Chapter 4: 4.1 Protein Function and Regulation

Question 1

What is a PTM?

Answer 1

Post-Translational Modifications (PTMs)
* Epigenetic marks that can alter the 3-D folding and/or function of a protein

Question 2

List:

PTMs (7)

Answer 2

1. Phosphorylation
2. Ubiquitination
3. Acetylation
4. Sumolylation
5. Glycosylation
6. Myristoylation
7. Farnesylation

Question 3

1. What is phosphorylation?
2. What does it do?

Answer 3

1. Adds a negative charge to an amino acid
2. Can activate or repress the function of a protein

Question 4

What is kinase?

Answer 4

A phosphorylating enzyme

Question 5

What are key amino acid residues that are phosphorylated?

Answer 5

• Serine (S)
• Threonine (T)
• Tyrosine (Y)

Question 6

1. What is ubiquitination?
2. What does it do?

Answer 6

1. Addition of the protein ubiquitin to an amino acid
2. Marks proteins for degredation (i.e. alters protein stability), alters the cellular location or alters the protein’s activity

Question 7

1. What is acetylation?
2. What does it do?

Answer 7

1. Addition of an acetyl group to an amino acid
2. Can alter sub-cellular localization and protein-protein interactions

Question 8

1. What is sumoylation?
2. What does it do?

Answer 8

1. Addition of Small Ubiquitin-like Modifiers (SUMO proteins) to amino acids
2. Can alter protein stability and solubility

Question 9

1. What is glycosylation?
2. What does it do?

Answer 9

1. Addition of a carbohydrate group to an amino acid
2. Affects solubility of a protein (i.e. can make it membrane permeable to allow protein to leave/enter organelles)

Question 10

1. What is myristoylation?
2. What does it do?

Answer 10

1. Addition of myristoyl group to N-terminal glycine
2. Alters cellular localization and protein-protein interactions

Question 11

1. What is farnesylation?
2. What does it do?

Answer 11

1. Addition of an isoprenyl group to a cysteine
2. Alters cellular localization and protein-protein interactions

Question 12

Define:

Ligands

Answer 12

Molecules to which proteins bind with a certain specificity and affinity

Question 13

In Ligand Binding, define:

Specificity

Answer 13

How specific is the ligand protein interaction
* Can the ligand bind to more than one protein or vice versa?

Question 14

In Ligand Binding, define:

Affinity

Answer 14

How strong is the ligand-binding interaction
* Is it easy for the ligand to dissociate from the protein?

Question 15

In Ligand Binding:

What is Kd?

Answer 15

Measure of ligand-protein affinity

Question 16

In Ligand Binding, state:

The formula for Kd

Answer 16

For a particular ligand binding interaction: PL <—-> P + L

Kd = [P] * [L] / [PL]

• P = Protein
• L = Ligand
• PL = Protein-Ligand complex

Question 17

True or False:

When Kd is SMALL, the protein-ligand interaction is WEAK

Answer 17

False, when Kd is SMALL the protein-ligand interaction is STRONG (and vice versa)

Question 18

In Ligand Binding

What do specificity and affinity depend on?

Answer 18

Physical and chemical properties of the protein’s ligand binding site

Question 19

What is myoglobin?

Answer 19

A protein that binds to oxygen (O2)

Question 20

What is the ligand binding interaction for Myoglobin?

Answer 20

Mb + O2 <—–> MbO2

Question 21

State:

The Kd formula for myoglobin

Answer 21

Kd = [Mb] * [O2] / [MbO2]

Question 22

At a given oxygen pressure, how do we determine how many myoglobin sites are bound to O2?

Answer 22

Y(O2) = [MbO2] / [Mb] + [MbO2]
* Y(O2) = Fraction of occupied binding sites

Question 23

What is another form of the Y(O2) equation for Myoglobin?

Answer 23

Y(O2) = pO2 / Kd + pO2
* Substitute the equation for Kd into the equation for Y(O2)
* Express O2 as it’s partial pressure

Question 24

K = p50 is where half of the myoblin or hemoglobin sites are…

Answer 24

Saturated (bound) to oxygen

Question 25

Hemoglobin exhibits a form of ——— called…

Answer 25

Allostery, “Cooperativity”

Question 26

Define:

Allostery

Answer 26

When a ligand (allosteric effector) binds to a protein at one ligand binding site and effects the binding affinity at ANOTHER ligand-binding site on the same protein by inducing a conformational change in the proteins’ tertiary or quarternary structure

Question 27

Describe:

Structure + Binding of Hemoglobin

Answer 27

• Contains FOUR subunits which each contain one heme molecule
• Heme molecule in one subunit binds to O2, it increases the affinity for the other three heme molecules

Question 28

What does increased affinity for a heme molecule mean?

Answer 28

They bind to O2 more easily