Proteins

Question 1

Where does a dipeptide form

Answer 1

1. Between carboxyl group and amino group

Question 2

Name the 4 levels of organisation of a protein

Answer 2

1. Primary structure- amino acid sequence of its polypeptide chain
2. Secondary structure- Alpha helix, beta sheets and loops
3. Tertiary structure- 3D structure of entire polypeptide
4. Quaternary structure- structure of multiple polypeptide chains (subunits) in a protein.

Question 3

Describe the structure of an alpha helix

Answer 3

1. Either left handed or right handed (normally right handed)
2. 3.6 residues per turn (13 main chain atoms)
3. Rise of 5.4 Å per turn (1.5 Å per residue)
4. Hydrogen bonds form between N-H and C=O groups
5. Contains a dipole moment

Question 4

Why does an alpha helix contain a dipole moment

Answer 4

1. All carbonyl groups are pointing one-way c terminus has slight negative charge.
2. Because all NH groups point down N terminus has slight positive charge.

Question 5

What is the N-terminus and C-terminus

Answer 5

1. End with NH2 group- N terminus
2. End with COOH group- C-terminus
3. Always read amino acid from N-terminus to C-terminus direction

Question 6

What are the two types of beta pleated sheets

Answer 6

1. Antiparallel- neighbouring hydrogen bonded polypeptide chains run in opposite directions
2. Parallel- hydrogen bonded chains run in same direction
3. Many proteins contain mixes of and antiparallel beta pleated sheets- may result in giving the protein a twist as mix of straight and wonky

Question 7

Why are parallel beta pleated sheets less stable

Answer 7

1. Amino groups and carbonyl groups don’t line up properly
2. Because of wonky interactions less stable
3. Hydrogen bonds not as stable because the N and O atoms are further apart

Question 8

Do beta pleated sheets have a dipole

Answer 8

1. Don’t have dipole moment.

2. Amino acids alternate their orientation, so the dipoles cancel out

Question 9

Name two other types of secondary structure

Answer 9

1. Alpha-pleated sheet- very rare

2. Beta helices- antifreeze protein found in beetles

Question 10

What are loops/ beta turns

Answer 10

1. Hydrogen bonds between two amino acids on opposite sides
2. Two types- main difference is the way the peptide plane faces
3. Used to connect beta sheets

Question 11

Describe the tertiary structure

Answer 11

1. Segments of secondary structure (e.g. α-helix)
2. Linked by less regular segments turns (loops)
3. Results in a compact, globular structure

Question 12

List 4 non-covalent interactions in polypeptides

Answer 12

1. Hydrogen bond - Form with amino group, carboxyl group and functional R group- internal hydrogen bonding cannot significantly stabilise structure-may even destabilise
2. Ionic interaction (salt bridge)- contribute little stability
3. Hydrophobic interaction- drive folding of protein to create core of hydrophobic amino acids which need to be on inside of protein
4. Van de Waals interaction- weaker- but significantly stabilise structure

Question 13

What is conformation

Answer 13

Conformation refers to the complete 3-D structure of a protein molecule

Question 14

Describe disulphide bonds in proteins

Answer 14

1. Covalent bonds which may stabilise the conformation of a protein
2. Covalent bond between cysteine side chains
3. Not all proteins have cys residues (cysteine amino acids)
4. Not all cys residues are involved in disulphides- free cys
5. Found in your hair
6. Broken by reducing agent- ammonium thioglycolate
7. Then add oxidising agent to reform

Question 15

What happens to the bonds when a protein is heated

Answer 15

1. Covalent bonds intact (peptide and disulphide)
2. Non-covalent interactions disrupted
3. Protein is denatured

Question 16

Name 8 post-translational modifications

Answer 16

1. Glycosylation
2. Glycation- glucose attacks positively charged amino acids- diabetes
3. Phosphorylation
4. Acetylation
5. Ubiquitination
6. Sumoylation
7. Methylation
8. Proteolytic cleavage