2. Protein structure and function

Question 1

Describe proteins (3pts)

Answer 1

1. Proteins are the fundamental functional molecules of the cell
2. Proteins provide both structural and functional molecules that underline the dynamic processes of the cell
3. Proteins are functional products of the genome providing:
4. Carrier functions= e.g glucose transports oxygen
5. Metabolic functions= e.g enzyme cascades utilising energy
6. Forms part of the cellular machinery
7. Make up the structural scaffold
8. Sensing molecules e,g receptors and their ligands.

Question 2

Describe Amino acids and their structure (5 pts)

Answer 2

1. Proteins are polymers made up of Amino acids
2. There are 20 naturally occurring amino acids including 9 essential amino acids.
3. Amino acids have a tetrahedral arrangement of atoms with the alpha carbon as its centre. The carboxyl and amine groups are attached to the central carbon.
4. The variable R chain confers the specific physiochemical properties.
5. low PH= Amino acid acts as a base and accepts H+. Becomes + charged.
6. High PH= Amino acid acts as an acid and donates H+. Becomes - charged.

Question 3

Describe the D and L Amino acid isomers

Answer 3

The arrangement of the atoms give rise to D and L isomers,.

Question 3

Describe the D and L Amino acid isomers

Answer 3

L form= 1. reads corn in a 
                  clockwise direction 
                 2. L amino acids 
                     found in naturally 
                     occurring 
                     proteins of all 
                     organisms.

 D form= 1. the groups read 
                   corn in an anti 
                    clockwise 
                    direction. 
                  2. Amino acids 
                      compromise cell 
                      walls in 
                      bacteria and are 
                      used in 
                      therapeutics.

Question 4

Describe a Polypeptide chain ( 4pts)

Answer 4

1. Amino acid + Amino acid= Polypeptide + water

• peptide bond
• condensation reaction

2. Amino and carboxyl groups have differing charge which provide the polypeptide chain with a degree of polarity.
3. Peptide residue= each repeating unit of the polypeptide chain .
4. Polypeptide chain is the primary structure

Question 5

Describe the secondary structure (4pts)

Answer 5

1. A secondary structure is formed from the folding of the polypeptide chain
2. e.g beta sheets, alpha helices, beta turns
3. The arrangement of the variable side chains give the proteins their properties and are important for structure and function.
4. The side chains in the alpha helix and the beta sheet protrude upwards from the structures.

Question 6

Describe a beta sheet ( 4 pts)

Answer 6

1. Beta sheets are held together by hydrogen bonds which stabilise the sheet
2. Beta sheets are formed from hydrogen bonding between adjacent beta strands either in antiparallel or parallel arrangement.
3. In an anti parallel arrangement the strands are in complimentary directions and the sheet has more stability. The loops in this arrangement are shorter.
4. Beta strands are connected by loops or short turns.

Question 7

Describe an alpha helix ( 4 pts)

Answer 7

1. Right handed helix
2. Stabilised by hydrogen bonds
3. Hydrogen bonds are 4 residues apart between residue 1 and 5
4. 3.6 residues per turn

Question 8

Describe the tertiary structure

Answer 8

Tertiary structure is combining secondary structures such as alpha helices, beta sheets and beta turns.

Question 9

Describe protein properties (4 pts)

Answer 9

1. Functional proteins are formed from two or more folded polypeptides that combine to form the mature protein.
2. e.g Haemoglobin is formed by combining 2 beta chains and 2 alpha chains.
3. Some proteins require cofactors for their function whilst some require cofactors for their folding e.g heme for haemoglobin.
4. Correct structure is essential for normal function.

Question 10

Describe water soluble proteins (3pts)

Answer 10

1. Water soluble proteins are globular in shape
2. The hydrophilic residues are found on the external surface whilst hydrophobic residues are buried inside the protein.
3. Some water soluble proteins assemble into filaments such as actin or tubes. In these proteins the hydrophilic amino acids face outwards with their charged side chains interacting with the surrounding aqueous environment.

Question 11

Describe membrane proteins ( 2 pts)

Answer 11

1. Membrane spanning regions have externally located hydrophobic residues that interact with the membrane lipids
2. have hydrophilic central channels