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GSBS Biochem > Proteins 1 > Flashcards

Proteins 1 Flashcards

1
Q

nonpolar amino acids

A

G
A
V
L
I
M
W
F
P

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2
Q

polar amino acids

A

S
T
C
Y
N
Q

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3
Q

acidic amino acids

A

E
D

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4
Q

basic amino acids

A

K
R
H

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5
Q

which amino acid has different hydrophobicity properties based on its charge

A

Histidine

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6
Q

pKa values of the acids

A

4.4

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7
Q

pKa value of Histidine

A

6

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8
Q

pKa value of cysteine

A

8.5

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9
Q

pKa value of tyrosine and lysine

A

10

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10
Q

pKa value of arginine

A

12

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11
Q

the higher the pKa value

A

the harder it is to remove a proton

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12
Q

pKa values are heavily affected by their

A

environment

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13
Q

conformations of proteins can change based on

A

pH and metals added

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14
Q

antibodies can only bind at

A

neutral pH

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15
Q

plant viruses are stable at

A

low pH

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16
Q

at neutral pH plant viruses

A

fall apart and release RNA into the cell

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17
Q

amino acids are connected to each other via

A

peptide bonds

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18
Q

the peptide bond cannot rotate and therefore

A

holds 6 atoms in a plane

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19
Q

the side chains will limit the rotations about

A

psi and phi

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20
Q

limitations of backbone rotations can be shown in

A

Ramachandran plots

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21
Q

glycine is known as

A

a helix breaker

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22
Q

proline is known as a

A

conformation breaker

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23
Q

5 types of interactions that hold proteins together

A

hydrogen bonds
hydrophobic interactions
van der waals
disulfide bridges
ionic bonds

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24
Q

hydrophobic interactions occur when

A

nonpolar (hydrophobic) amino acids associate with each other and cluster together to hide from water

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25
Q

van der waals forces are

A

weak attractions between atoms due to oppositely polarized electron clouds.

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26
Q

proteins are made up of

A

portions with increasing organization

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27
Q

primary structure

A

amino acid sequence

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28
Q

secondary structure

A

angels and structure dictated by the amino acid composition

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29
Q

motif

A

portion of a protein that is repeated in other proteins

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30
Q

domain

A

portion of a protein that is physically separate and often has a particular function

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31
Q

quaternary/tertiary structure

A

domains and subunits come together to make the full structure

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32
Q

examples of folds/domains

A

globin folds
rossmann folds

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33
Q

all alpha helices are

A

right handed unless otherwise specified

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34
Q

alpha helix

A

relatively rigid structures that can be hydrophilic, amphipathic or hydrophobic

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34
Q

function of an alpha helix can be determined via

A

an Edmunson Wheel

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35
Q

what makes alpha helixes so strong

A

hydrogen bonds

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36
Q

in an alpha helix, where are the bases

A

outside the helix

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37
Q

helices can form

A

unusual features in the structure by virtue of their rigidity

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38
Q

helices are important in

A

membrane proteins/transmembrane proteins

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39
Q

signal sequences are

A

helices

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40
Q

beta sheets

A

are extremly stable structures used for domains and proteins that require stability

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41
Q

in beta sheets here are the side chains

A

the side chains point up and down from the plane of the sheet

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42
Q

beta sheets can either be

A

parallel or antiparallel

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43
Q

the most famous beta sheet fold

A

immunoglobulin domain

44
Q

immunoglobulin domain

A

uses 7 beta strands to form a sandwich and is remarkably stable and protease resistant

45
Q

4 ways a protein folds/misfolds

A

thermodynamic
kinetic
helper
heaven only knows

46
Q

thermodynamic protein folding

A

usually small proteins
easily finds energy minimum on their own

47
Q

kinetic protein folding

A

translation order probably controls folding
thought to be related to proteins that do not refold after denaturation

48
Q

helper needed protein folding

A

mis-folded proteins need to be unfolded and refolded in chaperone protein complexes
includes improper cysteine bonds and proline conformations

49
Q

heaven only know protein folding

A

how do they move????????

50
Q

Hsp70 chaperones

A

DNaK and DnaJ

51
Q

the HSP70 chaperones stabilize the newly synthesized protein in a

A

nonaggregated folding-competent state

52
Q

Hsp60 chaperone

A

GroEL

53
Q

transfering the protein into the central cavity of Hsp60 requires

A

the nucleotide exchange factor GrpE

54
Q

what binds to GroEL in an ATP-dependent reaction and displaces the unfolded protein into an enclosed folding cage

A

GroES

55
Q

how long is the protein inside the GroESL cage

A

10 seconds
the time needed for GroEL to complete one round of ATP hydrolysis (7 ATP)

56
Q

binding of ATP to the opposite ring of GroEL induces

A

an allosteric change that triggers the opening of the folding chamber

57
Q

Protein Disulfide Isomerase (PDI)

A

an enzyme in the ER in eukaryotes that catalyzes the formation and breakage of disulfide bonds between cysteine residues within proteins as they fold.

58
Q

two proline conformations

A

cis and trans

59
Q

cis proline

A

very tight turn

60
Q

trans proline

A

less tight turn

61
Q

Prolyl isomerase
peptidylpropyl isomerase
PPIase

A

an enzyme found in both prokaryotes and eukaryotes that interconverts the cis and trans isomers of peptide bonds with the amino acid proline

62
Q

proline has an unusually conformationally restrained peptide bond due to

A

its cyclic structure with its side chain bonded to its secondary amine nitrogen

63
Q

most amino acids have a strong energetic preference for

A

the trans peptide bond conformation due to steric hindrance, but prolines unusual structure stabilizes the cis form so both isomers are populated under biologically relevant conditions.

64
Q

proteins with PPIase activity

A

cyclophilin
FKBPs
parvulin

65
Q

some proteins need sugars covalently bound for

A

function

66
Q

N-linked glycans attatch to a

A

nitrogen of asparagine or arginine side chains

67
Q

N-linked glycosylation requires participation of a special lipid called

A

dolichol phosphate

68
Q

o-linked glycans attatch to the

A

oxygen of serine, threonine, tyrosine, hydrolysine, or hydroxyproline side chains.

69
Q

phosphoglycans are linked via

A

the phosphate of a phosphoserine

70
Q

Why sugars?

A

stabilize proteins
increase solubility
important for function
monitor age
part of folding process
export in golgi

71
Q

sugars can be used to moniter age of serum proteins and

A

target them for distruction

72
Q

sugars on extracellular proteins are added

A

during export

73
Q

what kind of sugar linking happens in the ER

A

N-linked glycosylation

74
Q

what kind of sugar linking happens in the Golgi

A

O-glycosylation and N-glycosylation

75
Q

expression of glycoproteins in mammalian cells will result in

A

mammalian type glycosylation

76
Q

humans are the only species that produce

A

sialic acid

77
Q

plant cells typically have glycans that contain extra

A

fucose and xylose residues

78
Q

insect expression systems add

A

shorter N-glycans

79
Q

yeast expression systems have a very different glycosylation pattern with only

A

mannose containing glycans

80
Q

sugars in the mammalian expression system

A

fucose
GlcNAc
mannose
Galactose
sialic acid

81
Q

early steps in glycoprotein synthesis in the ER are

A

very similar across eukaryotes

82
Q

folding and ER glycosylation are connected processes so

A

any eukaryotic system could potentially yield a properly folded protein

83
Q

it is now established that bacteria posses

A

both N-linked and O-linked glycosylation pathways

84
Q

some phage carry their own transferases to ensure that the coat or genome is

A

glycosylated

85
Q

protein phosphorylation is a major

A

post-translation process

86
Q

protein phosphorylation happens on which amino acids

A

serine
threonine
tyrosine
OH group

87
Q

example of using mutagenesis to mimic phosphorylation

A

phosphoserine into aspartic acid

88
Q

lipidation is an example of a

A

post-translation process

89
Q

examples of lipidation

A

GPI anchor
cholesterylation
myristoylation
palmitoylation
farnesylation
geranylgeranylation

90
Q

what kinds of residues would you expect to see on the inside of the protein

A

greasy amino acids

91
Q

what kinds of residues would you find at a subunit interface

A

hydrophobic

92
Q

what kinds of residues would be in transmembrane helices

A

greasy
hydrophobic

93
Q

what amino acid would you want in a flexible hoop

A

glycine

94
Q

what amino acid would be in a catalytic active site where protons are thrown around

A

histidine

95
Q

what amino acid puts a sharp bend in a loop

A

proline

96
Q

the amino acid composition of a protein determines

A

the fold

97
Q

the fold and amino acid composition determines

A

stability that is often related to function

98
Q

some proteins are meant to move and flex to

A

do their job such as enzymes

99
Q

some proteins are meant to be rocks so that they can

A

hang around for long periods of time

100
Q

example of a stable protein

A

collagen

101
Q

main amino acids in collagen

A

alanine
glycine
proline

102
Q

why is collagen special

A

it is a left handed helix

103
Q

collagen is so stable because it has

A

few places where proteases can attack

104
Q

proteases attack

A

the peptide bond

105
Q

example of floppy protein

A

kinases

106
Q

signaling enzymes such as kinases are made to be

A

flexible to do their job, recognize and phosphorylate the target

107
Q

collagen has a higher…. than kinases

A

activation energy

GSBS Biochem (13 decks)

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