Proteins

Question 1

Name the 5 main functions of proteins

Answer 1

1. Enzymes
2. Storage
3. Immunity
4. Growth
5. Structure

Question 2

What is the basic structure of a protein?

Answer 2

• Linear polymer comprising of 20 different types of amino acids spontaneously forming a 3D structure
• Each amino acid is formed from a central carbon, H, NH3+ and COO- as well as an R side chain
• Only L-isomers found in nature
• linked by peptide bonds formed in a hydrolytic reaction

Question 3

How does the structure of an amino acid change depending on the pH?

Answer 3

neutral - zwitterions
acidic - both groups are protonated
basic - both groups are deprotonated

Question 4

What are the characteristics of a peptide bond?

Answer 4

• Planar with a partial double bond character

- Can be cis or trans depending on whether alpha-carbon atoms are on the same side of the peptide bond

Question 5

How can ‘R’ side chains differ?

Answer 5

• size
• shape
• H-bonding
• hydrophobicity
• chemical reactivity

Question 6

What are the amino acids with the 2 simplest side chains?

Answer 6

Glycine (Gly,G) - H

Alanine (Ala, A) - CH3

Question 7

Name an amino acid with a long aliphatic chain and what is its characteristics?

Answer 7

Valine (Val,V) CH3CHCH3

Hydrophobic

Question 8

Give an example of an amino acid with an aromatic ring and what are its characteristics?

Answer 8

Phenylalanine (Phe, P)

• Hydrophobic
• Can absorb light via delocalised electrons at the ring

Question 9

Give 2 examples of proteins which are aliphatic with a hydroxy group

Answer 9

Serine and threonine

Question 10

What is the defining characteristic of asparagine and glutamine?

Answer 10

Both have an amide group

Question 11

Give an example of a protein with a sulphydryl/thiol group, what properties does this have?

Answer 11

• cysteine

- can form disulphide bridges

Question 12

Which bonds in a protein have free rotation?

Answer 12

Bonds between amino group and C and bonds between carbonyl group and C

Question 13

What limits the number of possible protein structures?

Answer 13

Restricted rotation due to steric clashes and the rigidity of the peptide bond

Question 14

What are phi and psi torsion angles?

Answer 14

phi - clockwise rotation viewed from N gives a positive angle
psi - clockwise rotation viewed from C gives a positive angle

Question 15

What does a protein fold to do?

Answer 15

reduce free energy

Question 16

Why does glycine not obey the Ramachandran limits?

Answer 16

Confers energy pay off

Question 17

What are the main components of the secondary protein structure?

Answer 17

alpha-helix, beta-sheet and loop/turn

Mainly formed by H bonding between NH (donor) and COOH (acceptor)

Question 18

Describe the structure of an alpha-helix

Answer 18

• coiled backbone, H bonds occur with residues 4 ahead
• Each residue is 1.5A and rotated 100degrees from the next with 3.6 amino acids per turn
• Usually right handed

Question 19

Describe the structure of beta sheets

Answer 19

• 2 or more beta strands
• 3.5 A between acids and side chains
• Can be parallel/antiparallel

Question 20

Give 5 elements of the tertiary structure of a protein

Answer 20

• hydrophobic interactions
• H-bonds
• Van der Waals interactions
• Disulphide bonds (covalent)
• Ionic bonds

Question 21

What are motifs/supersecondary structures?

Answer 21

combinations of secondary structure occurring frequently and often with a conserved function