Protein Function

Question 1

What are the three functions of myoglobin?

Answer 1

1. Facilitates oxygen diffusion through muscle tissue.
2. Acts as a local reserve of oxygen during intense exercise.
3. Stores oxygen in aquatic animals.

Question 2

If K(d) is high, what does this mean for the concentration of ligand/protein in a solution?

Answer 2

K(d) is high = Lower concentrations of complexes compared to free-floating ligand and proteins.

Question 3

If K(d) is low, what does this mean for the concentration of ligand/protein in a solution?

Answer 3

K(d) is low = Higher concentrations of complexes compared to free-floating ligand and proteins.

Question 4

What is specificity?

Answer 4

Specificity is the interaction between protein and ligand in which a protein is specialized for interaction with that particular ligand.

Question 5

What is affinity?

Answer 5

The strength and efficacy at which a ligand can bind to a protein.

Question 6

What is the structure of myoglobin?

Answer 6

8 alpha-helices and irregular structures in a globular structure; 153 amino acids present in total. Heme prosthetic group appears in hydrophobic pocket to allow for binding of oxygen.

Question 7

What is the structure of Heme?

Answer 7

Circular and planar porphyrin ring containing a ferrous (2+) ion situated between 4 nitrogen atoms. Two propionyl (charged polar) groups extend from the bottom of the porphyrin ring.

Question 8

What compounds bind at the fifth and sixth binding site of the ferrous ion in Heme?

Answer 8

6: Histidine
5: Oxygen

Question 9

What is the proximal histidine?

Answer 9

The histidine present in the 6th position relative to the ferrous ion of myoglobin (Known also as HisF8).

Question 10

How is the Heme prosthetic group held in place?

Answer 10

Through hydrophobic inetractions and coordination of bonds between the ferrous ion and the proximal histidine.

Question 11

What is the function of HisF8?

Answer 11

1. Binds heme into heme-binding pocket.

2. Prevents oxidation of ferrous ion.

Question 12

What is the distal histidine?

Answer 12

A histidine group (HisE7) that binds to the oxygen present at heme position 6.

Question 13

What is the function of HisE7?

Answer 13

1. Increase oxygen-binding affinity.
2. Lower affinity for other molecules.
3. Increase specificity for oxygen.

Question 14

What is the structure of hemoglobin?

Answer 14

Tetramer with 2 alpha subunits, 2 beta subunits with a heme group present in each subunit.

Question 15

What are homologous proteins?

Answer 15

Proteins that stem from similar ancestors, often contain similar or identical amino acids in key locations in the protein.

Question 16

What are conservative substitutions?

Answer 16

Relatively minor effects on structure/function.

Question 17

What are critical substitutions?

Answer 17

Changes in structure and function based on amino acid substitutions.

Question 18

How is the binding curve of Myoglobin described?

Answer 18

As a hyperbolic curve.

Question 19

How is the binding curve of hemoglobin described?

Answer 19

As a sigmoidal curve.

Question 20

What are the two conformations of hemoglobin?

Answer 20

Tensed (T) and Relaxed (R) state.

Question 21

What happens to the hemoglobin during deoxygenation?

Answer 21

A histidine residue on the beta subunit fits between a threonine and proline residue inside an alpha subunit.

Question 22

What happens to the hemoglobin during oxygenation?

Answer 22

A histidine residue on the beta subunit fits between two threonine residues inside an alpha subunit. This results in a change of shape.

Question 23

When is the central cavity largest in hemoglobin? (T or R)

Answer 23

T state

Question 24

When is oxygen affinity highest in hemoglobin? (T or R)

Answer 24

R state

Question 25

What does homoallosteric mean?

Answer 25

Occurs when binding of the effector affects further binding of the same compound.

Question 26

What does heteroallosteric mean?

Answer 26

Occurs when binding of the effector affects further binding of a different compound.

Question 27

What is an activator?

Answer 27

A ligand that increases binding affinity.

Question 28

What is an inhibitor?

Answer 28

A ligand that decreases binding affinity.

Question 29

What is positive cooperativity?

Answer 29

When the binding of a ligand at one site on a macromolecule increases the affinity of other sites for the same ligand.

Question 30

How does hemoglobin exhibit cooperative binding?

Answer 30

Oxygen is a homoallosteric activator of Hb, therefore as one molecule of oxygen binds to a Hb subunit it will cause the conformational change of all surrounding subunits to the relaxed state in order to bind to more oxygen.

This is important because, during oxygenation in the lungs, hemoglobin must quickly change conformation to take up massive amounts of oxygen. This is why we see a sigmoidal curve in hemoglobin binding instead of a hyperbolic curve.

Question 31

How does oxygen bind to the T-state? (How does the conformation occur?)

Answer 31

Oxygen binds to a subunit, causing the ferrous ion to move into the plate of heme due to electrostatic attraction. Proximal histidine moves with the ferrous ion, causing the subsequent movement of the helix bound to HisF8. This results in a subunit interface change.

Question 32

What are the three allosteric effectors for hemoglobin?

Answer 32

1. Oxygen.
2. BPG.
3. Hydrogens (protons, pH)