1.2(c) - Protein Structure, Ligand Binding and Conformational Change

Question 1

Describe the structure of amino acids

Answer 1

Amino acids have the same basic structure however have different R groups. R groups of amino acids vary in size, shape, charge, hydrogen bonding capacity and chemical reactivity

Question 2

How do amino acids form polypeptides?

Answer 2

Amino acids are linked by peptide bonds to form polypeptide chains

Question 3

Name the different amino acid R groups

Answer 3

Basic (positively charged), acidic (negatively charged), polar and hydrophobic

Question 4

How do proteins have such a wide range of functions?

Answer 4

The diversity of R groups

Question 5

What is the primary structure of proteins?

Answer 5

The sequence in which amino acids are synthesised to form a polypeptide chain

Question 6

What is the secondary structure of proteins?

Answer 6

Hydrogen bonding along the backbone of the protein strand results in regions of secondary structure including alpha helices, beta-pleated sheets and turns

Question 7

What is the tertiary structure of a protein?

Answer 7

The final folded shape of the protein. It is stabilised by interactions between R groups including, hydrophobic interactions, ionic bonds, LDFs, hydrogen bonds and disulfide bridges

Question 8

What are disulfide bridges?

Answer 8

Covalent bonds between R groups containing sulfur

Question 9

What is the quaternary structure of protein?

Answer 9

Exists is proteins with two or more connected polypeptide subunits. It describes the spatial arrangement of the subunits

Question 10

What is a prosthetic group and give an example

Answer 10

ts a non-protein unit tightly bound to a protein which is necessary for its function

The ability of haemoglobin to bind to oxygen is dependent upon the the non-protein haem group

Question 11

What effect does increasing the temperature have on R groups?

Answer 11

What effect does increasing the temperature have on R groups?

Question 12

What effect does pH have on R groups?

Answer 12

The charges on acidic and basic R groups are affected. As pH increases or decreases from the optimum, the normal ionic interactions between charged groups are lost, which gradually changes the conformation of the protein until it becomes denatured

Question 13

Define a ligand

Answer 13

A ligand is a substance that can bind to a protein

Question 14

What can R groups not involved in protein folding do?

Answer 14

They can allow binding to ligands

Question 15

Describe what happens when a ligand binds

Answer 15

When a ligand binds to a protein-binding site the conformation of the protein changes. This change in conformation can cause functional changes in the protein

Question 16

Describe the structure of a binding site

Answer 16

The binding site will have a complementary shape to the ligand

Question 17

What happens when a substrate molecule binds to one active site of an allosteric and why is it important?

Answer 17

It increases the affinity of the other active sites for binding of subsequent substrate molecules

Its important because the activity of allosteric enzymes can vary greatly with small changes in substrate concentration

Question 18

What is cooperativity?

Answer 18

Changes in binding at one subunit alters the affinity for the remaining subunits

Question 19

What is the second site on an allosteric enzyme called?

Answer 19

An allosteric site

Question 20

What is the role a positive or negative modulator?

Answer 20

A positive modulator increases the enzyme’s affinity for the substrate whilst a negative modulator reduces the enzyme’s affinity

Question 21

What happens when a modulator binds?

Answer 21

Following binding of a modulator, the conformation of the enzyme changes and this alters the affinity of the active site for the substrate

Question 22

What do modulators do?

Answer 22

Once bound to the allosteric site they regulate the activity of the enzyme

Question 23

How does the binding and release of oxygen in haemoglobin show cooperativity?

Answer 23

Changes in binding of oxygen at one subunit alters the affinity of the remaining subunits for oxygen

Question 24

What influence does temperature have on the binding of oxygen?

Answer 24

An increase in temperature lowers the affinity of haemoglobin for oxygen so the binding of oxygen is reduced. This promotes increased oxygen delivery to tissue

Question 25

What influence does pH have on the binding of oxygen

Answer 25

Decrease in pH lowers the affinity of haemoglobin for oxygen so the binding of oxygen is reduced. This promotes increased oxygen delivery to tissue

Question 26

What does the addition or removal of a phosphate cause?

Answer 26

A reversible conformational change in proteins and is a common form of post-translational modification.

Question 27

What is the role of protein kinase?

Answer 27

It catalyses the transfer of a phosphate group to other proteins. (Phosphorylation)

Question 28

What is the role of protein phosphatase?

Answer 28

Catalyses the removal of a phosphate group (Dephosphorylation)

Question 29

How does phosphorylation affect the activity of the protein?

Answer 29

Some proteins are activated by phosphorylation while others are inhibited. Adding a phosphate group adds a negative charge which can disrupt ionic interactions in the unphosphorylated protein and new ones can be created

Question 30

Why is a protein’s activity affected by phosphorylation?

Answer 30

It causes a conformational change