8 - PROTEIN STRUCTURE & FUNCTION II

Question 1

Tertiary structure

Answer 1

the final 3D structure of a protein is produced by the association of the secondary structures into compact domains

Question 2

Non-covalent bonding in tertiary structure

Answer 2

important for correct tertiary structure:
• Ionic bonds
• Hydrogen bonds
• Van der Waals forces

Question 3

Disulphide bridges

Answer 3

The side chain of 1 CYSTEINE can form a crosslink with the side chain of another which is near to it in space.
This crosslink is called a DISULPHIDE BRIDGE, and is a covalent bond.
Disulphide bridges make proteins more resistant to degradation and denaturation

Question 4

Diagrammatic representation of tertiary structure

Answer 4

only the polypeptide backbone is usually shown as a thick line or ribbon.
The presence of an a-helix is usually indicated by the inclusion of a SPIRAL or CYLINDER within the ribbon.
b-strands are drawn as thick ARROWS, pointing from the N-terminal end to the C-terminal.

Question 5

Quaternary structure

Answer 5

The chains, SUBUNITS, associate into a MULTIMERIC COMPLEX which is held together by electrostatic, hydrogen and van der Waals bonds (and sometimes disulphide bridges)

Question 6

Haemoglobin I

Answer 6

Haemoglobin is composed of 4 polypeptides

2 identical a chains and 2 identical b chains

Question 7

Antibodies

Answer 7

Immunoglobulin G is a type of antibody

It is composed of 4 polypeptide chains and has intramolecular and intermolecular disulphide bridges

Question 8

GLOBULAR

Answer 8

Protein chain(s) are arranged in compact domains
Usually active components of the cellular ‘machinery’

Question 9

FIBROUS

Answer 9

Protein chains are arranged into fibres

Have a structural role

Question 10

3 main groups of fibrous proteins

Answer 10

coiled-coil (e.g. keratin and myosin)
b-sheets (e.g. amyloid fibres and silks)
triple helix (the collagens)

Question 11

α-Keratin I

Answer 11

• The keratins are a family of mechanically durable proteins found in hair, nails, feathers, etc
• The primary structure of a-keratin has a 7 amino acid repeat, a-b-c-d-e-f-g, which forms an a-helix
• Residues a and d are hydrophobic and lie on the same side of the a-helix; b, c, e, f, g can be any amino acid
• 2 a-keratin helices twist around each other, associating via the hydrophobic faces of the helices. This forms a COILED-COIL

Question 12

α-Keratin II

Answer 12

The coiled-coil dimer then lines up with another to form a staggered antiparallel tetramer
The tetramers are the building blocks of protofilaments which then form into protofibrils which then form microfibrils

Question 13

Fibroin I

Answer 13

Produced by silkworms
Long stretches of silk fibroin contain a six amino acid repeat (-Gly-Ser-Gly-Ala-Gly-Ala-)n which forms an antiparallel b-sheet
The glycine side chains (H) project from one side of the sheet and those of serine (CH2OH) and alanine (CH3) project from the other.

Question 14

Fibroin II

Answer 14

Silk is extremely strong as any stretching would require the breaking of covalent bonds, yet it is flexible because the b-sheets are interacting via weak van der Waals bonds
The b-sheets can stack into an array with layers of contacting Gly side chains alternating with layers of Ser/Ala side chains

Question 15

Collagen

Answer 15

Most abundant vertebrate protein - Forms strong fibres present in skin, bone, teeth, cartilage.
Nearly one-third of the amino acids are glycine. Another 15-30% are proline or hydroxyproline (Hyp)
The primary amino acid sequence consists of a repeating tripeptide of Gly-X-Y where X is often Pro and Y is often Hyp

Question 16

Why cant collagen form an a-helix?

Answer 16

because of the Pro and Hyp residues.

Instead it forms a ‘loose’ helix with around three residues per turn

Question 17

The collagen triple helix

Answer 17

The polypeptide chains form inter-chain hydrogen bonds
The Pro and Hyp residues confer rigidity
Every 3rd amino acid passes through the centre of the triple helix which is so crowded that only Gly can fit
Three collagen polypeptides wind around each other in a rope-like twist to form a TRIPLE HELIX
The triple-helical trimers can often associate to form large, strong fibres