Protein Function

Question 0

When a ligand binds to a protein what usually occurs? Why does it occur and what is the mechanism called?

Answer 0

Conformational changes in the protein. It occurs so the protein and ligand can bind more ‘tightly’ and it is called induced fit.

Question 1

What do many protein functions require? What is the name of the binding molecules involved?

Answer 1

Reversible binding of molecules to proteins.

Ligand.

Question 2

A conformational effect in a multi-subunit protein can cause what? What is this effect called?

Answer 2

Can cause conformational changes in the other subunits, this is an allosteric effect.

Question 3

Why is iron within a haeme group?
What is the Oxidative state of the iron atom in the haeme group?
How many coordination bonds bind the iron atom?

Answer 3

If iron was free floating it could bind to oxygen to form a highly reactive oxygen species such as hydroxyl radicals which can damage DNA.
The oxidation state is 2+
The iron atom is involved in six coordination bonds.

Question 4

Four of the coordination bonds are to what and why?
One or the coordination bonds is to what?
The final coordination bond is to what?

Answer 4

Four of the bonds are to the protoporphyrin ring. The nitrogen atoms involved in this prevent the Fe^2+ from changing to Fe^3+.
One of the bonds is to the nitrogen atom of a histidine residue.
The final bond would be to oxygen, it is the ligand binding site.

Question 5

What are globins?
Where is myoglobin found?
How many alpha helices does it possess?

Answer 5

Globins are a group of proteins which all have similar primary and tertiary structures. They are commonly found in eukaryotes but are found in some bacteria. Most function as oxygen transporters.
Myoglobin is found in the muscles of diving marine mammals.
It possesses eight alpha helices.

Question 6

Oxygen is transported around human blood via haemoglobin. Arterial blood is how much saturated with oxygen and venous blood is how much saturated with oxygen?

Answer 6

Arterial blood is 96% saturated.

Venous blood is 64% saturated.

Question 7

Haemoglobin can be described as what due to possessing four subunits and what are these individual subunits called?
How many amino acids are in each type of subunit?

Answer 7

Haemoglobin is a tetramer. It possesses two alpha subunits and two beta subunits. The alpha subunit has 141 amino acids within it and the beta subunit has 146 amino acids within it.

Question 8

Haemoglobin undergoes a structural change when oxygen binds to it, what are the two conformations? What subunit has a higher affinity for oxygen? What state is predominant in oxygen’s absence and why?

Answer 8

These conformations are labelled the R state and T state.
The R state has a higher affinity for oxygen.
The T state is predominant because it is more stable in oxygen’s absence.

Question 9

Why do the R and T conformations help the transport system?

What happens when one oxygen atom binds to a subunit?

Answer 9

They allow a balance in affinities to be formed. If haemoglobin was just in the R state it would have a very high affinity for oxygen but would not release it at the tissues, and vice versa for the T state.
When one oxygen atom binds to deoxygenated haemoglobin it binds weakly due to the presence of the T state however this T state would then change to the R state causing an allosteric effect on other subunits and increasing the affinity for oxygen.

Question 10

Haemoglobin also transports what molecules/ions and how much of the average body’s levels does it transport? High levels of what reduce the affinity of haemoglobin for oxygen? This reduction in the affinity of haemoglobin is called what?

Answer 10

It also transports H+ ions and CO2, with haemoglobin transporting 40% of the H+ and 20% of the CO2 produced.
High levels of H+ and CO2 reduce affinity, for H+ this is called the Bohr shift, for CO2 it is called the Haldane shift.

Question 11

Sickle cell anaemia is caused by what mutation? How does the effect result in sickle cell anaemia?

Answer 11

A point mutation resulting in glutamic acid being replaced by valine. It results in the haemoglobin being insoluble and forming polymers that aggregate into tubular fibre. These fibres deform the erythrocyte structure resulting in sickle structures that stick together to form clots.

Question 12

It is fundamental that ligand binding sites are what?

Answer 12

Able to discriminate between ligands, even those that are structurally similar.

Question 13

Immunity is brought about by what?

Name the cells involved in the immune system.

Answer 13

It is brought about by cooperation by different specialised cells.
Leukocytes are white blood cells that ingest large particles and cells via phagocytosis.
Lymphocytes are white blood cells: B-lymphocytes (B-plasma cells, B-memory cells), T-lymphocytes (cytotoxic T-cells, T-helper cells).

Question 14

Define an Antigen.
Define an Epitope.
Define Haptens.

Answer 14

An antigen is any molecule or pathogen that is capable of eliciting an immune response.
An epitope, also known as an antigenic determinant, is the particular molecular structure within an antigen to which an antibody or T-cell receptor binds.
Haptens are small molecules covalently coupled to carrier proteins to produce an immune response.

Question 15

What are MHC proteins? What are the two classes and give brief descriptions of each.

Answer 15

MHC proteins are major histocompatibility complex proteins. They exist on the surface of cells and there are two classes: class I and class II. Class I MHC proteins exist on the surface of all nucleated cells. Class II MHC proteins are on the surface of specialist cells, each individual cell produces up to twelve class II MHC proteins. They present peptides derived from extracellular foreign proteins.

Question 16

Describe the process of antigen presentation in relation to MHC proteins.

Answer 16

Firstly the antigen enters the cell where enzymes break it down into pieces. Antigen pieces bind to MHC proteins inside the endoplasmic reticulum. The MHC-antigen complex is transported to the cell surface via the Golgi apparatus. The MHC protein presents the antigen on the surface of the cell membrane.

Question 17

What is a cell mediated immune response?

What is a antibody mediated immune response?

Answer 17

Cell mediated immune responses do not involve antibodies but instead involve the activation of phagocytes, antigen-specific cytotoxic T-lymphocytes and the release of cytokines.
Antibody mediated immune responses create a memory system which immediately respond to a reintroduction of the antigen. Also antibodies are used to neutralised pathogens.

Question 18

What is the major class of antibody molecule?
Describe this molecule.
Identify the domains on typical antibody molecules.

Answer 18

Immunoglobulin G is the major class of antibody molecule. It possess four polypeptide chains: two heavy and two light chains. These are linked by covalent bonds and disulfide bridges. 
Antibodies are generally Y shaped with a hinge region that separates the base from the branches. The two domains are the constant domains and the variable domains.

Question 19

What determines the antibody binding specificity?
The lining of the antigen binding site is known as what?
Complete complementarity can be achieved how?

Answer 19

The amino acid residues in the variable regions of the heavy and light chains determine the specificity. The lining is known as hypervariable.
Complete complementarity may be achieved through conformational changes occurring as the antigen and antigen-binding site get closer together.

Question 20

What are polyclonal and monoclonal antibodies?

Answer 20

Polyclonal antibodies are antibodies produced by many different B-lymphocytes in response to one antigen. Monoclonal antibodies are antibodies produced from a population of identical B-lymphocytes.

Question 21

Describe the general technique of an immunoblot.

Answer 21

Coat surface with sample (antigens).
Block unoccupied sites with non-specific protein.
Incubate with primary antibody against specific antigen.
Incubate with antibody-enzyme complex that binds primary antibody.
Add substrate.
Formation of coloured product indicates the presence of specific antigen.

Question 22

List some protein interactions that are modulated by chemical energy.

Answer 22

Muscle contraction,
Movement of organelles along microtubules,
The rotation of bacterial flagella,
The movement of helicases and DNA polymerases along DNA.

Question 23

Describe the structure of myosin.

Answer 23

Myosin is made up of two heavy chains and four light chains. At the carboxyl terminus the chains are arranged in extended alpha helices wrapped around each other. At the amino terminus each heavy chain has a globular domain attached which is the site of ATP hydrolysis.

Question 24

What occurs when myosin is treated with trypsin and then with papain?

Answer 24

Much of the fibrous tail is cleaved off when treated with trypsin resulting in two fragments: light meromyosin and heavy meromyosin. When the heavy meromyosin is treated with papain the globular domain can be liberated, leaving two fragments: S1 (the globular domain) and S2.

Question 25

Describe actin filaments.

Answer 25

Actin filaments are formed from monomeric G-actin which associate to form long polymers called F-actin. When assembled the monomeric actin are bound to ATP which then hydrolysed to ADP. The F-actin chains interact to form helical chains. Tropomyosin then interacts with the F-actin, with troponin associating with tropomyosin, in muscle fibres.