2.3 Protein Structure, Ligand Binding and Conformational Change i Amino Acid Sequence Determines Protein Structure

Question 1

What are the polymers of an amino acid monomers known as?

Answer 1

Proteins

Question 2

What kind of bond links amino acids to form polypeptides?

Answer 2

Peptide bonds

Question 3

How do amino acids differentiate from each other?

Answer 3

Differing R groups

Question 4

In which ways do R groups on amino acids vary?

Answer 4

By shape, size, charge, hydrogen bonding capacity and chemical reactivity.

Question 5

Name the four different classifications of amino acids according to their R groups

Answer 5

Basic (positively charged)
Acidic (negatively charged)
Polar (hydrophilic)
Hydrophobic (non polar)

Question 6

What is the chemical formula of the acidic R group?

Answer 6

COOH

Question 7

What is the chemical formula of the basic R group?

Answer 7

NH2

Question 8

What is the chemical formula of the polar R group?

Answer 8

OH

Question 9

What is the chemical formula of the hydrophobic R group?

Answer 9

CH3

Question 10

What causes the wide range of functions carried out by proteins results from what?

Answer 10

The diversity of R groups

Question 11

What is the primary structure of a protein?

Answer 11

The sequence in which the amino acids are synthesised into the polypeptide

Question 12

What kind of structure is brought about by the presence of hydrogen bonding along the backbone of the protein?

Answer 12

Secondary structure

Question 13

Name three different kinds of secondary structure

Answer 13

Alpha helices.
Parallel or anti-parallel beta-pleated sheets.
Turns.

Question 14

How is the conformation of the tertiary structure stabilised?

Answer 14

Interactions between R groups such as hydrophobic interactions; ionic bonds; London dispersion forces; hydrogen bonds; disulphide bridges

Question 15

What are disulphide bridges?

Answer 15

Disulphide bridges are covalent bonds between R groups containing sulphur.

Question 16

Where does quaternary structure exist?

Answer 16

In proteins with two or more connected polypeptide subunits

Question 17

What does quaternary structure describe?

Answer 17

The spatial arrangement of the subunits.

Question 18

What is a prosthetic group?

Answer 18

A non-protein unit tightly bound to a protein and necessary for its function

Question 19

Example of a protein that requires a prosthetic group to function

Answer 19

The ability of haemoglobin to bind oxygen is dependent upon the non-protein haem group.

Question 20

Which two factors can interactions of R groups be influenced by?

Answer 20

Temperature and pH

Question 21

How can temperature affect R group interactions?

Answer 21

Increasing temperature disrupts the interactions that hold the protein in shape; the protein begins to unfold, eventually becoming denatured.

Question 22

How can pH affect R group interactions?

Answer 22

The charges on acidic and basic R groups are affected by pH. As pH increases or decreases from the optimum, the normal ionic interactions between charged groups are lost, which gradually changes the conformation of the protein until it becomes denatured