Protein structure and function 1

Question 1

Primary structure

Answer 1

Amino acid sequence

Disulfide bonds

Question 2

Secondary structure

Answer 2

Local organisation of polypeptide backbone

Beta pleated sheets and alpha helixes

Question 3

Tertiary structure

Answer 3

3D structure of polypeptide and the packing of secondary structure elements within it

Question 4

Quaternary structure

Answer 4

Number and position of polypeptide subunits

Question 5

Structure of amino acids

Answer 5

Amino group, R group, carboxyl group

Question 6

Formation of peptide bond

Answer 6

Between amino and carboxyl group of amino acids

Question 7

Disulfide bonds

Answer 7

Between two cysteine residues between chains

Question 8

Nature of peptide bond

Answer 8

Resonance hybrid
Delocalisation of pie electrons over entire bond instead of just C=O bond
Partial double bond character - restricted rotation, planar

Question 9

Peptide bond conformation

Answer 9

Trans or cis, trans favoured due to steric clash of R1 and R2 groups

Question 10

Advantages of alpha helix and beta sheets

Answer 10

Maximise hydrogen bonding and minimise steric repulsion while fitting with planar nature of peptide bond

Question 11

Beta sheet

Answer 11

Side chains point alternatively up and down

Question 12

Tertiary domains

Answer 12

Normally in polypeptides with more than 200 amino acids
Often serve as independent units of function
Act as platforms and offer functional variability
Composed of structural motifs

Question 13

Structural motifs

Answer 13

Secondary structures linked by loops in specific 3D arrangements
eg. Helix-loop-helix

Question 14

Major stabilisation forces of conformation

Answer 14

Hydrophobic interactions: non-polar residues are buried on the inside of polypeptide’s interior
Electrostatic attractions: van der Waals, H bonds, ionic interactions
Covalent linkages