BIOCHEM REVIEW 1 Flashcards
1
Q
domain protein folding
A
a region of a protein’s polypeptide chain that is self-stabilizing and that folds independently from the res
2
Q
super secondary protein folding
A
intermediate between secondary and tertiary structures
3
Q
if pH>pl the overall charge of the protien is?
A
negative (higher pH = -)
4
Q
hydroxyl group below pka
A
OH
5
Q
if pH < pl the overall chagre of the protein is
A
positive (lower pH = +)
6
Q
amino group above pka
A
NH2
6
Q
amino group below pka
A
NH3+
7
Q
hydroxul group above pka
A
O-
8
Q
SH-group below pka
A
SH
9
Q
SH-group above pka
A
S-
10
Q
carboxylate group below pka
A
COOH
11
Q
carboxylate gorup above pka
A
COO-
12
Q
imidazole below pka has one
A
positive charge but above pka it has no charge (looks similar to a histidine)
12
Q
N-termni pka is
A
8
13
Q
glutamic acid pka
A
4.2
13
Q
C-termni pka is
A
4
14
Q
arginine pka
A
12.5
15
Q
aspartic acid pka
A
3.9
16
Q
cysteine pka
A
8.3
17
Q
lysine pka
A
10.0
18
Q
histidine pka
A
6.0
19
Q
tyrosine pka
A
10.1
20
Q
in gel filtration chromatography do larger or smaller molecules elute first
A
larger
21
Q
what are the two ways to elute
A
- modulate pH
- increasing salt concentration
22
only reducing SDS-page will have 2
bands
22
under both however a homodimer without disulfide bonds would show up as a
single band
23
S>0
H<0
spontaneous
24
H>0
S>0
spontaneous high temp
25
H<0
S<0
spontaneous low temp
26
H>0
S<0
never spontaneous
27
myoglobin and hemoglobin share similar binding sites because the Fe(II) is octahedrally coordinated by
4 nitrogen groups of porphyrin ring, O2 and His F8
28
how are mycoglobin and hemoglobin different?
4° structure
29
T-state is energetically favored when
no oxygen is bound, BPG binds in the central cavity
29
R-state is energetically favored when
oxygen is bound
30
positive cooperativity for hemoglobin steps
O2 binds to the Fe(II)
Fe(II) moves into the plane of the heme group when O2 binds
the HisF8 interacting with the Fe(II) is pulled upward like a lever and moves helix F
surrounding subunits move relative to one another changing the pKa of certain amino acids involved in salt bridges needed to stabilize the T-state
protons are released in these amino acid groups and the T-state salt bridges break
The cavity in the center shrinks but the C2 symmetry remains in the R-state
30
hemoblobin has a sigmodial curve but myoglobin has a
hyperbolic curve
31
what 3 molecules favor the T state
H+, CO2, and BPG
31
what 2 molecules favor the R state
O2 and CO
32
what is the 4° of the cholera toxin
C5 symmetry, hetero-hexamer, B-pentamer + A-subunit -> AB5
33
globular actin has what symmetry
helical, has a 4-domain subunit that assembles into fibers->microfilaments
34
GroEL/GroES symmetry
C7 also its a chaperone protein and has a cis (ADP) and trans (NO ADP) rings
35
ATCase number of chains
-6 regulatory (R chains) -> Binding of CTP to the R subunits converts the R-state to the T-state by stabilizing the T-state which inhibits catalysis
-6 catalytic chains (C chains) -> Binding of CTP to the R subunits converts the R-state to the T-state by stabilizing the T-state which inhibits catalysis
35
myoglobin subunits and binding
-8 alpha helices
-one subunit
-Fe in the center
36
ATCase role in pyrimidine synthesis
ATCase catalyzes the first committed step in pyrimidine synthesis (CTP & UTP)
37
ATCase symmetry
D3
38
what type of molecules does chymotrypsin cleave
LARGE HYDROPHOBIC side chains -> tyr, Trp, Phe, Leu
38
Hemocyanin symmetry
D3 and Cu is in the center and is oxidized when O2 binds
39
Hb subunits and binding
2 alpha subunits -> C2 symmetry
2 beta subunits -> C2 symmetry
Fe in center
cooperativity
40
calmodulin conformational change is dependent on
calcium
40
what type of molecules does trypsin cleave
Lys or arg
40
what type of molecules does elastase cleave
ala, gly, val
41
all serine proteases cleave what?
n-terminal from amino acids
42
TIM structure contains
beta-barrel element and alpha helices
43
RNAse A structure
all-beta, 2 histidines in active site, endonuclease for ssRNA
44
what 3 proteins have cleavage specificity
trypsin, chymotrypsin, elastase
45
Km inc. but Vmax no change
competitive
45
Km reduced and Vmax reduced
uncompetitive
46
structure of neurminidase
tetramer with 4-beta-stranded sheet ie blades or propeller
47
what does neurminidase specifically do
sialic acid cleavage
48
Km unaffected (only when a and a' are the same) and Vmax reduced
mixed
49
intercepts for mixed inhibition
-x-intercept: -a'/aKm
-y-intercept: a'/Vmax
50
intercepts for competitive
-x-intercept: -1/aKm
-y-intercept: 1/Vmax
50
Ribonuclease A Catalysis steps
1. His12 acts as a general base abstracting a proton from the 2'-OH of the ribose
2. the 2'-OH carries out a nucleophillic attack on the adjacent phosphorus atom of the RNA
3. his119 acts as a general acid donating a protin to 5'-OH of the leaving ribose
4. A 2',3'-cyclic intermediate is formed
5. first product leaves
6. water comes in near his119
51
intercepts for uncompetitive
-x-intercept: -a'/Km
-y-intercept: a'/Vmax
52
how many ATP does GroEL/GroES need for 1 cycle
7
53
After the GroES cap binds GroEL and enlarges the cavity of the cis-ring, what is the next step in the GroEL/GroES chaperone system?
ATP hydrolysis to catalyze protein refolding
