Exam 1: M4 Flashcards
(124 cards)
1
Q
hemoglobin and myoglobin both bind to ___
A
O2
2
Q
T/F: Hb and Mb are paralogs
A
T
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
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
5
Q
both Mb and Hb contain
A
heme groups
6
Q
define prosthetic group
A
molecules permanently attached to a protein (small and organic)
7
Q
heme group have central ion surrounded by
A
porphyrin ring
8
Q
Fe (II) has ___ coordination positions
A
6
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
10
Q
both heme AND the protein are requierd to bind O2 ___
A
reversibly
11
Q
w/o protein, heme would bind O2 __
A
irreversibly
12
Q
if just had heme out there, Fe(II) gets oxidized to __
A
Fe (III)
13
Q
Mb structure
A
8 alpha helices connected by loops (A-H)
14
Q
which 2 helices of Mb are important for structure and function of Mb and its binding to heme
A
E and F
15
Q
where is the heme buried in Mb
A
deep hydrophobic cleft or pocket between alpha helix E and F
16
Q
hydrophobic cleft prevents heme from being
A
oxidized to Fe (III)
17
Q
what does Mb His E7 (distal) do
A
interacts w/ O2, important for maintaining O2 at that site
18
Q
what does Mb His F8 (proximal )do
A
coordinated w/ Fe in heme
19
Q
O2 binds to Mb at an
A
angle
20
Q
what faciliates O2 binding to Mb at an angle
A
His E7
21
Q
T/F: Mb undergoes significant structural change when binding to O2
A
F
22
Q
Mb function: improves ____ to facilitate O2 diffusion into muscle
A
solubility of O2
23
Q
heme is ___
A
hydrophobic
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
25
Mb function: prevents heme
oxidation
26
Mb function: prevents ______ binding
carbon monoxide
27
CO wants to bind heme in a ___ fashion
linear
28
what ensures O2 can bind and prevents CO binding
His E7
29
Mb binds to O2 ___
reversibly
30
Kd for Mb
[Mb][O2] / [MbO2]
31
define fractional saturation
what fraction of Mb is bound to O2
32
Y>= 0
no O2 bound
33
Y <= 1
all binding sites occupied
34
equation for Y for Mb
[MbO2]/[Mb] + [MbO2] and
[O2] / Kd + [O2]
35
O2 interacts ______ w binding sites on Mb
independently
36
p50 =
Kd
37
for Mb: inverse relationship btwn
Yo2 and Kd
38
high p50 implies _____ affinity for O2
low
39
low p50 implies _____ affinity for O2
high
40
p50 for myoglobin in blood is ____ torr
2.8
41
Hb structure
4 diff subunits--> 2a, 2b
2 ab dimers
42
quarternary structure of Hb
a2b2 tetramer
43
ab dimers are related by ______ symmetry
2-fold
44
each subunit binds ____ heme molecule and also binds ____ O2 molecule
1;1
45
a and b subunits are related to each other and to _____
myoglobin--> paralogs
46
do sequences or structures diverge more rapidly
sequences
47
some residues are conserved btwn a, B, and myoglobin like
distal and proximal His and also specific hydrophobic residues w/in hydrophobic binding pocket for heme
48
ab dimers come together to make
tetramer
49
what two states do Hb exist in
1)deoxy T state
2) oxy R state
50
what induces a conf change in Hb
binding of O2
51
size of the channel in the middle of the subunits is larger in what state of Hb
deoxy state
52
BPG binds in channel when it is bigger (deoxy state) which is important for
releasing O2
53
what causes channel in protein to narrow
some helices rotate and change angle of orientation wrt each other when going to T to R state
54
what are the 3 changes in quarternary structure when O2 binds
-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
Hb p50 in venous blood is ____
26 torr
56
Which does O2 bind more tightly to? Mb or Hb
Mb
57
what does a small kd or p50 imply
very tight binding
58
what does a high kd or p50 imply
low affinity
59
Why does Hb have lower O2 affinity than Mb
it wants to deliver O2
60
Mb O2 binding curve is
hyperbolic
61
Hb O2 binding curve is
sigmoidal
62
what does a sigmoidal binding curve imply
cooperative binding
63
define cooperativity
O2 binding to 1 site of the effects of O2 binding to another site
64
why is sigmoidal binding curve important for Hb function
allows Hb to deliver more O2 to tissues compared to if it didn't have sigmoidal
65
the difference btwn YO2 in arteries vs veins is
how much O2 Hb is able to deliver when it transitions from artery to veins
66
Hill equation assumes
Hb binds O2 w/ infinite cooperativity (all 4 O bind simultaneously)
67
hill constant is never greater than the
number of available binding sites
68
what does the hill coefficient (n) estimate
cooperativity btwn binding sites
69
if n=1, binding is ___
noncooperative
70
if n>1, binding is _____
positively cooperative
71
if n< 1, binding is____
negatively cooperative
72
on the double log plot, slope represents
n
73
max slope occurs at
YO2 of 0.5
74
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
has much higher affinity for O2 binding
75
decreasing Kd implies
higher affinity
76
Hb needs to bind O2 reversibly, or it won't effectively
deliver O2 to tissues
77
What 3 molecules promote O2 release from Hb
H+, CO2, BPG
78
increase in p50 causes
release of O2
79
to get n from graph, look for steepest part of slope, which is at
Yo2 = 0.5
80
mutant would have a ______ where you would expect to see cooperativity/steepest slope
shallower slope
81
changes in quarternary structure to Hb upon O2 binding
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
when O2 binds to Hb:
closing of central channel; alpha helices are tilting
83
define allosteric effect
ligand binding at one site effects ligand binding at 2nd distant site
84
all 4 subunits exist in 1 state at the same
time
85
O2 binding drives structural change throughout tetramer that convert the Hb molecule from
T to R state
86
first step of O2 binding to Hb
O2 pulls Fe+2 into more optimal position in heme plane (0.6A)
87
what is the driving force to change Hb from T to R state
O2 binding to heme
88
2nd step of O2 binding to Hb
Fe pulls proximal His bc they are coordinated which pulls all Helix F so the entire alpha helix moves
89
1 O2 binding to 1 heme group primes rest of subunits to position to bind to other O2 molecules, and now Hb is in
R state
90
If Fe moves, ____ also has to move
His
91
Overall binding of O2 to heme:
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
what causes helix to tilt
0.6A
93
other interaction happens at which interfaces
a1b2 and a2b1
94
allosteric effect in Hb
bc the helix gets shifted upwards, new H bonds formed and old ones broken
95
what other tertiary structure changes occurred between subunits
ion pairs 'break' @ C terminus of a and b subunits
96
ionic interactions help stabilize ___ state
T
97
these concerted structural changes make it _____ for other subunits to bind O2
easier
98
higher affinity = lower or high kd/p50?
lower
99
Bohr effect
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
as you inc [H+] or [CO2], ____ affinity for O2 binding
dec
101
T to R: ____ pk of bases
lowers
102
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
H+ ions
103
higher pH favors ___ state and drives ____ binding
R; more
104
why does lower pH favor T state
needs charge stabilization
105
what facilitates bicarbonate formation
H+ uptake by Hb
106
what triggers Hb to deliver O2 to a site
acidic env from carbon dioxide formation
107
CO2 can modify amino groups in blood proteins to form
carbamate
108
function of carbamate ion
promotes T state and R-->T transition in capillaries where O2 is high
109
carbamate formation ___ Ph
dec
110
BPG is allosteric _____ of Hb
effector
111
BPG is very
neg
112
BPG can only bind to ____ form of Hb
T/deoxy
113
BPG binds ...
2 Lys, 4 His, 2 a-NH3+
114
BPG stabilizes what state
T
115
BPG helps ____ O2
unload
116
BPG ____ affinity of Hb for O2 and ___ p50/Kd
dec; inc
117
w/o Bohr effect with pH, cO2, BPG, pure Hb O2 binding curve would be shifted
left; little O2 gets unloaded
118
Hb is a model protein for ____ and ____
allostery; cooperative binding
119
define allostery
separate molecule that affects affinity of ligand independelty of that ligand (H+. CO2, BPG)q
120
Bohr effect is ____ from BPG binding
separate
121
mutations in protein seq can be:
single point mutation
mulitple changes in aa sequence
change to overall fold
change to active site
122
what mutation is sickle cell
Glu (charged)--> Val(hphobic)
123
why is val bad for sickle cell
fits into hphobic pocket amd makes fibers
124
T/F: Sicle cell is the first evidence of disease being caused by changed protein structure
T
