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MICRO 442 > BIOCHEM REVIEW 1 > Flashcards

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

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2
Q

super secondary protein folding

A

intermediate between secondary and tertiary structures

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3
Q

if pH>pl the overall charge of the protien is?

A

negative (higher pH = -)

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4
Q

hydroxyl group below pka

A

OH

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5
Q

if pH < pl the overall chagre of the protein is

A

positive (lower pH = +)

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6
Q

amino group above pka

A

NH2

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6
Q

amino group below pka

A

NH3+

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7
Q

hydroxul group above pka

A

O-

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8
Q

SH-group below pka

A

SH

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9
Q

SH-group above pka

A

S-

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10
Q

carboxylate group below pka

A

COOH

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11
Q

carboxylate gorup above pka

A

COO-

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12
Q

imidazole below pka has one

A

positive charge but above pka it has no charge (looks similar to a histidine)

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12
Q

N-termni pka is

A

8

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13
Q

glutamic acid pka

A

4.2

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13
Q

C-termni pka is

A

4

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14
Q

arginine pka

A

12.5

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15
Q

aspartic acid pka

A

3.9

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16
Q

cysteine pka

A

8.3

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17
Q

lysine pka

A

10.0

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18
Q

histidine pka

A

6.0

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19
Q

tyrosine pka

A

10.1

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20
Q

in gel filtration chromatography do larger or smaller molecules elute first

A

larger

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21
Q

what are the two ways to elute

A
  1. modulate pH
  2. increasing salt concentration
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22
Q

only reducing SDS-page will have 2

A

bands

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22
Q

under both however a homodimer without disulfide bonds would show up as a

A

single band

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23
Q

S>0
H<0

A

spontaneous

24
Q

H>0
S>0

A

spontaneous high temp

25
Q

H<0
S<0

A

spontaneous low temp

26
Q

H>0
S<0

A

never spontaneous

27
Q

myoglobin and hemoglobin share similar binding sites because the Fe(II) is octahedrally coordinated by

A

4 nitrogen groups of porphyrin ring, O2 and His F8

28
Q

how are mycoglobin and hemoglobin different?

A

4° structure

29
Q

T-state is energetically favored when

A

no oxygen is bound, BPG binds in the central cavity

29
Q

R-state is energetically favored when

A

oxygen is bound

30
Q

positive cooperativity for hemoglobin steps

A

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
Q

hemoblobin has a sigmodial curve but myoglobin has a

A

hyperbolic curve

31
Q

what 3 molecules favor the T state

A

H+, CO2, and BPG

31
Q

what 2 molecules favor the R state

A

O2 and CO

32
Q

what is the 4° of the cholera toxin

A

C5 symmetry, hetero-hexamer, B-pentamer + A-subunit -> AB5

33
Q

globular actin has what symmetry

A

helical, has a 4-domain subunit that assembles into fibers->microfilaments

34
Q

GroEL/GroES symmetry

A

C7 also its a chaperone protein and has a cis (ADP) and trans (NO ADP) rings

35
Q

ATCase number of chains

A

-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
Q

myoglobin subunits and binding

A

-8 alpha helices
-one subunit
-Fe in the center

36
Q

ATCase role in pyrimidine synthesis

A

ATCase catalyzes the first committed step in pyrimidine synthesis (CTP & UTP)

37
Q

ATCase symmetry

A

D3

38
Q

what type of molecules does chymotrypsin cleave

A

LARGE HYDROPHOBIC side chains -> tyr, Trp, Phe, Leu

38
Q

Hemocyanin symmetry

A

D3 and Cu is in the center and is oxidized when O2 binds

39
Q

Hb subunits and binding

A

2 alpha subunits -> C2 symmetry
2 beta subunits -> C2 symmetry
Fe in center
cooperativity

40
Q

calmodulin conformational change is dependent on

A

calcium

40
Q

what type of molecules does trypsin cleave

A

Lys or arg

40
Q

what type of molecules does elastase cleave

A

ala, gly, val

41
Q

all serine proteases cleave what?

A

n-terminal from amino acids

42
Q

TIM structure contains

A

beta-barrel element and alpha helices

43
Q

RNAse A structure

A

all-beta, 2 histidines in active site, endonuclease for ssRNA

44
Q

what 3 proteins have cleavage specificity

A

trypsin, chymotrypsin, elastase

45
Q

Km inc. but Vmax no change

A

competitive

45
Q

Km reduced and Vmax reduced

A

uncompetitive

46
Q

structure of neurminidase

A

tetramer with 4-beta-stranded sheet ie blades or propeller

47
Q

what does neurminidase specifically do

A

sialic acid cleavage

48
Q

Km unaffected (only when a and a’ are the same) and Vmax reduced

A

mixed

49
Q

intercepts for mixed inhibition

A

-x-intercept: -a’/aKm
-y-intercept: a’/Vmax

50
Q

intercepts for competitive

A

-x-intercept: -1/aKm
-y-intercept: 1/Vmax

50
Q

Ribonuclease A Catalysis steps

A
  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
Q

intercepts for uncompetitive

A

-x-intercept: -a’/Km
-y-intercept: a’/Vmax

52
Q

how many ATP does GroEL/GroES need for 1 cycle

A

7

53
Q

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?

A

ATP hydrolysis to catalyze protein refolding

MICRO 442 (25 decks)

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