Section 1

1. Proteins are polymers of amino acids where the amino group of one amino acid reacts with
the carboxylic acid group of another to form an amide bond (peptide bond).
2. An amino acid has the structure below where R is one of 20 different groups.

3. Nearly all amino acids are chiral (except glycine where R = H) existing in one particular
configuration.
4. Protein structure is described in terms of four levels of organisation: primary, secondary,
tertiary and quaternary.

5. The primary structure of a protein is the sequence of amino acids of which it is composed,
and ultimately determines the shape that the protein adopts.

6. The peptide group formed between two amino acid residues has a rigid planar structure and
these planar groups can rotate around the Cα–N and Cα–C bonds. In a polypeptide, the angles of

rotation about these bonds ( and ψ respectively) specify the conformation of the backbone. A

Ramachandran plot of versus ψ, based on ‘allowed’ and ‘outer limit’ distances for contact

between atoms, identifies those conformations that are sterically favourable or unfavourable.
7. A polypeptide will tend to fold in such a way as to give a conformation that minimises its free
energy (i.e. the most stable conformation).
8. Secondary structure refers to the conformation adopted by the polypeptide backbone of a
protein and includes helices, pleated sheets (parallel and antiparallel) and turns. Secondary structures
are stabilised by non-covalent interactions between atoms and groups in the polypeptide backbone,
namely hydrogen bonds and van der Waals attractions.
9. Tertiary structure describes how the polypeptide folds as a whole. The structure is held
together by long-range forces such as hydrogen bonding, van der Waals forces, ionic interactions,
dipole-dipole interactions, dipole-induced dipole interactions and disulfide bonds. The hydrophobic effect
is important in ensuring non-polar amino acids remain in the centre of the protein whereas polar amino
acids are located at the surface. There are certain distinct folding patterns common to many different
proteins. Discrete independently folded structures within a single polypeptide are called domains and
often have distinct functions.
10. Quaternary structure applies only to those proteins that consist of more than one polypeptide
chain (subunit) and describes how subunits associate with each other.
11. The structure of a protein can be determined by first sequencing the order of amino acids
using an Edman degradation that identifies each amino acid in turn from the N-terminal end. This can
be automated. Alternatively mass spectrometry can be used.
12. The arrangement of the amino acids in space can be determined using X-ray crystallography
or NMR spectroscopy.
13. The structure of a protein is stored at the RCSB Protein Data Bank as a pdb file that can be
downloaded and visualised using molecular modelling packages such as Discovery Studio. Such
packages enable the secondary structure of the protein to be interrogated as well as the active site and
any bound substrates/inhibitors.

Section 2

1. An enzyme is a catalyst – it enables biological reactions to take place at a reasonable rate at

about pH7, 37 °C and atmospheric pressure. It also ensures reactions occur selectively favouring one
particular product.
2. Enzyme action involves a substrate reaction at an active site to form an enzyme substrate
complex that then decomposes to give the product and the enzyme back again. A lock-and-key analogy
is often used to describe the relationship between the substrate and the active site, although this has
been superseded by the induced fit model.
3. Enzymes catalyse reactions in different ways, by providing an alternative pathway involving
low-energy intermediates, binding the reactants close together, stabilising the transition state and
enabling proton transfer via local acidic/basic groups.
 4. An inhibitor interferes with the catalytic activity of the enzyme by binding to the enzyme (at
the active site or at another binding site) and preventing the substrate binding to the active site.
Irreversible inhibitors covalently bind with the enzyme but reversible inhibitors bind to the enzyme via
non-covalent interactions.
5. Enzymes are classified according to their function, e.g. oxidoreductases, transferases,
hydrolases (including proteases), lyases, isomerases and ligases.
6. A serine protease has an active site consisting of a catalytic triad; an aspartic acid, histidine
and serine amino acids. This increases the nucleophilicity of the serine so that it acts as a good
nucleophile and can cleave a peptide bond. The triad also ensure the serine acts as a good leaving
group so can be hydrolysed back to its active form. The presence of certain amino acids in the active
site leads to the specificity for hydrolysis of peptide bonds between particular amino acids.
7. HIV proteases are essential for the development of HIV. An understanding of the active site
has led to peptide mimic inhibitors that block the active site and reduce the development of the disease.

8. Kinases are enzymes that catalyse the transfer of phosphate groups from nucleotides.
Receptor tyrosine kinases involve a ligand binding site on one side of a membrane and a catalytic site
on the other where phosphorylation leads to cell signaling such as cell growth that if permanently on or
off can lead to cancer. Drugs such as Glivec® can be used to treat chronic myeloid leukaemia – they
bind to the protein to prevent the phosphorylation occurring.

9. Flu is caused by a virus which has two proteins embedded in the viral coat, one of which is
neuraminidase which is inhibited by Tamiflu® and Relenza® which both mimic 2-deoxy-2,3-dehydro-N-
acetyl-neuraminic acid, the normal substrate of neuramidase.

Sec 3

1. Receptors are protein molecules that are involved in signalling within or between cells. A
ligand attaches to the binding site which causes a conformational change which triggers other actions.

2. The molecule that binds to the receptor is called a ligand. The strength of the ligand–receptor
interaction is measured by its dissociation constant, Kd. Ligands that bind to receptors in the membrane
of the post-synaptic cell are called neurotransmitters. An agonist is a compound that binds to a
receptor, causing the same conformational change and the same signal response as the endogenous
ligand. An antagonist is a compound that binds to a receptor, preventing the binding of the endogenous
ligand but does not elicit a response. A partial agonist is a compound that binds to a receptor and
produces a response that is less intense, or lower, than that of the endogenous ligand. An inverse
agonist binds to a receptor and reduces its base activity.
3. Many receptors span a membrane with the binding site on one side of the membrane and the
trigger on the other side of the membrane that can be amplified, for example, by turning on an enzyme.
4. Many such transmembrane proteins involve clusters of α-helices that span the membrane.
The amino acids in these α-helices tend to involve non-polar residues.

5. G-protein coupled receptors (GPCRs) are ubiquitous transmembrane signalling proteins. They
bind the ligand on the outside of the cell and bind G protein on the cytoplasmic side of the membrane.
This leads to signalling and further downstream action.

6. Ion channels are proteins that are embedded in cell membranes and that control the
environment inside cells by allowing, or preventing, the passage of positively and negatively charged
ions into and out of cells. Ion channels form narrow pores or channels in the membranes that can
switch between the ‘open’ state, when they allow the passage of ions through the membrane and the
‘closed’ state, when they do not. Passive channels simply allow ions to diffuse down electrostatic
gradients, and active channels, or ion pumps, allow ions to cross ‘uphill’ against electrostatic gradients.
7. Hypertension can be treated using antagonists of adrenaline – beta blockers. There are three
types of beta-adrenoceptor, for example, beta-1 receptors are found in heart tissue but beta-2
receptors are found in the lungs. Thus antagonists need to be designed carefully to exhibit specificity.
8. Levodopa is metabolised into the neurotransmitter dopamine for treatment of Parkinson’s
disease.

9. Stomach ulcers caused by abnormally high levels of secretion of gastric acid can be treated
by antagonists at the histidine-2 receptor, such as cimetidine. Again specificity is required to avoid
H1 binding.
10. Antipsychotics are used for the treatment of psychotic disorders. They act as antagonists for
receptors in the brain.