Module 3: V1 - V2

Question 1

What is the structure of myoglobin?

Answer 1

myoglobin is a monomer with tertiary structure

Question 2

What is the structure of hemoglobin?

Answer 2

hemoglobin is composed of four subunits

a tetramer with quaternary structure

Question 3

Which subunits is hemoglobin composed of?

Answer 3

hemoglobin is a tetramer of two subunits ɑ2β2

each subunit is similar to myoglobin

Question 4

Which group is common to both myoglobin and hemoglobin and what is the function of this group? How is it able to do this?

Answer 4

the heme group which binds oxygen

contains an Fe(II) centre which coordinates the oxygen that binds

Question 5

How can hemoglobin be described?

Answer 5

as a tetramer of four subunits or, more correctly, a dimer of two ɑβ ‘protomers’

Question 6

What is a ‘protomer’?

Answer 6

a ‘protomer’ is the structural ‘unit’ of a protein with quaternary structure

Question 7

How many subunits is IgG composed of, what are these subunits called and what is their function?

Answer 7

four subunits: 2 heavy chains and 2 light chains which are both involved in binding to the antigen ligand

Question 8

What happens to the variable regions once they bind an antigen?

Answer 8

they undergo conformational (shape) change

Question 9

How can IgG be described?

Answer 9

not so much a tetramer, more so a dimer of light chain / heavy chain pairs

Question 10

What is the Fab region and how many domains is it composed of?

Answer 10

the fragment that allows for antigen binding

it is composed of four domains

Question 11

What is the immunoglobulin-like fold composed of?

Answer 11

a sandwich of two beta-sheets

Question 12

Where is the variable domain found?

Answer 12

one at each of the two tips of the antigen binding region

Question 13

Why have antibodies evolved to be multivalent?

Answer 13

multivalent binding is more effective due to ‘avidity’

Question 14

Why has hemoglobin evolved to be multimeric (bind more than one oxygen)?

Answer 14

not just simply that it can bind four times more oxygen as myoglobin
cooperative binding occurs in hemoglobin resulting in a sigmoidal graph of saturation with O2 against pO2
this can only happen in a multimeric complex

Question 15

What are the two functions of myoglobin?

Answer 15

storage of oxygen in muscles and release of oxygen when rapidly contracting muscle needs energy

Question 16

Where does oxygen bind to in the myoglobin protein?

Answer 16

the heme group

Question 17

Why are diving animals e.g. seals, otters and whales able to breathe for long periods underwater?

Answer 17

when starting to dive, they slow their heart rate, stop breathing, and shunt blood to the brain, heart, and muscles
the myoglobin concentration in muscles of diving mammals is ~10x that in humans

Question 18

Why is myoglobin positively charge in elephant seals?

Answer 18

so the molecules repel each other and do not clump at high concentration

Question 19

What is a common function of many proteins?

Answer 19

many involve the binding of another molecule - in the case of myoglobin, that molecule is oxygen

Question 20

What is oxygen referred to in terms of binding and where does it bind to on the protein?

Answer 20

oxygen is called a ligand and the ligand attaches to the binding site of the protein

Question 21

How does O2 bind to myoglobin?

Answer 21

binds reversibly to Fe2+ of the heme prosthetic group

Question 22

What type of coordination complex does oxygen form with the heme prosthetic group?

Answer 22

octahedral

Question 23

What is the equilibrium association and dissociation constant for an arbitrary system of A + B ⇌ AB?

Answer 23

Ka = [AB]/[A][B], units M^-1
Kd = [A][B]/AB, units M

Question 24

Is the dissociation or association constant preferred in biological sciences? Why?

Answer 24

the dissociation constant because it is useful in expressing ligand binding as it represents the concentration of a ligand at which the protein is 50% saturated (Kd)

Question 25

What is given by theta? Give the equation.

Answer 25

occupied protein sites divided by total protein binding sites
θ = [PL]/[P] + [PL]
θ = [L]/[L] + Kd

Question 26

What is biotin?

Answer 26

a vitamin which must be provided in the diet and is needed for decarboxylations
binds the protein avidin found in raw egg white of which the Kd is 10^-15 (almost irreversible)

Question 27

What is biotin deficiency associated with in humans?

Answer 27

long-term consumption of diets rich in raw eggs

the biotin-avidin complex survives digestion and is lost in faeces

Question 28

You read a research article that that says the epidermal growth factor (EFG) receptor binds its ligand with a Kd of 1 nanomolar. Generally speaking, is that weak intermediate or strong binding?

Answer 28

strong binding

Question 29

A truncated mutant version of the receptor (missing some of its sequence) binds EGF with a Kd of 0.2 micromolar. Does the mutant bind EGF more strongly or more weakly than the wild type receptor?

Answer 29

more weakly

Question 30

A diet overly rich in raw eggs can lead to biotin deficiency. Cooked eggs do not cause this problem. Why?

Answer 30

avidin is denatured during the cooking process which means that it can no longer bind to biotin in the body, therefore this will not be an issue