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Biochem 1 (WPH) > Proteins 2 - folding 09/05 Traish > Flashcards

Proteins 2 - folding 09/05 Traish Flashcards

1
Q

what is protein primary structure

A

order of aa’s

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2
Q

by convention, an aa polypeptide sequence is written from __-terminus to __-terminus

A

N-terminus to C-terminus

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3
Q

secondary structure consists of…

A

locally folded structures (a-helices, b-sheets, turns, random coils [loops]) dependent on H-bonding between a-N and a-C groups

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4
Q

T/F secondary structure depends upon H-bonding between R groups

A

False

depends upon H-bonding between primary amino and carbonyl

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5
Q

by convention, the __-terminus is left and the __-terminus is right in an aa polypeptide sequence

A

N-terminus left

C-terminus right

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6
Q

tertiary structure consists of…

A

3-D structure from interactions between domains in a single pp sequence

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7
Q

tertiary structure is dependent upon what kinds of intermolecular interactions

A

H-bonds, hydrophobic interactions, electrostatic interactions, van der Waal’s forces, disulfide bonds

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8
Q

quaternary structure is dependent upon what kinds of intermolecular interactions

A

H-bonds, hydrophobic interactions, electrostatic interactions, van der Waal’s forces, disulfide bonds (same as tertiary) BUT globular protein monomers are RARELY held together by disulfide bonds and never by other covalent linkages

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9
Q

do the same intermolecular interactions stabilize tertiary and quaternary structure?

A

yes they can

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10
Q

is hemoglobin a homo-oligomer or hetero-oligomer?

A

hetero-oligomer – 2 alpha subunits, 2 beta subunits

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11
Q

what is a homo-oligomer?

A

an oligomer composed of identical subunit monomers

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12
Q

what is a hetero-oligomer?

A

an oligomer composed of non-identical subunit monomers

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13
Q

a tetramer is__

A

an oligomer with 4 monomeric subunits

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14
Q

the bond between a-amino and a-carboxyl aa groups is called

A

a peptide bond

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15
Q

can a peptide bond twist/rotate? why?

A

very little – partial double bond character (delocalization of pi electrons)

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16
Q

quaternary structure consists of

A

the oligomerization of multiple monomeric subunits from separate pp sequences

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17
Q

how are the C=O and N-H bonds of a peptide bond oriented to one another?

A

parallel – usually antiparallel

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18
Q

T/F the O, C, N, and H of a peptide bond are nearly coplanar

A

true

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19
Q

what does it mean that a peptide bond is “metastable?”

A

proteins hydrolyze in an aqueous environment when a catalyst is present

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20
Q

T/F a peptide bond can rotate

A

false (double bond character)

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21
Q

T/F the N-C alpha and C-C alpha bonds can rotate?

A

true

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22
Q

the aa N-C alpha bond is called __

A

phi (O with |

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23
Q

the aa C-C alpha bond is called __

A

psi (pitchfork)

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24
Q

common secondary structures include

A

a helices, b sheets, turns, loops / coils (as yet unclassified)

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25
Q

what is a crystallographic repeat?

A

a periodically repeating pattern of atoms in 3D

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26
Q

what does a crystallographic repeat measurement (c) refer to?

A

distance parallel to the axis of a-helix over which the structure exactly repeats itself

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27
Q

a-helix pitch (p) refers to…

A

distance parallel to a-helix axis in one turn

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28
Q

a-helix rise (h) refers to

A

distance parallel to a-helix axis from one residue to next

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29
Q

a-helix (n) refers to

A

the number of residues… per turn, or repeat, or what have you

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30
Q

do R groups exist on exterior or interior of an a-helix?

A

exterior

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31
Q

2 aa’s that are likely to disrupt an a-helix include:

A

G, P

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32
Q

a “dihedral” angle is…

A

the angle between two planes

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33
Q

T/F the dihedral angle pairs, phi and psi, can differ from one residue from the next in an a-helix

A

false – dihedral angle pairs are the same for each residue

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34
Q

T/F a-helices are classified as “repetitive secondary structure”

A

true – their backbone phi and psi angles repeat

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35
Q

what are the phi and psi angles in an ideal, right-handed a-helix?

A

phi = -57.8
psi = -47.0
(- signifies counter clockwise)

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36
Q

what do + and - rotation angles in phi and psi refer to?

A 
\+ = clockwise rotation
- = ccw rotation
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37
Q

T/F a-helices are the most abundant helical conformation found in globular proteins

A

true

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38
Q

a-helices account for __ to __ percent of all globular protein residues

A

32-38%

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39
Q

average n in an a-helix is…

A

10 residues

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40
Q

H-bonds in an a-helix are between…

A

each backbone C=O and the backbone N-H 4 residues ahead (i+4)

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41
Q

T/F H-bonds in an a-helix are between each backbone N-H and the backbone C=O 4 residues ahead

A

false. between each backbone C=O and the backbone N-H 4 residues ahead (i+4)

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42
Q

X-ray data suggest that an a-helix repeats itself after __ residues

A

18

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43
Q

how many turns are there in an alpha helix repeat?

A

5

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44
Q

how many residues per a-helix turn?

A

3.6

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45
Q

a-helix pitch (p) is __ nm

A

.54 nm per turn

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46
Q

a-helix rise (h) is __ nm, or __ angstroms

A

.15 nm per residue

  • or-
    1. 5 A per residue
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47
Q

how many angstroms in a nanometer?

A

10

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48
Q

how many meters in an angstrom?

A

10^-10

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49
Q

how many angstroms in a meter?

A

10^10

50
Q

a stretched a-helix will have a (higher or lower) rise and a (higher or lower) n per turn

A

a stretched a-helix will have a higher rise and a lower number of residues per turn

51
Q

prolyl residues, adjacent bulky residues, adjacent branched residues ,and adjacent charged residues can all do what to an a-helix?

A

interrupt it

52
Q

how many polypeptide stretches are involved in an a-helix vs a b-sheet?

A

a-helix – single stretch

b-sheet – multiple stretch

53
Q

beta stretches consist of at least __ to __ aa’s

A

5-10

54
Q

a key difference between the H-bonds in a-helices vs b-sheets is…

A

b-sheets H-bond between different pp stretches

a-helices H-bond along the same strand

55
Q

why are b-sheets “pleated” ?

A

the alpha carbons alternate above and below the plane of the sheet

56
Q

T/F b-sheets can be parallel, antiparallel, or mixed

A

true

57
Q

what is a parallel b-sheet

A

adjacent stretches’ N-termini and C-termini run in same directions

58
Q

what is an anti-parallel b-sheet

A

adjacent stretches’ N-termini and C-termini run in opposite directions

59
Q

golubular proteins cointain __ to __ percent b-sheets

A

20-28%

60
Q

what is the basic unit of a b-sheet

A

b-strand (n=2 residues/turn)

61
Q

a b-strand can be thought of one turn of a helix with n = __ residues per turn

A

n=2 residues per turn

62
Q

the backbone dihedral angels, phi and psi, in a b-strand, are:

A 
phi = -120
psi = +120
63
Q

translational “rise” (h) in a beta sheet is __ for antiparallel strands

A

3.2 nm per residue

64
Q

translational “rise” (h) in a beta sheet is __ for parallel strands

A

3.4 nm per residue

65
Q

is translational “rise” (h) in a beta sheet greater for parallel strands or antiparallel strands?

A

h is greater in parallel strands (3.4 nm vs 3.2 nm)

66
Q

are there any intrasegment H-bonds or van der Waal’s forces in a b-sheet?

A

no – only intersegment forces – due to the extended nature of the chain

67
Q

what is the average length of a b-pleated sheet?

A

6 residues

68
Q

most b-pleated sheets contain fewer than __ strands

A

fewer than 6 strands

69
Q

do side chains from adjacent residues in a b-sheet interact with each other?

A

no – because they exist on alternating sides of the sheet

70
Q

can b-sheets exhibit amphiphilicity with one face polar and one face nonpolar? can a-helices?

A

yes in both cases

71
Q

can a-helices be formed from strands from distant portions of the pp chain? can b-sheets?

A

a-helices - no

b-sheets - yes

72
Q

which is thought to be more intrinsically stable, antiparallel b-sheets or parallel b-sheets? why?

A

antiparallel

  • more optimal orientation of hydrogen bonds
  • peptide dipoles cancel
73
Q

are side chains closer / interacting more strongly in parallel or antiparallel b-sheets?

A

same in both. side chains can match up above and below the plane of the sheet either way

74
Q

the most stretched “helix”, with n=2 residues per turn, is also known as…

A

a beta sheet

75
Q

what kind of secondary structure is pervasive in silk versus wool?

A 
silk = b-sheets (strong & inextensible because already maximally stretched, flexible because only H-bonding)
wool = a-helices (stretchy because coiled and H-bonds along axis of fiber, not perpendicular)
76
Q

what is the typical secondary structure of an immunoglobulin fold (hypervariable domain / antigen binding site) ?

A

two antiparallel b-sheets in a barrel structure

77
Q

what is the primary function of a “turn” in protein secondary structure?

A

reverse the direction of the polypeptide chain

78
Q

where are turns primarily located?

A

on the protein surface

79
Q

are residues on a turn mostly hydrophobic or hydrophilic?

A

polar and charged because they exist usually at surface where protein must be turned back in

80
Q

T/F antibody recognition, phosphorylation, glycosylation, and hydroxilation sites are frequently found at or adjacent to “turns”

A

True – turns mostly located at surface with polar and charged residues as it turns the pp sequence back toward protein

81
Q

approximately what proportion of globular protein residues are “turns” ?

A

~1/3

82
Q

approximately __ to __ percent of residues in globular proteins can be calssified as participating in a-helices, b-sheets, or reverse turns

A

80-90%

83
Q

this secondary structure is compact and globular in structure

A

loop

84
Q

loops contain between __ and __ residues

A

6 and 16

85
Q

T/F like turns, loops generally contain polar residues and are predominantly found at the protein surface

A

true

86
Q

between a-helices, b-sheets, turns, and loops, this is the order of frequence in globular proteins

A

a-helices & turns (most common)

loops & b-sheets (less common)

87
Q

T/F in globular proteins, a-helices and turns are more common than loops and b-sheets

A

true

88
Q

describe the hydrophobic effect in protein folding

A

non polar side chains tend to be buried in the center of proteins with polar chains on outside

89
Q

T/F hemoglobin exists as a single polypeptide chain

A

false – it is a tetramer

90
Q

T/F myoglobin exists as a single polypeptide chain

A

true – it is a monomer

91
Q

what is the name of the “O2 warehouse” protein that stores oxygen in muscle tissue?

A

myoglobin

92
Q

T/F fibrous proteins are elongated molecules with well-defined secondary structures that play structural roles in cells (skin, connective tissue, hair, silk)

A

true

93
Q

T/F alpha-keratin, fibroin, and collagen are examples of globular proteins

A

false – they are fibrous proteins

94
Q

T/F a “domain” is a compact, locally folded region of tertiary structure

A

true

95
Q

T/F a protein domain can be classified as predominantly a-helix, predominantly b-sheet, or mixed

A

true

96
Q

T/F beta sheets can be twisted

A

true – they are usually twisted or wrapped into barrel structures

97
Q

T/F “random coil” secondary structures are sometimes referred to as “turns”

A

false – they are sometimes referred to as “loops”

98
Q

is the conformational entropy change of protein folding + or -, favorable or unfavorable?

A

-, unfavorable

99
Q

is the enthalpy change arising from protein folding + or -, favorable or unfavorable?

A

-, favorable

100
Q

is the entropy change of burying hydrophobic groups in protein folding + or -, favorable or unfavorable?

A

+, favorable

101
Q

how does the hydrophobic effect in protein folding increase entropy?

A

it eliminates the orderly formation of “hydration shells” along hydrophobic surfaces. adjacent to hydrophilic surfaces, H2O is not restricted in orientation or mobility

102
Q

what two thermodynamic factors does Gibbs free energy combine?

A

enthalpy and entropy

103
Q

what is the equation for Gibbs free energy of a system

A 
dG = dH - TdS
"G = HoTS"
104
Q

T/F when calculating Gibbs free energy of protein folding, you must remember to account for dH, dS, and T of both protein and solvent

A

true.
dH = dHp + dHs
dS = dSp + dSs

105
Q

is protein folding spontaneous when dG is + or - ?

A

negative dG is spontaneous

106
Q

what scientist performed the experiment to demonstrate that protein folding depended on primary structure?

A

Nobel laureate Christian Anfinsen

107
Q

what protein did C. Anfinsen denature in his experiment with protein folding?

A

ribonuclease

108
Q

what is the normal function of ribonuclease?

A

hydrolyze RNA into single nucleotides

109
Q

what organic solvent did C. Anfinsen use to denature ribonuclease in his experiment with protein folding?

A

urea

(disrupts hydrogen bonds in protein by replacing them with hydrogen bonds with itself

110
Q

what substance did C. Anfinsen use to reduce the disulfide bonds in ribonuclease in his experiment with protein folding?

A

beta-mercaptoethanol

111
Q

why were small amounts of beta-mercaptoethanol needed to ensure appropriate renaturation of ribonuclease in c. Anfinsen’s experiments with protein folding?

A

2ME (b-mercaptoethanol) was needed to allow inappropriate disulfide bonds to break and find the most stable conformation

112
Q

how many disulfide bonds are involved in the tertiary structure of ribonuclease?

A

4

113
Q

how many cysteine residues are involved in the tertiary structure of ribonuclease?

A

8

114
Q

what are the odds of approprate renaturation of ribonuclease if determined randomly (not by primary pp sequence?)

A

1/71/51/3*1/1 = 1/105 = <1%

115
Q

what was the rate of ribonuclease function restoration (appropriate renaturation) achieved by C. Anfinsen in his experiments with protein folding?

A

97%

116
Q

how does beta-mercaptoethanol disrupt disulfide bonds?

A

it is a thiol agent that reduces disulfide bonds as it is oxidized into dimers joined by disulfide bonds itself

117
Q

T/F a molecule containing -S-S- bridges has a larger number of conformations available in the unfolded form than does a comparable protein without the bridges

A

False

-S-S- bridges reduce the number of conformations available to an unfolded protein

118
Q

what degree of protein structure is involved in allosteric regulation?

A 
quaternary structure
(requires interactions with other proteins / molecules -- e.g. hemoglobin)
119
Q

this amino acid, found in milk, eggs, and lime but not in corn or dry cereal, is a pre-courser of vitamin B3 and a lack may cause dermatitis

A

W

e.g. southern corn diet vs mexican lime+corn diet

120
Q

T/F the Linus Pauling postulates re polypeptide conformations include:

  • bond length and angles should be distorted as little as possible
  • no two atoms should violate each other’s van der Waal’s radii
  • amide group remains planar and trans config (phi & psi rotation only)
  • non-covalent usually H-bonds between N and C groups stabilize folding
A

true

Biochem 1 (WPH) (15 decks)

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