Amino Acids

Question 1

4 major functional groups

Answer 1

1. Binding -> always a binding effect
2. Catalysts -> enzymes
3. Switching -> receptors
4. Structural -> e.g. actin/myosin, keratin

Question 2

General Structure

Answer 2

1. Peptide bond = strong

2. Non-ionic form can never exist in nature

Question 3

The ionic form in a solution is dictated by

Answer 3

1. pH

2. Dissociation constants

Question 4

NH3+ pka

Answer 4

9.4

Question 5

COO- pka

Answer 5

2.2

Question 6

At pH’s above pka of side chain

Answer 6

Always negatively charged -> acidic

Question 7

At pH’s below pka of side chain

Answer 7

Always positively charged -> basic

Question 8

P.I. =

Answer 8

Isoelectric point of protein -> information about it your side chain is +ve or -ve -> predominantly L-amino acids

Question 9

R groups

Answer 9

give protein property

Question 10

Aliphatic R groups

Answer 10

1. As chain length increases, hydrophobia increases
2. Unless protein has a binding site for hydrophobic side chain/ bonds to other hydrophobic side chains
3. Small side chains generally found at tight turns

Question 11

Leusine

Answer 11

2 chiral centres so 4 stereoisomers

Question 12

Acidic R groups

Answer 12

Negative charge -> conjugate base

-> more hydrophiic

Question 13

Basic R groups

Answer 13

Tend to be on surface + space allows for binding processes

Question 14

Histidine

Answer 14

p.k. around neutrality -> act as acid + base in same mechanism + binds to metal ions

Question 15

Side chains with alcohol and sulphur groups

Answer 15

e. g. cysteine -> disulfide bond , 4 ribonucleise, in oxidising conditions
- > only covalent bond in side chains => tough proteins

Question 16

Methionine

Answer 16

Can be powerful nuclei

Question 17

Tyrosine and serine

Answer 17

Hydroxyl often phosphorylated -> switching on and off

Question 18

Side chains containing nitrogen heterocycles

Answer 18

1. Only bond involved in secondary bonding = peptide

2. Proline stops formation of helix (helix breaker) -> cis-configuration

Question 19

The peptide bond

Answer 19

1. Resonance stabilised structure
2. N-> planar trigonal shape, flat but bonds on either side are capable of rotation
3. Amount rotated dependent on size of R-group

Question 20

Ramachandron Plot

Answer 20

Rotation around peptide bond can be estimated -> start of how helix folds

Question 21

Structure of peptide bond

Answer 21

1. Nitrogen forms planar trigonal shape b/c partial double bond formed with adjacent carbon
2. Stereochemistry requires carbonyl carbon, nitrogen, oxygen, hydrogen atoms and 2 neighboring alpha carbons all constrained to lie in a plane
3. Restricts peptide bond to either cis or trans
4. Trans favored to reduce steric crowding except where proline involved

Question 22

The shape of polypeptides is defined by rotation about the

Answer 22

C-N bonds - phi

C-C bonds - psi

Question 23

In a repeated structure…

Answer 23

Phi and Psi angles are the same e.g. alpha helix or beta sheet