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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

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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

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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

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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)

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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

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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

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

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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

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Ionization of Amino Acids

Titration of histidine with NaOH

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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

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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

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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

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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

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