L3: From Amino Acids To Protein

Question 1

Structure of amino acid

Answer 1

1. Carboxylate group
2. Amino group
3. R chain
4. Alpha-Carbon

Question 2

Classification of amino acids

Answer 2

1. Nonpolar, aliphatic (Glycine, Alanine, Proline (cyclic ring, secondary amino group), Valine, Leucine, Isoleucine)
2. Polar uncharged (Asparagine, Threonine (-OH), Glutamine, Serine (-OH))
3. Basic: +ve charged (Lysine, Arginine, Histidine)
4. Acidic: -ve charged (Aspartate, Glutamate)
5. Aromatic (Phenylalanine, Tyrosine, Tryptophan)
6. Sulphur-containing (Methionine, Cysteine)

Question 3

How are amino acids linked together

Answer 3

Amide bond

Question 4

Characteristics of amide bond

Answer 4

Have resonance form:

1. Partial double bond (+ve on N, -ve on O, partial double bond N=C)
2. Rigid and planar (all bonds can rotate except amide bond)
3. Trans configuration
4. Uncharged but polar

Question 5

Describe primary, secondary, tertiary, quaternary structure of protein

Answer 5

Primary: Linear sequence of amino acid
Secondary: Local conformation of backbone, formed from folding
Tertiary: Geometric shape of SINGLE polypeptide chain protein determined by side chain interaction, formed from different domains
Quaternary: Arrangement of multiple protein subunits into multi-subunit complex (e.g. monomer, tetramer etc.)

Question 6

Secondary structures

Answer 6

1. Alpha helix:
   - R chain extend outwards
   - Intrachain H-bond parallel to backbone
   - Right hand twist
2. Beta sheet:
   - Parallel (N-terminals together)vs Antiparallel (N-terminals alternating)
   - Two or more peptide chains aligned laterally
   - Stabilised by inter + intrachain H-bond between N and O
   - R group extend in opposite direction in adjacent a.a.
   - Hairpin loop (in antiparallel) by 4 amino acids held together by H-bond (extremely stable)

Question 7

Interactions between R chain

Answer 7

1. Hydrophobic interaction
2. Electrostatic interaction
3. Hydrogen bond
4. Disulfide bond (between cysteine)

Question 8

Post-translational modification (covalent modification) of protein

Answer 8

1. Glycosylation
2. Hydroxylation
3. Phosphorylation
4. Carboxylation
5. Biotin addition
6. Fatty acylation

Question 9

What are the protein variations in primary structures

Answer 9

1. Polymorphism: sickle cell allele
2. Homologous family of protein (Myoglobin and Hb)
3. Developmental isoforms (HbF and HbA)
4. Tissue specific isoforms (CKMB and CKBB)
5. Between species (insulin)