MCAT Biochemistry: Amino Acids, Peptides, Proteins, and Enzymes

Amino Acids

Molecules containing an amino group ($-NH_2$) and a carboxyl group ($-COOH$).

$\alpha$-amino acids

Amino acids where the amino and carboxyl groups are bonded to the same carbon ($\alpha$-carbon).

$\alpha$-carbon

The central carbon of an amino acid to which the amino group, carboxyl group, hydrogen atom, and R group are attached.

Side chain (R group)

The specific group attached to the $\alpha$-carbon that determines the chemical properties and function of an amino acid.

Proteinogenic amino acids

The 20 $\alpha$-amino acids encoded by the human genetic code.

Achiral amino acid

Glycine, which has a hydrogen atom as its R group, making the $\alpha$-carbon non-stereogenic.

L-amino acids

The stereochemical form of all chiral amino acids used in eukaryotic proteins; the amino group is on the left in a Fischer projection.

(S) absolute configuration

The configuration of almost all chiral amino acids (except cysteine).

Cysteine absolute configuration

The only L-amino acid with an (R) absolute configuration because the $-CH_2SH$ group has higher priority.

Nonpolar, nonaromatic amino acids

Glycine, alanine, valine, leucine, isoleucine, methionine, and proline.

Glycine

The smallest amino acid; achiral; R group is a hydrogen atom.

Alanine

Nonpolar, nonaromatic amino acid with an alkyl side chain of one carbon.

Valine

Nonpolar, nonaromatic amino acid with an alkyl side chain of three carbons.

Leucine

Nonpolar, nonaromatic amino acid with an alkyl side chain of four carbons.

Isoleucine

Nonpolar, nonaromatic amino acid with an alkyl side chain of four carbons (isomer of leucine).

Methionine

One of two sulfur-containing amino acids; nonpolar due to a methyl group attached to the sulfur.

Proline

Unique cyclic amino acid where the amino nitrogen becomes part of a five-membered ring side chain.

Aromatic side chain amino acids

Tryptophan, phenylalanine, and tyrosine.

Tryptophan

The largest aromatic amino acid; contains a double-ring system with a nitrogen atom.

Phenylalanine

Relatively nonpolar aromatic amino acid with a benzyl side chain.

Tyrosine

Polar aromatic amino acid formed by adding an $-OH$ group to phenylalanine.

Polar, nonaromatic amino acids

Serine, threonine, asparagine, glutamine, and cysteine.

Serine

Highly polar amino acid containing an $-OH$ group; participates in hydrogen bonding.

Threonine

Highly polar amino acid containing an $-OH$ group; participates in hydrogen bonding.

Asparagine

Polar amino acid with an amide side chain that does not become charged with pH changes.

Glutamine

Polar amino acid with an amide side chain that does not become charged with pH changes.

Cysteine

Polar amino acid with a thiol ($-SH$) group; prone to oxidation.

Negatively charged (acidic) amino acids

Aspartic acid (aspartate) and glutamic acid (glutamate); contain carboxylate groups at physiological pH.

Aspartate

The deprotonated form of aspartic acid; negatively charged at pH 7.4.

Glutamate

The deprotonated form of glutamic acid; negatively charged at pH 7.4.

Positively charged (basic) amino acids

Lysine, arginine, and histidine.

Lysine

Basic amino acid with a terminal primary amino group in its side chain.

Arginine

Basic amino acid with three nitrogen atoms in its side chain; positive charge is delocalized.

Histidine

Basic amino acid with an imidazole ring; one nitrogen is protonated at acidic pH.

Hydrophobic amino acids

Amino acids with long alkyl side chains (Ala, Ile, Leu, Val, Phe) found in protein interiors.

Hydrophilic amino acids

Amino acids with charged side chains (His, Arg, Lys, Glu, Asp) or amides (Asn, Gln).

Ala

Three-letter abbreviation for Alanine.

A

One-letter abbreviation for Alanine.

Arg

Three-letter abbreviation for Arginine.

R

One-letter abbreviation for Arginine.

Asn

Three-letter abbreviation for Asparagine.

N

One-letter abbreviation for Asparagine.

Asp

Three-letter abbreviation for Aspartic acid.

D

One-letter abbreviation for Aspartic acid.

Cys

Three-letter abbreviation for Cysteine.

C

One-letter abbreviation for Cysteine.

Glu

Three-letter abbreviation for Glutamic acid.

E

One-letter abbreviation for Glutamic acid.

Gln

Three-letter abbreviation for Glutamine.

Q

One-letter abbreviation for Glutamine.

Gly

Three-letter abbreviation for Glycine.

G

One-letter abbreviation for Glycine.

His

Three-letter abbreviation for Histidine.

H

One-letter abbreviation for Histidine.

Ile

Three-letter abbreviation for Isoleucine.

I

One-letter abbreviation for Isoleucine.

Leu

Three-letter abbreviation for Leucine.

L

One-letter abbreviation for Leucine.

Lys

Three-letter abbreviation for Lysine.

K

One-letter abbreviation for Lysine.

Met

Three-letter abbreviation for Methionine.

M

One-letter abbreviation for Methionine.

Phe

Three-letter abbreviation for Phenylalanine.

F

One-letter abbreviation for Phenylalanine.

Pro

Three-letter abbreviation for Proline.

P

One-letter abbreviation for Proline.

Ser

Three-letter abbreviation for Serine.

S

One-letter abbreviation for Serine.

Thr

Three-letter abbreviation for Threonine.

T

One-letter abbreviation for Threonine.

Trp

Three-letter abbreviation for Tryptophan.

W

One-letter abbreviation for Tryptophan.

Tyr

Three-letter abbreviation for Tyrosine.

Y

One-letter abbreviation for Tyrosine.

Val

Three-letter abbreviation for Valine.

V

One-letter abbreviation for Valine.

Amphoteric species

Molecules that can either accept or donate a proton depending on the environmental pH.

Low pH condition

Ionizable groups tend to be protonated.

High pH condition

Ionizable groups tend to be deprotonated.

$$pK_a$$

The pH at which half of the molecules of a species are deprotonated; $[HA] = [A^-]$.

$$pK_{a1}$$

The $pK_a$ for the carboxyl group of an amino acid, typically around 2.

$$pK_{a2}$$

The $pK_a$ for the amino group of an amino acid, typically between 9 and 10.

Zwitterions

Dipolar ions that have both a positive and negative charge but are overall electrically neutral.

Internal salts

The form in which zwitterions exist in water.

Isoelectric point ($pI$)

The pH at which a molecule is electrically neutral.

$$pI_{neutral amino acid}$$

$$\frac{pK_{a,NH_3^+ group} + pK_{a,COOH group}}{2}$$

$$pI_{acidic amino acid}$$

$$\frac{pK_{a,R group} + pK_{a,COOH group}}{2}$$

$$pI_{basic amino acid}$$

$$\frac{pK_{a,NH_3^+ group} + pK_{a,R group}}{2}$$

Neutral amino acid $pI$

Usually around 6.

Acidic amino acid $pI$

Well below 6.

Basic amino acid $pI$

Well above 6.

Peptides

Compounds composed of amino acid subunits called residues.

Dipeptides

Peptides consisting of two amino acid residues.

Tripeptides

Peptides consisting of three amino acid residues.

Oligopeptide

Relatively small peptides with up to about 20 residues.

Polypeptides

Long chains of amino acid residues (greater than 20).

Peptide bond

A specialized amide bond between the $-COO^-$ group of one amino acid and the $-NH_3^+$ group of another.

Condensation/Dehydration reaction

A reaction resulting in the removal of a water molecule ($H_2O$), such as peptide bond formation.

Resonance in peptide bonds

Delocalizable $\pi$ electrons in the carbonyl and amino nitrogen lone pair give the $C-N$ bond partial double bond character.

N-terminus

The free amino end of a peptide chain; written on the left by convention.