Biology Exam 2

Question 1

Fractional saturation

Answer 1

occupied binding sites/ total binding sites
[PL]/[Pl]+[P]

Question 2

Kd

Answer 2

Kd is dissociation constant, and is the ligand at half saturation
[products]/[reactants]
[P][L]/[PL]

Question 3

What two factors determine how much protein is bound to a ligand at a given time

Answer 3

Concentration of ligand
affinity of a ligand to a protein

Question 4

How to define sigmoidal

Answer 4

It starts at a lower affinity and increases affinity as more ligand binds to a different subunit.

Question 5

What is a negative cooperativity

Answer 5

The binding of 1 ligand decreases the probability of the same ligand binding to a different subunit.

Question 6

Hemoglobin

Answer 6

Heterotetramer
4 heme subunits

Question 7

Bohr effect

Answer 7

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.

Question 8

Active muscles

Answer 8

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.

Question 9

Myglobin

Answer 9

Dimer or monomer
Higher affinity better suited to facilitate diffusion storage.

Question 10

Hemoglobin

Answer 10

Tetramer
Lower affinity due to cooperativity, efficiently transports O2 to tissues

Question 11

Structural features to make your protein allow cooperatively binding

Answer 11

The protein must have two affinity states and multiple subunits. The multiple subunits allow a switch in affinity inn other subunits.

Question 12

Why is Km a pesuado measure of affinity

Answer 12

The addition of the K2 allows idenity of the formation of product.

Question 13

4 features of proteins that make them idea catalyst

Answer 13

High reaction rates
Specificity
Mild reaction
Can be regulated

Question 14

High reaction rate

Answer 14

Rates significantly increased vs uncatalyzed and even chemical catalyst, therefor useful on biological time scale

Question 15

Specificity

Answer 15

Highly substrate and stereochemistry specific no side products, can also vary substrate specificity

Question 16

Can be regulated

Answer 16

Activity can be increased or decreased

Question 17

Mild reaction

Answer 17

Conditions can occur at biological temp, pressure and pH

Question 18

Transition state theory

Answer 18

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.

Question 19

What mechanism is used to increase the reaction

Answer 19

Proximity and Orientation, it increases effective substrate and alignment for rxn binding of the TS this then stabilizes the TS and lowers delta G.

Question 20

Active sites on Enzyme

Answer 20

3D structure by protein folding that binds substrate
(binding site)(Catalytic site)

Question 21

Regulating sites on Enzyme

Answer 21

binding site on enzyme for small molecules
(regulatory ligands)

Question 22

N-H

Answer 22

Base

Question 23

H-N

Answer 23

Acid