Mary K.

Campbell
Shawn O. Farrell

Chapter Three
Amino Acids and Peptides

Dr. M. khalifeh
Amino Acids
• Amino acid: a compound that contains
both an amino and a carboxyl group.
• -Amino acid has an amino group
attached to the carbon adjacent to
the carboxyl group
• -carbon also bound to side chain
group, R
• R gives identity to amino acid
• Two steroisomers of amino acids
are designated L- or D-. Based on
similarity to glyceraldehdye
(Figure 3.2)

Dr. M. khalifeh
Dr. M. khalifeh
Amino Acids steroisomers

• The two stereoisomers of each a.a  L and D a.a’s on

the basis of glyceraldehydes standard
• IF AMINO GROUP IS ON THE LEFT SIDE OF -
CARBON L FORM.
• IF AMINO GROUP IS ON THE RIGHT SIDE OF -
CARBON D FORM.
• Dashed represent bonds directed away from the
observer
• Solid triangles represent bonds directed toward the
observer

Dr. M. khalifeh
Amino Acid Structure and Properties
• With the exception of glycine all protein-derived
amino acids have at least one R group (the -
carbon) and are Chiral (stereoisomers)
• The simplest amino acid is glycine
• The vast majority of -amino acids have the L form-
configuration at the -carbon
• D-forms do not in proteins (antibiotics and bacterial cell
wall)
Amino Acid Structure and Properties
• Proline is usually cyclic structure where the amino
group is secondary amine (such called imino acid)
• All other amino group bond to one carbon ecxept proline
binds two carbons
• Side-chain carbons in other amino acids designated
with Greek symbols, starting at a carbon (…etc)
• Amino acids can be referred to by three-letter or one-
letter codes. Table 3.1 (KNOW THESE)

Dr. M. khalifeh
Non-Polar Amino Acids

 Proline is the only aa where the alpha amino

group is tied up in a ring structure. This
amino acid is only slightly hydrophobic.
 The ring structure decreases the flexibility of
the peptide backbone.

Dr. M. khalifeh
Individual Amino Acids
• Group A: non-polar (hydrophobic) side chains
• Ala, Val, Leu, Ile, Pro. Phe, Trp, Met.
• Ala, Val, Leu, Ile, Pro- contain aliphatic hydrocarbon
group
• (aliphatic = absence of benzene ring in the side chain).
• Pro has aliphatic cyclic structure.

Dr. M. khalifeh
Dr. M. khalifeh
Individual Amino Acids
• Group A (continue)
• Phe- hydrocarbon aromatic ring.
• Trp- Indole ring side chain, aromatic.
• Indole is an aromatic heterocyclic organic compound. It
has a bicyclic structure, consisting of a six-membered
benzene ring fused to a five-membered nitrogen-
containing pyrrole ring
• Met- Sulfur atom in side chain.

Dr. M. khalifeh
 Aromatic ring

ndole ring side

Dr. M. khalifeh
Ionic forms of amino acids

H R

C
COO-
H +
+
H3N H+
Zwitterion
H R pH 7 Net charge 0
H R

C C
+ COOH COO -
H3N H2N
pH 1 Net charge +1 pH 13 Net charge -1

Dr. M. khalifeh
Amino Acids (cont’d)
• Group B: electrically neutral side chains
• Has polar side that is uncharged at neutral pH
• Usually more soluble in water
• Exception is Tyr (most insoluble at 0.453 g/L at 25 C)
• Ser, Thr, Tyr, Cys, Glu, Asn
• Glycine sometimes included here because it lacks non-polar
end
• Ser, Thr- Side chain is polar hydroxyl group
• Tyr- hydroxyl group bonded to aromatic hydrocarbon
group
• Cys- Side chain contains thiol group (-SH)
• Gln, Asn- contain amide bonds (NH2) in side chain
Dr. M. khalifeh
 Uncharged polar side chains

Includes amino acids with alcohols in R-groups

- COO-
COO COO- +
+ + H3N C H
H3N C H H3N C H
lacks non-polar CH2 H C OH CH2
COO-
+ OH CH3
H3N C H Serine Threonine

H Ser Thr
OH
S T
Glycine Tyrosine
Gly Tyr
G Y Dr. M. khalifeh
Formation of cystine

Sulfhydryl group: Cys

Cys can form a disulfide bond (2 cysteines can make one cystine)

Dr. M. khalifeh
Uncharged polar side chains

Amide groups: Asn and Gln

COO-
COO- +
+ H3N C H
H3N C H
CH2
CH2
CH2
C
O C
NH2
O NH2
Asparagine
Glutamine
Asn
Gln
N
Q Dr. M. khalifeh
Amino Acids (cont’d)
• Group C: Acidic Side Chains: Glu, Asp
• Both have a carboxyl group in side chain
• Can lose a proton, forming a carboxylate ion
• These amino acids are negatively charged at
neutral pH

Dr. M. khalifeh
Charged polar (acidic) side chains

COO-
COO- +
+ H3N C H
H3N C H
CH2
CH2
CH2
C
O O- C
Aspartic acid
O O-
Glutamic acid
Asp
Glu
D
E

Dr. M. khalifeh
Amino Acids (cont’d)
• Group D: Basic side chains: His, Lys, Arg
• Side chains are positively charged at pH 7
• Arg-side chain is a guanidino group
• His-side chain is an imidazole group

Dr. M. khalifeh
Charged polar (basic) side chains

COO - COO-
+ COO-
+ H3N C H +
H3N C H C
H3N H
CH2 CH2
CH2 CH2 CH2
CH2 CH2 HC C
CH2 NH
H+N NH
NH3+ C
CH
Lysine NH2+ NH2
Histidine
Arginine
Lys His
Arg
K H
R Dr. M. khalifeh
Nonstandard (uncommon) amino acids

• 20 common amino acids programmed by genetic code

• Nature often needs more variation
• Nonstandard amino acids play a variety of roles:
• Structural
• Antibiotics
• Signals
• Hormones
• Neurotransmitters
• intermediates in metabolic cycles
• Nonstandard amino acids are usually the result of modification of a
standard amino acid after a polypeptide has been synthesized.

Dr. M. khalifeh
Nonstandard amino acids
Found in connective tissue
proteins (collagen)

Dr. M. khalifeh
Nonstandard amino acids

Modification of tyrosine present in thyroglobulin

(extra iodine containing aromatic ring
Produced only in thyroid gland
Released from thyroglobulin after proteolysis

Dr. M. khalifeh