Protein Structure 2

Question 1

What are the 2 main types of protein secondary structure?

Answer 1

• Alpha helix

- Beta sheet (of beta strands)

Question 2

Describe the structure of alpha helices.

Answer 2

• Right handed, 3.6 aa/turn, 0.54 nm pitch.

- Stabilised by H bonds between N-H and C=O every 4 aa residues away.

Question 3

Which aa promote or inhibit the formation of alpha-helices?

Answer 3

• Small hydrophobic residues such as alanine or leucine = strong helix formers.
• Proline = helix breaker as rotation around N-C alpha bond not possible.
• Glycine = helix breaker as tiny R group supports other conformations.

Question 4

Describe the structure of beta-sheets.

Answer 4

• Fully extended conformation, 0.35 nm between aa
• R groups alternate between opposite sides of chain.
• Stabilised by multiple inner H bonds.

Question 5

What is the difference between parallel and anti-parallel beta-sheets?

Answer 5

• Parallel: beta-strands in same directions

- Antiparallel: beta-strands in opposite directions

Question 6

Give examples of proteins that are mainly formed of alpha-helices or beta-sheets.

Answer 6

• Ferritin (iron storage) is largely alpha-helix.

- Fatty acid binding protein is largely beta-sheet.

Question 7

What are the 2 main forms of tertiary structure? Give example of each.

Answer 7

• Fibrous (e.g. Collagen)

- Globular (e.g. Carbonic anhydrase)

Question 8

Compare the properties of fibrous and globular proteins.

Answer 8

Fibrous:

• Long strands or sheets
• Single type of repeating secondary structure
• Role: support, shape, protection

Globular:

• Compact shape
• Several types of secondary structure
• Role: catalysis, regulation

Question 9

What is the aa sequence in collagen?

Answer 9

Gly-X-Y

Question 10

What is the different between motifs and domains in tertiary structure?

Answer 10

• Motifs: folding patterns containing 1 or more elements of 2ndary structure, e.g. Beta-alpha-beta loop, beta-barrel.
• Domains: part of a polypeptide chain that folds into a distinct shape. Often has a specific functional role, e.g. Calcium-binding domains of troponin C.

Question 11

Describe the tertiary structure of water-soluble proteins.

Answer 11

Fold so that:

• hydrophobic side chains are buried
• polar, charged chains are on the surface

E.g. Myoglobin

Question 12

Describe the tertiary structure of membrane proteins.

Answer 12

Often show ‘inside-out’ distribution of aa:

• water-filled hydrophilic channel at centre
• largely hydrophobic exterior.

E.g. Porins

Question 13

Describe the quaternary structure of haemoglobin and ribosomes.

Answer 13

• Haemoglobin: 2 alpha subunits, 2 beta subunits

- Ribosome: 55 protein subunits, 3 RNA molecules