Proteins 1 Flashcards
1
Q
nonpolar amino acids
A
G
A
V
L
I
M
W
F
P
2
Q
polar amino acids
A
S
T
C
Y
N
Q
3
Q
acidic amino acids
A
E
D
4
Q
basic amino acids
A
K
R
H
5
Q
which amino acid has different hydrophobicity properties based on its charge
A
Histidine
6
Q
pKa values of the acids
A
4.4
7
Q
pKa value of Histidine
A
6
8
Q
pKa value of cysteine
A
8.5
9
Q
pKa value of tyrosine and lysine
A
10
10
Q
pKa value of arginine
A
12
11
Q
the higher the pKa value
A
the harder it is to remove a proton
12
Q
pKa values are heavily affected by their
A
environment
13
Q
conformations of proteins can change based on
A
pH and metals added
14
Q
antibodies can only bind at
A
neutral pH
15
Q
plant viruses are stable at
A
low pH
16
Q
at neutral pH plant viruses
A
fall apart and release RNA into the cell
17
Q
amino acids are connected to each other via
A
peptide bonds
18
Q
the peptide bond cannot rotate and therefore
A
holds 6 atoms in a plane
19
Q
the side chains will limit the rotations about
A
psi and phi
20
Q
limitations of backbone rotations can be shown in
A
Ramachandran plots
21
Q
glycine is known as
A
a helix breaker
22
Q
proline is known as a
A
conformation breaker
23
Q
5 types of interactions that hold proteins together
A
hydrogen bonds
hydrophobic interactions
van der waals
disulfide bridges
ionic bonds
24
Q
hydrophobic interactions occur when
A
nonpolar (hydrophobic) amino acids associate with each other and cluster together to hide from water
25
van der waals forces are
weak attractions between atoms due to oppositely polarized electron clouds.
26
proteins are made up of
portions with increasing organization
27
primary structure
amino acid sequence
28
secondary structure
angels and structure dictated by the amino acid composition
29
motif
portion of a protein that is repeated in other proteins
30
domain
portion of a protein that is physically separate and often has a particular function
31
quaternary/tertiary structure
domains and subunits come together to make the full structure
32
examples of folds/domains
globin folds
rossmann folds
33
all alpha helices are
right handed unless otherwise specified
34
alpha helix
relatively rigid structures that can be hydrophilic, amphipathic or hydrophobic
34
function of an alpha helix can be determined via
an Edmunson Wheel
35
what makes alpha helixes so strong
hydrogen bonds
36
in an alpha helix, where are the bases
outside the helix
37
helices can form
unusual features in the structure by virtue of their rigidity
38
helices are important in
membrane proteins/transmembrane proteins
39
signal sequences are
helices
40
beta sheets
are extremly stable structures used for domains and proteins that require stability
41
in beta sheets here are the side chains
the side chains point up and down from the plane of the sheet
42
beta sheets can either be
parallel or antiparallel
43
the most famous beta sheet fold
immunoglobulin domain
44
immunoglobulin domain
uses 7 beta strands to form a sandwich and is remarkably stable and protease resistant
45
4 ways a protein folds/misfolds
thermodynamic
kinetic
helper
heaven only knows
46
thermodynamic protein folding
usually small proteins
easily finds energy minimum on their own
47
kinetic protein folding
translation order probably controls folding
thought to be related to proteins that do not refold after denaturation
48
helper needed protein folding
mis-folded proteins need to be unfolded and refolded in chaperone protein complexes
includes improper cysteine bonds and proline conformations
49
heaven only know protein folding
how do they move????????
50
Hsp70 chaperones
DNaK and DnaJ
51
the HSP70 chaperones stabilize the newly synthesized protein in a
nonaggregated folding-competent state
52
Hsp60 chaperone
GroEL
53
transfering the protein into the central cavity of Hsp60 requires
the nucleotide exchange factor GrpE
54
what binds to GroEL in an ATP-dependent reaction and displaces the unfolded protein into an enclosed folding cage
GroES
55
how long is the protein inside the GroESL cage
10 seconds
the time needed for GroEL to complete one round of ATP hydrolysis (7 ATP)
56
binding of ATP to the opposite ring of GroEL induces
an allosteric change that triggers the opening of the folding chamber
57
Protein Disulfide Isomerase (PDI)
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
two proline conformations
cis and trans
59
cis proline
very tight turn
60
trans proline
less tight turn
61
Prolyl isomerase
peptidylpropyl isomerase
PPIase
an enzyme found in both prokaryotes and eukaryotes that interconverts the cis and trans isomers of peptide bonds with the amino acid proline
62
proline has an unusually conformationally restrained peptide bond due to
its cyclic structure with its side chain bonded to its secondary amine nitrogen
63
most amino acids have a strong energetic preference for
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
proteins with PPIase activity
cyclophilin
FKBPs
parvulin
65
some proteins need sugars covalently bound for
function
66
N-linked glycans attatch to a
nitrogen of asparagine or arginine side chains
67
N-linked glycosylation requires participation of a special lipid called
dolichol phosphate
68
o-linked glycans attatch to the
oxygen of serine, threonine, tyrosine, hydrolysine, or hydroxyproline side chains.
69
phosphoglycans are linked via
the phosphate of a phosphoserine
70
Why sugars?
stabilize proteins
increase solubility
important for function
monitor age
part of folding process
export in golgi
71
sugars can be used to moniter age of serum proteins and
target them for distruction
72
sugars on extracellular proteins are added
during export
73
what kind of sugar linking happens in the ER
N-linked glycosylation
74
what kind of sugar linking happens in the Golgi
O-glycosylation and N-glycosylation
75
expression of glycoproteins in mammalian cells will result in
mammalian type glycosylation
76
humans are the only species that produce
sialic acid
77
plant cells typically have glycans that contain extra
fucose and xylose residues
78
insect expression systems add
shorter N-glycans
79
yeast expression systems have a very different glycosylation pattern with only
mannose containing glycans
80
sugars in the mammalian expression system
fucose
GlcNAc
mannose
Galactose
sialic acid
81
early steps in glycoprotein synthesis in the ER are
very similar across eukaryotes
82
folding and ER glycosylation are connected processes so
any eukaryotic system could potentially yield a properly folded protein
83
it is now established that bacteria posses
both N-linked and O-linked glycosylation pathways
84
some phage carry their own transferases to ensure that the coat or genome is
glycosylated
85
protein phosphorylation is a major
post-translation process
86
protein phosphorylation happens on which amino acids
serine
threonine
tyrosine
OH group
87
example of using mutagenesis to mimic phosphorylation
phosphoserine into aspartic acid
88
lipidation is an example of a
post-translation process
89
examples of lipidation
GPI anchor
cholesterylation
myristoylation
palmitoylation
farnesylation
geranylgeranylation
90
what kinds of residues would you expect to see on the inside of the protein
greasy amino acids
91
what kinds of residues would you find at a subunit interface
hydrophobic
92
what kinds of residues would be in transmembrane helices
greasy
hydrophobic
93
what amino acid would you want in a flexible hoop
glycine
94
what amino acid would be in a catalytic active site where protons are thrown around
histidine
95
what amino acid puts a sharp bend in a loop
proline
96
the amino acid composition of a protein determines
the fold
97
the fold and amino acid composition determines
stability that is often related to function
98
some proteins are meant to move and flex to
do their job such as enzymes
99
some proteins are meant to be rocks so that they can
hang around for long periods of time
100
example of a stable protein
collagen
101
main amino acids in collagen
alanine
glycine
proline
102
why is collagen special
it is a left handed helix
103
collagen is so stable because it has
few places where proteases can attack
104
proteases attack
the peptide bond
105
example of floppy protein
kinases
106
signaling enzymes such as kinases are made to be
flexible to do their job, recognize and phosphorylate the target
107
collagen has a higher.... than kinases
activation energy
