7. Myoglobin and molecular binding

Question 1

T or F: O2 is poorly soluble in aqueous solutions

Answer 1

true

Question 2

what is the role of myoglobin

Answer 2

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

Question 3

what animal is myoglobin very prevalent in and why

Answer 3

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

Question 4

how much more myoglobin do sperm whales have than humans

Answer 4

about 30x more

Question 5

how many polypeptides is myoglobin

Answer 5

1

Question 6

how many amino acids is myoglobin

Answer 6

153

Question 7

what is the molecular weight of myoglobin

Answer 7

Mr=16,700

Question 8

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

Answer 8

78% of residues are in alpha helices

Question 9

how many helices make up myoglobin

Answer 9

8

Question 10

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

Answer 10

hydrophobic residues

Question 11

which hydrophobic residues make up the interior of myoglobin

Answer 11

Valine, Leucine, Isoleucine, Phenylalanine, and methionine

VMILF

Question 12

what part of myoglobin binds O2

Answer 12

the associated heme group

Question 13

describe the structure of the heme group of myoglobin

Answer 13

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

Question 14

why is muscle and blood dark red

Answer 14

heme absorbs light at that wavelength

Question 15

how are the helices in myoglobin named

Answer 15

A-H

Question 16

how are the bands connecting the helices named

Answer 16

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

Question 17

how are residues in the helices named

Answer 17

named for their position in a given helix

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

Question 18

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

Answer 18

4 of 8 helices end with proline

Question 19

why do half of the helices end in proline

Answer 19

they break helices because they don’t fit

Question 20

in regards to the helices, where is the heme group

Answer 20

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

Question 21

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

Answer 21

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

Question 22

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

Answer 22

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

Question 23

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

Answer 23

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

Question 24

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

Answer 24

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

Question 25

what happens to O2 when it's bound to heme

Answer 25

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

Question 26

how does O2 with the negative charge become stabilized

Answer 26

stabilized electrostatically by His64 aka His E7, aka distal his

Question 27

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

Answer 27

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

Question 28

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

Answer 28

P + L ⇌ PL

Question 29

what is the equilibrium constant for proteins binding to ligands

Answer 29

Ka

Question 30

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

Answer 30

Ka = [PL]/[P][L] | products over reactants

Question 31

what does Ka represent

Answer 31

the affinity of the ligand to the protein

Question 32

what does a high Ka represent

Answer 32

high affinity

Question 33

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

Answer 33

M^-1

Question 34

what variable represents the rate of the forward reaction

Answer 34

ka

Question 35

what variable represents the rate of the reverse reaction

Answer 35

kd

Question 36

how do Ka, ka, and kd relate

Answer 36

Ka = ka/kd

Question 37

define first order reaction

Answer 37

when there's one reactant

Question 38

define second order reaction

Answer 38

when there's two reactants

Question 39

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

Answer 39

s^-1

Question 40

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

Answer 40

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

Question 41

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

Answer 41

true

Question 42

how do we graphically represent ligand binding

Answer 42

we consider the fractional saturation of the protein with the ligand = binding sites occupied/total binding sites

Question 43

what does Y equal

Answer 43

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

Question 44

what can the Y equation be simplified to

Answer 44

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

Question 45

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

Answer 45

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

Question 46

what is Kd

Answer 46

the dissociation constant, and the reciprocal of Ka

Question 47

what are the units of Kd

Answer 47

M

Question 48

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

Answer 48

half

Question 49

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

Answer 49

less ligand is bound

Question 50

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

Answer 50

more ligand is bound

Question 51

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

Answer 51

higher

Question 52

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

Answer 52

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

Question 53

what does P50 mean

Answer 53

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

Question 54

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

Answer 54

Y= pO2/pO2+P50

Question 55

does myoglobin have a low or high affinity for O2

Answer 55

VERY high, due to low Kd value

Question 56

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

Answer 56

true

Question 57

what different molecules can heme bind to

Answer 57

O2, CO, and NO

Question 58

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

Answer 58

CO has a MUCH higher affinity

Question 59

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

Answer 59

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

Question 60

which ligand binds to heme at an angle

Answer 60

O2

Question 61

which ligand binds to perpendicularly

Answer 61

CO

Question 62

which angle of binding is stronger: straight or angled

Answer 62

straight

Question 63

will O2 or CO be more stabilized when bound to heme

Answer 63

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

Question 64

what happens if CO outcompetes O2 to bind to heme

Answer 64

it can kill us