U1 - Protein structure, ligand binding and conformational change

Question 1

What determines a proteins structure

Answer 1

An amino acid sequence

Question 2

Proteins are _______ of amino acid _____

Answer 2

Proteins are polymers of amino acid monomers

Question 3

What are amino acids linked by and what is a chain of amino acids called?

Answer 3

Amino acids are linked by peptide bonds to form polypeptides.

Question 4

What do amino acid structures differ by?

Answer 4

They differ by R groups; size, shape, charge , hydrogen bonding capacity and chemical activity

Question 5

What are the four amino acid R groups?

Answer 5

Basic ( positively charged )
Acidic ( negatively charged )
Hydrophilic ( Polar )
Hydrophobic ( Non - Polar )

Question 6

What determines the functions of proteins ?

Answer 6

The diversity of amino acid R groups and structures.

Question 7

What is the primary structure

Answer 7

The sequence in which the amino acids are synthesised into the polypeptide.

Question 8

What results in secondary structure

Answer 8

Hydrogen bonding along the backbone of the protein strand.

Question 9

Name the different types of secondary structure

Answer 9

Alpha Helices
Parallel or anti parallel beta pleated sheets
Turns

Question 10

What stabilises a tertiary structure

Answer 10

By interactions between R groups; 
Hydrophobic interactions
Ionic bonds
London dispersion forces
Hydrogen bonds 
Disulphide bridges

Question 11

What are disulfide bridges

Answer 11

Disulfide bridges are covalent bonds between groups containing sulfur

Question 12

What forms a Quaternary structure

Answer 12

A quaternary structure is when two or more polypeptide subunits connect

Question 13

What describes a Quaternary structure

Answer 13

It describes the spatial arrangement of subunits.

Question 14

what is a prosthetic group?

Answer 14

A prosthetic group is a non-protein unit tightly bound to a protein and necessary for its function.

Question 15

What allows haemoglobin to bind oxygen

Answer 15

It is dependent upon the non-protein haem group.

Question 16

What can influence interactions of the R groups

Answer 16

Temperature

pH

Question 17

How does temperature effect the interactions of the R groups

Answer 17

Increasing temperature disrupts the interactions that hold the protein in shape, the protein unfolds and eventually becomes de-natured.

Question 18

How does pH effect the interactions of the R groups

Answer 18

As pH increases or decreases from optimum, the normal ionic interactions between charged groups are lost, which gradually changes the conformation of the protein until it becomes denatured.

Question 19

What is a ligand

Answer 19

A ligand is a substance that can bind to a protein

Question 20

What are the other functions of R groups, excluding protein folding

Answer 20

They allow ligands to bind

Question 21

How are binding sites welcoming to ligands

Answer 21

They will have complementary shape and chemistry to the ligand.

Question 22

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

Answer 22

The conformation of the protein changes

Question 23

what happens when the conformation of a protein is changed by a ligand

Answer 23

It causes a functional change in the protein

Question 24

What is an allosteric site

Answer 24

An active site that is spatially distinct from the main active site of the enzyme

Question 25

What happens to the affinity of active sites if a molecule binds to the allosteric site

Answer 25

The binding of a structure molecule to one active site of an allosteric enzyme increases the affinity of the other active sites for binding of subsequent substrate molecules.

Question 26

Why are allosteric enzymes of biological importance

Answer 26

This is of biological importance because the activity of allosteric enzymes can vary greatly with the small changes in substrate concentrations.

Question 27

Many allosteric proteins consist of multiple subunits (quaternary)

Answer 27

q

Question 28

What features do allosteric proteins with multiple subunits show?

Answer 28

Co-operativity in binding, in which changes in binding at one subunit alter the affinity of the remaining subunits

Question 29

What is the second site on the allosteric enzyme called?

Answer 29

Allosteric site

Question 30

What do modulators do?

Answer 30

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

Question 31

What happens after the binding of a modulator?

Answer 31

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

Question 32

what do the different types of modulators do?

Answer 32

Positive modulators increase the enzymes affinity for the substrate, whereas negative modulators reduce the enzymes affinity.

Question 33

What is the relation between co-operativity and release of oxygen in haemoglobin

Answer 33

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

if one substrate binds it loosens off the other and then more bind.

Question 34

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

Answer 34

A decrease in pH or an increase in temperature lowers the affinity of haemoglobin for oxygen, so the binding of oxygen is reduced. Reduced pH and increased temperature in actively respiring tissue will reduce the binding of oxygen to haemoglobin promoting increased oxygen delivery to tissue.