Term
| What are the characteristics of living systems? |
|
Definition
1. Complicated, highly organized
2. Structures have functional purpose
3. Energy transformations
4. Self-replication |
|
|
Term
| Organisms store the captured energy in 'energy-rich' molecules like |
|
Definition
- ATP and NADPH are two most prominent 'energy-rich' biomolecules.
- these molecules react with other molecules in the cell and release the stored energy
- the energy thus released is used to drive energy-requiring (unfavorable) cellular processes
- living systems, thus, is characterized by flow of energy through the organism, which maintains the intricate order and activity of the living system.
- overall, the living system is maintained in an apparent state of constancy (steady state)
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Term
| what kinds of molecules are biomolecules? |
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Definition
| H, O, C, N make up 99% of the composition of the earths crust, with H predominating |
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Term
|
Definition
| lightest elements capable of forming strong covalent bonds by electron pair sharing. |
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Term
| What two other covalent bond forming elements play an important role in the composition of biomolecules? |
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Definition
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Term
| The strength of covalent bonds is inversely proportional to what? |
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Definition
| The atomic weights of the atoms involved |
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Term
| What are two relevant properties of C that make it versatile such that it can form a large number of different biomolecules? |
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Definition
1. C can form 4 covalent bonds (sharing 4 electrons in its outer shell)
2. Tetrahedral geometry when C forms 4 single bonds |
|
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Term
|
Definition
- molecules self assemble into supra-molecular complexes
- the supra-molecular complexes self-assemble into organelles
- organelles self assemble into cells, which form tissues in the same fashion
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Term
| Describe the inorganic precursors for complex biomolecules |
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Definition
| Carbon dioxide, water, ammonia, nitrogen gas, nitrate |
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Term
| Describe the metabolites for complex biomolecules |
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Definition
Pyruvate, citrate, succinate, glyceraldehyde-3-phosphate, Fructose-1,6-bisphosphate, 3-phosphoglyceric acid
simple organic compounds that are intermediates in cellular energy transformations |
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Term
| What are the building blocks of complex biomolecules? |
|
Definition
amino acids, nucleotides, monosaccharides, fatty acids, glyceral.
covalent linkage of these form macromolecules |
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Term
| What are the macromolecules of complex biomolecules? |
|
Definition
proteins, nucleic acids, polysaccharides, lipids.
non-covalent interactions between different sets of macromolecules form supramolecular complexes |
|
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Term
| What are supramolecular complexes |
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Definition
| ribosomes, cytoskeleton, multienzyme complexes, chromosomes |
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Term
| What maintains supramolecular assemblies' structural integrity |
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Definition
| noncovalent forces such as H bonds, ionic attractions, van der walls forces, and hydrophobic interactions |
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Term
|
Definition
nucleus, mitochondria, chloroplasts, endoplasmic reticulum, golgi apparatus, vacuole
these are surrounded by membranes and present only in higher organisms (eukaryotes) |
|
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Term
| Describe biological membranes |
|
Definition
membranes define the boundaries of cells and also of organelles within a cell
membranes are complexes of proteins and lipid molecules maintained by noncovalent forces and hydrophobic interactions |
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Term
| macromolecules are formed by what? |
|
Definition
dehydration syntheses in which the elements of water are eliminated between monomeric unites
they have structural polarity (directionality) and are not symmetrical
they are informational and have a three-dimensional architecture |
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Term
|
Definition
| linear polymers of (usually) 20 amino acids, in which water is eliminated between the carboxyl group of one amino acid and the amino group of the next |
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Term
| polysaccharides are built by |
|
Definition
| joining sugars together by a (1,4) linkage |
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Term
|
Definition
polymers of nucleotides
each nucleotide unit has a 5'phosphate and a 3'OH group and are formed by linking the 5'-PO4 group of one nucleotide with the 3'-OH group of another nucleotide |
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Term
| Why are polysaccharides not as informational as proteins or nucleic acids? |
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Definition
| they are often compsed of the same sugar unit repeated over and over again |
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Term
| the strength of van der walls interactions depends on |
|
Definition
the relative size of the atoms or molecules and the distance between them
intrinsic attraction of one atom's positively charged nucleus with the negatively charged electrons of a neighboring atom |
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Term
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Definition
| weak, polar interactions that occur when an electropositive hydrogen donor is covalently attached to an electronegative atom which results in unshared electrons allowing the H to be shared with another electronegative acceptor atom |
|
|
Term
| how strong are van der waals forces |
|
Definition
| very weak, only .4-4 kJ/mol due to fluctuations within electron clouds |
|
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Term
| the limit of approach of two atoms in van der waals forces is determined by |
|
Definition
| the sum of their van der waals radii |
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|
Term
| hydrogen bond characteristics |
|
Definition
h bonds are highly directional and straight between donor H and acceptor atoms
H bonds are strongest when all three atoms are in a straight line
require the presence of complementary H donor and acceptor groups |
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Term
| Strength of H bonds and how are they weakened |
|
Definition
12-30 kJ/mole
weakened by water |
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Term
| ionic interactions are a result of |
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Definition
| attractive forces between oppositely charged groups with the electric charge readially distributed |
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|
Term
| ionic/ electrostatic interactions between biomolecules may involve |
|
Definition
| ions, permanent dipoles, or induced dipoles and thus have a high degree of structural specificity |
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Term
|
Definition
result from the strong tendency of water to exclude non polar groups or molecules
formation is entropically driven
strength is <40 kj/mol |
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Term
| two important points about weak forces |
|
Definition
1. biomolecular recognition is mediated by weak chemical forces
2. weak forces restrict organisms to a narrow range of enviro conditions |
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Term
|
Definition
UV light
mechanical sheer forces
heat
8 M urea |
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|
Term
|
Definition
The ordered reaction pathways by which cellular chemistry proceeds and biological energy transformations are accomplished
=maintains steady state against enviro pressures by controlling enzyme activity |
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Term
|
Definition
| the release of useful energy from the breakdown of food |
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Term
|
Definition
synthesis of biomolecules
biosynthesis |
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Term
| What are some common chemical ways of accelerating reaction rates and why are they not available in cells |
|
Definition
elevation of temperature, pressure; addition of acid/base; increasing reactant concentrations
the cells function at a very narrow range. any large fluctuations will result in cell death |
|
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Term
|
Definition
| the kinetics of a reaction (rate), not the thermodynamic (free energy) |
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Term
| cells are what type of thermodynamic systems and explain |
|
Definition
OPEN.
they exchange matter and energy with the surroundings and function as a highly regulated isothermal chemical engine |
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|
Term
| What does a golgi apparatus do in the eukaryotic cell? |
|
Definition
| processes and packages macromolecules for secretion and delivery to other cellular compartments |
|
|
Term
| What does the endoplasmic reticulum do in eukaryotic cells? |
|
Definition
| synthesizes membrane proteins and lipids |
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|
Term
| What does the lysosome hole and what does that do? |
|
Definition
| lysozyme: degrades cell components (macromolecules) |
|
|
Term
| Briefly describe a virus lifecycle |
|
Definition
1. Enters cell
2. take over of metabolic machinery of the host cell to produce more virus particles or be integrated into host dna
3. more virus particles are released by rupture of the host cell, sometimes by lysis |
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Term
| What are the strengths of H bonds verses the covalent bonds in water? |
|
Definition
| 23 kj/mol for hydrogen bonds between neighboring water molecules compared to 420 kj/mol for each H-O covalent bond |
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Term
| Compare the H bonds of water to those of ice |
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Definition
| Ice forms 4 H bonds per molecule compared to water's average 2.3 bonds. Ice H bonds also last much longer, a factor of 10^-5 |
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|
Term
| Describe the structure of normal ice |
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Definition
| the h bonds between water molecules form a rigid 3D network, resulting in the crystalline structure of water. |
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Term
| Why is liquid water denser than ice? |
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Definition
| Some of the H bonds that maintain the crystal structure of ice are broken, allowing water molecules in liquid water to pack close together |
|
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Term
| Describe the fluid network of water |
|
Definition
lacks the lattice-like structure of ice
The space around an O atom is not defined by the presence of four H atoms, but can be occupied by other water molecules, randomly oriented.
at least half of the H bonds are not colinear with a line joining the centers of the atoms involved
therefore the H bonds are weaker and water is fluid
H bonds are dynamically formed and broken |
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|
Term
| Describe the solvent properties of water derived from its polar nature |
|
Definition
water has a high dielectric constant
ions are always hydrated in water and carry around a "hydration shell"
water is able to form H bonds with polar solutes |
|
|
Term
| What is water an excellent solvent for? |
|
Definition
-ionic substances
-nonionic, but polar substances like sugars, alcohols, and amines
-carbonyl group containing molecules like aldehydes and ketons |
|
|
Term
| Describe hydration shells surrounding ions in water |
|
Definition
-sodium and chloride ions are hydrated by a shell of water molecules
-water molecules are oriented in an opposite direction about sodium and chloride ions, because the interaction is electrostatic
-hydration shells are stable but static
-each water molecule in the inner hydration shell around an Na+ ion is replaced by another water molecule every couple of nanoseconds |
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|
Term
| What does D stand for in "Water has a high dielectric constant (D)? |
|
Definition
| 'D' is a measure of the solvent's ability to surround ions in dipole interactions (hydration shells) and hence screen them from oppositely charged ions in solution |
|
|
Term
|
Definition
Water's dielectric constant
F=the attractive force between oppositely charged ions
e=charge on an ion
r=distance between the ions
D=dielectric constant |
|
|
Term
| Describe how water forms H bonds with non-ionic polar solutes |
|
Definition
The OH- groups serve as H bond donors
hence water dipoles readily H bond
These plar solvent oslute interactions are stronger than attractions between solute molecules caused by van der waals forces and H bonding |
|
|
Term
| explain non polar solutes in water |
|
Definition
non polar solutes cannot H bond with water dipoles
water dipoles significanly reorganize their extensive H bonded network to form a cage-like structure (clathrate) surrounding the non polar solute molecule
this results in order of water molecules since water molecules in the clathrate have markedly reduced freedom in 3d space
thus, significant decrease in entropy of water molecules accompanies clathrate formation around the non polar solute molecules |
|
|
Term
| what is a clathrate structure |
|
Definition
| an iceberg like structure that forms surrounding hydrocarbon tails in an aqueous environment |
|
|
Term
| describe hydrophobic interactions in water |
|
Definition
non polar solutes tend to cluster into larger aggregates
less number of water molecules are ordered
Significant increase in entropy of water molecules (= hihgly favorable process) |
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|
Term
| What are amphipathic molecules |
|
Definition
| contain both polar gourp and a non polar group, such as when fatty acids contain a polar head group and a non polar hydrocarbon 'tail' group |
|
|
Term
| explain micelle formation by amphiphilic molecules in aqueous solution |
|
Definition
the hydrophilic polar head group is exposed maximally to water and is efficiently hydrated by water dipoles
they hydrophobic non polar hydrocrabon tail groups cluster together with each other to minimize exposure to water |
|
|
Term
| what properties of water are effected by the presence of solutes |
|
Definition
-freezing point is lowered
-boiling point is elevated
-vapor pressure is lowered
-osmotic pressure changes
NOTE: these depend on the quantity of solute molecules, not their chemical properties |
|
|
Term
| what is the osmotic pressure of 1 molal (m) solution |
|
Definition
|
|
Term
| what are the assumptions of Kw ionization |
|
Definition
| 10^7 moles of H+ and OH- present in 1 L of pure water at 25ºC |
|
|
Term
|
Definition
| substances capable of generating ions in solution and thereby causing an increase in electrical conductivity of the solution |
|
|
Term
|
Definition
| Ka is called the acid dissociation constant or ionization constant of the weak acid. It represents the extent to which a substance forms ions in water |
|
|
Term
| Explain the henderson-hasselbalch equation |
|
Definition
there is one HH eqn for each group that titrates
the pKa of a weak acid is that pH where HA is half-titrated
HH equation allows to calculate the extent to which a weak acid dissociates and hence to calculate the change in pH of the weak acid solution |
|
|
Term
|
Definition
titration is an analytical method used to determine the amount of acid in a solution
a measured volume of the acid solution is titrated by slowl adding a solution of base in incremental amounts
the [H+] change in the acid solution is monitored by monitoring the pH of the acid solution
a titration curve is the plot of pH of the solution versus amount of OH- |
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|
Term
|
Definition
buffers are aqueous solutions that resist changes in pH as acid and base are added
a mixture of weak acid and it's conjugate base
maintains cellular pH |
|
|
Term
| What criteria must cellular buffers meet? |
|
Definition
the pka of buffer system must be near desired pH
buffer must be compatible with cell machinery |
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|
Term
| What is the first law of thermodynamics |
|
Definition
| the total energy of an isolated system is conserved and the energy of the universe is constant |
|
|
Term
|
Definition
| the internal energy- includes all energies that may be exchanged in physical or chemical processes (including rotational, vibrational and translational energies of molecules and the enrgy stored in covalent and noncovalent bonds) |
|
|
Term
|
Definition
| (H) the heat content of a system as a measure of the system's internal energy |
|
|
Term
| describe the changes in enthalpy |
|
Definition
if negative: reaction gives off heat = exothermic
if positive: reaction absorbs heat = endothermic |
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|
Term
| What are the characteristics of isolated, closed, and open systems |
|
Definition
isolated systems exchange neither matter nor energy with their surroundings
closed systems may exchange energy, but not matter, with their surroundings
open systems may exchange either matter or energy with their surroundings |
|
|
Term
| what is the second law of thermodynamics |
|
Definition
systems tend toward disorder and randomness (by which measures entropy)
systems tend to proceed from ordered (low entropy, small S) to high entropy, high S value) states
entropy does not change in reversible processes |
|
|
Term
|
Definition
| the criterion for predicting equilibrium and spontaneity of a biochemical reaction |
|
|
Term
| delta G will spontaneous proceed toward a state of |
|
Definition
| lower G, as close to 0 as possible |
|
|
Term
| protein folding is driven by |
|
Definition
entropy
this decreases the randomness of protein molecules |
|
|
Term
| Define the standard state for solutes in solution |
|
Definition
1 atm
298 K
1 M concentration |
|
|
Term
| Define the modified standard state for solutes in solution |
|
Definition
1 atm
10^-7 M for H+ ions, 1M for all other solutes
298 K |
|
|
Term
|
Definition
-nature of reactants and products
-conditions of the reaction |
|
|
Term
| The point of equilibrium for a reaction in solution is a function of the |
|
Definition
| standard state free energy change for the process |
|
|
Term
| What are two important properties of high-energy compounds |
|
Definition
1. Transient forms of stored energy: meant to carry energy from one point to another in metabolism. They are not long term energy storage containers
2. Do not hydrolyze unpredictably: they are not unstable
Rather, ATP requires a higher activation energy |
|
|
Term
| why is AMP not a high energy phosphate compound |
|
Definition
because it is not a phosphoanhydrate, but a phosphoester
it posesses a single phosphoryl group and is not markedly different from its hydrolysis product in terms of electrostatic repoulsion and resonance stabilization |
|
|
Term
| What Are the Structures and Properties of Amino Acids? |
|
Definition
Amino acids contain a central tetrahedral carbon atom (α-carbon)
There are 20 common amino acids in proteins
Amino acids can join via peptide bonds
Several amino acids occur only rarely in proteins
Some amino acids are not found in proteins |
|
|
Term
| What are the three relevant peptide bonds? |
|
Definition
Cα-CO bond
CO-N bond (peptide bond)
N-Cα bond |
|
|
Term
| What are the Consequences of the partial double bond nature of the peptide bond? |
|
Definition
The peptide bond (CO-N) is not free to rotate. The other two bonds ie Cα-CO and N-Cα are free to rotate.
- The six atoms of the peptide bond group (Cα, CO, O, N, H and Cα) are co-planar.
- This plane is called the ‘amide plane’ of the peptide backbone
- The R groups and the H atoms attached to the Cα atoms do not lie on the plane |
|
|
Term
| Why are amino acids WEAK, polyprotic acid |
|
Definition
| All amino acids have at least two dissociable protons (COOH and NH3+) |
|
|
Term
|
Definition
| Therefore at neutral pH, an amino acid molecule is neutral (zero charge: due to one positive and one negative charge) |
|
|
Term
| What is an isoelectric point? |
|
Definition
| pH where a molecule has a net charge of 0, can be calculated as (pK1 + pK2)/2. |
|
|
Term
| Describe how peptide pKa of an ionizable R group is affected by the presence of another nearby |
|
Definition
| α-amino and α-carboxyl groups of non-terminal amino acids are joined in peptide bonds do not ionize and hence do not contribute to acid-base properties of the peptide |
|
|
Term
| What are the Differences in pKa between free amino acid and peptides |
|
Definition
In a free amino acid:
-Opposite charges stabilize each other.
-Therefore, amino and carboxyl group both will want to stay charged (NH3+ and COO- respectively).
-For the amino group: To stay charged, it will not want to give up its proton. Hence Ka dec pKa inc
-For the carboxyl group: To stay charged, it will want to give up its proton. Hence Ka inc pKa dec
In a peptide:
-Opposite charges (on terminal amino and carboxyl groups) far from each other. The distance increases with the length of the peptide.
-Therefore no / less charge-stabilizing effect.
-Therefore, terminal amino and carboxyl groups both will want to stay uncharged (NH2and COOH respectively). |
|
|
Term
| The enantiomer that rotates incident light in CLOCKWISE direction is |
|
Definition
|
|
Term
| The enantiomer that rotates incident light in COUNTERCLOCKWISE direction is: |
|
Definition
|
|
Term
| dextrorotatory(+) and levorotatory(-) is the naming convention for chiral molecules by their |
|
Definition
|
|
Term
| D-amino acids (although not found in protein) are found in nature: |
|
Definition
- In the cell wall of bacteria
- In peptide antibiotics (example valinomycine, gramicidin) |
|
|
Term
| Edman reagent (phenylisothiocyanate /PITC) reacts with |
|
Definition
| the N-terminal amino acid of a peptide or protein to form a cyclic thiazoline derivative that reacts in weak aqueous acid to form a PTH-amino acid. |
|
|
Term
| Separation of amino acid mixtures depends on |
|
Definition
PARTITION properties: The tendency to associate with one phase over another – CHROMATOGRAPHY
ELECTRICAL charge: ELECTROPHORESIS |
|
|
Term
| what are the general principles of chromatography |
|
Definition
- The amino acid mixture is allowed (or forced) to flow through a medium consisting of two phases--- (solid-liquid), (liquid-liquid) or (gas-liquid)
The amino acids distribute themselves between the two phases depending on the property that is being exploited. |
|
|
Term
| What are the Most important chromatographic methods used to separate amino acid are: |
|
Definition
- Ion Exchange Chromatography
- High Performance Liquid Chromatography (HPLC) |
|
|
Term
| The set up for ion exchange chromatography consists of: |
|
Definition
- An immobilized solid phase (resin) that has +vely or –vely charged particles attached to it
- The amino acid mixture constitutes the liquid mobile phase |
|
|
Term
| What does an anion exchanger do |
|
Definition
| binds anions (-vely charged). Thus, the group attached to the anion exchange resin is +vely charged |
|
|
Term
| What does a cation exchanger do |
|
Definition
| binds cations (+vely charged). Thus, the group attached to the cation exchange resin is -vely charged. |
|
|
Term
| In electrophoresis, When pH of buffer > pI of amino acid: |
|
Definition
| deprotonated amino acid (-ve) predominates |
|
|
Term
| In electrophroesis, When pH of buffer < pI of amino acid: |
|
Definition
| protonated amino acid (+ve) predominates |
|
|
Term
| What is the Fundamental Structural Pattern in Proteins? |
|
Definition
Proteins are unbranched polymers of amino acids
Amino acids join head-to-tail through formation of covalent peptide bonds
Peptide bond formation results in release of water
The peptide backbone of a protein consists of the repeated sequence –N-Cα-Co-
“N” is the amide nitrogen of the amino acid
“Cα” is the alpha-C of the amino acid
“Co” is the carbonyl carbon of the amino acid |
|
|
Term
| what is the hierarchy of protein structure |
|
Definition
| 1. Primary structure (amino acid sequence) maintained by covalent bonds |
|
|
Term
What are the Non-covalent interactions and SH bonds stabilize the higher orders (2°, 3° and
4°) of protein structure |
|
Definition
-H-bonds
-Hydrophobic Interactions
-Ionic (electrostatic) Interactions
-Van der Waals Interactions
-Sulfohydryl bonds |
|
|
Term
| Charged groups in a protein that may participate in ionic interactions are: |
|
Definition
The N and the C terminus of the protein chain that are +vely and –vely charged respectively. Amino acid side chains that carry a +ve or –ve charge
Charged amino acid residues are usually located on the surface of a protein where they can effectively interact with water molecules or charged side chains of other protein molecules. It is energetically unfavorable for a charged residue to be buried in the hydrophobic interior of a protein |
|
|
Term
| What are alpha helix destablilizing factors |
|
Definition
1. Charge repulsion: Amino acid residues with charged side chains do not form α-helices due to charge repulsion.
E.g., at pH 7, the side chains of Asp and Glu are highly negatively charged and the side chain of Lys is highly positively charged. Hence charge repulsion destabilizes helix.
NOTE: However,
- For Asp and Glu: at pH below 2.0, their side chain COOH groups are protonated and hence not charged. Then, they can form α-helices.
- For Lys: at pH above 11, its side chain NH3+ group is deprotonated ie as NH2 and hence not charged. Then, it can form α-helices .
Steric repulsion between bulky side chains: E.g., Asparagine (Asn) |
|
|
Term
| This marginal stability is essential for cellular functions: |
|
Definition
Marginal stability means that the many weak forces that maintain the higher levels of protein structure can be broken and reformed (Conformational changes)
This means protein structure is flexible and is in motion, which makes cellular functions possible. |
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