CBS - Protein Structure and Function

Question 1

What are the two classes of proteins?

Answer 1

• globular proteins

- fibrillar proteins

Question 2

Describe a peptide bond (and how to break one).

Answer 2

. It is the bond between the carboxyl group and the amino group. It can be broken by hydrolysis.

Hydrolysis can only happen under certain conditions: the pH, and the enzymes needed to break the bonds, which can happen during digestion or through lysosome action.

Question 3

What are some features of a peptide bond?

Answer 3

It has some features of a ‘double bond’:

• shorter than expected C-N bond length, so there is no rotation
• rigid C-N bond, no rotation, trans arrangement of groups
• partial ⁻ve charge on O atom
• partial ⁺ve charge on N atom
• peptides can form H-bonds with other polar groups (including other peptide bonds) in polypeptide chain (e.g. a-helix)

Question 4

Describe the structure of a polypeptide.

Answer 4

The first amino acids has a has NH3⁺ group on the
N-terminal end, and the last amino acid has a COO⁻ group on the C-terminal end.

The R groups alternate on the plane (showing the trans-configuration). Thus, we end up with a peptide backbone, and alternating side chains.

Question 5

List (and describe) other covalent linkages, apart from peptide bonds.

Answer 5

DISULPHIDE (S-S) BRIDGES:
between two cysteines, joining subunits together e.g. insulin.

GLYCOSYLATION:

• O-linked -OH of threonine and serine
• N-linked -NH2 of asparegine

PHOSPHORYLATION: which are used in
- cell signal transduction e.g. phosphorylation of in tyrosine insulin receptor
- changing activity of an enzyme e.g. phosphorylation of
glycogen phosphorylase in response to glucagon

METHYLATION via -NH2 groups of lysein and argenine
- e.g. histones affecting gene expression

Question 6

Describe the levels of the 3D structure of a protein.

Answer 6

A 3D protein structure has 4 levels:
PRIMARY – the sequence of amino acids in the peptide chain

SECONDARY – folding/coiling of the peptide chain (usually into an α-helix or β-pleated sheet)

TERTIARY – how the whole polypeptide (sub-unit) is folded in 3D; it will consist of a number of different supersecondary structures (domains)

QUATERNARY – how the whole functional protein is formed in 3D, it may consist of a number of sub-units e.g haemoglobin α2β2

Question 7

Describe an α-helix.

Answer 7

It is formed by H-bonds in the same polypeptide chain (the backbone, not the side chains).

The H-bonds are formed between the peptide bond of the carbonyl-O & H of N-H every 4th peptide. This forms a regular right-handed helix.

There are 3.6 residues per turn, stabilised by H-bonds. The R groups are on the outside.

It is a rigid cylinder shape, and acts as an ‘architectural’ support for the protein.

Question 8

Describe β-pleated sheets.

Answer 8

They are linear peptide chains, with H-bonding between the peptide chain that holds the strands together in a β-sheet.

The side chains in each strand alternately lie above and below the plane of the sheet.

Question 9

Describe a collagen triple helix.

Answer 9

It is made up of three chains. It is found in collagen.

There are H-bonds between the chains (making it different to an alpha helix). There are 3 residues per turn, and is a left-handed helix.

It also has a repeating unit:
- Gly - X - Y - Gly - X - Y -

X= mainly proline
Y= mainly hydroxy-proline

This is an unusual structure. Proline cannot be form α helices, and is the hallmark of triple helices.

Question 10

List some forces that stabilise the protein structure.

Answer 10

COVALENT:
- disulphide bridges (not all proteins have them)

NON–COVALENT:

• hydrogen bonds
• electrostatic interactions
• Van der Waals forces
• hydrophobic effect

Question 11

Describe electrostatic interactions.

Answer 11

It occurs between charged side chains.

At physiological pH:

• Asp and Glu carboxyl groups are ionised (COO-)
• Lys and Arg amino groups are ionised (NH3+).

Depending on how a protein orients itself, its possible that there will be compatible residues that provide part of the stabilisation energy.

Question 12

Describe Van der Waals forces.

Answer 12

It is the sum of the attractive or repulsive forces between molecules. (excluding those due to covalent bonds, hydrogen bonds, and electrostatic interactions)

They are dependent on the dipole effect caused by the unequal distribution of electrons, such as the partial negative δ- and partial δ+ positive charge across a covalent bond.

Question 13

Describe hydrophobic effects.

Answer 13

Hydrophobic regions of a protein fold in such a way to minimise the contact with aqueous environment.

Hydrophobic regions are unable to form hydrogen bonds.

Question 14

List some examples of what proteins are sensitive to.

Answer 14

• pH
• temperature
• ionic strength

Question 15

Give some examples of how misfolded proteins can cause diseases.

Answer 15

Mutations can cause a protein to:

FOLD INCORRECTLY
- sickle cell disease (on beta chain of Hb molecule), changing Glu → Val (charged to hydrophobic), thus stablising the polymerization of HbS

FROM STABLE AGGREGATIONS

• amyloid proteins forming plaques in Alzheimer’s Disease
• prion protein polymerisation in Creutzfeldt-Jakob Disease

Question 16

Describe what happens in sickle cell disease.

Answer 16

The mutation is on the beta subunit of the haemoglobin at position 6.

The consequence of this mutation is the formation of a hydrophobic patch on the cell surface. This is unfavourable, thus the Hb orient themselves to prevent this region being in contact with the aqueous environment. They do that by polymerising together. This continues until it reaches an almost crystalline structure of filaments.

This causes problems with oxygen binding, etc. The Hb polymers can also disrupt the red blood cell membrane, bending it into the sickle shape that can find difficulty passing through narrow capillaries in laminar flow.