Exam 1

Question 1

What is the Gibbs free energy equation?

Answer 1

Δ G = Δ H - TΔ S, where Δ H is enthalpy and Δ S is entropy

Question 2

What does a Δ G < 0 indicate about a reaction?

Answer 2

The reaction proceeds spontaneously in the forward direction and is exergonic

Question 3

What does it mean when Δ G = 0?

Answer 3

The system is at equilibrium

Question 4

What is an endergonic reaction, and what does its Δ G look like?

Answer 4

An endergonic reaction requires additional energy to proceed and has a Δ G > 0

Question 5

Give an example of a reaction driven by both enthalpy and entropy.

Answer 5

Fermentation of glucose to ethanol

Question 6

What is the hydrophobic effect?

Answer 6

The tendency of nonpolar molecules to self-associate in water, increasing water entropy

Question 7

How does hydrogen bonding affect water molecules?

Answer 7

Hydrogen bonds between water molecules are weak and easily broken, contributing to favorable enthalpy

Question 8

Why do nonpolar molecules group together in water?

Answer 8

Grouping reduces the number of water molecules needed to surround them, increasing the entropy of the water

Question 9

What is the Henderson-Hasselbalch equation?

Answer 9

pH = pKa +
log([A-]/[A-][HA])

Question 10

What happens when the pH equals the pKa?

Answer 10

The concentration of the conjugate base [A-] equals the concentration of the acid [HA]

Question 11

What does a lower pKa indicate?

Answer 11

A stronger acid

Question 12

At pH = 7.4, what is the ratio of uncharged histidine to protonated histidine?

Answer 12

25:1 (96% uncharged)

Question 13

What is the structure of an amino acid?

Answer 13

An amino group (-NH2), a carboxyl group (-COOH), and a side chain (R)

Question 14

Name three neutral, weakly hydrophobic amino acids.

Answer 14

Alanine (A), Glycine (G), and Valine (V)

Question 15

What is a zwitterion?

Answer 15

A molecule with both positive and negative charges simultaneously

Question 16

Which amino acids have titratable groups?

Answer 16

Arginine, Aspartic acid, Cysteine, Glutamic acid, Histidine, Lysine, and Tyrosine

Question 17

What stabilizes secondary structures?

Answer 17

Hydrogen bonding between carbonyl oxygen and an amide hydrogen

Question 18

What technique allows one to view multiple conformations of small proteins?

Answer 18

Nuclear Magnetic Resonance

Question 19

How are the alpha-helicies in keratin and L-helicies in tropocollagen similar?

Answer 19

Both involve hydrogen bonding between a carbonyl oxygen and an amide hydrogen

Question 20

What happens if the proximal histidine in Mb is replaced by alanine?

Answer 20

No O2 will bind, regardless of P(O2)

Question 21

What happens if the distal histidine in Mb is replaced by alanine?

Answer 21

P50 will increase and binding is less efficient

Question 22

What would happen if a histidine that lines the water-filled cavity was replaced by lysine, assuming lysine still binds to 2,3-BPG?

Answer 22

The molecule will be less sensitive to pH change

Question 23

What stabilizes tropocollagen?

Answer 23

Covalent cross linking of lysine side chains

Question 24

What is a common strategy by which catalysis occurs?

Answer 24

Stabilization of the transition state

Question 25

What contributes to a favorable reaction?

Answer 25

Change in enthalpy < 0, change in entropy > 0

Question 26

How can an unfavorable reaction proceed?

Answer 26

By being coupled to a favorable reaction (commonly ATP hydrolysis)

Question 27

What molecules interact favorable with H2O, and what effect does this have on said molecules?

Answer 27

Polar/charged, increases solubility

Question 28

What stabilizes interactions between biological molecules?

Answer 28

Charged groups

Question 29

Why are charged groups important to enzymes?

Answer 29

used for substrate binding and/or catalysis

Question 30

What AAs are alipathic?

Answer 30

G, A, V, L, I (Glycine, Alanine, Valine, Leucine, Isoleucine)

Question 31

What traits do alipathic AAs have?

Answer 31

Side chains are entirely C and H, and are hydrophobic (except for glycine)

Question 32

What is the relationship between hydrophobicity and amount of Cs in the side chain?

Answer 32

Hydrophobicity increases as Cs increase (leucine > valine > alanine)

Question 33

What AAs are aromatic?

Answer 33

F, W, Y (phenylalanine, tryptophan, tyrosine)

Question 34

What is a unique trait of aromatic AAs?

Answer 34

They absorb UV light

Question 35

Which AAs contain oxygen or sulfur?

Answer 35

S, C, T, M (Serine, Cysteine, Threonine, Methionine)

Question 36

Of the oxygen/sulfur containing AAs, which can ionize?

Answer 36

Cysteine

Question 37

Of the oxygen/sulfur containing AAs, which behaves more alipathic?

Answer 37

Methionine

Question 38

What AAs are acidic?

Answer 38

D and E (Aspartic acid and glutamic acid)

Question 39

Where is histidine often found because of its ability to be either protonated or deprotonated

Answer 39

Active sites of enzymes, participating in acid-base catalysis

Question 40

How is proline different from other AAs?

Answer 40

It has a cyclic structure (amino group is secondary, attached to an alpha-carbon and a side chain carbon

Question 41

What is a unique characteristic of Cysteine?

Answer 41

Sulfur from one cysteine bonds to the sulfur of another cysteine, forming a disulfide bond

Question 42

What type of reaction is disulfide bond formation, and what do they do to proteins?

Answer 42

Oxidation, stabilize 3D structures of extracellular proteins

Question 43

What is the pKa of histidine, and why does that matter?

Answer 43

6, near physiological pH, allowing it to be a proton donor and acceptor, and the ability to be charged or not

Question 44

What is the isoelectric point (pl)?

Answer 44

pH where the net charge of a molecule that has mroe than one ionizable group equals zero

Question 45

What protein structure is important in the regulation f enzyme activity?

Answer 45

quaternary

Question 46

What is the beginning and end of a primary structure?

Answer 46

alpha amino group (amino or N terminus) at the beginning, free carboxyl (caboxyl or C terminus) at the end

Question 47

Most R groups have trans geometry, which AA allows for cis?

Answer 47

Proline

Question 48

Is peptide bond formation favorable? If not, what drive the reaction?

Answer 48

No, ATP hydrolysis

Question 49

What is the pitch of alpha-helices?

Answer 49

one turn/0.54 nm, or 3.6 residues/turn, or 0.15nm/residue

Question 50

What stabilizes alpha helices?

Answer 50

Hydrogen bonding between the carbonyl oxygen in residue n. and amide hydrogen of residue n+4

Question 51

What does proline indicate in alpha helices?

Answer 51

A kink or a bend

Question 52

What stabilizes beta sheets?

Answer 52

Hydrogen bonds between strands

Question 53

What influences stability of stacked beta sheets in tertiary structures?

Answer 53

Interactions between R groups

Question 54

How many residues does it take to complete a beta turn?

Answer 54

4

Question 55

What two AAs are commonly found in beta turns?

Answer 55

Proline and glycine

Question 56

Name five effects that stabilize tertiary structures

Answer 56

Hydrogen bonds, electrostatic interactions, van der Waals, hydrophobic effect, disulfide bonds

Question 57

Where is the information on folding tertiary structures contained?

Answer 57

In the primary structure

Question 58

What is the charge of the stationary phase of cation exchange and anion exchange?

Answer 58

Negative and positive, respectively

Question 59

What is the means of separation for gel filtration chromatography?

Answer 59

Size of protein

Question 60

What elutes out first for gel filtration?

Answer 60

Larger proteins

Question 61

What method of protein structure prediction generates very high resolution structures?

Answer 61

X-ray crystallography

Question 62

What defines fibrous protein's structure?

Answer 62

Secondary structure

Question 63

What is the pseudo-repeat of alpha kertain?

Answer 63

(AbcDefg), where 1st and 4th residues have similar properties to each other (having a hydrophobic side chain)

Question 64

What provides strength and stability to alpha-keratin helicies?

Answer 64

Disulfide bonds between cysteins

Question 65

What secondary structure makes up fibroin?

Answer 65

anti-parallel beta sheets

Question 66

What is the repeating unit of fibroin?

Answer 66

ser-gly-ala-gly

Question 67

What is the repeating unit of collagen?

Answer 67

Gly-X-Y, where X is usually proline and Y is usually either hydroxyproline or hydroxylysine

Question 68

Is collagen right or left handed, and how many residues per turn?

Answer 68

left handed; 3 residues per turn