Binding Sites, Enzymes, Chemical Signalling

Question 1

What is a ligand?

Answer 1

any molecule or ion that is bound to a protein by electrical attraction or hydrophobic attraction

Question 2

What does the binding of a ligand do to a protein?

Answer 2

It changes the conformation of the protein

Question 3

What is necessary for a ligand to bind to a protein?

Answer 3

the charges and conformational shapes must be complementary

Question 4

What is the affinity of a binding site to a ligand?

Answer 4

The strength of a ligand-protein binding, and the likeliness that the ligand will stay bound rather than returning to its unbound state

Question 5

What factors determine the percent saturation of a binding site with ligands?

Answer 5

• Concentration of unbound ligand

- affinity of the binding site for the ligand

Question 6

What are the two ways to control protein activity?

Answer 6

• Changing protein shape to alter ligand binding

- Regulating protein synthesis and breakdown

Question 7

What are the two mechanisms in cells that alter protein shape?

Answer 7

• Allosteric Modulation

- Covalent Modulation

Question 8

What is allosteric modulation?

Answer 8

When a protein has two binding sites and the binding of a protein to one of the sites alters the shape of the other.

Question 9

What is cooperativity?

Answer 9

When a ligand binds to the first of several functional sites on a molecule, inducing a change that increases the affinity of other functional sites

Question 10

What is covalent modulation?

Answer 10

The covalent bonding of charged chemical groups to some of the protein’s side chains.

Question 11

What is a common type of covalent modulation?

Answer 11

Phosphorylation

Question 12

what is the name for an enzyme that adds phosphate to another protein?

Answer 12

Kinase

Question 13

What is catabolism?

Answer 13

the break down of organic molecules

Question 14

What is anabolism, bro?

Answer 14

the synthesis of organic molecules

Question 15

What is the Law of Mass Action?

Answer 15

The concentration of reactants and products can determine the direction at which the net reaction proceeds

Question 16

What is the activation energy threshold?

Answer 16

Sufficient energy to overcome the mutual repulsion from electrons surrounding the atoms allowing them to collide

Question 17

What is a cofactor?

Answer 17

A trace metal (like Mg, Zinc, Cu, Fe) that binds to an enzyme changing its conformation so that it can bind substrate

Question 18

What is a coenzyme?

Answer 18

An organic molecule which directly participates as one of the substrates in a reaction

Question 19

What are the three main factors affecting enzyme mediated ractions?

Answer 19

Substrate concentration
Enzyme concentration
Enzyme Activity

Question 20

How does substrate concentration affect rate of enzyme mediated reactions?

Answer 20

Increases until saturated

Question 21

How does enzyme concentration affect rate of enzyme mediated reactions?

Answer 21

Increasing enzyme concentration increases the max rate (shift upwards in diagram).

Question 22

How does enzyme activity affect the rate of enzyme mediated reactions?

Answer 22

Increasing affinity through allosteric or covalent modulation increases the steepness of the diagram (think as efficiency)

Question 23

What is the difference between a neurotransmitter and a hormone?

Answer 23

Hormone = slow function over great distance
Neurotransmitter = rapid fuction over short distance

Question 24

What is down-regulation of receptors?

Answer 24

Where extra-cellular concentration of a messenger is maintained, the number of receptors on target cells is decreased, reducing the cell responsiveness to the chemical messenger

Question 25

What is up-regulation of receptors?

Answer 25

Exposing cells to low concentrations of messenger for long periods to increase the number of receptors on the cell surface

Question 26

What does binding of a chemical messenger to a receptor lead to a change in?

Answer 26

(the conformation, leading to a change in:)

• Permeability/Transport properties/electrical state
• Metabolism
• Secretory Activity
• Rate of proliferation and differentiation
• Contraction

Question 27

Explain the key points of the pathway of a lipid soluble chemical messenger

Answer 27

• Diffuses through the plasma membrane
• Binds to intracellular receptors
• Bind directly to recognised sequences in DNA
• Slower than membrane receptors but sustained

Question 28

Explain the key points of the pathway of a water soluble chemical messenger

Answer 28

• Bind to extracellular receptor proteins
• activate intracellular signalling cascades
• can have many effects including affecting DNA transcription
• Faster than lipid messengers but less sustained

Question 29

What are the different pathways for a water soluble chemical mssenger?

Answer 29

• Ligand gates ion channels
• Receptors that act as enzymes on the inside of the cell
• Receptors that interact with JAKs
• G-protein coupled receptors

Question 30

Explain the 4 methods of cessation of chemical signalling

Answer 30

• Metabolism of the first messenger
• Chemical alteration of messenger decreasing affinity and causing release of messenger
• Phosphorylation of receptor to prevent Gprotein binding
• Receptors being removed by endocytosis