AMINO ACIDS

AND
PEPTIDES
Marion G. Rivera, M.D.
 a-AMINO ACIDS
 Contain an amino and carboxylic groups
attached to the same a carbon
R
│
a
H ─ C ─ COOH
│
NH2
 AMINO ACIDS
 a-Carbon of all amino acids
except for glycine is chiral or
assymetric
• Chiral carbon – carbon in which all
four groups attached are different;
confers optical activity
 L- a-AMINO ACIDS
 Absolute
configuration of
amino acids are
referenced to
Glyceraldehyde
 All amino acids
derived from
natural proteins
are of the
L-configuration
 L- a-AMINO ACIDS

 Only 20 amino acids occur in

proteins from all forms of life
 Differ in their R group
THE
20
AMINO
ACIDS
CLASSIFICATION OF AMINO ACIDS
ACCORDING TO R GROUPS

A. WITH ALIPATHIC SIDE CHAINS

1. Glycine (G)
2. Alanine (A)
3. Valine (V)
4. Leucine (L)
5. Isoleucine (I)
CLASSIFICATION OF AMINO ACIDS
ACCORDING TO R GROUPS
B. WITH SIDE CHAINS CONTAINING -OH
GROUPS
6. Serine (S)
7. Threonine (T)
8. Tyrosine (Y)

C. WITH SIDE CHAINS CONTAINING

SULFUR ATOMS
9. Cysteine (C)
10. Methionine (M)
CLASSIFICATION OF AMINO ACIDS
ACCORDING TO R GROUPS

D. WITH SIDE CHAINS CONTAINING

ACIDIC GROUPS OR THEIR AMIDES
11. Aspartic acid (D)
12. Asparagine (N)
13. Glutamic acid (E)
14. Glutamine (Q)
CLASSIFICATION OF AMINO ACIDS
ACCORDING TO R GROUPS
E. WITH SIDE CHAINS CONTAINING
BASIC GROUPS
15. Arginine (R)
16. Lysine (K)
17. Histidine (H)
CLASSIFICATION OF AMINO ACIDS
ACCORDING TO R GROUPS
F. WITH AROMATIC RINGS
18. Phenylalanine (F)
19. Tryptophan (W)
Tyrosine
Histidine
G. IMINO ACID
20. Proline (P)
 Alanine A (Ala)
 Chemical
Properties:
Aliphatic

 Physical
Properties:
Non-polar
 Arginine R (Arg)
 Chemical
Properties:
Basic

 Physical
Properties:
Polar
(positively
charged)
 Aspartic Acid D (Asp)
 Chemical
Properties:
Acidic

 Physical
Properties: Polar
(negatively
charged)
 Asparagine N (Asn)
 Chemical
Properties:
Neutral
(Amide of an acidic
amino acid)

 Physical Properties:
Polar (uncharged)
 Cysteine C (Cys)
 Chemical
Properties:
Sulfur-
containing

 Physical
Properties:
Polar
(uncharged)
 Glutamic Acid E (Glu)
 Chemical
Properties:
Acidic

 Physical
Properties: Polar
(negatively
charged)
 Glutamine Q (Gln)
 Chemical
Properties: Neutral
(Amide of an acidic
amino acid)

 Physical Properties:
Polar (uncharged)
 Glycine G (Gly)
 Chemical
Properties:
Aliphatic

 Physical
Properties:
Nonpolar
 Histidine H (His)
 Chemical
Properties:
Basic

 Physical
Properties:
Polar
(positively
charged)
 Isoleucine I (Ile)
 Chemical
Properties:
Aliphatic

 Physical
Properties:
Nonpolar
 Leucine L (Leu)
 Chemical
Properties:
Aliphatic

 Physical
Properties:
Nonpolar
 Lysine K (Lys)
 Chemical
Properties:
Basic

 Physical
Properties:
Polar
(positively
charged)
 Methionine M (Met)
 Chemical
Properties:
Sulfur-
containing

 Physical
Properties:
Non polar
(hydrophobic)
 Phenylalanine F (Phe)
 Chemical
Properties:
Aromatic

 Physical
Properties:
Nonpolar
 Proline P (Pro)
 Chemical
Properties:
Cyclic

 Physical
Properties:
Nonpolar
 Serine S (Ser)
 Chemical
Properties:
Non-aromatic
hydroxyl

 Physical
Properties:
Polar
(uncharged)
 Threonine T (Thr)
 Chemical
Properties:
Non-aromatic
hydroxyl

 Physical
Properties:
Polar
(uncharged)
 Tryptophan W (Trp)
 Chemical
Properties:
Aromatic

 Physical
Properties:
Nonpolar
 Tyrosine Y (Tyr)
 Chemical
Properties:
Aromatic with
hydroxyl
group
 Physical
Properties:
Polar,
uncharged
 Valine V (Val)
 Chemical
Properties:
Aliphatic

 Physical
Properties:
Nonpolar
 SELENOCYSTEINE
 Commonly referred to as 21st amino
acid
 Selenium atom replaces the sulfur of
its structural analog, cysteine
 Present in the active site of several
enzymes eg, thioredoxin reductase,
glutathione peroxidase, deiodinase
SELENOCYSTEINE

a
 PROTONIC EQUILIBRIA OF
AMINO ACIDS
 Amino acids bear at least 2
ionizable weak acid groups

R – COOH R – COO- + H+

R – NH3+ R – NH2 + H+
 PROTONIC EQUILIBRIA OF
AMINO ACIDS

 R – COOH is a stronger
acid than R – NH3+

• pKa of –COOH = 2
• pKa of –NH3+ = 10
 pH = pKa + log [A-] / [HA]
 The pK of an acid group is that pH at
which the protonated and
unprotonated species (acid and its
conjugate base) is present in equal
concentration
R – COOH R – COO- + H+ pK= 2

R – NH3+ R – NH2 + H+ pK= 10

 At pH of blood, 7.4 or pH of
intracellular space, 7.1, exist as
R-COO- and R-NH3+

H H
│
R ─ C ─ COOH R – C – COO-
│
NH2 NH3+
cannot exist in any pH
 PROTONIC EQUILIBRIA OF
AMINO ACIDS
 Amino acids exist as zwitterions
• Zwitterions are molecules that contain an
equal number of ionizable groups of opposite
charge and therefore bear no net charge
 Functional groups present on amino
acids has different pKa values
 Net charge of an amino acid depends
upon the pH of the surrounding
solution
 RESONANCE HYBRIDS OF THE
PROTONATED FORMS OF THE R
GROUPS OF HISTIDINE AND ARGININE
Histidine
Imidazole
ring

Arginine

Guanidino
 ISOELECTRIC pH
 pH at which an amino acid bears no
net charge and hence does not move
in a direct current electrical field

 pH midway between pK values on

either side of the isoelectric species
 2.34 9.60

NC = +1 NC = 0 NC = -1
DETERMINATION OF ISOELECTRIC pH
OF ASPARTIC ACID
DETERMINATION OF ISOELECTRIC pH
OF ASPARTIC ACID

pI = pK1 + pK2
2
= 2.09 + 3.86
2
= 5.95
2
= 2.98
DETERMINATION OF ISOELECTRIC pH
OF HISTIDINE

1.8 6.0 9.3

NC = +2 NC = +1 NC = 0 NC = -1
 DETERMINATION OF ISOELECTRIC pH
OF HISTIDINE
pI = pK2 + pK3
2
= 6.0 + 9.3
2
= 15.3
2
= 7.65
DETERMINATION OF ISOELECTRIC pH
OF HISTIDINE
 ISOELECTRIC pH
 Knowledge of isoelectric pH
guides in the selection of
conditions for electrophoretic
separation
 Varying the pH of the

medium alters the charge of

the amino acids
 At pH < pI, amino acid is (+)

 At pH > pI, amino acid is (-)

 GENERAL PROPERTIES OF
AMINO ACIDS
 Soluble in polar solvents (water,
ethanol); insoluble in non-polar
solvents (benzene, ether)
 High melting point
 Do not absorb visible light with the
exception of the aromatic amino
acids
Specific properties of the
individual amino acids
are dictated by the
nature of their R groups
+
 Glycine
• Smallest amino acid
• Can fit in regions inaccessible to other amino
acids
 AA with alipathic or aromatic R group
• Hydrophobic
• Occurs in the interior of proteins
 AA with charged R group
• Basic and acidic AAs
• Role in stabilizing specific protein conformation
by formation of salt bonds
 -OH of serine and –SH of cysteine
• Nucleophile
• Function as such during enzymatic catalysis
 -OH of serine, tyrosine and threonine
• Undergoes phosphorylation which regulate
enzyme activity
 Imidazole group of histidine
• Important in enzyme catalysis
• pKa of 6.0 allows it to function as either a base
or acid catalyst at neutral pH
NON-PROTEIN AMINO
ACIDS
NON-PROTEIN AMINO ACIDS

HOMOCYSTEINE

ORNITHINE CITRULLINE
 TEST FOR AMINO ACIDS
 Treatment of a polypeptide with hot HCl
hydrolyzes the peptide bonds and releases
free amino acids; reaction with N-
hydroxysuccinimidyl carbamate forms
flourescent derivatives that can be
separated and identified
 Ninhydrin
• Also used in detecting amino acids; forms a
purple product with a-amino acids and yellow
with imine groups of proline
PEPTIDES
 PEPTIDES
 Consist of 2 or
more amino acid
residues linked by
peptide bond
 PEPTIDE BOND FORMATION
 Involves removal
of one mol of
water between
the a-amino
group of one
amino acid and
the a-carboxyl
group of a
second amino
acid
PEPTIDE BOND FORMATION

 Peptides written with the

• N-terminal residue at the left
• C-terminal residue at the right
NOMENCLATURE

Seryl–valyl-tyrosyl-cysteine

Ser-Val-Tyr-Cys

SVYC
 DRAWING A PEPTIDE STRUCTURE

 Draw a zigzag to represent the

peptide backbone
 DRAWING A PEPTIDE STRUCTURE

 The peptide backbone is made up of

repeating N, a-C and carbonyl C

C N C C
a
a a
N C N
C C
 DRAWING A PEPTIDE STRUCTURE

 Add hydrogen to each a-carbon and peptide

nitrogen, oxygen to carbonyl carbon and
appropriate R group to each a-carbon

CH3 CH3

CH O CH2 – SH
l ǁ
CH NH C CH
a a
a
C CH NH COO-
NH3+ ǁ
O
CH2 – CH2 – CH2 – CH2 – NH3+
 PEPTIDE BOND
O O ̿  Exhibit partial
double-bond
C C character
 No freedom of
rotation about the
N N+ bond that connects
the carbonyl
H H carbon and the
nitrogen of the
peptide bond
 A B C D E F

Identify the peptide bonds

 Peptide
Peptide bond
Peptide bond
bond
 TEST FOR PEPTIDE BONDS
 BIURET TEST
• Sample treated with alkaline copper sulfate
reagent
• Produces a violet color in the presence of at
least two peptide bonds
 PEPTIDES
 Formation of peptides from amino
acids is accompanied by a net loss of
one positive and one negative charge
per peptide bond formed
 Peptides are charged at physiologic
pH because of their terminal carboxyl
and amino groups and when present
the charged R group
 pKa VALUES FOR IONIZABLE
GROUPS IN PEPTIDES AND
PROTEINS
 pKa values of the R groups of free
amino acids in aqueous solution may
vary with the pKa values of the same
amino acids when present in proteins
 pKa values of functional groups will
depend upon its location within a
given protein
pKa VALUES FOR IONIZABLE GROUPS IN
PEPTIDES AND PROTEINS
Dissociating Group pKa Range
a-Carboxyl 3.5 – 4.0
Non-a-COOH of Asp or Glu 4.0 – 4.8
Imidazole of His 6.5 – 7.4
SH of Cys 8.5 – 9.0
OH of Tyr 9.5 – 10.5
a-Amino 8.0 – 9.5
e-amino of Lys 9.8 – 10.4
Guanidinium of Arg ~12.0
 PEPTIDES OF PHYSIOLOGIC
IMPORTANCE
 Bradykinin
• Vasodilator
• Involved in the
normal
inflammatory
process

Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg
 Polypeptide
antibiotics
• Gramicidin
 Glutathione
• Tripeptide (Glu-Cys-Gly)
• Participates in the formation of correct
disulfide bonds of many proteins
 TRH
• Pyro-glutamyl-histidyl-prolinamide
• Atyphical, N-terminal glutamate is cyclized
to pyroglutamate and C-terminal
prolylcarboxyl is amidated
 Aspartame
• Artificial sweetener, 200x sweeter than
sugar
• Dipeptide; L-aspartyl-L-phenylalanine
(methyl ester)