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Biochem Exam 1 > Exam 1 > Flashcards

Exam 1 Flashcards

1
Q

What is the Gibbs free energy equation?

A

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

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2
Q

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

A

The reaction proceeds spontaneously in the forward direction and is exergonic

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3
Q

What does it mean when Δ G = 0?

A

The system is at equilibrium

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4
Q

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

A

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

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5
Q

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

A

Fermentation of glucose to ethanol

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6
Q

What is the hydrophobic effect?

A

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

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7
Q

How does hydrogen bonding affect water molecules?

A

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

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8
Q

Why do nonpolar molecules group together in water?

A

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

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9
Q

What is the Henderson-Hasselbalch equation?

A

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

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10
Q

What happens when the pH equals the pKa?

A

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

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11
Q

What does a lower pKa indicate?

A

A stronger acid

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12
Q

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

A

25:1 (96% uncharged)

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13
Q

What is the structure of an amino acid?

A

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

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14
Q

Name three neutral, weakly hydrophobic amino acids.

A

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

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15
Q

What is a zwitterion?

A

A molecule with both positive and negative charges simultaneously

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16
Q

Which amino acids have titratable groups?

A

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

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17
Q

What stabilizes secondary structures?

A

Hydrogen bonding between carbonyl oxygen and an amide hydrogen

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18
Q

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

A

Nuclear Magnetic Resonance

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19
Q

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

A

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

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20
Q

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

A

No O2 will bind, regardless of P(O2)

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21
Q

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

A

P50 will increase and binding is less efficient

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22
Q

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

A

The molecule will be less sensitive to pH change

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23
Q

What stabilizes tropocollagen?

A

Covalent cross linking of lysine side chains

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24
Q

What is a common strategy by which catalysis occurs?

A

Stabilization of the transition state

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25
Q

What contributes to a favorable reaction?

A

Change in enthalpy < 0, change in entropy > 0

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26
Q

How can an unfavorable reaction proceed?

A

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

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27
Q

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

A

Polar/charged, increases solubility

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28
Q

What stabilizes interactions between biological molecules?

A

Charged groups

29
Q

Why are charged groups important to enzymes?

A

used for substrate binding and/or catalysis

30
Q

What AAs are alipathic?

A

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

31
Q

What traits do alipathic AAs have?

A

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

32
Q

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

A

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

33
Q

What AAs are aromatic?

A

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

34
Q

What is a unique trait of aromatic AAs?

A

They absorb UV light

35
Q

Which AAs contain oxygen or sulfur?

A

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

36
Q

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

A

Cysteine

37
Q

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

A

Methionine

38
Q

What AAs are acidic?

A

D and E (Aspartic acid and glutamic acid)

39
Q

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

A

Active sites of enzymes, participating in acid-base catalysis

40
Q

How is proline different from other AAs?

A

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

41
Q

What is a unique characteristic of Cysteine?

A

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

42
Q

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

A

Oxidation, stabilize 3D structures of extracellular proteins

43
Q

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

A

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

44
Q

What is the isoelectric point (pl)?

A

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

45
Q

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

A

quaternary

46
Q

What is the beginning and end of a primary structure?

A

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

47
Q

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

A

Proline

48
Q

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

A

No, ATP hydrolysis

49
Q

What is the pitch of alpha-helices?

A

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

50
Q

What stabilizes alpha helices?

A

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

51
Q

What does proline indicate in alpha helices?

A

A kink or a bend

52
Q

What stabilizes beta sheets?

A

Hydrogen bonds between strands

53
Q

What influences stability of stacked beta sheets in tertiary structures?

A

Interactions between R groups

54
Q

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

A

4

55
Q

What two AAs are commonly found in beta turns?

A

Proline and glycine

56
Q

Name five effects that stabilize tertiary structures

A

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

57
Q

Where is the information on folding tertiary structures contained?

A

In the primary structure

58
Q

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

A

Negative and positive, respectively

59
Q

What is the means of separation for gel filtration chromatography?

A

Size of protein

60
Q

What elutes out first for gel filtration?

A

Larger proteins

61
Q

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

A

X-ray crystallography

62
Q

What defines fibrous protein’s structure?

A

Secondary structure

63
Q

What is the pseudo-repeat of alpha kertain?

A

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

64
Q

What provides strength and stability to alpha-keratin helicies?

A

Disulfide bonds between cysteins

65
Q

What secondary structure makes up fibroin?

A

anti-parallel beta sheets

66
Q

What is the repeating unit of fibroin?

A

ser-gly-ala-gly

67
Q

What is the repeating unit of collagen?

A

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

68
Q

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

A

left handed; 3 residues per turn

69
Q
A

Biochem Exam 1 (3 decks)

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