AMINO ACIDS

AND
PEPTIDES
Maureen Baroro- De Guzman, MD
BIOMEDICAL IMPORTANCE
Provide the monomer units of polypeptide chains of proteins
Participate in cellular functions ( nerve transmission,
porphyrins, purines, pyrimidines, urea)
Peptides: short polymers of proteins (role in neuroendocrine
system)
D- and L- amino acids: by microorganisms (therapeutic value)
Humans: lack the capability to synthesize 10 of the 20
common L-amino acids, diet must contain adequate
quantities of these essential amino acids
PROPERTIES OF AMINO ACIDS
TABLE 3-1 PP 15
AMINO ACIDS: BUILDING BLOCKS FOR PROTEINS
Organic compound that contains both an amino
(-NH2) group and a carboxyl (-COOH) group

amino acids :amino and carboxyl groups are
attached to the carbon; AA in proteins

The Genetic Code Specifies 20 L- Amino
Acids
Redundancy of 3- letter genetic code: limits the
available codons to the 20 L-a amino acids

Some proteins: contain additional amino acids that
arise by modification of an amino acid already present
in a peptide
Conversion of peptidyl proline and lysine to 4-
hydroxyproline and 5- hydroxylysine
Peptidyl glutamate to - carboxyglutamate

Modifications: extend the biologic diversity of
proteins by altering their solubility, stability and
interaction with other proteins


Selenocysteine, the 21
st
L- amino acid?
Selenocysteine: L- a amino acid
found in peroxidases and
reductases
Participates in the catalysis of
electron transfer reaction
Selenium atom replaces the
sulfur of its structural analog
cysteine
Inserted into polypeptides during
translation: commonly referred to
as the 21
st
amino acid
Unlike the other 20 amino acid:
not specified by the 3-letter codon
THE ESSENTIAL AMINO ACIDS
amino acids needed by the body that must be
obtained from dietary sources because it cannot be
synthesized within the body from other substances
in adequate amounts
Arginine: required for growth in children but not
required in adults
Only L- Amino Acids Occur in Proteins
amino acids are chiral (except glycine)
Share absolute configuration of L-glyceraldehyde : L-
amino acids
Free amino acids: role in metabolic processes
ornithine, citrulline, argininosuccinate in urea
synthesis
Tyrosine: thyroid hormone synthesis
Glutamate: neurotransmitter biosynthesis
D- Amino acids that occur naturally:
D- serine and aspartate in brain tissue
D- alanine and glutamate: cell walls of G+ bacteria
In certain peptides and antibiotics produced by
bacteria , fungi, reptiles and nonmammalian
species






Acid- Base Properties Of Amino Acids
Pure form: white crystalline solids with high
decomposition points
Most are not very water soluble due to strong
intermolecular forces within in their crystal
structures
AA are charged species both in the solid state and
in solution
Both an acidic group (-COOH) and a basic group (-
NH2) are present
Neutral Solution: carboxyl groups have a tendency
to lose protons (H+) producing a negatively charged
species
-COOH -COO
-
+ H
+

Neutral solution: amino groups have a tendency to
accept protons (H+) producing a positively charged
species
-NH
2
+ H
+
-
+
NH
3
-COOH groups donates a proton to the NH2 of
the same amino acid; internal base reaction with a
net result


called a Zwitterion (German meaning: double ion)
A molecule that has a positive charge on one
atom and a negative charge on another atom
but which has no net charge
Net charge: zero
Strong intermolecular forces between the
positive and the negative centers: high melting
points of amino acids



Zwitterion ion structure change: pH of solution
containing an amino acid is changed from neutral
either to
acidic (low pH) by adding an acid such as HCl
basic (high pH) by adding a base such as NAOH

Acidic Solution: zwitterion accepts a proton (H+)
to form a positively charged ion





Basic Solution: the NH3 of the zwitterion loses a
proton and a negatively charged species is formed




In solution, 3 different solutions can exist (zwitterion,
negative and positive ion ion)
3 species in equilibrium with each other
Equilibrium shifts with pH change
Overall equilibrium process



Ability of amino acids to react with both H
3
0
+
and OH
-
ions:
can function as buffers

Guidelines for amino acid form as a function of
solution of pH
Low pH: All acid groups are protonated
(-COOH). All amino groups are protonated
(-
+
NH3)

High pH: All acid groups are deprotonated
(-COO
-
). All amino groups are deprotonated
(-NH2).

Neutral pH: All acid groups are deprotonated
(-COO
-
). All amino groups are protonated
(-
+
NH3).




Assumption that that the side chain (R chain) of an
amino remains unchanged in solution as the pH is
varied (for neutral amino acids)

Acidic and Basic Amino acids: side chain can also
acquire a charge because it contains an amino or a
carboxyl group that can gain of lose a proton
respectively

Protonated: gain of H+ ion
Deprotonated : loss of a H+ ion


With an extra site that can be protonated or
deprotonated, acidic and basic amino acids have
four charged forms in solution

Four forms of aspartic acid







Side chain carboxyl groups are weaker acids that
a- carbon carboxyl groups
pKa values express the strengths of Weak
Acids
pKa: acid strengths of weak acids
Molecules with multiple dissociable protons: pKa for
each acidic group is designated by replacing a
subscript a with a number
Net charge on amino acid: algebraic sum of all the
positively and negatively charged groups present-
depends upon the pKa values of its functional groups
and on the pH of the surrounding medium
Altering the charge by varying the pH facilitates the
physical separation of amino acids, peptides and
proteins

At its isoelectric pH, an Amino acid bears
no net charge
Zwiterrions: isoelectric species, equal number of
negative charges (electrically neutral)
Isoelectric pH (pI): pH midway between pKa values on
either side of the isoelectric species
Example: Alanine with 2 dissociating groups
1
st
pKa (R-COOH): 2.35
2
nd
pKa (R-NH3+): 9.69
pI: pK1 +pK2 = 2.35+ 9.69 =6.02
2 2










Polyfunctional acids: pI is also the pH midway
between the pKa values on either side of the isoionic
species
Also apply to Polyprotic acids (proteins): regardless
of the number of dissociating groups present
Laboratory: pI guides selection of conditions for
electrophoretic separations
Ex: Elecgtrophoresis at pH 7.0: separate 2
molecules with pI values 6.0 and 8.0
Because at pH 7, the molecule with a pI 6.0
with have a net positive charge, pI 8.0 with a
negative charge








pKa values vary with the environment
pKa values of the R groups of free amino acids:
provide only an approximate guide to the pKa values
of the same amino acids in proteins
Polar environment: favors charged form (R-COO or R-
NH3+), Non polar environment: favors uncharged form
(R-COOH and R-NH2); raises the pKa of a carboxyl
group (making it a weaker acid) but lowers that of an
amino group (making it a weaker acid)
Presence of adjacent charged groups: reinforce or
counteract solvent effect
pKa of a functional group: will depend on its location
with in a given protein
Variations in pKa can encompass whole pH units
(table 3-2)
Solubility of Amino Acids reflects their
Ionic Character
Charged functional groups of amino acids: ensure that
they are readily solvated by- and thus soluble in- polar
solvents such water and ethanol
But insoluble in nonpolar solvents (benzene,
hexane)
Amino acids: do not absorb visible light, colorles
Tyrosine, Phe, Tryp: absorb wavelength (250-290 nm)
UV
Tyrp: Absorbs UV light 10x more efficiently than
phe or Tyr, makes major contribution to the ability
of most proteins to absorb light in the region of 280
nm


THE - R GROUPS DETERMINE THE PROPERTIES
OF AMINO ACIDS
Glycine: smallest amino acid, accomodated in places
inaccessible to other amino acids, occur where peptides bend
sharply
Hydrophobic R groups (Ala, Val, Leu, Iso and aromatic R
groups of Phe, Tyr, Tryp): occur primarily in the interior of
cytosolic proteins
Charged R groups of basic and acidic amino acids: stabilize
specific protein conformations via ionic interactions or salt
bridges
Such interactions functions in charge relay systems
during enzymatic catalysis and electron transport in
respiring mitochondria


Histidine: unique role, pKA of its imidazole proton permits it
to function at neutral pH as either a base of an acid catalyst

Primary alcohol group of Ser and thioalcohol of Cysteine:
excellent nucleophiles, function during enzymatic catalysis

Secondary alcohol group of Threonine: good nucleophile,
doe not fulfill the same role of Ser and Cysteine

-OH groups of ser, try and threonine: regulation of activity of
enzymes whose catalytic activity depends on the
phosphorylation state of these residues
FUNCTIONAL GROUPS DICTATE THE CHEMICAL
REACTIONS OF AMINO ACIDS
Each functional group of an amino acids: exhibits all of its
characteristic chemical reaction
Carboxylic acid groups: formation of esters, amides and acid
anhydrides
Amino groups: acylation, amidation and esterification
-Oh and Sh groups: oxidation and esterification
FORMATION OF PEPTIDE BOND: most important reaction of
amino acids
Amino Acid Sequence Determines
Primary Structure
primary structure: Number and order of all of the
amino acid residues in a polypeptide chain
Aminoacyl residues: amino acids present in peptides
Named by replacing the ate or ine suffixes of
free amino acids with yl (alanyl, aspartyl, lysyl)
Peptides: named as derivatives of the carboxyl
terminal aminoacyl residues
Example: Lys-Leu-Tyr-Gln
Lysyl-Leucyl-Tyrosyl-Glutamine
-ine ending of Glutamine indicate that its a-carboxyl
group is not involved in the peptide bond formation

PEPTIDE
unbranched chain of amino acids, each joined to
the next by a peptide bond

Classified by the number of peptide bonds
Di- , tri-, oligo

Polypeptide: long, unbranched chain of amino
acids, each joined to the next by a peptide bond
NATURE OF PEPTIDE BOND
Carboxyl group of one amino acid interacts with
the amino group of the other amino acid







Products: water and molecule containing 2 amino
acids linked by an amide bond
Directionality: N- terminal end C- terminal end

NATURE OF PEPTIDE BOND
Sequence of amino acids in a peptide is written
with the N- terminal amino acid on the left

Amino acid residue: portion of an amino acid
structure that remains after release of H2O, when
an amino acid participates in peptide bond
formation as it becomes part of the peptide chain

Structural Formula: may be written in full or by
the standard 3-letter AA abbreviations; AA at the
N-terminal end of the peptide is always written on
the left
E.g. Glyc- Ala- Ser
PEPTIDE NOMENCLATURE
IUPAC Rules for Naming small peptides
1. The C- terminal amino acid residue keep its full
amino acid name
2. All of the other amino acid residues have names
that end in yl. The yl suffix replaces the ine
or ic acid ending of the amino acid name,
except for Tryptophan (tryptophyl), cysteine
(cysteinyl), glutamine (gluatminyl) and
asparagine (asparaginyl)
3. The amino acid naming sequence begins at the
N-terminal amino acid residue
Assign IUPAC names:

1. Glu- Ser- Ala
2. Gly- Tyr- Leu- Val


Answers:

1. Glutamylserylalanine
2. Glycyltyrosylleucylvaline


Some peptides contain unusual amino
acids
Mammals: peptide hormones typically contain only a-
amino acids of proteins linked by standard peptide
bonds
Others: contain nonproteins amino acids, derivatives
of amino acids or amino acids linked by an atypical
peptide bond
Ex: amino terminal of glutathione (participates in
folding and in the metabolism of xenobiotics): linked to
cysteine by a non- a peptide bond


Peptides are polyelectrolytes
Peptide bond: uncharged at any pH of physiologic pH
Formation of peptides from amino acids:
accompanied by a net loss of one positive and one
negative charge per peptide bond formed
Charged at physiologic pH: carboxyl and amino
terminal groups and where present, their acidic or
basic R groups
Amino acids: the net charge on a peptide depends on
the pH of its environment and the pKa values of its
dissociating groups
The Peptide Bond Has Partial Double- Bond
Character
Single bond linked to the a-carboxyl
and a-nitrogen atoms: exhibits partial
double bond
Thus, no freedom of rotation about
the bond that connects the carbonyl
and the nitrogen of a peptide bond
O, C, N, H are co planar
Imposed semi-rigidity of the peptide
bond: important consequences for
the manner in which peptides and
proteins fold to generate higher
orders of structure
Noncovalent Forces Constrain Peptide
Conformations
Folding of a peptide bond: coincident with its
biosynthesis
Physiologically active conformation of : reflects the
collective contributions of the amino acid sequences,
steric hindrance, non covalent interactions
Common conformations: a- helices and B- pleated
sheets
Analysis of the Amino Acid Content of
Biologic Materials
Determine the identity and quality of each amino acid
in a sample of biologic material: necessary to hydrolyze
the peptide bonds that link the amino acids together
by treatment with hot HCl
Resulting mixture of free amino acids: treated with 6-
amino-N-hydroxysuccinimidyl carbamate which reacts
with their a-amino groups to form fluorescent
dreivatives that are separated and identified using high
pressure liquid chromatography
Ninhydrin : used for detecting amino acids and a
yellow adduct with the imine groups of proline and
hydroxylproline