Term
| some nonpolar, hydrophobic amino acids |
|
Definition
-glycine
-alanine
-valine
-leucine
-isoleucine
-methionine
-proline
-phenylalanine
-tryptophan |
|
|
Term
| some polar, but uncharged, amino acids |
|
Definition
-serine
-threonine
-tyrosine
-cysteine
-asparagine
-glutamine |
|
|
Term
| some positively charged amino acids |
|
Definition
-lysine
-arginine
-histidine |
|
|
Term
| some negatively charged amino acids |
|
Definition
|
|
Term
acid or base form?
[image] |
|
Definition
|
|
Term
acid or base form?
[image] |
|
Definition
|
|
Term
acid or base form?
[image] |
|
Definition
|
|
Term
acid or base form?
[image] |
|
Definition
|
|
Term
acid or base form?
[image] |
|
Definition
|
|
Term
acid or base form?
[image] |
|
Definition
|
|
Term
acid or base form?
[image] |
|
Definition
|
|
Term
acid or base form?
[image] |
|
Definition
|
|
Term
acid or base form?
[image] |
|
Definition
|
|
Term
acid or base form?
[image] |
|
Definition
|
|
Term
acid or base form?
[image] |
|
Definition
|
|
Term
acid or base form?
[image] |
|
Definition
|
|
Term
|
Definition
| arrays of atoms that have distinctive chemical properties |
|
|
Term
| some key functional groups in biochem |
|
Definition
| some key functional groups in biochem |
|
|
Term
| class(es) of compounds with hydrophobic functional group |
|
Definition
-hydrocarbon chains (aliphatic)
-aromatic (hydrocarbons in a ring structure with multiple double bonds) |
|
|
Term
| class(es) of compounds with hydroxyl functional group |
|
Definition
|
|
Term
| class(es) of compounds with aldehyde functional group |
|
Definition
|
|
Term
| class(es) of compounds with keto functional group |
|
Definition
|
|
Term
| class(es) of compounds with carboxyl functional group |
|
Definition
|
|
Term
| class(es) of compounds with amino functional group |
|
Definition
|
|
Term
| class(es) of compounds with phosphate functional group |
|
Definition
|
|
Term
| class(es) of compounds with sulhydryl functional group |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| aliphatic hydrocarbon chain |
|
Definition
|
|
Term
|
Definition
| aliphatic hydrocarbon chain |
|
|
Term
| aromatic hydrocarbon ring |
|
Definition
|
|
Term
|
Definition
| aromatic hydrocarbon ring |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| some things we'll be looking at in Biochem |
|
Definition
-How macromolecules are made and broken down,
-How the structures of macromolecules relates their funcPons,
-How energy and elements (especially carbon, oxygen, and nitrogen) flow
through biological systems,
-How biological reactions are catalyzed, and
-How biological pathways are regulated. |
|
|
Term
| the 4 types of macromolecules in biochem |
|
Definition
-lipids
-proteins
-nucleic acids
-carbohydrates |
|
|
Term
|
Definition
| the chemistry of life processes; life processes thru the lens of chemistry |
|
|
Term
| where most of the focus is in Biochem |
|
Definition
| most of the focus is on the molecules, their structure, and their activity |
|
|
Term
|
Definition
|
|
Term
| water content of a typical cell |
|
Definition
|
|
Term
| the role of water in biochem |
|
Definition
Water is the solvent of life.
• Most biomolecules dissolve in water
• Biological reactions take place in water
• Water participates in essential biological reactions.
• Water is essentially responsible for the remarkable structure and
function of the biomolecules, organelles and cells. |
|
|
Term
| how water affects biomolecules, organelles, and cells |
|
Definition
| Water is essentially responsible for the remarkable structure and function of the biomolecules, organelles and cells. |
|
|
Term
|
Definition
| Transient, non-covalent, chemical interactions |
|
|
Term
| importance of weak interactions |
|
Definition
| they form the basis of biochemistry and life itself |
|
|
Term
| why H bonds occur in water |
|
Definition
| because of water's polarity |
|
|
Term
| this accounts for the cohesiveness of water |
|
Definition
The polarity of water allows the formation of
hydrogen bonds between water molecules |
|
|
Term
| why water can dissolve many important biochemicals |
|
Definition
|
|
Term
| what causes the hydrophobic effect? |
|
Definition
| The inability of water to dissolve nonpolar molecules |
|
|
Term
| some things that can be attributed to the polarity of water |
|
Definition
-formation of H bonds
-cohesiveness of water
ability to dissolve many important biomolecules |
|
|
Term
|
Definition
| an important organizing principle caused by the inability of water to dissolve nonpolar molecules |
|
|
Term
| some of the interactions we'll be studying |
|
Definition
-electrostatic interactions
-H bonds
-van der Waals interactions |
|
|
Term
| ElectrostaPc Interactions |
|
Definition
Interactions between distinct electrical charges on atoms
example: water molecules dissolving NaCl |
|
|
Term
| electrostatic interactions aka... |
|
Definition
-ionic bonds
-salt bridges |
|
|
Term
|
Definition
| Forms between an electronegative atom (e.g., F, O, N) and Hydrogen |
|
|
Term
|
Definition
| seems to be the F, O, or N that's covalently bound to the H |
|
|
Term
|
Definition
| seems to be the F, O, or N that's not covalently bound to that H |
|
|
Term
| depiction of H bond donors and acceptors (might wanna draw this) |
|
Definition
|
|
Term
|
Definition
| when H is covalently bonded to an electronegative atom |
|
|
Term
| how water disrupts hydrogen bonds between two molecules |
|
Definition
by competing for the hydrogen bonding capability
example:
[image] |
|
|
Term
| where van der Waals interactions take place |
|
Definition
| between nonpolar and uncharged molecules |
|
|
Term
| van der Waals interactions take place between ______ and ______ molecules |
|
Definition
|
|
Term
| The basis of the van der Waals interaction |
|
Definition
| transient asymmetry in one molecule will induce complementary asymmetry in a nearby molecule |
|
|
Term
| energy of a van der Waals interaction vs. distance (might wanna draw this) |
|
Definition
|
|
Term
|
Definition
| the measure of randomness for the whole system itself |
|
|
Term
| one reason water doesn't dissolve nonpolar molecules |
|
Definition
| because water has greater entropy if it doesn't dissolve nonpolar molecules |
|
|
Term
| Hydrophobic molecules such as benzene tend to ______ in aqueous soluPons. |
|
Definition
|
|
Term
|
Definition
| the clustering of hydrophobic molecules in water |
|
|
Term
| Second Law of Thermodynamics |
|
Definition
| The total entropy of a system and its surroundings always increases in a spontaneous process. |
|
|
Term
| biological importance of hydrophobic effect |
|
Definition
| Hydrophobic effect is a powerful organizing force in biological systems |
|
|
Term
| membrane formation is powered by... |
|
Definition
|
|
Term
| composition of a phospholipid |
|
Definition
| hydrophilic head and hydrophobic tail |
|
|
Term
| what happens to phospholipids when they are exposed to water? |
|
Definition
|
|
Term
| how the formation of a phospholipid membrane increases entropy |
|
Definition
| by releasing water into the environment, allowing the water to have greater entropy |
|
|
Term
| protein folding is powered by... |
|
Definition
|
|
Term
| which version of protein has less entropy: folded or unfolded? |
|
Definition
|
|
Term
| why the folding of a protein into something ordered happens spontaneously |
|
Definition
| because it is powered by the hydrophobic effect and increases the entropy of the water |
|
|
Term
|
Definition
| H+ concentration of a solution |
|
|
Term
|
Definition
| pH = log(1/[H+]) = -log([H+]) |
|
|
Term
| acid is a proton donor or acceptor? |
|
Definition
|
|
Term
| base is a proton donor or acceptor? |
|
Definition
|
|
Term
| what the proton does in water |
|
Definition
| complexes with water to form hydronium ion |
|
|
Term
| what strong acids do in solution |
|
Definition
|
|
Term
| what weak acids do in solution |
|
Definition
| partially dissociate and establish e'librium |
|
|
Term
| what happens at a'librium? |
|
Definition
| formation of products and reactants happens at the same time at the same rate |
|
|
Term
|
Definition
| The chemical formed upon ionization of an acid |
|
|
Term
|
Definition
| the acid formed when a base binds a proton |
|
|
Term
| how to calculate the ionization equilibrium of a weak acid |
|
Definition
|
|
Term
| how to calculate the e'librium constant of a weak acid |
|
Definition
|
|
Term
|
Definition
| pKa = log(1/Ka) = -log(Ka) |
|
|
Term
| relationship between pH and pKa (Henderson-Hasselbach equation) |
|
Definition
| pH = pKa + log([A-]/[HA])
A- = conjugate base |
|
|
Term
|
Definition
| the pH at which the acid is half dissociated |
|
|
Term
| the protonated form is the acid or base? |
|
Definition
|
|
Term
| the deprotonated form is the acid or base? |
|
Definition
|
|
Term
|
Definition
| A- (deprotonated form) predominates |
|
|
Term
|
Definition
| HA (protonated form) predominates |
|
|
Term
|
Definition
| An acid-base conjugate pair that resists changes in the pH of a solution |
|
|
Term
| when a buffer is most effective |
|
Definition
| when the pH is near its pKa |
|
|
Term
| what buffers the pH of blood? |
|
Definition
| the conjugate acid-base pair of carbonic acid and bicarbonate (H2CO3/HCO3
-) |
|
|
Term
| the rxn that happens with CO2 in blood |
|
Definition
| CO2 + H2O <--> H2CO3 <--> H+ + HCO3- |
|
|
Term
| electrostatic interaction forms between... |
|
Definition
| distinct electrical charges |
|
|
Term
|
Definition
| an electronegative atom and Hydrogen |
|
|
Term
| van der Waals interaction forms between... |
|
Definition
| nonpolar and uncharged molecules due to transient asymmetry in electrical charge |
|
|
Term
| what causes van der Waals forces? |
|
Definition
| dipole-dipole interaction |
|
|
Term
| dipole-dipole interaction |
|
Definition
| interactions of atoms due to transient asymmetry in electrical charge |
|
|
Term
|
Definition
| clustering of hydrophobic molecules in water |
|
|
Term
| The hydrophobic effect is powered by... |
|
Definition
| the increase in the entropy of water that results when hydrophobic molecules come together. |
|
|
Term
| Protein folding is powered by... |
|
Definition
|
|
Term
| use of weak interactions in proteins |
|
Definition
| used to stabilize 3D structure |
|
|
Term
| depiction of how an amino acid changes in response to pH |
|
Definition
|
|
Term
| depiction of how peptide bonds are formed |
|
Definition
|
|
Term
| this is considered the beginning of the polypeptide chain |
|
Definition
|
|
Term
| this is considered the end of the polypeptide chain |
|
Definition
|
|
Term
| the only covalent rxn that can happen in a protein other than formation of peptide bonds |
|
Definition
| formation of disulfide bridge |
|
|
Term
| depiction of how a disulfide bridge is formed |
|
Definition
|
|
Term
| the resonance that occurs in a peptide bond |
|
Definition
|
|
Term
| distance between R groups in energetically favorable form |
|
Definition
| energetically favorable form has R groups far from each other |
|
|
Term
| configuration of most peptide bonds |
|
Definition
|
|
Term
| why most peptide bonds are in trans conformation |
|
Definition
| to minimize steric clashes between R groups |
|
|
Term
|
Definition
| the three-dimensional structure formed by hydrogen bonds between pep |
|
|
Term
| some prominent examples of protein secondary structure |
|
Definition
|
|
Term
| the most common secondary structure |
|
Definition
|
|
Term
| where H bonding occurs in the α-helix |
|
Definition
| it's always 4 amino acids ahead |
|
|
Term
| some things that determine likelihood of an amino acid being in an α-helix |
|
Definition
-crowding on the beta C
-distance of H bonding O from backbone |
|
|
Term
| Beta sheets are formed by... |
|
Definition
|
|
Term
| some ways beta sheets can be aligned |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| how polypeptides are stabilized in secondary structure |
|
Definition
| by H bonding in the backbone |
|
|
Term
|
Definition
| just the sequence thru peptide bonds |
|
|
Term
|
Definition
| the result of H bonding along the backbone |
|
|
Term
|
Definition
| the result of the protein folding into its structure |
|
|
Term
| what determines the structure a protein folds into? |
|
Definition
|
|
Term
| formation of tertiary structure is powered by... |
|
Definition
|
|
Term
| interactions that occur between hydrophobic molecules within a protein |
|
Definition
| van der Waals interactions |
|
|
Term
|
Definition
| multiple polypeptide chains called subunits |
|
|
Term
| depiction of how electrophoresis separates mixtures of molecules |
|
Definition
|
|
Term
|
Definition
|
|
Term
| how much enzymes speed up rxns |
|
Definition
|
|
Term
| the an- in anhydrase means... |
|
Definition
|
|
Term
|
Definition
| breaking of a bond by addition of a water molecule |
|
|
Term
|
Definition
|
|
Term
|
Definition
| catalyze the hydrolysis of peptide bonds |
|
|
Term
| are all enzymes equally specific? |
|
Definition
|
|
Term
| the 6 major classes of enzymes |
|
Definition
-Oxidoreductase
-Transferases
-Hydrolyases
-Lyases
-Isomerases
-Ligases |
|
|
Term
|
Definition
| catalyze oxidation-reduction reactions |
|
|
Term
|
Definition
| move functional groups between molecules |
|
|
Term
|
Definition
| cleave bonds with the addition of water |
|
|
Term
|
Definition
| remove atoms to form double bonds or add atoms to double bonds |
|
|
Term
|
Definition
move functional groups within a molecule
converts molecule to another isomer |
|
|
Term
|
Definition
| join two molecules at the expense of ATP |
|
|
Term
|
Definition
a measure of energy capable of doing work
this is the energy within the bonds of a molecule that is capable of doing work |
|
|
Term
| do enzymes alter the ΔG of a reaction? |
|
Definition
|
|
Term
| when rxn occurs spontaneously |
|
Definition
|
|
Term
|
Definition
|
|
Term
| when rxn does not occur spontaneously |
|
Definition
|
|
Term
|
Definition
|
|
Term
| when rxn is at e'librium,... |
|
Definition
there is no net change in the amount of reactant or product
ΔG = 0 |
|
|
Term
| The ΔG of a reaction depends only on... |
|
Definition
| the free energy difference between reactants and products |
|
|
Term
| does the ΔG of a reaction provide any ΔG of a reaction? |
|
Definition
|
|
Term
| do enzymes alter rxn rate? |
|
Definition
|
|
Term
| do enzymes alter rxn e'librium? |
|
Definition
|
|
Term
| The reaction equilibrium is determined only by... |
|
Definition
| the free energy difference between the products and reactants |
|
|
Term
|
Definition
| a molecular form that is no longer substrate but not yet product |
|
|
Term
|
Definition
| the formation of the transition state |
|
|
Term
|
Definition
| The energy required to form the transition state from the substrate |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| how to calculate activation energy |
|
Definition
|
|
Term
| the first step in enzymatic catalysis |
|
Definition
| the formation of an enzyme-substrate complex |
|
|
Term
|
Definition
| region of an enzyme where the enzyme-substrate complex forms |
|
|
Term
| this promotes the formation of the transition state |
|
Definition
| The interaction of the enzyme and substrates at the active site |
|
|
Term
| some common features of active sites of enzymes |
|
Definition
1. The active site is a three-dimensional cleft or crevice created by amino acids from different parts of the primary structure.
2. The active site constitutes a small portion of the enzyme volume.
3. Active sites create unique microenvironments.
4. The interaction of the enzyme and substrate at the active site involves multiple weak interactions.
5. Enzyme specificity depends on the molecular architecture at the active site. |
|
|
Term
| structure of the active site |
|
Definition
| a three-dimensional cleft or crevice created by amino acids from different parts of the primary structure |
|
|
Term
| how much of the enzyme is taken up by the active site? |
|
Definition
|
|
Term
|
Definition
|
|
Term
| The interaction of the enzyme and substrate at the active site involves... |
|
Definition
| multiple weak interactions |
|
|
Term
| Enzyme specificity depends on... |
|
Definition
| the molecular architecture at the active site |
|
|
Term
| do enzymes follow the lock-and-key model? |
|
Definition
|
|
Term
| what model do enzymes almost always follow? |
|
Definition
|
|
Term
|
Definition
| the enzyme changing shape upon substrate binding |
|
|
Term
|
Definition
| the free energy released upon interaction of the enzyme and substrate |
|
|
Term
| Binding energy is greatest when... |
|
Definition
| the enzyme interacts with the transition state |
|
|
Term
| what facilitates the formation of a transition state when an enzyme is involved? |
|
Definition
|
|
Term
| important characteristic of an enzyme inhibitor |
|
Definition
| has to resemble the transition state |
|
|
Term
| how to calculate binding energy |
|
Definition
| binding energy = uncatalyzed activation energy - catalyzed activation energy |
|
|
Term
| which amino acids would you expect to be on the outside of an alpha-helix in a plasma membrane? |
|
Definition
| hydrophobic/nonpolar amino acids |
|
|
Term
| which amino acids would you expect to be on the inside of an alpha-helix in a plasma membrane? |
|
Definition
| polar/hydrophilic amino acids |
|
|
Term
| What reaction does CA catalyze? |
|
Definition
|
|
Term
|
Definition
|
|
Term
| how water complexes with the Zn ion in carbonic anhydrase |
|
Definition
| -Zn2+ acts as a Lewis acid
-water then compensates for loss of electrons by releasing a proton |
|
|
Term
| how a water molecule compensates for loss of electrons |
|
Definition
|
|
Term
| why the pKa of water is 15.7 |
|
Definition
| because for every 55.5 mols of water, there's 10-7 mols of H+ and 10-7 mols of OH-
therefore,...
Ka = (10-7 X 10-7) / 55.5 = 1.8 X 10-16
therefore,...
pKa = -log (1.8 X 10-16) = 15.7 |
|
|
Term
| depiction of how carbonic anhydrase reacts with water |
|
Definition
|
|
Term
|
Definition
|
|
Term
| some reasons tyrosine replacing a histidine can affect the function of CA |
|
Definition
-at physiological pH, histidine can be protonated or deprotonated, but tyrosine can only be protonated
-histidine can make 2 H bonds while tyrosine can make only one H bond |
|
|
Term
| why tyrosine is not a good AA for the active site of CA |
|
Definition
| -Does not interact with H2O or OH-
-Does not interact with Zn2+
-Slower rate of catalysis |
|
|
Term
|
Definition
| Bone cells that break down and remove bone Issue – dissolve the fibers and matrix of bone |
|
|
Term
|
Definition
| breaking bonds by addition of water |
|
|
Term
| why is initial velocity (V0) used in measuring catalysis? |
|
Definition
| because you're interested in the initial product formation |
|
|
Term
| the kinetics of Michaelis-Menten enzymes |
|
Definition
| starts off first order with respect to S, then seems to be zero order with respect to S |
|
|
Term
| when the kinetics of a Michaleis-Menten enzyme become zero-order |
|
Definition
| when all the enzyme is bound to substrate |
|
|
Term
| in this rxn, why do we ignore k2?
[image] |
|
Definition
| Because we examine only the initial rates |
|
|
Term
| quantities of enzymes compared to quantities of substrates |
|
Definition
| enzymes are almost always in way less quantities than substrates |
|
|
Term
| how calculate V0 (initial velocity) (the Michaelis-Menten equation) |
|
Definition
| V0 = (Vmax[S]) / (KM + [S])
this is the Michaelis-Menten equation |
|
|
Term
| how to calculate KM (the Michaelis-Menten constant) |
|
Definition
| KM = (k-1 + k2) / k1 = (ES falls apart) / (ES forms)
here's a depiction of it:
[image] |
|
|
Term
| KM is an indication of... |
|
Definition
| -the stability of the [ES] complex
-Tells how much substrate will saturate E (~10 × KM) |
|
|
Term
| KM vs. enzyme affinity for substrate |
|
Definition
|
|
Term
|
Definition
| Vmax = k2 X [E]Total
or
Vmax = kcat X [E]Total
k2 is a constant |
|
|
Term
|
Definition
|
|
Term
|
Definition
| k2 or kcat = Vmax / [E]Total |
|
|
Term
| in Michaelis-Menten Kinetics, what happens when you change [E]? |
|
Definition
| k2 or kcat doesn't change, but Vmax does |
|
|
Term
|
Definition
| the rate constant of the rate-limiting step |
|
|
Term
| relationship between k2 and kcat |
|
Definition
|
|
Term
|
Definition
| The number of molecules of substrate converted per unit time per enzyme molecule |
|
|
Term
| kcat/KM is a measure of... |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
| How fast the ES makes product |
|
|
Term
|
Definition
|
|
Term
| relationship between kcat and KM |
|
Definition
| kcat/KM = (How fast the ES makes product)/(How easily ES is formed) |
|
|
Term
| for an enzyme to be highly efficient, you want kcat to be ______ and KM to be ______ |
|
Definition
|
|
Term
| for an enzyme to be highly efficient, you want ______ to be high and ______ to be low |
|
Definition
|
|
Term
| is Vmax estimated or measured? |
|
Definition
|
|
Term
| the Lineweaver-Burk equation |
|
Definition
| (1/V0) = ((KM/Vmax) X (1/[S])) + (1/Vmax)
y = ax + b
y = 1/V0
a = KM/Vmax
x = 1/[S]
b = 1/Vmax |
|
|
Term
| value of kcat/KM vs. enzyme efficiency |
|
Definition
|
|
Term
| enzymes that do not follow standard Michaelis-Menten kinetics |
|
Definition
| allosteric enzymes/proteins |
|
|
Term
| allosteric enzymes/proteins |
|
Definition
| enzymes that “switch” between functioning and non-functioning (or more and less active) conformations |
|
|
Term
| how allosteric enzymes/proteins are regulated |
|
Definition
-Binding of a regulator at a site distant from the active site
-Cooperative binding of multiple substrate molecules
-Or both |
|
|
Term
| regulators of allosteric enzymes/proteins |
|
Definition
molecules that bind at a site distant from the active site to regulate the activity of the enzyme
they are inhibitors and activators |
|
|
Term
| how regulators affect allosteric enzymes/proteins |
|
Definition
| they induce changes in 4° structure |
|
|
Term
| the structure allosteric enzymes/proteins have |
|
Definition
|
|
Term
| a step in metabolic pathways that's always regulated by allosteric enzymes |
|
Definition
|
|
Term
|
Definition
| end product binding to regulatory site on allosteric enzyme distinct from active site |
|
|
Term
| the enzymes that facilitate steps in biochemical pathways other than the committed step |
|
Definition
|
|
Term
| composition of hemoglobin |
|
Definition
| 4 O2 binding subunits: 2 α and 2β (pair of identical αβ dimers) |
|
|
Term
| how O bonding affects the structure of hemoglobin |
|
Definition
| Binds O2 cooperatively: as one subunit binds O2, Hb conformation changes, increasing O2 affinity of other subunits |
|
|
Term
| how the structure of myoglobin differs from that of hemoglobin |
|
Definition
| hemoglobin has 4 polypeptide chains while myoglobin has only 1 |
|
|
Term
| behavior of myoglobin compared to that of hemoglobin |
|
Definition
| hemoglobin behaves like an allosteric enzyme while myoglobin behaves like a Michaelis-Menten enzyme |
|
|
Term
| where hemoglobin takes up O |
|
Definition
|
|
Term
| where hemoglobin releases O |
|
Definition
|
|
Term
| when hemoglobin has low affinity for O |
|
Definition
| when there's no O bound to it |
|
|
Term
| T state of hemoglobin is favored until... |
|
Definition
| O has bound to one subunit of each αβ dimer |
|
|
Term
| R state of hemoglobin is favored until... |
|
Definition
| O is released from one complete αβ dimer |
|
|
Term
| what O does to the Fe atom in hemoglobin when O bonds to hemoglobin |
|
Definition
|
|
Term
| the 2 oxidation states of Fe |
|
Definition
|
|
Term
| depiction of how O bonding to hemoglobin alters the structure of the molecule |
|
Definition
[image]
this induces conformational changes in one Hb chain, which triggers a conformational change in other Hb chains |
|
|
Term
| the bonds that occur between O and hemoglobin |
|
Definition
-covalent with Fe
-H bond with distal Histidine |
|
|
Term
|
Definition
| decrease in pH or increase in CO2 leads to stabilization of the T state of Hb and unloading of O2 (and the reverse...) |
|
|
Term
| the role of 2,3-Biphosphoglycerate (2,3-BPG) |
|
Definition
| binds to the interior of the hemoglobin to reduce its affinity for O |
|
|
Term
| what CO2 does with amino acid side chains to help hemoglobin release O |
|
Definition
| covalently binds with side chains to form carbamate |
|
|
Term
| depiction of CO2 binding with side chains to form carbamate |
|
Definition
| [image]
this also helps us exhale CO2 |
|
|
Term
| why mutant hemoglobin forms 2 bands in electrophoresis as oppose to normal hemoglobin forming one band |
|
Definition
| people with mutant hemoglobin produce both normal and mutant hemoglobin; the mutant hemoglobin has greater negative charge, making it move faster to the positive end |
|
|
Term
|
Definition
| dissociation over binding |
|
|
Term
| types of gel electrophoresis with proteins |
|
Definition
|
|
Term
| native gel electrophoresis |
|
Definition
| electrophoresis with protein as it occurs naturally in the organism |
|
|
Term
| native gel electrophoresis separates proteins based on... |
|
Definition
|
|
Term
| denatured gel electrophoresis |
|
Definition
| protein gets denatured, often by a salt called SDS that covers protein in negative charge |
|
|
Term
| denatured gel electrophoresis separates proteins based on... |
|
Definition
|
|
Term
| types of bonds that form in reversible enzyme-inhibitor binding |
|
Definition
| mostly electrostatic and weak interactions with the enzyme rather than covalent |
|
|
Term
| types of bonds that form in irreversible enzyme-inhibitor binding |
|
Definition
| mostly covalent bonds with the enzyme rather than electrostatic and weak interactions |
|
|
Term
| equation for enzyme catalysis |
|
Definition
|
|
Term
| mechanism for competitive inhibition |
|
Definition
|
|
Term
| mechanism for uncompetitive inhibition |
|
Definition
|
|
Term
| mechanism for noncompetitive inhibition |
|
Definition
|
|
Term
| what competitive inhibitors bind to |
|
Definition
|
|
Term
| how competitive inhibitors affect the catalysis rxn |
|
Definition
|
|
Term
| what happens wen you add extra substrate when there's a competitive inhibitor? |
|
Definition
| substrate outcompetes comprtitive inhibitor |
|
|
Term
|
Definition
|
|
Term
| how competitive inhibitor affects Vmax |
|
Definition
|
|
Term
|
Definition
when enzyme is saturated with substrate
happens only when there's excess amounts of substrate |
|
|
Term
| how competitive inhibitor affects KM |
|
Definition
|
|
Term
| why competitive inhibitor increases KM |
|
Definition
| because of effectively reduced affinity for enzyme |
|
|
Term
|
Definition
| the [S] at which 1/2 Vmax is reached |
|
|
Term
| what uncompetitive inhibitors bind to |
|
Definition
|
|
Term
| how uncompetitive inhibitors affect the catalysis rxn |
|
Definition
| effectively increases [ES] |
|
|
Term
| how uncompetitive inhibitor affects Vmax |
|
Definition
|
|
Term
| why competitive inhibitor lowers Vmax |
|
Definition
| because of increased [ES] |
|
|
Term
| how uncompetitive inhibitor affects KM |
|
Definition
|
|
Term
| why competitive inhibitor increases KM |
|
Definition
| because of increased [ES] |
|
|
Term
| what noncompetitive inhibitor binds to |
|
Definition
| both enzyme and ES complex |
|
|
Term
| structure of noncompetitive inhibitor |
|
Definition
| not similar to that of substrate |
|
|
Term
| how noncompetitive inhibitor affects catalysis rxn |
|
Definition
| could lower concentrations of E and ES, but proportions of E and ES stay the same |
|
|
Term
|
Definition
| inhibitor that results in unequal proportions of EI and ESI |
|
|
Term
| how noncompetitive inhibitor affects Vmax |
|
Definition
|
|
Term
| how noncompetitive inhibitor affects KM |
|
Definition
|
|
Term
| why KM stays the same when there's a noncompetitive inhibitor |
|
Definition
| same affinity for substrate |
|
|
Term
what inhibitor is this?
[image] |
|
Definition
|
|
Term
what inhibitor is this?
[image] |
|
Definition
|
|
Term
what inhibitor is this?
[image] |
|
Definition
|
|
Term
what inhibitor is this?
[image] |
|
Definition
|
|
Term
what inhibitor is this?
[image] |
|
Definition
|
|
Term
what inhibitor is this?
[image] |
|
Definition
|
|
Term
|
Definition
| to understand what it means to be alive at the molecular level |
|
|
Term
| tyhe chemical unity of life |
|
Definition
| all living things seem to be remarkably uniform at the molecular level |
|
|
Term
| the 3 elements that make up 98% of the atoms in living organisms |
|
Definition
|
|
Term
| one reason O and H are so comon in living things |
|
Definition
|
|
Term
| importance of C in living things |
|
Definition
| large biomolecules have C backbones |
|
|
Term
| why C is better for life than Si is |
|
Definition
because C-C bonds are more stable than Si-Si bonds
also because more energy is released when C-C bonds are broken than when Si-Si bonds are broken |
|
|
Term
| the 4 classes of biomolecules |
|
Definition
-proteins
-nucleic acids
-lipids
-carbohydrates |
|
|
Term
| the composition of proteins |
|
Definition
| amino acids linked by peptide bonds to form long, unbranched polymers |
|
|
Term
| the building blocks of proteins |
|
Definition
| amino acids (there's 20 of them) |
|
|
Term
| what happens after the polypeptide chain of amino acids is synthesized? |
|
Definition
| it folds into a protein with a precise 3d structure |
|
|
Term
| some functions of proteins |
|
Definition
-signal
-receptor
-structural
-mobility
-defense
-enzymes |
|
|
Term
|
Definition
| usually proteins, these catalyze biochemical reactions |
|
|
Term
| the 3d folding of a protein is dictated by... |
|
Definition
| the sequence of amino acids in the protein |
|
|
Term
| primary function of nucleic acids |
|
Definition
| to store and transfer informaation |
|
|
Term
| the building blocks of nucleic acids |
|
Definition
|
|
Term
| composition of a nucleotide |
|
Definition
| made of a 5 carbon sugar attached to a heterocyclic ring structure called a base, and at least one phosphoryl group |
|
|
Term
| the 2 types of nucleic acid |
|
Definition
-deoxyribonucleic acid (DNA)
-ribonucleic acid (RNA) |
|
|
Term
| the interaction of DNA with RNA |
|
Definition
| info from DNA is transcribed onto mRNA, which acts as a template for protein synthesis |
|
|
Term
| what happens to mRNA after use? |
|
Definition
| frequently gets broken doen |
|
|
Term
| differences in composition of DNA and RNA |
|
Definition
-RNA uses U instead of T
-in RNA, the sugar component of the ribonucleotides contains an extra -OH group |
|
|
Term
| size of lipids compared to proteins and nucleic acids |
|
Definition
| lipids tend to be a lot smaller |
|
|
Term
| are lipids polymers composed of repeating monomers? |
|
Definition
|
|
Term
| a key characteristic of many biochemically important lipids |
|
Definition
| their dual chemical nature; part being hydrophilic and the other part being hydrophobic |
|
|
Term
| what the dual nature (part hydrophilic and part hydrophobic) nature of lipids makes possible |
|
Definition
allows cells to form barriers that delineate the cell from its environment and to establish intracellular compartments
basically allows formation of inside and outside at the biochem level |
|
|
Term
| why it's possible for a cell to form barriers that delineate the cell from its environment and to establish intracellular compartments |
|
Definition
| because of the dual nature (part hydrophilic and part hydrophobic) nature of lipids |
|
|
Term
|
Definition
-forming membranes and compartments
-energy storage
-signaling |
|
|
Term
| the most common carbohydrate fuel |
|
Definition
|
|
Term
| how glucose is stored in animals |
|
Definition
|
|
Term
| how glucose is stored in plants |
|
Definition
|
|
Term
| the structure of glycogen |
|
Definition
many glucose molecules linked end-to-end, with occasional branches
starch has similar structure |
|
|
Term
| some functions of carbohydrate chains |
|
Definition
-energy storage
-cell-to-cell communication, such as helping cells recognize each other |
|
|
Term
| the Central Dogma as described by Francis Crick |
|
Definition
|
|
Term
| the heritable information |
|
Definition
|
|
Term
| the discrete units of heredity in the genome |
|
Definition
|
|
Term
| enzymes that catalyze the DNA replication process |
|
Definition
|
|
Term
| how info from a gene becomes accessible |
|
Definition
| gets transcribed onto RNA |
|
|
Term
| enzymes that catalyzes transcription |
|
Definition
|
|
Term
| what defines the function of a cell or tissue? |
|
Definition
| the genes that are expressed in that cell or tissue |
|
|
Term
| info from DNA is transcribed onto... |
|
Definition
|
|
Term
| genetic info is realized in the process of... |
|
Definition
|
|
Term
|
Definition
| renders the genetic info into a functional form |
|
|
Term
| where translation takes place |
|
Definition
| large macromolecular complexes called ribosomes |
|
|
Term
|
Definition
|
|
Term
|
Definition
| translates info from mRNA into the amino acid sequence of a protein |
|
|
Term
| each cell is delineated by... |
|
Definition
|
|
Term
|
Definition
| lipid bilayer with the hydrophobic chains interacting with each other on the inside and the hydrophilic heads interacting with the environment |
|
|
Term
| difference between prokaryotic and eukaryotic cells |
|
Definition
| eukaryotes have membrane-enclosed compartments and prokaryotes don't |
|
|
Term
| structure of a prokaryotic cell wall |
|
Definition
|
|
Term
| the 2 biochemical features that constitute a cell |
|
Definition
1: a barrier that separates the cell from its environment
2: an inside that is chemically different from the environment and that accommodates the biochemistry of living |
|
|
Term
|
Definition
| barrier between the cell and the environment |
|
|
Term
|
Definition
| the inner substance of the cell, the material that is surrounded by the plasma membrane |
|
|
Term
| function of proteins in the plasma membrane |
|
Definition
-facilitate the entrance of certain fuels and building blocks that need to enter
-transduce information |
|
|
Term
|
Definition
| proteins that penetrate the cell membrane |
|
|
Term
|
Definition
| proteins that don't penetrate the cell membrane |
|
|
Term
| the cell wall of plants is made of... |
|
Definition
|
|
Term
| some important biochemical processes that occur in the cytoplasm |
|
Definition
-initial stage of glucose metabolism
-fatty acid synthesis
-protein synthesis |
|
|
Term
|
Definition
| network of structural filaments that organize the biochemistry of the cytoplasm |
|
|
Term
| some types of filaments that occur in the cytoskeleton of eukaryotes |
|
Definition
-actin filaments
-intermediate filaments
-microtubules |
|
|
Term
| some functions of the filaments in the cytoskeleton |
|
Definition
-support the structure of the cell
-help to localize certain biochemical activities
-even serve as "molecular highways" by which molecules can be shuttled around the cell |
|
|
Term
|
Definition
| membrane-bound compartments within eukaryotic cells |
|
|
Term
|
Definition
|
|
Term
|
Definition
-the information center of the cell
-double-membrane-bound
-contains an organism's genome |
|
|
Term
| function of pores in the nuclear membrane |
|
Definition
| allow transpoirt into and out of the nucleus, such as the machinery needed for gene expression |
|
|
Term
| the 2 membranes of the mitochondrion |
|
Definition
|
|
Term
| outer mitochondrial membrane |
|
Definition
| in touch with the cytoplasm |
|
|
Term
| inner mitochondrial membrane |
|
Definition
| defines the matrix of the mitochondrion- mitochondrial equivalent of cytoplasm |
|
|
Term
|
Definition
| mitochondrial equivalent of cytoplasm |
|
|
Term
|
Definition
| the space between the 2 membranes in a mitochondrion |
|
|
Term
| what happens in mitochondria? |
|
Definition
| fuel molecules undergo combustion into CO2 and water with the generation of ATP |
|
|
Term
| how much energy is produced by the mitochondria? |
|
Definition
| about 90% of a eukarytotic cell's energy |
|
|
Term
| why CO and cyanide are so desadly |
|
Definition
| because they disrupt the mitochondria |
|
|
Term
|
Definition
| organelle in plant cells responsible for converting sunlight into useable energy |
|
|
Term
|
Definition
| basically a series of membranous sacs |
|
|
Term
| important role of smooth ER |
|
Definition
|
|
Term
| what happens to proteins synthesized by ribosomes that are floating freely in the cell? |
|
Definition
|
|
Term
| what happens to proteins synthesized by ribosomes attached to the rough ER? |
|
Definition
| they will either enter thru cellular membranes or be secreted from the cell |
|
|
Term
|
Definition
| basically a series of stacked membranes |
|
|
Term
| function of the Golgi complex |
|
Definition
| sorting and further processing of proteins from the rough ER |
|
|
Term
| something the rough ER does to some proteins that enter it |
|
Definition
| add carbohydrates to that protein |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
formed when a vesicle filled with the proteins destined for secretion buds off the Golgi complex
dumps cargo into extracellular environment |
|
|
Term
|
Definition
| cell emptying some contents into extracellular environment |
|
|
Term
|
Definition
| taking small amounts of something into a cell |
|
|
Term
|
Definition
| taking large amounts of something into a cell |
|
|
Term
|
Definition
| organelle that contains a wide array of digestive enzymes |
|
|
Term
| some organelles unique to plants |
|
Definition
|
|
Term
| the bonds that stabilize biomolecules (lipids, carbohydrates, proteins, and nucleic acids) |
|
Definition
|
|
Term
|
Definition
| allow for dynamic interactions and transmission of energy and information |
|
|
Term
| this forms the basis for biochem and life itself |
|
Definition
| transient chemical interactions |
|
|
Term
|
Definition
| random movement of particles due to fluctuations in temperature |
|
|
Term
|
Definition
| random fluctuation of the energy content of the environment |
|
|
Term
| what initiates biochemical interactions? |
|
Definition
|
|
Term
| the medium for Brownian motion |
|
Definition
|
|
Term
| something water does for living organisms |
|
Definition
| dissolving important molecules to render them mobile and available |
|
|
Term
| the type of covalent molecule water is |
|
Definition
|
|
Term
| why the polarity of water is important for biochemistry |
|
Definition
| because the polarity enables water to dissolve polar and charged molecules |
|
|
Term
| the type of bonding that occurs between water molecules |
|
Definition
|
|
Term
| molecules water can't dissolve |
|
Definition
|
|
Term
| the 3 fundamental noncovalent bonds |
|
Definition
1: ionic bonds / electrostatic interactions
2: H bonds
3: van der Waals interactions |
|
|
Term
|
Definition
| electrostatic interaction / ionic bond |
|
|
Term
|
Definition
| E = (kq1q2) / Dr
E = force
k = proportionality constant
q1 and q2 = charges on the 2 atoms
r = distance between 2 atoms (in Angstroms)
D = dielectric constant |
|
|
Term
| why NaCl dissolves in water |
|
Definition
| because the individual ions bind to the water instead of each other |
|
|
Term
| how to calculate the energy of an electrostatic interaction |
|
Definition
| Coulomb's law
E = (kq1q2) / Dr
E = force
k = proportionality constant
q1 and q2 = charges on the 2 atoms
r = distance between 2 atoms (in Angstroms)
D = dielectric constant |
|
|
Term
|
Definition
| between H and electronegative element |
|
|
Term
| the basis for van der Waals interactions |
|
Definition
| the distribution of electronic charge around an atom changes with time, and, at any instant, the charge distribution will not be perfectly symmetric; this creates momentary positive and negative |
|
|
Term
| why geckos can defy gravity |
|
Definition
| van der Waals interactions |
|
|
Term
| the second law of termodynamics |
|
Definition
| the total entropy of a system and its surroundings always increases in a spontaneous process |
|
|
Term
|
Definition
|
|
Term
|
Definition
| the aggregation of nonpolar groups in water increases the entropy in the water |
|
|
Term
| why nonpolar molecules congregate in water |
|
Definition
| because when they come into contact with each other, they release water molecules |
|
|
Term
|
Definition
| interactions driven by the hydrophobic effect |
|
|
Term
| depiction of how congregation of nonpolar molecules in water increases entropy |
|
Definition
|
|
Term
| membrane formation is powered by... |
|
Definition
|
|
Term
|
Definition
| molecule that has both a hydrophilic side and a hydrophobic side |
|
|
Term
|
Definition
| molecule that has both a hydrophilic side and a hydrophobic side |
|
|
Term
| the hydrophobic interior of the bilayer is stabilized by... |
|
Definition
| van der Waals interactions between the tails |
|
|
Term
| protein folding is powered by... |
|
Definition
|
|
Term
| why proteins can do so many things in living things |
|
Definition
| because they can form complex 3D structures that allow specific interactions with other biomolecules |
|
|
Term
|
Definition
| groups of atoms with distinct chemical properties |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| the hydroxyl functional group is found in... |
|
Definition
|
|
Term
| the aldehyde functional group is found in... |
|
Definition
|
|
Term
| the keto functional group is found in... |
|
Definition
|
|
Term
| the carboxyl functional group is found in... |
|
Definition
|
|
Term
| the amino functional group is found in... |
|
Definition
|
|
Term
| the phosphate functional group is found in... |
|
Definition
|
|
Term
| the sulfhydryl functional group is found in... |
|
Definition
|
|
Term
| why it's important for living things to maintain constant pH |
|
Definition
| because alterations in pH can drastically affect the internal electrostatic environment, of an organism, which can alter the weak bonds that maintain the structure of biomolecules; altered structure messes with function |
|
|
Term
| what water will ionize into |
|
Definition
|
|
Term
| the e'librium equation of water |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
| Keq = [H+][OH-]/[H2O]
the brackets denote c'tration in molarity (M) |
|
|
Term
|
Definition
|
|
Term
|
Definition
| Kw = Keq X [H2O]
simplifies to...
Kw = [H+][OH-] |
|
|
Term
|
Definition
| pH = -log[H+]
or
pH = log(1/[H+]) |
|
|
Term
| acid is proton (donor or acceptor) |
|
Definition
|
|
Term
| base is proton (donor or acceptor) |
|
Definition
|
|
Term
| what happens to acid in solution? |
|
Definition
| ionizes to produce a proton and a base
acid <---> H+ + base |
|
|
Term
|
Definition
| the base that results when an acid dissociates in solution |
|
|
Term
|
Definition
| the acid that results when a base dissociates in solution |
|
|
Term
| ionization e'librium of a weak acid (HA) |
|
Definition
|
|
Term
| the e'librium constant (Ka) for HA |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
| pH = pKa + log([A-]/[HA])
A- = ionized acid
HA = unionized acid
this is the Henderson-Hasselbach equation |
|
|
Term
| the Henderson-Hasselbach equation |
|
Definition
| pH = pKa + log([A-]/[HA])
A- = ionized acid
HA = unionized acid |
|
|
Term
|
Definition
| the pH at which the acid is half dissociated |
|
|
Term
| what's dominant above pKa? |
|
Definition
|
|
Term
| what's dominant below pKa? |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
| in the vicinity of their pKa |
|
|
Term
| why knowledge of buffers is important |
|
Definition
1: biomolecules are sensitive to pH, so a good buffer is needed for a successful experiment
2: to understand how an organism controls its own pH |
|
|
Term
| compensatory respiratory alkalosis |
|
Definition
| mechanism by which the amount of carbonic acid and bicarbonate is adjusted in the blood in response to carbon dioxide |
|
|
Term
| some functions of amino acids |
|
Definition
-signal molecules, such as neurotransmitters
-precursors to other biomolecules, such as hormones, nucleic acids, lipids, and proteins |
|
|
Term
| the unique part of each amino acid |
|
Definition
|
|
Term
| the isomers of amino acids |
|
Definition
| D and L; they are enantiomers |
|
|
Term
| the type of amino acids that make up proteins |
|
Definition
|
|
Term
| how amino acids typically exist in physiological condition |
|
Definition
|
|
Term
|
Definition
|
|
Term
| how an amino acid is in zwitterionic (dipolar ion) form |
|
Definition
| has protonated amino group (NH3+) and deprotonated carboxyl group (COO-) |
|
|
Term
| state of amino acid at low pH |
|
Definition
| both amino and carboxyl protonated |
|
|
Term
| state of amino acid at high pH |
|
Definition
| both amino and carboxyl deprotonated |
|
|
Term
| the 4 groups of amino acids |
|
Definition
1: hydrophobic w/ nonpolar R groups
2: polar w/ neutral R groups
3: positively charged w/ positive in R group
4: negatively charged w/ negative in R group |
|
|
Term
| characteristic of the hydrophobic amino acids |
|
Definition
| have side chains consisting mainly of C and H |
|
|
Term
| what the hydrophobic amino acids do in protein formation |
|
Definition
| they tend to cluster together inside the protein away from the aqueous environment |
|
|
Term
| characteristic of polar amino acids |
|
Definition
| their side chains contain electronegative atoms |
|
|
Term
| characteristics of positively charged amino acids |
|
Definition
-positive charge in side chain
-hydrophilic |
|
|
Term
| characteristic of negatively charged amino acids |
|
Definition
| have acidic side chains that have a negative charge |
|
|
Term
| what ionizeable side chains do for amino acids |
|
Definition
| enhance reactivity and bonding |
|
|
Term
|
Definition
| the ability to donate or accept protons |
|
|
Term
| primary structure of a protein |
|
Definition
|
|
Term
| secondary structure of a protein |
|
Definition
| 3D structure resulting from a regular pattern of H bonds between the CO and NH components of the amino acids in the polypeptide chain |
|
|
Term
| tertiary structure of a protein |
|
Definition
| occurs when the R groups of the amino acids bond with one another |
|
|
Term
|
Definition
| seems to be proteins working with each other |
|
|
Term
| the bond between 2 amino acids |
|
Definition
|
|
Term
|
Definition
|
|
Term
| how a peptide bond is formed |
|
Definition
| by linking the a-carboxyl group of one amino acid to the a-amino group of the other |
|
|
Term
| depiction of how a peptide bond is formed |
|
Definition
|
|
Term
|
Definition
| each amino acid unit in a polypeptide chain |
|
|
Term
| the directionality of a polypeptide chain |
|
Definition
| has a-amino group at one end and a-carboxyl group on the other end |
|
|
Term
| the end that's taken to be the beginning of the polypeptide chain |
|
Definition
|
|
Term
| general structure of a polypeptide chain |
|
Definition
C-N backbone with carbonyl groups and side chains, as shown here
[image] |
|
|
Term
| the most common cross-linking that occurs in polypeptide chains |
|
Definition
|
|
Term
| why it's important to know amino acid sequences |
|
Definition
1: sequence determines structure
2: knowledge of sequence is essential to elucidating its function
3: alterations in sequence can produce abnormal functions and disease
4: sequence of a protein can reveal something about its evolutionary history |
|
|
Term
| what determines 3D structure of a protein? |
|
Definition
|
|
Term
| what determines function of a protein? |
|
Definition
|
|
Term
| are peptide bonds in proteins cis or trans? |
|
Definition
| almost all of them are trans |
|
|
Term
| why do peptide bonds prefer trans configuration? |
|
Definition
| because there's steric clash between the R groups in cis configuration |
|
|
Term
|
Definition
| the fact that 2 atoms can't be in the same place at the same time |
|
|
Term
| what steric exclusion does for proteins |
|
Definition
| restricts the number of possible peptide conformations |
|
|
Term
| some types of structures that occur in a protein's secondary structure |
|
Definition
-a-helices
-B pleated sheets
-turns |
|
|
Term
|
Definition
| coiled structure stabilized by intrachain H bonds |
|
|
Term
|
Definition
|
|
Term
| the a-helix is stabilized by... |
|
Definition
| H bonds between the NH and CO groups of the main chain |
|
|
Term
| are a-helices right or left handed? |
|
Definition
| essentially all right handed |
|
|
Term
| how B sheets are stabilized |
|
Definition
| stabilized by H bonding between polypeptide strands |
|
|
Term
| structure of a single polypeptide B strand |
|
Definition
|
|
Term
| structure of polypeptide B strands H bonded to each other |
|
Definition
[image]
the top is antiparallel and the bottom is parallel |
|
|
Term
|
Definition
| H bonding between 2 or more B strands |
|
|
Term
|
Definition
| can be almost flat, but most adopt an almost twisted shape |
|
|
Term
| polypeptide chains can change direction by... |
|
Definition
| making reverse turns and loops |
|
|
Term
|
Definition
|
|
Term
| the compact globular shape of most proteins requires this of their polypeptide chains |
|
Definition
| reversals in the direction |
|
|
Term
| where the turns and loops in polypeptide chains are in proteins |
|
Definition
| on the surface of the proteins |
|
|
Term
| function of fibrous proteins |
|
Definition
| provide structural support for cells and tissues |
|
|
Term
| ther general structure of fibrous proteins |
|
Definition
| mostly extensive stretches of secondary structure |
|
|
Term
| examples of fibrous proteins |
|
Definition
|
|
Term
| depiction of a fibrous protein |
|
Definition
|
|
Term
| 2 ways intertwined strands in fibrous proteins can be stabilized |
|
Definition
-H bonding inside
-steric repulsion outside |
|
|
Term
| the only residue that can fit in an interior position in a protein helix |
|
Definition
|
|
Term
| the interior of the triple-stranded helical cable that forms collagen |
|
Definition
| very crowded; only glycine can fit in there |
|
|
Term
| tertiary structure is caused by... |
|
Definition
| interactions between R groups |
|
|
Term
| protein with tertiary structure |
|
Definition
| has a compact, 3D structure |
|
|
Term
| the type of protein that performs most of the chemical transactions in the cell |
|
Definition
| compact, globular proteins with specific 3D structure |
|
|
Term
| how a protein folds in an aqueous environment |
|
Definition
folds such that the hydrophobic parts are on the inside and the hydrophilic parts are on the outside
driven by the hydrophobic effect |
|
|
Term
| how proteins that span the biological membrane, such as porins, are arranged |
|
Definition
-hydrophobic and hydrophilic on inside
-outside interacts with hydrophobic environment and inside permits a channel of water |
|
|
Term
| motif or supersecondary structure |
|
Definition
| some combinations of secondary structure |
|
|
Term
| the tertiary structure of many proteins can be divided into... |
|
Definition
| structural and functional units |
|
|
Term
| subunit (in the context of proteins) |
|
Definition
| polypeptide chain in a protein that consists of more than 1 polypeptide chain |
|
|
Term
|
Definition
| multiple polypeptide chains working together as a single unit |
|
|
Term
|
Definition
protein that doesn't have its characteristic shape
randomly coiled peptide without its normal activity |
|
|
Term
| the mpost stable structure of a protein |
|
Definition
|
|
Term
|
Definition
| proteins that prevent other proteins from tangling with each other, something like that |
|
|
Term
|
Definition
| protein correctly folds much quicker than it would if it randomly tried every single possibility |
|
|
Term
| one way proteins make themselves fold more correctly |
|
Definition
| by retaining partly correct intermediates, which are slightly more stable than unfolded regions |
|
|
Term
| stability of correctly folded proteins |
|
Definition
|
|
Term
| mechanism by which proteins fold |
|
Definition
| by progressive stabilization of intermediates |
|
|
Term
| intrinsically unstructured proteins (IUP's) |
|
Definition
| proteins that lack 3D structure under physiological conditions |
|
|
Term
| advantage of a protein being able to assume different shapes |
|
Definition
| versatility, being able to interact with different partners and yield different biochemical functions |
|
|
Term
| intrinsically unstructured proteins (IUP's) appear to be important for... |
|
Definition
| signaling and regulatory pathways |
|
|
Term
| when intrinsically unstructured proteins (IUP's) assume a defined structure |
|
Definition
| when they interact with other proteins |
|
|
Term
|
Definition
| proteins that appear to exist in an ensemble of approx equal energy that are in e'librium |
|
|
Term
| one way to study proteins |
|
Definition
| purify them and study them in vitro |
|
|
Term
|
Definition
the functional representation of the genome
encompassesd the types, functions, and interactions of proteins that yield a functional unit |
|
|
Term
| something the proteome tells us |
|
Definition
| what proteins are functionally present |
|
|
Term
| how proteins interact in the body |
|
Definition
| interact with each other to form complexes with specific functional properties |
|
|
Term
| how we acquire an understanding of the proteome |
|
Definition
| by isolating, characterizing, and cataloging proteins |
|
|
Term
| the first step in understanding a protein's function |
|
Definition
|
|
Term
| proteins can be purified based on... |
|
Definition
| their chemical properties |
|
|
Term
|
Definition
| procedure to measure the activity of a biomolecule, such as an enzyme |
|
|
Term
|
Definition
| the ratio of enzyme activity to the amount of protein in the enzyme assay at the end of each step of purification |
|
|
Term
| information you need in order to make sure the protein purification scheme is working |
|
Definition
-enzyme activity
-amount of total protein in mixture |
|
|
Term
| the fractions that result from centrifugation |
|
Definition
-pellet
-supernatant
called fractions because we fractionate the homogenate cell contents |
|
|
Term
| differential centrifugation |
|
Definition
putting the supernatant thru increasingly forceful rounds of centrifugation
yields pellets of decreasing density |
|
|
Term
|
Definition
| the fraction that is used as a source for further purification |
|
|
Term
| properties by which proteins can be purified |
|
Definition
-solubility
-size
-charge
-specific binding affinity |
|
|
Term
| some separation mechanisms that can be used to purify a protein |
|
Definition
-salting out
-separation by size
-ion-exchange chromatography
-affinity chromatography
-high-pressure liquid chromatography |
|
|
Term
|
Definition
| increase in salt concentration to make a protein dissolve in solution |
|
|
Term
|
Definition
| protein precipitation caused by increasing salt concentration |
|
|
Term
| salt concentration vs. protein solubility |
|
Definition
|
|
Term
| disadvantage of salting out |
|
Definition
| can make the protein lose its function |
|
|
Term
| what you gotta do to after salting out a protein |
|
Definition
| put the solution thru dialysis |
|
|
Term
|
Definition
the protein-salt solution is closed in a semipermeable bag which itself is immersed in a solution of low salt concentration (the dialysate)
small molecules diffuse from the bag |
|
|
Term
| molecular exclusion chromatography aka gel-filtration chromatography |
|
Definition
| separates proteins on the basis of size |
|
|
Term
| how molecular exclusion chromatography aka gel-filtration chromatography is done |
|
Definition
| percolating mix of proteins thru column of beads that increase in size as you go down the column |
|
|
Term
| ion-exchange chromatography |
|
Definition
| separating proteins on the basis of their net charge |
|
|
Term
| how ion-exchange chromatography is done |
|
Definition
| percolating mix of proteins thru column of beads that contain charged groups |
|
|
Term
| how salting out precipitates out proteins |
|
Definition
| by competition between the salt ions and the protein to keep the ion in solution |
|
|
Term
|
Definition
| separates proteins by their affinity for certain substances |
|
|
Term
| high-pressure liquid chromatography |
|
Definition
| similar to the other chromatography techniques, but uses much finer beads and high pressure is used |
|
|
Term
|
Definition
| a molecule with a net charge moving in an electric field |
|
|
Term
| how gel electrophoresis is done |
|
Definition
| proteins move thru the gel, the speed and distance depending on molecular weight and charge |
|
|
Term
|
Definition
| type of electrophoresis that uses SDS to linearize the proteins and "swamp" the charges on them, such that they differ only in size |
|
|
Term
|
Definition
| separating proteins electrophoretically based on the relative content of acidic and basic residues of the proteins |
|
|
Term
| how isoelectric focusing is done |
|
Definition
-mix of proteins undergoes electrophoresis in a pH gradient
-each protein migrates in the gel until it reaches pI |
|
|
Term
|
Definition
isoelectric point
this is the pH at which a protein has no net charge |
|
|
Term
| two-dimensional electrophoresis |
|
Definition
| first putting proteins thru isoelectric focusing, then putting them thru SDS-PAGE in a perpendicular direction |
|
|
Term
| how the success of a protein purification scheme is determined |
|
Definition
| by determining specific activity and performing an SDS-PAGE analysis |
|
|
Term
| parameters that are measured when purifying a protein |
|
Definition
-total protein
-total activity
-specific activity
-yield
-purification level |
|
|
Term
| how the quantity of protein in a fraction is measured |
|
Definition
| quantity = protein c'tration X volume |
|
|
Term
| how the enzyme activity for a fraction is obtained |
|
Definition
| total enzyme activity = enzyme activity in fraction X volume of fraction |
|
|
Term
| how specific activity is obtained |
|
Definition
| specific activity = total activity / total protein |
|
|
Term
|
Definition
measured as the total activity retained after each purification step as a percentage of the activity in the crude extract
activity in initial extract = 100% |
|
|
Term
| how purification level is measured |
|
Definition
| purification level = specific activity / specific activity of initial extract |
|
|
Term
|
Definition
|
|
Term
| the type of catalysts enzymes are |
|
Definition
| powerful and highly specific |
|
|
Term
|
Definition
| reactant an enzyme interacts with |
|
|
Term
|
Definition
| the hydrolysis of a peptide bond |
|
|
Term
| what causes an enzyme to be specific? |
|
Definition
| the precise interaction of the substrate with the enzyme |
|
|
Term
|
Definition
| because of its intricate, 3D structure |
|
|
Term
| 6 major classes of enzymes |
|
Definition
1: oxidoreductases
2: transferases
3: hydrolyases
4: lyases
5: isomerases
6: ligases |
|
|
Term
|
Definition
| transfer electrons between molecules to catalyze redox rxns |
|
|
Term
|
Definition
| transfer functional groups between molecules |
|
|
Term
|
Definition
| cleaves molecules by the addition of water |
|
|
Term
|
Definition
| adds atoms or functional groups to a double bond or removes them to form double bonds |
|
|
Term
|
Definition
| they move functional groups within a molecule |
|
|
Term
|
Definition
| they join 2 molecules in a rxn powered by ATP hydrolysis |
|
|
Term
| many enzymes require this for activity |
|
Definition
|
|
Term
|
Definition
| small molecules that help activate an enzyme |
|
|
Term
|
Definition
| enzyme without its cofactor |
|
|
Term
|
Definition
| the complete, catalytically active, enzyme; has the cofactor |
|
|
Term
|
Definition
|
|
Term
|
Definition
| small organic molecules derived from vitamins; type of cofactor |
|
|
Term
| prosthetic (helper) groups |
|
Definition
|
|
Term
| loosely associated coenzymes are more like... |
|
Definition
cosubstrates
they bind to and are released from enzymes |
|
|
Term
| difference between coenzymes and normal substrates |
|
Definition
| coenzymes are derived from vitamins and used by a variety of enzymes |
|
|
Term
|
Definition
| measures the amount of useful energy, the energy capable of doing work |
|
|
Term
| thermodynamic properties that need to be considered to understand how enzymes operate |
|
Definition
1: the free energy difference (ΔG) between the products and the reactants
2: the free energy required to initiate the conversion of reactants into products (activation energy) |
|
|
Term
| thermodynamic property affected by enzymes |
|
Definition
| the free energy required to initiate the rxn (activation energy) |
|
|
Term
| ΔG of a rxn determines... |
|
Definition
| whether or not the rxn will take place spontaneously |
|
|
Term
| a rxn can occur spontaneously only if... |
|
Definition
|
|
Term
|
Definition
-rxn that releases energy
-occurs spontaneously
-ΔG negative |
|
|
Term
|
Definition
-requires energy input
-not spontaneous
-ΔG positive |
|
|
Term
|
Definition
| rxn can't be spontaneous and energy input is required |
|
|
Term
|
Definition
| rxn is spontaneous and energy is released |
|
|
Term
|
Definition
| the system is at e'librium and there's no net change in energy |
|
|
Term
|
Definition
ΔG rxn = ΔG products - ΔG reactants
this is independent of path |
|
|
Term
| some info ΔG does not provide |
|
Definition
|
|
Term
| the rate of a rxn depends on... |
|
Definition
| the free energy of activation (ΔGt) |
|
|
Term
|
Definition
| free energy of activation |
|
|
Term
| the standard free-energy change of a rxn is related to... |
|
Definition
|
|
Term
| how to calculate ΔG of a rxn |
|
Definition
ΔG = ΔG° + RTln([each product]/[each reactant])
ΔG = free energy change of a rxn
ΔG° = standard free energy change
R = gas constant
T = absolute temperature |
|
|
Term
|
Definition
standard free energy change
expressed in kJ/mol |
|
|
Term
|
Definition
| gas constant (standard 8.315 X 10-3kJ mol-1 K-1) |
|
|
Term
|
Definition
| absolute temperature (standard 298 K) |
|
|
Term
|
Definition
standard free energy change at pH 7
expressed in kJ/mol |
|
|
Term
|
Definition
0 = ΔG°' + RTln([each product]/[each reactant])
so
ΔG°' = -RTln([each product]/[each reactant])
ΔG = free energy change of a rxn
ΔG°' = standard free energy change at pH 7
R = gas constant
T = absolute temperature |
|
|
Term
|
Definition
| e'librium constant under standard conditions |
|
|
Term
|
Definition
| K'eq = ([each product]/[each reactant]) |
|
|
Term
|
Definition
| ΔG°' = -RTln([each product]/[each reactant])
ΔG°' = -RTln(K'eq) |
|
|
Term
|
Definition
| K'eq = [each product]/[each reactant]
K'eq = e-ΔG°'/RT
K'eq = e-ΔG°'/2.47 |
|
|
Term
| the size of ΔG relative to ΔG°' depends on... |
|
Definition
| the concentrations of the reactants and products |
|
|
Term
| what enzymes do to e'librium |
|
Definition
| accelerate the attainment of e'librium |
|
|
Term
| the e'librium position is a function of... |
|
Definition
| only the free energy difference between rxns and products |
|
|
Term
|
Definition
|
|
Term
|
Definition
| free energy of activation / activation energy |
|
|
Term
|
Definition
| difference between free energy of substrate and free energy of transition state |
|
|
Term
| how enzymes lower activation energy |
|
Definition
| by facilitating the formation of the transition state |
|
|
Term
| the first step in enzymatic catalysis |
|
Definition
| the formation of an enzyme-substrate complex |
|
|
Term
|
Definition
| the region of an enzyme that binds to the substrate and cofactor |
|
|
Term
|
Definition
| the amino acid residues within active sites that directly participate in making and breaking bonds |
|
|
Term
| the binding of enzyme to substrate is mediated by... |
|
Definition
| weak forces, such as H bonding, van der Waals, and electrostatic forces |
|
|
Term
| an enzyme's specificity of binding depends on... |
|
Definition
| the percisely defined arrangement of atoms in an active site |
|
|
Term
|
Definition
| enzyme adjusting to fit with the substrate |
|
|
Term
|
Definition
| certain conformations of an enzyme that a substrate may bind to |
|
|
Term
|
Definition
| the free energy released when an enzyme binds to the substrate |
|
|
Term
|
Definition
| compound that resembles the transition state of a rxn, but isn't capable of being acted on by the enzyme |
|
|
Term
| what transition-state analogs do to enzymes |
|
Definition
| inhibit them by resembling the transition state, but the enzyme can't act on it |
|
|
Term
| An enzyme will specifically bind its substrate primarily because of... |
|
Definition
| A large number of weak interactions at the active site |
|
|
Term
|
Definition
|
|
Term
|
Definition
| study of the rates of enzyme-catalyzed rxns |
|
|
Term
|
Definition
| quantity of reactant that disappears in a specified unit of time |
|
|
Term
| how to calculate velocity of a rxn (V) |
|
Definition
V = -d[A]/dt = d[P]/dt
V = velocity of rxn
d = decrease in substrate concxentration or increase in product concentration
t = time
A = reactant A
P = product P |
|
|
Term
| velocity of rxn (V) vs. rate constant (k) |
|
Definition
V = k[each reactant]
V = velocity of rxn
k = rate constant |
|
|
Term
|
Definition
| rxn in which the velocity is directly proportional to the reactant concentration
have unit s-1 |
|
|
Term
|
Definition
| rxn that includes 2 reactants
have units M-1 s-1 (per mole per second) |
|
|
Term
|
Definition
| second-order rxns that appear to be first-order rxns |
|
|
Term
|
Definition
| rxn in which rate is independent of rxn concentration |
|
|
Term
| rate equation of a first-order rxn |
|
Definition
|
|
Term
| rate equation of a second-order rxn |
|
Definition
|
|
Term
| this is a necessary intermediate in catalysis |
|
Definition
|
|
Term
| Michaelis-Menton equation |
|
Definition
| V0 = Vmax X ([S]/([S] + KM))
V0 = initial velocity
Vmak = maximum velocity
S = substrate
KM = Michaelis constant |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| when Vmax can be obtained |
|
Definition
| when total enzyme (ET) is attained |
|
|
Term
| when the enzyme is said to be saturated |
|
Definition
| when all the available enzyme is bound to the substrate and displaying zero-order kinetics |
|
|
Term
|
Definition
| the substrate concentration at which the rxn velocity is half its maximal value |
|
|
Term
|
Definition
| 1/V0 = (KM/Vmax) X (1/S) + (1/Vmax) |
|
|
Term
| the KM value of an enzyme varies based on... |
|
Definition
| substrate and environmental conditions |
|
|
Term
| enzymes when substrate concentration is below KM |
|
Definition
| enzymes have little activity and are sensitive to changes in substrate concentration |
|
|
Term
| enzymes when substrate concentration is above KM |
|
Definition
| enzymes have much activity and are insensitive to changes in substrate concentration |
|
|
Term
| enzymes when substrate concentration is approximately KM |
|
Definition
| enzymes have much activity and are sensitive to changes in substrate concentration |
|
|
Term
| maximal velocity (Vmax) reveals... |
|
Definition
| an enzyme's turnover number |
|
|
Term
| an enzyme's turnover number |
|
Definition
| the number of substrate molecules than an enzyme can convert into product per unit time when the enzyme is fully saturated with substrate |
|
|
Term
| this limits theb rate of formation of the ES complex |
|
Definition
| diffusion; can't be faster than the diffusion controlled enzyme-substrate encounter |
|
|
Term
|
Definition
| when catalytic velocity is restricted only by the rate at which enzymes encounter substrate in the solution |
|
|
Term
| when enzymes have kinetic perfection |
|
Definition
| when they have their Kcat/KM ratios at their upper limits |
|
|
Term
| the 2 classes of multiple substrate rxns |
|
Definition
1: sequential rxns
2: double-displacement rxns |
|
|
Term
|
Definition
| all substrates must bind to the enzyme before any product is released |
|
|
Term
|
Definition
| rxn where a ternary complex forms |
|
|
Term
|
Definition
| consists of enzyme and both substrates |
|
|
Term
| the types of sequential mechanisms for sequential rxns |
|
Definition
|
|
Term
| ordered mechanism for sequential rxns |
|
Definition
| substrates bind to the enzyme in a defined sequence |
|
|
Term
| double-displacement (ping-pong) rxns |
|
Definition
| one or more products are released before all substrates bind the enzyme |
|
|
Term
| the defining feature of double-displacement rxns |
|
Definition
| the existence of a substituted enzyme intermediate |
|
|
Term
| substituted enzyme intermediate |
|
Definition
| in a double-displacement rxn, this is when the enzyme is temporarily modified |
|
|
Term
| representation of sequential rxn |
|
Definition
|
|
Term
| representation of double-displacement rxn |
|
Definition
|
|
Term
| which parameter of an enzyme-catalyzed rxn depends on enzyme concentration? |
|
Definition
|
|
Term
| KM is the equivalent of... |
|
Definition
| Substrate concentration when 1/2 Vmax is reached |
|
|
Term
| what parameter of an enzyme-catalyzed rxn is a measure for the affinity of its substrate? |
|
Definition
|
|
Term
| When a substrate concentration is MUCH greater than KM, the rate of catalysis is almost equal to... |
|
Definition
|
|
Term
|
Definition
| enzymes that follow Michaelis-Menten kinetics |
|
|
Term
| how Michaelis-Menten enzyme action is governed |
|
Definition
| simply by mass action; they catalyze when substrate is present |
|
|
Term
| the type of enzymes most enzymes in the cell are |
|
Definition
| Michaelis-Menten enzymes; not regulated in the cell |
|
|
Term
| an effective way to regulate metabolic traffic |
|
Definition
| regulating enzyme activity |
|
|
Term
| the enzymes that regulate metabolic traffic |
|
Definition
|
|
Term
| key features of allosteric enzymes |
|
Definition
-regulation of catalytic activity by environmental signals
-kinetics more complex than those of Michaelis-Menten enzymes
-quaternary structure with multiple active sites in each enzyme |
|
|
Term
|
Definition
| seems to be the step after which the rxn that yields the final product will take place |
|
|
Term
|
Definition
| seems to be the final product of a pathway binding reversibly to the committed step to inhibit the rxn |
|
|
Term
| depiction of feedback inhibition |
|
Definition
[image]
here, the final product binds to an alternate site on the allosteric enzyme to inhibit the committed step |
|
|
Term
| enzymes that catalyze the committed step of metabolic pathways |
|
Definition
| allosteric enzymes always do this |
|
|
Term
| some molecules allosteric enzymes can recognize to regulate production of the final product |
|
Definition
-inhibitor molecules
-stimulatory molecules |
|
|
Term
| depiction of a pathway that uses both inhibition and stimulation |
|
Definition
[image]
here, F and I stimulate the production of each other, F inhibits production of itself, I inhibits production of itself, and K inhibits production of both F and I, thus inhibiting production of itself |
|
|
Term
| how allosteric enzymes are regulated |
|
Definition
-changes in substrate concentration
-other molecules, i.e., non-substrate molecules |
|
|
Term
| how Michaelis-Menten enzymes and allosteric enzymes differ in kinetics |
|
Definition
[image]
the curve for allosteric is sigmoidal because it resembles the letter S |
|
|
Term
| 2 properties unique to allosteric enzymes |
|
Definition
1: regulation of catalytic activity
2: sigmoidal kinetics |
|
|
Term
| the kinetics of allosteric enzymes |
|
Definition
| sigmoidal (resembles S on a graph) |
|
|
Term
| the concerted model or MWC model of allosteric enzyme regulation |
|
Definition
based on several premises
-allosteric enzymes have multiple active sites on different polypeptide chains
-the enzyme can exist in the R (relaxed, more active) or T (tense, less active) conformation state
-all subunits or active sites must be in the same state; no hybrids (this is the symmetry rule)
-substrate (S) binds more readily with R form than T form |
|
|
Term
| the active sites on allosteric enzymes |
|
Definition
| have multiple active sites on different polypeptide chains |
|
|
Term
| the 2 conformations or states an allosteric enzyme can be in |
|
Definition
-R (relaxed, active)
-T (tense, less active) |
|
|
Term
| state of allosteric enzyme when there's no substrate |
|
Definition
| R and T states in e'librium, with T being more stable and thus more common |
|
|
Term
|
Definition
| the t/r ratio, which is in the hundreds when there's no substrate |
|
|
Term
|
Definition
| rule that all the subunits or active sites of an allosteric enzyme be in the same state |
|
|
Term
| the form of allosteric enzyme substrates more readily bind to |
|
Definition
|
|
Term
| why allosteric enzymes have sigmoidal (S-shaped) kinetics |
|
Definition
| because the binding of substrate disrupts the T <--> R e'librium in favor of R |
|
|
Term
|
Definition
accumulation of substrate binding and disrupting the T <--> R e'librium in favor of R
this accounts for the sharp increase in velocity of rxn |
|
|
Term
| the physiological significance of cooperativity in allosteric enzymes (accumulation of substrate binding and disrupting the T <--> R e'librium in favor of R) |
|
Definition
| allosteric enzymes are more sensitive to changes in substrate concentration near KM than Michaelis-Menten enzymes with the same Vmax |
|
|
Term
|
Definition
| rapid increase in enzyme activity above a certain threshold |
|
|
Term
| how the T <--> R e'librium of allosteric enzymes is regulated |
|
Definition
| regulator molecules, such as positive and negative effectors |
|
|
Term
|
Definition
binds to the R form of an allosteric enzyme at a regulatory site, distinct from the active site, to stabilize it, increasing c'tration of R and making that enzyme more likely to bind with substrate
make allosteric enzyme more sensitive to substrate |
|
|
Term
|
Definition
binds to T form of an allosteric enzyme and stabilizes it, increasing c'tration of T, which makes the R form less likely to bind with substrate
make allosteric enzyme less sensitive to substrate |
|
|
Term
|
Definition
| effects of regulatory molecules on allosteric enzymes |
|
|
Term
|
Definition
| effects of substrates on allosteric enzymes |
|
|
Term
|
Definition
| the binding of substrate to one site of the allosteric enzyme influencing substrate binding to the neighboring sites without necessarily inducing a transition encompassing the entire enzyme |
|
|
Term
| depiction of sequential model |
|
Definition
|
|
Term
|
Definition
| the binding of one substrate decreasing the affinity of other sites on an allosteric enzyme for the substrate |
|
|
Term
| the model many allosteric enzymes follow |
|
Definition
| some combination of the concerted and sequential model |
|
|
Term
| what hemoglobin does for the body |
|
Definition
| carries oxygen to tissues and contributes to the transport of CO2 and H ions back to the lungs |
|
|
Term
| is allostery limited to enzymes? |
|
Definition
| no; hemoglobin is an allosteric protein |
|
|
Term
|
Definition
| found in muscle, this protein facilitates the diffusion of O to cellular sites and provides reserve supply of O |
|
|
Term
| the kinetics of hemoglobin |
|
Definition
|
|
Term
| the kinetics of myoglobin |
|
Definition
| hyperbolic curve (like that of a Michaelis-Menten enzyme) |
|
|
Term
| what determines the amount of O hemoglobin releases as it passes thru the tissues? |
|
Definition
| allosteric regulators at the tissues |
|
|
Term
| why does hemoglobin release more O than myoglobin would? |
|
Definition
| because of cooperativity between O binding sites in hemoglobin |
|
|
Term
| the 2 forms myoglobin can exist in |
|
Definition
-deoxymyoglobin
-oxymyoglobin |
|
|
Term
| where O binds in hemoglobin and myoglobin |
|
Definition
|
|
Term
| depiction of a heme group |
|
Definition
|
|
Term
| oxidation state of hemoglobin's Fe in normal conditions |
|
Definition
|
|
Term
|
Definition
| the histidine residue that occupies the 5th coordination site of the Fe atom in hemoglobin; it's on one side of the plane of the heme group |
|
|
Term
| the part of the Fe atom in hemoglobin available for binding with O |
|
Definition
| the 6th coordination site; this is on the opposite side of the proximal histidine |
|
|
Term
|
Definition
| resides on the opposite side of the heme group from the proximal histidine |
|
|
Term
| what the distal histidine does for hemoglobin |
|
Definition
| -prevents oxidation of the heme to the ferric (Fe+3) ion
-reduces the ability of CO to bind to the heme
-H bonds with bound O to stabilize it |
|
|
Term
| depiction of deoxyhemoglobin and oxyhemoglobin |
|
Definition
[image]
in deoxy form, the Fe is slightly outside the plane, but in the oxy form, the Fe is in the plane |
|
|
Term
| how O bound to hemoglobin is stabilized |
|
Definition
| by forming a H bond wit the distal histidine |
|
|
Term
| the structure of hemoglobin |
|
Definition
|
|
Term
| the subunits of hemoglobin |
|
Definition
| -2 α subunits
-2 β subunits
functions as a pair of identical αβ dimers, together forming a tetramer
α1β1 dimer and α2β2 dimer |
|
|
Term
| the αβ dimers of hemoglobin are linked by... |
|
Definition
| an extensive interface which includes, among other regions, the carboxyl terminus of each chain |
|
|
Term
| the interface between the αβ dimers of hemoglobin consists of... |
|
Definition
| among other regions, the carboxyl terminus of each chain |
|
|
Term
| the allosteric state deoxyhemoglobin corresponds to |
|
Definition
|
|
Term
| the allosteric state oxyhemoglobin corresponds to |
|
Definition
|
|
Term
| how O binding to hemoglobin affects the quaternary state of hemoglobin |
|
Definition
| binding of O on one subunit makes the α1β1 and α2β2 dimers rotate about 15 degrees with respect to each other
converts from T to R state |
|
|
Term
| the molecule that regulates hemoglobin within red blood cells |
|
Definition
2,3-biphosphoglycerate (2,3-BPG)
regulates hemoglobin's affinity for O such that sufficient amounts are supplied to aerobic tissues |
|
|
Term
| how 2,3-biphosphoglycerate (2,3-BPG) regulates hemoglobin's O affinity |
|
Definition
| goes in the center of the deoxyhemoglobin (T state) and binds to 3 positively charged groups on each β chain by way of ionic bonds, stabilizing the T state and reducing its affinity for O |
|
|
Term
| what must happen to 2,3-biphosphoglycerate (2,3-BPG) for hemoglobin to change from the T to the R state? |
|
Definition
| the bonds between hemoglobin and 2,3-biphosphoglycerate (2,3-BPG) must break ad the 2,3-biphosphoglycerate (2,3-BPG) must be expelled from the molecule |
|
|
Term
| depiction of 2,3-biphosphoglycerate (2,3-BPG) in deoxyhemoglobin (T state) |
|
Definition
|
|
Term
| the β chain groups 2,3-biphosphoglycerate (2,3-BPG) ionically bonds with |
|
Definition
|
|
Term
| depiction of 2,3-biphosphoglycerate (2,3-BPG) and the β chain groups it ionically bonds with |
|
Definition
|
|
Term
| is 2,3-BPG the only allosteric regulator of hemoglobin? |
|
Definition
|
|
Term
| how tissues most in need of O, such as muscle, get the O they need |
|
Definition
| 1: muscle releases CO2
2: CO2 diffuses into the red blood cell
3: this rxn occurs in the red blood cell: CO2 + H2O <--> H2CO3 <--> HCO3- + H+
this enhances the release of O fromn hemoglobin |
|
|
Term
|
Definition
| the regulation of O binding by H+ and CO2 |
|
|
Term
| other than regulatory molecules, what can affect hemoglobin's affinity for O? |
|
Definition
|
|
Term
| effect of pH on hemoglobin's affinity for O |
|
Definition
| lower pH leads to lower affinity for O |
|
|
Term
| effect of partial pressure on hemoglobin's affinity for O |
|
Definition
| lower partial pressure leads to lower affinity for O |
|
|
Term
| the chemical basis of pH regulating hemoglobin's affinity for O (Bohr effect) |
|
Definition
| at low pH, the side chain of histidine gets protonated to form a salt bridge with the CO2- group on the aspartate, stabilizing the T state, favorin greater release of O at actively metabolizing tissues
at high pH, histidine's side chain is not protonated and the salt bridge does not form, favoring O binding |
|
|
Term
| how CO2 reduces hemoglobin's affinity for O |
|
Definition
| CO2 binds with the terminal amino groups to form negatively charged carbamate groups, stabilizing the T state, favoring the release of O |
|
|
Term
| where the amino termini are in hemoglobin |
|
Definition
| at the interface between the αβ dimers |
|
|
Term
| some strategies enzymes use to facilitate the formation of transition states |
|
Definition
1: covalent catalysis
2: general acid-base catalysis
3: metal ion catalysis
4: catalysis by approximation and orientation |
|
|
Term
|
Definition
| active site contains reactive group, usually a powerful nucleophile that becomes temporarily covalently modified in the course of catalysis |
|
|
Term
| general acid-base catalysis |
|
Definition
| molecule other than water plays role of proton donor or acceptor |
|
|
Term
|
Definition
metal acts as an electrophilic catalyst either by stabilizing a negative charge on a rxn intermediate, generating a nucleophile by increasing the acidity of nearby molecules, or increasing the binding energy of the enzyme-substrate interaction by binding to substrates
basically, metal ion draws electrons away from substrate |
|
|
Term
| catalysis by approximation and orientation |
|
Definition
| enhancing rxn rate by bringing 2 substrates into proximity and in the proper orientation on a single binding surface on the enzyme |
|
|
Term
| enzyme activity can be modulated by... |
|
Definition
-temp
-pH
-inhibitory molecules |
|
|
Term
| why increased heat increases enzyme activity |
|
Definition
| because it increases the Brownian motion, and therefore the chance of collision, making activity more likely |
|
|
Term
| enzyme activity increases with temp until... |
|
Definition
| the enzyme becomes denatured |
|
|
Term
| the pH dependence of enzymes is due to... |
|
Definition
|
|
Term
| how enzyme inhibitors can be useful |
|
Definition
| specific inhibitors can be used to identify residues critical for catalysis |
|
|
Term
| an especially potent type of inhibitor |
|
Definition
|
|
Term
|
Definition
| characterized by rapid dissociation of the enzyme-inhibitor complex |
|
|
Term
| 3 common types of reversible inhibition |
|
Definition
-competitive inhibition
-uncompetitive inhibition
-noncompetitive inhibition |
|
|
Term
|
Definition
| inhibitor resembles the substrate and binds to the active site |
|
|
Term
| how competitive inhibition can be alleviated |
|
Definition
| by increasing the concentration of substrate |
|
|
Term
|
Definition
| inhibitor binds to enzyme-substrate complex; binding of enzyme to substrate creates active site for uncompetitive inhibitor |
|
|
Term
| can increased concentration of substrate overcome uncompetive inhibition? |
|
Definition
|
|
Term
| noncompetitive inhibition |
|
Definition
| noncompetitive inhibitor binds to alternate site to make enzyme less functional |
|
|
Term
| can noncompetitive inhibition be overcome by increasing the concentration of substrate? |
|
Definition
|
|
Term
| depiction of competitive inhibition |
|
Definition
|
|
Term
| depiction of uncompetitive inhibition |
|
Definition
|
|
Term
| depiction of noncompetitive inhibition |
|
Definition
|
|
Term
| the hallmark of competitive inhibition |
|
Definition
| it can be overcome by sufficient concentrations of substrate |
|
|
Term
| kinetics of a competitive inhibitor |
|
Definition
| raises the KM (this new apparent value is called (KMapp)
does not affect the Vmax |
|
|
Term
| what uncompetitive inhibition of an enzyme does to that enzyme's rxn |
|
Definition
| makes the ES complex not proceed to form any product |
|
|
Term
| kinetics of an uncompetitive inhibitor |
|
Definition
| lower Vmax, now called VMapp
lower KM, now called KMapp |
|
|
Term
| kinetics of noncompetitive inhibition |
|
Definition
| lower Vmax, now called VMapp
KM unchanged
it's as if there's less enzyme |
|
|
Term
| something irreversible inhibitors can be used for |
|
Definition
|
|
Term
|
Definition
| dissociates very slowly from target enzyme due to tight bonding, either covalent or noncovalent |
|
|
Term
| irreversible inhibitors that covalently bind to enzymes are used for... |
|
Definition
elucidating mechanisms of enzymes
if inhibitor decreases function, this suggests that modified group is needed for proper function |
|
|
Term
| the first step in determining the chemical mechanism of an enzyme |
|
Definition
| to determine which functional groups are required for enzyme activity |
|
|
Term
| 4 categories of irreversible inhibitors |
|
Definition
1: group-specific reagents
2: affinity labels (substrate analogs)
3: suicide inhibitors
4: transition-state analogs |
|
|
Term
|
Definition
| type of irreversible inhibitor that modifies specific R groups of amino acids |
|
|
Term
| affinity labels (substrate analogs) |
|
Definition
type of irreversible inhibitor covalently modifies active site residues and is structurally similar to an enzyme's substrate
thus more specific for active site than group-specific reagents |
|
|
Term
| suicide inhibitors aka mechanism-based inhibitors |
|
Definition
type of irreversible inhibitor that is a chemically modified substrate
binds to enzyme as substrate to produce reactive intermediate that inactivates enzyme by covalent modification |
|
|
Term
| type of irreversible inhibitor that provides researchers the most specific means of modifying an enzyme's active site |
|
Definition
| suicide inhibitors aka mechanism-based inhibitors |
|
|
Term
|
Definition
| type of irreversible inhibitor that closely resembles the transition state and potently inhibits the enzyme |
|
|
Term
| important piece of info supporting the role of the formation of transition states in enzyme catalysis |
|
Definition
| the inhibitory power of transition-state analogs |
|
|
Term
| composition of carbohydrates |
|
Definition
| they are C based molecules rich in hydroxyl (-OH) groups |
|
|
Term
| empirical formula for many carbohydrates |
|
Definition
|
|
Term
| why carbohydrates can be used for functions as simple as energy storage to as complex as cell-cell recognition |
|
Definition
| because of the vast array of 3d structures that can arise due to the variety of monosaccharides and the multiplicity of linkages that form within carbohydrate polymers |
|
|
Term
| why carbohydrates can form a variety of 3d structures |
|
Definition
| because of the vast array of 3d structures that can arise due to the variety of monosaccharides and the multiplicity of linkages that form within carbohydrate polymers |
|
|
Term
|
Definition
| aldehydes or ketones that have 2 or more hydroxyl (-OH) groups |
|
|
Term
|
Definition
| carbohydrate that contains a ketone group |
|
|
Term
|
Definition
| carbohydrate that contains an aldehyde group |
|
|
Term
|
Definition
| carbohydrates that contain 3 C's |
|
|
Term
|
Definition
| have identical molecular formula, but differ in how the atoms are ordered |
|
|
Term
|
Definition
| isomers that differ in spatial arrangement |
|
|
Term
|
Definition
|
|
Term
|
Definition
| stereoisomers that are not mirror images of each other; they're not enantiomers |
|
|
Term
|
Definition
| diastereoisomers that differ in one of several C atoms |
|
|
Term
|
Definition
| diastereoisomers that differ at a new asymmetric C atom formed on ring closure |
|
|
Term
| the predominant forms of some monosaccharides in solution |
|
Definition
| cyclic rings instead of open chains |
|
|
Term
| the chemical basis for ring formation |
|
Definition
| an aldehyde can react with an alcohol to form a hemiacetal |
|
|
Term
|
Definition
| formed when an aldehyde complexes with an alcohol |
|
|
Term
|
Definition
| formed when a ketone complexes with an alcohol |
|
|
Term
|
Definition
| OH groups on same side of ring |
|
|
Term
|
Definition
| OH groups on different sides of ring |
|
|
Term
|
Definition
| the C atom where the molecule can be either the α or β anomer |
|
|
Term
|
Definition
| substituents that are nearly perpendicular to the ring |
|
|
Term
|
Definition
| nearly parallel to the plane of the ring |
|
|
Term
| which tend to be more crowded? axial or equatorial substituents? |
|
Definition
|
|
Term
|
Definition
| bonds that join monosaccharides to alcohols and amines |
|
|
Term
|
Definition
| bond between the anomeric C atom of a glucose and the O atom of an alcohol |
|
|
Term
|
Definition
| bond between the anomeric C atom of a glucose and the N atom of an amine |
|
|
Term
| 3 common reactants in the modification of monosaccharides |
|
Definition
-alcohols
-amines
-phosphates |
|
|
Term
| the type of bond between adjacent monosaccharides in oligo- and polysaccharides |
|
Definition
|
|
Term
|
Definition
| catalyze the formation of glycosidic bonds |
|
|
Term
|
Definition
| carbohydrate that has a substituent on it attached by a glycosidic bond |
|
|
Term
| some common disaccharides |
|
Definition
|
|
Term
| some storage forms of glucose |
|
Definition
|
|
Term
|
Definition
| polysaccharide in which all the monomer units are the same |
|
|
Term
|
Definition
| a polysaccharide that is a storage form of glucose in animals; it's the most common storage form of glucose in animal cells |
|
|
Term
| in human tissues, glycogen is most common in... |
|
Definition
|
|
Term
|
Definition
| homopolymer storage form of glucose in plants |
|
|
Term
|
Definition
|
|
Term
|
Definition
| unbranched form of starch, consisting of glucose molomers in α-1,4 linkage |
|
|
Term
|
Definition
| branched form of starch having about 1 α-1,6 linkage per 30 α-1,4 linkages |
|
|
Term
|
Definition
| enzyme secreted by the salivary glands that readily breaks down amylose, amylopectin, and glycogen |
|
|
Term
|
Definition
| structural polysaccharide in plants that is made of glucose monomers joined by a β-1,4 linkage |
|
|
Term
| what α and β linkages do for structure of polysaccharides |
|
Definition
| β linkages favor straight chains with H bonding between the strands while α linkages favor bent and helical structures, which are better for storage |
|
|
Term
|
Definition
| protein with a carbohydrate covalently attached to it |
|
|
Term
| amount of glycoproteins in the proteome |
|
Definition
| glycoproteins are 50% of the proteome |
|
|
Term
| 3 classes of glycoproteins |
|
Definition
-glycoproteins
-proteoglycans
-mucins/mucoproteins |
|
|
Term
| composition of glycoproteins |
|
Definition
| protein component is the largest constituent by weight |
|
|
Term
| function of glycoproteins |
|
Definition
| many, such as components of cell membranes, where they take part in processes such as cell adhesion and binding of sperm to eggs |
|
|
Term
| composition of proteoglycans |
|
Definition
protein component is conjugated to a type of polysac called a glycosyaminoglycan
carbohydrates take up a significant portion of proteoglycans |
|
|
Term
| function of proteoglycans |
|
Definition
-structural components
-lubricants |
|
|
Term
|
Definition
| type of polysac that a proteoglycan is conjugated to |
|
|
Term
| composition of mucins/mucoproteins |
|
Definition
| predominantly carbohydrate |
|
|
Term
| function of mucins/mucoproteins |
|
Definition
|
|
Term
| what determines polysac structure? |
|
Definition
|
|
Term
| amino acids that carbohydrates may be linked to |
|
Definition
-asparagine
-serine
-threonine |
|
|
Term
|
Definition
| linking of carbohydrates to asparagine, serine, or threonine |
|
|
Term
| some structural functions of proteoglycans |
|
Definition
-connective tissue
-mediate adhesion of cells to the extracellular matrix
-bind factors that regulate cell proliferation |
|
|
Term
| the properties of proteoglycans are determined primarily by... |
|
Definition
| the glycosaminoglycan component |
|
|
Term
| composition of many glycosaminoglycans |
|
Definition
made of repeating units of disaccharides containing a derivative of an amino sugar, either glucosamine or galactosamine
at least one of the 2 sugars in the repeating unit has a negatively charged sulfate group |
|
|
Term
|
Definition
| they bind specific carbohydrate structures on neighboring cell surfaces |
|
|
Term
|
Definition
| they facilitate cell-cell contact |
|
|
Term
| how lectins facilitate cell-cell contact |
|
Definition
| the lectins on the surface of one cell interact with arrays of carbohydrates displayed on the surface of another cell |
|
|
Term
| the 3 stages of generating energy from the oxidation of food |
|
Definition
1: digestion (large molecules being broken down into smaller molecules)
2: numerous small molecules being degraded into a few simple units that play a central role in metabolism; most of these simple units are converted into acetyl CoA
3: producing ATP from the complete oxidation of acetyl CoA; this involves the citric acid cycle and oxidative phosphorylation |
|
|
Term
|
Definition
| large molecules being broken down into smaller molecules |
|
|
Term
|
Definition
-tricarboxylic acid (TCA) cycle
-Krebs cycle |
|
|
Term
|
Definition
| the extraction of energy from fuels |
|
|
Term
| depiction of the stages of catabolism |
|
Definition
|
|
Term
| 3 things living organisms need energy for |
|
Definition
1: mechanical work in muscle contraction and cellular movements
2: active transport of molecules and ions
3: synthesis of macromolecules and other biomolecules from simple precursors |
|
|
Term
|
Definition
| photosynthetic organisms that obtain energy by trapping sunlight in a chemical form |
|
|
Term
|
Definition
| organisms that obtain energy thru the oxidation of C fuels |
|
|
Term
| some basic principles that underlie energy flow in all living systems |
|
Definition
1: fuels are degraded and large molecules are constructed step by step in a series of linked rxns called metabolic pathways
2: an energy currency common to all life forms, ATP, links energy releasing pathways with energy requiring pathways
3: the oxidation of C fuels powers the formation of ATP
4: although there are many metabolic pathways, a limited number of types of reactions and particular intermediates are common to many pathways
5: metabolic pathways are highly regulated to allow the efficient use of fuels and to coordinate biosynthetic processes |
|
|
Term
|
Definition
| series of linked rxns in which fuels are degraded and large molecules are constructed |
|
|
Term
|
Definition
links energy releasing pathways with energy requiring pathways
this is the energy currency |
|
|
Term
| what powers the formation of ATP? |
|
Definition
|
|
Term
|
Definition
| a linked series of chemical rxns that begins with a particular biomolecule and converts it into some other required biomolecule in a carefully defined fasion |
|
|
Term
|
Definition
| defined metabolic pathways in the cell |
|
|
Term
| 2 broad classes of metabolic pathways |
|
Definition
1: those that convert energy from fuel into biologically useful forms (catabolic)
2: those that require input of energy to proceed (anabolic) |
|
|
Term
|
Definition
| breaking down fuels to release cellular energy |
|
|
Term
|
Definition
| using energy to synthesize biomolecules |
|
|
Term
|
Definition
| can be either anabolic or catabolic, depending on conditions in the cell |
|
|
Term
| an important principle of metabolism |
|
Definition
| although biosynthetic and degradative pathways often have rxns in common, the regulated, irreversible reactions of each pathway are almost always distinct from each other |
|
|
Term
| how anabolic and catabolic rxns interact |
|
Definition
| energy released from catabolic rxns is used to power anabolic rxns |
|
|
Term
| 2 criteria a metabolic pathway has to meet |
|
Definition
1: the individual rxns must be specific
2: the entire set of rxns that constitute the pathway must be thermodynamically favored |
|
|
Term
| the nature of a rxn depends on... |
|
Definition
-the nature of the reactants and products
-the concentrations of reactants and products |
|
|
Term
| a thermodynamically unfavorable rxn can be driven by... |
|
Definition
| a thermodynamically favorable rxn |
|
|
Term
| ATP can be thought of as... |
|
Definition
| the currency that facilitates the commerce of the cell (metabolism) |
|
|
Term
|
Definition
|
|
Term
|
Definition
| adenine with a triphosphate unit attached |
|
|
Term
|
Definition
| because its triphosphate unit contains 2 phosphoanhydride linkages |
|
|
Term
| phosphoanhydride linkages |
|
Definition
| formed between 2 phosphoryl groups accompanied by the loss of a water molecule |
|
|
Term
| how energy is released from ATP |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| phosphates that can be released from ATP hydrolysis |
|
Definition
|
|
Term
| when ATP is formed from ADP and Pi in chemotrophs |
|
Definition
| when fuel molecules are oxidized |
|
|
Term
| when ATP is formed from ADP and Pi in phototrophs |
|
Definition
|
|
Term
| how an otherwise unfavorable rxn can be made possible |
|
Definition
| by coupling it to ATP hydrolysis |
|
|
Term
| standard free energy of hydrolysis |
|
Definition
| the energy released when the phosphorylated compound transfers the phosphoryl group to water under standard conditions |
|
|
Term
| magnitude of ΔG⁰' vs. phosphoryl-transfer potential |
|
Definition
|
|
Term
| factors that differentiate the stability of the reactants and products |
|
Definition
1: electrostatic repulsion
2: resonance stabilization
3: increase in entropy
4: stabilization due to hydration |
|
|
Term
| how electrostatic repulsion affects stability of reactants and products |
|
Definition
| ATP has 4 negative charges in close proximity to each other; the repulsion between them is reduced when ATP is hydrolyzed |
|
|
Term
| how resonance stabilization affects stability of reactants and products |
|
Definition
| phosphate has greater resonance stabilization when released from ATP |
|
|
Term
| how increase in entropy affects stability of reactants and products |
|
Definition
| products of ATP hydrolysis have 2 molecules instead of 1 |
|
|
Term
| how stabilization due to hydration affects stability of reactants and products |
|
Definition
| water binds to ADP and Pi, making the synthesis of ATP less favorable |
|
|
Term
| why ATP is an efficient carrier of phosphoryl groups |
|
Definition
| because its phosphoryl-transfer potential is intermediate among the biologically important phosphorylated molecules |
|
|
Term
| characteristics of phosphate and its esters that render it useful for biochemical systems |
|
Definition
1: they are thermodynamically unstable, but kinetically stable, thus their energy can be manipulated by enzymes
2: the stability of phosphate esters is due to the negative charges that make them resistant to hydrolysis in the absence of enzymes
3: their kinetic stability makes them ideal regulatory molecules, added to proteins by kinases and removed only by phosphatases |
|
|
Term
| one of the primary roles of catabolism |
|
Definition
|
|
Term
| is ATP an immediate or ling term donor of free energy? |
|
Definition
|
|
Term
| the fundamental mode of energy exchange in biological systems |
|
Definition
|
|
Term
| depiction of the ATP-ADP cycle |
|
Definition
|
|
Term
| some things that require ATP |
|
Definition
-motion
-active transport
-biosynthesis
-signal amplification |
|
|
Term
| some things that turn ADP into ATP |
|
Definition
-oxidation of fuel molecules
-photosynthesis |
|
|
Term
|
Definition
| rxns where one atom loses electrons (oxidation) and another gains electrons (reduction) |
|
|
Term
| reduction of a C atom vs. free energy released by its oxidation |
|
Definition
proportional
the more reduced it tis to begin with, the higher the free energy released by its oxidation |
|
|
Term
| why fats are more efficient fuels than carbohydrates |
|
Definition
| because the C's in fats are more reduced |
|
|
Term
| what happens to the energy of oxidation in ATP synthesis? |
|
Definition
| it is initially trapped as a high-phosphoryl-transfer-potential compound and then used to form ATP |
|
|
Term
| what C oxidation energy is used for in the formation of ATP |
|
Definition
-creating a compound with high phosphoryl-transfer potential
-creating an ion gradient |
|
|
Term
| what is glucose usually metabolized into? |
|
Definition
| CO2 and water; this happens when oxygen delivery is adequate |
|
|
Term
| what happens when ATP needs outpace oxygen delivery? |
|
Definition
| glucose is metabolized to lactate |
|
|
Term
| some speculated reasons for glucose being such a prominent fuel as opposed to other monosaccharides |
|
Definition
1: it is one of several monosacs formed from formaldehyde under prebiotic conditions, so it might have been available for primitive biochem systems
2: glucose is a stable hexose because the hydroxyl groups and hydroxyymethyl group are all equatorial, minimizing steric clashes
3: relative to other monosacs, glucose has a low tendency to glycolysate proteins; this is due to its strong tendency to form rings |
|
|
Term
| why glucose might have been available for primitive biochem systems |
|
Definition
| because it is one of several monosacs formed from formaldehyde under prebiotic conditions |
|
|
Term
| why glucose is a stable hexose |
|
Definition
| because the hydroxyl groups and hydroxyymethyl group are all equatorial, minimizing steric clashes |
|
|
Term
| why glucose has a low tendency to glycolysate proteins |
|
Definition
| because of its strong tendency to form rings |
|
|
Term
| where glycolysis occurs in eukaryotic cells |
|
Definition
|
|
Term
| what glucose is converted to in gylycolysis |
|
Definition
| 2 molecules of pyruvate with the concomitant generation of 2 molecules of ATP |
|
|
Term
| stage 1 of glycolysis begins with... |
|
Definition
| the conversion of glucose into fructose 1,6-biphosphate |
|
|
Term
| the 3 steps of converting glucose into fructose 1,6-biphosphate |
|
Definition
1: phosphorylation
2: isomerization
3: 2nd phosphorylation |
|
|
Term
| the strategy of the initial steps of glycolysis |
|
Definition
| to trap the glucose in the cell and form a compound that can be readily cleaved into phosphorylated 3-C units |
|
|
Term
| stage 1 of glycolysis is completed by... |
|
Definition
| the cleavage of fructose 1,6-biphosphate into 2 phosphorylated, 3-C fragments |
|
|
Term
| what happens in stage 1 of glycolysis? |
|
Definition
| glucose is trapped, destabilized, and cleaved into 2 interconvertible 3-C molecules, generated by the cleavage of 6-C fructose |
|
|
Term
| what happens in stage 2 of glycolysis? |
|
Definition
| the 2 3-C units are oxidized to pyruvate, generating ATP |
|
|
Term
| depiction of the stages of glycolysis |
|
Definition
|
|
Term
| the one principal fate glucose has inside the cell |
|
Definition
| it is phosphorylated by ATP to form glucose 6-phosphate |
|
|
Term
|
Definition
catalyzes the transfer of the phosphoryl group from ATP to the hydroxyl group on C6 of glucose
traps glucose in the cell and begins glycolysis |
|
|
Term
| depiction of the function of hexokinase |
|
Definition
|
|
Term
|
Definition
| enzyme that catalyzes the transfer of a phosphoryl group from ATP to an acceptor |
|
|
Term
| something kinases require for activity |
|
Definition
| divalent metal cations, such as Mg2+ and Mn2+
this forms a complex with ATP |
|
|
Term
| fructose 1,6-biphosphate is generated from... |
|
Definition
|
|
Term
|
Definition
catalyzes the isomerization of glucose 6-phosphate to to fructose 6-phosphate
this is the conversion of an aldose to a ketose |
|
|
Term
| depiction of the function of phosphoglucose isomerase |
|
Definition
|
|
Term
| what happens to fructose 6-phosphate during glycolysis? |
|
Definition
| gets phosphorylated by ATP to fructose 1,6-biphosphate |
|
|
Term
| phosphofructokinase (PFK) |
|
Definition
| catalyzes the phosphorylation of fructose 6-phosphate to fructose 1,6-biphosphate |
|
|
Term
| depiction of the function of phosphofructokinase (PFK) |
|
Definition
|
|
Term
| an allosteric enzyme that is the key regulatory enzyme for glycolysis |
|
Definition
|
|
Term
| what the oxidation of aldehyde does in glycolysis |
|
Definition
| powers the formation of a compound having high phosphoryl-transfer potential |
|
|
Term
| glyceraldehyde 3-phosphate dehydrogenase |
|
Definition
| catalyzes the conversion of glyceraldehyde 3-phosphate into 1,3-biphosphoglycerate |
|
|
Term
|
Definition
| enzyme that catalyzes redox rxns, often transferring a hydride ion from a donor molecule to NAD+ or transferring a hydride ion from NADH to an acceptor molecule |
|
|
Term
| depiction of the function of glyceraldehyde 3-phosphate dehydrogenase |
|
Definition
|
|
Term
| the energy of C oxidation is transferred as... |
|
Definition
| high phosphoryl-transfer potential |
|
|
Term
| detailed depiction of the conversion of glyceraldehyde 3-phosphate into 1,3-biphosphoglycerate |
|
Definition
|
|
Term
| what couples the aldehyde oxidation to drive the formation of the acyl phosphate? |
|
Definition
| an enzyme that forms a thioester intermediate, replacing the H on the aldehyde group and later being replaced by an orthophosphate group |
|
|
Term
| depiction of the function of the thioester intermediate that couples the aldehyde oxidation to drive the formation of the acyl phosphate |
|
Definition
[image]
reduces the activation energy; intermediate more stable than reactants, but more stable than products, making it spontaneous |
|
|
Term
| in glycolysis, ATP is formed by... |
|
Definition
| phosphoryl transfer from 1,3-biphosphoglycerate |
|
|
Term
|
Definition
| catalyzes the transfer of the phosphoryl group from the acyl phosphate of 1,3-biphosphoglycerate to ADP, which yields ATP and 3-phosphoglycerate |
|
|
Term
| depiction of the function of phodsphoglycerate kinase |
|
Definition
|
|
Term
| how additional ATP is generated at the end of glycolysis |
|
Definition
| by converting 3-phosphoglycerate into pyruvate, which forms a 2nd molecule of ASTP |
|
|
Term
| depiction of 3-phosphoglycerate being converted into pyruvate to form ATP |
|
Definition
|
|
Term
|
Definition
| shifts the position of the phosphoryl group to convert 3-phosphoglycerate into 2-phosphoglycerate |
|
|
Term
| depiction of the function of phosphoglycerate mutase |
|
Definition
|
|
Term
|
Definition
| catalyzes the intramolecular shift of a chemical group |
|
|
Term
|
Definition
| catalyzes the formation of the enol phosphate phosphoenolpyruvate (PEP), which is unstable and has a high phosphoryl transfer potential |
|
|
Term
| depiction of the function of enolase |
|
Definition
|
|
Term
|
Definition
| catalyzes the irreversible transfer of a phosphoryl group from phosphoenolpyruvate (PEP) to ADP |
|
|
Term
| depiction of the function of pyruvate kinase |
|
Definition
|
|
Term
| the net rxn of the transformation of glucose into pyruvate |
|
Definition
| glucose + 2 Pi + 2 ADP + 2 NAD+ ---> 2 pyruvate + 2 ATP + 2 NADH + 2 H+ + 2 H2O |
|
|
Term
| why a glycolysis pathway that ends with pyruvate will not proceed |
|
Definition
| because this would result in oxidation-reduction imbalance |
|
|
Term
| the final process in glycolysis |
|
Definition
| the regeneration of NAD+ thru the metabolism of pyruvate |
|
|
Term
| 3 rxns of pyruvate that can occur in living things |
|
Definition
| -conversion into ethanol
-conversion into lactate
-conversion into CO2 and water |
|
|
Term
| types of fermentation that can occur with pyruvate in the absence of O |
|
Definition
-conversion into ethanol
-conversion into lactate |
|
|
Term
|
Definition
| ATP-generating process in which organic compounds act as both donors and acceptors of electrons |
|
|
Term
| what happens to pyruvate in the presence of O? |
|
Definition
| gets metabolized to CO2 and water thru the citric acid cycle and the electron transport chain |
|
|
Term
| depiction of the possible fates of pyruvate |
|
Definition
|
|
Term
|
Definition
| catalyzes the decarboxylation of pyruvate |
|
|
Term
| depiction of the function of pyruvate decarboxylase |
|
Definition
|
|
Term
|
Definition
| catalyzes the reduction of acetaldehyde to ethanol by NADH |
|
|
Term
| depiction of the function of alcohol dehydrogenase |
|
Definition
|
|
Term
|
Definition
| converting glucose into alcohol |
|
|
Term
| the net result of the anaerobic conversion of glucose into ethanol |
|
Definition
| glucose + 2Pi + 2 ADP + 2 H+ --> 2 ethanol 2 CO2 + 2 ATP + 2 H2O |
|
|
Term
| how redox balance is maintained in alcohol fermentation |
|
Definition
| production and later consumption of NADH; no net proiduction of NADH or NAD+ |
|
|
Term
| depiction of how redox balance is maintained in alcoholic fermentation |
|
Definition
|
|
Term
|
Definition
| converting glucose into lactate |
|
|
Term
|
Definition
| catalyzes the conversion of pyruvate to lactate |
|
|
Term
| depiction of the function of lactate dehydrogenase |
|
Definition
|
|
Term
| overall rxn in the conversion of glucose to lactate |
|
Definition
| glucose + 2Pi + 2 ADP --> 2 lactate + 2 ATP + 2 H2O |
|
|
Term
| how redox balance is maintained in lactate fermentation |
|
Definition
| production and later consumption of NADH; no net proiduction of NADH or NAD+ |
|
|
Term
| this sustains glycolysis under anaerobic conditions |
|
Definition
| the regeneration of NAD+ from NADH; using the NAD+ that's produced and using the NADH that's produced |
|
|
Term
| depiction of how redox balance is maintained in lactic acid fermentation |
|
Definition
|
|
Term
| type of cell in animals that can function anaerobically for a short time |
|
Definition
| fast twitch, or type IIb, muscle |
|
|
Term
| which type of glycolysis releases more energy? aerobic or anaerobic? |
|
Definition
|
|
Term
| how energy is extracted aerobically |
|
Definition
| by means of the citric acid cycle and the electron transport chain, which combust, or oxidize, glucose into H2O and CO2 |
|
|
Term
| the entry point to the oxidative pathway in aerobic glycolysis |
|
Definition
| acetyl coenzyme A (acetyl CoA) |
|
|
Term
|
Definition
| formed from pyruvate inside mitochondria |
|
|
Term
| the process by which mitochondria form acetyl CoA |
|
Definition
| pyruvate + NAD+ + CoA --> acetyl CoA + CO2 + NADH |
|
|
Term
| how the NAD+ needed for aerobic glycolysis is regenerated |
|
Definition
| regenerated by the electron transport chain in mitochondria |
|
|
Term
| some recurring motifs in biochemistry |
|
Definition
1: the use of activated carriers
2: the existence of a recurring set of activated characters in all organisms |
|
|
Term
| why ATP is an activated carrier of phosphoryl groups |
|
Definition
| because phosphoryl transfer from ATP is energetically favorable |
|
|
Term
| a recurring motif in biochem |
|
Definition
| the use of activated carriers |
|
|
Term
|
Definition
| small molecule carrying activate functional groups that can be donated to another molecule |
|
|
Term
| examples of activated carriers |
|
Definition
-ATP carries activated phosphoryl groups
-coenzyme A carries activated acyl groups
-activated carriers of electrons for fuel oxidation
-activated carriers of electrons for the synthesis of biomolecules
-an activated carrier of 2-Carbon fragments |
|
|
Term
| many activated carriers function as... |
|
Definition
|
|
Term
|
Definition
| small organic molecules that serve as cofactors for enzymes |
|
|
Term
| the ultimate electron acceptor in the oxidation of fuel molecules |
|
Definition
|
|
Term
| the flow of electrons from fuel molecules to O2 |
|
Definition
| fuel molecules --> pyridine nucleotides or flavins --> O2 |
|
|
Term
| an example of a pyridine nucleotide |
|
Definition
|
|
Term
|
Definition
| a pyridine nucleotide that is a major electron carrier in the oxidation of fuel molecules |
|
|
Term
|
Definition
|
|
Term
| depiction of NAD+ reduction |
|
Definition
|
|
Term
| depiction of redox rxn involving NAD+ |
|
Definition
|
|
Term
| major electron carriers in the oxidation of fuel molecules |
|
Definition
| -NAD+
-FAD
these are both oxidized forms |
|
|
Term
|
Definition
|
|
Term
| depiction of redox rxn involving FAD |
|
Definition
|
|
Term
| oxidized and reduced forms of FAD/FADH2 |
|
Definition
|
|
Term
|
Definition
| synthesizing something from precursors that are more oxidized than the products |
|
|
Term
| most biosynthesis is this type of biosynthesis |
|
Definition
|
|
Term
| the electron donor in most biosynthesis |
|
Definition
|
|
Term
|
Definition
|
|
Term
| key difference between NADH and NADPH |
|
Definition
| NADPH contains one more phosphate group |
|
|
Term
| key difference between the uses of NADH and NADPH |
|
Definition
| NADPH used almost exclusively for reductive biosynthesis while NADH is used primarily for the generation of ATP |
|
|
Term
|
Definition
| almost exclusively for reductive biosynthesis while NADH is used primarily for the generation of ATP |
|
|
Term
|
Definition
| primarily the generation of ATP |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| why acetyl CoA has high acetyl group transfer potential |
|
Definition
| because transfer of the acetyl group is exergonic (i.e., thermodynamically favorable) |
|
|
Term
| why the kinetic stability of NADH, NADPH, FADH2, ATP, and acetyl CoA in the absence of specific catalysts is essential foor their biological function |
|
Definition
| because it allows enzymes to control the flow of free energy and reducing power |
|
|
Term
| one of the unifying motifs in biochem |
|
Definition
| the existence of a recurring set of activated characters in all organisms |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| many activated carriers are derived from... |
|
Definition
|
|
Term
|
Definition
| organic molecules needed in small amounts in the diets of many higher animals |
|
|
Term
| the dual role of the glycolytic pathway |
|
Definition
-degrades glucose to generate ATP
-provides building blocks for biosynthetic rxns |
|
|
Term
| potential sites of control in metabolic pathways |
|
Definition
| enzymes catalyzing irreversible rxns |
|
|
Term
| the control sites (i.e., enzymes tat catalyze irreversible rxns) in glycolysis |
|
Definition
-hexokinase
-phosphofructokinase
-pyruvate kinase |
|
|
Term
| the type of enzymes that regulate glycolysis |
|
Definition
|
|
Term
| what glycolysis in muscle does |
|
Definition
| primarily provides power for muscle contraction |
|
|
Term
| the primary control of muscle glycolysis |
|
Definition
| energy charge of the cell- ratio of ATP to AMP |
|
|
Term
| energy charge of the cell |
|
Definition
|
|
Term
| glycolysis in muscle is regulated by... |
|
Definition
| feedback inhibition to meet the need for ATP |
|
|
Term
| the most important control site in the mammalian glycolytic pathway |
|
Definition
|
|
Term
| how phosphofructokinase is inhibited in muscle |
|
Definition
ATP binds with phosphofructokinase at a distinct site to lower its affinity for fructose 6-phosphate
can also be inhibited by declining pH |
|
|
Term
| how phosphofructokinase is stimulated in muscle |
|
Definition
| AMP binds with phosphofructokinase at the same site to increase its affinity for fructose 6-phosphate |
|
|
Term
| how muscle cells are protected from excess acidity |
|
Definition
| lactic acid lowers the pH, augmenting the inhibitory effect of ATP on phosphofructokinase |
|
|
Term
| why AMP, not ADP, stimulates phosphofructokinase activity |
|
Definition
| because while ATP is being used, aldenylate kinase can convert ADP into ATP |
|
|
Term
|
Definition
|
|
Term
| the rxn aldenylate kinase is involved in |
|
Definition
|
|
Term
| the primary regulatory enzyme in glycolysis |
|
Definition
|
|
Term
| how hexokinase is regulated in muscle |
|
Definition
| it is inhibited by accumulation of glucose 6-phosphate |
|
|
Term
| how inhibition of phosphofructokinase leads to inhibition of hexokinase |
|
Definition
| inhibition of PFK leads to accumulation of fructose 6-phosphate, leading to accumulation of glucose 6-phosphate, leading to inhibition of hexokinase |
|
|
Term
| why hexokinase is not the committed step in glycolysis |
|
Definition
| because glucose 6-phosphate can also be converted into glycogen |
|
|
Term
| why PFK is the committed step in glycolysis |
|
Definition
| because it's the first step unique to glycolysis |
|
|
Term
| why the committed step is the most important controlled element in a biochemical pathway |
|
Definition
| because it regulates flux down the pathway |
|
|
Term
| how pyruvate kinase is inhibited in muscle |
|
Definition
| ATP binds to pyruvate kinase to decrease its affinity for phosphoenolpyruvate |
|
|
Term
| how pyruvate kinase is stimulated in muscle |
|
Definition
| fructose 1,6-bisphosphate activates the kinase to enable it to keep pace with the oncoming flux of intermediates |
|
|
Term
| depiction of glycolysis being inhibited in muscle (at rest) |
|
Definition
|
|
Term
| depiction of glycolysis being stimulated in muscle (during exercise) |
|
Definition
|
|
Term
| the regulation of glycolysis in the liver corresponds to... |
|
Definition
| the biochemical versatility of the liver |
|
|
Term
| how the liver regulates blood glucose |
|
Definition
-stores it as glycogen when high
-releases glucose when low |
|
|
Term
| some things the liver does with glucose |
|
Definition
-stores it as glycogen when high
-releases glucose when low
-uses glucose to generate reducing power for biosynthesis
-synthesize a host of building blocks for other biomolecules |
|
|
Term
| how PFK in the liver is inhibited |
|
Definition
| citrate, since citrate accumulation indicates that there's already enough biosynthetic precursors |
|
|
Term
| the key means by which PFK in the liver responds to changes in blood glucose |
|
Definition
| thru the signal molecule fructose 2,6-bisphosphate (F-2,6-BP) |
|
|
Term
| how PFK in the liver is stimulated |
|
Definition
| fructose 2,6-bisphosphate stimulates PFK by increasing its affinity for fructose 6-phosphate |
|
|
Term
| the enzyme primarily responsible for phosphorylating glucose in the liver |
|
Definition
| glucokinase (hexokinase IV) |
|
|
Term
| glucokinase (hexokinase IV) |
|
Definition
| isozyme of hexokinase; this is what's primarily responsible for phosphorylating glucose in the liver |
|
|
Term
|
Definition
| enzymes encoded by different genes with different amino acid sequences, but catalyze the same rxns |
|
|
Term
| how isozymes/isoenzymes differ |
|
Definition
| usually by kinetic or regulatory properties |
|
|
Term
| some differences between hexokinase and glucokinase |
|
Definition
| glucokinase has a higher KM value and is not inhibited by its product, glucose 6-phosphate |
|
|
Term
|
Definition
| to provide glucose 6-phosphate for the synthesis of glycogen and for the formation of fatty acids |
|
|
Term
|
Definition
| the need to remove glucose from thew blood for storage as glycogen or conversion into fat |
|
|
Term
| some important forms of pyruvate kinase |
|
Definition
|
|
Term
| the form of pyruvate kinase that predominates in the liver |
|
Definition
|
|
Term
| the form of pyruvate kinase that predominates in the muscle and brain |
|
Definition
|
|
Term
| which form of pyruvate kinase is inhibited by alanine? |
|
Definition
| the L form (liver enzyme) |
|
|
Term
| reversible phosphorylation regulates the catalytic properties of which form of pyruvate kinase? |
|
Definition
| the L form (liver enzyme) |
|
|
Term
| the importance of reversible phosphorylation regulating the catalytic properties of the L form of pyruvate kinase (liver enzyme) |
|
Definition
| prevents the liver from consuming glucose when it is more urgently needed by brain and muscle |
|
|
Term
| the function of the GLUT1 to GLUT5 proteins |
|
Definition
| enable glucose to enter and leave animal cells |
|
|
Term
| where the GLUT1 protein is found |
|
Definition
| nearly all mammalian cells |
|
|
Term
| where the GLUT3 protein is found |
|
Definition
| nearly all mammalian cells |
|
|
Term
| the GLUT proteins that essentially continuously transport glucose into cells at a constant rate (function in basal glucose uptake) |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| where the GLUT2 protein is found |
|
Definition
| liver and pancreatic β cells |
|
|
Term
| when glucose enters through the GLUT2 protein at a significant rate |
|
Definition
| when there is much glucose in the blood |
|
|
Term
|
Definition
in pancreas: helps regulate insulin
in liver: removes excess glucose from the blood |
|
|
Term
| where the GLUT4 protein is found |
|
Definition
|
|
Term
| how the number of GLUT4 proteins increases |
|
Definition
-increased insulin, which signals the presence of glucose
-endurance exercise |
|
|
Term
| where the GLUT5 protein is found |
|
Definition
|
|
Term
|
Definition
| primarily as fructose transporter |
|
|
Term
|
Definition
| the synthesis of glucose from noncarboydrate precursors |
|
|
Term
| why it's important to maintain glucose levels |
|
Definition
| because red blood cells need it and the brain uses it as its only fuel source |
|
|
Term
| the part of the body that needs most of the glucose |
|
Definition
|
|
Term
| when gng is especially important |
|
Definition
| during fasting or starvation |
|
|
Term
|
Definition
| mostly liver with small amount occurring in kidney |
|
|
Term
|
Definition
| helps maintain blood glucose so tissues that need it can access it |
|
|
Term
| the gng pathway converts ______ into ______ |
|
Definition
|
|
Term
| the major noncarbohydrate precursors that get involved in gng |
|
Definition
-lactate
-amino acids
-glycerol |
|
|
Term
| how glycerol may enter the gng pathway |
|
Definition
| by conversion of glycerol to dihydroxyacetone phosphate |
|
|
Term
| depiction of the conversion of glycerol to dihydroxyacetone phosphate |
|
Definition
|
|
Term
| is gng a complete reversal of glycolysis? |
|
Definition
|
|
Term
| why is gng not a complete reversal of glycolysis? |
|
Definition
| because the free energy of glycolysis is -90 kJ/mol, making it irreversible and necessary for gng to bypass the irreversible steps |
|
|
Term
|
Definition
|
|
Term
| the conversion of pyruvate into phosphoenolpyruvate begins with... |
|
Definition
| the formation of oxaloacetate |
|
|
Term
|
Definition
| carboxylation of pyruvate to form oxaloacetate |
|
|
Term
|
Definition
| enyme that catalyzes the carboxylation of pyruvate to form oxaloacetate |
|
|
Term
| where the carboxylation of pyruvate to form oxaloacetate occurs |
|
Definition
|
|
Term
| depiction of the carboxylation of pyruvate to form oxaloacetate |
|
Definition
|
|
Term
| importance of biotin to pyruvate carboxylase |
|
Definition
| biotin is a covalently attached prosthetic group that serves as the carrier of activated CO2 |
|
|
Term
| the 3 stages of pyruvate carboxylation |
|
Definition
|
|
Term
| how oxaloacetate is processed in the mitochondria |
|
Definition
in matrix: pyruvate --> oxaloacetate --> malate
in cytoplasm: malate --> oxaloacetate |
|
|
Term
| depiction of how oxaloacetate is processed in the mitochondria |
|
Definition
|
|
Term
| phosphoenolpyruvate carboxykinase (PEPCK) |
|
Definition
| catalyzes the decarboxylation and phosphorylation of of oxaloiacetate |
|
|
Term
| depiction of the function of phosphoenolpyruvate carboxykinase (PEPCK) |
|
Definition
|
|
Term
| the sum of the rxns catalyzed by pyruvate carboxylase and phosphoenolpyruvate carboxylase |
|
Definition
| pyruvate + ATP + GTP + H2O --> phosphoenolpyruvate + ADP + GDP + Pi + 2 H+ |
|
|
Term
| importance of decarboxylation |
|
Definition
| often drives rxns that are otherwise highly endergonic |
|
|
Term
| fructose 1,6-bisphosphotase |
|
Definition
| catalyzes conversion of fructose 1,6-bisphosphate to fructose 6-phosphate |
|
|
Term
| depiction of the function of fructose 1,6-bisphosphotase |
|
Definition
|
|
Term
| where gng ends in most tissues |
|
Definition
| conversion of fructose 6-phosphate into glucose 6-phosphate, which is often stored as glycogen |
|
|
Term
| where the final step in the generation of free glucose occurs |
|
Definition
|
|
Term
| metabolic duty of the liver |
|
Definition
| to maintain adequate levels of glucose in the blood for use by other organs |
|
|
Term
| how glucose 6-phosphate gets converted to free glucose |
|
Definition
| transported into lumen of endoplasmic reticulum, where it is hydrolyzed to glucose by glucose 6-phosphatase, which is bound to the ER membrane.
glucose and Pi are then shuttled out into the cytoplasm by transporters |
|
|
Term
| depiction of generation of glucose from glucose 6-phosphate |
|
Definition
|
|
Term
| the NTP difference between glycolysis and gng |
|
Definition
| glycolysis yields 2 ATP while gng requires 4 ATP and 2 GTP (6 NTP) |
|
|
Term
| when glycolysis predominates |
|
Definition
|
|
Term
|
Definition
|
|
Term
| what determines whether glycolysis or gng will be more active? |
|
Definition
|
|
Term
| the key regulation site in the gng pathway |
|
Definition
| the interconversion of fructose 6-phosphate and fructose 1,6-bisphosphate |
|
|
Term
|
Definition
| seems to be ratio of ATP/AMP |
|
|
Term
| something indicated by high AMP concentration |
|
Definition
| energy is needed, thus stimulating glycolysis and inhibiting gng |
|
|
Term
| something indicated by high ATP concentration |
|
Definition
| the energy charge is high and biosynthetic intermediates are abundant, thus inhibiting glycolysis |
|
|
Term
| something indicated by high citrate concentration |
|
Definition
| reports the status of the citric acid cycle; high citrate indicates energy rich situation and precursors for biosynthesis, inhibiting glycolysis and stimulating gng |
|
|
Term
| where the interconversion of phosphoenolpyruvate and pyruvate occurs |
|
Definition
|
|
Term
| something indicated by high alanine concentration |
|
Definition
| energy charge is hidh and building blocks are abundant, inhibiting pyruvate kinase in glycolysis |
|
|
Term
| depiction of the reciprocal regulation of glycolysis and gng in the liver |
|
Definition
|
|
Term
| phosphofructokinase 2 (PFK2) |
|
Definition
| catalyzes the conversion of fructose 6-phosphate to fructose 2,6-bisphosphate |
|
|
Term
| fructose bisphosphatase 2 (FBPase2) |
|
Definition
| catalyzes conversion of fructose 2,6-bisphosphate to frucose 6-phosphate |
|
|
Term
| something striking about PFK2 and FBPase2 |
|
Definition
| they're both in a single 55-kDa polypeptide chain; it's a bifunctional enzyme |
|
|
Term
| composition of the bifunctional PFK2/FBPase2 enzyme |
|
Definition
| N-terminal regulatory domain followed by a kinase domain and a phosphatase domain |
|
|
Term
| how it is determined whether a bifunctional PFK2/FBPase2 enzyme functions as PFK2 or FBPase2 |
|
Definition
| the activities of PFK2 and FBPase2 are reciprocally controlled by the phosphorylation of a single serine residue |
|
|
Term
| when the bifunctional PFK2/FBPase2 enzyme functions as FBPase2 |
|
Definition
when blood glucose is low
gng predominates |
|
|
Term
| how low blood glucose causes the bifunctional PFK2/FBPase2 enzyme to act as FBPase2 |
|
Definition
| when glucose in scarce, blood glucagon rises and triggers a cyclic AMP signal cascade, leading to the phospkorylation of this enzyme by protein kinase A; this activates FBPase2 and inhibits PFK2 |
|
|
Term
| when the bifunctional PFK2/FBPase2 enzyme functions as PFK2 |
|
Definition
when blood glucose is high
glycolysis predominates |
|
|
Term
| how high blood glucose causes the bifunctional PFK2/FBPase2 enzyme to act as PFK2 |
|
Definition
| glucagon falls and insulin rises, causing the phosphoryl group to be removed; this activates PFK2 and inhibits FBPase2 |
|
|
Term
|
Definition
|
|
Term
| depiction of the bifunctional PFK2/FBPase2 enzyme |
|
Definition
|
|
Term
| depiction of the control of the synthesis and degradation of fructose 2,6-bisphosphate |
|
Definition
|
|
Term
| what lets contracting skeletal muscle generate ATP in the absence of oxygen? |
|
Definition
| the formation and release of lactate |
|
|
Term
| 2 possible fates of lactate |
|
Definition
1: diffuses into cardiac and slow-twitch (type 1) muscle to be reverted to pyruvate to be metabolized thru the citric acid cycle and oxidative phosphorylation to generate ATP
2: excess lactate enters the liver to be converted into pyruvate, then to glucose by the gng pathway |
|
|
Term
| what the liver does for active muscles |
|
Definition
| restores the levels of glucose needed for active muscle cells, which derive ATP from the conversion of glucose into lactate |
|
|
Term
| depiction of a substrate cycle |
|
Definition
|
|
Term
| depiction of the Cori cycle |
|
Definition
|
|
Term
|
Definition
|
|
Term
| the one way link between glycolysis and cellular respiration |
|
Definition
|
|
Term
| what happens to pyruvate in anaerobic conditions? |
|
Definition
| converted to lactic acid or ethanol |
|
|
Term
| what happens to pyruvate in aerobic conditions |
|
Definition
| converted into acetyl coenzyme A (acetyl CoA), which enters the citric acid cycle |
|
|
Term
| what happens to pyruvate when a cell's oxygen supply is insufficient? |
|
Definition
| gets converted to lactate |
|
|
Term
| simplified overview of the citric acid cycle |
|
Definition
|
|
Term
| pyruvate dehydrogenase complex |
|
Definition
| oxidatively decarboxylates pyruvate to form acetyl CoA |
|
|
Term
| the chemical rxn of the pyruvate dehydrogenase complex |
|
Definition
| pyruvate + CoA + NAD+ --> acetyl CoA + CO2 NADH + H+ |
|
|
Term
| where oxidative decarboxylation of pyruvate occurs |
|
Definition
|
|
Term
| where citric acid cycle occurs |
|
Definition
|
|
Term
| the rxn E1 in the pyruvate dehydrogenase complex catalyzes |
|
Definition
| oxidative decarboxylation of pyruvate |
|
|
Term
| the rxn E2 in the pyruvate dehydrogenase complex catalyzes |
|
Definition
| transfer of acetyl group to CoA |
|
|
Term
| the rxn E3 in the pyruvate dehydrogenase complex catalyzes |
|
Definition
| regeneration of the oxidized form of lipoamide |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| the link between glycolysis and the citric acid cycle |
|
Definition
| the irreversible conversion of pyruvate into acetyl CoA |
|
|
Term
| depiction of the link between glycolysis and the citric acid cycle |
|
Definition
|
|
Term
|
Definition
| function as enzymes; not permanently altered by participation in rxn |
|
|
Term
|
Definition
| they function as substrates |
|
|
Term
| the 3 steps of the conversion of pyruvate into acetyl CoA |
|
Definition
1: decarboxylation
2: oxidation
3: the transfer of the resultant acetyl group to CoA |
|
|
Term
| depiction of the conversion of pyruvate into acetyl CoA |
|
Definition
|
|
Term
|
Definition
| proteins tightly associated with FAD |
|
|
Term
| what allows lipoamide to move between different active sites? |
|
Definition
|
|
Term
| depiction of the structure of the pyruvate dehydrogenase complex |
|
Definition
| [image]
-has 8 E2 (α3) trimers at the core to make a hollow cube
-the cube is surrounded by 12 E3 (αβ) dimers and 24 E1 (α2β2) |
|
|
Term
| depiction of the structure of the E2 within the pyruvate dehydrogenase complex |
|
Definition
[image]
contains 8 trimers |
|
|
Term
| depiction of the domains within each E2 (α3) trimer |
|
Definition
|
|
Term
| how the pyruvate dehydrogenase (PDH) complex differs in mammals |
|
Definition
| the core contains another protein, E3-binding protein (E3-BP) |
|
|
Term
| depiction of the reactions of the pyruvate dehydrogenase (PDH) complex |
|
Definition
|
|
Term
| what happens when the pyruvate dehydrogenase (PDH) complex is missing the E3-binding protein (E3-BP)? |
|
Definition
| the PDH complex has greatly reduced activity |
|
|
Term
| how do the 3 distinct active sites of the PDH complex work in concert? |
|
Definition
| the flexible lipoamide arm of the E2 subunit carries substrate from active site to active site |
|
|
Term
|
Definition
| oxidative decarboxylation of pyruvate to acetyl CoA |
|
|
Term
| 2 principal fates of the carbons in acetyl CoA |
|
Definition
| 1: oxidation to CO2 by the citric acid cycle with the concomitant generation of energy
2: incorporation into lipid, because acetyl CoA is an essential precursor for lipid synthesis |
|
|
Term
| simple depiction of the conversion of glucose to pyruvate to acetyl CoA to CO2 and fatty acids |
|
Definition
|
|
Term
| the key means of regulation of the PDH complex in eukaryotes |
|
Definition
| covalent modification in the form of phosphorylation |
|
|
Term
| what phosphorylation does to the PDH complex |
|
Definition
|
|
Term
| what dephosphorylation does to the PDH complex |
|
Definition
|
|
Term
|
Definition
| catalyzes phoisphorylation of PDH complex to deactivate it |
|
|
Term
|
Definition
| catalyzes dephosphorylation of PDH complex to reactivate it |
|
|
Term
| depiction of the regulation of the PDH complex |
|
Definition
|
|
Term
| PDH phosphatase is activated by... |
|
Definition
|
|
Term
| depiction of PDH regulation under high energy charge |
|
Definition
|
|
Term
| depiction of PDH regulation under low energy charge |
|
Definition
|
|
Term
|
Definition
| carbon compounds capable of being oxidized |
|
|
Term
| the function of the citric acid cycle |
|
Definition
| the harvesting of high energy electrons from carbon fuels |
|
|
Term
| how the citric acid cycle begins |
|
Definition
| the 2-carbon acetyl unit condenses with a 4-carbon oxaloacetate to yield the 6-Carbon tricarboxylic acid citrate |
|
|
Term
| simple depiction of an overview of the citric acid cycle |
|
Definition
|
|
Term
| oxidative phosphorylation |
|
Definition
| forming ATP by by the transfer of electrons from NADH or FADH2 to O2 by a series of electron carriers |
|
|
Term
|
Definition
| series of membrane proteins electrons from NADH or FADH2 floe thru to generate proton gradient |
|
|
Term
| what proton gradient is used for |
|
Definition
| to generate ATP from ADP and inorganic phosphate |
|
|
Term
| the stagers of cellular respiration |
|
Definition
1: citric acid cycle
2: oxidative phosphorylation |
|
|
Term
| depiction of cellular respiration |
|
Definition
|
|
Term
| the 2 stages of the citric acid cycle |
|
Definition
1: oxidizing 2 carbon atoms to gather energy rich electrons
2: regenerating oxaloacetate and harvesting energy rich electrons |
|
|
Term
| oxidative decarboxylation |
|
Definition
| citrate being oxidized by releasing 2 CO2 to yield a 4-carbon molecule and high transfer potential electrons captured as 2 molecules of NADH |
|
|
Term
| how the citric acid cycle begins |
|
Definition
| joining of 4-Carbon oxaloacetate with the 2-carbon acetyl group acetyl CoA to form citryl CoA, which gets hydrolyzed to form citrate |
|
|
Term
| depiction of the formation of citrate |
|
Definition
[image]
citrate synthase involved in both steps |
|
|
Term
|
Definition
| catalyzes the merging of 4-carbon oxaloacetate to the 2-carbon acetyl group to form citrate |
|
|
Term
|
Definition
| enzyme that catalyzes a synthetic rxn in which 2 subunits are joined usually without the direct participation of ATP or another nucleoside triphosphate |
|
|
Term
| this powers the synthesis of citrate |
|
Definition
| the hydrolysis of the thioester in citryl CoA |
|
|
Term
| composition of mammalian citrate synthase |
|
Definition
| dimer of identical 49-kDa subunitswith a cleft present between the large and small domains of the subunits, adjacent to the subunit interface |
|
|
Term
| the reason for ordered binding in citrate synthase |
|
Definition
| because oxaloacetate induces a major structural rearrangement leading to the creation of a binding site for acetyl CoA |
|
|
Term
| depiction of the structure of citrate synthase |
|
Definition
|
|
Term
| how the wasteful hydrolysis of acetyl CoA is prevented |
|
Definition
| because citrate synthase is well suited for the hydrolysis of citryl CoA but not acetyl CoA |
|
|
Term
| why citrate is isomerized into isocitrate |
|
Definition
| because the hydroxyl (-OH) group in citrate is not properly located in the molecuule for the oxidative decarboxylations that follow |
|
|
Term
| how citrate is isomerized into isocitrate |
|
Definition
| dehydrateion, then hydration |
|
|
Term
|
Definition
| catalyzes isomerization of citrate into isocitrate |
|
|
Term
| depiction of how citrate is isomerized into isocitrate |
|
Definition
[image]
aconitase involved in both steps |
|
|
Term
|
Definition
| catalyzes the oxidative decarboxylation of isocitrate to α-ketoglutarate |
|
|
Term
| net rxn that oxidizes and decarboxylates isocitrate to α-ketoglutarate |
|
Definition
| isocitrate + NAD+ --> α-ketoglutarate + CO2 + NADH |
|
|
Term
| depiction of the oxidative decarboxylation of isocitrate to α-ketoglutarate |
|
Definition
[image]
catalyzed by isocitrate dehydrogenase |
|
|
Term
| depiction of the oxidative decarboxylation of α-ketoglutarate |
|
Definition
|
|
Term
| α-ketoglutarate dehydrogenase complex |
|
Definition
catalyzes the oxidative decarboxylation of α-ketoglutarate
structurally similar to PDH |
|
|
Term
| how the citric acid cycle produces ATP |
|
Definition
| the cleavage of the thioester of succinyl CoA is coupled with the phosphorylation of ADP |
|
|
Term
| succinyl CoA synthetase (succinate thiokinase) |
|
Definition
| catalyzes the cleavage of the thioester of succinyl CoA that gets coupled with the phosphorylation of ADP |
|
|
Term
| depiction of the cleavage of the thioester of succinyl CoA that gets coupled with the phosphorylation of ADP to yield ATP |
|
Definition
[image]
catalyzed by succinyl CoA synthetase (succinate thiokinase) |
|
|
Term
| the 2 forms of succinyl CoA synthetase (succinate thiokinase) in mammals |
|
Definition
1: ADP acceptor
2: GDP acceptor |
|
|
Term
| tissue where the ADP accepting version of succinyl CoA synthetase (succinate thiokinase) dominates in mammals |
|
Definition
| tissues that perform lost of cellular respiration, such as skeletal and heart muscle |
|
|
Term
| tissue where the GDP accepting version of succinyl CoA synthetase (succinate thiokinase) dominates in mammals |
|
Definition
| tissues that perform lost of anabolic rxns, such as liver |
|
|
Term
| how the GDP-requiring form of succinyl CoA synthetase (succinate thiokinase) is believed to work |
|
Definition
| in reverse of the direction observed in the citric acid cycle; that is, GTP is used to power the synthesis of succinyl CoA, which is a precursor for heme synthesis |
|
|
Term
| substrate-level phosphorylation |
|
Definition
| generation of ATP a rxn in which a high-phosphoryl-transfer-potential compound (succinyl phosphate) transfers the phosphate to ADP to generate ATP |
|
|
Term
| types of rxns glycolysis uses to form ATP |
|
Definition
| substrate-level phosphorylation rxns |
|
|
Term
| depiction of the rxn mechanism of succinyl CoA synthetase |
|
Definition
|
|
Term
| how oxaloacetate is regenerated |
|
Definition
| by the oxidation of succinate |
|
|
Term
| depiction of the oxidation of succinate |
|
Definition
|
|
Term
| how succinate is oxidized to regenerate oxaloacetate |
|
Definition
1: oxidation
2: hydration
3: 2nd oxidation |
|
|
Term
|
Definition
| catalyzes the oxidation of succinate to fumarate |
|
|
Term
| depiction of the function of succinate dehydrogenase |
|
Definition
|
|
Term
| how succinate dehydrogenase differs from other enzymes in the citric acid cycle |
|
Definition
| it is embedded in the inner mitochondrial membrane in association with the electron transport chain, which is also set in the inner mitochondrial membrane |
|
|
Term
| the link between the citric acid cycle and ATP formation |
|
Definition
| the electron transport chain |
|
|
Term
|
Definition
| catalyzes hydration of fumarate to form L-malate |
|
|
Term
| depiction of the function of fumarase |
|
Definition
|
|
Term
|
Definition
| catalyzes oxidation of malate to form oxaloacetate |
|
|
Term
| depiction of the function of malate dehydrogenase |
|
Definition
|
|
Term
| how the energetically unfavorable oxidation of malate is driven |
|
Definition
| driven by the use of the products; oxaloacetate by citrate synthase and NADH by the electron-transport chain |
|
|
Term
| the net rxn of the citric acid cycle |
|
Definition
| acetyl CoA + 3 NAD+ + FAD + ADP + pi + 2 H2O --> 2 CO2 + 3 NADH + FADH2 + ATP + 2 H+ + CoA |
|
|
Term
| depiction of the complete citric acid cycle |
|
Definition
|
|
Term
|
Definition
| rxn products passing directly from one active site to the nest thru connecting channels |
|
|
Term
| the key catabolic function of the citric acid cycle |
|
Definition
| the production of high energy electrons in the form of NADH and FADH2 |
|
|
Term
| does molecular oxygen participate directly in the citric acid cycle? |
|
Definition
|
|
Term
| why the citric acid cycle operates only under aerobic conditions |
|
Definition
| because NAD+ and FAD can be regenerated in mitochondria only by the transfer of electrons to molecular oxygen |
|
|
Term
| how NAD+ and FAD can be regenerated in mitochondria |
|
Definition
| only by the transfer of electrons to molecular oxygen |
|
|
Term
| why glycolysis can proceed under anaerobic conditions |
|
Definition
| because NAD+ is regenerated in the conversion of pyruvate into lactate or ethanol |
|
|
Term
| depiction of the control of the citric acid cycle |
|
Definition
|
|
Term
| the primary control points to control the rate of the citric acid cycle |
|
Definition
-isocitrate dehydrogenase
-α-ketoglutarate dehydrogenase |
|
|
Term
| the citric acid cycle is regulated primarily by the concentrations of... |
|
Definition
|
|
Term
| something succinyl CoA from the citric acid cycle is used to make |
|
Definition
| the heme groups of hemoglobin and myoglobin |
|
|
Term
| something α-ketoglutarate from the citric acid cycle is used to make |
|
Definition
|
|
Term
| something oxaloacetate from the citric acid cycle is used to make |
|
Definition
|
|
Term
| depiction of the biosynthetic roles of the citric acid cycle |
|
Definition
|
|
Term
| when the citric acid cycle creates intermediates for biosynthesis |
|
Definition
| when the energy needs of the cell are met |
|
|
Term
| how are citric acid cycle intermediates replenished when they are drawn out for biosynthesis |
|
Definition
| conversion of pyruvate to oxaloacetate |
|
|
Term
|
Definition
| catalyzes the conversion of pyruvate to oxaloacetate |
|
|
Term
| rxn that converts pyruvate to oxaloacetate |
|
Definition
| pyruvate + CO?2 + ATP + H2O --> oxaloacetate + ADP + Pi + 2 H+ |
|
|
Term
| depiction of pyruvate carboxylase replenishing the citric acid cycle |
|
Definition
|
|
Term
| when pyruvate carboxylase is active |
|
Definition
| only in the presence of acetyl CoA |
|
|
Term
| what happens to oxaloacetate when the energy charge is high? |
|
Definition
| oxaloacetate gets converted into glucose |
|
|
Term
| what happens to oxaloacetate when the energy charge is low? |
|
Definition
| oxaloacetate replenishes the citric acid cycle |
|
|
Term
|
Definition
| rxn that leads to the net synthesis, or replenishment, of pathway components |
|
|
Term
| example of an anaplerotic rxn |
|
Definition
| synthesis of oxaloacetate by the carboxylation of pyruvate |
|
|
Term
| the fate of acetyl CoA that enters the citric acid cycle |
|
Definition
|
|
Term
| what the glyoxylate cycle enables plants and bacteria to do |
|
Definition
| convert fats into carbohydrates |
|
|
Term
| some ways the glyoxylate cycle differs from the citric acid cycle |
|
Definition
-bypasses the 2 decarboxylation steps of the cycle
-2 acetyl CoA's enter the cycle instead of just 1 |
|
|
Term
|
Definition
| cleaves isocitrate into succinate and glyoxylate |
|
|
Term
|
Definition
| catalyzes the condensation of acetyl CoA with glyoxylate to form malate |
|
|
Term
| depiction of the glyoxylate pathway |
|
Definition
|
|
Term
|
Definition
| organelles in plants where the glyoxylate pathway takes place |
|
|
Term
| electron transport chain aka respiratory chain |
|
Definition
| 4 large protein complexes that are embedded in the inner mitochondrial membrane |
|
|
Term
| where the electron transport chain is located |
|
Definition
| inner mitochondrial membrane |
|
|
Term
|
Definition
| generation of high-transfer-potential electrons by the citric acid cycle, the respiratory chain, and the accompanying synthesis of ATP |
|
|
Term
| depiction of a simple overview of oxidative phosphorylation |
|
Definition
|
|
Term
| where the flow of electrons thru the electron transport chain takes place |
|
Definition
| inner mitochondrial membrane |
|
|
Term
|
Definition
| folds in the mitochondrion's inner membrane |
|
|
Term
| the 2 compartments of the mitochondrion |
|
Definition
1: intermembrane space
2: matrix |
|
|
Term
| permeability of the mitochondrion's outer membrane |
|
Definition
|
|
Term
| why the mitochondrion's outer membrane is very permeable |
|
Definition
| because it contains many mitochondrial porins, which create pores |
|
|
Term
| function of mitochondrial porin |
|
Definition
| regulates flux of molecules crucial to the function of cellular respiration |
|
|
Term
| permeability of mitochondrion's inner membrane |
|
Definition
| intrinsically permeable to nearly all ions and polar molecules |
|
|
Term
|
Definition
| inside mitochondrion's inner membrane |
|
|
Term
|
Definition
| intermembrane space in mitochondrion; called this because it is freely accessible to most small molecules in the cytoplasm cytoplasm |
|
|
Term
| simple depiction of the anatomy of a mitochondrion |
|
Definition
|
|
Term
| what oxidative phosphorylation does to O2 |
|
Definition
|
|
Term
| how oxidative phosphorylation reduces O2 to water |
|
Definition
| using electrons from NADH and FADH2 |
|
|
Term
|
Definition
| set of membrane proteins in which the transfer of electrons to reduce O2 to water takes place |
|
|
Term
| a conversion of potential that occurs in oxidative phosphorylation |
|
Definition
| the electron-transfer potential of NADH or FADH2 being converted into the phosphoryl-transfer potential of ATP |
|
|
Term
| how phosphoryl-transfer potential is expressed |
|
Definition
|
|
Term
|
Definition
| expression for electron transfer potential |
|
|
Term
| how reduction potential is expressed |
|
Definition
|
|
Term
|
Definition
| substance that exists as oxidized and reduced forms |
|
|
Term
| how the reduction potential of a redox couple is determined |
|
Definition
| by measuring the electromotive force generated by a sample half cell connected to a standard reference half cell |
|
|
Term
| depiction of how redox potential is measured |
|
Definition
[image]
electrons flow thru the wire and ions flow thru the agar bridge |
|
|
Term
| the reduction potential of the X:X- couple |
|
Definition
| the observed voltage at the start of the experiment |
|
|
Term
| the reduction potential of the H+:H2 couple |
|
Definition
|
|
Term
| what a positive reduction potential (ΔE0') indicates |
|
Definition
|
|
Term
| what a negative reduction potential (ΔE0') indicates |
|
Definition
|
|
Term
|
Definition
| faraday proportionality constant (96.48 kJ mol-1 V-1, or 23.06 kcal mol-1 V-1) |
|
|
Term
| relationship between ΔE0' and ΔG°' |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| the driving force of oxidative phosphorylation |
|
Definition
| the electron-transfer potential of NADH or FADH2 relative to that of O2 |
|
|
Term
| where does the energy that produces the proton gradient to make ATP come from? |
|
Definition
| the energy released by the reduction of each electron carrier |
|
|
Term
|
Definition
| supramolecular complex composed of complexes that carries electrons down the electron transport chain |
|
|
Term
| depiction of the components of the electron transport chain |
|
Definition
|
|
Term
| why FADh2 derived electrons pump fewer protons and ATP than NADH derived electrons |
|
Definition
| electrons from FADH2 feed into the chain downstream from those from NADH because those from FADH2 have lower reduction potential |
|
|
Term
| why electrons from FADH2 feed into the chain downstream from those from NADH |
|
Definition
| because those from FADH2 have lower reduction potential |
|
|
Term
| the 2 types of Fe proteins in the electron transport chain |
|
Definition
1: iron-sulfur proteins aka nonheme-iron proteins
2: cytochromes, which are components of heme prothetic groups |
|
|
Term
|
Definition
| Fe containing protein that is a component of a heme prosthetic group |
|
|
Term
| another metal that can participate in the electron transport chain |
|
Definition
|
|
Term
| how electron transfer works for quinones |
|
Definition
| for quinones, electron-transfer rxns are coupled to proton binding and release |
|
|
Term
| how the electron transport chain creates a proton gradient |
|
Definition
| electron flow within it leads to the transport of protons accross the inner membrane |
|
|
Term
| a protein complex that does not pump electrons |
|
Definition
|
|
Term
| where the electrons from NADH enter the electron transport chain |
|
Definition
| at NADH-Q oxidoreductase (complex 1) |
|
|
Term
| depiction of the electron transport chain's complexes |
|
Definition
|
|
Term
| depiction of coupled electron-proton transfer rxns thru NADH-Q oxidoreductase |
|
Definition
|
|
Term
|
Definition
| funnels electrons from a 2 electron carrier to a 1 electron carrier and pumps protons |
|
|
Term
|
Definition
| the mechanism for the coupling of electron transfer from Q to cytochrome C to transmembrane proton transport |
|
|
Term
|
Definition
|
|
Term
| depiction of the cytochrome oxidase mechanism |
|
Definition
|
|
Term
| depiction of proton transport by cytochrome c oxidase |
|
Definition
|
|
Term
| depiction of the electron-transport chain |
|
Definition
|
|
Term
| some dangerous radicals that can form from O2 |
|
Definition
| -superoxide (O2-)
-peroxide (O22-) |
|
|
Term
|
Definition
| -superoxide (O2-)
-peroxide (O22-)
-hydroxyl radical (OH•) |
|
|
Term
| some things reactive oxygen species can cause |
|
Definition
-aging
-some other diseases |
|
|
Term
|
Definition
| catalyzes the conversion of 2 superoxides into hydrogen peroxide and molecular oxygen |
|
|
Term
| depiction of the function of superoxide dismutase |
|
Definition
|
|
Term
|
Definition
| catalyzes the dismutation of hydrogen peroxide into water and molecular oxygen |
|
|
Term
| depiction of the function of catalase |
|
Definition
|
|
Term
|
Definition
| rxn in which a single reactant is converted into 2 different products |
|
|
Term
|
Definition
| protein protons move thru to generate ATP |
|
|
Term
|
Definition
proposes that electron transport and ATP synthesis are coupled by a proton gradient across the inner mitochondrial membrane
basically says that flow of protons drives production of ATP by ATP synthase |
|
|
Term
| how electron transport and ATP synthesis are coupled |
|
Definition
| by a proton gradient across the inner mitochondrial membrane |
|
|
Term
| depiction of the chemostatic hypothesis |
|
Definition
|
|
Term
|
Definition
| the energy rich, unequal distribution of protons across the inner mitochondrial membrane |
|
|
Term
| the 2 components of the proton motive force |
|
Definition
1: chemical gradient
2: charge gradient |
|
|
Term
| chemical gradient for protons |
|
Definition
| can be represented as a pH gradient |
|
|
Term
|
Definition
| created by the positive charge on the unequally distributed protons forming the chemical gradient |
|
|
Term
| how protons are transported out of the matrix into the intermembrane space |
|
Definition
| electron transfer thru the respiratory chain leads to the pumping of protons |
|
|
Term
| how to calculate proton-motive force |
|
Definition
| proton-motive force (Δp) = chemical gradient (ΔH) + charge gradient (Δψ) |
|
|
Term
| the respiratory chain and ATP synthase are biochemically separate. what links them? |
|
Definition
| only the proton-motive force |
|
|
Term
| depiction of the link between the respiratory chain and ATP synthase |
|
Definition
|
|
Term
| how NADH oxidation is coupled to ATP synthesis |
|
Definition
1: electron transport generates a proton-motive force
2: ATP synthesis by ATP synthase is powered by a proton-motive force |
|
|
Term
| depiction of ATP synthase |
|
Definition
|
|
Term
| what makes each of the 3 β subunits different? |
|
Definition
| they each interact with a different face of the γ subunit |
|
|
Term
| how formation of cristae makes ATP synthesis more efficient |
|
Definition
| localizing the proton gradient to where the ATP synthases are |
|
|
Term
| depiction of how ATP synthase assists in the formation of cristae |
|
Definition
|
|
Term
| the rxn ATP synthase catalyzes |
|
Definition
| formation of ATP from ADP and orthophosphate
ADP3- + HPO42- + H+ <--> ATP4- + H2O |
|
|
Term
| the 3 different functions performed by the 3 active sites in ATP synthase |
|
Definition
| 1: trapping of ADP and Pi
2: ATP synthesis
3: ATP release and ADP and Pi binding |
|
|
Term
| the 2 parts of ATP synthase |
|
Definition
1: moving unit (rotor) consisting of c ring and γε stalk
2: the stationary unit (stator) consisting of the remainder of the molecule |
|
|
Term
| depiction of the distinct ATP synthase nucleotide-binding sites |
|
Definition
|
|
Term
| order in which subunits of ATP synthase change state |
|
Definition
T --> O --> L
repeatedly rotates counterclockwise |
|
|
Term
| depiction of a binding-change mechanism for ATP synthase |
|
Definition
|
|
Term
| what drives the rotation of the γ subunit in ATP synthase? |
|
Definition
|
|
Term
| depiction of the components of the proton-conducting unit of ATP synthase |
|
Definition
|
|
Term
| what powers the rtation of the c ring in ATP synthase? |
|
Definition
| movement of protons thru the half channels from high proton c'tration of intermembrane space to low proton c'tration of matrix |
|
|
Term
| depiction of proton motion across the membrane |
|
Definition
|
|
Term
| depiction of the proton path thru the membrane |
|
Definition
|
|
Term
| number of c subunits in ring vs. efficiency of ATP synthase |
|
Definition
| the more subunits in the ring, the less efficient, that is, the more protons needed to synthesize 1 ATP |
|
|
Term
| depiction of an overview of oxidative phosphorylation |
|
Definition
|
|
Term
| how electrons from intermembrane space enter matrix |
|
Definition
|
|
Term
| how NADH is reoxidized to NAD+ |
|
Definition
| electrons from NADH, rather than NADH itself, are carried across the mitochondrial membrane |
|
|
Term
| the glycerol 3-phosphate shuttle |
|
Definition
| introduces electrons from NADH into the electron transport chain |
|
|
Term
| depiction of the glycerol 3-phosphate shuttle |
|
Definition
|
|
Term
|
Definition
| transfers electrons from NADH to oxaloacetate, forming malate |
|
|
Term
| depiction of the malate-aspartate shuttle |
|
Definition
|
|
Term
| the major function of oxidative phosphorylation |
|
Definition
|
|
Term
|
Definition
| transports ATP out of matrix and ADP into matrix |
|
|
Term
| when ATP enters the mitochondrial matrix |
|
Definition
|
|
Term
| when ADP enters the mitochondrial matrix |
|
Definition
|
|
Term
| depiction of the mechanism of ATP-ADP translocase |
|
Definition
|
|
Term
|
Definition
| large complex of proteins that provide the substrates needed for ATP synthesis |
|
|
Term
| depiction of the mitochondrial transporters |
|
Definition
|
|
Term
| cellular respiration is regulated by... |
|
Definition
| the need for ATP, since it's the ultimate and product of cellular respiration |
|
|
Term
| how many molecules of ATP are formed when glucose is completely oxidzed to co2? |
|
Definition
|
|
Term
| which step of cellular respiration generates most of the ATP? |
|
Definition
| oxidative phosphorylation (26 of 30) |
|
|
Term
| how many ATP does anaerobic glycolysis yield? |
|
Definition
|
|
Term
| the rate of oxidative phosphorylation is determined by... |
|
Definition
|
|
Term
| when electrons flow thru the electron transport chain to O2 |
|
Definition
| they usually do this only when ADP is simultaneously phosphorylated to ATP |
|
|
Term
| respiratory control or acceptor control |
|
Definition
| regulation of the rate of oxidative phosphorylation by the ADP level |
|
|
Term
| when electrons flow from fuel molecules to O2 |
|
Definition
| only when ATP needs to be synthesized |
|
|
Term
| depiction of how energy charge regulates the use of fuels |
|
Definition
|
|
Term
| depiction of some things proton gradient can be used for |
|
Definition
|
|
Term
| depiction of degrading glycogen to release glucose |
|
Definition
|
|
Term
|
Definition
| degrades glycogen into glucose |
|
|
Term
| difference between muscle glycogen and liver glycogen |
|
Definition
| they are 2 isozymes (kinda 2 forms of the same enzyme), 90% identical on the amino acid level |
|
|
Term
| where glycogen phosphorylase can cleave glycogen |
|
Definition
| at 1,4-linkages up to 4 residues away from 1,6-linkages |
|
|
Term
| where branches occur in glycogen |
|
Definition
|
|
Term
| depiction of the function of glycogen phosphorylase |
|
Definition
|
|
Term
|
Definition
| transfers 3 glycosyl residues onto one of the branches |
|
|
Term
| depiction of the function of transerase |
|
Definition
|
|
Term
|
Definition
| cleaves remaining glucose (free sugar, hexokinase phosphorylates) |
|
|
Term
| depiction of the function of α-1,6-Glucosidase |
|
Definition
|
|
Term
| depiction of the entire degradation of glycogen |
|
Definition
|
|
Term
|
Definition
| converts glucose 1-P into a usable form, glucose 6-P |
|
|
Term
| depiction of the function of phosphoglucomutase |
|
Definition
[image]
note that the phosphate ends up on a different residue |
|
|
Term
| what glycogen stored in liver is used for |
|
Definition
| to deliver glucose elsewhere (i.e., maintaining blood glucose levels) |
|
|
Term
| what glycogen stored in muscle is used for |
|
Definition
| provides glucose for its own energy demands |
|
|
Term
| does glucose 1-P enter glycolysis? |
|
Definition
|
|
Term
| are phosphorylated forms of glucose exported? |
|
Definition
|
|
Term
|
Definition
| catalyzes the dephosphorylation of glucose 6-P into glucose and Pi
glucose 6-P + water --> glucose + PPi |
|
|
Term
| where is glucose-6-phosphatase expressed? |
|
Definition
|
|
Term
| depiction of the general regulation of phosphorylase (might wanna draw this) |
|
Definition
|
|
Term
| the more active form of glycogen phosphorylase |
|
Definition
|
|
Term
| the less active form of glycogen phosphorylase |
|
Definition
|
|
Term
| how phosphorylase gets activated |
|
Definition
|
|
Term
| activity of phosphorylase is modulated by... |
|
Definition
|
|
Term
|
Definition
| phosphorylates phosphorylase |
|
|
Term
| how phosphorylase is deactivated |
|
Definition
|
|
Term
| some molecules that can bind to phosphorylase to stabilize the R or T states |
|
Definition
-ATP
-AMP
-glucose 6-P
-glucose |
|
|
Term
| hormones in muscle that affect phosphorylase |
|
Definition
|
|
Term
| how phosphorylation is stimulated in muscle |
|
Definition
| Hormones: epinephrine, adrenaline (fear/excitement), increase phosphorylation (a state) by stimulating phosphorylase kinase.
Muscle contraction: Ca2+ release, increase phosphorylation (a state) by stimulating phosphorylase kinase. |
|
|
Term
| how muscle contraction stimulates phosphorylation in muscle |
|
Definition
|
|
Term
| Allosteric effectors that stabilize phosphorylase b, T state in muscle |
|
Definition
|
|
Term
| Allosteric effector that stabilizes phosphorylase a, R state in muscle |
|
Definition
|
|
Term
| form of phosphorylase that predominates in muscle |
|
Definition
DBT
Dephosphorylated
B form
T state |
|
|
Term
| depiction of how allosteric affectors regulate muscle phorphorylase b (less active) |
|
Definition
|
|
Term
| what insulin does for glycogen |
|
Definition
| signals fed state, high blood glucose, and need to synthesize glucagon |
|
|
Term
| what insulin does for phosphorylase |
|
Definition
|
|
Term
| what glucagon does for glycogen |
|
Definition
| signals starved state, low blood glucose, and need to degrade glycogen |
|
|
Term
| what glucagon does for phosphorylase |
|
Definition
|
|
Term
| when phosphorylase kinase is active |
|
Definition
| when Phosphorylated by Protein Kinase A, glucagon signal, cAMP |
|
|
Term
| when phosphorylase phosphatase PP1 is inactive |
|
Definition
| when bound to phosphorylase, glucose releases and activates |
|
|
Term
| allosteric affectors for phosphorylase in liver |
|
Definition
|
|
Term
| how glucose regulates phosphorylase |
|
Definition
- Binds to PP1/phosphorylase, PP1 released from phosphorylase, (released PP1 more active, dephosphorylates phosphorylase)
- Binds to phosphorylase a, stabilizes T state |
|
|
Term
| form of phosphorylase that predominates in the liver |
|
Definition
PAR
Phosphorylated
a form
Relaxed state |
|
|
Term
| depiction of how phosphorylase a is regulated in the liver |
|
Definition
|
|
Term
|
Definition
|
|
Term
| depiction of the overall regulation of phosphorylase kinase |
|
Definition
|
|
Term
| depiction of the signal transduction cascacde to activate phosphorylase |
|
Definition
|
|
Term
| what epinephrine signals to the muscle |
|
Definition
| demand for muscle contraction |
|
|
Term
| equation for glycogen synthesis |
|
Definition
| glycogenn + UDP-glucose --> glycogenn+1 + UDP |
|
|
Term
| equation for glycogen degradation |
|
Definition
| glycogenn+1 + Pi --> glycogenn + glucose 1-phosphate |
|
|
Term
| the product of glycogen degradation |
|
Definition
|
|
Term
| how glucose 1-P is activated |
|
Definition
| by coupling with UTP, which releases PPi |
|
|
Term
| UDP-glucose pyrophosphorylase |
|
Definition
| catalyzes the activation of glucose 1-P by coupling to UTP |
|
|
Term
| depiction of the activation of glucose 1-P by coupling to UTP |
|
Definition
|
|
Term
| depiction of synthesis of 1,4 linkages in glycogen |
|
Definition
|
|
Term
| the priming enzyme for glycogen |
|
Definition
|
|
Term
| cross section of glycogen showing glycogenin |
|
Definition
|
|
Term
|
Definition
| transfers glucose from UDP to growing glycogen chain using 1,4-linkage |
|
|
Term
|
Definition
| breaks 1,4-linkage after > 4 units and creates 1,6-linkage |
|
|
Term
| depiction of the creation of 1,6 linkages in glycogen to create branching |
|
Definition
|
|
Term
| advantage of branching in glycogen |
|
Definition
| gives you more sites to degrade from |
|
|
Term
| why would it be harder to store proteins than glycogen? |
|
Definition
| because amino acids are more reactive |
|
|
Term
| net rxn of glycogen synthesis |
|
Definition
| glucose + 2 ATP + glycogenn + H2O --> glycogenn+1 + ADP + 2 Pi |
|
|
Term
|
Definition
| binds to it and stabilizes R state |
|
|
Term
| depiction of the Cori cycle (might wanna draw this) |
|
Definition
|
|
Term
| how the body recovers lactic acid into glucose |
|
Definition
the Cori cycle
lactate enters liver to participate in gng |
|
|
Term
| what causes the burning sensation in muscles? |
|
Definition
|
|
Term
| depiction of reciprocal regulation of glycogen during exercise or fasting |
|
Definition
|
|
Term
| the regulated step in glycogen synthesis |
|
Definition
|
|
Term
| the 2 kinases that can phosphorylate glycogen synthase |
|
Definition
-PKA
-glycogen synthase kinase |
|
|
Term
| What removes the phosphoryl groups from phosphorylase and glycogen synthase? |
|
Definition
|
|
Term
| what PP1 does to phosphorylase |
|
Definition
| dephosphorylates it a-->b to lower its activity |
|
|
Term
|
Definition
| dephosphorylates it to lower its activity |
|
|
Term
| what PP1 does to glycogen synthase |
|
Definition
| dephosphorylates it b-->a to activate it |
|
|
Term
| the more active form of glycogen synthase |
|
Definition
| the dephosphorylated a form |
|
|
Term
| the less active form of glycogen synthase |
|
Definition
| the phosphorylated b form |
|
|
Term
| depiction of insulin regulation in liver |
|
Definition
|
|
Term
|
Definition
| insulin receptor substrates |
|
|
Term
|
Definition
|
|
Term
| how insulin stimulates PP1 activity |
|
Definition
| An insulin sensitive protein kinase also phosphorylates a subunit of PP1, increasing the activity of PP1. |
|
|
Term
|
Definition
|
|
Term
| glycogen synthase is allosterically activated by... |
|
Definition
|
|
Term
| what glucose 6-P does to glycogen synthase |
|
Definition
| allosterically activates it |
|
|
Term
| PP1 is bound to ______ – this keeps PP1 from ______ |
|
Definition
liver phosphorylase a
dephosphorylating phosphorylase |
|
|
Term
| is phosphorylase more or less active after eating pasta? |
|
Definition
| less active because of all that glucose from the pasts |
|
|
Term
| is phosphorylase phosphorylated or dephosphorylated after eating pasta? |
|
Definition
|
|
Term
| is PP1 more or less active after eating pasta? |
|
Definition
|
|
Term
| depiction of how PP1 allows for "crosstalk" between phosphorylase and glycogen synthase (draw this) |
|
Definition
[image]
it seems excess glucose cleaves the PP1 from phosphorylase so PP1 can dephosphorylase glycogen synthase and glycogen phosphorylase |
|
|
Term
|
Definition
| activates glycogen phosphorylase and deactivates glycogen synthase, both by phosphorylation |
|
|
Term
| depiction of regulation of glycogen synthesis after a meal or at rest (draw this) |
|
Definition
|
|
Term
| when a lot of glycogen synthesis occurs |
|
Definition
|
|
Term
| the role of liver glycogen metabolism |
|
Definition
| maintains blood glucose level |
|
|
Term
| normal range of blood glucose concentration |
|
Definition
|
|
Term
| one way to tell if someone's diabetic |
|
Definition
| the whopping amount of glucose they give you stays high |
|
|
Term
| depiction of glycogen phosphorylase and glycogen synthase activity in response to added glucose |
|
Definition
|
|
Term
| what glucose does to glycogen phosphorylase a |
|
Definition
|
|
Term
|
Definition
| insulin-sensitive protein kinase |
|
|
Term
| how activation of PP1 by insulin sensitive protein kinase leads to less phosphorylase activity |
|
Definition
| because less of it gets activated |
|
|
Term
| what PP1 does to phosphorylase |
|
Definition
| deactivates it from a to b by dephosphorylation |
|
|
Term
| what PP1 does to glycogen synthase |
|
Definition
| activates it from b to a by dephosphorylation |
|
|
Term
| what can activate glycogen synthase other than PP1? |
|
Definition
|
|
Term
| which stays more constant throughout the day? glucose or A1c? |
|
Definition
|
|
Term
| A1c is an indication of... |
|
Definition
| the amount of glucose that becomes associated with hemoglobin; glycated with hemoglobin |
|
|
Term
| where non-enzymatic glycosylation takes place |
|
Definition
| in all proteins with a free-reacting lysine or valine in the presence of glucose |
|
|
Term
| what part of hemoglobin reacts with glucose? |
|
Definition
| the amino terminus of the beta chain |
|
|
Term
| why glycosylated hemoglobin is a widely used reporter for blood glucose levels |
|
Definition
| because red blood cells last 2-3 months and replenished continuously |
|
|
Term
|
Definition
stuck in a glucose insensitive state
the body always thinks it's starved of glucose |
|
|
Term
| description of type 1 diabetes |
|
Definition
| autoimmune disease resulting in destruction of insulin producing cells. |
|
|
Term
| description of type 2 diabetes |
|
Definition
| Insulin-resistance, insulin is usually made at normal levels but is not utilized properly, and glycogen synthesis is 50% lower. |
|
|
Term
| physiological response to diabetes |
|
Definition
|
|
Term
| what the body can't do when it has diabetes |
|
Definition
| can't convert glucose to glycogen |
|
|
Term
| what happens to excess glucose when you have diabetes? |
|
Definition
| that excess glucose gets incorporated into other pathways |
|
|
Term
| some problems that can be caused by excess glucose |
|
Definition
|
|
Term
| About ______ of the US population has Type 2 diabetes. |
|
Definition
|
|
Term
| About 80% of people with Type 2 diabetes are ______. |
|
Definition
|
|
Term
| one possible treatment for type 2 diabetes |
|
Definition
| increasing production of glucose transporters to get more glucose out of the bloodstream |
|
|
Term
| to activate glycogen synthesis, you wanna deactivate... |
|
Definition
|
|
Term
| increasing activity of ______ should create more active form of glycogen synthase |
|
Definition
|
|
Term
| 2 things that activate PP1 |
|
Definition
-glycogen phosphorylase a
-insulin-sensitive protein kinase |
|
|
Term
| what releases PP1 from glycogen phosphorylase a? |
|
Definition
|
|
Term
| the key enzyme when there's a need to synthesize glycogen |
|
Definition
|
|
Term
| Hydrolysis of _____ drives the formation of UDP-glucose used in glycogen synthesis. |
|
Definition
| P-Pi
this is true because of Le Chatlier's principle |
|
|
Term
| The core of glycogen contains ______. |
|
Definition
|
|
Term
| Glycogen synthase is converted into more active form by the enzyme _______ . |
|
Definition
PP1
more active when dephosphorylated |
|
|
Term
| Insulin stimulates glycogen synthase activity and decreases ______ activity. |
|
Definition
phosphorylase a
this is because phosphorylase degrades glycogen and insulin signals making glycogen |
|
|
Term
| Phosphorylation has the __________ affect on the enzymatic activities of glycogen phosphorylase and glycogen synthase. |
|
Definition
|
|
Term
| During fasting, _____ acts along with glycogen synthase kinase to phosphorylase glycogen synthase, ____ glycogen synthase activity. |
|
Definition
|
|
Term
|
Definition
| cell that stores lipids; fat cell |
|
|
Term
| depiction of an adipocyte |
|
Definition
|
|
Term
| general pathway of triacylglycerol metabolism |
|
Definition
|
|
Term
| metabolism of triacylglycerol in the fat cell is stimulated by... |
|
Definition
|
|
Term
| some lipoprotein complexes |
|
Definition
-HDL
-LDL
-VLDL
-serum albumin |
|
|
Term
|
Definition
| not really, but has cholesterol in it |
|
|
Term
|
Definition
| triggers inflammatory response in vessels, leading to vessel sclerosis |
|
|
Term
| triacylglycerol can be converted into... |
|
Definition
|
|
Term
| what converts triacylglycerol into glycerol or fatty acids? |
|
Definition
|
|
Term
| pathways that glycerol that enters liver cells can get incorporated into |
|
Definition
|
|
Term
| pathways that fatty acids that enter cells outside the liver can get incorporated into |
|
Definition
| fatty acid oxidation, leading to citric acid cycle |
|
|
Term
|
Definition
| converts triacylglycerol into glycerol and fatty acids |
|
|
Term
| structure of triacylglyceride |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| depiction of triacylglyceride being converted into fatty acids and glycerol |
|
Definition
|
|
Term
| Triacylglycerol is stored in... |
|
Definition
| adipocytes as lipid droplets |
|
|
Term
| how epinephrine and glucagon signal for energy |
|
Definition
| by acting through 7TM receptors, stimulate lipid breakdown or lipolysis. |
|
|
Term
| depiction of pathway by which a hormone signals for triacylglycerol degradation (diagram this into something that makes better sense) |
|
Definition
|
|
Term
| hormones that can signal for triacylglycerol degradation |
|
Definition
|
|
Term
| Glycerol released during lipolysis is absorbed by the liver or other cells for use in... |
|
Definition
| glycolysis or gluconeogenesis |
|
|
Term
| depiction of glycerol metabolism |
|
Definition
|
|
Term
| fatty acids are linked to ______ before they are oxidized |
|
Definition
|
|
Term
| the first stage of fatty acid oxidation is basically... |
|
Definition
| conversion of fatty acid to acyl CoA |
|
|
Term
|
Definition
| catalyzes the conversion of fatty acid to acyl CoA |
|
|
Term
| where the first stage of fatty acid degradation occurs |
|
Definition
| on outer mitochondrial membrane |
|
|
Term
| depiction of stage 1 of fatty acid degradation |
|
Definition
|
|
Term
| depiction of an acyl adenylate |
|
Definition
|
|
Term
|
Definition
|
|
Term
| structure of an acyl group |
|
Definition
|
|
Term
| depiction of stage 2 of fatty acid degradation |
|
Definition
|
|
Term
| depiction of how fatty acids, in the form of acyl, cross the inner mitochondrial membrane |
|
Definition
|
|
Term
| why buying cartinine is nuts |
|
Definition
| because we can make it and there's lots of food we eat that contains it |
|
|
Term
| depiction of stage 3 of fatty acid degradation |
|
Definition
|
|
Term
| the rxn for one round of β-oxidation of a fatty acid |
|
Definition
| Cn-acyl CoA + FAD + NAD+ + H2O + CoA --> Cn-2-acyl CoA + FADH2 + NADH + acetyl CoA + H+ |
|
|
Term
| the complete rxn for palmitoyl CoA |
|
Definition
| palmitoyl CoA + 7 FAD + 7 NAD+ + 7 H2O + 7 CoA --> 7 FADH2 + 7 NADH + 8 acetyl CoA + 7 H+ |
|
|
Term
| How much ATP is generated from C16 palmitoyl-CoA? |
|
Definition
net 106
produces 108 at the expense of 2 |
|
|
Term
| depiction of how ketone bodies are formed |
|
Definition
|
|
Term
| when formation of ketone bodies occurs |
|
Definition
| basically happens when acetyl CoA goes wild |
|
|
Term
| the 2 ketone bodies that can be produced |
|
Definition
-acetone
-D-3-hydroxybutyrate |
|
|
Term
| when production of acetone occurs |
|
Definition
| basically happens as a result of running out of citric acid cycle intermediates |
|
|
Term
|
Definition
2-30% lost in breath and urine.
during starvation, some converted to pyruvate, enters gluconeogenesis |
|
|
Term
| depiction of how D-3-hydroxybutyrate can be used for energy |
|
Definition
|
|
Term
| some tissues that can use ketone bodies as fuel |
|
Definition
-liver
-heart
-renal cortex
-brain |
|
|
Term
| choice of fuel vs. days of starvation |
|
Definition
|
|
Term
| the first thing that goes during starvation |
|
Definition
|
|
Term
| depiction of Diabetic ketosis (ketoacidosis) |
|
Definition
|
|
Term
|
Definition
-physiology thinks you have no glucose in your bloodstream
-this can happen when you produce no insulin
-this results in lots of acetone |
|
|
Term
| depiction of the pathways that contribute to fatty acid synthesis |
|
Definition
|
|
Term
| when you make fatty acids, you have big demand for... |
|
Definition
|
|
Term
|
Definition
| rule of thumb: NADPH in biosynth and NADH in catabolism |
|
|
Term
| stage 1 of fatty acid synthesis |
|
Definition
| transfer citrate from the mitochondria to the cytoplasm, cleaved to form acetyl CoA and OAA (ATP citrate lyase) |
|
|
Term
| stage 2 of fatty acid synthesis |
|
Definition
activation of acetyl CoA + carbonate to form malonyl CoA
Key regulatory and committed step (acetyl CoA carboxylase) |
|
|
Term
| stage 3 of fatty acid synthesis |
|
Definition
repetitive addition and reduction of two carbon units to synthesize fatty acids.
Synthesis occurs on an acyl carrier protein (ACP), which acts as a molecular scaffold (can also think of it as a tag). |
|
|
Term
| which occurs in fatty acid synthesis? reduction or oxidation? |
|
Definition
|
|
Term
| which occurs in fatty acid synthesis? hydration or dehydration? |
|
Definition
|
|
Term
| which occurs in fatty acid degradation? reduction or oxidation? |
|
Definition
|
|
Term
| which occurs in fatty acid degradation? hydration or dehydration? |
|
Definition
|
|
Term
| depiction of stage 1 of fatty acid synthesis |
|
Definition
|
|
Term
|
Definition
| catalyzes synthesis of malonyl CoA |
|
|
Term
| depiction of stage 2 of fatty acid synthesis |
|
Definition
|
|
Term
|
Definition
| catalyzes the formation of fatty acids |
|
|
Term
| where fatty acid synthesis occurs |
|
Definition
| on the acyl carrier protein (ACP), a polypeptide linked to CoA |
|
|
Term
| depiction of stage 3 of fatty acid synthesis |
|
Definition
|
|
Term
| depiction of round 1 of stage 3 of fatty acid synthesis |
|
Definition
|
|
Term
| depiction of round 2 of stage 3 of fatty acid synthesis |
|
Definition
|
|
Term
| the activities of fatty acid synthase |
|
Definition
-condensation
-reduction
-dehydration
-reduction |
|
|
Term
| fatty acid synthesis keeps running until... |
|
Definition
|
|
Term
| regulators of acetyl CoA carboxylase |
|
Definition
-citrate
-malonyl CoA
-fatty acid (in this case, palmitoyl CoA) |
|
|
Term
| when acetyl CoA carboxylase is inhibited |
|
Definition
| when phosphorylated by AMP-dependent protein kinase (AMPK) |
|
|
Term
| how acetyl CoA carboxylase gets activated |
|
Definition
| gets dephosphorylated by protein phospahatase 2A (PP2A) |
|
|
Term
| the hub of fatty acid biosynthesis |
|
Definition
|
|
Term
|
Definition
|
|
Term
| how citrate activates carboxylase |
|
Definition
| by facilitating the formation of active polymers of the enzyme |
|
|
Term
|
Definition
| phosphofructokinase, lowers flux through glycolysis |
|
|
Term
| major end product of fatty acid biosynthesis |
|
Definition
|
|
Term
| how palmitoyl CoA inhibits carboxylase |
|
Definition
| by causing depolymerization of the enzyme polymers |
|
|
Term
| how palmitoyl CoA affects citrate |
|
Definition
| Inhibits export of citrate from mitochondria |
|
|
Term
| Malonyl CoA is the product of... |
|
Definition
|
|
Term
| what malonyl CoA does to carnitine acyl transferase 1 |
|
Definition
|
|
Term
| depiction of Regulation by AMPK and PP2A |
|
Definition
|
|
Term
| this is basically the fuel gage for fatty acid metabolism |
|
Definition
| AMP-activated protein kinase |
|
|
Term
| what insulin signals in fatty acid metabolism |
|
Definition
| fed state, basically signaling to synthesize fatty acids |
|
|
Term
| depiction of the involvement of citrate in fatty acid metabolism |
|
Definition
|
|
Term
| depiction of palmitoyl CoA inhibiting fatty acid synthesis |
|
Definition
|
|
Term
| how carboxylase inhibits fatty acid degradation |
|
Definition
| it's product, malonyl CoA, prevents the entry of fatty acid acyl CoA into mitochondria by inhibiting carnitine acyl transferase I |
|
|
Term
| depiction of malonyl CoA (product of carboxylase) inhibiting fatty acid degradation |
|
Definition
|
|
Term
| general depiction of the synthesis of storage lipids and cholesterol |
|
Definition
|
|
Term
| depiction of a cell membrane with cholesterol in it |
|
Definition
|
|
Term
| structure of a cholesterol molecule |
|
Definition
|
|
Term
| phosphatidate is a precursor to... |
|
Definition
-storage lipids
-many membrane lipids |
|
|
Term
| Phosphatidate is formed by... |
|
Definition
| the addition of two fatty acids to glycerol 3-phosphate in the liver. |
|
|
Term
| where phosphatidate formation occurs |
|
Definition
|
|
Term
| depiction of phosphatidate formation |
|
Definition
|
|
Term
| structure of phosphatidate |
|
Definition
|
|
Term
| what phosphatidate can be used for |
|
Definition
| can be used to make lipids, such as phospholipids |
|
|
Term
|
Definition
| synthesizes triacylglycerol from phosphatidate and acyl CoA. |
|
|
Term
| the primary fuel storage in humans |
|
Definition
|
|
Term
| depiction of metabolism of phosphatidate into phospholipids and triacylglycerols |
|
Definition
|
|
Term
| depiction of phospholipid synthesis |
|
Definition
|
|
Term
| depiction of triacylglycerol synthesis |
|
Definition
|
|
Term
| most of the fat droplet in adipocytes is... |
|
Definition
|
|
Term
| something cholesterol helps with in the membrane |
|
Definition
| helps form lipid rafts, which help with lots of functions in the membrane |
|
|
Term
| why you should never put a baby on a low cholesterol diet |
|
Definition
| because they need cholesterol to form lipid rafts |
|
|
Term
| depiction of cholesterol synthesis |
|
Definition
|
|
Term
| steroid hormones are derived from... |
|
Definition
|
|
Term
| some steroid hormones derived from cholesterol |
|
Definition
-androgens
-glucocorticoids |
|
|
Term
| cortisol is derived from... |
|
Definition
|
|
Term
| drugs used to lower cholesterol |
|
Definition
|
|
Term
| how statins lower cholesterol |
|
Definition
| inhibit HMG CoA reductase |
|
|
Term
| The rate of synthesis of HMG CoA reductase mRNA is controlled by... |
|
Definition
| the sterol regulatory element binding protein (SREBP). Too little cholesterol. |
|
|
Term
| The rate of translation of the reductase mRNA is controlled by... |
|
Definition
| metabolites of mevalonate and dietary cholesterol (molecular mechanism not understood) |
|
|
Term
| Increases in cholesterol concentration result in... |
|
Definition
| proteolytic degradation of the reductase. |
|
|
Term
| how HMG CoA reductase is inactivated |
|
Definition
| Phosphorylation of the reductase by AMP-dependent protein kinase inactivates the enzyme. |
|
|
Term
| depiction of transcription control |
|
Definition
|
|
Term
| depiction of Degradation of HMG CoA reductase in response to cholesterol |
|
Definition
|
|
Term
| role of ubiquitin in the Degradation of HMG CoA reductase in response to cholesterol |
|
Definition
| acts as a tag for protein degradation |
|
|
Term
| the role of Degradation of HMG CoA reductase in response to cholesterol |
|
Definition
this is basically the protein turnover machine in cells
triggered by changes in cholesterol |
|
|
Term
| depiction of Phosphorylation of HMG-CoA reductase |
|
Definition
|
|
Term
| ethanol metabolism in liver leads to excess... |
|
Definition
NADH and fatty acids
(fatty liver) |
|
|
Term
| why it's not good to have acetylaldehyde in the system |
|
Definition
| because it is highly reactive and messes with lots of things; can even mess with DNA |
|
|
Term
| rxns that occur during ethanol metabolism |
|
Definition
|
|
Term
| the role of acetyl CoA synthase in fatty acid synthesis |
|
Definition
| produces acetyl-CoA from the acetate derived from ethanol (think of it as a very very short fatty acid!) |
|
|
Term
| how acetyl-CoA can be used for fatty acid synthesis |
|
Definition
| by converting to malonyl-CoA (acetyl-CoA carboxylase) after substituting CoA with ACP (acetyl transacylase). |
|
|
Term
| Consequences of acetaldehyde (very reactive) |
|
Definition
- Damages DNA, leads to esophageal cancer
- Outcomes depend on personal genetics |
|
|
Term
| depiction of the flowchart of what happens as a result of too much acetaldehyde |
|
Definition
|
|
Term
| what acetaldehyde does to DNA |
|
Definition
| causes DNA strands to crosslink |
|
|
Term
| depiction of the different fates of pyruvate |
|
Definition
|
|
Term
| Excess NADH/acetate inhibits... |
|
Definition
inhibits citric acid cycle
NADH inhibits α KG dehydrogenase and isocitrate dehydrogenase |
|
|
Term
| Excess NADH/acetate stimulates... |
|
Definition
-lactic acidosis; excess NADH pushes lactate dehydrogenase rxn towards lactate
-fatty acid synthesis due to excess acetyl-CoA; leads to fatty liver
-ketone body formation as a result of more acetyl-CoA; this leads to more acidosis |
|
|
Term
| why some people are more vulnerable to alcohol induced cancer |
|
Definition
| because they have an allele that increases acetaldehyde production when drinking alcohol |
|
|
Term
| depiction of the Molecular basis of the ALDH2*E487K variant |
|
Definition
|
|
Term
| why do we not store amino acids or proteins? |
|
Definition
| amino acids are more diverse and therefore proteins are more complex and less stable |
|
|
Term
| What happens to the ammonia produced when amino acids are used as fuel? |
|
Definition
| gets converted to urea, because it's toxic |
|
|
Term
| the 1st step in the degradation of amino acids |
|
Definition
|
|
Term
| how N gets removed from amino acids |
|
Definition
| alpha amino groups are converted into ammonium ions by the oxidative deanimation of glutamate
Amino groups from amino acids are funneled to glutamate, which is deaminated to form NH4+. |
|
|
Term
| depiction of N being removed from amino acids |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| Aminotransferases (transaminases) |
|
Definition
| transfer amino groups from an amino acid to α-ketoglutarate to generate glutamate. |
|
|
Term
| depiction of the function of aminotransferases (transaminases) |
|
Definition
|
|
Term
|
Definition
| a mitochondrial enzyme, releases NH4+ in the oxidative deamination of glutamate |
|
|
Term
| depiction of the function of glutamate dehydrogenase |
|
Definition
|
|
Term
| why you gotta regulate how much glutamate is produced |
|
Definition
| because glutamate is also a neurotransmitter |
|
|
Term
| allosteric regulators of glutamate dehydrogenase |
|
Definition
- GTP and ATP Inhibit
- GDP and ADP Activate |
|
|
Term
| what GTP and ATP do to glutamate dehydrogenase |
|
Definition
|
|
Term
| what GDP and ADP do to glutamate dehydrogenase |
|
Definition
|
|
Term
| depiction of the major flow of ammonia |
|
Definition
[image]
note that it gives you ONE of the N's in urea |
|
|
Term
| depiction of how NH4+ is processed in the liver |
|
Definition
|
|
Term
| how muscle processes NH4+ |
|
Definition
- Lacks urea cycle
- Transaminations to Alanine, which is exported to the liver to be converted to glutamate |
|
|
Term
| do muscle cells have a urea cycle? |
|
Definition
|
|
Term
| how do muscle cells get around not having a urea cycle? |
|
Definition
| Transaminations to Alanine, which is exported to the liver to be converted to glutamate |
|
|
Term
| depiction of the urea cycle (draw this) |
|
Definition
|
|
Term
| understand these things about pathways: |
|
Definition
1: function
2: energetics
3: regulation
4: compartmentalized?
5: pathway connections |
|
|
Term
| the types of molecules citrulline and ornithine are |
|
Definition
| amino acids, but they're never used to make proteins |
|
|
Term
|
Definition
| to get rid of ammonia by producing urea |
|
|
Term
|
Definition
| urea cycle consumes energy (note that it consumes ATP) |
|
|
Term
| how is the urea cycle compartmentalized? |
|
Definition
| mitochondria and cytoplasm |
|
|
Term
| pathway connection from urea cycle |
|
Definition
|
|
Term
| Carbamoyl phosphate synthase |
|
Definition
| Couples ammonia to bicarbonate |
|
|
Term
| allosteric activator of Carbamoyl phosphate synthase |
|
Definition
|
|
Term
| how arginine affects urea cycle |
|
Definition
| high concentration of arginine activates the Urea cycle |
|
|
Term
| depiction of the function of Carbamoyl phosphate synthase (how Carbamoyl phosphate is synthesized) |
|
Definition
|
|
Term
| Ornithine transcarbamoylase |
|
Definition
| forms citrulline from ornithine and carbamoyl phosphate |
|
|
Term
| depiction of the function of Ornithine transcarbamoylase (how ornithine is converted to citrulline) |
|
Definition
[image]
the pink is what becomes urea |
|
|
Term
| how citrulline and ornithine are thansported accross the mitochondrial membrane |
|
Definition
| co-transport of ornithine (in) and citrulline (out) |
|
|
Term
|
Definition
| condenses citrulline and aspartate |
|
|
Term
| depiction of the function of Arginosuccinate synthase (how arginosuccinate is synthesized) |
|
Definition
|
|
Term
|
Definition
degrades arginosuccinate into arginine and fumarate
fumarate enters gng |
|
|
Term
| depiction of the function of Argininosuccinase |
|
Definition
|
|
Term
|
Definition
| catalyzes hydrolysis of arginine into ornithine and urea |
|
|
Term
| the rxn arginase is involved in |
|
Definition
| Arginine + water --> ornithine + UREA |
|
|
Term
| where do the N's in urea come from? |
|
Definition
|
|
Term
| the urea cycle is linked to... |
|
Definition
|
|
Term
| how the urea cycle is linked to gng |
|
Definition
| CO2 + NH4+ + 3 ATP + aspartate + 2 H2O --> urea + 2 ADP + 2 Pi + AMP + PPi + fumarate
the fumarate can enter gng |
|
|
Term
| depiction of what links gng and the urea cycle |
|
Definition
|
|
Term
| depiction of the fates of C backbones of amino acids in metabolism |
|
Definition
[image]
the yellow are ketogenic and the pink are glucogenic |
|
|
Term
| ______ are required for degradation of aromatic amino acids |
|
Definition
|
|
Term
| aromatic amino acids require ______ for degradation |
|
Definition
| monooxygenases (mixed-function oxygenases) |
|
|
Term
| what monooxygenases use as substrates |
|
Definition
|
|
Term
|
Definition
| use O2 as a substrate and incorporate one O into theproduct and the other into water |
|
|
Term
| phenylalanine hydroxylase |
|
Definition
| monooxygenase that converts phenylalanine into tyrosine with the assistance of the cofactor tetrahydrobiopterin |
|
|
Term
| depiction of the function of phenylalanine hydroxylase (conversion of phenylalanine to tyrosine) |
|
Definition
|
|
Term
| something deficient in Phenylketonuria (PKU) |
|
Definition
|
|
Term
| the genetics details of the PKU allele |
|
Definition
- Recessive
- about 1/60 carriers
- about 1/15,000 live births |
|
|
Term
| PKU causes mental retardation. the mechanism is unknown, but what's one possibility? |
|
Definition
| if the phenylalanine c'tration gets too high, it causes neurological damage by preventing uptake of some amino acids into the brain |
|
|
Term
| depiction of phenylalanine and tyrosine degradation |
|
Definition
|
|
Term
| why phenylalanine and tyrosine have glucogenic character as well as ketogenic character |
|
Definition
| because degradation produces acetone and fumarate; the fumarate can enter gng pathway |
|
|
Term
|
Definition
| missing or deficient phenylalanine hydroxylase |
|
|
Term
| in PKU, some of the excess phenylalanine is converted into... |
|
Definition
|
|
Term
|
Definition
| urine turns green with FeCl3 |
|
|
Term
| what happene when someone is diagnosed with PKU? |
|
Definition
| put on strict diet to prevent mental retardation |
|
|
Term
|
Definition
| current hypothesis: excess Phenylalanine blocks a large neutral amino acid transporter at the blood brain barrier called LAT-1 |
|
|
Term
| depiction of conversion of phenylalanine into phenylpyruvate |
|
Definition
|
|
Term
| can we synthesize phenylalanine? |
|
Definition
|
|
Term
| important characteristic of a PKU patient's diet |
|
Definition
| must avoid too much phenylalanine, but phenylalanine is an essential amino acid, so we must consume some of it |
|
|
Term
| Biosynthetic families of amino acids in bacteria and plants |
|
Definition
[image]
the ones with E are essential for humans |
|
|
Term
| depiction of the synthesis of serine and glycine |
|
Definition
|
|
Term
| why it's bad to have too much homocystein in the system |
|
Definition
oxidizes:
- Blood vessel lining
- Vascular smooth muscle |
|
|
Term
| depiction of the synthesis of homocysteine and cysteine |
|
Definition
|
|
Term
| something used frequrntly in biosynthetic pathways |
|
Definition
| One carbon donors/acceptors |
|
|
Term
| why S-adenosylmethionine (SAM) is an effective methyl group donor |
|
Definition
| because the positive charge on S gives it higher methyl transfer potential |
|
|
Term
| depiction of synthesis of S-adenosylmethionine (SAM) |
|
Definition
|
|
Term
| when fasting, why is there an initial surge of N excretion? |
|
Definition
| utilization of dietary protein |
|
|
Term
| Why does nitrogen excretion fall after several weeks of fasting? |
|
Definition
| using fatty acids, and then ketone bodies |
|
|
Term
| why there's an increase in nitrogen secretion when the lipid stores are depleted |
|
Definition
| starts degrading your own proteins; last ditch effort |
|
|
Term
Which of the following compounds serves as an acceptor for amino groups of many
amino acids during catabolism? Glutamine, Asparagine, Alpha-ketoglutarate, or Histidine |
|
Definition
|
|
Term
|
Definition
| deficiency phenylalanine hydroxylase or tetrahydrobiopterin |
|
|
Term
|
Definition
| buildup of phenylalanine in the body |
|
|
Term
| how PKU causes mental retardation |
|
Definition
|
|
Term
| two examples of direct transmination between CAC intermediates and amino acids |
|
Definition
alpha-ketoglutarate --> glutamate
oxaloacetate --> aspartate |
|
|
Term
| Can an amino acid be both ketogenic and glucogenic? |
|
Definition
|
|
Term
| an unborn baby's neural tube closure requires lots of... |
|
Definition
|
|
Term
| Triacylglycerols are stored in _____ in mammals |
|
Definition
|
|
Term
| Feedback inhibition usually occurs at the ______ step in a biosynthetic pathway. |
|
Definition
|
|
Term
| Degradation of ketogenic amino acids gives rise to _______. |
|
Definition
-acetyl CoA
-acetoacetyl CoA |
|
|
Term
| Carnitine is the carrier used to transfer fatty acids into the _______ for degradation. |
|
Definition
|
|
Term
| Complete beta oxidation of myristyl-CoA (14:0) yields |
|
Definition
| 7 acetyl CoA + 6 FADH2 + 6 NADH + 6 H+ |
|
|
Term
| Fatty acid synthesis begins with the export of ______ from the mitochondria. |
|
Definition
|
|
Term
| Fatty acid synthesis adds a total of ___ carbon units per cycle after removal of ___ unit(s) as CO2. |
|
Definition
| 2
1
you add 3, but lose 1 as CO2, so the net is 2, 1 |
|
|
Term
| Fatty acid synthesis and degradation occurs using similar intermediates. What allows these pathways to function independently without a creating a futile cycle? |
|
Definition
-Synthesis occurs in the cytoplasm, degradation in the mitochondria.
-Acyl-carnitine used for degradation.
-Acyl-ACP used for synthesis |
|
|
Term
| Type 2 diabetes is a condition where insulin is produced but cannot perform its function (insulin resistance), allowing blood glucose levels to remain above normal. Research is underway to develop drugs for glycogen phosphorylase as a possible treatment. Provide a rationale for this strategy. |
|
Definition
| A drug that inhibits phosphorylase should reduce the level of glucose. |
|
|
Term
| Excessive alcohol consumption results in abnormally high levels of... |
|
Definition
|
|
Term
| The level of HMG-CoA reductase is regulated by... |
|
Definition
-protein degradation mediated by the proteasome.
-transcription of the HMG-CoA reductase gene in response to low levels of sterols.
-the level of protein phosphorylation modulated through signaling pathways. |
|
|
Term
| Increasing the level of insulin secretion should stimulate ____. |
|
Definition
| cholesterol and glycogen synthesis |
|
|
Term
| Under what physiological condition would acetyl CoA carboxylase and HMG CoA reductase be phosphorylated by AMP-activated protein kinase? |
|
Definition
A starved state should increase phosphorylation of these enzymes, lowering their activity.
under starved state, you wanna degrade, not synthesize, stuff |
|
|
Term
| What role does acetyl CoA carboxylase play in fatty acid degradation? |
|
Definition
| The product of acetyl CoA carboxylase, malonyl-CoA, inhibits acyl carnitine transferase I import of acyl carnitine into the mitochondria where fatty acid degradation occurs |
|
|
Term
| how protein phosphatase 1 (PP1) regulates glycogen synthesis in liver |
|
Definition
-Glucose releases PP1, where it dephosphorylates phosphorylase A to form the less active form phosphorylase B.
-Inactivates phosphorylase kinase by dephosphorylation.
-Activates glycogen synthase by dephosphorylation |
|
|
Term
| The urea cycle removes ____ atoms of nitrogen per cycle |
|
Definition
2
1 coming from ammonium and the other coming from the amino group of aspartate |
|
|
Term
| two pathways that contribute precursors for amino acid synthesis |
|
Definition
-glycolysis
-citric acid cycle |
|
|
Term
| How might increased synthesis of glutamate and aspartate affect energy production in the cell? |
|
Definition
| Loss of oxaloacetate and alpha ketoglutarate would slow the citric acid cycle. |
|
|
Term
| Nitrogen is funneled through _____ prior to entering the urea cycle |
|
Definition
|
|
Term
| Statins lower cholesterol levels because they partially inhibit the committed step in cholesterol biosynthesis catalyzed by ______. |
|
Definition
|
|
Term
| common site of regulation in feedback inhibition |
|
Definition
|
|
Term
| depiction of feedback inhibition |
|
Definition
|
|
Term
| which step is usually the committed step? |
|
Definition
| the first step using the first enzyme |
|
|
Term
| what you gotta give bacteria for them to grow |
|
Definition
| the end product of the pathway |
|
|
Term
| 3-phosphoglycerate dehydrogenase |
|
Definition
| catalyzes the committed step in serine synthesis |
|
|
Term
| The committed step in serine synthesis, catalyzed by 3-phosphoglycerate dehydrogenase, is inhibited by... |
|
Definition
|
|
Term
| 3-phosphoglycerate is an intermediate of... |
|
Definition
|
|
Term
| structure of 3-phosphoglycerate dehydrogenase |
|
Definition
|
|
Term
| how binding of serine affects 3-phosphoglycerate dehydrogenase |
|
Definition
| decreases Vmax by conformational changes that alter the active site of the catalytic domain |
|
|
Term
| kinetics graph of serine as an inhibitor (might wanna draw this) |
|
Definition
[image]
this is kinda cooperativity turned on its head to analyze the inhibitor |
|
|
Term
| types of feedback that can occur in branched pathways |
|
Definition
-feedback inhibition (plus) activation
-enzyme multiplicity
-cumulative feedback inhibition |
|
|
Term
| Feedback inhibition (plus) activation |
|
Definition
| If two pathways have an initial common step, one pathway is inhibited by its own product and stimulated by the product of the other pathway. Threonine deaminase illustrates this type of regulation. |
|
|
Term
|
Definition
| The committed step is catalyzed by two or more enzymes with differing regulatory properties. For example, three distinct aspartate kinases control the synthesis of threonine, methionine, and lysine in E. coli. |
|
|
Term
| Cumulative feedback inhibition |
|
Definition
| A common step for several pathways is inhibited by each of the various end products. One issue is the number of allosteric sites. The Amino Acid Case is an example of this type of feedback inhibition. |
|
|
Term
| depiction of feedback inhibition and activation in a branched pathway |
|
Definition
|
|
Term
| one advantage of inhibition and activation by a branched pathway |
|
Definition
| in the end, you want a balance of products |
|
|
Term
| depiction of enzyme multiplicity in a branched pathway |
|
Definition
|
|
Term
| a microbe that can degrade raw biomass |
|
Definition
| Caldicellulosiruptor bescii,
isolated from a thermal spring in Russia |
|
|
Term
| objective of degrading raw biomass |
|
Definition
|
|
Term
| advantage C. Bescii has when it come to the bioethanol production process |
|
Definition
| you heat it up to about 75°C, which frees up some useful carbohydrates and it's a temp the microbe likes |
|
|
Term
| fermentative pathways in C. bescii for hexose sugars |
|
Definition
|
|
Term
| strategy in engineering C. bescii for use in bioethanol production |
|
Definition
| Targeted insertion and expression of C. thermocellum adhE in C. bescii |
|
|
Term
| what knocking out the Idh gene in C. bescii does |
|
Definition
|
|
Term
| another characteristic that makes C. bescii more suitable for ethanol production |
|
Definition
| C. bescii itself is fairly tolerant to ethanol
tolerant to 300 mM |
|
|
Term
| Amino acid synthesis is generally regulated by... |
|
Definition
|
|
Term
| In a linear biosynthetic pathway, what step is usually regulated? What molecule is usually the feedback inhibitor? Why? |
|
Definition
Committed step
end product
saves energy
pathway won't function if committed step is inhibited |
|
|
Term
| If an animal is fed N15-labeled aspartate, name a major compound that will be labeled. |
|
Definition
|
|
Term
| Feeding past a nutritional block resulting from a mutation is an effective way to understand ____ . |
|
Definition
| gene/enzyme relationships |
|
|
Term
|
Definition
|
|
Term
| structure of triacylglyceride |
|
Definition
|
|
Term
| structure of carboxylic acid |
|
Definition
|
|
Term
|
Definition
| very large, branched polymer of glucose residues |
|
|
Term
| the linkage between most of the glucose residues in glycogen |
|
Definition
|
|
Term
| frequency of branching in glycogen |
|
Definition
|
|
Term
| type of linkage at branch points in glycogen |
|
Definition
|
|
Term
| why glycogen is not as energy rich as fatty acids |
|
Definition
| because glycogen is less reduced (more oxidized) than fatty acids |
|
|
Term
| one advantage of glycogen over fatty acids |
|
Definition
| the glucose released from glycogen can provide energy in the absence of oxygen, while fatty acids can't |
|
|
Term
| what glycogen does for blood glucose |
|
Definition
| maintains blood glucose concentration between meals |
|
|
Term
| when the brain can use a fuel other than glucose |
|
Definition
| during prolonged starvation |
|
|
Term
| plants store glucose as... |
|
Definition
|
|
Term
| the 2 major sites of glycogen storage in humans |
|
Definition
|
|
Term
| glycogen is present in the cytoplasm as... |
|
Definition
| 10-40 nm granules, containing about 55,000 glucose molecules |
|
|
Term
| why glycogen synthesis and degradation are regulated in the liver |
|
Definition
| to maintain glucose concentration in the blood, such as to degrade glycogen between meals |
|
|
Term
| why glycogen synthesis and degradation are regulated in the liver |
|
Definition
| to meet the needs of the muscle itself, such as to meet ATP needs |
|
|
Term
| this is thought to be a major component of exhaustion |
|
Definition
| depletion of muscle glycogen |
|
|
Term
| depiction of the structure of glycogen |
|
Definition
|
|
Term
| the protein at the core of glycogen |
|
Definition
|
|
Term
| these form the ends of the glycogen granule |
|
Definition
| the nonreducing ends of the glycogen molecule |
|
|
Term
| some steps required for the efficient breakdown of glycogen |
|
Definition
-degrade glycogen
-remodel glycogen so that it remains a substrate for degradation
-convert the product of glycogen breakdown into a product suitable for further metabolism |
|
|
Term
| the key regulatory enzyme in glycogen breakdown |
|
Definition
|
|
Term
|
Definition
| the key regulatory enzyme in glycogen breakdown; it cleaves its substrate by the addition of orthophosphate (Pi) to yield glucose 1-phosphate |
|
|
Term
|
Definition
| the cleavage of a bond by the addition of orthophosphate |
|
|
Term
| depiction of the function of glycogen phosphorylase |
|
Definition
|
|
Term
| where glycogen phosphorylase catalyzes the removal of glucose molecules from glycogen |
|
Definition
| the nonreducing ends of the glycogen molecule, that is, it cleaves off the residues at the ends of the chains |
|
|
Term
|
Definition
|
|
Term
| how the glucose 1-phosphate released by the phosphorolysis of glycogen can become useful |
|
Definition
| it can be readily converted into glucose 6-phosphate, which is an important metabolic intermediate |
|
|
Term
|
Definition
| converts glucose 1-phosphate into glucose 6-phosphate |
|
|
Term
| depiction of phosphorolysis |
|
Definition
|
|
Term
| depiction of the branching in glycogen |
|
Definition
|
|
Term
| why the phosphorolytic cleavage of glycogen is energetically advantageous |
|
Definition
| because the released sugar is already phosphorylated |
|
|
Term
| why phosphorolytic cleavage of glycogen is advantageous over hydrolytic cleavage of glycogen |
|
Definition
| because phosphorolytic cleavage releases a sugar that is already phosphorolated, while the unphosphorylated sugar released by hydrolysis would have to be later phosphorolated at the expense of an ATP to enter the glycolytic pathway |
|
|
Term
| additional advantage of glycohen phosphorolysis in muscle cells |
|
Definition
| can't be transported out of the cell, since there's no transporters for it |
|
|
Term
| when glycogen phosphorolase stops degrading glycogen |
|
Definition
| when it reaches a residue 4 residues away from a branch point |
|
|
Term
| what enzymes remodel the glycogen such that glycogen phosphorolase can continue degrading it? |
|
Definition
-a transferase
-α-1,6-glucosidase (aka debranching enzyme) |
|
|
Term
| what transferase does to glycogen |
|
Definition
| shifts a block of 3 glucosyl residues from one outer branch to another, exposing a single α-1,6-glycosidic linked, branched, glucose residue |
|
|
Term
| what α-1,6-glucosidase (aka debranching enzyme) does to glycogen |
|
Definition
| hydrolyzes the α-1,6-glycosidic bond at the branching glucose residue |
|
|
Term
| depiction of the function of α-1,6-glucosidase (aka debranching enzyme) |
|
Definition
|
|
Term
|
Definition
| phosphorylates a free glucose molecule |
|
|
Term
| where the activities of transferase and α-1,6-glucosidase (aka debranching enzyme) are in eukaryotes |
|
Definition
| a single 160-kDa polypeptide chain, that is, a bifunctional enzyme |
|
|
Term
| depiction of glycogen remodeling |
|
Definition
|
|
Term
| what must happen t the glucose 1-phosphate formed in the phosphorolytic cleavage of glycogen before it can enter the metabolic mainstream? |
|
Definition
| has to be converted into glucose 6-phosphate |
|
|
Term
|
Definition
| catalyzes the shift of a phosphoryl group to convert glucose 1-phosphate into glucose 6-phosphate |
|
|
Term
| depiction of the function of phosphoglucomutase |
|
Definition
|
|
Term
| when the liver releases glucose into the blood |
|
Definition
| during muscular activity and between meals |
|
|
Term
| why liver can release glucose |
|
Definition
| because it has glucose 6-phosphatase, a hydrolytic enzyme absent in muscle |
|
|
Term
|
Definition
| removes the phosphoryl group from glucose 6-phosphate to yield free glucose and Pi (orthophosphate) |
|
|
Term
| depiction of the function of glucose 6-phosphatase |
|
Definition
|
|
Term
| role of glucose 6-phosphatase in anoyther biochemical pathway we've already discussed |
|
Definition
| releases free glucose at the end of gluconeogenesis |
|
|
Term
| where glucose 6-phosphatase is found inside liver cells |
|
Definition
| on the lumenal side of the smooth ER membrane |
|
|
Term
| what happens to glucose 6-phosphate in liver cells? |
|
Definition
| glucose 6-phosphate gets transported into ER; glucose and Pi (ortyhophosphate) are then shuttled back into the cytoplasm |
|
|
Term
| what tissues other than liver use glucose 6-phosphate for |
|
Definition
|
|
Term
| is glucose a major fuel for the liver? |
|
Definition
|
|
Term
| some things that regulate glycogen phosphorylase |
|
Definition
-several allosteric effectors that signal the energy state of the cell
-reversible phosphorylation |
|
|
Term
| reversible phosphorylation is responsive to... |
|
Definition
hormones, such as...
-epinephrine
-glucagon
-insulin |
|
|
Term
| why liver and skeletal muscle muscle have different forms of glycogen phosphorylase |
|
Definition
| because the liver maintains glucose homeostasis for the organism as a whole while the skeletal muscle uses glucose to produce energy for itself |
|
|
Term
| the 2 interconvertible forms of dimeric phosphorylase in the liver |
|
Definition
-usually active phosphorylase a
-usually inactive phosphorylase b |
|
|
Term
| the usually active form of glycogen phosphorylase in the liver |
|
Definition
|
|
Term
| the usually inactive form of glycogen phosphorylase in the liver |
|
Definition
|
|
Term
|
Definition
| enzymes coded by different genes, but catalyze same rxn |
|
|
Term
| state favored by e'librium for phosphorylase a |
|
Definition
|
|
Term
| state favored by e'librium for phosphorylase b |
|
Definition
|
|
Term
| depiction of the structures of phosphorylase a and phosphorylase b |
|
Definition
|
|
Term
| depiction of phosphorylase regulation and its e'librium |
|
Definition
|
|
Term
| then role of glycogen degradation in the liver |
|
Definition
| to form glucose for export to other tissues when blood glucose is low |
|
|
Term
| the default state of liver phosphorylase |
|
Definition
| a form (R state); degrades glycogen to release glucose unless signaled otherwise |
|
|
Term
| molecule that inhibits liver phosphorylase |
|
Definition
|
|
Term
| depiction of the allosteric regulation of liver phosphorylase |
|
Definition
|
|
Term
| why glycogen is not mobilized when glucose is already abundant |
|
Definition
| because glucose inhibits phosphorylase |
|
|
Term
| why is muscle phosphorylase (phosphorylase b) usually in the T state? |
|
Definition
| because phosphorylase needs to be active primarily during muscle contraction |
|
|
Term
| what activates muscle phosphorylase (phosphorylase b) into the R state? |
|
Definition
| high concentrations of AMP |
|
|
Term
| how muscle phosphorylase (pjhosphorylase b) is activated into the R state |
|
Definition
| AMP binds to the nucleotide binding site and stabilizes the R state |
|
|
Term
| how AMP and ATP regulate muscle phosphorylase (phosphorylase b) |
|
Definition
| they compete with each other for the same site on the phosphorylase b enzyme; therefore, phosphorylase b is regulated by the energy charge of the cell |
|
|
Term
| the transition of muscle phosphorylase (phosphorylase b) is regulated by... |
|
Definition
| the energy charge of the cell |
|
|
Term
| why muscle phosphorylase (phosphorylase b) is usually inactive under physiological conditions |
|
Definition
| because of the inhibitory effects of ATP and glucose 6-phosphate |
|
|
Term
| depiction of the allosteric regulation of muscle phosphorylase |
|
Definition
|
|
Term
| the similarity between liver and muscle phosphorylase |
|
Definition
| 90% identical in amino acid sequence, but the 10% difference confers important differences |
|
|
Term
| different types of fiber in skeletal muscle |
|
Definition
-type I (slow-twitch)
-type IIa (intermediate between type I and type IIb)
-type IIb (fast-twitch) |
|
|
Term
| primary fuel source for type I (slow-twitch) muscle fibers |
|
Definition
| fatty acid degradation and cellular respiration; rich in mitochondria |
|
|
Term
| primary fuel source for type I (fast-twitch) muscle fibers |
|
Definition
|
|
Term
| how phosphorylase b is converted into phosphorylase a |
|
Definition
| by the phosphorylation of a single serine residue in each subunit |
|
|
Term
| what causes phosphorylase b in liver to convert into phosphorylase a? |
|
Definition
|
|
Term
| what causes phosphorylase b in muscle to convert into phosphorylase a? |
|
Definition
|
|
Term
|
Definition
| catalyzes the conversion of phosphorylase b to phosphorylase a |
|
|
Term
| the transition from the T state (prevalent in phosphorylase b) to the R state (prevalent in phosphorylase a) is associated with... |
|
Definition
| structural changes in α helices that move a loop out of the active site of each subunit |
|
|
Term
| why the active site of phosphorylase is less active in the T state |
|
Definition
| because it is partly blocked |
|
|
Term
| why tyhe R state of phosphorylase is more active |
|
Definition
| because the active site is open and a binding site for orthophosphate (Pi) is well organized |
|
|
Term
| how phosphorylase kinase activates phosphorylase b |
|
Definition
| by attaching a phosphoryl group |
|
|
Term
|
Definition
| Ca binding protein that functions as a Ca sensor that stimulates many enzymes in eukaryotes |
|
|
Term
| the part of phosphorylase kinase occupied by calmodulin |
|
Definition
|
|
Term
| the parts of phosphorylase kinase that are the targets of protein kinase A (PKA) |
|
Definition
|
|
Term
| sequence of phosphorylation of phosphorylase kinase |
|
Definition
| the β unit is phosphorylated first, followed by the α unit |
|
|
Term
| when activation of phosphorylase kinase is initiated |
|
Definition
| when Ca2+ binds to the δ subunit (calmodulin) |
|
|
Term
| contraction of muscle is triggered by... |
|
Definition
| the release of Ca2+ from the sarcoplasmic reticulum |
|
|
Term
| maximal activation of phosphorylase kinase is achieved with... |
|
Definition
| the phosphorylation of the α and β subunits when of the Ca2+ bound kinase |
|
|
Term
| depiction of the activation of phosphorylase kinase |
|
Definition
|
|
Term
| sequence of activation in activating phosphorylase |
|
Definition
| PKA activates phosphorylase kinase, which activates glycogen phosphorylase |
|
|
Term
| 2 hormones that signal the need for glycogen breakdown |
|
Definition
|
|
Term
| what leads to the release of epinephrine? |
|
Definition
| muscular activity or its anticipation |
|
|
Term
| the hormone liver is more responsive to |
|
Definition
|
|
Term
|
Definition
|
|
Term
| depiction of the hormonal control of glycogen breakdown |
|
Definition
|
|
Term
| how hormones trigger the breakdown of glycogen |
|
Definition
| they initiate a cyclic AMP (cAMP) signal-transduction cascade |
|
|
Term
| depiction of the regulatory cascade for glycogen breakdown |
|
Definition
|
|
Term
| this leads to maximal mobilization of liver glycogen |
|
Definition
| stimulation by both glucagon and epinephrine |
|
|
Term
| when is glycogen synthesis turned off? |
|
Definition
| when glucose needs have been met |
|
|
Term
| how is glycogen breakdown turned off? |
|
Definition
phosphorylase kinase and glycogen phosphorylase are dephosphorylated and inactivated
simultaneously, glycogen synthesis is activated |
|
|
Term
| protein phosphatase 1 (PP1) |
|
Definition
| removes phosphoryl groups from phosphorylase kinase and glycogen phosphorylase into the less active b form, inactivating them; this helps turn off glycogen breakdown when need be |
|
|
Term
| advantage of separate pathways being used in synthesis and breakdown |
|
Definition
| much greater flexibility, both in energetics and control |
|
|
Term
| common requirement for biosynthesis |
|
Definition
| use of an activated precursor |
|
|
Term
| precursor used in glycogen synthesis |
|
Definition
| uridine diphosphate glucose (UDP-glucose) |
|
|
Term
| structure of uridine diphosphate glucose (UDP-glucose) |
|
Definition
|
|
Term
| overall pathway of glycogen synthesis |
|
Definition
| glycogenn + UDP-glucose --> glycogenn+1 + UDP |
|
|
Term
| overall pathway of glycogen degradation |
|
Definition
| glycogenn+1 + Pi --> glycogenn + glucose 1-phosphate |
|
|
Term
| the activated form of glucose used in the synthesis of glycogen |
|
Definition
|
|
Term
| UDP-glucose is synthesized from... |
|
Definition
| glucose 1-phosphate and uridine triphosphate (UTP) |
|
|
Term
| rxn that yields UDP-glucose |
|
Definition
| glucose 1-phosphate + UTP <--> UDP-glucose + PPi |
|
|
Term
| UDP-glucose phosphorylase |
|
Definition
| catalyzes the synthesis of UDP-glucose from glucose 1-phosphate and UTP |
|
|
Term
| depiction of the synthesis of UDP-glucose from glucose 1-phosphate and UTP |
|
Definition
|
|
Term
| depiction of the function of UDP-glucose phosphorylase |
|
Definition
|
|
Term
| by itself, the synthesis of UDP-glucose is readily reversible. what is it coupled with to make it irreversible? |
|
Definition
| the essentially irreversible hydrolysis of pyrophosphate (PPi) into orthophosphate (2 Pi) |
|
|
Term
| what drives the synthesis of UDP-glucose? |
|
Definition
| the essentially irreversible hydrolysis of pyrophosphate (PPi) into orthophosphate (2 Pi) |
|
|
Term
| inorganic pyrophosphatase |
|
Definition
| catalyzes the essentially irreversible hydrolysis of pyrophosphate (PPi) into orthophosphate (2 Pi) |
|
|
Term
| depiction of UDP-glucose synthesis being coupled with pyrophosphate (PPi) hydrolysis |
|
Definition
|
|
Term
| importance of the essentially irreversible hydrolysis of pyrophosphate (PPi) into orthophosphate (2 Pi) elsewhere in biochem |
|
Definition
| drives many biosynthetic rxns |
|
|
Term
| where new glucosyl units are added to glycogen during glycogen synthesis |
|
Definition
| the nonreducing terminal residues of glycogen |
|
|
Term
|
Definition
| catalyzes the transfer of glucose from UDP-glucose to a growing chain |
|
|
Term
| the key regulatory enzyme in glycogen synthesis |
|
Definition
|
|
Term
| the 2 isozymic forms of glycogen synthase in humans |
|
Definition
-one specific to the liver
-the other expressed in muscle and other tissues |
|
|
Term
| where glycogen synthase can add glucosyl residues |
|
Definition
| only where there's a polysac chain containing 5+ residues |
|
|
Term
|
Definition
catalyzes the formation of α-1,4-glucose polymers
this is the primer for glycogen synthesis |
|
|
Term
| depiction of a cross section of a glycogen molecule |
|
Definition
|
|
Term
| how glycogen gets branched |
|
Definition
| a branching enzyme breaks α-1,4 linkages and forms branches with α-1,6 linkages to the main chain |
|
|
Term
| function of branching enzyme |
|
Definition
| breaks α-1,4 linkages and forms branches with α-1,6 linkages to the main chain |
|
|
Term
| how exact branching enzyme is |
|
Definition
-the block of 7 or so residues must contain the nonreducing terminus and come from a chain 11+ residues long
-the new branch point must be 4+ residues away from a preexisting one |
|
|
Term
| depiction of the branching rxn in glycogen synthesis |
|
Definition
|
|
Term
| why branching is important for glycogen |
|
Definition
-increases solubility of glycogen
-increases number of terminal residues, increasing rate of glycogen synthesis and degradation |
|
|
Term
| the 2 forms of glycogen synthase |
|
Definition
|
|
Term
| a form of glycogen synthase |
|
Definition
| active, nonphosphorylated form |
|
|
Term
| b form of glycogen synthase |
|
Definition
| inactive, phosphorylated form |
|
|
Term
| the key means of regulating glycogen synthase |
|
Definition
| allosteric regulation of the phosphorylated b form |
|
|
Term
| powerful activator of glycogen synthase b |
|
Definition
| glucose 6-phosphate, which stabilizes the R state |
|
|
Term
| glycogen synthase kinase (GSK) |
|
Definition
| phosphorylates glycogen synthase |
|
|
Term
| what regulates glycogen synthase kinase (GSK)? |
|
Definition
-insulin
-protein kinase A (PKA) |
|
|
Term
| effects of phosphorylation glycogen synthase and glycogen phosphorylase |
|
Definition
opposite effects
activates phosphorylase and inactivates synthase |
|
|
Term
| nucleoside diphosphokinase |
|
Definition
| catalyzes the regeneration of UTP from UDP |
|
|
Term
| the summation of the rxns in glycogen synthesis |
|
Definition
| 1: glucose + ATP --> glucose 6-phosphate + ADP
2: glucose 6-phosphate --> glucose 1-phosphate
3: glucose 1-phosphate + UTP --> UDP-glucose + PPi
4: PPi + H2O --> 2 Pi
5: UDP-glucose + glycogenn --> glycogenn+1 + UDP
6: UDP + ATP --> UTP + ADP
sum: glucose + 2 ATP + glycogenn + H2O --> glycogenn+1 + 1 ADP + 2 Pi |
|
|
Term
| the overall efficiency of glycogen storage |
|
Definition
|
|
Term
| glucagon and epinephrine control both glycogen breakdown and synthesis through... |
|
Definition
|
|
Term
| how glycogen synthesis and breakdown are reciprocally regulated |
|
Definition
| phosphorylation activates glycogen phosphorylase and inactivates glycogen synthase |
|
|
Term
| depiction of the coordinate control of glycogen metabolism |
|
Definition
|
|
Term
| protein phosphatase 1 (PP1) |
|
Definition
| catalyzes dephosphorylation of glycogen phosphorylase and glycogen synthase |
|
|
Term
| how protein phosphatase 1 (PP1) |
|
Definition
catalyzes dephosphorylation of glycogen phosphorylase and glycogen synthase
inhibits phosphorylase a and phosphorylase kinase by dephosphorylating them
activates glycogen phosphorylase b into glycogen phosphorylase a by dephosphorylating it |
|
|
Term
| depiction of the regulation of glycogen synthesis by protein phosphatase 1 (PP1) |
|
Definition
|
|
Term
|
Definition
| catalytic subunit of protein phosphatase 1 (PP1) in muscle |
|
|
Term
|
Definition
| catalytic subunit of protein phosphatase 1 (PP1) in liver |
|
|
Term
| the role of regulatory subunits (GM and GL) in the context of glycogen |
|
Definition
| they act as scaffolds, bringing together the protein phosphatase and its substrates in the context of a glycogen particle |
|
|
Term
| how protein phosphatase 1 (PP1) is regulated in muscle |
|
Definition
| 1: phosphorylation, which releases PP1 from GM
2: phosphorylated inhibitors that inhibit PP1 |
|
|
Term
| depiction of the regulation of protein phosphatase 1 (PP1) in muscle |
|
Definition
|
|
Term
| how insulin regulates blood glucose |
|
Definition
| increases amount of glucose in cell and stimulates synthesis of glycogen |
|
|
Term
| how insulin stimulates glycogen synthesis |
|
Definition
-increases glucose in cell by increasing number of glucose transporters (GLUT4) in cell membrane
-leads to the inactivation of glycogen synthase kinase, which leads to the activation of glycogen synthase |
|
|
Term
| depiction of how insulin inactivates glycogen synthase kinase |
|
Definition
|
|
Term
|
Definition
| insulin-receptor substrate |
|
|
Term
| what insulin binds to in te plasma membrane |
|
Definition
| its receptor tyrosine kinase |
|
|
Term
|
Definition
| replenishment of glycogen stores |
|
|
Term
| other than insulin, this can signal the liver to synthesize glycogen |
|
Definition
| blood glucose concentration |
|
|
Term
| what happens to liver phosphorylase a when glucose is infused into the blood? |
|
Definition
| the amount of liver phosphorylase a rapidly decreases |
|
|
Term
| this is the glucose sensor in liver cells |
|
Definition
|
|
Term
| how glucose regulates inactivates phosphorylase A |
|
Definition
| binding of glucose to phosphorylase a shifts it from the R form to the T form, making PP1 dissociate from it to make the phosphorylase b, stabilizing the T form |
|
|
Term
| is the R <--> T transition of muscle phosphorylase a affected by glucose? |
|
Definition
| no; therefore, it is not affected by blood glucose concentration |
|
|
Term
| the conversion of phosphorylase a into phosphorylase b is accompanied by... |
|
Definition
|
|
Term
| PP1 activates ______ and inactivates ______ |
|
Definition
glycogen synthase
glycogen phosphorylase |
|
|
Term
| when the activity of gycogen synthase begins to increase |
|
Definition
| only after most of the phosphorylase is inactivated |
|
|
Term
| advantage of the lag between glycogen degradation and glycogen synthesis |
|
Definition
| prevents the 2 pathways from operating simultaneously |
|
|
Term
| the 3 elements of the remarkable glucose-sensing system in the liver |
|
Definition
1: communication between the allosteric site for glucose and the serine phosphate
2: the use of PP1 to inactivate phosphorylase and activate glycogen synthase
3: the binding of the phiosphatase to phosphorylase a to prevent the premature activation of glycogen synthase |
|
|
Term
| depiction of how glucose regulates liver-glycogen metabolism |
|
Definition
|
|
Term
| key energy source during hibernation |
|
Definition
|
|
Term
| how fatty acids are stored |
|
Definition
| stored as triacylglycerols in adipose tissue |
|
|
Term
|
Definition
|
|
Term
|
Definition
| surrounding intertnal organs |
|
|
Term
|
Definition
| degradation of triaclyglycerol into free fatty acids and glycerol; this mobilizes triacylglycerols |
|
|
Term
|
Definition
| oxidation of fatty acids to acetyl CoA |
|
|
Term
| a fat derived fuel source important during fasting |
|
Definition
|
|
Term
| when ketone bodies are impoirtant |
|
Definition
|
|
Term
| how peripheral tissues, such as muscle, gain access to the lipid energy reserves stored in adipose tissue |
|
Definition
1: mobilization of lipids by lipolysis; fatty acids get released from adipose tissue
2: at the tissues that need the fatty acids, the fatty acids are activated and transported into mitochondria for degradation
3: fatty acids are broken down into acetyl CoA, which is then processed in the citric acid cycle |
|
|
Term
| lipids are hydrolyzed by... |
|
Definition
|
|
Term
| glycerol enters the liver, where it can be metabolized by these pathways |
|
Definition
-glycolysis
-gluconeogenesis |
|
|
Term
| depiction of lipid degradation |
|
Definition
|
|
Term
| triacylglycerols in adipose tissue are converted into free fatty acids in response to... |
|
Definition
|
|
Term
| depiction of triacyglycerols in adipose tissue being converted into free fatty acids |
|
Definition
|
|
Term
| what hormones induce lipolysis? |
|
Definition
|
|
Term
| fatty acids are not soluble in aqueous solutions, so how do they get to the tissues that need them? |
|
Definition
| released fatty acids bind to the blood protein albumin, which delivers them to tissues in need of fuel |
|
|
Term
| blood protein released fatty acids bind to |
|
Definition
|
|
Term
| what happens to glycerol formed by lipolysis? |
|
Definition
| gets absorbed by the liver and gets phosphorylated |
|
|
Term
| the end product of glycerol after phosphorylation, dehydration, and isomerization? |
|
Definition
| D-glyceraldehyde 3-phosphate |
|
|
Term
| importance of D-glyceraldehyde 3-phosphate |
|
Definition
| intermediate in both glycolysis and gluconeogenesis |
|
|
Term
| depiction of phosphorylation of glycerol |
|
Definition
|
|
Term
| what glycerol can be converted into in the liver |
|
Definition
|
|
Term
| depiction of how glycerol and fatty acids are used by the liver and other tissues, respectively |
|
Definition
|
|
Term
| what glycerol is used for in liver cells |
|
Definition
-glycolysis to generate pyruvate
-gluconeogenesis to generate glucose |
|
|
Term
| what fatty acids are used for in tissues other than liver |
|
Definition
| fatty acid oxidation into acetyl CoA |
|
|
Term
| how fatty acids enter cells |
|
Definition
| they separate from the albumin in the bloodstream and diffuse through transport proteins into the cells |
|
|
Term
| how fatty acids are shuttled about inside cells |
|
Definition
| in association with fatty-acid-binding proteins |
|
|
Term
| fatty acid degradation occurs in... |
|
Definition
|
|
Term
| how fatty acids gain access to mitochondria to be oxidized |
|
Definition
by being activated by reacting with coenzyme A to form acyl CoA
this takes place on the outer mitochondrial membrane |
|
|
Term
| how fatty acids get activated |
|
Definition
| by reacting with coenzyme A to form acyl CoA |
|
|
Term
|
Definition
| catalyzes the activation of fatty acids |
|
|
Term
| depiction of the activation of fatty acids into acyl CoA |
|
Definition
|
|
Term
| the 2 steps of fatty acid activation |
|
Definition
|
|
Term
| what drives forward the activation of fatty acids? |
|
Definition
| the hydrolysis of pyrophosphate (PPi) by pyrophosphatase |
|
|
Term
|
Definition
| catalyzes the hydrolysis of pyrophosphate (PPi) |
|
|
Term
| depiction of the function of pyrophosphatase |
|
Definition
|
|
Term
| what hydrolysis of inorganic pyrophosphate (PPi) does for biosynthetic rxns |
|
Definition
|
|
Term
| the complete rxn for fatty acid activation |
|
Definition
| RCOO- + CoA + ATP +H2O --> RCO-CoA + AMP + 2 Pi |
|
|
Term
| activated fatty acids cross outer motochondrial membrane thru... |
|
Definition
| voltage-dependent ion channels, also called porin channels |
|
|
Term
| what's required for fatty acids to be transported across the inner mitochondrial membrane? |
|
Definition
| fatty acids must be linked to the alcohol cartinine |
|
|
Term
| how a fatty acid gets linked to cartinine |
|
Definition
| the acyl group in acyl CoA gets transferred to the OH on cartinine |
|
|
Term
| cartinine acetyltransferase I (aka cartinine palmitoyl transferase I) |
|
Definition
| catalyzes transfer of acyl CoA to cartinine to form acyl cartinine |
|
|
Term
| where cartinine acetyltransferase I (aka cartinine palmitoyl transferase I) is |
|
Definition
| bound to the outer mitochondrial membrane |
|
|
Term
| structure of an acyl group |
|
Definition
|
|
Term
| depiction of a fatty acid getting linked to cartinine |
|
Definition
|
|
Term
| depiction of the function of cartinine acetyltransferase I (aka cartinine palmitoyl transferase I) |
|
Definition
|
|
Term
|
Definition
| shuttles acyl carnitine to the matrix side of the inner mitochondrial membrane and carnitine to the cytoplasmic side of the inner mitochondrial membrane |
|
|
Term
| cartinine acetyltransferase II (aka cartinine palmitoyl transferase II) |
|
Definition
| catalyzes the transfer of an acyl group from carnitine back to CoA |
|
|
Term
| where cartinine acetyltransferase II (aka cartinine palmitoyl transferase II) is located |
|
Definition
| matrix side of inner mitochondrial membrane |
|
|
Term
| depiction of the function of acyl carnitine translocase |
|
Definition
|
|
Term
|
Definition
| to oxidize the fatty acid, 2 C atoms at a time, into acetyl CoA and to gather the released high energy electrons to power oxidative phosphorylation |
|
|
Term
| what the electrons released from β-oxidation are used for |
|
Definition
| to power oxidative phosphorylation |
|
|
Term
| recurring sequence of 4 rxns that degrades a saturated acyl CoA |
|
Definition
| 1: oxidation by FAD
2: hydration
3: oxidation by NAD+
4: thiolysis by CoA |
|
|
Term
| what happens to the fatty acid in β-oxidation? |
|
Definition
| gets shortened by 2 C atoms |
|
|
Term
| some byproducts that are generated from β-oxidation |
|
Definition
|
|
Term
| why degradation of fatty acids is called β-oxidation |
|
Definition
| because it occurs at the C in a fatty acid |
|
|
Term
|
Definition
| the oxidative degradation of fatty acids |
|
|
Term
| structure of the fatty acid that undergoes β-oxidation |
|
Definition
|
|
Term
| depiction of the β-oxidation pathway |
|
Definition
|
|
Term
| the first rxn in each round of β-oxidation of fatty acids |
|
Definition
| oxidation of acyl CoA by acyl CoA dehydrogenase |
|
|
Term
|
Definition
| catalyzes the oxidation of acyl CoA |
|
|
Term
| depiction of the function of acyl CoA dehydrogenase |
|
Definition
|
|
Term
|
Definition
| catalyzes the hydration of the double bond between C-2 and C-3 in trans-Δ2-Enoyl CoA to yield L-3-hydroxyacyl CoA |
|
|
Term
| depiction of the function of enoyl CoA hydratase |
|
Definition
|
|
Term
| L-3-hydroxyacyl CoA dehydrogenase |
|
Definition
| catalyzes oxidation of L-3-hydroxyacyl CoA into 3-ketoacyl CoA |
|
|
Term
| depiction of the function of L-3-hydroxyacyl CoA dehydrogenase |
|
Definition
|
|
Term
|
Definition
| catalyzes the cleavage of 3-ketoacyl CoA to yield acetyl CoA and acyl CoA |
|
|
Term
| depiction of the function of β-ketothiolase |
|
Definition
|
|
Term
| depiction of the first 3 rounds in the degradation of palmitate |
|
Definition
|
|
Term
| the net rxn of β-oxidation |
|
Definition
| Cn-acyl CoA + FAD + NAD+ H2O + CoA --> Cn-2-acyl CoA + FADH2 + NADH + acetyl CoA + H+ |
|
|
Term
|
Definition
|
|
Term
| the degradation of palmitoyl CoA (C16-acyl CoA) requires how many rxn cycles? |
|
Definition
|
|
Term
| net rxn of the β-oxidation of palmitoyl CoA |
|
Definition
| palmitoyl CoA + 7 FAD + 7 NAD+ 7 H2O + 7 CoA --> 7 FADH2 + 7 NADH + 8 acetyl CoA + 7 H+ |
|
|
Term
| net ATP yield of the complete oxidation of 1 molecule of palmitate |
|
Definition
106 molecules of ATP
consumes 2 and produces 108, therefore net of 106 |
|
|
Term
| what happens to most acetyl CoA produced by fatty acid degradation? |
|
Definition
|
|
Term
| what ketone bodies are formed from |
|
Definition
|
|
Term
| the ketone bodies formed from acetyl CoA |
|
Definition
-acetoacetate
-D-3-hydroxybutyrate (β-hydroxybutyrate)
-acetone |
|
|
Term
| advantage of ketone bodies over fatty acids |
|
Definition
| ketone bodies are water soluble, so they are an easily transportable form of acetyl units |
|
|
Term
|
Definition
| by the slow, spontaneous decarboxylation of acetoacetate |
|
|
Term
| when acetone may be captured to synthesize glucose |
|
Definition
| under starvation conditions |
|
|
Term
|
Definition
| production of acetoacetate and D-3-hydroxybutyrate |
|
|
Term
|
Definition
| the mitochondria of the liver |
|
|
Term
| the net rxn of the formation of acetoacetate |
|
Definition
| 2 acetyl CoA + H2O --> acetoacetate + 2 CoA + H+ |
|
|
Term
| depiction of the formation of ketone bodies |
|
Definition
|
|
Term
| how ketone bodies are used as fuel |
|
Definition
| metabolized to generate NADH and acetyl CoA |
|
|
Term
| depiction of the utilization of D-3-hydroxybutyrate and acetoacetate as a fuel |
|
Definition
|
|
Term
| regulatory role of acetoacetate |
|
Definition
| high levels of acetoacetate signify abunbdance of acetyl units, leading to less lipolysis in adipose tissue |
|
|
Term
| why animals are unable to effect the net synthesis of glucose from fatty acids |
|
Definition
because the acetyl CoA generated by fatty acid oxidation can't be converted to pyruvate or oxaloacetate in animals
(recall that converting pyruvate into acetyl CoA is irreversible) |
|
|
Term
| why net synthesis of oxaloacetate from fatty acid degradation is impossible in animals |
|
Definition
| because 2 C atoms enter the citric acid cycle as an acetyl group and leave the cycle as CO2 |
|
|
Term
| type of organisms that can convert the C atoms of acetyl CoA into oxaloacetate |
|
Definition
|
|
Term
| why plants can convert the C atoms of acetyl CoA into oxaloacetate |
|
Definition
| because they have 2 additional enzymes that enable them to do that |
|
|
Term
| some crucial roles of fatty acids |
|
Definition
-fuel reserves
-signal molecules
-components of membrane lipids |
|
|
Term
| some tissues that can synthesize fatty acids under certain conditions |
|
Definition
|
|
Term
| some times fatty acid synthesis is necessary |
|
Definition
-embryonic development
-lactation |
|
|
Term
| the precursor to virtually all fatty acids |
|
Definition
| acetyl CoA, which is the end product of fatty acid degradation |
|
|
Term
| the 3 stages of fatty acid synthesis |
|
Definition
1: acetyl CoA transported in the form of citrate out of mitochondria into cytoplasm; the citrate that is formed yields acetyl CoA and oxaloacetate
2: acetyl CoA is activated into malonyl CoA
3: rxn intermediates attached to acyl carrier protein, which serves as the foundation for fatty acid synthesis, which happens 2 C atoms at a time in a 5-step elongation cycle |
|
|
Term
| where fatty acid synthesis occurs |
|
Definition
|
|
Term
| fatty acid synthesis begins with... |
|
Definition
| activation of acetyl CoA into malonyl CoA |
|
|
Term
| molecular foundation for fatty acid synthesis |
|
Definition
|
|
Term
| the raw material fgor fatty acid synthesis |
|
Definition
|
|
Term
| how acetyl CoiA is transported out of mitochondria into cytoplasm |
|
Definition
| transported out in the form of citrate |
|
|
Term
| when mitochondria transports citrate into the cytolasm |
|
Definition
| when the energy needs of a cell have been met |
|
|
Term
|
Definition
| catalyzes the cleavage of citrate into acetyl CoA and oxaloacetate at the expense of an ATP molecule |
|
|
Term
| depiction of the function of ATP-citrate lyase |
|
Definition
|
|
Term
| ATP-citrate lyase is stimulated by... |
|
Definition
|
|
Term
| how insulin stimulates ATP-citrate lyase |
|
Definition
| initiating a signal transduction pathway that ultimately results in the phosphorylation and activation of the lyase by Akt (aka protein kinase B) |
|
|
Term
| Akt (aka protein kinase B) |
|
Definition
| phosphorylates and activates ATP-citrate lyase |
|
|
Term
| how citrate serves as a signal molecule |
|
Definition
| inhibits phosphofructokinase, which controls the rate of glycolysis |
|
|
Term
| depiction of the transfer of acetyl CoA to the cytoplasm |
|
Definition
|
|
Term
|
Definition
| catalyzes the reduction of oxaloacetate to malate by NADH |
|
|
Term
| depiction of the function of malate dehydrogenase |
|
Definition
|
|
Term
| NADP+-linked malate enzyme (aka malic enzyme) |
|
Definition
| catalyzes the oxidative decarboxylation of malate into pyruvate |
|
|
Term
| depiction of the function of NADP+-linked malate enzyme (aka malic enzyme) |
|
Definition
|
|
Term
|
Definition
| catalyzes the carboxylation pyruvate into oxaloacetate |
|
|
Term
| depiction of the function of pyruvate carboxylase |
|
Definition
|
|
Term
| the net rxn of converting oxaloacetate into pyruvate |
|
Definition
| NADP+ + NADH + ATP + H2O --> NADPH + NAD+ + ADP Pi + H+ |
|
|
Term
| pathways that provide the C atoms needed for reducing power in fatty acid synthesis |
|
Definition
-citric acid cycle
-transport of citrate from mitochondria to cytoplasm
-pentose phosphate pathway |
|
|
Term
| pathways that provide the ATP needed for fatty acid synthesis |
|
Definition
-glycolysis
-oxidative phosphorylation |
|
|
Term
| depiction of pathway integration for fatty acid synthesis |
|
Definition
|
|
Term
| the committed step in fatty acid synthesis |
|
Definition
|
|
Term
|
Definition
| catalyzes the activation of acetyl CoA into malonyl CoA |
|
|
Term
| depiction of the activation of acetyl CoA into malonyl CoA |
|
Definition
|
|
Term
| the 2 steps of the synthesis of malonyl CoA |
|
Definition
| 1: a carboxybiotin intermediate is formed at the expense of the hydrolysis of a molecule of ATP
2: the activated CO2 group is then transferred to acetyl CoA to form malonyl CoA |
|
|
Term
| the essential regulatory enzyme for fatty acid degradation |
|
Definition
|
|
Term
|
Definition
| the enzyme system that catalyzes the synthesis of saturated, long-chain fatty acids from acetyl CoA, malonyl CoA, and NADPH |
|
|
Term
|
Definition
| catalyzes the conversion of acetyl CoA into acetyl ACP |
|
|
Term
|
Definition
| catalyzes the conversion of malonyl CoA into malonyl ACP |
|
|
Term
| depiction of the function of acetyl transacylase and malonyl transacylase |
|
Definition
|
|
Term
| the synthesis of fatty acids with an odd number of C atoms starts with... |
|
Definition
|
|
Term
| the active unit on acyl carrier protein |
|
Definition
|
|
Term
|
Definition
|
|
Term
| β-ketoacyl synthase aka condensing enzyme |
|
Definition
| catalyzes the formation of acetoacetyl ACP |
|
|
Term
| depiction of the function of β-ketoacyl synthase aka condensing enzyme |
|
Definition
|
|
Term
| depiction of fatty acid synthesis |
|
Definition
|
|
Term
| where the C atoms in fatty acids containing an even number of C atoms come from |
|
Definition
| they are all derived from acetyl CoA |
|
|
Term
| general difference between NADPH and NADH |
|
Definition
-NADPH consumed in biiosynthetic rxns
-NADH generated in energy-yielding rxns |
|
|
Term
| elongation of fatty acids continues until... |
|
Definition
|
|
Term
| this acts as a ruler to determine fatty acid chain length |
|
Definition
|
|
Term
| why thioesterase acts as a ruler for fatty acid chain length |
|
Definition
| because it acts selectively on C16-acyl ACP |
|
|
Term
| net rxn for the synthesis of palmitate |
|
Definition
| 8 acetyl CoA + 7 ATP + 14 NADPH --> palmitate + NADP+ + 8 CoA + 6 H2O 7 ADP + 7 Pi |
|
|
Term
| general composition of fatty acid synthase |
|
Definition
| dimer of 2 identical 270 kDa subunits, each containing all the active sites required for activity and an acyl carrier protein tethered to the complex |
|
|
Term
| depiction of the fatty acid synthase in animals |
|
Definition
|
|
Term
| characteristic of many eukaryotic multienzyme complexes |
|
Definition
| they are multifunctional proteins in which the enzymes are linked covalently |
|
|
Term
| advantage of enzymes being linked covalentle in a multienzyme complex |
|
Definition
| intermediates can be efficiently handed from one active site to another without leaving the assembly |
|
|
Term
| when fatty acid synthesis is maximal |
|
Definition
| when carbohydrates and energy are plentiful and when fatty acids are scarce |
|
|
Term
| enzymes that play essential roles in fatty acid synthesis and degradation |
|
Definition
| acetyl CoA carboxylase 1 and 2 |
|
|
Term
|
Definition
| catalyzes the production of malonyl CoA (the active 2 C donor), which is the committed step in fatty acid synthesis |
|
|
Term
| how acetyl CoA carboxylase 1 is activated |
|
Definition
|
|
Term
| how acetyl CoA carboxylase 1 is deactivated |
|
Definition
|
|
Term
| when fats are not synthesized |
|
Definition
|
|
Term
| depiction of how acetyl CoA carboxylase 1 is regulated |
|
Definition
|
|
Term
| when the level of citrate is high |
|
Definition
| when both acetyl CoA and ATP are abundant, signifying that raw materials for fatty acid synthesis are available |
|
|
Term
|
Definition
| facilitates the citrate induced polymerization of inactive dimers into active filaments |
|
|
Term
| function of palmitoyl CoA |
|
Definition
-counteracts the stimulatory effect of citrate on the carboxylase
-causes the filaments to disassemble into inactive subunits
-inhibits some other enzymes |
|
|
Term
| when palmitoyl CoA is abundant |
|
Definition
| when there is an excess of fatty acids |
|
|
Term
| depiction of the citrate-induced polymerization of inactive dimers into active filaments |
|
Definition
|
|
Term
| when malonyl CoA is abundant |
|
Definition
| when fuel molecules are abundant |
|
|
Term
| the role of mitochondrial malonyl CoA in the regulation of fatty acid synthesis |
|
Definition
| it inhibits carnitine acetyltransferase I, preventing the entry of fatty acyl CoA's into the mitochondrial matrix in times of plenty |
|
|
Term
| depiction of the dependence of the catalytic activity of acetyl CoA carboxylase on the concentration of citrate |
|
Definition
|
|
Term
| some things that can regulate fatty acid synthesis and degradation |
|
Definition
-glucagon
-epinephrine
-insulin
-diet |
|
|
Term
| when glucagon and epinephrine are present |
|
Definition
| under conditions of fasting and exercise |
|
|
Term
| stimulatory effect of glucagon and epinephrine on fatty acids |
|
Definition
| they stimulate the mobilization of fatty acids from triacylglycerols in fat cells such that they can be used as fuel |
|
|
Term
| inhibitory effect of glucagon and epinephrine on fatty acids |
|
Definition
| inhibit fatty acid synthesis |
|
|
Term
| how glucagon and epinephrine inhibit fatty acid synthesis |
|
Definition
by inhibiting acetyl CoA carboxylase 1
this augments the inhibition by the AMP-activated kinase |
|
|
Term
| how glucagon and epinephrine regulate acetyl CoA carboxylase 1 |
|
Definition
| they switch off fattyb acid synthesis by keeping the carboxylase in the inactive phosphorylated state |
|
|
Term
| effect of insulin on fatty acids |
|
Definition
| inhibits the mobilization of fatty acids and stimulates their accumulation as triacylglycerols by muscle and adipose tissue |
|
|
Term
| effect of insulin on fatty acid synthesis |
|
Definition
|
|
Term
| how insulin stimulates fatty acid synthesis |
|
Definition
| by activating acetyl CoA carboxylase 1 |
|
|
Term
| how insulin activates acetyl CoA carboxylase 1 |
|
Definition
| by enhancing the phosphorylation of AMPK by Akt, which inhibits AMPK, as well as by stimulating the activity of a protein phosphatase that dephosphorylates and activates acetyl CoA carboxylase |
|
|
Term
| the 2 steps of ethanol metabolism |
|
Definition
1: conversion of ethanol to acetaldehyde; this happens in the cytoplasm
2: conversion of acetaldehyde to acetate; this happens in the mitochondria |
|
|
Term
|
Definition
| catalyzes the conversion of ethanol to acetaldehyde |
|
|
Term
| depiction of the function of alcohol dehydrogenase |
|
Definition
|
|
Term
|
Definition
| catalyzes the conversion of acetaldehyde to acetate |
|
|
Term
| depiction of the function of aldehyde dehydrogenase |
|
Definition
|
|
Term
| ethanol consumption leads to accumulation of... |
|
Definition
|
|
Term
| effect of NADH accumulation |
|
Definition
| inhibits gluconeogenesis by preventing the oxidation of lactate to pyruvate |
|
|
Term
| how NADH accumulation inhibits gluconeogenesis |
|
Definition
| by preventing the oxidation of lactate to pyruvate |
|
|
Term
| NADH accumulation will cause this to accumulate |
|
Definition
|
|
Term
| these could happen as a result of lactate accumulation |
|
Definition
-hypoglycemia
-lactic acidosis |
|
|
Term
| how too moch NADH affects fatty acid metabolism |
|
Definition
| inhibits fatty acid oxidation |
|
|
Term
| the metabolic purpose of fatty acid oxidation |
|
Definition
| to generate NADH for ATP generation by oxidative phosphorylation |
|
|
Term
| why alcohol consumption leads to fatty liver |
|
Definition
| because the excess NADH from alcohol consumption is a signal to synthesize tiaclyglycerols |
|
|
Term
| liver mitochondria can convert acetate into... |
|
Definition
| acetyl CoA in a rxn requiring ATP |
|
|
Term
| function of acyl CoA synthetase in the context of alcohol metabolism |
|
Definition
| converts acetate into acetyl CoA |
|
|
Term
| depiction of the function of acyl CoA synthetase in the context of alcohol metabolism |
|
Definition
|
|
Term
| why alcohol consumption leads to the accumulation of acetyl CoA |
|
Definition
| because further processing of the acetyl CoA by the citric acid cycle is blocked because of NADH inhibiting 2 important citric acid cycle regulating enzymes |
|
|
Term
| some consequences of acetyl CoA accumulation |
|
Definition
1: ketone bodies form and get released into the blood, exacerbating the acidic condition already created by high lactate concentration
2: processing of acetate in liver becomes inefficient, leading to buildup of acetaldehyde, which impairs proteins by forming covalent bonds with them |
|
|
Term
| effect of ketone body accumulation in bloodstream |
|
Definition
| they exacerbate the acidic condition already created by high lactate concentration |
|
|
Term
| how acetaldehyde messes with proteins |
|
Definition
| by forming covalent bonds with them |
|
|
Term
| 2 sites of cholesterol synthesis in mammals |
|
Definition
-liver (major site)
-intestine (significant) |
|
|
Term
| how the rate of cholesterol formation is regulated |
|
Definition
| primarily by changes in the amount and activity of 3-hydroxy-3-methylglutaryl CoA reductase (HMG-CoA reductase) |
|
|
Term
| 3-hydroxy-3-methylglutaryl CoA reductase (HMG-CoA reductase) |
|
Definition
| helps regulate the rate of cholesterol formation |
|
|
Term
| the committed step in cholesterol biosynthesis |
|
Definition
| the formation of mevalonate |
|
|
Term
| some ways HMG-CoA reductase is controlled |
|
Definition
1: rate of synthesis of HMG-CoA reductase mRNA is controlled by the sterol regulatory element binding protein (SREBP)
2: the rate of translation of HMG-CoA reductase nRNA is inhibited by nonsterol metabolites derived from mevalonate as well as by dietary cholesterol
3: the degradation of HMG-CoA reductase is stringently controlled by interactions involving the cytoplasmic and membrane domains
4: phosphorylation decreases the activity of HMG-CoA reductase |
|
|
Term
| the rate of synthesis of HMG-CoA reductase mRNA is controlled by... |
|
Definition
| the sterol regulatory element binding protein (SREBP) |
|
|
Term
|
Definition
| a short DNA sequence called the sterol regulatory element (SRE) on the 5' side of the reductase gene |
|
|
Term
|
Definition
| when cholesterol levels are low |
|
|
Term
| when SREBP binding to SRE does for transcription |
|
Definition
|
|
Term
| membrane protein that acts as the cholesterol sensor |
|
Definition
| SREB cleavage activating protein (SCAP) |
|
|
Term
| what SCAP does when cholesterol levels are low |
|
Definition
| escorts SREBP in small membrane vesicles to the Golgi complex, where it is released from the membrane |
|
|
Term
| how SREBP enhances transcription |
|
Definition
| migrates to nucleus and binds to the SRE of the HMG-CoA reductase gene, as well as several other genes in the cholesterol biosynthetic pathway |
|
|
Term
| what happens to SREBP when cholesterol levels are high? |
|
Definition
| release of SREBP is blocked and SREBP in nucleus is rapidly degraded |
|
|
Term
| what SCAP in the endoplasmic reticulum does when cholesterol is low |
|
Definition
| binds to vesicular proteins that facilitate the transport of SCAP-SREBP to the Golgi apparatus |
|
|
Term
| what SCAP in the endoplasmic reticulum does when cholesterol is present |
|
Definition
| binds cholesterol, which causes a structural change in SCAP so that it binds to insig (insulin-induced gene), another endoplasmic reticulum protein |
|
|
Term
|
Definition
|
|
Term
| the importance of insig when cholesterol is present |
|
Definition
| it is the anchor that retains SCAP and thus SREBP in the endoplasmic reticulum in the presence of cholesterol |
|
|
Term
| depiction of the site of cholesterol synthesis |
|
Definition
[image]
the arrow points to a vesicle that is releasing its content of VLDL particles |
|
|
Term
| depiction of the SREBP pathway |
|
Definition
|
|
Term
| the rate of translation of HMG-CoA reductase nRNA is inhibited by... |
|
Definition
| nonsterol metabolites derived from mevalonate as well as by dietary cholesterol |
|
|
Term
| the 2 domains of HMG-CoA reductase |
|
Definition
-cytoplasmic domain, which carries out catalysis
-membrane domain, which senses signals that lead to its degradation |
|
|
Term
| function of the cytoplasmic domain of HMG-CoA reductase |
|
Definition
|
|
Term
| function of the membrane domain of HMG-CoA reductase |
|
Definition
| senses signals that lead to its degradation |
|
|
Term
| effect of phosphorylation on the activity of HMG-CoA reductase |
|
Definition
|
|
Term
| why cholesterol synthesis ceases when ATP is low |
|
Definition
| because HMG-CoA reductase is switched off by an AMP-activated protein kinase |
|
|
Term
| some sources of amino acids |
|
Definition
-dietary protein
-degradation of unneded or defective cellular proteins |
|
|
Term
|
Definition
| the degradation and resynthesis of proteins |
|
|
Term
| some proteins that are short lived |
|
Definition
| those that are involved in metabolic regulation |
|
|
Term
| some causes of defective proteins |
|
Definition
-errors in translation
-oxidative damage
-altered in other ways with the passage of time |
|
|
Term
| something that happens to excess amino acids |
|
Definition
| they are first used as building blocks for anabolic rxns, such as protein synthy and nucleotide synth |
|
|
Term
| what happens to excess amino acids after then needs for anabolic rxns are met? |
|
Definition
| the amino acids are degraded and the C skeletons are used in catabolism or anabolism |
|
|
Term
| why it's important to safely remove the excess N from amino acids |
|
Definition
| because excess N in the form of ammonia is toxic |
|
|
Term
| how most vertebrates get rid of excess N from amino acids |
|
Definition
| convert the ammonia into urea, which is then excreted |
|
|
Term
| the first step in the degradation of amino acids |
|
Definition
|
|
Term
| the major site of amino acid degradation in mammals |
|
Definition
|
|
Term
|
Definition
| what's left over after the N is removed from amino acids |
|
|
Term
| what happens after the N is removed fro amino acids? |
|
Definition
| the resulting α-ketoacids so that the C skeletons can enter the metabolic mainstream as precursors of glucose or citric acid cycle intermediates |
|
|
Term
| how alpha-amino groups are converted into ammonium ions |
|
Definition
| by the oxidative deanimation of glutamate |
|
|
Term
| depiction of oxidative deanimation of glutamate |
|
Definition
|
|
Term
| aminotransferases aka transaminases |
|
Definition
catalyze the transfer of an α-amino groupfrom an α-amino acid to an α-ketoacid
generally funnel α-amino groups from a variety of amino acids to α-ketoglutarate for conversion into ammonia |
|
|
Term
| depiction of the function of aminotransferases aka transaminases |
|
Definition
|
|
Term
| aspartate aminotransferase |
|
Definition
| catalyzes the transfer of the aminotransferases aka transaminases-amino group of aspartate to aminotransferases aka transaminases-ketoglutarate |
|
|
Term
| depiction of the function of aspartate aminotransferase |
|
Definition
|
|
Term
|
Definition
| catalyzes the transfer of the amino group of alanine to aminotransferases aka transaminases-ketoglutarate |
|
|
Term
| depiction of the function of alanine aminotransferase |
|
Definition
|
|
Term
| depiction of the oxidative deanimation of glutamate, regenerating α-ketoglutarate |
|
Definition
|
|
Term
|
Definition
| catalyzes the oxidative deanimation of glutamate |
|
|
Term
| depiction of the function of glutamate dehydrogenase |
|
Definition
|
|
Term
| something unusual about glutamate dehydrogenase |
|
Definition
| it can use either NADH or NADPH as reducing power |
|
|
Term
| how toxic free ammonia is sequestered |
|
Definition
| some liver specific enzymes in mitochondria such that there's compartmentalization |
|
|
Term
| how glutamate dehydrogenase is regulated in mammals, but not other organisms |
|
Definition
| allosterically inhibited by GTP and stimulated by ADP |
|
|
Term
|
Definition
| this is formed on an enzyme when a product is replaced by substrate before the rxn is complete |
|
|
Term
| the net rxn catalyzed by aminotransferases and glutamate dehydrogenases |
|
Definition
| α-amino acid + NAD(P)H+ + H2O --> α-ketoacid + NH4+ + NAD(P)H +
H+ |
|
|
Term
| what happens to the N atoms of amino acids, except for serine and threonine, before their removal? |
|
Definition
| they get transferred to α-ketoglutarate before their removal |
|
|
Term
| how the N atoms of serine and threonine are removed |
|
Definition
| they are directly deanimated |
|
|
Term
|
Definition
| catalyze the direct deanimation of serine, which yields pyruvate and ammonia |
|
|
Term
|
Definition
| catalyze the direct deanimation of thrionine, which yields α-ketobutyrate and ammonia |
|
|
Term
| the prosthetic group on serine dehydratase and thrionine dehydratase |
|
Definition
| pyridoxal phosphate (PLP) |
|
|
Term
| depiction of the function of serine dehydratase |
|
Definition
|
|
Term
| depiction of the function of threonine dehydratase |
|
Definition
|
|
Term
| depiction of how ammonia is converted into urea in most terrestrial vertibrates |
|
Definition
|
|
Term
| the amino acids liver can not deanimate |
|
Definition
| the branched-chain amino acids leucine, valine, and isoleucine |
|
|
Term
| one way muscle uses branched-chain amino acids |
|
Definition
|
|
Term
| how N from amino acids is processed in the muscle |
|
Definition
| gets released into a form that can be absorbed by the liver and converted into urea |
|
|
Term
| 2 principal transport forms in which N is transported from muscle to liver |
|
Definition
|
|
Term
|
Definition
| evidently the interconversion of alanina and glucose |
|
|
Term
| depiction of the glucose-alanine cycle |
|
Definition
|
|
Term
| when muscles use branched-chain amino acids as fuel |
|
Definition
| during prolonged exercise and fasting |
|
|
Term
| a key transport form of N |
|
Definition
|
|
Term
|
Definition
| catalyzes the synthesis of glutamine from glutamate and ammonia in an ATP-dependent rxn |
|
|
Term
| depiction of the function of glutamine synthetase |
|
Definition
|
|
Term
| how ammonia from the breakdown of amino acids can be used by the organism |
|
Definition
| in the biosynthesis of N compounds |
|
|
Term
| what happens to excess ammonia in most terrestrial vertebrates? |
|
Definition
| gets converted to urea by the urea cycle and excreted |
|
|
Term
|
Definition
| organisms that use the urea cycle to convert excess ammonia into urea to ne excreted |
|
|
Term
| depiction of the urea cycle |
|
Definition
|
|
Term
|
Definition
|
|
Term
| urea cycle begins in ______ with ______ |
|
Definition
| mitochondrial matrix
coupling of free NH4+ and HCO3- to form carbamoyl phosphate |
|
|
Term
| carbamoyl phosphate synthetase I (CPS I) |
|
Definition
| catalyzes the coupling of free NH4+ and HCO3- to form carbamoyl phosphate |
|
|
Term
| the committed step in the urea cycle |
|
Definition
| the coupling of free NH4+ and HCO3- to form carbamoyl phosphate using carbamoyl phosphate synthetase I (CPS I) |
|
|
Term
| depiction of the rxn sequence that forms carbamoly phosphate |
|
Definition
|
|
Term
| why the synthesis of carbamoyl phosphate is irreversible |
|
Definition
| because it consumes 2 ATP's |
|
|
Term
| the key regulatory enzyme for urea synthesis |
|
Definition
| carbamoyl phosphate synthetase |
|
|
Term
| when carbamoyl phosphate synthetase is maximally active |
|
Definition
| when amino acids are being metabolized for fuel use |
|
|
Term
| N-acetylglutamate synthase |
|
Definition
| catalyzes the synthesis of N-acetylglutamate |
|
|
Term
| depiction of the function of N-acetylglutamate synthase |
|
Definition
|
|
Term
| N-acetylglutamate synthase is itself activated by... |
|
Definition
|
|
Term
| how the urea cycle begins |
|
Definition
| carbamoyl phosphate reacts with ornithine to begin the urea cycle |
|
|
Term
| ornithine transcarbamoylase |
|
Definition
| catalyzes the rxn of ornithine with carbamoyl phosphate to form citrulline |
|
|
Term
| depiction of the function of ornithine transcarbamoylase |
|
Definition
|
|
Term
| argininosuccinate synthetase |
|
Definition
| catalyzes the formation of argininosuccinate from citrulline and aspartate |
|
|
Term
| depiction of the function of argininosuccinate synthetase |
|
Definition
|
|
Term
| argininosuccinase aka argininosuccinate lyase) |
|
Definition
| cleaves argininosuccinate into arginine and fumarate |
|
|
Term
| depiction of the function of argininosuccinase aka argininosuccinate lyase |
|
Definition
|
|
Term
|
Definition
| catalyzes the hydrolysis of arginine to form urea and ornithine |
|
|
Term
| the net rxn of urea synthesis |
|
Definition
| CO2 + NH4+ + 3 ATP + aspartate + 2 H2O --> urea + 2 ADP + 2 Pi + AMP + PPi + fumarate |
|
|
Term
| importance of fumarate derived from urea cycle |
|
Definition
-fumarate is a precursor for glucose
-fumarate can be hydrated to malate, which is an intermediate in the citric acid cycle |
|
|
Term
| the urea cycle, citric acid cycle, and transamination of oxaloacetate are linked by... |
|
Definition
|
|
Term
| depiction of the connection between the urea cycle, the citric acid cycle, and the transamination of oxaloacetate |
|
Definition
|
|
Term
| the strategy of amino acid degradation |
|
Definition
| to transform the C skeletons into major metabolic intermediates that can be converted into glucose or oxidized by the citric acid cycle |
|
|
Term
| the C skeletons from the 20 fundamental amino acids are funneled into these 7 molecules. |
|
Definition
-pyruvate
-acetyl CoA
-acetoacetyl CoA
-α-ketoglutarate
-succinyl CoA
-fumarate
-oxaloacetate |
|
|
Term
|
Definition
amino acids that are degraded into acetyl CoA or acetoacetyl CoA
they are called this because they give rise to ketone bodies or fatty acids but can not be used to synthesize glucose |
|
|
Term
| ketogenic amino acids give rise to... |
|
Definition
| ketone bodies or fatty acids |
|
|
Term
| ketogenic amino acids give rise to ketone bodies or fatty acids but can not be used to synthesize... |
|
Definition
|
|
Term
|
Definition
| amino acids that are degraded to pyruvate, α-ketoglutarate, succinyl CoA, fumarate, or oxaloacetate |
|
|
Term
| what oxaloacetate and pyruvate derived from the degradation of glucogenic amino acids can be used for |
|
Definition
|
|
Term
| the only 2 amino acids that are solely ketogenic |
|
Definition
|
|
Term
| the amino acids that are both ketogenic and glucogenic |
|
Definition
-threonine
-isoleucine
-phenylalanine
-tryptophan
-tyrosine |
|
|
Term
| the amino acids that are solely glucogenic |
|
Definition
-alanine
-cysteine
-glycine
-serine
-threonine
-asparagine
-aspartate
-methionine
-valine
-arginine
-glutamate
-glutamine
-histidine
-proline |
|
|
Term
| how the poathways of amino acid degradation are identified |
|
Definition
| by entry point into metabolism |
|
|
Term
| depiction of the fates of the C skeletons of amino acids |
|
Definition
|
|
Term
| amino acids that enter the metabolic mainstream by pyruvate |
|
Definition
-alanine
-serine
-cysteine
-glycine
-threonine
-tryptophan |
|
|
Term
| how alanine gets converted into pyruvate |
|
Definition
transamination of alanine
alanine + α-ketoglutarate <--> pyruvate + glutamate |
|
|
Term
| how serine gets converted into pyruvate |
|
Definition
| deanimation by dehydratase
serine --> pyruvate + NH4+ |
|
|
Term
|
Definition
| catalyzes the deanimation of serine to pyruvate |
|
|
Term
| depiction of the function of serine dehydratase |
|
Definition
|
|
Term
| depiction of pyruvate formation from amino acids |
|
Definition
|
|
Term
| the amino acids that enter the mainstream metabolism by way of oxaloacetate |
|
Definition
|
|
Term
| how aspartate enters mainstream metabolism by way of oxaloacetate |
|
Definition
gets directly transaminated to oxaloacetate
aspartate + α-ketoglutarate <--> oxaloacetate + glutamate |
|
|
Term
| how asparagine enters mainstream metabolism by way of oxaloacetate |
|
Definition
| gets hydrolyzed into aspartate, which is then transaminated into oxaloacetate |
|
|
Term
|
Definition
| catalyzes the hydrolysis of asparagine into aspartate and NH4+ |
|
|
Term
| amino acids that can enter mainstream metabolism by α-ketoglutarate |
|
Definition
-glutamine
-arginine
-proline
-histidine
-glutamate |
|
|
Term
| how glutamate enters mainstream metabolism by way of α-ketoglutarate |
|
Definition
| gets converted into α-ketoglutarate |
|
|
Term
| how glutamine, proline, arginine, and histidine enter mainstream metabolism by way of α-ketoglutarate |
|
Definition
| by getting converted into glutamate, which can be converted into α-ketoglutarate |
|
|
Term
| depiction of α-ketoglutarate formation from amino acids |
|
Definition
|
|
Term
| depiction of histidine degradation (the conversion of histidine into glutamate) |
|
Definition
|
|
Term
| how glutamine enters mainstream metabolism by way of α-ketoglutarate |
|
Definition
| gets hydrolyzed into glutamate, which can be converted into α-ketoglutarate |
|
|
Term
|
Definition
| hydrolyzes glutamine into glutamate and NH4+ |
|
|
Term
| depiction of glutamate formation from proline and arginine |
|
Definition
|
|
Term
| amino acids that enter mainsteram metabolism by way of succinyl CoA |
|
Definition
-methionine
-isoleucine
-valine |
|
|
Term
| depiction of succinyl CoA formation from methionine, isoleucine, and valine |
|
Definition
|
|
Term
| the branched chain amino acids that enter mainstream metabolism |
|
Definition
-leucine
-isoleucine
-valine |
|
|
Term
| branched-chain α-ketoacid dehydrogenase complex |
|
Definition
| catalyzes the oxidative decatboxylation of α-ketoisocaproate into isovaletyl CoA |
|
|
Term
| depiction of leucine being converted into isovaleryl CoA |
|
Definition
|
|
Term
| depiction of the function of the branched-chain α-ketoacid dehydrogenase complex |
|
Definition
|
|
Term
| depiction of isovaleryl CoA being converted into β-methylglutaconyl CoA |
|
Definition
|
|
Term
| depiction of β-methylglutaconyl CoA being converted into acetyl CoA and acetoacetate |
|
Definition
|
|
Term
| overall conversion of leucine into acetyl CoA and acetoacetate |
|
Definition
| make a composite picture of the 3 rxn sequences on p. 563 |
|
|
Term
| what is used to break the aromatic ring in aromatic amino acids? |
|
Definition
|
|
Term
| phenylalanine hydroxylase |
|
Definition
| catalyzes the hydroxylation of phenylalanine to tyrosine |
|
|
Term
| depiction of the function of phenylalanine hydroxylase |
|
Definition
|
|
Term
| monooxygenase or mixed-function oxygenase |
|
Definition
| oxygenase that makes 1 O atom of O2 go to the product and the other go to H2O
example: phenylalanine hydroxylase |
|
|
Term
| net rxn for the hydroxylation of phenylalanine to tyrosine |
|
Definition
| phenylalanine + H2O + NADH + H+ --> tyrosine + NAD+ + H2O |
|
|
Term
| depiction of phenylalanine and tyrosine degradation |
|
Definition
|
|
Term
| the end products of phenylalanine and tyrosine degradation |
|
Definition
| acetoacetate and fumarate |
|
|
Term
| nearly all cleavages of aromatic rings in biological systems are catalyzed by... |
|
Definition
|
|
Term
|
Definition
| enzyme that incorporates both O atoms into the product |
|
|
Term
| depiction of tryptophan degradation |
|
Definition
|
|
Term
| end products of tryptophan degradation |
|
Definition
|
|
Term
| the end product of methionine degradation |
|
Definition
|
|
Term
| depiction of methionine metabolism |
|
Definition
|
|
Term
| the sources of the C skeletons of amino acids |
|
Definition
intermediates of...
-glycolysis
-citric acid cycle
-pentose phosphate pathway |
|
|
Term
| depiction of the biosynthetic families of amino acids in bacteria and plants |
|
Definition
|
|
Term
|
Definition
| amino acids that must be obtained from the diet |
|
|
Term
|
Definition
| amino acids that can be biosynthesized |
|
|
Term
| the 3 α-ketoacids that can be converted into amino acids simply by transamination (the addition of an amino group) |
|
Definition
-α-ketoglutarate
-oxaloacetate
-pyruvate |
|
|
Term
|
Definition
| transfer of an amino group |
|
|
Term
| equation for aspartate biosynthesis |
|
Definition
| oxaloacetate + glutamate <--> aspartate + α-ketoglutarate |
|
|
Term
| equation for alanine biosynthesis |
|
Definition
| pyruvate + glutamate <--> alanine + α-ketoglutarate |
|
|
Term
| transamination rxns are carried out by... |
|
Definition
| pyridoxal phosphate-dependent aminotransferases |
|
|
Term
| pyridoxal phosphate-dependent aminotransferases |
|
Definition
| enzymes that carry out transamination rxns |
|
|
Term
| type of rxn that participates in the synthesis of most amino acids |
|
Definition
|
|
Term
| all aminotransferases contain this prosthetic group |
|
Definition
| pyridoxal phosphate (PLP) |
|
|
Term
| pyridoxal phosphate (PLP) |
|
Definition
| thisd is the prosthetic group of all aminotransferases |
|
|
Term
| pyridoxal phosphate (PLP) is derived from... |
|
Definition
|
|
Term
| what pyridoxal phosphate (PLP) does in transamination rxns |
|
Definition
| accepts an amino group to form a cofactor prominent in many enzymes, pyridoxamine phosphate (PMP) |
|
|
Term
| depiction of the biosynthesis of serine |
|
Definition
|
|
Term
|
Definition
|
|
Term
| the major donor of methyl groups in biosynthetic methylation rxns |
|
Definition
| S-adenoslymethionine (SAM) |
|
|
Term
| S-adenoslymethionine (SAM) |
|
Definition
| this is the major donor of methyl groups in biosynthetic methylation rxns |
|
|
Term
| S-adenoslymethionine (SAM) is synthesized from... |
|
Definition
|
|
Term
| depiction of the synthesis of S-adenoslymethionine (SAM) |
|
Definition
|
|
Term
| depiction of the conversion of S-adenoslymethionine (SAM) into homocysteine |
|
Definition
|
|
Term
| methionine synthase aka homocysteine methyltransferase |
|
Definition
| catalyzes the transfer of a methyl group from N5-methyltetrahydrofolate |
|
|
Term
|
Definition
| mediates the transfer of a methyl group from N5-methyltetrahydrofolate; it's a cofactor for methionine synthase aka homocysteine methyltransferase |
|
|
Term
| methylcobalamin is derived from... |
|
Definition
|
|
Term
| depiction of the activated methyl cycle |
|
Definition
|
|
Term
| how the methyl group of methionine is activated |
|
Definition
| by the formation of S-adenoslymethionine (SAM) |
|
|
Term
| the rate of amino acid synthesis depends mainly on... |
|
Definition
-amount of biosynthetic enzymes
-activities of those enzymes |
|
|
Term
| the first irreversible step in a biosynthetic rxn |
|
Definition
|
|
Term
| the step of a biosynthetic pathway that's often allosterically regulated |
|
Definition
|
|
Term
| essential role of feedback inhibition (type of allosteric regulation) |
|
Definition
| conservation of building blocks and metabolic energy |
|
|
Term
| the regulation of branched pathways is more complicated because... |
|
Definition
| 2 end products must be accounted for |
|
|
Term
|
Definition
| the PLP enzyme that catalyzes the formation of α-ketobutyrate |
|
|
Term
| depiction of the function of threonine deaminase |
|
Definition
|
|
Term
| depiction of the regulation of threonine deaminase |
|
Definition
|
|
Term
|
Definition
| the committed step being catalyzed by 2 or more enzymes with different regulatory properties |
|
|
Term
| depiction of enzyme multiplicity |
|
Definition
|
|
Term
| cumulative feedback inhibition |
|
Definition
a common step being partly inhibited by each of the final products, acting independently
each inhibitor can reduce the activity of the enzyme, even when other inhibitors are exerting their own maximal inhibition |
|
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Term
|
Definition
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Term
|
Definition
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|
Term
|
Definition
|
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Term
|
Definition
|
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Term
|
Definition
|
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Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| structure of a pyrimidine |
|
Definition
|
|
Term
|
Definition
|
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Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
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Term
|
Definition
|
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Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| something epigenetic that can happen to cytosine when adde to nucleotide strand |
|
Definition
| the H atom where the arrow is pointing gets replaced by CH3; gets methylated
[image] |
|
|
Term
| where adenosine comes from |
|
Definition
adenine
Adenine becomes the nucleoside Adenosine when it becomes combined with a ribose |
|
|
Term
| when adenine becomes adenosine |
|
Definition
| when it becomes combined with a ribose |
|
|
Term
|
Definition
|
|
Term
| macromolecule ATP seems to be present in |
|
Definition
|
|
Term
| the phosphate you want to tag in ATP |
|
Definition
| the alpha phosphate, which is the closest to the ribose |
|
|
Term
| how a phosphate is tagged |
|
Definition
|
|
Term
|
Definition
|
|
Term
| what happens if you label the gamma phosphate? |
|
Definition
| it'll wind up in pyrophosphate |
|
|
Term
| the form of ATP that seems to be present in DNA |
|
Definition
|
|
Term
| in essence, our genetic material is basically... |
|
Definition
|
|
Term
|
Definition
|
|
Term
| structure of deoxyribose ATP |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| why RNA is less stable than DNA |
|
Definition
| because RNA contains that reactive OH group |
|
|
Term
| some questions the structure of DNA can answer |
|
Definition
1: replication
2: nature/function of a gene
3: genetic basis of heredity
4: molecular basis of evolution (this is a more modern matter because it requires ability to sequence DNA; the technology for that wasn't developed until 1970's) |
|
|
Term
| why genetics is important to a cell |
|
Definition
| because cells have to keep their genetic constitution to stay alive |
|
|
Term
| how Rosalind Franklin contributed to discovering the structure of DNA |
|
Definition
Franklin was a great crystallographer; got hired to determine structure of D-form DNA
Wilkins released Franklin's data and Franklin was oblivious to this |
|
|
Term
|
Definition
A = T
G = C
DNA obeys the rule, but RNA doesn't; it's a universal role of double-stranded DNA |
|
|
Term
| things to consider with DNA structure |
|
Definition
1: stabilizing forces
2: Double helix is directional/antiparallel
3: Major and minor grooves (asymmetrical threads of a screw) |
|
|
Term
| some stabilizing forces in DNA |
|
Definition
- Hydrophobic interactions
- H-bonding, W/C (Watson/Crick) pairing
- van der Waals forces act on adjacent stacked base pairs |
|
|
Term
|
Definition
|
|
Term
| distance between consecutive bases in DNA |
|
Definition
|
|
Term
|
Definition
| 1 100millionth of a centimeter
10-10 |
|
|
Term
| what the asymmetric threading of the "screw" does for the DNA molecule |
|
Definition
| presents different faces of the strands of the helix to the outside |
|
|
Term
| one reason the phosphate backbone is on the outside of the DNA molecule |
|
Definition
| because phosphates are more hydrophilic than bases |
|
|
Term
| side view of DNA molecule |
|
Definition
|
|
Term
|
Definition
|
|
Term
| depiction of the asymmetric "screw" of DNA |
|
Definition
|
|
Term
| depiction of the bonding between guanine and cytosine |
|
Definition
|
|
Term
| depiction of the bonding between adenine and thymine |
|
Definition
|
|
Term
| depiction of the van der Waals interactions in base stacking |
|
Definition
|
|
Term
| how DNA strands can be separated in the lab |
|
Definition
|
|
Term
|
Definition
The temperature at which half of the DNA
molecules are denatured |
|
|
Term
|
Definition
| separated DNA strands combining to form the double helix |
|
|
Term
| what alkali or chaotropic agents do to DNA |
|
Definition
| denature DNA by disrupting non-covalent interactions |
|
|
Term
| how chaotropic agents break down DNA |
|
Definition
|
|
Term
| which DNA absorbs more light? single stranded or double stranded? |
|
Definition
|
|
Term
| chart showing wavelength absorbance of single stranded and double stranded DNA |
|
Definition
|
|
Term
|
Definition
| the increase in light absorption that occurs when single strands flop around |
|
|
Term
| depiction of a hyperchromic shift |
|
Definition
|
|
Term
| dsDNA can be denatured by... |
|
Definition
| heat or chaotropic agents |
|
|
Term
| Extent of denaturation can be measured by... |
|
Definition
|
|
Term
|
Definition
| duplexes that are all A's and T's |
|
|
Term
|
Definition
| duplexes that are all G's and C's |
|
|
Term
| depiction of a Tm chart vs. UV absorbance by DNA |
|
Definition
[image]
Any DNA you put in there has to be between those 2 extremes |
|
|
Term
| the hallmarks of DNA structure |
|
Definition
-DNA consists of two chains of polynucleotides
-Paired via hydrogen bonds
-Running in opposite directions
-right-handed helix around a central axis
-Bases found on the inside of the helix
-Phosphates and sugars on the outside
-bases perpendicular to the axis (Bform) |
|
|
Term
| this accounts for some of the compaction of the DNA |
|
Definition
|
|
Term
| Further compaction of DNA occurs by... |
|
Definition
| binding certain proteins to the DNA |
|
|
Term
| how much does an average chromosome have to be compacted? |
|
Definition
|
|
Term
|
Definition
| modifications of histones and effect of histones on DNA expression |
|
|
Term
| can epigenetic factors be inherited? |
|
Definition
|
|
Term
|
Definition
| protein octamers that have a strong affinity for DNA and bind to it in a certain way |
|
|
Term
| depiction of the histone octamer |
|
Definition
|
|
Term
| depiction of nucleosome core particle |
|
Definition
|
|
Term
| depiction of nucleosome core particle and linker DNA |
|
Definition
|
|
Term
| depiction of all the compaction that occurs with DNA |
|
Definition
|
|
Term
| the amount of DNA compaction we seem to have accounted for so far |
|
Definition
|
|
Term
| can characteristics of chromatin be inherited? |
|
Definition
|
|
Term
| A common structural motif seen in nucleic acids, most notably RNA |
|
Definition
|
|
Term
| the stem-loop occurs when... |
|
Definition
complementary
sequences in the same strand form a double helix |
|
|
Term
| do Non-Watson-Crick base pairs occur frequently in RNA? |
|
Definition
|
|
Term
| More elaborate structures of RNA are |
|
Definition
| often stabilized by Mg2+ ions |
|
|
Term
| depiction of stem loop structure |
|
Definition
|
|
Term
| depiction of Prokaryotic gene expression |
|
Definition
|
|
Term
| can RNA in prokaryotes have multiple protein coding sequences? |
|
Definition
|
|
Term
| depiction of Euokaryotic gene expression |
|
Definition
|
|
Term
| what occurs at each end of the mRNA molecule in eukaryotic gene expression? |
|
Definition
| covalent modifications to form a cap |
|
|
Term
| in eukaryotic gene expression, every step along the way has the potential to be... |
|
Definition
|
|
Term
| genetic mapping reveals... |
|
Definition
| order of genes on specific chromosomes |
|
|
Term
| composition of the human geneome |
|
Definition
|
|
Term
| how much of the human genome encodes proteins? |
|
Definition
|
|
Term
|
Definition
| gene that encodes RNA that never codes a protein product |
|
|
Term
| how much of the genome contains sequences linked to biological function? |
|
Definition
|
|
Term
| how much of the genome is transcribed at some point? |
|
Definition
|
|
Term
|
Definition
|
|
Term
| can transcripts be synthesized by both strands? |
|
Definition
|
|
Term
|
Definition
| Genome Wide ASsociation variants associated with diseases such as schizophrenia and type 2 diabetes |
|
|
Term
| GWAS studies try to understand... |
|
Definition
| pleiotropic things in the genome |
|
|
Term
| some challenges to defining a gene |
|
Definition
• Gene regulatory sequences
• Overlapping genes (introns and exons)
• Parasitic and mobile genes (transposons)
• “Junk” DNA is conserved
• Pseudogenes (duplicated genes)
• Pervasive transcription |
|
|
Term
|
Definition
| Parasitic and mobile genes |
|
|
Term
| what happens to “Junk” DNA? |
|
Definition
|
|
Term
| depiction of gene complexity |
|
Definition
|
|
Term
| why RNA is more unstable than DNA |
|
Definition
| because it has that reactive OH group |
|
|
Term
| depiction of the difference between DNA and RNA |
|
Definition
|
|
Term
| depiction of what happens to RNA when it is treated with NaOH |
|
Definition
|
|
Term
|
Definition
|
|
Term
| what CsCl does for separation of light and heavy DNA |
|
Definition
| forms density gradient along the centrifuge tube |
|
|
Term
| The reaction catalyzed by DNA polymerase |
|
Definition
| (DNA)n + dNTP <--> (DNA)n + 1 + PPi |
|
|
Term
| depiction of The reaction catalyzed by DNA polymerase |
|
Definition
|
|
Term
| depiction of RNA strand-elongation rxn |
|
Definition
|
|
Term
| Key characteristics of DNA synthesis in vitro |
|
Definition
| 1. Four deoxynucleoside triphosphates and Mg2+ are required in the buffer.
2. A template strand is used to direct DNA synthesis.
3. A primer from which the new strand grows must be present. |
|
|
Term
| what's required in the buffer for DNA synthesis? |
|
Definition
| Four deoxynucleoside triphosphates and Mg2+ |
|
|
Term
| ion required for DNA synthesis |
|
Definition
|
|
Term
| table of E. coli DNA polymerases |
|
Definition
|
|
Term
| where in the molecule does exonuclease start? |
|
Definition
|
|
Term
| where in the molecule does endonuclease start? |
|
Definition
|
|
Term
|
Definition
| nicks or 2bl stranded breaks |
|
|
Term
| general depiction of replication fork |
|
Definition
|
|
Term
| depiction of DNA polymerase holoenzyme |
|
Definition
| [image]
the β2 is basically a Sliding Clamp |
|
|
Term
| how the DNA polymerase holoenzyme is processive |
|
Definition
| it doesn't let go of the substrate; it can replicate many bases before it falls off the substrate |
|
|
Term
| what the clamp loader in the DNA polymerase holoenzyme does |
|
Definition
| opens and closes the beta 2 donut ring |
|
|
Term
| depiction of the trombone model of the DNA polymerase holoenzyme |
|
Definition
|
|
Term
| single strand binding protein (SSB) |
|
Definition
| coats single stranded DNA to protect it from degradation |
|
|
Term
| what primase does for DNA synthesis in the lagging strand |
|
Definition
| adds RNA to the DNA to serve as a primer |
|
|
Term
| depiction of DNA synthesis from primer |
|
Definition
|
|
Term
| depiction of the type of nick sealed by ligase |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
| relieves tension by introducing negative supercoils ahead of the fork |
|
|
Term
| depiction of Topoisomerase II in the replication fork |
|
Definition
|
|
Term
|
Definition
| the enzyme responsible for telomeres |
|
|
Term
| depiction of replication and telomeres |
|
Definition
|
|
Term
| depiction of telomeres in embryonic and adult stem cells |
|
Definition
|
|
Term
| depiction of extending the length of a telomere |
|
Definition
|
|
Term
| what happens with telomerases in aging? |
|
Definition
|
|
Term
| what happens with telomerases in cancer? |
|
Definition
|
|
Term
| the type of enzyme telomerase is |
|
Definition
|
|
Term
| something telomerase conains |
|
Definition
| RNA molecule; this makes it a reverse transcriptase |
|
|
Term
| The simplest source of DNA damage |
|
Definition
| the incorporation of an incorrect base during replication that escapes the proofreading capabilities of the DNA polymerases |
|
|
Term
| some types of errors that can halt DNA synthesis |
|
Definition
| insertion, deletions or breaks in one or both strands |
|
|
Term
| depiction of Proofreading by replicative DNA polymerase |
|
Definition
|
|
Term
| how replicative DNA polymerase proofreads DNA |
|
Definition
-removes incorrect base
-repeats synthesis rxn |
|
|
Term
| depiction of triplet repeat expansion |
|
Definition
|
|
Term
| what triplet repeat expansion can do to mRNA |
|
Definition
|
|
Term
| how DNA is replicated when intrinsic repair mediated by replicative DNA polymerase fails |
|
Definition
1. Recognize the inappropriate base(s).
2. Remove the inappropriate base(s).
3. Fill in the resulting gap with repair DNA polymerase.
4. DNA ligase removes SS breaks, restores DS DNA. |
|
|
Term
| Last resort to remove inappropriatebase(s) |
|
Definition
|
|
Term
| depiction of DNA mismatch repair |
|
Definition
|
|
Term
| what distinguishes old from newly replicated strands in E. coli? |
|
Definition
| adenine-methylation; new strands are unmethylated |
|
|
Term
|
Definition
|
|
Term
|
Definition
| enhances ability to recognize error |
|
|
Term
|
Definition
| makes single stranded break |
|
|
Term
| Damage to bases can occur by... |
|
Definition
|
|
Term
| types of mutagenic agents that can damage bases |
|
Definition
|
|
Term
| Hydroxyl radicals aka Reactive Oxygen Species |
|
Definition
| oxidize guanine to 8-oxoguanine |
|
|
Term
|
Definition
| deaminates adenine, forming hypoxanthine |
|
|
Term
| types of chemical addition of DNA adducts |
|
Definition
-alkylation
-addition of bulky side groups |
|
|
Term
| how chemical addition of DNA adducts inhibits DNA replication |
|
Definition
|
|
Term
| what UV irradiation does to DNA |
|
Definition
forms covalent bonds between adjacent thymidines to form thymidine dimers
enzyme system can't fix the damage; this causes skin cancer |
|
|
Term
| depiction of how Hydroxyl radicals aka reactive oxygen species affect duanine |
|
Definition
|
|
Term
| depiction of Base Excision Repair (BER) |
|
Definition
|
|
Term
|
Definition
|
|
Term
| depiction of Adenine deamination: A to C transversion |
|
Definition
|
|
Term
| how Adenine deamination helps create immunity |
|
Definition
| mutates DNA at specific points in immunoglobulin genes in response to specific diseases; helps create immunity |
|
|
Term
| some things that can cause bulky adducts to be added to DNA bases |
|
Definition
-Tobacco smoke
-Aflatoxin
-Nitrated polycyclic hydrocarbons (Eat →Die)
-Some require oxidation by liver cytochrome P450 to react with DNA
-Nucleotide Excision Repair |
|
|
Term
| depiction of bulky adduct being added to DNA base |
|
Definition
|
|
Term
| If BER fails to recognize the damaged base, the mutation may be corrected by... |
|
Definition
| NER (bulky adducts, alkylated bases) |
|
|
Term
| how is a mutation corrected when all else fails? |
|
Definition
| translesion repair polymerases synthesize past the damage (error prone) |
|
|
Term
| depiction of Repair of thymine dimers by DNA photolyase |
|
Definition
|
|
Term
| what thymine dimers do to cells |
|
Definition
-causes replication to halt
-causes cells to die by apoptosis |
|
|
Term
| depiction of creation of a double stranded break |
|
Definition
[image]
X-rays can cause this type of DNA damage |
|
|
Term
| why Dideoxynucleotide triphosphates (ddNTPs) stop chain growth |
|
Definition
| because it is missing a 3' hydroxyl, which means there's nothing to be added to |
|
|
Term
| depiction of Dye terminator sequencing (pool rxns) |
|
Definition
|
|
Term
| Why is RNA synthesis essential for DNA replication? |
|
Definition
| because it can be used as a primer and DNA synthesis is activated by primers |
|
|
Term
| What are the functions of helicases and topoisomerases during replication? |
|
Definition
| helicase unwinds DNA and topoisomerase relieves tension by making nicks ahead of replication fork |
|
|
Term
|
Definition
|
|
Term
| function of topoisomerase |
|
Definition
| relieves tension by making nicks ahead of replication fork |
|
|
Term
| One simple way to avoid the end-replication problem |
|
Definition
circular genome
some viruses add more viral DNA at the end |
|
|
Term
| What are the steps required of most DNA repair systems? |
|
Definition
1: recognize error
2: remove error
3: resynthesize
4: reseal with ligase |
|
|
Term
| depiction of the Ames test |
|
Definition
|
|
Term
| sign of defective telomerase |
|
Definition
|
|
Term
| what you can do with PacBio SMRT sequencing |
|
Definition
| allows you to signal single molecules of DNA |
|
|
Term
|
Definition
| sequence of DNA that is transcribed and its RNA product |
|
|
Term
|
Definition
| by new genes being created |
|
|
Term
| depiction of pseudogene formation |
|
Definition
|
|
Term
| how much of our genome is made of pseudogenes? |
|
Definition
|
|
Term
|
Definition
|
|
Term
| depiction of how retroviruses contribute to our genome |
|
Definition
|
|
Term
| depiction of the flow of genetic information |
|
Definition
|
|
Term
|
Definition
|
|
Term
| a lot of the specialization in the flow of genetic information comes from... |
|
Definition
|
|
Term
| what prions can do to proteins |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
| has to be replicated into the + strand for transcription to occur |
|
|
Term
|
Definition
| just circular ssRNA, No coding potential! |
|
|
Term
|
Definition
| transcripts with a function |
|
|
Term
| Major classes of RNA synthesized in bacteria |
|
Definition
|
|
Term
|
Definition
| encodes the information to generate a protein |
|
|
Term
| Transfer RNA (tRNA) and ribosomal RNA (rRNA) |
|
Definition
| play key roles in translating mRNA information into protein |
|
|
Term
|
Definition
| something encoded in ribosomes to enhance expression |
|
|
Term
| the current frontier in terms of gene expression |
|
Definition
|
|
Term
| depiction of coding (sense) and template (antisense) strands of DNA and one strand of mRNA |
|
Definition
|
|
Term
| depiction of transcription bubble and synthesis of mRNA strand |
|
Definition
|
|
Term
| ______ specifies the coding and noncoding strands |
|
Definition
| Direction of transcription |
|
|
Term
| does RNA polymerase require a primer? |
|
Definition
|
|
Term
| why does RNA have more mistakes than DNA? |
|
Definition
| because RNA doesn't undergo any repair rxns |
|
|
Term
| table of subunits of E. coli RNA polymerase |
|
Definition
|
|
Term
| depiction of the Core + σ = holoenzyme |
|
Definition
|
|
Term
| depiction of the RNA polymerase rxn |
|
Definition
|
|
Term
| which polymerase is faster? RNA polymerase or DNA polymerase? |
|
Definition
|
|
Term
| depiction of how sigma factors act catalytically |
|
Definition
|
|
Term
| the steps of gene transcription |
|
Definition
1: Initiation: closed to open complex
2: Elongation |
|
|
Term
| how RNA polymerase generates mRNA |
|
Definition
1: polymerase and sigma factor bind to promoter
2: polymerase generates mRNA
3: sigma subunit breaks off to help another RNA polymerase transcribe another gene |
|
|
Term
| depiction of RNA–DNA hybrid separation |
|
Definition
|
|
Term
| how the RNA–DNA hybrid is separated |
|
Definition
| RNA polymerase extrudes the strand and DNA polymerase wants to keep the base pairing intact |
|
|
Term
| 2 types of termination of RNA synthesis |
|
Definition
-Rho independent
-Rho dependent |
|
|
Term
| Rho independent termination |
|
Definition
| has all the signals present for termination on the RNA |
|
|
Term
| depiction of Rho independent termination |
|
Definition
|
|
Term
| Rho dependent termination |
|
Definition
| uses Rho protein to dislodge polymerase from template |
|
|
Term
| depiction of Rho dependent termination |
|
Definition
|
|
Term
| what Rho independent and Rho dependent termination have in common |
|
Definition
| termination signals lie in newly synthesized RNA rather than DNA |
|
|
Term
| depiction of riboswitches with M ligand |
|
Definition
|
|
Term
| depiction of riboswitches without M ligand |
|
Definition
|
|
Term
|
Definition
| end product of a pathway, vitamin for example |
|
|
Term
| some similarities between DNA and RNA polymerase |
|
Definition
-need templates
-all 5'-->3'
-chemistry the same
-have replication bubbles; this means helicases are involved
-tend to be multiple subunit proteins |
|
|
Term
| some differences between DNA and RNA polymerase |
|
Definition
-speed (RNA pol slower)
-RNA pol doesn't need primer, but DNA pol does
-dNTP's vs. NTP's
-U/A differences
-error rate/proofreading
-DNA pol designed to maintain H bonding over replicated DNA; RNA pol doesn't |
|
|
Term
| transcription factors aka DNA binding proteins |
|
Definition
proteins that initiate or stop transcription of genes
they are upstream of the transcription start site |
|
|
Term
|
Definition
| where RNA polymerase transcribes mRNA from the DNA template |
|
|
Term
| The DNA components of an operon consist of... |
|
Definition
-a regulator gene
-an operator (binding site for a regulatory protein)
-a promoter
-structural genes |
|
|
Term
| gene specific behavior of the Lac operon |
|
Definition
| the regulatory gene encodes a protein called the lac repressor (lacI) that binds to the operator site (lacO) in the absence of lactose and prevents transcription of the structural genes |
|
|
Term
| global behavior of the Lac operon |
|
Definition
| In the absence of glucose, cAMP binds to the cAMP activator protein CRP. CRP-cAMP binds the promoter where contact is made with RNA Pol, which increases initiation of transcription. CRP-cAMP affects the expression of several hundred genes in addition to the Lac operon. |
|
|
Term
| Combinatorial gene regulation |
|
Definition
| Gene specific + global regulation |
|
|
Term
| depiction of the Lac operon and its repressor |
|
Definition
|
|
Term
| what has to happen for the Lac operon to be activated? |
|
Definition
| lactose has to be converted to allolactose, which binds to some receptor |
|
|
Term
| are regulatory circuits ever 100% induced or 100% off? |
|
Definition
|
|
Term
| depiction of Binding of Lac repressor to the Lac operator |
|
Definition
|
|
Term
| how allolactose activates the lac operon |
|
Definition
| Binding of the inducer allolactose to the repressor decreases binding affinity for the operator |
|
|
Term
| depiction of E. coli global control when glucose is present |
|
Definition
|
|
Term
| depiction of E. coli global control when glucose is absent |
|
Definition
|
|
Term
| what happens in E. coli in the absence of glucose? |
|
Definition
| enzyme III (EIII) transfers a phosphate group to adenylate cyclase, activating the cyclase, cAMP increases |
|
|
Term
| what CRP /CAP-cAMP binding does |
|
Definition
| activates transcription of other genes |
|
|
Term
| depiction of Positive activation by CRP-cAMP; global combinatorial control in E. coli |
|
Definition
|
|
Term
| other than allolactose, what else further activates transcription of the lac operon? |
|
Definition
|
|
Term
|
Definition
| encodes the Lac repressor, which binds to the Lac Operator |
|
|
Term
| Defective Lac repressor results in... |
|
Definition
| Lac expression regardless if lactose is present |
|
|
Term
|
Definition
| LacO operator is a region, O1 and O2 , of the promoter that binds LacI and blocks transcription of the Lac operon |
|
|
Term
| Defective LacO that can no longer bind LacI results in... |
|
Definition
| a Lac expression that is also independent of lactose |
|
|
Term
|
Definition
|
|
Term
| Loss of Lac promoter function (ie mutations in the -10 and -35 region) results in... |
|
Definition
| lower levels of expression under all conditions |
|
|
Term
| Lac merodiploid or partial diploid |
|
Definition
| Two copies of the Lac operon in one cell |
|
|
Term
| how the Lac operon is distributed when the cell is Lac merodiploid or partial diploid |
|
Definition
| Usually one copy is the Lac operon on the E. coli chromosome, and the second Lac operon is carried on a plasmid integrated into the chromosome at another location. Important controls are cells containing individual copies of Lac. |
|
|
Term
| Combinatorial gene regulation controls... |
|
Definition
|
|
Term
| depiction of how proteins attached to DNA affect the results of a DNA gel shift assay (EMSA) |
|
Definition
|
|
Term
|
Definition
|
|
Term
| depiction of shift and supershift caused by proteins bound to DNA |
|
Definition
|
|
Term
| Why does a regulatory circuit like the Lac operon require basal level expression? |
|
Definition
| because you need a little permease gene |
|
|
Term
| what allolactose does to the repressor in the Lac operon |
|
Definition
| binds to it to decrease the binding affinity for the operator |
|
|
Term
| Transcription from the Lac promoter occurs when... |
|
Definition
|
|
Term
| Transcription from the Lac promoter is further activated by... |
|
Definition
|
|
Term
| the 2 components of the combinatorial control circuit of the Lac operon |
|
Definition
1: Transcription from the Lac promoter occurs when allolactose is present
2: further activation of the Lac promoter by binding of cAMP to CRP |
|
|
Term
| transcription is low when... |
|
Definition
| you can't bind to promoter |
|
|
Term
|
Definition
| artificial inducer of the Lac operon |
|
|
Term
|
Definition
-DNA bound to 2 proteins
-DNA-protein complex |
|
|
Term
| What are the three major classes of bacterial RNA? |
|
Definition
|
|
Term
| most abundant type of bacterial RNA |
|
Definition
|
|
Term
| least abundant type of bacterial RNA |
|
Definition
| mRNA; it's the least stable |
|
|
Term
| How does sigma help RNA polymerase transition from the closed to open promoter complex? |
|
Definition
| changes the binding constant for the promoter; lowers it almost 10,000 fold |
|
|
Term
| What would be the effect of a promoter mutation in the Lac operon? |
|
Definition
| less or no transcription, depending on strength of mutation |
|
|
Term
| Does the Rho transcription termination factor act on DNA or RNA? |
|
Definition
|
|
Term
| In E. coli, the inability of the Lac repressor to bind an inducer would result in... |
|
Definition
no substantial synthesis of b–galactosidase
the repressor would be bound to the operator and you can't get it off |
|
|
Term
| What is the reason for basal level expression of the Lac operon? |
|
Definition
| permease to get a little bit of lactose into the cell |
|
|
Term
| depiction of the difference between prokaryote and eukaryote gene expression |
|
Definition
|
|
Term
| transcription and translation in prokaryotes |
|
Definition
|
|
Term
| transcription and translation in eukaryotes |
|
Definition
| transcribed in nucleus and translated outside of nucleus |
|
|
Term
| One scheme used for activation of transcription by estrogen |
|
Definition
|
|
Term
|
Definition
| nucleosomes wrapped around histone proteins |
|
|
Term
| how estrogen initiates activation of transcription |
|
Definition
| recognizes transcription factor and recruits coactivator |
|
|
Term
| coactivator is activated by... |
|
Definition
|
|
Term
| how activation of transcription by estrogen leads to loosening of DNA |
|
Definition
| acetylation of lysine in the histones |
|
|
Term
| all the steps in activation of transcription by estrogen |
|
Definition
0: Activate transcription factor
1: Recruitment of a coactivator
2: Coactivator recruits HAT, acetylation of lysine residues in the histone tails,
3: Binding of a chromatin remodeling complex to the acetylated lysine residues
4: ATP-dependent remodeling of the chromatin structure to expose DNA
5: Recruitment of RNA polymerase II, starting with TFIID/TBP
6: Mediator stabilizes Pol II, bridges activator, stimulates transcription |
|
|
Term
| depiction of Nuclear hormone receptor activation |
|
Definition
|
|
Term
| depiction of Recruitment of a coactivator triggered by estrogen |
|
Definition
|
|
Term
| what estrogen does to receptor protein |
|
Definition
| causes it to go under allosteric change, making it a good binding site for coactivator |
|
|
Term
|
Definition
| binds to the receptor but “antagonizes” its activation. |
|
|
Term
| estrogen tamoxifen can... |
|
Definition
| activate estrogen ligand in other tissues, such as uterus |
|
|
Term
| depiction of H3 lysine acetylation |
|
Definition
|
|
Term
| Recruitment of chromatin remodelers to acetylated histones |
|
Definition
|
|
Term
| what dictates the next steps after histone acetylation? |
|
Definition
|
|
Term
| some bromodomain proteins |
|
Definition
- Chromatin remodelers, some ATP dependent
- TAFs [TATA-box binding protein associated (TBP), factors], in particular TAF1 |
|
|
Term
| depiction of Assembly of Pol II |
|
Definition
|
|
Term
| depiction of Action of Mediator |
|
Definition
|
|
Term
| when transcription can occur |
|
Definition
| when mediator connects with both transcription factor and RNA polymerase II |
|
|
Term
| how the transcription factor gets activated |
|
Definition
|
|
Term
| how mediator contributes to transcription |
|
Definition
-stabilizes Pol II
-bridges activator
-stimulates transcription |
|
|
Term
|
Definition
| genes required for the function of all cells |
|
|
Term
| what acetylation does to lysine residues in histones |
|
Definition
| causes a charge change; changes it to something that's more acidic |
|
|
Term
|
Definition
| they are very basic proteins |
|
|
Term
| depiction of acetylation of lysine |
|
Definition
|
|
Term
| common method for studying DNA-protein interactions |
|
Definition
| DNA gel shift assay (EMSA) |
|
|
Term
| you can get a supershift if... |
|
Definition
| you have an antibody that's specific to the protein bound to the DNA |
|
|
Term
| depiction of prokaryotic gene expression |
|
Definition
|
|
Term
| depiction of eukaryotic gene expression |
|
Definition
|
|
Term
| some primary transcripts that must be further processed to be active |
|
Definition
|
|
Term
|
Definition
1. Removal of nucleotides
2. Addition of nucleotides
3. Covalent modification of nucleotides
4. Substituting nucleotides |
|
|
Term
| some things that happen in mRNA processing |
|
Definition
- Capping the 5’ end of the mRNA
- pA addition to the 3’ end of the mRNA
- RNA splicing
- RNA editing |
|
|
Term
| in mRNA processing, what goes on the 5' end? |
|
Definition
|
|
Term
| in mRNA processing, what goes on the 3' end? |
|
Definition
|
|
Term
| some reasons mRNA is processed |
|
Definition
- Protect mRNAs from premature degradation (some transcripts are huge)
- Additional levels of gene regulation possible (posttranscriptional)
- Assists in engaging the ribosome |
|
|
Term
| depiction of Capping the 5’ end of mRNA |
|
Definition
|
|
Term
| the nucleotide that's always in the 5' cap |
|
Definition
|
|
Term
| depiction of 3’ polyadenylation of a primary transcript |
|
Definition
|
|
Term
| what 3’ polyadenylation of a primary transcript does for mRNA |
|
Definition
-Stabilizes RNA
-Enhances translation
-Regulated turnover |
|
|
Term
| depiction of the torpedo model for transcription termination (human beta globulin gene) |
|
Definition
|
|
Term
| what disengages mRNA from the DNA strands in eukaryotes? |
|
Definition
| seems to be the torpedo model for transcription termination |
|
|
Term
| Pre-mRNA splicing takes place on... |
|
Definition
|
|
Term
|
Definition
| complexes of 45 proteins & 5 RNAs called small nuclear RNA (snRNA): U1, U2, U4, U5, U6 |
|
|
Term
| depiction of alternate splicing |
|
Definition
|
|
Term
| Advantages of alternative splicing |
|
Definition
| expands the amount of proteins you can make, because you can mix and match exons |
|
|
Term
| molecular basis of thalassemia and muscular dystrophies |
|
Definition
| problems with RNA splicing |
|
|
Term
|
Definition
| often as the mRNA is getting created |
|
|
Term
| depiction of Consensus sequences at splice sites in vertebrates |
|
Definition
|
|
Term
| the object of alternate splicing |
|
Definition
| to remove the intron and join the exons |
|
|
Term
| depiction of Spliceosome assembly and action |
|
Definition
|
|
Term
| what degrades this lariat? |
|
Definition
|
|
Term
| depiction of Intron removal in mRNA precursors |
|
Definition
|
|
Term
| depiction of First transesterifcation in splicing |
|
Definition
|
|
Term
| depiction of formation of a lariat |
|
Definition
|
|
Term
| depiction of separation of lariat from rest of mRNA precursor |
|
Definition
|
|
Term
| what happens to the lariat after it gets separated from the rest of the mRNA precursor? |
|
Definition
| gets degraded; the lariat is the intron |
|
|
Term
| depiction of 2’- 5’ circular lariat |
|
Definition
|
|
Term
| depiction of possible results of splicing mutations |
|
Definition
|
|
Term
| one reason a stop codon ignored in wild type |
|
Definition
| because it's in the intron |
|
|
Term
| when are mutations more severe? when the problem is with the exons or when the problem is with splicing? |
|
Definition
|
|
Term
| depiction of RNA transcription error that has good effect |
|
Definition
|
|
Term
| depiction of Coupling transcription to pre-mRNA processing: CTD |
|
Definition
|
|
Term
| can splicing occur at the same time as transcription? |
|
Definition
|
|
Term
| Genetic code Should explain... |
|
Definition
-how you get from DNA to protein
-heridity
-mutation
-molecular evolution |
|
|
Term
|
Definition
| defects in specific enzymes |
|
|
Term
| some ways the genetic code was deciphered |
|
Definition
-Synthesize or isolate short RNA sequences
-Develop a cell-free protein synthesis extract from E. coli
-Add RNA + individual radioactive amino acids
-Relate incorporation of labeled amino acids to RNA sequence |
|
|
Term
| depiction of the genetic code |
|
Definition
|
|
Term
| some amino acids that are not in the standard 20 |
|
Definition
-Selenocysteine (Archaea, Eubacteria, animals)
-Pyrrolysine (Archaea, bacteria) |
|
|
Term
| depiction of multiple open reading frames in the code |
|
Definition
[image]
the stars are the stop codons |
|
|
Term
| where degeneracy is in the codons |
|
Definition
|
|
Term
| is there any repair or proofreading of proteins? |
|
Definition
|
|
Term
| are there any tRNA's associated with stop codons? |
|
Definition
|
|
Term
| how DNA gets translated depends on... |
|
Definition
| what frame you're translating |
|
|
Term
| depiction of tRNA anatomy |
|
Definition
|
|
Term
| how tRNA links codons with amino acids |
|
Definition
| serves as the adaptor molecule |
|
|
Term
| amino acids are added to tRNA by... |
|
Definition
|
|
Term
| inosine (I) is derived from... |
|
Definition
|
|
Term
| where amino acid is added to the tRNA |
|
Definition
| the A residue at the 3’ end |
|
|
Term
| general depiction of tRNA, anticodon, codon, and amino acid |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| depiction of deamination of adenosine to form inosine |
|
Definition
|
|
Term
| depiction of how inosine binds with C, U, and A |
|
Definition
|
|
Term
| the smart enzymes in protein synthesis |
|
Definition
| Aminoacyl-tRNA synthetases |
|
|
Term
| Aminoacyl-tRNA synthetases |
|
Definition
| synthesize Aminoacyl-tRNAs (specific amino acid covalently attached to 3’ end of specific tRNAs (ie alanyl-tRNAAla) |
|
|
Term
| how many aminoacyl-tRNA synthetases are there? |
|
Definition
| At least 20 (1 per amino acid) |
|
|
Term
|
Definition
| high-energy molecules in which the amino acid has been “activated or charged” |
|
|
Term
| rxn by which aminoacyl-tRNA synthetase activates amino acids |
|
Definition
| Amino acid + tRNA + ATP --> Aminoacyl-tRNA + AMP + PPi |
|
|
Term
| steps of the Activation of amino acid by aminoacyl-tRNA synthetase |
|
Definition
Step 1: ATP + amino acid → aminoacyladenylate intermediate + PP
Step 2: aminoacyl-adenylate + tRNA → aminoacyl-tRNA + AMP |
|
|
Term
| depiction of the entire Activation of amino acid by aminoacyl-tRNA synthetase |
|
Definition
|
|
Term
| what part of the aminoacyl tRNA is used in protein synthesis? |
|
Definition
| the charged or activated tRNA |
|
|
Term
| Determinants of tRNA synthetase specificity |
|
Definition
1. Recognize the correct amino acid
2. Recognize the structure of the tRNA and the anticodon |
|
|
Term
| depiction of Determinants of tRNA synthetase specificity |
|
Definition
|
|
Term
| depiction of Threonyl tRNA synthetase |
|
Definition
|
|
Term
| comparison of Prokaryotic and eukaryotic ribosomes |
|
Definition
|
|
Term
| depiction of Sites for tRNA binding in ribosomes |
|
Definition
|
|
Term
| simple depiction of Position of tRNAs |
|
Definition
|
|
Term
| where prokaryotes and eukaryotes differ in translation |
|
Definition
|
|
Term
|
Definition
1: initiation
2: elongation
3: termination |
|
|
Term
| depiction of Shine-Dalgarno sequence |
|
Definition
|
|
Term
| depiction of Initiation of fMet-tRNA |
|
Definition
|
|
Term
| depiction of The initiation complex |
|
Definition
|
|
Term
| depiction of the Elongation cycle |
|
Definition
|
|
Term
| depiction of Peptide bond formation |
|
Definition
|
|
Term
| depiction of translocation step of translation |
|
Definition
|
|
Term
| what basically happens in translocation |
|
Definition
| polypeptide chain grows from N to C as ribosome moves 5’-3’ |
|
|
Term
| depiction of elongation of polypeptide |
|
Definition
|
|
Term
| direction of protein synthesis |
|
Definition
|
|
Term
| depiction of termination of translation |
|
Definition
|
|
Term
| how initiation occurs in prokaryotes |
|
Definition
| Scans for the first AUG (recognizes Cap, ATP dependent scan) |
|
|
Term
| depiction of how initiation occurs in prokaryotes |
|
Definition
|
|
Term
|
Definition
|
|
Term
| depiction of circular eukaryotic mRNA |
|
Definition
|
|
Term
| table of antibiotic inhibitors of protein synthesis |
|
Definition
|
|
Term
| what step is inhibited when mRNA freezes in position? |
|
Definition
|
|
Term
| how a ricin molecule kills a cell |
|
Definition
| causes elongation factors to be unable to bind |
|
|
Term
| an aspect of translation does not require GTP |
|
Definition
| charging tRNAs because it requires ATP |
|
|
Term
| things that could lead to an increase in the synthesis of a particular protein |
|
Definition
-Shine-Dalgarno sequence because you could make the sequence better
-3’ untranslated region because degradation occurs on the 3' end |
|
|
Term
| where does degradation occur within a gene? |
|
Definition
|
|
Term
| Why aren’t eukaryotic mRNAs polycistronic? |
|
Definition
| Since eukaryotic mRNAs don’t have sequences equivalent to the Shine-Dalgarno sequence, there is no way to identify which internal methionines might be used for initiation. |
|
|
Term
| composition of each monomer in the nucleic acid sequence |
|
Definition
|
|
Term
| this uniquely characterizes a nucleic acid |
|
Definition
| the sequence of bases that forms linear information |
|
|
Term
| depiction of DNA replication |
|
Definition
|
|
Term
| depiction of the polymeric structure of nucleic acids |
|
Definition
|
|
Term
| difference between ribose and deoxyribose |
|
Definition
| deoxyribose lacks the O at the 2' C |
|
|
Term
| depiction of the structure of ribose |
|
Definition
|
|
Term
| depiction of the structure of deoxyribose |
|
Definition
|
|
Term
| how monomers are linked in nucleic acids |
|
Definition
the 3' OH group of the sugar component of one nucleotide binds to the phosphate attached to the 5' C on the adjacent sugar
3' --> 5' phosphodiester linkages |
|
|
Term
| 2 ways RNA differs from DNA |
|
Definition
1: RNA uses riboses instead of deoxyriboses
2: RNA uses U instead of T |
|
|
Term
| one way DNA and RNA maintain stability |
|
Definition
| they have a negative charge, which repels nucleophilic species that would otherwise hydrolyze tham |
|
|
Term
| why DNA is more resistant to hydrolysis than RNA |
|
Definition
| because DNA lacks the 2' OH croup |
|
|
Term
| the backbone of nucleic acids |
|
Definition
|
|
Term
| depiction of the backbones of DNA and RNA |
|
Definition
|
|
Term
|
Definition
|
|
Term
| depiction of the pyrimidines |
|
Definition
|
|
Term
|
Definition
| a unit consisting of a base bonded to a sugar |
|
|
Term
| the 4 nucleoside units in DNA |
|
Definition
-deoxyadenosine
-deoxyguanosine
-deoxycytidine
-thymidine (no, that's not a misprint) |
|
|
Term
| why the prefix deoxy- is not added to thymidine |
|
Definition
| because thymine-containing nucleotides are found only rarely in RNA |
|
|
Term
| the 4 nucleoside units in RNA |
|
Definition
-adenosine
-guanosine
-cytidine
-uridine |
|
|
Term
| the C in the ribose/deoxyribose the nucleotide base is always attached to |
|
Definition
|
|
Term
| the type of linkage in a purine nucleoside |
|
Definition
|
|
Term
| depiction of the β-glycosidic linkage in a purine nucleoside |
|
Definition
|
|
Term
|
Definition
| nucleoside joined to 1 or more phosphoryl groups by an ester linkage |
|
|
Term
| the monomers that link to form DNA and RNA |
|
Definition
| nucleoside triphosphates (this includes ATP!) |
|
|
Term
| 5'nucleotide or nucleoside 5'-phosphate |
|
Definition
| compound formed by the attachment of a phosphoryl group to C-5' of a nucleoside sugar |
|
|
Term
| the most common site of phosphate esterfication |
|
Definition
|
|
Term
|
Definition
adenosine 5'-triphosphate
[image] |
|
|
Term
| the direction a sequence of DNA is written in |
|
Definition
|
|
Term
| depiction of the structure of a DNA strand |
|
Definition
|
|
Term
| replication of DNA is the basis for these cellular processes |
|
Definition
-duplication
-growth
-ultimately, reproduction |
|
|
Term
| distance between adjacent bases in nucleic acids |
|
Definition
|
|
Term
| how many bases does it take for the double helix to go 360⁰? |
|
Definition
|
|
Term
| side view of a DNA double helix |
|
Definition
|
|
Term
| end view of a DNA double helix |
|
Definition
|
|
Term
| some features of the Watson-Crick model |
|
Definition
1: right-handed helix with antiparallel strands
2: the sugar-phosphate backbone is on the outside and the purine and pyrimidine bases are on the inside
3: bases nearly perpendicular to axis, 3.4 angstroms between adjacent bases, and 10.4 bases per turn of helix
4: diameter of the helix is about 20 angstroms |
|
|
Term
| handednes of DNA 2bl helix |
|
Definition
|
|
Term
| diameter of DNA 2bl helix |
|
Definition
|
|
Term
| depiction of the structures of the base pairs proposed by Watson and Crick |
|
Definition
|
|
Term
| 2 forces that stabilize the DNA double helix |
|
Definition
1: hydrophobic effect between bases on opposite strands
2: van der Waals forces between stacked bases, known as base stacking |
|
|
Term
| depiction of semiconservative replication |
|
Definition
|
|
Term
| depiction of the detection of semiconservative replication of E. coli DNA by density-gradient centrifugation |
|
Definition
|
|
Term
| 2 ways to break the DNA double helix |
|
Definition
-heating it to break the H bonds between the bases on opposite strands
-adding acid or alkali to ionize bases and disrupt base pairing |
|
|
Term
|
Definition
| the temperature at which half the helical structure is lost |
|
|
Term
|
Definition
| renaturation of the double helix below the melting temperature (Tm) |
|
|
Term
|
Definition
-B-DNA (this is the form you're already familiar with)
-A-form
-Z-form |
|
|
Term
| depiction of B-form and A-form DNA |
|
Definition
|
|
Term
|
Definition
|
|
Term
| some things that can resemble A-DNA |
|
Definition
-double-stranded regions of RNA
-at least some RNA-DNA hybrids |
|
|
Term
|
Definition
|
|
Term
| why Z-DNA contains the letter Z |
|
Definition
| because the phosphate backbone zig-zags |
|
|
Term
|
Definition
|
|
Term
| comparison of A-, B-, and Z-DNA |
|
Definition
|
|
Term
| 2 types of grooves in B-DNA |
|
Definition
-major groove
-minor groove |
|
|
Term
| why B-DNA has major and minor grooves |
|
Definition
| because the glycosidic bonds of a base pair are not diametrically opposite to each other |
|
|
Term
| depiction of the major- and minor- groove sides of nucleotide pairs |
|
Definition
|
|
Term
| depiction of the major and minor grooves in B-DNA |
|
Definition
|
|
Term
| the importance of grooves in B-DNA |
|
Definition
| exposing potential H-bond donors and acceptors to enable interactions with proteins |
|
|
Term
|
Definition
| the axis of a double helix being twisted into a superhelix |
|
|
Term
| depiction of a negative superhelix |
|
Definition
|
|
Term
| the coiling of most naturally occurring DNA molecules |
|
Definition
|
|
Term
| negative supercoiling arises from... |
|
Definition
| the unwinding or underwinding of DNA |
|
|
Term
| what negative supercoiling does for DNA |
|
Definition
| prepares it for processes requiring separation of the DNA strands, such as replication and transcription |
|
|
Term
| why negative supercoiling is better for DNA than positive supercoiling |
|
Definition
| condenses DNA as effectively, but makes strand separation more difficult |
|
|
Term
| this has to happen to coiled DNA for it to be replicated |
|
Definition
| local unwinding to allow separation of the 2 strands |
|
|
Term
| what local unwinding of DNA causes to happen to the other DNA in the strand |
|
Definition
| overwinding or supercoiling |
|
|
Term
| what prevents the strain induced by overwinding? |
|
Definition
| specialized set of enzymes introduces supercoils that favor strand separation |
|
|
Term
|
Definition
| the final DNA-protein complex |
|
|
Term
|
Definition
| small basic proteins that DNA tightly binds to |
|
|
Term
|
Definition
| the entire complex of a cell's DNA and its associated protein |
|
|
Term
| the 5 major histones present in chromatin |
|
Definition
-H1
-H2A
-H2B
-H3
-H4
H2A, H2B, H3, and H4 associate with one another |
|
|
Term
| histones have strikingly basic properties because... |
|
Definition
| a quarter of the residues in each histone are either arginine or lysine |
|
|
Term
|
Definition
| repeating units, each containing 200 bp of DNA and 2 copies each of H2A, H2B, H3, and H4, called the histone octamer |
|
|
Term
|
Definition
| comtains 2 copies each of H2A, H2B, H3, and H4 |
|
|
Term
|
Definition
the repeating units of chromatin
repeating units, each containing 200 bp of DNA and 2 copies each of H2A, H2B, H3, and H4, called the histone octamer |
|
|
Term
|
Definition
| smaller complex of the histone octamer and the 145-bp DNA fragment |
|
|
Term
|
Definition
| the DNA connecting core particles in undigested chromatin |
|
|
Term
| what binds to linker DNA? |
|
Definition
| histone H1 binds, in part, to the linker DNA |
|
|
Term
| depiction of chromatin structure |
|
Definition
|
|
Term
| depiction of linked core particles |
|
Definition
|
|
Term
| depiction of a nucleosome core |
|
Definition
|
|
Term
| something that is done to histones to affect DNA transcription |
|
Definition
| covalent modifications of their tails play an essential role in modulating the accessibility of DNA for transcription |
|
|
Term
| the handedness of the superhelix that forms around the histone octamer |
|
Definition
|
|
Term
| how the protein core interacts with the superhelix that wraps around it |
|
Definition
| forms contacts with the inner surface of it, particularly along the phosphodiester backbone and the minor groove of the DNA |
|
|
Term
| how histone H1 interacts with the DNA wrapped around the core protein |
|
Definition
| seals off the nucleosome at the location at which the linker DNA enters and leaves the nucleosome |
|
|
Term
| how wrapping around histones contributes to the packing of DNA |
|
Definition
| by decreasing its linear extent |
|
|
Term
| wrapping around histones is just the 1st step in DNA packing. what's the next step? |
|
Definition
it's thought to be nucleosomes being packed into 2 interwound helical stacks; folding of nucleosomes into loops
this is higher order chromatin structure |
|
|
Term
| depiction of higher-order chromatin structure |
|
Definition
|
|
Term
| depiction of the compaction of DNA into a eukaryotic chromosome |
|
Definition
|
|
Term
| depiction of how cispaltin alters the structure of DNA |
|
Definition
|
|
Term
| why RNA can perform a host of functions that DNA can not |
|
Definition
because RNA is single stranded, enabling it to adopt a variety of elaborate structures
this includes some functions that were once thought to be exclusively done by proteins |
|
|
Term
| the simplest and most common structural motif in nucleic acids |
|
Definition
|
|
Term
| depiction of stem-loop structures |
|
Definition
|
|
Term
| some things that can happen to stem-loop structures |
|
Definition
-many have paired bases
-some have mismatched or unpaired bases that can bulge out and destabilize local structure, but introduce deviations from the standard 2bl helix that can be important for higher order folding and for function |
|
|
Term
| how some more complex structures in nucleic acids can form |
|
Definition
| by way of interactions between more distant bases |
|
|
Term
| depiction of the complex structure of an RNA molecule |
|
Definition
|
|
Term
|
Definition
catalyze the copying of DNA sequences
promote the formation of the phosphodiester linkages joining the units of the ADNA backbone |
|
|
Term
| the types of DNA polymerases |
|
Definition
-polymerase I
-polymerase II
-polymerase III
-polymerase IV
-polymerase V |
|
|
Term
| the better understood DNA polymerases |
|
Definition
-polymerase I
-polymerase II |
|
|
Term
| function of DNA polymerase I |
|
Definition
| primer removal and DNA repair |
|
|
Term
| function of DNA polymerase II |
|
Definition
| repairs attachment of bulky hydrocarbons to bases |
|
|
Term
| function of DNA polymerase III |
|
Definition
|
|
Term
| function of DNA polymerase IV |
|
Definition
| repairs attachment of bulky hydrocarbons to bases |
|
|
Term
| function of DNA polymerase V |
|
Definition
| repairs attachment of bulky hydrocarbons to bases |
|
|
Term
| additional enzyme activities of DNA polymerase I |
|
Definition
|
|
Term
| additional enzyme activities of DNA polymerase II |
|
Definition
|
|
Term
| additional enzyme activities of DNA polymerase III |
|
Definition
|
|
Term
| additional enzyme activities of DNA polymerase IV |
|
Definition
|
|
Term
| table of E. coli DNA polymerases |
|
Definition
|
|
Term
| DNA polymerases catalyze... |
|
Definition
| the step-by-step addition of deoxyribonucleotides to a DNA strand |
|
|
Term
| rxn of the addition of DNA strands, in its simplest form |
|
Definition
| (DNA)n + dNTP <--> (DNA)n + 1 PPi |
|
|
Term
|
Definition
|
|
Term
|
Definition
| sequence of nucleic acids that determines the sequence of a complementary nucleic acid |
|
|
Term
| depiction of a polymerization rxn catalyzed by DNA polymerases |
|
Definition
|
|
Term
| some characteristics of DNA synthesis |
|
Definition
| 1: requires all 4 aqctivated precursors -- that is, the deoxynucleoside 5'-triphosphates dATP, dGTP, dCTP, and TTP -- as well as the Mg2+ ion
2: the new DNA strand is assembled directly onto a preexisting DNA template; the DNA polymerase is a template-directed enzyme that synthesizes a complementary product
3: DNA polymerases require a primer to begin synthesis. Elongation proceeds from 5' to 3' direction
4: many DNA polymerases are able to correct mistakes by removing mismatched nucleotides |
|
|
Term
| what is required for DNA synthesis to occur? |
|
Definition
| -deoxynucleoside 5'-triphosphates
-Mg+2 ion |
|
|
Term
| the deoxynucleoside 5'-triphosphates |
|
Definition
|
|
Term
| how the phosphodiester bond between adjacent nucleotides is formed |
|
Definition
| nucleophilic attack by the 3' end of the growing strand on the innermost P atom of the dinucleoside triphosphate (dNTP) |
|
|
Term
|
Definition
| initial segment of of a polymer that is to be extended on which elongation depends |
|
|
Term
| the 3 distinct active sites of DNA polymerase I |
|
Definition
-polymerase site
-3' --> 5' exonuclease site
-5' --> 3' exonuclease site |
|
|
Term
| what the 3' --> 5' nuclease activity of DNA polymerase I does |
|
Definition
| contributes to the remarkable high fidelity of DNA replication; error rate is less than 10-8 base pair |
|
|
Term
| error rate of DNA replication |
|
Definition
|
|
Term
| depiction of the strand-elongation rxn |
|
Definition
|
|
Term
| depiction of DNA polymerase structure (Klenow fragment) |
|
Definition
|
|
Term
| depiction of shape complementarity of bases (in this case, adenosine) |
|
Definition
|
|
Term
| one reason DNA polymerase has such a low error rate |
|
Definition
| conformational change by induced fit triggered by the binding of a dNTP into the active site such that it forms a tight pocket in which only a properly shaped base will fit |
|
|
Term
| depiction of shape selectivity of DNA polymerase |
|
Definition
|
|
Term
| depiction of the helicase mechanism |
|
Definition
|
|
Term
|
Definition
|
|
Term
| negative supercoiling arises from... |
|
Definition
| the unwinding or underwinding of DNA |
|
|
Term
| negative supercoiling prepares DNA for... |
|
Definition
| processes requiring separation of the DNA strands, such as replication |
|
|
Term
| what unwinding of part of a strand does to adjacent DNA |
|
Definition
|
|
Term
| why DNA must be locally unwound |
|
Definition
| to expose single-stranded templates for replication |
|
|
Term
| depiction of the consequences of strand separation |
|
Definition
|
|
Term
|
Definition
| to move in a circle or spiral or to revolve, usually about a fixed point or on an axis |
|
|
Term
|
Definition
| introduce or eliminate supercoils by temporarily cleaving DNA |
|
|
Term
|
Definition
| catalyze the relaxation of supercoiled DNA, which is thermodynamically favorable |
|
|
Term
|
Definition
| utilize free energy from hydrolysis to add negative supercoils to DNA |
|
|
Term
|
Definition
| type II topoisomerases in bacteria |
|
|
Term
| function of the exonuclease on DNA polymerase I |
|
Definition
| removes mismatched nucleotides from the 3' end of DNA by hydrolysis |
|
|
Term
| why it's easy for mismatched nucleotides to be removed |
|
Definition
weaker H bonding due to mismatch of nucleotides makes the malformed product flop around and be hot held as tightly in the polymerase active site
it finds itself in the exonuclease active site, where the trespassing nucleotide is removed |
|
|
Term
| depiction of proofreading of DNA |
|
Definition
|
|
Term
| what happens if an incorrect base is incorporated into the DNA strand? |
|
Definition
enzyme stalls due to structural disruption caused by the mismatch
the pause gives it time to wander into te exonuclease active site |
|
|
Term
| cost of exonuclease activity |
|
Definition
| DNA polymerase I removes about 1 correct nucleotide in 20; slight wasteful energetically |
|
|
Term
| origin of replication (oriC locus) |
|
Definition
| unique site within the genome where replication begins |
|
|
Term
|
Definition
|
|
Term
| what the origin of replication is in E. coli |
|
Definition
| a 245-bp region that has several unusual features |
|
|
Term
| composition of the oriC locus in E. coli |
|
Definition
-binding sites for DnaA protein
-tandem array of 13-bp sequences (AT rich) |
|
|
Term
|
Definition
| structure in the E. coli chromosome where replication begins |
|
|
Term
| how the prepriming complex is formed |
|
Definition
1: oriC locus wraps around DnaA protein
2: DnaB (a helicase) unwinds strand, including AT rich regions
3: single-strand-binding proteins (SSB) bind to newly generated single strands, preventing re-forming of 2bl helix |
|
|
Term
| depiction of the origin of replication in E. coli and formation of the prepriming complex |
|
Definition
|
|
Term
| depiction of the oriC locus in E. coli |
|
Definition
| refer to p. 634 (figure 34.11 A) |
|
|
Term
| DNA polymerases can add nucleotides only to... |
|
Definition
|
|
Term
| why a primer is required for DNA synthesis |
|
Definition
| because DNA polymerases can't start a strand de novo |
|
|
Term
| what primes the synthesis of DNA? |
|
Definition
|
|
Term
|
Definition
| specialized RNA polymerase that joins the prepriming complex in a multisubunit assembly called the primosome |
|
|
Term
|
Definition
| multisubunit assembly that primase joins the prepriming complex in |
|
|
Term
|
Definition
| synthesizes a stretch of about 10 RNA nucleotides that is complementary to one of the template DNA strands |
|
|
Term
| what removes the RNA primer? |
|
Definition
|
|
Term
|
Definition
|
|
Term
| depiction of DNA replication at low resolution |
|
Definition
|
|
Term
| how Okazaki fragments are joined |
|
Definition
| covalently by way of DNA ligase, which uses ATP hydrolysis to power the joining of DNA fragments |
|
|
Term
|
Definition
| strand formed from Okazaki fragments |
|
|
Term
|
Definition
| strand synthesized continuously 5' --> 3' |
|
|
Term
| depiction of Okazaki fragments |
|
Definition
|
|
Term
| the enzyme responsible for the rapid and accurate synthesis of DNA in E. coli |
|
Definition
| the holoenzyme DNA polymerase III |
|
|
Term
| hallmarks of the holoenzyme DNA polymerase III |
|
Definition
-its fidelity
-its very high catalytic potency
-its processitivity |
|
|
Term
|
Definition
| the ability of an enzyme to catalyze many consecutive rxns without releasing its substrate |
|
|
Term
| the amount of phosphodiester linkages formed by the holoenzyme DNA polymerase III before releasing its template |
|
Definition
| many thousands, compared with only 20 for DNA polymerase I |
|
|
Term
| catalytic potency of the holoenzyme DNA polymerase III |
|
Definition
| adds 1000 nucleotides per second compared to only 10 per second by DNA polymerase I |
|
|
Term
| why the holoenzyme DNA polymerase III is able to add 1000 nucleotides per second |
|
Definition
| largely because of its processitivity |
|
|
Term
| the source of the holoenzyme DNA polymerase III's processitivity |
|
Definition
| the β2 subunit, which has the form of a star shaped ring that can readily accommodate the DNA strand, encircle it, and spin around it to add nucleotides |
|
|
Term
| function of the β2 subunit in the holoenzyme DNA polymerase III |
|
Definition
| functions as a sliding clamp that spins around the molecule and adds nucleotides as it spins |
|
|
Term
| depiction of the structure of a sliding DNA clamp (the β2 subunit in the holoenzyme DNA polymerase III) |
|
Definition
|
|
Term
| how DNA gets into the β2 subunit in the holoenzyme DNA polymerase III |
|
Definition
| by way of sliding clamp loaders |
|
|
Term
|
Definition
| unwinds the DNA duplex ahead of the DNA polymerase |
|
|
Term
| single-strand-binding proteins |
|
Definition
| they bind to unwound strands to keep the strands separated so that both strands can serve as templates |
|
|
Term
|
Definition
| introduces negative supercoils ahead of the replication fork to avoid a topological crisis |
|
|
Term
| depiction of the replication fork |
|
Definition
|
|
Term
| depiction of the DNA polymerase holoenzyme |
|
Definition
|
|
Term
| the DNA polymerase holoenzyme consists of... |
|
Definition
-2 copies of the polymerase core enzyme linked to a central structure
-the central structure includes the clamp-loader complex, which binds to the hexameric helicase Dnab |
|
|
Term
| what fills the gaps between fragments of the nascent lagging strand in the trombone model? |
|
Definition
|
|
Term
| what removes the RNA primers in the lagging strand? |
|
Definition
| the 5' --> 3' exonuclease activity in DNA polymerase I |
|
|
Term
| why DNA polymerase III can't erase the RNA primers |
|
Definition
| because it doesn't have 5' --> 3' editing capacity |
|
|
Term
| how DNA ligase joins fragments of DNA |
|
Definition
| catalyzes the formation of a phosphodiester linkage between the 3'-hydroxyl group at the end of one DNA chain and the 5'-phosphate group at the end of the other |
|
|
Term
| depiction of the trombone model |
|
Definition
|
|
Term
| depiction of the DNA ligase rxn |
|
Definition
refer to p. 638
this is how it occurs in archaea and eukaryotes |
|
|
Term
| why DNA synthesis is more complex in eukaryotes than in bacteria |
|
Definition
-size of genome
-eukaryotes have pairs of chromosomes that must be replicated
-eukaryotes have linear instead of circular chromosomes
-the nature of DNA synthesis on the lagging strand; linear chromosomes subject to shporteninbg on each round of replication unless countermeasures are taken |
|
|
Term
| how the challenges of size of genome and number of chromosomes are dealt with |
|
Definition
| multiple origins of replication |
|
|
Term
| how far apart are the different origins of replication? |
|
Definition
| 30-300 kilobase pairs (kbp) apart |
|
|
Term
| how many origins of replication are in humans? |
|
Definition
| about 30,000, with each chromosome having several hundred |
|
|
Term
|
Definition
|
|
Term
|
Definition
proteins that bind to the origin of replication and permit (license) the DNA synthesis initiation complex
they ensure that each each replicon is replicated only once in each round of DNA synthesis |
|
|
Term
| how replicons are controlled such that each replicon is replicated only once in each cell division |
|
Definition
licensing factors bind to the origin of replication and get destroyed after the initiation of the initiation complex
license expires after 1 use |
|
|
Term
| the 2 distinct polymerases needed to copy a eukaryotic replicon |
|
Definition
-DNA polymerase α
-DNA polymerase δ |
|
|
Term
|
Definition
begins the copying of a replicon
includes primase subunit to synthesize RNA primer as well as an active DNA polymerase
adds about 20 deoxynucleotides to the primer |
|
|
Term
|
Definition
replaces DNA polymerase α
more processive than DNA polymerase α and is the principal replicative polymerase in eukaryotes |
|
|
Term
|
Definition
| DNA polymerase α being replaced by DNA polymerase δ |
|
|
Term
| complications introduced by having linear chromosomes |
|
Definition
-unprotected termini at the ends of chromosomes more vulnerable to digestion by exonuclease if left to dangle at the end of the chromosome during replication
-complete replication of DNA ends is difficult because polymerases act in 5' --> 3' direction and the lagging strand would have an incomplete 5' end after the removal of the RNA primer; each round of replication would shorten the chromosome |
|
|
Term
| depiction of telomere shortening |
|
Definition
|
|
Term
|
Definition
| the DNA at the end of a chromosome; consists of hundreds of repeats of a hexanucleotide sequence characteristic of the organism |
|
|
Term
| the most notable feature of telomeric DNA |
|
Definition
| it contains hundreds of tandem repeats of a hexanucleotide sequence |
|
|
Term
| how the telomere is structured in humans |
|
Definition
one of the strands is G rich at the 3' end and is slightly longer than the other
it is proporsed to loop back to form a DNA duplex with another part of the repeating sequence, displacing part of the original telomeric duplex |
|
|
Term
| the G rich repeating strand in human telomeres |
|
Definition
|
|
Term
| depiction of a proposed model for telomeres |
|
Definition
|
|
Term
| the simplest source of damage in the DNA double helix |
|
Definition
| errors introduced in the replication process |
|
|
Term
| how mismatching DNA bases causes damage |
|
Definition
| distorts double helix, which can become mutagenic |
|
|
Term
| how a mismatch of bases is mutagenic |
|
Definition
| results in daughter helices with different sequences |
|
|
Term
| some types of errors in DNA |
|
Definition
-mismatches
-insertions
-deletions
-breaks in one or both strands |
|
|
Term
| how errors in DNA can inhibit replication |
|
Definition
| replicative polymerases can stall or fall off the damaged template entirely, making replication of the genome halt before it's complete |
|
|
Term
| one way to repair damage in DNA |
|
Definition
| translesion or error-prone polymerases |
|
|
Term
| function of translesion or error-prone polymerases |
|
Definition
| allow for the completion of a draft sequence of the damaged area of the genome that can be at least partly repaired by DNA-repair processes |
|
|
Term
| drawback to the use of translesion or error-prone polymerases |
|
Definition
| substantially more error prone than other polymerases when replicating DNA |
|
|
Term
| depiction of triplet-repeat expansion |
|
Definition
|
|
Term
| bases in DNA can be damaged by... |
|
Definition
-oxidizing agents
-alkylating agents
-light |
|
|
Term
|
Definition
| chemical agents that alter specific bases within DNA after replication is complete |
|
|
Term
| how hydroxyl radical (a reactive oxygen species) is mutagenic |
|
Definition
| converts guanine to 8-oxoguanine, which is mutagenic because it pairs with adenine instead of cytosine |
|
|
Term
| depiction of guanine oxidation |
|
Definition
refer to p. 645
this is mutagenic |
|
|
Term
| how deamination causes mutations |
|
Definition
| example: deaminates adenine to form hypoxanthine, which pairs with cytosine instead of thymine |
|
|
Term
| depiction of adenine deamination |
|
Definition
refer to p. 645
this causes mutations |
|
|
Term
|
Definition
| aflatoxin B1, which is produced by molds that grow on peanuts and other foods |
|
|
Term
| how aflatoxin B1 causes mutations |
|
Definition
| cytochrome P450 enzyme converts it into a highly reactive epoxide, which reacts with the N-7 atom of guanine to form a mutagenic adduct that binds with adenine instead of cystine |
|
|
Term
| depiction of aflatoxin B1 activation |
|
Definition
refer to p. 646
causes mutations |
|
|
Term
| the most pertvasive DNA-damaging agent |
|
Definition
| the UV light from sunlight |
|
|
Term
|
Definition
| by covalently linking adjacent pyrimidine residues along the DNA strand |
|
|
Term
| depiction of a cross-linked dimer of 2 thymine bases |
|
Definition
|
|
Term
| how high energy em radiation, such as X-rays, damages DNA |
|
Definition
by producing high concentrations of reactive chemicals
also causes sinbgle- and double-stranded breaks |
|
|
Term
| many systems repair DNA by... |
|
Definition
| using sequence information from the uncompromised strand |
|
|
Term
| mechanistic outline followed by many single-strand replication systems |
|
Definition
1: recognize the offending base(s)
2: remove the offending base(s)
3: repair the resulting gap with a DNA polymerase ad a DNA ligase |
|
|
Term
| a mechanism in essentially all cells that corrects errors not corrected by proofreading |
|
Definition
|
|
Term
| how mismatch repair works in E. coli |
|
Definition
1: detecting mismatch
2: removing part of the strand containing the mismatch
3: replace it with correct sequence |
|
|
Term
| the mismatch repair proteins in E. coli |
|
Definition
|
|
Term
| the endonuclease in E. coli |
|
Definition
|
|
Term
| depiction of mismatch repair |
|
Definition
|
|
Term
| how mismatch repair machinery determines incorrect base in E. coli |
|
Definition
| some adenine bases in the parent strand are methylated, whereas the newly synthesized daughter strand is not yet methylated. thus, the machinery recognizes that the methylated base is correct and the unmethylated mismatch is incorrect |
|
|
Term
|
Definition
| repairing damage to DNA without having to remove any fragments of the DNA |
|
|
Term
|
Definition
| a photoreactivating enzyme that direct repairs DNA by photochemical cleavage of pyrimidine dimers |
|
|
Term
| how photochemical cleavage works |
|
Definition
| photolytic enzyme binds to distorted region and absorbs photon to form an excited state that cleaves the dimer into its component bases |
|
|
Term
| what happens to damaged bases in E. coli? |
|
Definition
|
|
Term
|
Definition
| replacing damaged bases with undamaged bases |
|
|
Term
| depiction of base-excision repair |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
| site in DNA strand devoid of base |
|
|
Term
|
Definition
| knicks the backbone adjacent to the missing base |
|
|
Term
| deoxyribose phosphodiesterase |
|
Definition
| excites residual phosphate unit |
|
|
Term
| role of DNA polymerase I in base-excision repair |
|
Definition
| inserts undamaged nucleotide |
|
|
Term
| how the base-excision-repair system know to remove T in the T-G pair |
|
Definition
| because the C-->T mutation is so common |
|
|
Term
| depiction of the deamination of 5-methylcytosine forms thymine. |
|
Definition
|
|
Term
| what mechanism recognizes improper nucleotide pairs that escape the base-excision-repair system? |
|
Definition
| nucleotide-excision repair |
|
|
Term
| what the nucleotide-excision repair system does |
|
Definition
| recognizes distortions in the DNA double-helix caused by the presence of a damaged base |
|
|
Term
| depiction of nucleotide-excision repair |
|
Definition
|
|
Term
|
Definition
| in nucleotide-excision repair, this cuts out DNA sequence that contains the defective base |
|
|
Term
| why DNA uses thymine instead of uracil |
|
Definition
-cytosine spontaneously deaminates to form uracil
-thymine contains methyl group, but uravil instead contains an H in that place
-thus, the methyl group is a tag that distinguishes thymine from deaminated cytosine, which is uracil; this mechanism enhances the fidelity of the genetic message |
|
|
Term
| depiction of uracil repair |
|
Definition
|
|
Term
|
Definition
| hydrolyzes the glycosidic bond between the uracil and deoxyribose moieties, but does not attack thymine-containing nucleotides |
|
|
Term
| double-strand breaks arise when... |
|
Definition
|
|
Term
| one thing that can cause replication to stall |
|
Definition
| when the polymerase encounters an unrepaired nick in one of the template strands at the replication fork |
|
|
Term
| depiction of generation of a double-strand break |
|
Definition
|
|
Term
| things that can cause double-strand breaks |
|
Definition
-unrepaired nicks
-ionizing radiation, such as gamma rays and X-rays |
|
|
Term
| what happens when the replication machinery encounters a nick in the DNA? |
|
Definition
| the replication fork collapses, leaving a double-stranded break on one of the daughter helices |
|
|
Term
| types of ionizing radiation that can cause double-stranded breaks |
|
Definition
-x-rays
-gamma rays
they are powerful enough to break the DNA backbone |
|
|
Term
| where recombination is most efficient |
|
Definition
| between stretches of DNA that are similar in sequence |
|
|
Term
|
Definition
| parent DNA duplexes align at regions of sequence similarity, and new DNA molecules are formed by the breaking and joining of homologous segments |
|
|
Term
| one key protein in recombination in humans |
|
Definition
| RAD 51, which is an ATPase that binds single-stranded DNA |
|
|
Term
| depiction of repair of double-strand break by using recombination |
|
Definition
|
|
Term
| something recombination between alleles can be used for |
|
Definition
| generation of new DNA sequences and molecular diversity |
|
|
Term
| a biochemical tool recombination is the foundation for |
|
Definition
-gene knock-out
-gene knock-in |
|
|
Term
|
Definition
|
|
Term
|
Definition
| specific gene is inserted |
|
|
Term
| depiction of RNA polymerase |
|
Definition
|
|
Term
| the role of Mg2+ in RNA polymerase |
|
Definition
| part of the active site at the center of the structure |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| the 2 substrates required by RNA polymerase |
|
Definition
-DNA template strand
-nucleoside triphosphates |
|
|
Term
| the ribonucleoside triphosphates that are usen to synthesize RNA |
|
Definition
|
|
Term
| 2 divalent metal cations that can work in RNA polymerase |
|
Definition
|
|
Term
| depiction of complementarity between mRNA and DNA |
|
Definition
|
|
Term
|
Definition
| (RNA)n residues + ribonucleoside triphosphate <--> (RNA)n+1 residues + PPi |
|
|
Term
| difference between RNA polymerase and DNA polymerase |
|
Definition
| RNA polymerase doesn't require a primer |
|
|
Term
| depiction of the RNA strand-elongation rxn |
|
Definition
|
|
Term
|
Definition
| the segments of DNA that encode the various species of RNA |
|
|
Term
| 3 types of RNA in all cells |
|
Definition
|
|
Term
| composition of the RNA polymerase holoenzyme |
|
Definition
|
|
Term
| role of the σ subunit in the RNA polymerase holoenzyme |
|
Definition
-helps to find a site where transcription begins
-participates in the initiation of RNA synthesis
-it then dissociates from the rest of the enzyme |
|
|
Term
| composition of the RNA polymerase core enzyme |
|
Definition
|
|
Term
| table of the subunits of E. coli RNA polymerase |
|
Definition
|
|
Term
| the 3 stages of RNA synthesis |
|
Definition
1: initiation
2: elongation
3: termination |
|
|
Term
| how RNA polymerase knows where to begin transcription |
|
Definition
| promoters direct it to the proper site |
|
|
Term
| where the promoters are in DNA |
|
Definition
| about 10 and 35 nucleotides upstream of the start site |
|
|
Term
| depiction of bacterial promoter sequences |
|
Definition
|
|
Term
| depiction of consensus (average) sequences deduced from the analysis of many promoters |
|
Definition
|
|
Term
| how strength of promoter affects transcription |
|
Definition
| genes with stronger promoters get transcribed more frequently |
|
|
Term
|
Definition
| regulatory proteins that bind to specific sequences near promoter sites and interact with RNA polymerase |
|
|
Term
| how the upstream element (UP element) increases efficiency of transcription |
|
Definition
| by binding to the α subunit of RNA polymerase, creating an additional binding site for the polymerase |
|
|
Term
| the role of the σ subunit in RNA polymerase |
|
Definition
| helps to recognize promoter sites |
|
|
Term
| how the σ subunit helps RNA polymerase recognize promoter sites |
|
Definition
| 1: decreases affinity of RNA polymerase for general regions of DNA by a factor of 104, allowing t to slide rapidly in search of the promoter
2: enables RNA polymerase to recognize promoter sites |
|
|
Term
| depiction of the RNA polymerase holoenzyme complex |
|
Definition
|
|
Term
| depiction of how sigma factors act catalytically |
|
Definition
|
|
Term
| depiction of DNA unwinding |
|
Definition
|
|
Term
| depiction of RNA strand growth |
|
Definition
|
|
Term
|
Definition
region containing RNA polymerase, DNA, and nascent RNA
contains "bubble" of about 17 separated base pairs |
|
|
Term
| depiction of transcription bubble |
|
Definition
|
|
Term
| depiction of RNA-DNA hybrid separation |
|
Definition
|
|
Term
| why the higher error rate of RNA polymerase can be tolerated |
|
Definition
| because mistakes in RNA are not transmitted to progeny |
|
|
Term
|
Definition
| RNA polymerase can backtrack and remove the incorrect nucleotide using its inherent nuclease activity |
|
|
Term
|
Definition
termination of DNA transcription onto RNA within or just after a GC rich stem-and-loop structure followed by 4 U residues
terminates within or just after the termination signal |
|
|
Term
| depiction of termination signal |
|
Definition
|
|
Term
| how the combination hairpin-oligo(U) strucvture terminates transcription |
|
Definition
1: RNA polymerase appears to pause immediately after synthesising sequence that folds into a hairpin
2: RNA-DNA hybrid helix in the oligo(U) tail is unstable because rU-dA base pairs are the weakest of the Watson-Crick base pairs, thus allowing the pause caused by the hairpin to dissociate from the DNA template and the enzyme |
|
|
Term
| protein-dependent termination |
|
Definition
| termination that requires the participation of with ATPase activity caller the rho (p) protein |
|
|
Term
| how the rho (p) protein terminates RNA transcription |
|
Definition
1: hexameric p gets brought into action by sequences rich in C and poor in G
2: p then races down the strand searching for the RNA polymerase
3: p collides with RNA polymerase at the transcription bubble, breaking the RNA-DNA hybrid helix, unwinding the hybrid helix and stopping transcription |
|
|
Term
| common feature of protein-independent and protein-dependent termination |
|
Definition
| the functioning signals lie in the RNA rather than the DNA |
|
|
Term
| depiction of the mechanism for the termination of transcription by p protein |
|
Definition
|
|
Term
| tRNA and rRNA are generated by... |
|
Definition
| cleavage and other modifications of the transcription product |
|
|
Term
|
Definition
| noncoding regions of RNA product |
|
|
Term
| depiction of primary transcript of RNA |
|
Definition
|
|
Term
| S value vs. how fast RNA molecules move in a centrifugal field |
|
Definition
| the larger the S value, the larger the molecule moves |
|
|
Term
| some ways rRNA's and tRNA's are processed |
|
Definition
-excision from precursor
-addition of nucleotides to the termini of some strands (common for tRNA)
-modification of bases and ribose units |
|
|
Term
| type of RNA processing common for tRNA |
|
Definition
| addition of nucleotides to termini of molecules |
|
|
Term
| how bases and ribose units are modified in mRNA and tRNA |
|
Definition
-some bases being methylated (bacteria)
-unusual bases formed in all tRNA molecules by the enzymatic modification of a standard ribonucleotide in a tRNA precursor |
|
|
Term
| depiction of base pair modifications in RNA |
|
Definition
|
|
Term
| depiction of antibiotic action |
|
Definition
|
|
Term
| an essential enzyme in the metabolism of lactose |
|
Definition
|
|
Term
|
Definition
| hydrolyzes lactose into galactose and glucose |
|
|
Term
| depiction of β-galactosidase induction |
|
Definition
|
|
Term
| the 2 other proteins that are synthesized when β-galactosidase is synthesized |
|
Definition
-galactoside permease
-thiogalactoside transacetylase |
|
|
Term
| function of galactoside permease |
|
Definition
| it is required for the transport of lactose across the bacterial cell membrane |
|
|
Term
| function of thiogalactoside transacetylase |
|
Definition
| not essential for lactose metabolism, but may play a role in the detoxification of compounds that also may be transported by the permease |
|
|
Term
|
Definition
| coordinated unit of genes that cnahge expression in response to environmental changes |
|
|
Term
| the DNA components of the regulatory system of the lac operon |
|
Definition
-regulator gene
-operator site
-set of structural genes |
|
|
Term
| depiction of the general structure of an operon |
|
Definition
|
|
Term
| depiction of the lac operon |
|
Definition
|
|
Term
which part of the lac operon is i?
[image] |
|
Definition
| the gene encoding the repressor |
|
|
Term
which part of the lac operon is o?
[image] |
|
Definition
|
|
Term
which part of the lac operon is z?
[image] |
|
Definition
| structural gene for β-galactosidase |
|
|
Term
which part of the lac operon is y?
[image] |
|
Definition
|
|
Term
which part of the lac operon is a?
[image] |
|
Definition
|
|
Term
which part of the lac operon is p?
[image] |
|
Definition
|
|
Term
| function of the promoter site in the lac operon |
|
Definition
| directs the RNA polymerase to the correct transcription-initiation site |
|
|
Term
| function of the z, y, and a proteins |
|
Definition
| they are transcribed to yield a single mRNA molecule that codes for all 3 proteins |
|
|
Term
| polygenic or polycistronic transcript |
|
Definition
| mRNA molecule encoding more than 1 protein |
|
|
Term
| how does the lac repressor inhibit the expression of the lac operon? |
|
Definition
| in the absence of lactose, the repressor binds very tightly to the operator to block the bound RNA polymerase from using the DNA as a template |
|
|
Term
| how the repressor is removed from the lac operon |
|
Definition
| inducer binds to repressor, causing a structural change that greatly reduces the affinity of the repressor for the operator DNA |
|
|
Term
| depiction of the induction of the lac operon |
|
Definition
|
|
Term
| a type of lac operon inducer |
|
Definition
|
|
Term
|
Definition
| combination of galactose and glucose with an α-1,6 rather than an α-1,4 linkage |
|
|
Term
| what generates allolactose? |
|
Definition
| it's a side product of the few molecules of β-galactosidase that are always present before induction |
|
|
Term
| structure of 1,6-allolactose |
|
Definition
|
|
Term
| one DNA-sequence specific protein that stimulates the transcription of the lac operon when glucose is in short supply |
|
Definition
| catabolite activator protein (CAP), aka cyclic AMP (cAMP) response protein (CRP) |
|
|
Term
|
Definition
| in this case, it's glucose inhibiting the expression of the lac operon |
|
|
Term
| cellular glucose concentration vs. concentration of cAMP |
|
Definition
|
|
Term
| depiction of the binding site forcatabolite activator protein (CAP) |
|
Definition
|
|
Term
| how the level of cAMP is controlled in bacteria |
|
Definition
-enzyme IIA (EIIA) is phosphorylated at the expense of the glycolytic intermediate phosphoenolpyruvate
-phosphorylated EIIA then transfers phosphate to glucose, generating G6P
-if glucose is absent, phosphorylated EIIA activates adenylate cyclase, leading to an increase in cAMP and enhanced transcription of the lac operon |
|
|
Term
|
Definition
| mRNA molecules that form secondary structures capable of binding small molecules, thus preventing further transcription of mRNA |
|
|
Term
| how multicellular eukaryotes differentiate cells, in general |
|
Definition
| they differentially use transcriptional regulation of DNA common to all cells to create different cell types |
|
|
Term
| 3 important characteristics unique to eukaryotes that influence gene expression |
|
Definition
1: more complex transcriptional regulation
2: RNA processing
3: nuclear membrane |
|
|
Term
| depiction of transcription and translation |
|
Definition
|
|
Term
| how many types of RNA polymerases are there in bacteria? |
|
Definition
|
|
Term
| how many types of RNA polymerases are there in eukaryotes? |
|
Definition
|
|
Term
| table of the different types of eukaryotic RNA polymerases |
|
Definition
|
|
Term
| location of RNA polymerase I |
|
Definition
|
|
Term
| location of RNA polymerase II |
|
Definition
|
|
Term
| location of RNA polymerase III |
|
Definition
|
|
Term
| what RNA polymerase I synthesizes |
|
Definition
-18S rRNA
-5.8S rRNA
-28S rRNA |
|
|
Term
| what RNA polymerase II synthesizes |
|
Definition
|
|
Term
| what RNA polymerase III synthesizes |
|
Definition
|
|
Term
| depiction of additional classes of RNA |
|
Definition
|
|
Term
| something unique about RNA polymerase II |
|
Definition
| contains carboxyl-terminal domain (CTD) |
|
|
Term
| how RNA polymerase II is regulated |
|
Definition
| by phosphorylation mainly on the serine residues of the carboxyl-terminal domain (CTD) |
|
|
Term
| what phosphorylation of the carboxyl-terminal domain (CTD) does to RNA polymerase II |
|
Definition
| enhances transcription and recruits other factors required to process the RNA polymerase II product |
|
|
Term
| some types of eukaryotic RNA polymerase promoters |
|
Definition
-RNA polymerase I promoters
-RNA polymerase II promoters
-RNA polymerase III promoters |
|
|
Term
| depiction of common eukaryotic promoter elements (RNA promoters) |
|
Definition
|
|
Term
| characteristics of promoters for RNA polymerase I |
|
Definition
| have one at the start site (ribosomal initiator element (rInr)) and one 125-150 bp upstream of the start site (upstream promoter element (UPE)) |
|
|
Term
| ribosomal initiator element (rInr) |
|
Definition
| a sequence at the transcription start site that helps recruit RNA polymerase I to start transcription |
|
|
Term
| upstream promoter element (UPE) |
|
Definition
| sequence 150-200 bp further upstream of ribosomal initiator element (rInr); helps recruit RNA polymerase I to initiate transcription |
|
|
Term
| how ribosomal initiator element (rInr) and upstream promoter element (UPE) aid transcription |
|
Definition
| by binding proteins that recruit RNA polymerase I |
|
|
Term
| how transcription gets started |
|
Definition
| ribosomal initiator element (rInr) and upstream promoter element (UPE) aid transcription by binding proteins that recruit RNA polymerase I |
|
|
Term
| characteristics of promoters for RNA polymerase II |
|
Definition
-have set of conserved-sequence elements that define the start site and include the polymerase
-can contain any combination of possible elements, such as enhancer elements, which are unique to eukaryotes |
|
|
Term
| characteristics of promoters for RNA polymerase III |
|
Definition
| they are within the transcribed sequence, downstream of the start site |
|
|
Term
|
Definition
| DNA sequences that regulate the expression of a gene located on the same molecule of DNA |
|
|
Term
| trans-acting elements aka transcription factors |
|
Definition
| proteins that recognize cis-acting elements and regulate RNA synthesis |
|
|
Term
| importance of the regulation of RNA polymerase II |
|
Definition
| accounts for cell differentiation and development in higher organisms |
|
|
Term
|
Definition
| the most common cis-acting element for our genes transcribed by RNA polymerase II |
|
|
Term
| depiction of the TATA box |
|
Definition
|
|
Term
| the TASTA box is often paired with... |
|
Definition
| an initiator element (Inr) |
|
|
Term
|
Definition
| sequence found at the transcriptional start site |
|
|
Term
| downstream core promoter element (DPE) |
|
Definition
| found downstream of the start site and is commonly found in conjunction with the Inr in transcripts that lack the TATA box |
|
|
Term
|
Definition
| genes that tend to be continuously expressed instead of regulated |
|
|
Term
| genes that tend to have GC boxes in their promoters |
|
Definition
|
|
Term
| strands GC and CAAT boxes can be effective on |
|
Definition
-template (antisense)
-coding (sense) |
|
|
Term
| depiction of the CAAT and GC boxes |
|
Definition
|
|
Term
| RNA polymerase II is guided to the start site by... |
|
Definition
a set of transcription factors known collectively as TFII
TF stands for transcription factor and II stands for RNA polymerase II |
|
|
Term
| how transcription initiation using TFII begins |
|
Definition
| TFIID binding to the TATA box |
|
|
Term
| depiction of transcription initiation |
|
Definition
|
|
Term
| the key initial event in TATA-box promoters |
|
Definition
| recognition of the TATA box by the TATA-box-binding protein (TBP); this widens the minor groove |
|
|
Term
| the part of TFIID that binds to the TATA-box |
|
Definition
| the TATA-box-binding protein (TBP) |
|
|
Term
| depiction of the complex formed by the TATA-box-binding protein and DNA |
|
Definition
|
|
Term
| essential catalytic activities of TFIIH |
|
Definition
-it is an ATP-deppendent helicase that unwinds the DNA as a prelude to transcription
-the protein is also a kinase that phosphorylates the CTD of the polymerase |
|
|
Term
| this marks the transition from initiation to elongation |
|
Definition
| phosphorylation of the CTD by TFIIH |
|
|
Term
|
Definition
a type of cis-acting element that greatly increases the activities of many promoters in higher eukaryotes
they have no promoter activity of their own, but can exert their stimulatory actions over the span of several thousand base pairs |
|
|
Term
|
Definition
| upstream, downstream, or even in the midst of a transcribed gene |
|
|
Term
| something enhancers have in common with promoter sequences |
|
Definition
| they are bound by transcription activators that participate in the regulation of transcription |
|
|
Term
| transcription factors in eukaryotes don't act on their own, but instead... |
|
Definition
| recruit other proteins to form a complex that interacts with the transcriptional machinery to activate or repress transcription |
|
|
Term
|
Definition
| huge complex of 25-30 subunits that joins the transcription machinery (transcription factor and RNA polymerase II) before transcription takes place |
|
|
Term
|
Definition
refer to p. 680
in this case, it's basically acting in combinatorial control |
|
|
Term
|
Definition
| means of controlling gene expression in eukaryotes in which each transcription factor, rather than acting on its own to effect transcription, recruits other proteins to build up large complexes that regulate the transcription machinery |
|
|
Term
| advantage of combinatorial control |
|
Definition
a given regulatory protein can have different effects, depending on the other proteins present in the cell
helps eukaryotes with different cell types |
|
|
Term
| one way steroid receptors are different from other receptors |
|
Definition
| they are soluble and found in the cytoplasm or nucleoplasm rather than being bound to the membranes |
|
|
Term
| the general mode of action for steroid hormone receptors |
|
Definition
| on binding with the signal molecule (geberic term ligand), the ligand-receptor complex modifies the expression of specific genes by binding to control elements in the DNA |
|
|
Term
| nuclear hormone receptors |
|
Definition
| large family of transcription factors that, on the binding of a signal molecule such as a steroid hormone, modify the expression of specific genes by binding to control elements in DNA |
|
|
Term
|
Definition
| specific DNA sites that nuclear hormone receptors bind to |
|
|
Term
| 2 highly conserved domains of the nuclear hormone-receptor family |
|
Definition
-DNA-binding domain
-ligand-binding domain |
|
|
Term
|
Definition
| DNA-binding domains in which eight of the cysteine residues bind zinc ions to form DNA-binding domains that are called zinc-binding domains |
|
|
Term
| depiction of the structure of 2 nuclear hormone-receptor domains |
|
Definition
|
|
Term
| how ligand binding leads to transcription |
|
Definition
| causes significant structural change in the receptor and allows the receptor to recruit other proteins that facilitate transcription |
|
|
Term
| depiction of ligand binding to nuclear hormone receptor |
|
Definition
|
|
Term
|
Definition
| proteins that bind to the receptor only after it has bound to the steroid |
|
|
Term
| when the site for the interaction between the nuclear hormone-receptor complex and the coactivators is fully formed |
|
Definition
| only when the ligand is bound |
|
|
Term
| depiction of coactivator recruitment |
|
Definition
|
|
Term
|
Definition
| binds to a site in the ligand-binding domain that overlaps the coactivator binding site |
|
|
Term
| the template for RNA synthesis in eukaryotes |
|
Definition
|
|
Term
|
Definition
| complex of DNA and histones |
|
|
Term
| one way DNA gets loosened around histones |
|
Definition
| enzymatic attachment of acetyl groups to histones |
|
|
Term
| depiction of acetylation of histones |
|
Definition
|
|
Term
| histone acetyltransferases |
|
Definition
| catalyzes the acetylation of histones |
|
|
Term
| depiction of the structure of histone acetyltransferase |
|
Definition
|
|
Term
| how histone acetylation loosens DNA |
|
Definition
| dramatically reduces the affinity of the histone for DNA by neutralizing the positive charge of the lysine residfue while adding a negative charge to it |
|
|
Term
|
Definition
an acetyl binding domain that is present in many proteins that regulate eukaryotic transcription
these proteins serve as docking sites to recruit proteins that play a variety of roles in transcription and chromatin remodeling |
|
|
Term
| how acetylation of histone tails provides a mechanism for recruiting other components of the transcriptional machinery |
|
Definition
| they serve as docking sites to recruit proteins that play a variety of roles in transcription and chromatin remodeling |
|
|
Term
| a large complex bromodomains are also present in |
|
Definition
| chromatin-remodeling engines |
|
|
Term
| chromatin-remodeling engines |
|
Definition
-large complexes that contain bromodomains and domains somilar to those of helicases
-utilize the free energy of ATP hydrolysis to shift the positions of nucleosomes along the DNA and induce other conformational changes in the DNA |
|
|
Term
| 3 mechanisms histone acetylation can activate transcription |
|
Definition
1: reducing the affinity of the histones for DNA
2: recruiting other components of the transcriptional machinery
3: initiating the remodeling of the chromatin structure |
|
|
Term
| some means by which histones can be modified |
|
Definition
-acetylation
-methylation
-phosphorylation |
|
|
Term
| depiction of chromatin remodeling |
|
Definition
|
|
Term
| table of selected histone modifications |
|
Definition
|
|
Term
| general effect of acetylation on histones |
|
Definition
|
|
Term
| general effect of methylation on histones |
|
Definition
|
|
Term
| general effect of phosphorylation on histones |
|
Definition
|
|
Term
| key reaction in repression |
|
Definition
| deacetylation of acetylated lysine |
|
|
Term
|
Definition
| catalyze deacetylation of lysine residues in histone tails |
|
|
Term
| the products of RNA polymerase II action |
|
Definition
| pre-mRNA molecules (the primary transcripts) |
|
|
Term
| what happens to nearly all mRNA precursors in higher eukaryotes? |
|
Definition
|
|
Term
|
Definition
| encoding regions of genes that are kept after splicing |
|
|
Term
|
Definition
| noncoding regions of genes that are removed by splicing |
|
|
Term
| depiction of the processing of eukaryotic pre-rRNA |
|
Definition
|
|
Term
| how eukaryotic pre-rRNA gets processed |
|
Definition
1: extensive modification of certain sequences on the pre-rRNA, on both ribose and base components, directed by many small nucleolar ribonucleoproteins (snoRNPs)
2: the pre-rRNA is assembled with ribosomal proteins in a large ribonucleoprotein
3: cleavage of modified pre-rRNA |
|
|
Term
| small nucleolar ribonucleoproteins (snoRNPs) |
|
Definition
direct the modification of certain sequences on the pre-rRNA, both on the ribose and base components
each of these proteins consists of 1 small nucleolar RNA (snoRNA) and several proteins |
|
|
Term
| where more of the modification of pre-rRNA takes place |
|
Definition
|
|
Term
|
Definition
| cleaves nucleotides from the 5' end of the tRNA precursor |
|
|
Term
|
Definition
| cleaves nucleotides from the 3' end of the tRNA precursor |
|
|
Term
| tRNA nucleotidyltransferase |
|
Definition
| adds CCA to the tRNA precursor |
|
|
Term
| depiction of transfer RNA precursor processing |
|
Definition
|
|
Term
| what endonuclease does to tRNA precursor |
|
Definition
|
|
Term
| the most extensively modified transcription product |
|
Definition
| that of RNA polymerase II |
|
|
Term
| what happens to most of the transcription product of RNA polymerase II? |
|
Definition
| most of it gets processed to mRNA |
|
|
Term
| how the 5' end of the nascent RNA strand is modified shortly after the initiation of RNA synthesis |
|
Definition
1: phosphoryl group removed by hydrolysis by RNA triphosphatase
2: the diphosphate 5' end of the RNA attacks the α-phosphorus atom of a molecule of GTP to form an unusual 5'-5' triphosphate linkage, catalyzed by guanylyltransferase; this forms the 5' cap
3: the N-7 N atom of the terminal guanine is then methylated by RNA N-7 guanine methyltransferase, which uses S-adenosylmethionine as the methyl donor; this forms cap 0 |
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Term
| how the 5' cap is formed during RNA synthesis |
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Definition
| the diphosphate 5' end of the RNA attacks the α-phosphorus atom of a molecule of GTP to form an unusual 5'-5' triphosphate linkage, catalyzed by guanylyltransferase |
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Term
|
Definition
| the N-7 N atom of the terminal guanine is then methylated by RNA N-7 guanine methyltransferase, which uses S-adenosylmethionine as the methyl donor |
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Term
| how 5' caps make mRNAs more stable |
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Definition
| by protecting their 5' ends from nucleases and phosphatases |
|
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Term
| how caps enhance translation |
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Definition
| they enhance translation by eukaryotic protein-synthesizing systems |
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Term
| depiction of capping the 5' end |
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Definition
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Term
| something most eukaryotic mRNAs have added to their 3' end after transcription |
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Definition
| a polyadenylate (poly(A)) tail |
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Term
| how is the final form of the 3' end of the pre-mRNA created? |
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Definition
| the 3' end of the pre-mRNA is generated by a complex that contains a specific endonuclease (the cleavage and polyadenylation specifity factor, CPSF) that recognizes the sequence AAUAAA |
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Term
| depiction of polyadenylation of a primary transcript |
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Definition
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|
Term
| possible roles of the poly (A) tail that is added to mRNA |
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Definition
-might enhance translation efficiency
-might make the mRNA more stable
-more effective template for protein synthesis |
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Term
|
Definition
| the removal of introns and combining of exons to form the final product |
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|
Term
| this is required for accurate splicing of mRNA |
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Definition
| clear marking of correct splice sites |
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Term
| common structural motif of splice sites in eukaryotes |
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Definition
| the intron begins with GU and ends with AG |
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Term
| depiction of the transcription and translation of the β-globin gene |
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Definition
|
|
Term
| depiction of splice sites |
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Definition
|
|
Term
| what are the molecular machines that so precisely excise introns and join exons? |
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Definition
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Term
|
Definition
| large splicing complex formed by a group of special RNAs and more than 300 proteins that combine with pre-mRNA |
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Term
| small nuclear RNAs (snRNAs) |
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Definition
| class of RNAs that is essential in the spliceosome |
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Term
| small nuclear ribonucleoprotein particles (snRNPs) (pronounced "snurps") |
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Definition
| RNA-protein complexes that are composed of small nuclear RNAs (snRNAs) and their associated proteins |
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Term
| depiction of spliceosome assembly and action |
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Definition
|
|
Term
| what forms the catalytic center of the spliceosome? |
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Definition
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|
Term
| depiction of the splicing catalytic center |
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Definition
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Term
| 2 noteworthy features of the splicing process |
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Definition
1: RNA molecules play key roles in directing the alignment of splice sites and in carrying out catalysis
2: ATP-powered helicases unwind RNA duplex intermediates that facilitate catalysis and induce the release of snRNPs from the mRNA |
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Term
|
Definition
| rxn of an alcohol with an ester to form a different alcohol and a different ester |
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Term
| mRNA transcription and processing seem to be coordinated by... |
|
Definition
| the carboxyl-terminal domain (CTD) of RNA polymerase II |
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Term
| how the carboxyl-terminal domain (CTD) of RNA polymerase II contributes to efficient transcription |
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Definition
| by recruiting proteins to the pre-mRNA |
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Term
| depiction of the CTD: coupling transcription to pre-mRNA processing |
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Definition
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Term
| proteins recruited by the carboxyl-terminal domain (CTD) of RNA polymerase II |
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Definition
-capping enzymes
-components of the splicing machinery
-an endonuclease that cleaves the transcript at the poly(A) addition site |
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Term
|
Definition
| methylate the 5' guanine on the pre-mRNA immediately after transcription begins |
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Term
| what endonuclease does to the pre-mRNA |
|
Definition
| cleaves it at the poly(A) addition site, creating a free 3'-OH group that is the target for 3' adenylation |
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Term
| why protein synthesis is called translation |
|
Definition
| because the 4 letter alphabet of nucleic acids is translated into the 20 letter alphabet of proteins |
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Term
| some characteristics of the genetic code |
|
Definition
1: 3 nucleotides encode an amino acid
2: the code is nonoverlapping
3: the code has no punctuation; it is read sequentially from a fixed starting point without punctuation
4: the genetic code has directionality (5'-->3')
5: the genetic code is degenerate |
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Term
|
Definition
| group of 3 bases that encodes an amino acid |
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|
Term
| is the genetic code overlapping or nonoverlapping? |
|
Definition
|
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Term
|
Definition
| sequentially from a fixed starting point with no punctuation |
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|
Term
| direction the genetic code is read |
|
Definition
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|
Term
| how the genetic code is degenerate |
|
Definition
| this means that some amino acids are encoded by more than 1 codon |
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Term
|
Definition
| codons that specify the same amino acid |
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|
Term
| depiction of the genetic code |
|
Definition
|
|
Term
| why the degeneracy of the genetic code is advantageous |
|
Definition
| because it minimizes the deleterious effects of mutations |
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|
Term
| why the genetic code is almost, but not entirely, universal |
|
Definition
| because some codons translate differently in different organisms |
|
|
Term
| why the genetic code of mitochondria differs from the rest of the cell |
|
Definition
| because mitochondrial DNA encodes a distinct set of transfer RNAs, adaptor molecules that recognize the alternative codons |
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Term
| depiction of the distinctive codons of human mitochondria |
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Definition
|
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Term
|
Definition
| serves as the adaptor molecule between the codon and its specified amino acid |
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Term
| how tRNA acts as an adaptor |
|
Definition
| by binding to a specific codon and brings with it an amino acid for incorporation into the polypeptide chain |
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Term
| some features of all known transfer RNA molecules |
|
Definition
1: single strand containing 73-93 ribonucleotides
2: the 3D molecule is L-shaped
3: contain many unusual bases, typically 7-15 per tRNA, such as methylated derivatives of A, U, C, and G
4: can be arranged in a clover leaf pattern when depicted in 2D; it also has about half the nucleotides base-paired to form double-helices; also has 5 groups of bases that are not base paired
5: the 5' end is phosphorylated, with the 5' residue usually being pG
6: the activated amino acid is attached to a hydroxyl group of the adenosine residue located at the end of the 3' CCA component of the acceptor stem
7: the anticodon is present in a loop near the center of the sequence |
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|
Term
| depiction of transfer RNA structure |
|
Definition
|
|
Term
| what methylation of certain bases does for tRNA |
|
Definition
-prevents the formation of certain base pairs, rendering some of the bases accessible for for interactions with other components of the translation machinery
-gives some regions of tRNA hydrophobic character |
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|
Term
| the 5 groups of bases that are not base paired in tRNAs |
|
Definition
-the 3' CCA terminal region, which is part of the acceptor system
-the TψC loop, which got its name from ribothymine-pseudouracil-cytosine
-the "extra arm," which contains a variable number of residues
-the DHU loop, which contains several dihydrouracil residues
-the anticodon loop |
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|
Term
| depiction of the general structure of transfer RNA molecules |
|
Definition
|
|
Term
| why some tRNAs can recognize more than 1 codon |
|
Definition
|
|
Term
|
Definition
| states that some tRNAs can recognize more than 1 codon because of steric freedom in pairing of the 3rd base of the codon |
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|
Term
| depiction of allowed pairings at the third base of the codon according to the wobble hypothesis |
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Definition
|
|
Term
| 2 generalizations that can be made concerning the codon-anticodon interaction |
|
Definition
1: codons that differ in either of their first 2 bases must be recognized by different tRNAs
2: the first baser of an anticodon determines whether a particular tRNA molecule reads 1, 2, or 3 kinds of codons; thus, part of the degeneracy of the genetic code arises from imprecision in the pairing of the third base of the codon with the first base of the anticodon |
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Term
| part of the degeneracy of the genetic code arises from... |
|
Definition
| imprecision in the pairing of the third base of the codon with the first base of the anticodon |
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|
Term
| the observed error rate of protein synthesis |
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Definition
|
|
Term
| table of the accuracy of protein synthesis |
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Definition
|
|
Term
| aminoacyl-tRNA synthetases |
|
Definition
| catalyze the activation of amino acids |
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|
Term
| 2 reasons the specific linkages between amino acids and specific tRNAs are crucial |
|
Definition
1: the attachment of a given amino acid to a particular tRNA establishes the genetic code
2: the formation of a peptide bond is not thermodynamically favorable, so the amino acid must first be activated |
|
|
Term
| what establishes the genetic code? |
|
Definition
| the attachment of a given amino acid to a particular tRNA |
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|
Term
| why an amino acid must be activated before being added to the polypeptide chain |
|
Definition
| because the formation of that bond is thermodynamically unfavorable |
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Term
| the activated intermediates in protein synthesis |
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Definition
|
|
Term
|
Definition
|
|
Term
| aminoacyl-tRNA aka charged tRNA |
|
Definition
| an amino acid ester of tRNA |
|
|
Term
| amino acids are activated by... |
|
Definition
| attachment to transfer RNA |
|
|
Term
| depiction of aminoacyl-tRNA |
|
Definition
|
|
Term
| amino acids are first activated by... |
|
Definition
|
|
Term
| the first step in the activation of amino acids |
|
Definition
| the formation of an aminoacyl adenylate from the amino acid and the ATP |
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|
Term
| depiction of aminoacyl adenylate aka aminoacyl-AMP |
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Definition
|
|
Term
| the 2 steps of activation of an amino acid by adenylation |
|
Definition
1: formation of an aminoacyl adenylate from an amino acid and ATP
2: the transfer of the aminoacyl group to a particular tRNA molecule to form aminoacyl-tRNA |
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Term
| the net rxn of the activation of amino acids |
|
Definition
| amino acid + ATP + tRNA + H2O --> aminoacyl-tRNA + AMP + 2 Pi |
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|
Term
| the energy consumed in the synthesis of aminoacyl-tRNA |
|
Definition
| equivalent of 2 molecules of ATP consumed in the synthesis of each aminoacyl-tRNA |
|
|
Term
| how translation takes place |
|
Definition
| takes place with the formation of the ester linkage between an amino acid and a specific tRNA |
|
|
Term
| the actual translators of the genetic code |
|
Definition
| the aminoacyl-tRNA synthetases |
|
|
Term
| how aminoacyl-tRNA synthetases are specific in their binding |
|
Definition
| they have highly discriminating amino acid activation sites |
|
|
Term
| depiction of the active site of threonyl-tRNA synthetase |
|
Definition
|
|
Term
| one way the fidelity of protein synthesis is increased |
|
Definition
| proofreading by aminoacyl-tRNA syntyhetases |
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|
Term
| how the aminoacyl-tRNA can be edited without dissociating from the synthetase |
|
Definition
| the CCA arm with the amino acid attached to it can swing out of the activation site and into the editing site, which hydrolyzes the bond between the amino acid and the tRNA, providing an opportunity for correction |
|
|
Term
| depiction of the editing of aminoacyl-tRNA |
|
Definition
|
|
Term
| the point at which translation takes place |
|
Definition
| synthetases choosing their tRNA partners |
|
|
Term
| depiction of the recognition sites on tRNA |
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Definition
|
|
Term
| depiction of the ribosome at high resolution |
|
Definition
|
|
Term
|
Definition
| the molecular machines that coordinate the interplay of aminoacyl-tRNAs, mRNA, and proteins |
|
|
Term
|
Definition
-large subunit
-small subunit
-both subunits made of nearly 2/3 RNA and 1/3 protein |
|
|
Term
| depiction of ribosomal RNA folding pattern |
|
Definition
|
|
Term
| the catalytic sites in the ribosome are composed almost entirely of... |
|
Definition
|
|
Term
| one reason it's advatageous for mRNA to be translated in the 5' --> 3' direction |
|
Definition
| allows for translation to take place as it's being transcribed |
|
|
Term
| a key feature of bacterial gene expression |
|
Definition
| translation and transcription are closely coupled in space and time |
|
|
Term
|
Definition
| a group of ribosomes bound to an mRNA molecule |
|
|
Term
|
Definition
|
|
Term
| the 3 parts of protein synthesis |
|
Definition
1: initiation
2: elongation
3: termination |
|
|
Term
| protein-synthesis initiation requires the the cooperation of... |
|
Definition
-the ribosome
-tRNA
-mRNA
-various protein factors |
|
|
Term
| the 3 tRNA binding sites in ribosomes |
|
Definition
-A site (aminoacyl)
-P site (peptidyl)
-E site (exit) |
|
|
Term
| depiction of the binding sites of transfer RNA |
|
Definition
|
|
Term
| depiction of an active ribosome |
|
Definition
|
|
Term
| the start signal for translation is usually... |
|
Definition
|
|
Term
|
Definition
| when an mRNA encodes 2 or more polypeptide chains |
|
|
Term
| all known mRNA molecules contain... |
|
Definition
| the start and stop signals of the polypeptide chain(s) they encode |
|
|
Term
| other than the initiating codon, what else is involved in initiation in bacteria? |
|
Definition
| a purine-rich sequence called the Shine-Dalgarno sequence |
|
|
Term
|
Definition
| purine-rich sequence upstream of start codon that helps initiate translation |
|
|
Term
| depiction of initiation sites |
|
Definition
|
|
Term
| function of untranslated regions of mRNA |
|
Definition
| usually to regulate the usage of mRNA molecules |
|
|
Term
| the 2 kinds of interactions that determine where protein synthesis starts in bacteria |
|
Definition
1: pairing of mRNA bases with the 3' end of 16S rRNA
2: pairing of the initiator codon on mRNA with the anticodon of an initiator tRNA molecule |
|
|
Term
| bacterial protein synthesis is initiated by... |
|
Definition
|
|
Term
| protein synthesis in bacteria starts with... |
|
Definition
| the modified amino acid N-formylmethionine (fMet) |
|
|
Term
| depiction of N-formylmethionine (fMet) |
|
Definition
|
|
Term
| depiction of the formylation of methionyl-tRNA |
|
Definition
|
|
Term
| the rate-limiting step in protein synthesis |
|
Definition
| formation of the 70S complex |
|
|
Term
| depiction of translation initiation in bacteria |
|
Definition
|
|
Term
|
Definition
| basically where the ribosome reads the mRNA |
|
|
Term
|
Definition
| deliver aminoacyl-tRNA to the ribosome |
|
|
Term
|
Definition
rotation of the aminoacyl-tRNA in the A site so that the amino acid is brought into proximity with the aminoacyl-tRNA in the P site on the ribosome
this process aligns the amino acids for peptide bond formation |
|
|
Term
| are internal AUG codons read by the initiator tRNA? |
|
Definition
|
|
Term
| peptidyl transferase center |
|
Definition
| catalyzes the formation of a peptide bond |
|
|
Term
| the ribosome gets much of its catalytic power from... |
|
Definition
| catalysis by proximity and orientation |
|
|
Term
| depiction of peptide bond formation |
|
Definition
|
|
Term
| depiction of the mechanism of protein synthesis |
|
Definition
|
|
Term
| translocation in ribosomes is enhanced by... |
|
Definition
| elongation factor G (EF-G) aka translocase |
|
|
Term
| elongation factor G (EF-G) aka translocase |
|
Definition
| enhances elongation in ribosomes |
|
|
Term
| depiction of the translocation mechanism |
|
Definition
|
|
Term
| where the peptide chain stays during translation |
|
Definition
| in the P site of the ribosome; it leaves thru the exit tunnel |
|
|
Term
| how tRNA moves thru the ribosome |
|
Definition
| in the A site, thru the P site, and out the E site |
|
|
Term
| direction the polypeptide chain is synthesized in |
|
Definition
| amino-terminal-to-carboxyl-terminal |
|
|
Term
| depiction of polypeptide chain growth |
|
Definition
|
|
Term
| which terminus are new amino acids added to in protein synthesis? |
|
Definition
|
|
Term
| protein synthesis is terminated by... |
|
Definition
| release factors that read stop codons |
|
|
Term
| stop codons are recognized by... |
|
Definition
|
|
Term
| depiction of the termination of protein synthesis |
|
Definition
|
|
Term
| what a release factor does |
|
Definition
| recognizes a stop codon in the A site and stimulates the release of the completed protein from the tRNA in the P site |
|
|
Term
| where bacteria and eukaryotes differ in protein synthesis |
|
Definition
|
|
Term
| some areas where bacteria and eukaryotes differ in the initiation of protein synthesis |
|
Definition
1: ribosomes
2: initiator tRNA
3: initiation
4: the structure of mRNA
5: elongation and termination
6: organization |
|
|
Term
| difference between bacterial and eukaryotic ribosomes |
|
Definition
| eukaryotic ribosomes are larger |
|
|
Term
| difference in initiator tRNA between bacteria and eukaryotes |
|
Definition
-the initiator in bacteria is N-formylmethionine
-the initiator in eukaryotes is methionine |
|
|
Term
| the initiating amino acid in bacteria |
|
Definition
|
|
Term
| the initiating amino acid in eukaryotes |
|
Definition
|
|
Term
| the initiating codon in eukaryotes |
|
Definition
|
|
Term
| initiation in eukaryotes begins with... |
|
Definition
| the formation of the ternary complex consisting of the 40S ribosome and Met-tRNAi in association with eIF-2 |
|
|
Term
| why a bacterial mRNA can serve as the template for the synthesis of several proteins |
|
Definition
| because it can have multiple Shine-Dalgarno sequences, thus multiple start sites, making it able to serve as the template for multiple proteins |
|
|
Term
| part of the reason the initiation mechanisms between bacteria and eukaryotes are different |
|
Definition
| difference in RNA processing |
|
|
Term
| depiction of eukaryotic translation initiation |
|
Definition
|
|
Term
| the shape of eukaryotic mRNA |
|
Definition
|
|
Term
| depiction of how protein interactions circularize eukaryotic mRNA |
|
Definition
|
|
Term
| how the translation machinery is organized in higher eukaryotes |
|
Definition
| organized into large complexes associated with the cytoskeleton |
|
|
Term
| some antibiotic inhibitors of protein synthesis |
|
Definition
-streptomycin and other aminoglycosides
-tetracycline
-chloramphenicol
-cycloheximide
-erythromycin
-puromycin |
|
|
Term
| table of antibiotic inhibitors of protein synthesis |
|
Definition
|
|
Term
| depiction of the antibiotic action of puromycin |
|
Definition
|
|
