Proteins

Question 1

Amino acid

Answer 1

N-terminus - H2NRCHCOOH - C-terminus

alpha-carbon + 4 groups:

(i) Hydrogen atom
(ii) Amino group (NH2)
(iii) Carboxyl group (COOH)
(iv) Variable R group/side chain

Question 2

Types of R groups

Answer 2

Neutral

• Non-polar side chains; hydrophobic
• Polar side chains; hydrophilic

Electrically charged side chains; hydrophilic

• Acidic (negatively charged)
• Basic (positively charged)

Question 3

Properties of amino acids

Answer 3

1. Exist as zwitterions
   Generally soluble in water -> ionised -> dipolar ions
2. Act as buffers
   Amphoteric

Question 4

Polypeptides

Answer 4

Condensation between residues
COOH group linked with NH2 group
Peptide bond
Catalysed by peptidyl transferase at ribosomes

Folds into 3D arrangement

Question 5

Primary structure

Answer 5

Sequence, number and type of amino acids in a single polypeptide chain
Maintained by peptide bonds
Determines specific 3D conformation of protein
Specified by nucleotide sequences in genes

Question 6

Secondary structure

Answer 6

Regular coiling or pleating of a single polypeptide chain
Maintained by hydrogen bonds between CO and NH groups of polypeptide backbone

1. alpha-helix
Coiled/spiral structure
H-bonds between groups at every 4th peptide bond
O of CO group and H of NH group
3.6 amino acid residues in every turn

2. beta-pleated sheet
   Two or more regions of a single polypeptide chain lying side by side
   H-bonds between adjacent regions
   May run parallel or anti-parallel -> flat sheet

Question 7

Tertiary structure

Answer 7

Further extensive folding and bending of a single polypeptide chain -> compact globular/spherical molecule -> specific conformation

Maintained by 4 types of interactions between R groups:
1. Hydrogen bonds
O and N are electronegative (δ-), H is electropositive (δ+)

2. Ionic bonds (excess [H+] or [OH-] may affect ionisation)
   Formed between oppositely-charged* R groups* of amino acids
3. Hydrophobic interactions
   Formed between non-polar* R groups* which are hydrophobic
4. Disulfide bonds (between cysteine residues - oxidation of sulfydryl groups, which contains sulphur) -> strong covalent bonds

Question 8

Quaternary structure

Answer 8

Two or more polypeptide chains into one functional protein molecule
Each polypeptide is a subunit
Maintained by 4 types of interactions

Question 9

Types of proteins

Answer 9

Fibrous -> structural roles

Globular -> metabolic roles

Question 10

Haemoglobin

Answer 10

Globular (quaternary structure)
2 alpha-globin, 2 beta-globin subunits

Each subunit -> hydrophilic amino acid side chains on external surface, non-polar, hydrophobic ones in interior -> soluble in water

Polypeptide subunits (globin) + prosthetic component (haem group)
Haem group = porphyrin ring + iron ion (Fe2+)
Fe2+ binds reversibly to O2 -> oxyhaemoglobin

Question 11

Structure -> function of haemoglobin

Answer 11

No disulfide bonds (too strong) -> allow subunits to move wrt each other -> change of position influences affinity for oxygen -> tertiary structure changes

Binding of O2 to one subunit -> conformation change -> other subunit’s affinity for O2 increases (cooperative binding) -> bind more efficiently to oxygen

Question 12

Sickle cell anaemia

Answer 12

Normal haemoglobin: 6th residue is glutamic acid (hydrophilic)

Abnormal haemoglobin: 6th residue is valine (hydrophobic)

Conformation of polypeptide changes

Haemoglobin molecules aggregate together at low oxygen concentrations -> RBC changes shape

Question 13

Collagen

Answer 13

Fibrous (secondary and quaternary structure) -> connective tissue

Collagen molecule/tropocollagen molecule consists of 3 helical polypeptide chains

Question 14

Each individual helix

Answer 14

1 helical polypeptide chain

Loose helix -> 3.3 residues per turn
Repeating tripeptide unit: glycine-X-Y (X usually proline, Y usually hydroxyproline)

Question 15

Assembly to form tropocollagen molecule

Answer 15

3 helical polypeptides -> 1 tropocollagen molecule

Tight triple helix -> every 3rd amino acid is glycine, smallest one -> fit into restricted space at centre of triple helix

Hydrogen bonds between adjacent chains
Increase tensile strength
Make molecule insoluble

Bulky and inflexible proline and hydroxyproline residues confer rigidity

Question 16

Assembly to form fibril

Answer 16

Many tropocollagen molecules -> fibril

Cross-linking between lysine residues (covalent bonds)
Increases tensile strength
Staggered arrangement minimises points of weaknesses

Question 17

Assembly to form collagen fibre

Answer 17

Many fibrils -> fibre

Question 18

Properties of proteins (Solubility)

Answer 18

Depends on size and ability to interact with water
Globular soluble (mostly hydrophilic R groups on exterior -> interact with water)

Fibrous insoluble (mainly hydrophobic R groups on exterior + large + cross linked)

Question 19

Properties of proteins (Denaturation)

Answer 19

Loss of conformation -> lose function
Disruption of interactions
Primary structure remains unaffected

High temperatures -> increase kinetic energy and intramolecular vibrations -> breaks interactions

Extreme pH -> affect ionisation of R-groups of charged amino acids -> affect ionic bonds
H+ + COO- -> COOH
OH- + NH3+ -> NH2

Question 20

Test for proteins

Answer 20

Biuret test
Test for peptide bonds
2cm3 protein solution + equal 5% KOH + 2 drops 1%CuSO4