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CH531—Biochemistry > Chp 3 & 7—Proteins & Enzymes > Flashcards

Chp 3 & 7—Proteins & Enzymes Flashcards

1
Q
A

selenocysteine

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2
Q
A

pyrrolysine

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3
Q

draw a disulfide bond

A
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4
Q
A

competitive inhibition

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5
Q
A

noncompetitive inhibition

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6
Q
A

uncompetitive inhibition

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7
Q

only AA without a steric center

A

glycine

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8
Q

absolute AA configuration rules

A

R/S designation
R clockwise, S counterclockwise

S > O > N > C > H

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9
Q

relative AA configuration rules

A

D/L designation
D clockwise, L counterclockwise
COOH > R > N (corn)

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10
Q

most of nature uses ____ AAs

A

L

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11
Q

AA configuration fischer projections

A

H may be on top or bottom and it can be read normally

if H is on the side, flip the configuration

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12
Q

zwitterion

A

two ionizable groups with a 0 net charge

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13
Q

—- AAs have a 3rd ionizable group on the R chain

AAs?

A

7

REDCHKY
arginine, glutamic acid, aspartic acid, cysteine, histidine, lysine, tyrosine

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14
Q

AAs being amphoteric allows them to act as ——

A

buffers

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15
Q

isoelectic point (pI)

A

pH at which the zwitterion molecule exists

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16
Q

how to find pI

A

take average of pKa values “flanking” the 0 charge on the molecule

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17
Q

AA charge before pKa1

A

positive
COOH is present, not COO-

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18
Q

AA charge after pKa associated with N’

A

deprotonates to H2N
charge decreases

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19
Q

selenocysteine used in…

A

all organisms, though rarely

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20
Q

pyrrolysine used in…

A

archaea

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21
Q

phosphorylation

PTM

A

adds a phosphate to serine, threonine, or tyrosine

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22
Q

glycosylation

PTM

A

attaches a sugar, usually to an N or O, in an AA side chain

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23
Q

ubiquitination

PTM

A

adds ubiquitin to lysine of a target protein for degradation

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24
Q

SUMOylation

PTM

A

adds a small protein SUMO to a target protein
(similar to ubiqutin)

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25
Q

disulfide bond

PTM

A

covalently links the S atoms of 2 cysteine residues

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26
Q

acetylation

PTM

A

adds an acetyl group to N’ of a protein, or to lysine

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27
Q

lipidation

PTM

A

attaches a lipid to a protein

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28
Q

methylation

PTM

A

adds methyl group, usually at lysine or arginine

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29
Q

why is gene:protein complexity not 1:1?

A

folding
PTMs

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30
Q

how to draw peptide chains

A

H3N+ — wedge R — down carbonyl — N — dash R — up carbonyl — o-

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31
Q

draw peptides from —- to —

A

N’ to C’

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32
Q

nature of peptide bond

A

resonance gives double bond character (40%) which restricts rotation - planar

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33
Q

bonds flanking peptide bond

A

psi bond: C – C
phi bond: N – C

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34
Q

rotation of phi and psi bonds

A

allowed by limited by sterics
favored conformers given by Ramachandran plot

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35
Q

how to find possible proteins from # of AAs

A

20^#AAs = possible proteins

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36
Q

define 2° structure

A

series of conformations adopted by polypeptide strands

primarily alpha helices and beta sheets

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37
Q

helix promoter

A

alanine

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38
Q

helix breaker

A

proline

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39
Q

arrangement of B-sheets

A

parallel or antiparallel

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40
Q

motifs

A

supersecondary structures
unstable and cannot be isolated

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41
Q

examples of motifs (4)

A

B-turn/hairpin turn
Greek key
B barrel
B-a-B loop

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42
Q

define 3° structure

A

3D configuration of all 2° structures

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43
Q

globular proteins vs fibrous proteins

A

globular: spherical, soluble, diverse, domains & motifs

fibrous: 2° level, structural, insoluble

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44
Q

domains

A

large, stable functional regions of a globular protein

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45
Q

examples of domains

A

core/interior
exterior

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46
Q

core/interior residue characteristics
examples (5)

A

nonpolar

valine, leucine, isoleucine, methionine, phenylalanine

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47
Q

exterior residue characteristics
examples (5)

A

charged, polar
arginine, histidine, lysine, aspartic acid, glutamic acid

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48
Q

residues that can be in interior or exterior
examples (6)

A

uncharged polar (neutralized by H bonds in core)
serione, threonine, asparagine, glutamine, tyrosine, tryptophan

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49
Q

define 4° structure

A

association of 2+ 3° structures to form a multisubunit protein

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50
Q

fate of misfolded protein

A

labelled by ubiquitin and chopped

OR accumulate in RER and cause neurodegenerative disease

51
Q

speed of translation and folding

A

translation: 4 AA/sec
folding: nearly spontaneous

52
Q

Anfinsen’s dogma – postulate

A

N is determined by primary sequence

53
Q

Anfinsen’s dogma – evidence

A

spontaneous refolding of ribonuclease after denaturation

54
Q

Anfinsen’s dogma – caveats

A

experiment performed in vitro
ribonuclease is small
unfolded proteins are well known to exist

55
Q

Levinthal’s paradox – postulate

A

if folding was random, it would take a protein longer than the existence of the universe to find N

56
Q

3 folding models

A

Diffusion-collision model
Nucleation-condensation model
Hydrophobic-collapse theory

57
Q

explain diffusion collision

A

as a polypeptide is translated, “microdomains” form into 2° structures, which randomly collide, coalescing into 3° structures

stepwise

fewer conformations to sample as it goes

58
Q

explain nucleation condensation

A

a large stable nucleus acts as a seed/template for the remainder of folding

concerted mechanism for 2° and 3° folding

59
Q

explain hydrophobic collapse

A

as a polypeptide is translated, hydrophobic residues rapidly collapse to form a “core”, leading 2°/3° structure formation around the core

60
Q

problem with hydrophobic collapse

A

some proteins have no hydrophobic core

61
Q

5 energy landscapes

A

Levinthal’s golfcourse
idealized funnel
moat landscape
pathway landscape
rugged landscape

62
Q

levinthal’s golf course

A

represents the impossibility for U to find N
impossibility of Anfinsen’s dogma

63
Q

idealized funnel

A

represents Anfinsens’ dogma
does not account for unfolded proteins

64
Q

first landscape to have an energy barrier

A

moat

65
Q

problem with pathway landscape

A

too binary for our current understanding

66
Q

most accurage landscape

A

rugged landscape

67
Q

TS and I are represented by —— on landscape
unfolded proteins are represented by ——- on landscape

A

hills

kinetic traps

68
Q

molecular chaperones

A

bind to unfolded proteins to aid in folding or prevent misfolding

help escape kinetic traps

69
Q

amyloid fibrils

A

stable aggregates of misfolded proteins

70
Q

4 methods of protein sequencing

A

Berman degradation
Sanger’s method
Dansyl chloride method
Edman degradation

71
Q

modifies C’ to azide

A

Berman degradation

72
Q

allows us to identify 1st AA

A

Sanger’s method

73
Q

uses fluorescence to identify AAs

A

Dansyl chloride method

74
Q

best polypeptide sequencing

A

Edman degradation

75
Q

method for peptide synthesis

A

solid-phase peptide synthesis (SPPS)

76
Q

uses a resin bead

A

SPPS

77
Q

protects R groups during SPPS

A

PGs

78
Q

attached to N’ during SPPS

A

Fmoc

79
Q

only non protein enzyme

A

ribozymes

80
Q

simple protein enzymes

A

AAs only

81
Q

conjugated protein enzymes

A

AAs plus a non-protein component

82
Q

apoenzyme

A

protein component of enzyme

83
Q

cofactor

A

nonprotein component of enzyme

84
Q

holoenzyme

A

apoenzyme + cofactor

85
Q

two divisions of cofactors

A

inorganic (metallic)
organic (coenzymes)

86
Q

two divisions of inorganic cofactors

A

metal associated
metalloproteins

87
Q

two divisions of coenzymes

A

cosubstrates
prosthetic groups

88
Q

metal-associated metallic cofactors

A

bind, then leave

89
Q

metalloprotein

A

form tight associations; don’t leave even when digested

90
Q

cosubstrates

A

forms IMFs with enzyme; then leaves

91
Q

prosthetic groups

A

covalently linked to enzyme; don’t leave

92
Q

EC1

A

oxidoreductases

93
Q

EC2

A

transferases

94
Q

EC3

A

hydrolases

95
Q

EC4

A

lyases

96
Q

EC5

A

isomerases

97
Q

EC6

A

ligases

98
Q

oxidoreduxes

A

redox reactions

99
Q

transferases

A

transfer of functional groups

100
Q

hydrolases

A

hydrolysis reactions

101
Q

lyases

A

bond cleavage

102
Q

isomerases

A
103
Q

isomerases

A

isomerization

104
Q

ligases

A

bond formation/synthesis

105
Q

lock and key substrate binding

A

complementary shape of substrate and active site of enzyme

106
Q

induced fit substrate binding

A

substrate binding causes conformational change of enzyme

107
Q

enzyme kinetics equation

A
108
Q

enzymes use ——– reactions

A

energy coupling

109
Q

linease phase initially taken from——- graph

A

time vs [P]

110
Q

how to find Km

A

1/2 Vmax = y value
find x value on graph

111
Q

used to compare enzymes

A

specificity constant

112
Q

linear representation of V0 vs [S]

A

Lineweaver-Burk plot

113
Q

lineweaver burk plot axes

A

y: 1/V0
x: 1/[S]

114
Q

L-B plot y intercept

A

1/Vmax

115
Q

L-B plot x intercept

A

-1/Km

116
Q

3 types of reversible inhibition

A

competitive
noncompetitive
uncompetitive

117
Q

competitive inhibition

A

inhibitor has similar structure to substrate

118
Q

noncompetitive inhibition

A

inhibitor binds somewhere on enzyme besides active site, changing its conformation

119
Q

competitive inhibition effect on Vmax, Km

A

Vmax same
Km increases

120
Q

noncompetitive inhibition on Vmax, Km

A

Vmax decreases
Km no change

121
Q

uncompetitive inhibition

A

inhibitor binds after the substrate binds

122
Q

uncompetitive effect on Vmax, Km

A

both decrease

123
Q

uncompetitive effect on Vmax, Km

A

both decrease

CH531—Biochemistry (11 decks)

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