Ligands

Question 1

What is a ligand

Answer 1

A ligand is a substance that can bind to a protein. R groups not involved in protein folding can allow binding to these other molecules. Binding sites will have complementary shape and chemistry to the ligand.

Question 2

How does DNA bind to a number of proteins?

Answer 2

Positively charged histone proteins bind to the negatively charged sugar-phosphate backbone of DNA in eukaryotes. The DNA is wrapped around histones to form nucleosomes packing the DNA in chromosomes.

Question 3

What do other proteins have?

Answer 3

Other proteins have binding sites that are specific to particular sequences of double stranded DNA and when bound to can either stimulate or inhibit initiation of transcription.

Question 4

What happens when a ligand binds to a protein?

Answer 4

As a ligand binds to a protein binding site or a substrate binds to an enzymes active site, the conformation of the protein changes. This change in conformation causes a functional change in the protein.

Question 5

Describe the induced fit model

Answer 5

Induced fit in enzymes occurs when the correct substrate starts to bind resulting in a temporary change in shape of the active site increasing the binding and interaction with the substrate.

Question 6

Describe the control of allosteric enzymes.

Answer 6

In allosteric enzymes, modulators bind to secondary binding sites. The conformation of the enzyme alters the affinity for the substrate.

Question 7

Describe the role of positive and negative modulators.

Answer 7

Positive modulators increase the enzyme’s affinity whereas negative modulators reduce the enzyme’s affinity for the substrate.

Question 8

Explain cooperativity

Answer 8

Some proteins with quaternary structure show cooperativity in which changes in binding at one subunit alter the affinity of the remaining subunits.

Question 9

Explain cooperativity in the binding and release of oxygen in haemoglobin

Answer 9

In haemoglobin when one of the subunits binds to a molecule of oxygen, the second binds more easily and the third and fourth easier still. When oxyhaemoglobin releases oxygen, the same process occurs. Once one subunit has released its oxygen the next subunit is more likely to release oxygen and so on.

Question 10

What are the main factors which can affect haemoglobin’s ability to bind to oxygen

Answer 10

Temperature - as temperature increases, affinity for oxygen decreases.
pH - as pH decreases, affinity for oxygen decreases.