Ligand Binding

Question 1

What is the importance of ligand binding?

Answer 1

1. Carrier proteins must bind a ligand
2. Receptors must being a ligand agonist/antagonist for effect
3. Proteins in switching must bind trigger molecule -> conformational change -> activation/deactivation of another component in signalling system
4. Structural proteins often bind other monomericproteins of same type to form polymeric structures e.g. F-actin
5. DNA + RNA binding proteins + ribosomal proteins must effectively bind macromolcelular structures/ associate with other large proteins
6. Enzyme -> substrates

Question 2

For an enzyme reaction to occur:

Answer 2

1. Ligand must undergo chemical transformations in stereochemistry, charge configuration or covalent bonding
2. Free energy barrier must be overcome (higher the barrier slower the reaction)

Question 3

Transition State

Answer 3

1. Highest point of free energy in pathway
2. Where bonds are being made/broken
3. 10^-13s

Question 4

How do enzymes speed up reaction rates?

Answer 4

1. Raising energy of ground state
2. Lowering free energy of transition state
3. Provide an alternative route of reaction

Question 5

pH optima

Answer 5

The pH at which binding and catalytic groups are correctly ionised for binding and carrying out chemistry of catalysts

Question 6

How do enzymes achieve catalysis?

Answer 6

1. Reactive groups in active site -> optimally positioned to interact with substrate -> effectively increases conc. of reacting species in active site
2. Substrate bound in correct orientation -> catalytic efficiency
3. Some enzymes bind substrates in a way that destabilises the ground state for substrate
4. Some enzymes stabilise TS or preferentially bind TS structure

Question 7

What other factors contribute to catalysis?

Answer 7

1. Protein flexibility
2. Displacement of water from active site leading to local movement of amino acid side chains -> correct alignment + orientation of substrate

Question 8

4 General types of chemical transformation

Answer 8

1. REDOX
2. Addition/Elimination
3. Cleavage of esters, amides or acetals by reaction with water -> formation of these groups by removal of water
4. Removal of single carbon atom by loss of CO2

Question 9

How do active sites promote acid-base chemistry?

Answer 9

They use conjugate base of acidic amino acid or conjugate acid of more basic amino acids

Question 10

Histidine

Answer 10

Can act as both acid and base and is found in many active sites

Question 11

Cofactors

Answer 11

Molecules that are recruited to assist with catalysis. Can either be essential metal ions or coenzymes

Question 12

Co-enzymes

Answer 12

Cofactors that are organic compounds and assist in catalytic chemistry

Question 13

Activator ions and Cosubstrates are

Answer 13

weakly bound

Question 14

Active site ions and Prosthetic groups are

Answer 14

tightly bound

Question 15

Hydrolases

Answer 15

AB + H2O -> AH + HO-B

Question 16

Oxidoreductases

Answer 16

AH2 + B -> A + BH2

Question 17

Transferases

Answer 17

AB + C -> A + BC

Question 18

Isomerases

Answer 18

A -> isoA

Question 19

Lyases

Answer 19

AB -> A + B

Question 20

Ligases

Answer 20

A + B -> AB