Protein Structure and Functions

Question 1

Being functional products of the genome, what functions do proteins have?

Answer 1

• carrier functions e.g. trafficking oxygen
• metabolic functions e.g. enzyme producing and utilising energy
• forms parts of cellular scaffolding e.g. microtubules, nucleosomes
• sensing molecules e.g. receptors and their ligands

Question 2

Explain the basic structure that amino acids have.

Answer 2

The basic structure of an amino acid is a tetrahedral arrangement of atoms around a central alpha carbon which have a carboxyl, amine, hydrogen groups and a variable ‘R’ side chain.

Question 3

What are the two isomers that amino acids are able to give rise to?

Answer 3

The arrangement around the alpha carbon atom is said to be asymmetrical due to the chiral centre carbon so it gives rise to D & L isomers ( this does not apply to glycine).
L isomers- they are found in naturally occuring proteins of all living organisms
D isomers can be found in the cell walls of bacteria and used as therapeutics.

Question 4

What are the different levels to proteins structure?

Answer 4

• Primary structure- covalent bond forming a polymer i.e. the sequence of amino acids
• Secondary structure- regular folded form that is stabilised by hydrogen bonds e.g. helices sheets#
• Tertiary structure- overall 3D structure that is stabilised by HID, hydrophobic/hydrophilic and Van der Waals interactions.
• Quaternary structures- organisation of macromolecules into assemblies, often stabled by ionic bonding.

Question 5

How are peptides created?

Answer 5

They can be created through a condensation reaction between amino acids to form a peptide bond as well as removing water.

Question 6

What are the properties of amino acids that are determined by their structure?

Answer 6

• amino acids have a single and triple letter code
• proteins are made by ribosomes during translation
• there are 20 naturally occurring amino acids which includes the 9 amino acids that are essential.
• they have primary, secondary, tertiary and quaternary structures.

Question 7

What confirmation is the R variable side chain usually in and why?

Answer 7

It is usually found in the trans confirmations so that the R side chain alternates in orientation
*there is a 0.% chance to find them in the same orientation a.k.a cis transformation.

Question 8

What does the term residue mean?

Answer 8

The repeating unit in a polypeptide chain is called a residue.