Protein structure and function

Question 1

List the main functions of proteins

Answer 1

Carrier functions e.g. trafficking oxygen or glucose
Metabolic functions e.g. enzyme cascades like the TCA cycle
Forms parts of the cellular machinery e.g. spliceosomes
Make up the structural scaffold e.g. microtubules
Sensing molecules such as the receptors and their ligands

Question 2

What are the ionic properties of amino acids?

Answer 2

Amine and carboxyl groups readily ionise
The amino acid can act as a base where the NH2 group will ionise to NH3+
The amino acid can behave as an acid where the COOH ionises with the loss of its hydrogen to form COO-
At a neutral pH, the amino acid is a zwitterion where both groups are ionised

Question 3

What do D and L isomers mean, what is the exception,

and where does each occur?

Answer 3

The arrangement around the alpha carbon is said to be chiral.
The D and L isomer forms equate to ‘handedness’
The exception is Glycine whose R chain is a hydrogen
When viewed along the hydrogen-Ca bond:
The L-form reads CORN clockwise
The D-form reads CORN in the anticlockwise direction
All AA incorporated into the proteins by living organisms are in the L-form
D-amino acids comprise cell walls in some bacteria and are also used in some therapeutics

Question 4

What conformation is the variable R chain in a peptide residue?

Answer 4

Trans conformation because the cis formation is less energetically favourably

Question 5

What is a residue?

Answer 5

each repeating unit os a polypeptide chain is termed a residue

Question 6

What arrangements are beta sheets in and why?

Answer 6

Beta sheets exist either in antiparallel or parallel arrangement
The orientation of the strands determines the relative positioning of the groups forming the hydrogen bonds affecting the strand’s strength and stability
By that logic the anti-parallel arrangement produces a beta sheet with greater stability

Question 7

Describe an alpha helix

Answer 7

A right-handed helix
Stabilised by hydrogen bonds
H-bonds are 4 residues apart between residue 1 and 5
3.6 residues per turn or 0.54nm per turn
The arrangement of the variable side-chains gives proteins their properties and are important for structure and function

Question 8

Describe tertiary and quaternary structure

Answer 8

Formed from folding into densely packed generally globular structures
Formation depends on:
interaction between outward-facing side chains
many weak chemical bonds
but may sometimes be stabilised by covalent bonds

Question 9

Give two examples of cofactors for proteins

Answer 9

Haem of haemoglobin
Nicotinamide adenine diphosphate (NAD)
Flavin adenine dinucleotide (FAD)
Organic cofactors are sometimes called coenzymes
Other proteins might include Zn2+, Mg2+, Ca2+ or other ions