amino acids and proteins

Question 1

structure of amino acids
- bonding
- from what reaction
- biproduct
- composition
- how many different types

Answer 1

monomers of proteins
- peptide bonds (covalent)
- condensation
- releases water
- amino group (H2N), carboxyl group (COOH), R-group, central carbon atom and hydrogen
- 20

Question 2

4 different types of R-groups

Answer 2

• non-polar
• polar but uncharged
• polar charged (basic+ and acidic-)
• special

Question 3

properties of non-polar side chains

Answer 3

• hydrocarbon chains or rings
• hydrophobic

Question 4

2 examples of non-polar side chains

Answer 4

1. alanine (Ala, A)
   simple methyl group (CH3)
2. phenylalanine (Phe, F)
   CH2 + phenyl ring

Question 5

properties of polar but uncharged side chains

Answer 5

• contains hydroxyl or amide groups
• hydrophilic (from hydroxyl group (OH))

Question 6

2 examples of polar but uncharged side chains

Answer 6

1. serine (Ser, S)
   CH2 + hydroxyl group (OH)
2. tyrosine (Try, Y)
   CH2 + phenyl ring + hydroxyl group (OH)

Question 7

properties of polar charged side chains

Answer 7

• basic and acidic

basic = contains basic groups = positively charged at physiological pH

acidic = contains carboxylic acid groups = negatively charged at physiological pH
- often involved in catalysis

Question 8

example of a basic polar charged side chain

Answer 8

lysine (Lys, K)
hydrocarbon chain + amide group (NH3+)- this gives it its hydrophilic nature

Question 9

2 examples of acidic polar charged side chains

Answer 9

1. aspartic acid (Asp, D)
   CH2 + carboxylic acid group (COOH)- which has been ionised at physiological pH to COO-
2. glutamic acid (Glu, E)

Question 10

properties of special side chains

Answer 10

don’t fit into any other groups

Question 11

3 examples of special side chains

Answer 11

1. cysteine (Cys, C)
   CH2 + thiol group (SH)
2. glycine (Gly, G)
   single hydrogen atom
3. proline (Pro, P)

Question 12

properties of primary protein structure
- what is it
- what is it determined by
- what does it determine

Answer 12

• the basic sequence of amino acids in a polypeptide chain
• by the DNA code of the gene
• the subsequent levels of protein structure

Question 13

features of a-helix

Answer 13

• coiled + rod like
• hydrogen bonds form between the carboxyl (the O) of one + the amino group (the H) of another the 4th amino acid away
• 3.6 amino acids per turn
• R-groups face outwards

Question 14

features of b-pleated sheets

Answer 14

• hydrogen bonds form between the carboxyl (the O) of one + the amino group (the H) of another elsewhere on the chain
• R-groups alternate between above + below the plane of the strand
• can be parallel or anti-parallel depending on the relative direction of the polypeptide chains
• parallel = 2 chains running in the same direction
  anti-parallel = 2 chains running in opposite directions

Question 15

properties of tertiary protein structure
- what is it
- how is it folded
- held together by what

Answer 15

• the bending and folding of the secondary structure forming the overall 3D configuration
• folded into the structure with the lowest potential energy level required
• by interactions between R-groups

Question 16

name the bonds/forces involved in tertiary protein structure

Answer 16

• hydrogen
  between carboxyl (the O) and amino (the H) groups
• ionic (electrostatic)
  between oppositely charged polar molecules
• disulphide bridges
  covalent bonds between 2 cysteine residues
• hydrophobic interactions
  between non-polar R-groups, often found in the middle of the 3D structure to avoid the solvent