BIOCHEM REVIEW 1 Flashcards
domain protein folding
a region of a protein’s polypeptide chain that is self-stabilizing and that folds independently from the res
super secondary protein folding
intermediate between secondary and tertiary structures
if pH>pl the overall charge of the protien is?
negative (higher pH = -)
hydroxyl group below pka
OH
if pH < pl the overall chagre of the protein is
positive (lower pH = +)
amino group above pka
NH2
amino group below pka
NH3+
hydroxul group above pka
O-
SH-group below pka
SH
SH-group above pka
S-
carboxylate group below pka
COOH
carboxylate gorup above pka
COO-
imidazole below pka has one
positive charge but above pka it has no charge (looks similar to a histidine)
N-termni pka is
8
glutamic acid pka
4.2
C-termni pka is
4
arginine pka
12.5
aspartic acid pka
3.9
cysteine pka
8.3
lysine pka
10.0
histidine pka
6.0
tyrosine pka
10.1
in gel filtration chromatography do larger or smaller molecules elute first
larger
what are the two ways to elute
- modulate pH
- increasing salt concentration
only reducing SDS-page will have 2
bands
under both however a homodimer without disulfide bonds would show up as a
single band
S>0
H<0
spontaneous
H>0
S>0
spontaneous high temp
H<0
S<0
spontaneous low temp
H>0
S<0
never spontaneous
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
how are mycoglobin and hemoglobin different?
4° structure
T-state is energetically favored when
no oxygen is bound, BPG binds in the central cavity
R-state is energetically favored when
oxygen is bound
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
hemoblobin has a sigmodial curve but myoglobin has a
hyperbolic curve
what 3 molecules favor the T state
H+, CO2, and BPG
what 2 molecules favor the R state
O2 and CO
what is the 4° of the cholera toxin
C5 symmetry, hetero-hexamer, B-pentamer + A-subunit -> AB5
globular actin has what symmetry
helical, has a 4-domain subunit that assembles into fibers->microfilaments
GroEL/GroES symmetry
C7 also its a chaperone protein and has a cis (ADP) and trans (NO ADP) rings
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
myoglobin subunits and binding
-8 alpha helices
-one subunit
-Fe in the center
ATCase role in pyrimidine synthesis
ATCase catalyzes the first committed step in pyrimidine synthesis (CTP & UTP)
ATCase symmetry
D3
what type of molecules does chymotrypsin cleave
LARGE HYDROPHOBIC side chains -> tyr, Trp, Phe, Leu
Hemocyanin symmetry
D3 and Cu is in the center and is oxidized when O2 binds
Hb subunits and binding
2 alpha subunits -> C2 symmetry
2 beta subunits -> C2 symmetry
Fe in center
cooperativity
calmodulin conformational change is dependent on
calcium
what type of molecules does trypsin cleave
Lys or arg
what type of molecules does elastase cleave
ala, gly, val
all serine proteases cleave what?
n-terminal from amino acids
TIM structure contains
beta-barrel element and alpha helices
RNAse A structure
all-beta, 2 histidines in active site, endonuclease for ssRNA
what 3 proteins have cleavage specificity
trypsin, chymotrypsin, elastase
Km inc. but Vmax no change
competitive
Km reduced and Vmax reduced
uncompetitive
structure of neurminidase
tetramer with 4-beta-stranded sheet ie blades or propeller
what does neurminidase specifically do
sialic acid cleavage
Km unaffected (only when a and a’ are the same) and Vmax reduced
mixed
intercepts for mixed inhibition
-x-intercept: -a’/aKm
-y-intercept: a’/Vmax
intercepts for competitive
-x-intercept: -1/aKm
-y-intercept: 1/Vmax
Ribonuclease A Catalysis steps
- His12 acts as a general base abstracting a proton from the 2’-OH of the ribose
- the 2’-OH carries out a nucleophillic attack on the adjacent phosphorus atom of the RNA
- his119 acts as a general acid donating a protin to 5’-OH of the leaving ribose
- A 2’,3’-cyclic intermediate is formed
- first product leaves
- water comes in near his119
intercepts for uncompetitive
-x-intercept: -a’/Km
-y-intercept: a’/Vmax
how many ATP does GroEL/GroES need for 1 cycle
7
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
