Protien Structure, Ligand Binding- Lecture 3 Flashcards
Amino acids of proteins that form ______ determine the ______ that are compatible with that site.
binding sites
molecular interactions
What is the main principle guiding the binding of a ligand to a site that?
complementarity
What are ligands?
molecules that bind to specific sites in proteins with high affinity
What is Kd and how is it calculated?
dissociation constant/ the equilibrium constant for the dissociation reaction
[P] [L]
Kd = ———–
[PL]
When half of the protein is bound to the ligand, what is Kd?
Kd = [L] because at this point [PL}=[L]
What is the relationship between Kd and affinity?
the lower the Kd, the higher the affinity of a ligand for proteins (because it takes a smaller amount of ligand to half-saturate its binding partner)
What is the composition of HbA?
two alpha globin chains and two beta globin chains (each bound to a ferrous iron [Fe2+])
Describe the process of O2 binding to HbA.
Oxygen binds to the ferrous iron (Fe2+) in the heme group and by forming a H bond with a histidine in globin, causing a conformational state
______ are molecules that bind to a protein on one site and cause a conformational change in the protein that affects its function at a distant site.
allosteric effectors
What molecules are allosteric effectors of hemoglobin?
O2
CO2
protons
2,3-bisphosphoglycerate
What is the Bohr effect?
the lowering of the pH by high concentrations of dissolved CO2 (shifts bicarbonate system equilibrium R) decreases the affinity of hemoglobin for oxygen
Other than the Bohr effect, what other effect does CO2 have on binding of O2 to hemoglobin?
CO2 binds directly to hemoglobin, decreasing its affinity for O2 resulting in the release of O2 in tissues that contain high concentrations of CO2
How does 2,3-bisphosphonate effect O2 binding to hemoglobin?
it is a product of glucose breakdown that can bind to hemoglonin and decrease affinity for O2
What increases the endogenous levels of 2,3-bisphosphonate?
pathological conditions such as anemia or chronic hypoxia due to lung disease
decreases in partial pressure of O2 in the air (high altitude adaptation)
What is the composition of fetal hemoglobin?
two gamma globin chains and two alpha globin chains
