Lecture 2 - Protein

Question 1

What is the basic structure of amino acid?

Answer 1

Amino group (NH2), carboxyl group (COOH), H and R side chain

Question 2

3 main categories of amino acids

Answer 2

Non polar (hydrophobic), Polar (charged), Polar (uncharged)

Question 3

2 example of hydrophobic non polar AA

Answer 3

Tryptophan and Glycine

Question 4

2 examples of uncharged polar AA

Answer 4

Serine and Asparagine

Question 5

2 examples of charged polar AA

Answer 5

Lysine and aspartic acid

Question 6

What are ampholytes?

Answer 6

They can act as either base or acid

Question 7

Define zwitterions

Answer 7

Molecules have both positive and negative charge

Question 8

What are the characteristics of AA

Answer 8

AA are ampholytes, zwitterions and due to their ionic nature, they have extremely high melting temperatures

Question 9

What is primary structure of AA

Answer 9

Linear sequence of AA joined together by peptide bond

Question 10

What is secondary structure of AA

Answer 10

Local folding by hydrogen bonding of residues into regular patterns such as alpha helix and beta sheet structure

Question 11

What is alpha helix structure

Answer 11

Helical arrangement of AA in the polypeptide chain maintained by hydrogen bonds parallel to the helix axis

Question 12

What is beta sheet?

Answer 12

Hydrogen bonding formed between adjacent sections of polypeptides that are either running in the same direction (parallel) or opposite direction (anti-parallel)

Question 13

What is beta turn reverse?

Answer 13

There is a reversal in the direction of the polypeptide chain and it is found in the connecting ends of anti-parallel beta pleated sheets

Question 14

Definition of tertiary structure of protein

Answer 14

3D arrangement of the amino acids in the polypeptide chain. It is biologically active

Question 15

Definition of quaternary structure of protein

Answer 15

Composed of more than one polypeptide chain in a spatial arrangement. It is fully developed and functional

Question 16

What are the 3 main classes of protein?

Answer 16

1) Functional - enzymes, structural, transport and defence
2) Structural - globular and fibrous
3) Cellular localization -membrane, water soluble

Question 17

Definition of enzyme

Answer 17

1) Biological catalysts that control a reaction without being changed itself
2) Convert substrates into product
3) lower the action energy to speed up the rate of reaction

Question 18

Definition of activation energy

Answer 18

Energy required to initiate a chemical reaction

Question 19

Define induced fit model

Answer 19

This model describes the formation of the enzyme-substrate complex as a result of the interaction between the substrate and a flexible active site. The substrate produces slight changes in the active site of the enzyme for better bonding of substrate and catalytic effects

Question 20

Describe Lock and Key model

Answer 20

This model describes the formation of substrate and enzyme complex by substrate bonding onto the active site of the enzyme. There is no change to the active site as the product is being formed.

The active site is highly specific and substrate which has a complementary shape as active will be able to bind.

Question 21

What are the factors affecting enzyme structure and activity?

Answer 21

1) Temperature - At high temperatures, hydrogen bonding and other forces that stabilise protein structure is disrupted causing the enzyme to change its shape and lose activity
2) pH - alters the charge of the amino acids of a protein, thus affecting the structure and the ability for substrate to bind

Question 22

What are nucleotides composed of?

Answer 22

Sugar (pentose), phosphate group and base

Question 23

What are the characteristics of DNA?

Answer 23

1) Genetic blueprint - carries all the instructions needed to build a new material, one gene codes for information to make one protein
2) Arranged into chromosomes and is located in the nucleus
3) Genes are located in the chromosome

Question 24

What are the different types of RNA?

Answer 24

Messenger, transfer and ribosomal