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 |
|
|
