Proteins

Question 1

Amino Acid Structure

Answer 1

1. ALL AAs have amino group and carbonyl group attached to alpha carbon
2. Can be non-polar, polar or charged
   - Acidic AAs have negatively charged R groups like COOH while basic ones have positively charged R groups
3. Exist as zwitterions carrying both + and - charges in water
4. Act as buffers as they are amphoteric
   - Amino groups can act as bases to neutralise H+ while carbonyl groups can act as acids to neutralise OH-

Question 2

Polypeptide Structure

Answer 2

1. Condensation links carboxyl group of 1st AA and amino group of 2nd AA by forming a covalent peptide bond with removal of 1 H2O each (label peptide bond)
   - Polypeptides thus have direction from N-terminus to C-terminus
2. Polypeptide folds into a specific 3D conformation to determine protein function

Question 3

Primary Structure

Answer 3

Unique number and sequence of AAs in single polypeptide chain linked by peptide bonds, determined by genes

Question 4

Secondary Structure

Answer 4

Regular coiling/pleating of single polypeptide chain maintained by H bonds formed between CO and NH groups of polypeptide backbone (no R groups involved)
1. Alpha Helix
- coiled/spiral structure linked by H bonds between C=O and N-H group 4 AAs away, forming a-helix with *3.6 AA residues per turn**
- Bulky R groups/those with irregular structure can hinder a helix formation

2. Beta-pleated sheet
   - 2 or more regions of a single chain lying side by side linked together, with hydrogen bonds forming between adjacent regions (either parallel or anti-parallel)

Question 5

Tertiary Structure

Answer 5

Refers to further extensive folding of a single polypeptide chain via hydrogen bonds, hydrophobic interactions, ionic bonds and disulfide bridges formed between R groups of different AAs that give rise to specific 3D conformation
- Disulfide bridges are formed only between 2 cysteine AAs and are strong covalent bonds that are heat stable and increase molecule stability

Question 6

Quaternary Structure

Answer 6

2 or more polypeptide chains form 1 functional protein molecule with a specific 3D conformation for that proteins specific function

Question 7

Explain how a mutation can lead to a change in protein structure

Answer 7

1. Single base substitution/frameshift mutations change the DNA genetic code
2. This changes the mRNA codon sequence after transcription and the primary sequence of AAs after translation
3. This thus affects 4 interactions between R groups of AAs in tertiary and quaternary structure, affecting overall 3D conformation of protein and resulting in an abnormal/non-functioning protein

Question 8

Biuret Test

Answer 8

1. 2 cm3 protein and KOH each add to test tube, mix and add 2 drops of CuSO4
2. Violet = positive, remain blue = negative

Question 9

Structure + Function of Haemoglobin

Answer 9

1. Haemoglobin has a quaternary structure of 4 polypeptides, 2 alpha globin and 2 beta globin chains. Hydrophilic AA chains face external surface while hydrophobic AA chains face interior
   Function: Allow Hb to be a compact globular protein soluble in water
2. Each polypeptide chain made of globin polypeptide + prosthetic haem group. Each haem group consists of 1 porphyrin ring and a Fe2+ ion
   Function: Haemoglobin can bind reversibly to 4 O2 to form oxyhaemoglobin
3. 4 polypeptide subunits held together by ionic bonds, hydrogen bonds and hydrophobic interactions but not disulfide bridges.
   Function: Allows subunits to move wrt each other, allowing for cooperative binding where binding of 1 O2 induced conformation change that makes it easier for other 3 O2 to bind

Question 10

Structure + Function of Collagen

Answer 10

Collagen is a fibrous structural protein that builds connective tissue

1. A collagen molecule consists of 3 helical polypeptide chains wound around each other like a rope, thus giving it the name of tropocollagen.
2. Each individual chain is a loose helix stabilised by hydrogen bonds of peptide backbone. Hydrogen bonds formed between 3 adjacent chains to form a tight triple helix. The triple helix has 3.3 residues per turn and collagen thus has a secondary and quaternary structure but NOT tertiary
   Function: Gives high tensile strength and makes molecule insoluble
3. AA sequence is repeating tripeptide unit: glycine-X-Y. Glycine residues allow for formation of tight triple helix as small and can fit into centre. X and Y are usually bulky and inflexible proline and hydroxyproline that confer rigidity
4. Each tropocollagen molecule cross-links with parallel tropocollagen molecules to form fibrils. These cross links are covalent bonds formed between lysine residues**. Bundles of microfibrils unit to form a collagen fibre
   Function: This forms a staggered arrangement that minimises points of weakness, increasing tensile strength

Question 11

Globular vs Fibrous

Answer 11

1. Roughly spherical shape vs Long straight chains
2. Larger variety of AAs used with no repetitive, regular AA sequence vs less variety with mostly repetitive regular AA sequences
3. Small variety in polypeptide length and sequence while protein still functional vs Always identical AA sequence to keep it functional
4. Soluble in water vs insoluble in water (no H bonds available with water + large macromolecule)

(only if function, not structure) Metabolic vs structural function