Proteins: Structure and Function

Question 1

Draw an Amino Acid (3)

Answer 1

Allocate:

1. Amino Group
2. Carboxyl Group
3. R Group

Question 2

What type of bonds exist between amino acids? What reaction makes bond? (2)

Answer 2

1. Peptide Bond

2. Condensation Reaction

Question 3

How is folding determined in primary structure of a protein? (3)

Answer 3

1. By the distribution of the hydrophobic and hydrophillic side chains.
2. Hydrophillic (polar) side chains form hydrogen bonds with water on outside
3. Hydrophobic (non-polar) side chains are packed into core.

Question 4

What are the most stable Secondary protein structures? How does their shape form?

Answer 4

1. Alpha - helice and Beta Pleated sheet

2. Shape forms due to hydrogen bonds between carbonyl groups and amino groups along the chain.

Question 5

What are the arrangements of Alpha Helix and Beta Pleated sheet (Shape, AA length, Side chains, normal environment) (4)

Answer 5

Alpha Helix - Spiral, 5-20aa, Sidechains face outwards, - Abundant in the phospholipid bilayer. Hydrophobic side chains interact with hydrocarbon tails of the phospholids.

Beta Pleated sheet - Flat and arranged laterally, Sidechains extend above and below Beta Sheet

Question 6

What are other secondary structures of proteins? (2)

Answer 6

1. Loops and Turns (3-5 aa, have hydrophilic residues and found on the surface of proteins)
2. Random Coils - Chains with random configuration

Question 7

What are the weak side-chain interactions in proteins? (3)

Answer 7

1. Hydrogen Bonds
2. Van Der Waals
3. Electrostatic Attractions.

Question 8

What type of structure are Keratin and Collagen, what is the arrangement? (3)

Answer 8

Tetiary Structure (Coiled Coils)

These are formed from 2/3 Alpha helices wound around each other with hydrophobic core.

Question 9

What are Quaternary Structures. Give an example? (2)

Answer 9

1. When proteins associate with each other to generate high order structures.
   Example: Haemoglobin is formed of 2 alpha subunits and 2 beta subunits

Question 10

What is post-translational modification? (2)

Answer 10

1. Proteolytic cleavage or adding a modifying group to a protein
2. It modulates function of eukaryotic proteins altering activity, turnover, and interaction.

Question 11

What are the types of post-translational modification? (2)

Answer 11

1. Phosphorylation: Addition of phosphate to amino acid.

2. Glycosylation: Addition of Carbohydrates to specific site of protein.

Question 12

What type of bond do excreted tertiary structure proteins typically have? What role does it play? (3)

Answer 12

1. Disulfide bond.
2. Commonly between Cysteines between each other in folded structure.
3. Gives Strength but does not alter shape.

Question 13

What is ‘Folding Funnel’ in Protein formation? Why is it important (2)

Answer 13

1. Proteins spontaneously fold into 3-D conformation of the lowest free energy.
2. This folding process is energetically favourable as releases heat and increases disorder in the universe.

Question 14

For proteins that do not fold spontaneously, what molecules can help? (2)

Answer 14

Molecular Chaperones (Heat shock Proteins and Chaperonins).

They do not change 3D structure, speed up folding, prevent protein aggregation and prevent unproductive intermediates.

Question 15

What is the charge of these amino acid side chains? (2)

Glutamic acid
Aspartic acid
Lysine
Arginine 
histidine

Answer 15

-ve charge (carboxylic group):
Glutamic acid
Aspartic acid

+ve charge (N group)
Lysine
Arginine
histidine

Question 16

What role does mutated CFTR play in Cystic Fibrosis?

Answer 16

Mutation occurs due to deletion of amino acid Phenylalanine at 508.

Mutant CTFR protein becomes stuck in the endoplasmic reticulum leading to abnormal chloride conductance out of the cells

Question 17

What is Creutzfeldt–Jakob disease (CJD ) and how does it develop? (4)

Answer 17

It is a variant of Mad Cow Disease.
Transmitted by misfolded prions. They promote refolding of other prions into a disease conformation upon contact.

They are shaped as Beta-sheets (amyloid fibril) so are very stable, causing slow death of nerves in brain.