Chapter 4: 4.1 Protein Function and Regulation Flashcards
What is a PTM?
Post-Translational Modifications (PTMs)
* Epigenetic marks that can alter the 3-D folding and/or function of a protein
List:
PTMs (7)
- Phosphorylation
- Ubiquitination
- Acetylation
- Sumolylation
- Glycosylation
- Myristoylation
- Farnesylation
- What is phosphorylation?
- What does it do?
- Adds a negative charge to an amino acid
- Can activate or repress the function of a protein
What is kinase?
A phosphorylating enzyme
What are key amino acid residues that are phosphorylated?
- Serine (S)
- Threonine (T)
- Tyrosine (Y)
- What is ubiquitination?
- What does it do?
- Addition of the protein ubiquitin to an amino acid
- Marks proteins for degredation (i.e. alters protein stability), alters the cellular location or alters the protein’s activity
- What is acetylation?
- What does it do?
- Addition of an acetyl group to an amino acid
- Can alter sub-cellular localization and protein-protein interactions
- What is sumoylation?
- What does it do?
- Addition of Small Ubiquitin-like Modifiers (SUMO proteins) to amino acids
- Can alter protein stability and solubility
- What is glycosylation?
- What does it do?
- Addition of a carbohydrate group to an amino acid
- Affects solubility of a protein (i.e. can make it membrane permeable to allow protein to leave/enter organelles)
- What is myristoylation?
- What does it do?
- Addition of myristoyl group to N-terminal glycine
- Alters cellular localization and protein-protein interactions
- What is farnesylation?
- What does it do?
- Addition of an isoprenyl group to a cysteine
- Alters cellular localization and protein-protein interactions
Define:
Ligands
Molecules to which proteins bind with a certain specificity and affinity
In Ligand Binding, define:
Specificity
How specific is the ligand protein interaction
* Can the ligand bind to more than one protein or vice versa?
In Ligand Binding, define:
Affinity
How strong is the ligand-binding interaction
* Is it easy for the ligand to dissociate from the protein?
In Ligand Binding:
What is Kd?
Measure of ligand-protein affinity
In Ligand Binding, state:
The formula for Kd
For a particular ligand binding interaction: PL <—-> P + L
Kd = [P] * [L] / [PL]
- P = Protein
- L = Ligand
- PL = Protein-Ligand complex
True or False:
When Kd is SMALL, the protein-ligand interaction is WEAK
False, when Kd is SMALL the protein-ligand interaction is STRONG (and vice versa)
In Ligand Binding
What do specificity and affinity depend on?
Physical and chemical properties of the protein’s ligand binding site
What is myoglobin?
A protein that binds to oxygen (O2)
What is the ligand binding interaction for Myoglobin?
Mb + O2 <—–> MbO2
State:
The Kd formula for myoglobin
Kd = [Mb] * [O2] / [MbO2]
At a given oxygen pressure, how do we determine how many myoglobin sites are bound to O2?
Y(O2) = [MbO2] / [Mb] + [MbO2]
* Y(O2) = Fraction of occupied binding sites
What is another form of the Y(O2) equation for Myoglobin?
Y(O2) = pO2 / Kd + pO2
* Substitute the equation for Kd into the equation for Y(O2)
* Express O2 as it’s partial pressure
K = p50 is where half of the myoblin or hemoglobin sites are…
Saturated (bound) to oxygen
Hemoglobin exhibits a form of ——— called…
Allostery, “Cooperativity”
Define:
Allostery
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
Describe:
Structure + Binding of Hemoglobin
- 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
What does increased affinity for a heme molecule mean?
They bind to O2 more easily
