Protein Structure and Function

Question 1

Describe the different functions that proteins provide.

Answer 1

They are functional products of the genome providing:

• CARRIER FUNCTIONS: trafficking oxygen
• METABOLIC FUNCTIONS: enzymes producing and utilising energy
• FORM PARTS OF THE CELLULAR MACHINERY: spliceosomes, ribosomes
• MAKE UP STRUCTURAL SCAFFOLD: microtubules, nucleosomes
• SENSING MOLECULES: receptors and their ligands

Question 2

How do we differentiate between L (levo) and D (dextro) forms of amino acids?

Answer 2

All amino acids (except for Glycine) have the two isomers due to them being tetrahedral in arrangement and due to the α carbon being chiral.
An L isomer reads Co-R-N CLOCKWISE, while a D isomer reads Co-R-N ANTICLOCKWISE.

All amino acids incorporated into proteins by living organisms are in the L-form. D-amino acid residues comprise cell walls in bacteria and are often used in therapeutics.

Question 3

What is termed a residue?

Answer 3

A residue is each repeating unit in a polypeptide chain.

- Each residue consists of an invariable unit compromising - alpha carbon, c=o and an NH group

Question 4

Briefly describe the four categories that protein structure is divided into.

Answer 4

1) PRIMARY STRUCTURE: covalent bonds forming a polypeptide chain - ie. the order of amino acids residues
2) SECONDARY STRUCTURE: regular folded form, eg. α helices, β sheets and β turns
3) TERTIARY STRUCTURE: overall 3D structure, stabilised by non-covalent bonds and forces, and sometimes by intra-chain covalent bonds
4) QUATERNARY STRUCTURE: organisation of polypeptide chains into assemblies, stabilised by non-covalent bonds and forces (like tertiary), and sometimes by intra-chain covalent bonds

Question 5

Describe SECONDARY STRUCTURE.

Answer 5

They are formed by H bonds between the β strands. In sheets, the H bonds are between the strands. The sheet can have anti-parallel or parallel sheets. In turns, there are loops or turns linking the β sheets.

With the α helix:
It’s a right-handed helix, stablilised by H bonds between two amino acids four residues apart.

The arrangement of the variable side chains is important for structure and function. The side chains of both the α and β (sheets) protrude outwards from the structures.

Question 6

Describe TERTIARY STRUCTURE.

Answer 6

The secondary structure is then folded into more densely packed, generally globular structures. The formation of these structures depends on weak chemical bonds between the side chains.

Question 7

Describe QUATERNARY STRUCTURE.

Answer 7

In some cases, 2 or more folded polypeptides may be combined to form a mature protein. The same bonds used in the tertiary structure are used to hold the subunits together.

Question 8

List some cofactors that some proteins may require to work.

Answer 8

• Zn2+ or Mg2+
• haem of haemoglobin
• Nicotinamide Adenine Diphosphate (NAD)
• Flavin Adenine Dinucleotide (FAD)
• organic cofactors are sometimes a called coenzymes.

Question 9

Describe water-soluble proteins.

Answer 9

Water-soluble proteins are often globular in shape.
Some water-soluble proteins may arrange into:
- filaments (actin)
- tubes (tubulin)
- coiled coils (cortexillin)

Normally, the hydrophilic residues are mostly on the external surface while the hydrophobic residues are mostly buried inside.
However, this formation is reversed in membrane proteins. The membrane spanning region will have externally located hydrophobic residues that interact with membrane lipids.