KA2: Proteins: Protein structure, ligand binding and conformational change: Ligand binding changes the conformation of a protein

Question 1

Define the term ligand

Answer 1

A substance that can bind to a protein

Question 2

what do R groups not involved in protein folding do?

Answer 2

allow binding to ligands

Question 3

binding sites will have…

Answer 3

complementary shape and chemistry to the ligand

Question 4

what happens when a ligand binds to the protein-binding site?

and what does this do?

Answer 4

the conformation of the protein changes

this change in conformation causes a functional change in the protein

Question 5

describe the allosteric interactions occuring between spatially distinct sites and why these interactions are of biological importance

Answer 5

*binding of substrate molecule to one active site of an allosteric enzyme increases the affinity of the other active sites for binding of a subsequent substrate molecule

*because the activity of allosteric enzymes can very greatly with small changes in substrate concentration

Question 6

describe how allosteric interactions occur between spatially distinct sites

Answer 6

multiple subunits (quaternary structure)

Question 7

what do many allosteric proteins consist of?

Answer 7

multiple subunits (quaternary structure)

Question 8

describe the process of co-operativity in binding

Answer 8

Allosteric proteins with multiple subunits show co-operativity in binding, in which changes in binding at one subunit affect the binding of the remaining subunits

Question 9

what do allosteric enzymes contain and what are they called

Answer 9

a second type of site, called an allosteric site

Question 10

What do modulators do?

Answer 10

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

Question 11

describe the effect the binding of a modulator may have on a protein

Answer 11

the conformation of the changes and this alters the affinity of the active site for the substrate.

Question 12

what is the effect of a positive modulator?

Answer 12

increase the enzyme’s affinity for the substrate

Question 13

what is the effect of a negative modulator?

Answer 13

reduce the enzyme’s affinity

Question 14

what in haemoglobin shows cooperativity?

Answer 14

The binding and release of oxygen

Question 15

what alters the affinty of the remaining subunits for oxygen?

Answer 15

changes in binding of oxygen at one subunit

Question 16

describe the influence and physiological importance of temperature and pH on the binding of oxygen

Answer 16

decrease pH/increase temperature=>
lowers the affinity of haemoglobin for oxygen. Binding of oxygen is reduced.

Reduced increased temperature in actively respiring tissue =>

reduce the binding of oxygen to haemoglobin promoting increased oxygen delivery to tissue

Question 17

what does the addition or removal of phosphate cause?

what is this a common form of?

Answer 17

reversible conformational change in proteins

post-transitional modification

Question 18

what is the role of protein kinases?

Answer 18

catalyse the transfer of a phosphate group to other proteins

Question 19

Describe the use of ATP in phosphorylation reactions.

Answer 19

The terminal phosphate of ATP is transferred to specific R groups

Question 20

describe the role of protein phosphatases

Answer 20

• catalyse the reverse reaction of kinases (they take the phosphate away from a protein)

Question 21

what does phosphorylation bring about and what does this affect?

give an example

Answer 21

conformational change, which affects the protein’s activity and teh activity of cellular proteins

e.g. enzymes and receptors

Question 22

how are proteins activated?

Answer 22

some by phosphorylation, some by inhibition

Question 23

what affect does adding a phosphate group have?

Answer 23

adds negative charges

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