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Biochem > Exam 1: M4 > Flashcards

Exam 1: M4 Flashcards

1
Q

hemoglobin and myoglobin both bind to ___

A

O2

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2
Q

T/F: Hb and Mb are paralogs

A

T

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3
Q

characteristics of Mb

A

monomer (1 polypeptide chain)
found in muscle tissue of vertebrates
simple O2 binding behavior
1st xray crystal strucutre determined

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4
Q

characteristics of Hb

A

tetramer (4 diff polypeptide chains)
2 conformations
found in RBC of vertebrates
complex O2 binding behavior
one of 1st proteins described as a physiological function

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5
Q

both Mb and Hb contain

A

heme groups

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6
Q

define prosthetic group

A

molecules permanently attached to a protein (small and organic)

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7
Q

heme group have central ion surrounded by

A

porphyrin ring

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8
Q

Fe (II) has ___ coordination positions

A

6

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9
Q

what are the 6 coordination positions of Fe (II)

A

4 w/ N in pyrrole group
1 w/ His residue
1 position coordinated w/ O2

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10
Q

both heme AND the protein are requierd to bind O2 ___

A

reversibly

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11
Q

w/o protein, heme would bind O2 __

A

irreversibly

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12
Q

if just had heme out there, Fe(II) gets oxidized to __

A

Fe (III)

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13
Q

Mb structure

A

8 alpha helices connected by loops (A-H)

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14
Q

which 2 helices of Mb are important for structure and function of Mb and its binding to heme

A

E and F

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15
Q

where is the heme buried in Mb

A

deep hydrophobic cleft or pocket between alpha helix E and F

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16
Q

hydrophobic cleft prevents heme from being

A

oxidized to Fe (III)

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17
Q

what does Mb His E7 (distal) do

A

interacts w/ O2, important for maintaining O2 at that site

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18
Q

what does Mb His F8 (proximal )do

A

coordinated w/ Fe in heme

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19
Q

O2 binds to Mb at an

A

angle

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20
Q

what faciliates O2 binding to Mb at an angle

A

His E7

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21
Q

T/F: Mb undergoes significant structural change when binding to O2

A

F

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22
Q

Mb function: improves ____ to facilitate O2 diffusion into muscle

A

solubility of O2

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23
Q

heme is ___

A

hydrophobic

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24
Q

Mb function: O2 is not very soluble in aqeous soln, so presence of

A

protein and O2 binding partner facilitates diffusion of O2 to get into muscle

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25
Q

Mb function: prevents heme

A

oxidation

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26
Q

Mb function: prevents ______ binding

A

carbon monoxide

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27
Q

CO wants to bind heme in a ___ fashion

A

linear

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28
Q

what ensures O2 can bind and prevents CO binding

A

His E7

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29
Q

Mb binds to O2 ___

A

reversibly

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30
Q

Kd for Mb

A

[Mb][O2] / [MbO2]

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31
Q

define fractional saturation

A

what fraction of Mb is bound to O2

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32
Q

Y>= 0

A

no O2 bound

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33
Q

Y <= 1

A

all binding sites occupied

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34
Q

equation for Y for Mb

A

[MbO2]/[Mb] + [MbO2] and
[O2] / Kd + [O2]

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35
Q

O2 interacts ______ w binding sites on Mb

A

independently

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36
Q

p50 =

A

Kd

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37
Q

for Mb: inverse relationship btwn

A

Yo2 and Kd

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38
Q

high p50 implies _____ affinity for O2

A

low

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39
Q

low p50 implies _____ affinity for O2

A

high

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40
Q

p50 for myoglobin in blood is ____ torr

A

2.8

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41
Q

Hb structure

A

4 diff subunits–> 2a, 2b
2 ab dimers

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42
Q

quarternary structure of Hb

A

a2b2 tetramer

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43
Q

ab dimers are related by ______ symmetry

A

2-fold

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44
Q

each subunit binds ____ heme molecule and also binds ____ O2 molecule

A

1;1

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45
Q

a and b subunits are related to each other and to _____

A

myoglobin–> paralogs

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46
Q

do sequences or structures diverge more rapidly

A

sequences

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47
Q

some residues are conserved btwn a, B, and myoglobin like

A

distal and proximal His and also specific hydrophobic residues w/in hydrophobic binding pocket for heme

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48
Q

ab dimers come together to make

A

tetramer

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49
Q

what two states do Hb exist in

A

1)deoxy T state
2) oxy R state

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50
Q

what induces a conf change in Hb

A

binding of O2

51
Q

size of the channel in the middle of the subunits is larger in what state of Hb

A

deoxy state

52
Q

BPG binds in channel when it is bigger (deoxy state) which is important for

A

releasing O2

53
Q

what causes channel in protein to narrow

A

some helices rotate and change angle of orientation wrt each other when going to T to R state

54
Q

what are the 3 changes in quarternary structure when O2 binds

A

-each ab dimer rotates 15 degrees wrt symmetry mate
-brings b subunits closer together and narrows central channel
-changes contacts btwn subunits (a1b2 and a2b1 interfaces)

55
Q

Hb p50 in venous blood is ____

A

26 torr

56
Q

Which does O2 bind more tightly to? Mb or Hb

A

Mb

57
Q

what does a small kd or p50 imply

A

very tight binding

58
Q

what does a high kd or p50 imply

A

low affinity

59
Q

Why does Hb have lower O2 affinity than Mb

A

it wants to deliver O2

60
Q

Mb O2 binding curve is

A

hyperbolic

61
Q

Hb O2 binding curve is

A

sigmoidal

62
Q

what does a sigmoidal binding curve imply

A

cooperative binding

63
Q

define cooperativity

A

O2 binding to 1 site of the effects of O2 binding to another site

64
Q

why is sigmoidal binding curve important for Hb function

A

allows Hb to deliver more O2 to tissues compared to if it didn’t have sigmoidal

65
Q

the difference btwn YO2 in arteries vs veins is

A

how much O2 Hb is able to deliver when it transitions from artery to veins

66
Q

Hill equation assumes

A

Hb binds O2 w/ infinite cooperativity (all 4 O bind simultaneously)

67
Q

hill constant is never greater than the

A

number of available binding sites

68
Q

what does the hill coefficient (n) estimate

A

cooperativity btwn binding sites

69
Q

if n=1, binding is ___

A

noncooperative

70
Q

if n>1, binding is _____

A

positively cooperative

71
Q

if n< 1, binding is____

A

negatively cooperative

72
Q

on the double log plot, slope represents

A

n

73
Q

max slope occurs at

A

YO2 of 0.5

74
Q

1st O2 binds noncooperatively bc its binding 1st available site and once that O2 binds to Hb, induces conf. change in Hb and now Hb

A

has much higher affinity for O2 binding

75
Q

decreasing Kd implies

A

higher affinity

76
Q

Hb needs to bind O2 reversibly, or it won’t effectively

A

deliver O2 to tissues

77
Q

What 3 molecules promote O2 release from Hb

A

H+, CO2, BPG

78
Q

increase in p50 causes

A

release of O2

79
Q

to get n from graph, look for steepest part of slope, which is at

A

Yo2 = 0.5

80
Q

mutant would have a ______ where you would expect to see cooperativity/steepest slope

A

shallower slope

81
Q

changes in quarternary structure to Hb upon O2 binding

A
  1. 1 ab dimer rotates 15 degree wrt symmetry mate
  2. Brings b subunits closer together and narrow central channel
  3. changes contacts btwn subunits (a1-b2 and a2-b1)
82
Q

when O2 binds to Hb:

A

closing of central channel; alpha helices are tilting

83
Q

define allosteric effect

A

ligand binding at one site effects ligand binding at 2nd distant site

84
Q

all 4 subunits exist in 1 state at the same

A

time

85
Q

O2 binding drives structural change throughout tetramer that convert the Hb molecule from

A

T to R state

86
Q

first step of O2 binding to Hb

A

O2 pulls Fe+2 into more optimal position in heme plane (0.6A)

87
Q

what is the driving force to change Hb from T to R state

A

O2 binding to heme

88
Q

2nd step of O2 binding to Hb

A

Fe pulls proximal His bc they are coordinated which pulls all Helix F so the entire alpha helix moves

89
Q

1 O2 binding to 1 heme group primes rest of subunits to position to bind to other O2 molecules, and now Hb is in

A

R state

90
Q

If Fe moves, ____ also has to move

A

His

91
Q

Overall binding of O2 to heme:

A

O2 binds Fe at angle in T state; Fe kinked in T state so when O2 binds, it pulls heme straight by pulling Fe down by 0.6A which brings down His with it but will sterically clash so helix just tilts

92
Q

what causes helix to tilt

A

0.6A

93
Q

other interaction happens at which interfaces

A

a1b2 and a2b1

94
Q

allosteric effect in Hb

A

bc the helix gets shifted upwards, new H bonds formed and old ones broken

95
Q

what other tertiary structure changes occurred between subunits

A

ion pairs ‘break’ @ C terminus of a and b subunits

96
Q

ionic interactions help stabilize ___ state

A

T

97
Q

these concerted structural changes make it _____ for other subunits to bind O2

A

easier

98
Q

higher affinity = lower or high kd/p50?

A

lower

99
Q

Bohr effect

A

O2 dependent on pH;
O2 binding affinity changed as [H+] and [CO2] conc changed–> O2 binding affinity of Hb is inversely related to [H+] and [CO2];
promotes O2 release in capillaries

100
Q

as you inc [H+] or [CO2], ____ affinity for O2 binding

A

dec

101
Q

T to R: ____ pk of bases

A

lowers

102
Q

In T state, forming ionic interactions, pk is artificially high and when separated by conf change, pk drops to physiological levels and have release of

A

H+ ions

103
Q

higher pH favors ___ state and drives ____ binding

A

R; more

104
Q

why does lower pH favor T state

A

needs charge stabilization

105
Q

what facilitates bicarbonate formation

A

H+ uptake by Hb

106
Q

what triggers Hb to deliver O2 to a site

A

acidic env from carbon dioxide formation

107
Q

CO2 can modify amino groups in blood proteins to form

A

carbamate

108
Q

function of carbamate ion

A

promotes T state and R–>T transition in capillaries where O2 is high

109
Q

carbamate formation ___ Ph

A

dec

110
Q

BPG is allosteric _____ of Hb

A

effector

111
Q

BPG is very

A

neg

112
Q

BPG can only bind to ____ form of Hb

A

T/deoxy

113
Q

BPG binds …

A

2 Lys, 4 His, 2 a-NH3+

114
Q

BPG stabilizes what state

A

T

115
Q

BPG helps ____ O2

A

unload

116
Q

BPG ____ affinity of Hb for O2 and ___ p50/Kd

A

dec; inc

117
Q

w/o Bohr effect with pH, cO2, BPG, pure Hb O2 binding curve would be shifted

A

left; little O2 gets unloaded

118
Q

Hb is a model protein for ____ and ____

A

allostery; cooperative binding

119
Q

define allostery

A

separate molecule that affects affinity of ligand independelty of that ligand (H+. CO2, BPG)q

120
Q

Bohr effect is ____ from BPG binding

A

separate

121
Q

mutations in protein seq can be:

A

single point mutation
mulitple changes in aa sequence
change to overall fold
change to active site

122
Q

what mutation is sickle cell

A

Glu (charged)–> Val(hphobic)

123
Q

why is val bad for sickle cell

A

fits into hphobic pocket amd makes fibers

124
Q

T/F: Sicle cell is the first evidence of disease being caused by changed protein structure

A

T

Biochem (6 decks)

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