1.2c ligand binding and conformational change

Question 1

What does ligand binding do?

Answer 1

changes the conformation of a protein

Question 2

What is a ligand?

Answer 2

a substance that can bind to a protein

Question 3

What R groups can be allowed to bind to ligands

Answer 3

those not involved in protein folding

Question 4

What will binding sites have?

Answer 4

complementary shape and chemistry to the ligand

Question 5

What happens as a ligand binds to a protein-binding site and what effect does it have?

Answer 5

-the conformation of the protein changes
-and it causes a functional change in the protein

Question 6

When do allosteric interactions occur?

Answer 6

between spatially distinct sites

Question 7

Describe the binding of substrate molecules to allosteric enzymes

Answer 7

-binding to one active site increases the affinity of the other active sites for binding of subsequent substrate molecules

-of biological importance because the activity of allosteric enzymes can very greatly with small changes in substrate concentration

Question 8

Describe the structure of many allosteric proteins

Answer 8

many allosteric proteins consist of multiple subunits (quaternery structure)

Question 9

What do allosteric proteins with multiple subunits show?

Answer 9

co-operativity in binding

Question 10

What is cooperativity?

Answer 10

changes in binding at one subunit alter the affinity of the remaining subunits

Question 11

What is the second site on allosteric enzymes calles?

Answer 11

allosteric site

Question 12

What are modulators?

Answer 12

they regulate the activity of the enzyme when they bind to the allosteric site

Question 13

What happens following the binding of a modulator and what is the effect of this?

Answer 13

-the conformation of the enzyme changes

-alters the affinity of the active site for the substrate

Question 14

What do positive modulators do?

Answer 14

increase the enzymes affinity for the substrate

Question 15

What do negative modulators do?

Answer 15

reduce the enzymes affinity for the substrate

Question 16

What shows co-operativity in haemoglobin?

Answer 16

the binding and release of oxygen

Question 17

Describe co-operativity in haemoglobin

Answer 17

changes in the binding of oxygen at one subunit alter the affinity of the remaining subunits for oxygen

Question 18

What is the influence and physiological importance of temperature and pH on the binding of oxygen?

Answer 18

-decreased in pH or increase in temperature lowers the affinity of haemoglobin for oxygen, so the binding of oxygen is reduced

-in actively respiring tissue will reduce the binding of oxygen to haemoglobin

-promoting increased oxygen delivery to tissue

Question 19

What does the addition or removal of a phosphate cause?

Answer 19

-reversible conformational change in proteins

-this is a common form of post-translational modification

Question 20

What do protein kinases do?

Answer 20

catalyse the transfer of a phosphate group to other proteins

Question 21

What happens to the terminal phosphate of ATP?

Answer 21

transferred to specific R groups

Question 22

What do protein phosphatases do?

Answer 22

catalyse the reverse reaction (the removal of phosphate groups from proteins)

Question 23

What is the effect of phosphorylation and give examples?

Answer 23

-brings about the conformational changes, which can affect a protein’s activity

-the activity of many cellular proteins such as enzymes and receptors, is regulated in this way

Question 24

State the effect of phosphorylation on proteins

Answer 24

some are activated, others are inhibited

Question 25

What charges does adding a phosphate group add and what is the effect?

Answer 25

-negative
-ionic interactions in the unphosphorylated protein can be disrupted and new ones created