Protein Function (myoglobin and hemoglobin)

Question 1

Ligand

Answer 1

anything reversibly bound by a protein
- can be any kind of molecule, including another protein
- when binded can cause conformational change

Question 2

binding site

Answer 2

specific sit a ligand binds to
- complementary to the ligand in terms of shape, charge, etc.
- single protein may have many

Question 3

What are the ligand of hemoglobin?

Answer 3

2,3 bisphosphoglycerate:
- regulates hemoglobin
- a lot of negative charge (a bunch of positive charge i the binding pocket)

Question 4

Protein breathing

Answer 4

Lots of flexibility and changing by ligand bonding

Question 5

Induced fit

Answer 5

Protein pushed towards a particular shape by the binding of a ligand
- change properties of proteins

Question 6

What is the issue with oxygen delivery to cells?

Answer 6

• oxygen has low solubility in blood so it can’t do passive diffusion
• amino acids chains not well suited for reversible binding of oxygen
• transition metals are good for binding with oxygen but release free radicals

Question 7

How do is the issue of the oxygen delivery/storage solved?

Answer 7

• specialized proteins are made
• heme group safely binds iron to oxygen

Question 8

Myoglobin

Answer 8

monomeric protein that is used as a oxygen storage in peripheral tissue?
- Binds single oxygen (hugs)
- tertiary structure
- Have high affinity for oxygen (strong binding)

Question 9

Hemoglobin

Answer 9

tetrameric protein found in red blood cells that transport oxygen from lungs to periphery
- hugs and releases oxygen
- goes back to lungs
- quaternary structure
- essentially 4 myoglobins together

Question 10

Structure of Heme group

Answer 10

• Fe(II) is in the middle while four protoporphyrin rings surround it each presenting a N
• electron donating from N prevents the Fe(II) from turning into Fe (III)
• needs a specialized system to make these groups

Question 11

Fe(II) seeks six interactions:

Answer 11

• four coming from heme group
• Fifth comes from a histidine (imidazole group)
• sixth is from oxygen
• another distal histidine binds onto oxygen for stabilization (transport oxygen)

Question 12

How does carbon monoxide poisoning work?

Answer 12

• instead of oxygen binding to the heme group carbon monoxide does instead since it has a similar structure
• greater affinity

Question 13

P50 value

Answer 13

amount of oxygen needed to half saturate a protein
Myoglobin - 3
Hemoglobin - 30

Question 14

Myoglobin vs Hemoglobin curves

Answer 14

Myoglobin:
- more to the left (has higher affinity for oxygen)
- curve is constant instant binding (first oxygen makes it easier for the rest to bind)

Hemoglobin:
- more to the right (has lower affinity for oxygen
- s shaped curve (takes more energy for hemoglobin to be saturated)

Question 15

What does it mean by Hemoglobin is an allosteric?

Answer 15

It has T (inactive) and R (active) forms (adopt different function)
- in rapid equilibrium

Question 16

Difference between R and T form

Answer 16

T state:
- deoxy form (doesn’t have any oxygen bound)

** R state:**
- as more oxygens bind it does to R state
- lower affinity for oxygen

Question 17

Why does Hemoglobin need to have an equal state of both high and low affinity?

Answer 17

• At high affinity it is not a very effective delivery system (holds onto oxygen)
• At low affinity it does not saturate itself fully at the lungs (not much to offload)
  - equal with fully saturated and offload half of the amount

Question 18

Allosteric modulators

Answer 18

Bind allosteric proteins at specific sites
- can be either activators or inhibitors
- activators stabilize the R state and inhibitors stabilize the T state

Question 19

Homotrophic

Answer 19

Normal ligand and modulator are the same

Question 20

Heterotrophic

Answer 20

Normal ligand and modulator are different from each other

Question 21

describe how oxygen is a homotropic allosteric activator for hemoglobin

Answer 21

• each subunit of hemoglobin start out in the T state (no oxygen)
• as more oxygen is added not much is going to happen since it’s in the T state (low affinity)
• eventually an oxygen binds to a subunit (ligand), changing to an R state
• promote the other subunits to go to the R state even though they don’t have an oxygen bound
• saturated with oxygen very quickly
• serves as primary ligand for first subunit but allosteric modulators for the others

Question 22

What kind of modulator is 2,3 bisphosphoglycerate?

Answer 22

Heterotropic allosteric inhibitor
- decreases hemoglobin’s affinity for oxygen

Question 23

How does the binding site work for bonding 2,3 bisphosphoglycerate?

Answer 23

• BPG is a very negatively charged protein
• The binding site of histidines and lysines are going to be very positive
• electrostatic interaction
• favors T state