Biology Exam 2 Flashcards
More info after studying
Fractional saturation
occupied binding sites/ total binding sites
[PL]/[Pl]+[P]
Kd
Kd is dissociation constant, and is the ligand at half saturation
[products]/[reactants]
[P][L]/[PL]
What two factors determine how much protein is bound to a ligand at a given time
Concentration of ligand
affinity of a ligand to a protein
How to define sigmoidal
It starts at a lower affinity and increases affinity as more ligand binds to a different subunit.
What is a negative cooperativity
The binding of 1 ligand decreases the probability of the same ligand binding to a different subunit.
Hemoglobin
Heterotetramer
4 heme subunits
Bohr effect
The influence of CO2 and H+ on the HB. Specific residues on the HB become protonated allowing them to form interactions that stabilize the Transition State.
Active muscles
An increase in metabolism produces CO2 and H+ which stabilize the Transition state which leads to less )2 binding in tissue.
Active muscles decrease the PO2 in the tissues causing additonal release of )2 by hemoglobin.
Myglobin
Dimer or monomer
Higher affinity better suited to facilitate diffusion storage.
Hemoglobin
Tetramer
Lower affinity due to cooperativity, efficiently transports O2 to tissues
Structural features to make your protein allow cooperatively binding
The protein must have two affinity states and multiple subunits. The multiple subunits allow a switch in affinity inn other subunits.
Why is Km a pesuado measure of affinity
The addition of the K2 allows idenity of the formation of product.
4 features of proteins that make them idea catalyst
High reaction rates
Specificity
Mild reaction
Can be regulated
High reaction rate
Rates significantly increased vs uncatalyzed and even chemical catalyst, therefor useful on biological time scale
Specificity
Highly substrate and stereochemistry specific no side products, can also vary substrate specificity
Can be regulated
Activity can be increased or decreased
Mild reaction
Conditions can occur at biological temp, pressure and pH
Transition state theory
Reactions proceed through an unstable intermediate to products. The rate is determined by delta G between reactants and the transition state. Enzymes accelerate the rate of rxn by stabilizing the transition state or changing the pathway. This then decreases delta G between reactants and the Transition State.
What mechanism is used to increase the reaction
Proximity and Orientation, it increases effective substrate and alignment for rxn binding of the TS this then stabilizes the TS and lowers delta G.
Active sites on Enzyme
3D structure by protein folding that binds substrate
(binding site)(Catalytic site)
Regulating sites on Enzyme
binding site on enzyme for small molecules
(regulatory ligands)
N-H
Base
H-N
Acid
