Unit 2

AMINO ACIDS and PEPTIDES

AMINO ACID: Building block of Peptide/Protein
Contains the ff. chemical groups
attached to -carbon:
Amino group
Carboxyl group
Side chain group (R) gives the
identity to amino acid
All amino acids (except glycine)
have at least one stereocenter (-C)
and are chiral (stereoisomers).
Two stereoisomers:
L- and D-amino acid
Majority of -amino acids are in
L-configuration at the -C
Classification of Amino Acid
According to type of side chain, R group
Neutral amino acids
Acidic amino acids
Basic amino acids
According to Polarity
Uncharged nonpolar
Uncharged polar
Charged polar
According to Nutritional Requirements
Non-essential
Essential
Common Amino Acids
Neutral amino acids
with aliphatic hydrocarbon group
Glycine (Gly, G): hydrogen Alanine (Ala, A): methyl group

Valine (Val, V): isopropyl group Isoleucine (Ile, I): isobutyl group
Common Amino Acids
Neutral amino acids
with aliphatic hydrocarbon group
Leucine (Leu, L): sec-butyl group Proline (Pro, P): cyclic structure

with sulfur-containing side chain

Cysteine (Cys, C): thiol group Methionine (Met, M): thioether group
Common Amino Acids
Neutral amino acids
with hydroxyl group
Serine (Ser, S): primary alcohol Threonine (Thr, T): secondary alcohol

with aromatic ring

Phenylalanine (Phe, F): benzyl group Tryptophan (Trp, W): indole group
Common Amino Acids
Neutral amino acids
with aromatic ring
Tyrosine (Tyr, Y): phenolic group

with amide group

Asparagine (Asn, N) Glutamine (Gln, Q)
Common Amino Acids
Basic amino acids
Lysine (Lys, K): -amino group Arginine (Arg, R): guanidino group

Histidine (His, H): imidazole group

Common Amino Acids
Acidic amino acids
Aspartic acid (Asp, D): -carboxylate Glutamic acid (Gln, E): -carboxylate
Classification of Amino Acid
According to type of side chain, R group
Neutral amino acids
Acidic amino acids
Basic amino acids
According to Polarity
Uncharged nonpolar A, V, L, I, M, F, P, W
Uncharged polar G, C, S, T, Y, N, Q
Charged polar K, R, H, D, E
According to Nutritional Requirements
Non-essential
Essential
Classification of Amino Acid
According to type of side chain, R group
Neutral amino acids
Acidic amino acids
Basic amino acids
According to Polarity
Uncharged nonpolar
Uncharged polar
Charged polar
According to Nutritional Requirements (based on the
ability to synthesize de novo by the organism)
Non-essential A, N, Q, D, C, E, G, P, S, Y
Essential H, I, L, K, M, F, T, W, V, R
Acid-Base Properties of an Amino Acid
Remember: An amino acid contains ionizable
chemical groups (carboxyl and amino groups)
attached to -carbon.
Carboxyl group (-) and amino group (+) are charged at
neutral pH.

Without charged groups on side chain, amino acids

exist in neutral solution as zwitterions with no net
charge
Titration of Amino Acids
When an amino acid is titrated,
the titration curve represents
the reaction of each functional
group with the hydroxide ion
Ionization of Amino Acids
Titration of histidine with NaOH
Problem Set 1
With the ff. amino acids (alanine, aspartic acid, lysine),
answer the ff:
Draw all ionic forms of the amino acids.
Identify the zwitterion.
What is the net charge of the amino acid when dissolved in
a solution with the following pH:
2.00
4.50
7.40
10.00
Isoelectric pH
Isoelectric pH, pI: the pH at which the majority of molecules of
a compound in solution have no net charge

the pI for glycine, for example, falls midway between the pKa
values for the carboxyl and amino groups

Net charge of an amino acid:

pH < pI negative
pH = pI neutral
pH > pI positive
Problem Set 2
What is the pI of the ff amino acids?
Cysteine
Glutamic acid
Lysine
The Peptide Bond
Individual amino acids can
be linked by forming covalent
bonds.
Peptide bond: amide bond
between the -carboxyl
group of one amino acid and
the -amino group of another
amino acid
Amino acid residues: what
remains of each amino acid
Dipeptide: one peptide bond
and 2 amino acid residues;
tripeptide: two peptide bonds
and 3 amino acid residues;
and so on
The Peptide Bond
The peptide bond has considerable C-N double bond
character; stabilized by resonance.
Rotation about the peptide is restricted.
Peptide bond structure is planar.
The Peptide Bond
In contrast to the peptide bond, rotations are permitted at the bonds
between the amino group and the carbonyl group with the -carbon;
allowing for two possible conformations in respect to the -carbons, trans
(highly favored) and cis conformations.

N-terminal: residue that has free amino group

C-terminal: residue that has free carboxyl group
Problem Set 3
Draw the ff. peptides:
DK
YES
CHEM
What is the pI of each peptide?
Predict the ionic form of the peptide (given above) that will
predominate at:
pH 1
pH 7
pH 13