Amino Acids

Question 1

Non polar amino acids (non aromatic)

Answer 1

Side chains have no polar bonds, structures predominantly hydrophobic

1. Glycine (Gly, G): single hydrogen side chain, only achiral amino acid

2. Alanine (Ala, A): methyl group side chain

3. Valine (Val, V): two methyl groups (isopropyl group)

• substitution of glutamic acid and hemoglobin causes sickle cell disease

4. Leucine (Leu, L): extra carbon before isopropyl group

5. Isoleucine (Ile, I): tertiary carbon appears closer to amino acid structure

ALIV

6. Methionine (Met, M): one of two aminos with sulfer atom (cysteine)

• large quantity in eggs, used for DNA methylation

7. Proline (Pro, P): nitrogen in amine group is part of cyclic side chain, can break up secondary structure with proline kinks

Question 2

Aromatic nonpolar aminos

Answer 2

Side chains based on benzene rings

1. Phenylalanine (Phe, F): side chain is benzene ring attached to methyl group

2. Tyrosine (Tyr, Y): amphipathic side chain with OH group bonded to benzene ring, more nonpolar due to bulky ring

3. Tryptophan (Trp, W): two rings, precursor for serotonin and melatonin

• W = double ring

Question 3

Polar uncharged aminos

Answer 3

Side groups contain at least one polar bond that shapes behavior

Alcohols

1. Serine (Ser, S): alcohol, OH group, relatively reactive and targeted by phosphorylation and other posttranslational modification

2. Threonine (Thr, T): alcohol, side chain has additional carbon

Amides

1. Asparagine (Asn, N): amide side chain

2. Glutamine (Gln, Q): amide side chain but longer

Cysteine (Cys, C): thiol side chain (SH), not strongly polar but participates in H bonding

• covalent disulfide bonds b/w two cysteine molecules forms Cystine, important part of protein tertiary structure

Question 4

Basic amino acids

Special property for each?

Answer 4

Zwitterionic form is positively charged (has already picked a proton)

1. Lysine (Lys, K): simplest basic amino, hydrocarbon side chain with primary amine group at end

• fairly reactive target for methylation, acetylation

2. Arginine (Arg, R): hydrocarbon chain which terminates with 3 nitrogens

• positive charge can be resonance stabilized = most basic amino acid

3. Histidine (His, H): cyclic side chain containing two nitrogens, **under physiological conditions its uncharged

• usually neutral

Question 5

Bronsted Lowry acid base definitions

Answer 5

acids = proton donors

bases = proton acceptors

Question 6

Acidic amino acids

Answer 6

Both have COOH carboxylic acid group, deprotonated form is predominant in physiological conditions (pH 7.4)

Negatively charged

1. Aspartic acid (Asp, D): COOH side chain

Also called aspartate, which refers to deprotonated form

2. Glutamic acid (Glu, E): COOH side chain with extra carbon

Also glutamate when negative, important neurotransmitter

Two acidic aminos have one letter abbreviation next to each other in alphabet, D and E

Question 7

types of missense mutations

Answer 7

Amino acid is changed when DNA sequence is translated

conservative- new amino acid has similar structure to old, partially conserve original function

• ex. threonine to serine

minimal effects

nonconservative- replaces original amino acid with one with very different structure

• threonine to proline
• can greatly impact final protein

Question 8

Essential amino acids

Answer 8

cannot be made by the body. As a result, they must come from food.

The 9 essential amino acids are:

histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine.

Question 9

Special property of glycine

Answer 9

Achiral so doesn’t rotate plane polarized light