Question

Amino acids can have very specific properties. Some specific properties of interest are size (small/medium/large), If its is bulky/rigid/flexible, if it is hydrophilic or hydrophobic and if is positively or negatively charged.

1A. For the properies of size, bulk/rigidity/flexibility, hydrophilic or hydrophobic and positive or negatively charged, provide detailed descriptions of what we woud look for in the "R" group of the amino acid to decide what traits give it these properties. (10 points)

1B. For each of the twenty amino acids, name if it is big/medium/small, bulky/rigid/flexible, hydrophilic or hydrophobic and positive or negatively charged.

If any of the twenty amino acids you describe do not follow the trend that you provided in part A, provide a detailed explanation for why. (30 points)

Answer 1

Answer 1A

• Property Size: On the basis of size, amino acids can be very small, small, medium and large

Very Small are those with smallest R groups just one atom or one functional moiety

Small are those which have two carbon atoms (or carbon and sulfur) in side chain

Medium are those with three carbon atoms in side chain

Large are those containing long chain side groups (more than four carbons)

Very Large are with aromatic side chains

• Property Charge: On the basis of charge amino acids can be positively charged, negatively charged, uncharged

Amino acid would be considered negatively charged if it has more carboxylic groups than amino groups i.e. it has overall -ve charge at pH 7.

Amino acid would be considered positively charged if it has more amino groups than carboxylic groups i.e. it has overall +ve charge at pH 7.

Amino acid would be considered uncharged if it has equal number of carboxylic groups and amino groups i.e. it has overall zero charge at pH 7.

• Property Hydrophilicity: On the basis of Hydrophilicity, amino acid may be hydrophilic or hydrophobic

Amino acid is considered hydrophilic if it has groups which can form hydrogen bonds with water like those having carboxylic (COOH), amino (-NH₂) in its side chain.

Amino acid is considered slightly hydrophilic if it has groups like hydroxyl (OH), sulphahydral (SH) in its side chain

Amino acid is considered hydrophobic if it lacks the groups like carboxylic (COOH), amino (-NH₂), hydroxyl (OH), sulphahydral (SH) in its side chain.

• Property : Rigidity/Bulkiness/Flexibility

??Amino acid is considered Rigid if it has side chain heterocyclic groups or rigid bonds like double bonds in side chain

Amino acid is bulky if it has benzene ring in side chain.

Amino acid is considered Flexible if side chains are of carbon chain and no ring or cyclic structure.

Answer 1B

The amino acids with the above properties are tabulated as follows:

S.No.	Name of amino acid	Hydrophilicity	Charge at pH 7	Size	Flexibility/Rigidity/Bulkiness
1	Glycine	Slightly hydrophilic	Uncharged	Very Small	Flexible
2	Alanine	Hydrophobic	Uncharged	Very Small	Flexible
3	Leucine	Hydrophobic	Uncharged	Large	Flexible
4	Isoleucine	Hydrophobic	Uncharged	Large	Flexible
5	Phenylalanine	Hydrophobic	Uncharged	Very Large	Bulky
6	Cysteine	Hydrophobic	Uncharged	Small	Flexible
7	Methionine	Hydrophobic	Uncharged	Large	Flexible
8	Tyrosine	Slightly hydrophilic	Uncharged	Very Large	Bulky
9	Tryptophan	Hydrophobic	Uncharged	Very Large	Bulky
10	Arginine	Hydrophilic	Positive	Large	Rigid
11	Lysine	Hydrophilic	Positive	Large	Flexible
12	Glutamic acid	Hydrophilic	Negative	Medium	Flexible
13	Aspartic Acid	Hydrophilic	Negative	Small	Flexible
14	Glutamine	Hydrophilic	Uncharged	Medium	Flexible
15	Asparagine	Hydrophilic	Uncharged	Small	Flexible
16	Histidine	Hydrophilic	Positive	Medium	Rigid
17	Proline	Hydrophobic	Uncharged	Small	Rigid
18	Valine	Hydrophobic	Uncharged	Medium	Flexible
19	Serine	Slightly hydrophilic	Uncharged	Very Small	Flexible
20	Threonine	Slightly hydrophilic	Uncharged	Small	Flexible