Proteins

Question 1

Describe properties of amino acids.

Answer 1

-Exist as zwitterions in solution - carry both positive (NH3+) and negative (COO-) charge

-Act as buffers:
1. Can donate or accept H+, therefore able to act as an acid or a base i.e. amphoteric
2. Essential in biological systems - sudden change in pH could adversely affect performance of proteins e.g. enzymes.

Question 2

Explain primary structure.

Answer 2

Primary structure
-refers to the number and sequence of amino acids in a single polypeptide chain
-amino acids are linked by peptide bonds

Question 3

Explain secondary structure.

Answer 3

-Structure formed by regular coiling or folding of a single polypeptide chain.
-Maintained by hydrogen bonds
1. between C=O and N-H groups of the polypeptide backbone
2. R groups are not involved
Examples of secondary structures:

a-helix:
-Made up of a single polypeptide chain which is wound into a coiled/spiral structure.
-a hydrogen bond forms between C=O group of one amino acid residue and the N-H group of another amino acid residue four AAs away along the backbone of a single polypeptide
-there are 3.6 amino acid residues in every turn of the helix

b-pleated sheet:
-two or more regions/segments of a single polypeptide chain lying side by side are linked together by hydrogen bonds
-a hydrogen bond forms between the C=O group of an amino acid residue and a N-H group of another amino acid residue on an adjacent segment along the backbone of a single polypeptide
-chains may run parallel or anti-parallel
-forms flat sheet which becomes folded

Question 4

Explain tertiary structure.

Answer 4

-Structure formed by further extensive folding and bending of a single polypeptide chain, giving rise to a spherical, globular protein with a specific 3D conformation.
-Maintained by all 4 types of interactions: hydrogen, disulfide, ionic bonds and hydrophobic interactions

Question 5

Explain quaternary structure.

Answer 5

-Refers to the association of two or more polypeptide chains into one functional protein molecule
-Maintained by all 4 types of interactions

Question 6

Describe molecular structure of haemoglobin and explain it relates to its function:

Answer 6

1. Haemoglobin has a quaternary structure -> 2 a-globin, 2 b-globin subunits. Each subunit made of globin polypeptide and a prosthetic component, haem group. Each haem group consists of a porphyrin ring and Fe2+. —> Fe2+ of the haem group binds reversibly to O2, 1 Hb molecule carries up to 4 O2, forming oxyhaemoglobin
2. Each subunit arranged so that most of its hydrophilic amino acid side chains are on external surface, hydrophobic amino acid side chains buried in interior –> haemoglobin is soluble in an aqueous environment, can take part in chemical reactions in red blood cells, enables transport of oxygen
3. 4 subunits held together by intermolecular interactions formed between R groups (H bonds, H interactions, ionic bonds) Thus subunits can move wrt to each other, allowing a change in position that influences haemoglobin’s affinity for oxygen –> binding of one O2 molecule to one Hb subunit induces a conformational change in remaining 3 subunits such that affinity for O2 increases (known as cooperative binding of oxygen)

Question 7

Describe molecular structure of collagen and explain how it relates to its function:

Answer 7

1. A collagen molecule consists of three helical polypeptide chains wound around each other like a rope. Each chains contains ~1000 amino acids, repeating sequence: glycine-X(proline)-Y(hydroxyproline).

–> Tropocollagen molecule can form tight, compact coil as almost every third AA is glycine, smallest AA. Allows R group (H) to fit into restricted space in the centre of the triple helix. Bulky and relatively inflexible proline and hydroxyproline residues confer rigidity on the molecule.

2. Extensive H bonds form between amino acid residues of adjacent polypeptides
   –> increases tensile strenght and interaction with water molecules limited, insoluble
3. Adjacent tropocollagen molecules are arranged in a staggered manner (longitudinal displacement) –> staggered arrangement minimizes points of weaknesses along fibrils
4. Covalent cross-links/bonds between lysine residues at C and N ends of adjacent tropocollagen molecules results in the formation of fibrils –> increases tensile strength
5. Bundles of fibrils unite to form long collagen fibres –> increase tensile strength.