Chp 3 & 7—Proteins & Enzymes Flashcards
(123 cards)
1
Q
A
selenocysteine
2
Q
A
pyrrolysine
3
Q
draw a disulfide bond
A
4
Q
A
competitive inhibition
5
Q
A
noncompetitive inhibition
6
Q
A
uncompetitive inhibition
7
Q
only AA without a steric center
A
glycine
8
Q
absolute AA configuration rules
A
R/S designation
R clockwise, S counterclockwise
S > O > N > C > H
9
Q
relative AA configuration rules
A
D/L designation
D clockwise, L counterclockwise
COOH > R > N (corn)
10
Q
most of nature uses ____ AAs
A
L
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
12
Q
zwitterion
A
two ionizable groups with a 0 net charge
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
14
Q
AAs being amphoteric allows them to act as ——
A
buffers
15
Q
isoelectic point (pI)
A
pH at which the zwitterion molecule exists
16
Q
how to find pI
A
take average of pKa values “flanking” the 0 charge on the molecule
17
Q
AA charge before pKa1
A
positive
COOH is present, not COO-
18
Q
AA charge after pKa associated with N’
A
deprotonates to H2N
charge decreases
19
Q
selenocysteine used in…
A
all organisms, though rarely
20
Q
pyrrolysine used in…
A
archaea
21
Q
phosphorylation
PTM
A
adds a phosphate to serine, threonine, or tyrosine
22
Q
glycosylation
PTM
A
attaches a sugar, usually to an N or O, in an AA side chain
23
Q
ubiquitination
PTM
A
adds ubiquitin to lysine of a target protein for degradation
24
Q
SUMOylation
PTM
A
adds a small protein SUMO to a target protein
(similar to ubiqutin)
25
disulfide bond
| PTM
covalently links the S atoms of 2 cysteine residues
26
acetylation
| PTM
adds an acetyl group to N' of a protein, or to lysine
27
lipidation
| PTM
attaches a lipid to a protein
28
methylation
| PTM
adds methyl group, usually at lysine or arginine
29
why is gene:protein complexity not 1:1?
folding
PTMs
30
how to draw peptide chains
H3N+ --- wedge R --- down carbonyl --- N --- dash R --- up carbonyl --- o-
31
draw peptides from ---- to ---
N' to C'
32
nature of peptide bond
resonance gives double bond character (40%) which restricts rotation - planar
33
bonds flanking peptide bond
psi bond: C -- C
phi bond: N -- C
34
rotation of phi and psi bonds
allowed by limited by sterics
favored conformers given by Ramachandran plot
35
how to find possible proteins from # of AAs
20^#AAs = possible proteins
36
define 2° structure
series of conformations adopted by polypeptide strands
primarily alpha helices and beta sheets
37
helix promoter
alanine
38
helix breaker
proline
39
arrangement of B-sheets
parallel or antiparallel
40
motifs
supersecondary structures
unstable and cannot be isolated
41
examples of motifs (4)
B-turn/hairpin turn
Greek key
B barrel
B-a-B loop
42
define 3° structure
3D configuration of all 2° structures
43
globular proteins vs fibrous proteins
globular: spherical, soluble, diverse, domains & motifs
fibrous: 2° level, structural, insoluble
44
domains
large, stable functional regions of a globular protein
45
examples of domains
core/interior
exterior
46
core/interior residue characteristics
examples (5)
nonpolar
valine, leucine, isoleucine, methionine, phenylalanine
47
exterior residue characteristics
examples (5)
charged, polar
arginine, histidine, lysine, aspartic acid, glutamic acid
48
residues that can be in interior or exterior
examples (6)
uncharged polar (neutralized by H bonds in core)
serione, threonine, asparagine, glutamine, tyrosine, tryptophan
49
define 4° structure
association of 2+ 3° structures to form a multisubunit protein
50
fate of misfolded protein
labelled by ubiquitin and chopped
OR accumulate in RER and cause neurodegenerative disease
51
speed of translation and folding
translation: 4 AA/sec
folding: nearly spontaneous
52
Anfinsen's dogma -- postulate
N is determined by primary sequence
53
Anfinsen's dogma -- evidence
spontaneous refolding of ribonuclease after denaturation
54
Anfinsen's dogma -- caveats
experiment performed in vitro
ribonuclease is small
unfolded proteins are well known to exist
55
Levinthal's paradox -- postulate
if folding was random, it would take a protein longer than the existence of the universe to find N
56
3 folding models
Diffusion-collision model
Nucleation-condensation model
Hydrophobic-collapse theory
57
explain diffusion collision
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
explain nucleation condensation
a large stable nucleus acts as a seed/template for the remainder of folding
concerted mechanism for 2° and 3° folding
59
explain hydrophobic collapse
as a polypeptide is translated, hydrophobic residues rapidly collapse to form a "core", leading 2°/3° structure formation around the core
60
problem with hydrophobic collapse
some proteins have no hydrophobic core
61
5 energy landscapes
Levinthal's golfcourse
idealized funnel
moat landscape
pathway landscape
rugged landscape
62
levinthal's golf course
represents the impossibility for U to find N
impossibility of Anfinsen's dogma
63
idealized funnel
represents Anfinsens' dogma
does not account for unfolded proteins
64
first landscape to have an energy barrier
moat
65
problem with pathway landscape
too binary for our current understanding
66
most accurage landscape
rugged landscape
67
TS and I are represented by ------ on landscape
unfolded proteins are represented by ------- on landscape
hills
kinetic traps
68
molecular chaperones
bind to unfolded proteins to aid in folding or prevent misfolding
help escape kinetic traps
69
amyloid fibrils
stable aggregates of misfolded proteins
70
4 methods of protein sequencing
Berman degradation
Sanger's method
Dansyl chloride method
Edman degradation
71
modifies C' to azide
Berman degradation
72
allows us to identify 1st AA
Sanger's method
73
uses fluorescence to identify AAs
Dansyl chloride method
74
best polypeptide sequencing
Edman degradation
75
method for peptide synthesis
solid-phase peptide synthesis (SPPS)
76
uses a resin bead
SPPS
77
protects R groups during SPPS
PGs
78
attached to N' during SPPS
Fmoc
79
only non protein enzyme
ribozymes
80
simple protein enzymes
AAs only
81
conjugated protein enzymes
AAs plus a non-protein component
82
apoenzyme
protein component of enzyme
83
cofactor
nonprotein component of enzyme
84
holoenzyme
apoenzyme + cofactor
85
two divisions of cofactors
inorganic (metallic)
organic (coenzymes)
86
two divisions of inorganic cofactors
metal associated
metalloproteins
87
two divisions of coenzymes
cosubstrates
prosthetic groups
88
metal-associated metallic cofactors
bind, then leave
89
metalloprotein
form tight associations; don't leave even when digested
90
cosubstrates
forms IMFs with enzyme; then leaves
91
prosthetic groups
covalently linked to enzyme; don't leave
92
EC1
oxidoreductases
93
EC2
transferases
94
EC3
hydrolases
95
EC4
lyases
96
EC5
isomerases
97
EC6
ligases
98
oxidoreduxes
redox reactions
99
transferases
transfer of functional groups
100
hydrolases
hydrolysis reactions
101
lyases
bond cleavage
102
isomerases
103
isomerases
isomerization
104
ligases
bond formation/synthesis
105
lock and key substrate binding
complementary shape of substrate and active site of enzyme
106
induced fit substrate binding
substrate binding causes conformational change of enzyme
107
enzyme kinetics equation
108
enzymes use -------- reactions
energy coupling
109
linease phase initially taken from------- graph
time vs [P]
110
how to find Km
1/2 Vmax = y value
find x value on graph
111
used to compare enzymes
specificity constant
112
linear representation of V0 vs [S]
Lineweaver-Burk plot
113
lineweaver burk plot axes
y: 1/V0
x: 1/[S]
114
L-B plot y intercept
1/Vmax
115
L-B plot x intercept
-1/Km
116
3 types of reversible inhibition
competitive
noncompetitive
uncompetitive
117
competitive inhibition
inhibitor has similar structure to substrate
118
noncompetitive inhibition
inhibitor binds somewhere on enzyme besides active site, changing its conformation
119
competitive inhibition effect on Vmax, Km
Vmax same
Km increases
120
noncompetitive inhibition on Vmax, Km
Vmax decreases
Km no change
121
uncompetitive inhibition
inhibitor binds after the substrate binds
122
uncompetitive effect on Vmax, Km
both decrease
123
uncompetitive effect on Vmax, Km
both decrease
