Exam 1 Flashcards
What is the Gibbs free energy equation?
Δ G = Δ H - TΔ S, where Δ H is enthalpy and Δ S is entropy
What does a Δ G < 0 indicate about a reaction?
The reaction proceeds spontaneously in the forward direction and is exergonic
What does it mean when Δ G = 0?
The system is at equilibrium
What is an endergonic reaction, and what does its Δ G look like?
An endergonic reaction requires additional energy to proceed and has a Δ G > 0
Give an example of a reaction driven by both enthalpy and entropy.
Fermentation of glucose to ethanol
What is the hydrophobic effect?
The tendency of nonpolar molecules to self-associate in water, increasing water entropy
How does hydrogen bonding affect water molecules?
Hydrogen bonds between water molecules are weak and easily broken, contributing to favorable enthalpy
Why do nonpolar molecules group together in water?
Grouping reduces the number of water molecules needed to surround them, increasing the entropy of the water
What is the Henderson-Hasselbalch equation?
pH = pKa +
log([A-]/[A-][HA])
What happens when the pH equals the pKa?
The concentration of the conjugate base [A-] equals the concentration of the acid [HA]
What does a lower pKa indicate?
A stronger acid
At pH = 7.4, what is the ratio of uncharged histidine to protonated histidine?
25:1 (96% uncharged)
What is the structure of an amino acid?
An amino group (-NH2), a carboxyl group (-COOH), and a side chain (R)
Name three neutral, weakly hydrophobic amino acids.
Alanine (A), Glycine (G), and Valine (V)
What is a zwitterion?
A molecule with both positive and negative charges simultaneously
Which amino acids have titratable groups?
Arginine, Aspartic acid, Cysteine, Glutamic acid, Histidine, Lysine, and Tyrosine
What stabilizes secondary structures?
Hydrogen bonding between carbonyl oxygen and an amide hydrogen
What technique allows one to view multiple conformations of small proteins?
Nuclear Magnetic Resonance
How are the alpha-helicies in keratin and L-helicies in tropocollagen similar?
Both involve hydrogen bonding between a carbonyl oxygen and an amide hydrogen
What happens if the proximal histidine in Mb is replaced by alanine?
No O2 will bind, regardless of P(O2)
What happens if the distal histidine in Mb is replaced by alanine?
P50 will increase and binding is less efficient
What would happen if a histidine that lines the water-filled cavity was replaced by lysine, assuming lysine still binds to 2,3-BPG?
The molecule will be less sensitive to pH change
What stabilizes tropocollagen?
Covalent cross linking of lysine side chains
What is a common strategy by which catalysis occurs?
Stabilization of the transition state
What contributes to a favorable reaction?
Change in enthalpy < 0, change in entropy > 0
How can an unfavorable reaction proceed?
By being coupled to a favorable reaction (commonly ATP hydrolysis)
What molecules interact favorable with H2O, and what effect does this have on said molecules?
Polar/charged, increases solubility
What stabilizes interactions between biological molecules?
Charged groups
Why are charged groups important to enzymes?
used for substrate binding and/or catalysis
What AAs are alipathic?
G, A, V, L, I (Glycine, Alanine, Valine, Leucine, Isoleucine)
What traits do alipathic AAs have?
Side chains are entirely C and H, and are hydrophobic (except for glycine)
What is the relationship between hydrophobicity and amount of Cs in the side chain?
Hydrophobicity increases as Cs increase (leucine > valine > alanine)
What AAs are aromatic?
F, W, Y (phenylalanine, tryptophan, tyrosine)
What is a unique trait of aromatic AAs?
They absorb UV light
Which AAs contain oxygen or sulfur?
S, C, T, M (Serine, Cysteine, Threonine, Methionine)
Of the oxygen/sulfur containing AAs, which can ionize?
Cysteine
Of the oxygen/sulfur containing AAs, which behaves more alipathic?
Methionine
What AAs are acidic?
D and E (Aspartic acid and glutamic acid)
Where is histidine often found because of its ability to be either protonated or deprotonated
Active sites of enzymes, participating in acid-base catalysis
How is proline different from other AAs?
It has a cyclic structure (amino group is secondary, attached to an alpha-carbon and a side chain carbon
What is a unique characteristic of Cysteine?
Sulfur from one cysteine bonds to the sulfur of another cysteine, forming a disulfide bond
What type of reaction is disulfide bond formation, and what do they do to proteins?
Oxidation, stabilize 3D structures of extracellular proteins
What is the pKa of histidine, and why does that matter?
6, near physiological pH, allowing it to be a proton donor and acceptor, and the ability to be charged or not
What is the isoelectric point (pl)?
pH where the net charge of a molecule that has mroe than one ionizable group equals zero
What protein structure is important in the regulation f enzyme activity?
quaternary
What is the beginning and end of a primary structure?
alpha amino group (amino or N terminus) at the beginning, free carboxyl (caboxyl or C terminus) at the end
Most R groups have trans geometry, which AA allows for cis?
Proline
Is peptide bond formation favorable? If not, what drive the reaction?
No, ATP hydrolysis
What is the pitch of alpha-helices?
one turn/0.54 nm, or 3.6 residues/turn, or 0.15nm/residue
What stabilizes alpha helices?
Hydrogen bonding between the carbonyl oxygen in residue n. and amide hydrogen of residue n+4
What does proline indicate in alpha helices?
A kink or a bend
What stabilizes beta sheets?
Hydrogen bonds between strands
What influences stability of stacked beta sheets in tertiary structures?
Interactions between R groups
How many residues does it take to complete a beta turn?
4
What two AAs are commonly found in beta turns?
Proline and glycine
Name five effects that stabilize tertiary structures
Hydrogen bonds, electrostatic interactions, van der Waals, hydrophobic effect, disulfide bonds
Where is the information on folding tertiary structures contained?
In the primary structure
What is the charge of the stationary phase of cation exchange and anion exchange?
Negative and positive, respectively
What is the means of separation for gel filtration chromatography?
Size of protein
What elutes out first for gel filtration?
Larger proteins
What method of protein structure prediction generates very high resolution structures?
X-ray crystallography
What defines fibrous protein’s structure?
Secondary structure
What is the pseudo-repeat of alpha kertain?
(AbcDefg), where 1st and 4th residues have similar properties to each other (having a hydrophobic side chain)
What provides strength and stability to alpha-keratin helicies?
Disulfide bonds between cysteins
What secondary structure makes up fibroin?
anti-parallel beta sheets
What is the repeating unit of fibroin?
ser-gly-ala-gly
What is the repeating unit of collagen?
Gly-X-Y, where X is usually proline and Y is usually either hydroxyproline or hydroxylysine
Is collagen right or left handed, and how many residues per turn?
left handed; 3 residues per turn
