Chapter 5: Protein Function Flashcards
What are ligands?
Small organic molecules or other macromolecules that bind to a specific region of a protein (binding site) with specific orientation.
What is affinity and selectivity of a ligand-protein complex?
Affinity: how tightly the ligand binds to the protein.
Selectivity: how well the protein discriminates between structurally similar ligands.
What is the receptor protein-ligand complex?
-Binds to hormones and other signaling molecules.
- Undergo conformational change and activate signaling process within the cell.
What is the immunoglobulin protein-ligand complex?
- Antibodies (bind to antigens).
- Recognize foreign macromolecules.
What is the lectin protein-ligand complex?
- Binds to ogliosaccharides.
- Various functions, all involving the highly specific binding of particular carbohydrate groups.
What is the DNA-binding protein-ligand complex?
- Binds to DNA
- Transcription factors: bind DNA to regulate transcription of genes.
- May also bind to other ligands to regulate when they can bind to DNA.
What are transport proteins?
- Bind to various ligands.
- O2 binding proteins (myoglobin, hemoglobin)
- Membrane transporters.
What is meant by induced fit?
When ligand binding is accompanied by conformational change of protein and/or ligand to accommodate tighter binding.
What does a high Ka imply about protein-ligand interactions?
A high Ka means a high concentration of the protein-ligand complex with means there’s a high affinity (tight binding).
What is the fractional occupancy (Y)?
Y = (# of occupied binding sites) / (total # of binding sites)
What is Kd a measure of?
Affinity
What allows proteins and ligands to bind?
H-bonds, van der Waals interactions, electrostatic interactions, and the hydrophobic effect.
What are lectins?
Proteins that bind specific oligosaccharides.
What is the final electron acceptor in mitochondria during ATP synthesis?
O2
What is Heme?
Complexes metal with organic ligands to protect metal from oxidation.
What is Myoglobin (Mb)?
Globin found in muscle cells of mammals and other vertebrates.
What is proximal His and distal His?
Proximal His (His 93 or His F8): Closer to Fe than distal His and forms a coordination complex with De.
Distal His (His 64 or His E7)
What is the physiological function of Mb?
Provides a reservoir of O2 in the muscle.
What is Myoglobin most effective for?
O2 storage.
What is Hemoglobin (Hb)?
Hemoglobin is the primary O2 transport protein in animals.
- Found in red blood cells.
What is an allosteric protein?
The binding of a ligand (modulator - the second ligand) to one binding site affects the affinity of a different binding site for another ligand.
What is homotropic regulation?
When the modulator and affected ligand are the same.
- O2 is a positive homotropic regulator for Hb binding to O2.
What is heterotropic regulation?
When the modulator and affected ligand are different.
What does the Hill Equation describe?
The Hill Equation described the saturation (fractional occupancy) for a multisubunit protein as a function of [L].
- For a protein with n binding sites for ligand, if the ligands bind with infinite cooperativity (either all sites occupied or no sites occupied):
Y = ([L]^n)/(Kd + [L]^n)
What is nH?
nH is the Hill coefficient.
- nH < n
What does it mean when nH = 1, nH > 1, and nH < 1?
nH = 1: no cooperativity.
nH > 1: positive cooperativity.
nH < 1: negative cooperativity.
What kind of cooperativity does Mb and Hb have?
Mb: No cooperativity as there is only one binding site (nH = 1).
Hb: No cooperativity less then 1 kPa or higher than 10 kPa. In between 1-10 kPa, there’s a higher affinity (nH = 3).
