PROTEINS AND

AMINO ACIDS
BY
DR. SEHRISH LODHI
M.B.B.S, M.PHIL (GENETICS AND MOLECULAR BIOLOGY)
DEMONSTRATOR, BIOCHEMISTRY DEPARTMENT
KING EDWARD MEDICAL UNIVERSITY
 COURSE CONTENTS

• PROTEIN CHEMISTRY
• AMINO ACIDS
• STRUCTURE OF PROTEINS
• FIBROUS PROTEINS

• PROTEIN METABOLISM
• DISPOSAL OF NITROGEN
• DEGRADATION AND SYNTHESIS OF AMINO ACID
 AMINO ACIDS

• LEARNING GOALS:

• To know the structure and naming of all 20 protein amino acids

• To know the classification of amino acids on the basis of their side chains.
• To know the acid and basic properties of amino acids
• To know the application of Handerson-Hasselbalch equation
 AMINO ACIDS:
BUILDING BLOCKS OF PROTEIN

• Proteins are linear heteropolymers of -amino acids

• There are about 300 amino acids occur in nature. Only 20

of them occur in proteins.
STRUCTURE OF AMINO ACIDS
Proline is an IMINO ACID
ZWITTER ION:
• At physiological PH (7.4),
COOH group is dissociated
forming a negatively charged
carboxylate ion (COO-) and
amino group is protonated
forming positively charged ion
(NH3+) forming zwitter ion

• It is an isoelectric form, net

charge is zero.
CLASSIFICATION OF AMINO
ACIDS
Classification on the basis of side
chain character
1. Amino acids with nonpolar side chains
2. Amino acids with uncharged polar side chains
3. Amino acids with acidic side chains.
4. Amino acids with basic side chains.
 Amino Acids with
Nonpolar Side Chains
 Amino Acids with
Uncharged Polar Side Chains
• Can form:
• H bond
• Di-sulfide bond (cysteine)
• Bonds with other structures like phosphate
group
• Can attach oligosaccharides
• Histidine is weakly basic, and the free amino acid is largely
uncharged at physiologic pH.
• Histidine is incorporated into a protein, Its R group can be either
positively charged (protonated) or neutral, depending on the Ionic
environment provided by the protein.
• Histidine is the only amino acid with a side chain that can ionize within
the physiologic pH range.
• This is an important property of histidine that contributes to the
buffering role it plays in the functioning of proteins such as
Hemoglobin.
OPTICAL PROPERTIES OF AMINO ACIDS
• The α-carbon of amino acid is attached to four different
chemical groups is a chiral or optically active carbon atom.
• Amino acids exist in two forms, d and l, that are mirror images
of each other.
• Glycine is the exception – OPTICALY INACTIVE
• All amino acids found in proteins are of the L-configuration.
 ACIDIC AND BASIC PROPERTIES
OF AMINO ACIDS
• Amino acids are AMPHOTERIC, that is in aqueous solution
contain both weakly acidic α-carboxyl groups and weakly basic
α-amino groups.

• Each of the acidic and basic amino acids contains an ionizable

group in its side chain.

• Thus, both free and some of the combined amino acids in

peptide linkages can act as Buffers.
• Buffers = weak acid [HA] + conjugate base [A-]
 HENDERSON-HASSELBALCH EQUATION
• For the reaction (HA A- + H+ )
[H+] [A-]
• Ka = ─────
[HA]

• The relation between a weak acid (HA) and its conjugate base(A-) is described by the
HENDERSON-HASSELBALCH EQUATION
[A-]
• pH= pKa + log ───
[HA]

• pKa: is the pH at which half of the protons is removed from the group.
• pKa=log 1/Ka … strong acid  high Ka  low pKa

weak acid  low Ka  high pKa

 BUFFERS
• Maximum buffering capacity of any weak acid is at
pH = pKa ---- this happens when [HA] = [A-]
• When pH < pKa ---- depronated form [HA] predominates
• When pH > pKa ---- pronated form [A-] predominates
TITRATION SOLUTION OF AN AMINO ACID
• Isoelectric point, pI, is the pH at
which amino acid has no net charge
(is in isoelectric form).
• pI is average of pK1 and pK2
• pH above pI -ve charge
• pH bellow pI +ve charge

TITRATION CURVE
OF ALANINE
TITRATION CURVE OF HISTIDINE
 OTHER APPLICATIONS OF THE
HENDERSON-HASSELBALCH EQUATION
 Drug Absorbtion

• Acidic drugs: HA A - + H+
• Basic drugs ; BH+ B + H+
• A drug passes through membranes more
readily if it is uncharged.
• Thus, for a weak acid, such as aspirin, the
uncharged HA can permeate through
membranes, but A– cannot.
• For a weak base, such as morphine, the
uncharged form, B, penetrates through the
cell membrane, but BH+ does not.
• Therefore, the effective concentration of the permeable form of each
drug at its absorption site is determined by the relative concentrations
of the charged (impermeant) and uncharged (permeant) forms.
• The ratio between the two forms is determined by the pH at the site of
absorption, and by the pKa of the ionizable group.
• The Henderson-Hasselbalch equation is useful in determining how
much drug is found on either side of a membrane that separates two
compartments that differ in pH, for example, the stomach (ph 1.0–1.5)
and blood plasma (ph 7.4).
 STRUCTURE AND FUNCTION OF
PROTEINS
• LEARNING GOALS:

• To know the function of proteins.

• To know all the four levels of protein structure.

• To understand protein msfolding

FUNCTION OF PROTEINS
 DIFFERENCE BETWEEN A PEPTIDE AND A
PROTEIN
• The basic distinguishing factors are size and structure.

• Peptides:
• are defined as molecules that consist of between 2 and 50 amino acids,
• peptides tend to be less well defined in structure than proteins
• subdivided into
• Oligopeptides, which have few amino acids (e.g. 2 to 20), and
• Polypeptides, which have many amino acids.

•  Proteins:
• are made up of 50 or more amino acids.
• Proteins are formed from one or more polypeptides joined together.
• can adopt complex conformations known as secondary, tertiary, and
quaternary structures
 STRUCTURE OF PROTEINS-
LEVEL OF ORGANIZATION

PRIMARY Assembly
STRUCTURE

PR OC ESS
SECONDARY Folding

Packing
TERTIARY

Interaction
QUATERNARY
 PRIMARY STRUCTURE OF
PROTEINS
• The sequence of amino acids in a protein is called the primary structure of
the protein.
• In proteins, amino acids are joined covalently by peptide bonds.
• Each component amino acid in a polypeptide is called a “residue”.
• Peptide bonds are resistant to conditions that denature proteins, such as
heating and high concentrations of urea.
• Prolonged exposure to a strong acid or base at elevated temperatures is
required to break these bonds nonenzymically.
• Peptide bonds are amide linkages between the α-carboxyl group of one
amino acid and the α-amino group of another.

• All amino acid sequences are read from the N- to the C-terminal end of the peptide.
 DETERMINATION OF THE AMINO ACID COMPOSITION
OF A POLYPEPTIDE

I. Cation-exchange chromatography
II. Sequencing of the peptide from its N-terminal end
III. Determination of a protein’s primary structure by DNA sequencing

• Enzymes that hydrolyze peptide bonds are termed peptidases

(proteases).
• Exopeptidases cut at the ends of proteins and are divided into
aminopeptidases and carboxypeptidases.
• Endopeptidases cleave within a protein.
 SECONDARY STRUCTURE
OF PROTEINS
• Localized arrangement of adjacent amino acids formed as the
polypeptide chain folds are called secondary structure of protein
 ALPHA HELIX
• Spiral structure
• Can easily be stretched due to
tight coiling.
• Side chain extend outwards
• Stabilized by H bonding b/w
carbonyl oxygen and amide
hydrogen. 14
• Amino acids per turn – 3.6
• Alpha helical segments are found
in many globular proteins like
myoglobins, troponin- c etc.
AMINO ACIDS THAT DISRUPT AN α-HELIX:
• Proline - because its secondary amino group is not geometrically
compatible. Instead, it inserts a kink in the chain
• Charged amino acids – in large numbers, by forming ionic bonds or
by electrostatically repelling each other.
• Amino acids with bulky side chains, such as tryptophan.
• Amino acids that branch at the β-carbon , such as valine or
isoleucine,
 BETA PLEATED SHEET
• Formed when 2 or more polypeptides or
segments of polypeptides line up side by
side.
• Individual polypeptide - β strand, each β
strand is fully extended- inelastic.
• They are stabilized by H bond b/w N-H
and carbonyl groups of adjacent chains.
• All peptide bonds are involved, either
interchain or intrachain
• 2 types
• parallel
• anti -parallel
 Β-BENDS
(REVERSE TURNS, Β-TURNS)
• Permits the change of direction of the peptide
chain to get a folded structure.
• Involve four successive amino acid residues. 1
4
• It gives a protein globularity rather than
linearity.
• H bond and ionic bonds stabilizes the beta
bend structure.
• Proline and glycine are frequently found in
beta turns.
• Beta turns often promote the formation of
antiparallel beta sheets.
• Occur at protein surfaces.
 NON REPETITIVE STRUCTURES

• A significant portion of globular

protein’s structure may be irregular or
unique.
• They include coils and loops.
• Not random, but rather simply have a
less regular structure
• Connect two alpha helix or beta
sheath.
• Present in those area where bend is
required.
 SUPER SECONDARY STRUCTURES
(MOTIFS)

• Present in globular protein.

• Certain groupings of secondary structural elements are called motifs.
 TERTIARY STRUCTURE
• Non-linear
• 3 dimensional
• Refers both to the
• folding of domains
• final arrangement of domains in the
polypeptide.

• The hydrophobic side chains are buried

in the interior, whereas hydrophilic
groups are generally found on the
surface of the molecule.
 DOMAINS
• Polypeptide chains containing more than 200
residues usually fold into two or more globular
clusters known as domains.
• Fundamental functional and 3 dimensional
structural unit of proteins.
• Part of protein that can fold into a stable
structure independently
• The core of a domain is built from combinations
of supersecondary structural elements (motifs).
• Domains often have a specific function such as
the binding of a small molecule.
• Many domains are structurally independent units
that have the characteristics of small globular
proteins.
 INTERACTIONS STABILIZING
TERTIARY STRUCTURE
• The unique three-dimensional
structure of each polypeptide is
determined by its amino acid
sequence. Interactions between the
amino acid side chains guide the
folding of the polypeptide to form a
compact structure.
• Hydrogen bonds
• Ionic bonds
• Disulphide bridges
• Hydrophobic interactions
 QUATERNARY STRUCTURE
OF PROTEINS
• Proteins: a single polypeptide chain -
monomeric proteins.
• Proteins: multiple polypeptide chains -
multimeric proteins.
• The arrangement of these polypeptide subunits
is called the quaternary structure of the protein.
• Held together primarily by noncovalent
interactions.
• Subunits may either function independently or
may work cooperatively.
 PROTEIN FOLDING
• Interactions between the side chains of amino
acids determine how a long polypeptide chain
folds into the intricate three-dimensional shape
of the functional protein.

• Folding is a facilitated process that requires a

specialized group of proteins, “molecular
chaperones,” also known as “heat shock
proteins” (Hsp) and ATP hydrolysis.

• The chaperones, interact with a polypeptide at

various stages during the folding process.
 DENATURATION OF PROTEINS
• Protein denaturation results in the unfolding and disorganization of a protein’s
secondary and tertiary structures without the hydrolysis of peptide bonds.
• Denaturing agents include:
• Heat,
• Organic solvents,
• Strong acids or bases,
• Detergents and
• Ions of heavy metals such as lead.

• Denaturation may, under ideal conditions, be reversible. However, most

proteins, once denatured, remain permanently disordered.
• Denatured proteins are often insoluble and precipitate from solution.
 PROTEIN MISFOLDING
• Misfolded proteins are usually tagged and degraded within the cell
• Deposits of misfolded proteins are associated with a number of
diseases:
• A. Amyloid diseases
• B. Prion diseases

• Misfolding of proteins:
• Spontaneously
• Altered protein – mutation
• Abnormal proteolytic cleavage
 AMYLOID DISEASES

• Amyloids: Accumulation of insoluble, long, fibrillar

protein assemblies consisting of β-pleated sheets.
• Spontaneously aggregating proteins.
• Degenerative diseases
• Parkinson
• Huntington
• Alzheimer disease
 A. ALZHEIMER DISEASE

• Amyloid β (Aβ), an extracellular peptide containing 40–42 amino

acid residues – Neurotoxic
Tau (τ) protein: Helps in the
assembly of the microtubular
structure.

• Abnormal form -
hyperphosphorylated and
insoluble - block the
normal action

• A key component of
neurofibrillary tangles
inside neurons.
B. PRION DISEASES
• The Prion Protein (PrP)
-causative agent of
transmissible spongiform
encephalopathies (TSEs),
including
• Creutzfeldt-Jakob disease in
humans,
• Scrapie in sheep, and
• Bovine spongiform
encephalopathy in cattle -
“mad cow” disease

• PrPC is present in normal

mammalian brains on the
surface of neurons and glial
cells.
 CLASSIFICATION OF PROTEINS
BASED ON SHAPE
1. GLOBULAR PROTEINS
• Compact shape like a ball
with irregular surfaces

• Enzymes are globular

2. FIBROUS PROTEINS
• usually span a long distance
in the cell

• 3-D structure is usually long

and rod shaped