CHEMISTRY OF

PROTEINS AND AMINO ACIDS

Dr Girish K S
Assistant professor
Department of Biochemistry
 Amino acids : Classification,
properties, side chains of
Chemistry of amino acids, charge properties.
Proteins,
Proteins: Definitions,
Amino Acids Classifications and functions
and Peptides
(6hrs.) Peptides : Biologically active
peptides - Examples such as
GSH, Insulin - its structure.
 ARE PROTEINS AND
AMINO ACIDS ESSENTIAL
FOR LIFE ?
 ARE PROTEINS AND
AMINO ACIDS
ESSENTIAL FOR LIFE ?
Most abundant macromolecules in living cells

Constitutes 50% of the dry weight of a cell

Each cell contains hundreds of proteins

Exhibit enormous diversity and perform a variety of functions

Polymers of amino acids which are covalently linked to one

another
Amino acids

Classification

Properties

Side chains of amino acids

Charge properties
PROTEIN COMES FROM THE GREEK WORD PROTEIOS,

"PRIMARY" OR "HOLDING THE FIRST PLACE

DUTCH CHEMIST GERARD JOHANN MULDER, COINED

THE WORD PROTEIN IN 1838

 1 2 3

Amino acids Peptides Proteins

AMINO ACIDS
 AMINO ACIDS

• All the proteins in a living system are made from a set of 20 amino acids

• Genetically encoded

• Central dogma of life

• DNA – RNA – Proteins - Function
 AMINO ACIDS

• All the amino acids found in proteins

are called

• Alpha amino acids

• Amino group and carboxyl group are
attached to the same carbon atom

• Exception: proline – imino acid

AMINO
ACIDS
• Selenocysteine is called as the 21st amino acid
• Present in some proteins
• Sulphur in cysteine is replaced by selenium

• Pyrrolysine – is the 22nd aminoacid – found in

methyltransferase enzyme of some bacteria
 DERIVED AMINOACIDS

• Amino acids not found in proteins – (non-protein amino acids)

• L-ornithine, L-citrulline, homocysteine, gamma amino butyric
acid

• Present in proteins - after post-translational modification

• hydroxyproline, hydroxy lysine, gamma carboxy glutamate
 DERIVED AMINO ACIDS
• Non alpha amino acids – GABA – Gamma amino butyric acid,
Beta alanine

• D aminoacids –
• D serine in fore brain and D – aspartate - Brain – exact function is
not know
• Cell wall of bacteria – resistant to enzymes peptidase
• Antibiotics – Valinomycinm, actinomycin – D, gramicidin - A
NOMENCLATURE
CLASSIFICATION OF
AMINOACIDS
 Classification of Amino acids

• Based on polarity and charge on R group

• Based on metabolic fate – glucogenic, ketogenic, both
glucogenic and ketogenic
• BASED ON NUTRITIONAL SIGNIFICANCE – ESSENTIAL AND NON
ESSENTIAL
 Classification of Amino acids

• Based on side chains – R GROUP – simple, hydroxy, branched

chain, acidic, basic, amidic, sulfur containing

• Based on charge – neutral, acidic, basic

• Based on chemical nature – Aliphatic, Aromatic, Imino

 Classification of Amino acids

Based on polarity and charge on R group

• Non polar side chain
• Uncharged polar R group
• Charged polar R group
NONPOLAR SIDE CHAINS
NONPOLAR SIDE CHAINS
NONPOLAR SIDE CHAINS
UNCHARGED POLAR SIDE CHAINS
Charged polar side chain - ACIDIC SIDE CHAINS
Charged polar side chain - BASIC SIDE CHAINS
Selenocysteine

Se
Pyrrolysine
 CLASSIFICATION OF AMINO ACIDS
BASED ON NUTRITIONAL SIGNIFICANCE

• Essential - Not synthesized : hence needs to be supplied in the diet

• Semi-essential – required only in certain conditions

• Non-essential – Can be synthesized them in vivo; hence need not be

supplied in the diet
 CLASSIFICATION OF AMINO ACIDS
BASED ON NUTRITIONAL SIGNIFICANCE
Methionine
Arginine
Threonine
Tryptophan
Valine MATT VIL PHLy
Isoleucine
Leucine
Phenylalanine
Histidine
Lysine
 CLASSIFICATION OF AMINO ACIDS
BASED ON NUTRITIONAL SIGNIFICANCE

• Semi-essential (Arginine & Histidine)

• Required only in growing children but not in adults

• ALL OTHER AMINOACIDS ARE NON ESSENTIAL

CLASSIFICATION OF AMINO ACIDS
BASED ON METABOLIC FATE
CLASSIFICATION BASED ON STRUCTURE THE SIDE
CHAIN
Aliphatic Imino acid
side chain proline
Glycine, alanine

Side chains with Containing

OH group Amino acids aromatic ring
Serine, Threonine Phenyl alanine,
Histidine, Tyrosine

Side chains Side chains

with sulfur Side chains with basic
atoms With acidic Groups
Cysteine, Methionine group Arginine, Lysine
Aspartic acid,
glutamic acid
 PROPERTIES OF AMINO ACIDS

• Ionic forms of amino acid & isoelectric pH

• Isomerism in amino acids

• Absorption of ultraviolet light by aromatic

amino acids

• Reactions of amino acids

 IONIC FORMS OF AMINO ACID & ISOELECTRIC PH

• Amino acids can exist as ampholytes or

zwitterions in solution, depending on the pH.
• Amino acids contain two weekly ionizable
weak acid groups. COOH and NH3+
• The net charge carried by an amino acid
depends on the pH of the medium.
 ISOELECTRIC PH

• In acidic solutions, the amino acids are cationic

• In alkaline solutions, the amino acids are anionic
• At Isoelectric pH, amino acids carry no net charge
 ISOELECTRIC PH

The pH at which 50% of the molecules are in zwitterion and

50% are in cationic form is known as pK1

The pH at which 50% of the molecules are in zwitterion and

50% are in anionic form is known as pK2

pK1 + pK2
Isoelectric pH (pI) =
𝟐
IONIC FORMS OF AMINO ACID & ISOELECTRIC PH

Iso-electric point or iso-electric pH (pI)

The pH at which an amino acid carries

no net charge in a solution.

 ISOELECTRIC PH

• The buffering action is maximum at pK1 or pK2 and

minimum at pI
• Normal pH of blood is 7.4 (7.35 – 7.45)
• Only histidine which has an imidazole group has a pK
value of 6.1 which is close to physiologic pH
• For this reason, proteins present in the blood and
hemoglobin can act as buffers
 ISOMERISM OF AMINO ACIDS

• Stereochemistry – spatial arrangement of

atoms in a molecule
• Amino acids can exist as L or D isomers;
both the forms are mirror images of each
other
 ISOMERISM OF

AMINO ACIDS

• They arise because of the presence of asymmetric carbon atom

• These are called enantiomers

• All amino acids found in proteins are L-α-amino acids with few exceptions
• Some D isomers exist - some microorganisms, constituents in certain
antibiotics
• Glycine shows no isomerism as it contains no asymmetric carbon
Glycine shows no
isomerism

Simple

GLYCINE
Asymmetric
carbon atom
ABSENT
 ABSORPTION OF ULTRAVIOLET LIGHT BY
AROMATIC AMINO ACIDS

• Aromatic amino acids namely phenylalanine, tyrosine and

tryptophan can absorb ultraviolet light at 280 nm
• Tryptophan is responsible for most of the absorbance due to
proteins
• This property is useful in the quantitation of proteins by
spectrophotometer
 INDIVIDUAL REACTIONS OF AMINO ACIDS

• Reactions due to carboxyl group

• Reactions due to amino group

• Reactions due to side chains

• Peptide bond formation

 REACTIONS DUE TO CARBOXYL GROUP

Decarboxylation:
Ex. Histidine is converted to histamine

The amino acid on decarboxylation is converted to the

corresponding amine
 REACTIONS DUE TO CARBOXYL GROUP

Amide formation:
Ex. Conversion of glutamic acid
to glutamine

The extra carboxylic acid group

other than that bound to the α-
carbon will combine with
ammonia and forms the
corresponding amide Source of nitrogen for nucleic acid synthesis
 REACTIONS DUE TO AMINO GROUP

Transamination:
• Transfer of amino group from an amino acid to a keto acid
Results in inter-conversion of amino acids
• Non-essential amino acids are synthesized by this type of
reaction
 REACTIONS DUE TO AMINO GROUP

Oxidative Deamination reactions :

• Glutamic acid commonly undergoes this reaction
• Results in formation of alpha ketoglutarate with release of
free ammonia
 REACTIONS DUE TO AMINO GROUP
Formation of Carbamino compounds
• Carbondioxide is added to alpha amino group of aminoacid
• Alkaline pH
• Mechanism for transport of carbondioxide from tissue to
lungs – non enzymatic – 6% CO2 is transported
REACTIONS DUE TO AMINO GROUP
• Ester formation: Amino acids containing – OH group can react
with phosphoric acid
• seen in phosphoproteins
REACTIONS DUE TO AMINO GROUP

• Reaction of amide group: Glutamine and asparagine can

react with carbohydrates to form glycoproteins
 REACTIONS DUE TO–SH GROUP

• Two cysteine residues can

react together and form a
disulphide bond
• Two polypeptides can be
linked together by such bonds
 REACTIONS WITH NINHYDRIN

• All amino acids except proline when heated with ninhydrin

can form purple coloured complexes called Ruhemann’s
purple
• Proline produces yellow colour complex with ninhydrin
• This reaction is used for the detection of amino acids in
chromatography
PEPTIDE BOND BETWEEN
TWO AMINO ACIDS
BIOMEDICAL IMPORTANCE OF AMINO ACIDS
 BIOMEDICAL IMPORTANCE OF AMINO ACIDS

• Synthesis of body proteins

• Precursors for the synthesis of biologically important
compounds
• Catabolized to yield energy – 5-10% of the total energy
requirement of the body
• Inborn errors of amino acid metabolism can result from
deficiency in enzymes involved in it
• Classification of amino acids – essential and non essential

• Amino acids with specific R groups

• Important derivatives of each amino acids

• Isoelectric pH

• Why proteins like hemoglobin has highest buffering capacity

• Reactions of amino acids

PEPTIDE BOND BETWEEN
TWO AMINO ACIDS
 Peptide bond

PEPTIDE
BONDS LINK
AMINO Formed by condensation of the
ACIDS IN a-carboxyl of one amino acid
with the
PROTEINS
a-amino of another amino acid
(loss of H2O molecule)
 PROPERTIES OF A
PEPTIDE BOND

• Cα—C—N—Cα
• Of the three covalent bonds, the peptide bond C—N
exhibits a partial double bond character
• limited rotation of the peptide bond and they are said to be
rigid and coplanar
 PROPERTIES OF A
PEPTIDE BOND

• Rotation is permitted about Cα—C and N—Cα bonds

• In a protein molecule, the rigid planes of peptide bond
form a backbone while the other adjacent R groups can
assume different conformations