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BIOL 2421 - Cellular Biochem > 7. Myoglobin and molecular binding > Flashcards

7. Myoglobin and molecular binding Flashcards

1
Q

T or F: O2 is poorly soluble in aqueous solutions

A

true

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2
Q

what is the role of myoglobin

A

functions to both store oxygen and facilitate oxygen diffusion in rapidly contracting muscle tissue

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3
Q

what animal is myoglobin very prevalent in and why

A

sperm whales, because they need to be under the water for up to 2 hours at a time

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4
Q

how much more myoglobin do sperm whales have than humans

A

about 30x more

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5
Q

how many polypeptides is myoglobin

A

1

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6
Q

how many amino acids is myoglobin

A

153

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7
Q

what is the molecular weight of myoglobin

A

Mr=16,700

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8
Q

what is the main secondary structure of myoglobin. What percentage is this

A

78% of residues are in alpha helices

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9
Q

how many helices make up myoglobin

A

8

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10
Q

what type of amino acids make up the majority of the interior of myoglobin

A

hydrophobic residues

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11
Q

which hydrophobic residues make up the interior of myoglobin

A

Valine, Leucine, Isoleucine, Phenylalanine, and methionine

VMILF

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12
Q

what part of myoglobin binds O2

A

the associated heme group

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13
Q

describe the structure of the heme group of myoglobin

A

it’s a flat porphyrin ring with a single iron atom in the center. The iron is between 4 nitrogen molcules in the ring, and one atom binds above and one below

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14
Q

why is muscle and blood dark red

A

heme absorbs light at that wavelength

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15
Q

how are the helices in myoglobin named

A

A-H

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16
Q

how are the bands connecting the helices named

A

named after the helices they connect: ie AB, BC, CD, etc

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17
Q

how are residues in the helices named

A

named for their position in a given helix

ie His F8 is in helix F in the 8th position

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18
Q

what residue do many of the helices end with? how many helices end with this

A

4 of 8 helices end with proline

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19
Q

why do half of the helices end in proline

A

they break helices because they don’t fit

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20
Q

in regards to the helices, where is the heme group

A

it sits in a hydrophobic myoglobin pocket formed by 3 of the 8 helices, shielding it from solvent

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21
Q

what happens to the heme when it’s outside of the pocket

A

Fe2+ is almost instantly oxidized to Fe3+, which cannot bind O2

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22
Q

which conformation of iron cannot bind O2. When do we see this confirmation

A

Fe3+ cannot bind O2, and we get this when the heme group is outside of the pocket

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23
Q

what binds to the iron atom in the center of the heme group

A

N atom (from histidine) binds perpendicular to the plane of the ring, and then O2 binds as well

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24
Q

which histidine does the N come from that binds with the heme group

A

His F8, aka His residue #93, aka proximal histidine

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25
Q

what happens to O2 when it’s bound to heme

A

it has a partial negative charge due to its interaction with Fe2+ (this isn’t normal btw)

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26
Q

how does O2 with the negative charge become stabilized

A

stabilized electrostatically by His64 aka His E7, aka distal his

27
Q

where does the hydrogen bond form in regards to proximal and distal his and the heme group

A

hydrogen bond forms between O2 and an N-H on the distal His side chain

28
Q

what expression is used to represent the reversible binding of a protein to a ligand

A

P + L ⇌ PL

29
Q

what is the equilibrium constant for proteins binding to ligands

A

Ka

30
Q

what is the expression for Ka (ie how is Ka expressed)

A

Ka = [PL]/[P][L]

products over reactants

31
Q

what does Ka represent

A

the affinity of the ligand to the protein

32
Q

what does a high Ka represent

A

high affinity

33
Q

what are the units of Ka = [PL]/[P][L]

A

M^-1

34
Q

what variable represents the rate of the forward reaction

A

ka

35
Q

what variable represents the rate of the reverse reaction

A

kd

36
Q

how do Ka, ka, and kd relate

A

Ka = ka/kd

37
Q

define first order reaction

A

when there’s one reactant

38
Q

define second order reaction

A

when there’s two reactants

39
Q

what are the units for the rate constant in a first order reaction

A

s^-1

40
Q

what are the units for the rate constant in a second order reaction

A

(M^-1)(s^-1)

41
Q

T or F: the more ligand we have, the more ligand can bind

A

true

42
Q

how do we graphically represent ligand binding

A

we consider the fractional saturation of the protein with the ligand

= binding sites occupied/total binding sites

43
Q

what does Y equal

A

Y=fraction saturation= binding sites occupied/total binding sites = [PL]/([PL]+[P])

44
Q

what can the Y equation be simplified to

A

Y = [L]/([L]+1/Ka)

45
Q

at what value of Y does 1/Ka=[L] on the graph

A

Y=0.5 corresponds to the [L] that’s equal to 1/Ka

46
Q

what is Kd

A

the dissociation constant, and the reciprocal of Ka

47
Q

what are the units of Kd

A

M

48
Q

when [L]=Kd, how many of the ligand binding sites are filled

A

half

49
Q

how much ligand is bound as [L] falls below Kd

A

less ligand is bound

50
Q

how much ligand is bound as [L] rises above Kd

A

more ligand is bound

51
Q

a low Kd value corresponds to a (higher/lower) affinity of the ligand for the protein

A

higher

52
Q

since the ligand of myoglobin is O2 (gas), what adjustments do we make

A

we measure the partial pressure of O2 (pO2) instead of concentration

53
Q

what does P50 mean

A

the partial pressure of O2 at which 50% of ligand binding sites are occupied

54
Q

using partial pressure of O2, what is the equation for Y

A

Y= pO2/pO2+P50

55
Q

does myoglobin have a low or high affinity for O2

A

VERY high, due to low Kd value

56
Q

T or F: the binding of a ligand to any protein is affected by the protein structure and is often accompanied by conformational changes in the protein

A

true

57
Q

what different molecules can heme bind to

A

O2, CO, and NO

58
Q

describe the affinities heme has for CO and O2 when heme is free

A

CO has a MUCH higher affinity

59
Q

describe the affinities heme has for CO and O2 when heme is bound to myoglobin

A

CO still has greater affinity, but the difference is much less significant

60
Q

which ligand binds to heme at an angle

A

O2

61
Q

which ligand binds to perpendicularly

A

CO

62
Q

which angle of binding is stronger: straight or angled

A

straight

63
Q

will O2 or CO be more stabilized when bound to heme

A

O2, via the distal His. CO will not be stabilized by anything

64
Q

what happens if CO outcompetes O2 to bind to heme

A

it can kill us

BIOL 2421 - Cellular Biochem (21 decks)

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