I.

AMINO ACIDS, PEPTIDES &

PROTEINS: STRUCTURE, SEQUENCES
&CONFORMATIONS
II. PLASMA PROTEINS, HEMOPROTEINS
&PORPHYRINS
MDB 202.1: MEDICAL BIOCHEMISTRY
BCH 201: GENERAL BIOCHEMISTRY I

DR. M. M. ADEYANJU
DEPT. OF BIOCHEMISTRY, OOU
Learning Objectives
i. Introduction into Proteins
ii. General Structure of Amino Acids
iii. Classification of amino acids
-based on structure
-based on side chain character
-based on metabolism
-based on nutritional requirements
iv. Properties of Amino Acids: Iso-electric point, zwitterions, ampholytes
v. Reactions due to carboxyl group
vi. Reactions due to amino group
vii. Reactions of SH group
viii. Peptide-Bond formation
ix. Sequence of Amino acids
 Introduction
• Proteins are large biological molecules, or macromolecules,
consisting of one or more chains of amino acid residues.

• They are the most widely distributed, the most abundant (45% of
human body) and the most complex bio-molecules with the most
diversified biological functions.

• Proteins differ from one another primarily in their sequence of

amino acids, which is dictated by the nucleotide sequence of
their genes, and which usually results in folding of the protein into
a specific three-dimensional structure that determines its activity.
Components of Proteins
The major elements of proteins are Carbon, Hydrogen, Oxygen, and
Nitrogen;
C (50~55%), H (~7%), O (19~20%), N (13~19%), S (~4%)
Trace elements include Phosphorus (P), Iron (Fe), Copper (Cu), Zinc (Zn),
Iodine (I)
Protein Classification
Over the past years several protein classifications have been developed
that aim to group proteins based on their structural relationships. Some
of these classification schemes explore the concept of structural
neighbourhood (structural continuum), whereas other utilize the notion
of protein evolution and thus provide a discrete rather than continuum
view of protein structure space.
Proteins can be classified based on the composition, structure, shape
and solubility
Classification based on Composition:
Simple proteins: They are composed of only amino acid residues. On
hydrolysis these proteins yield only constituent amino acids. e.g.
albumins, globulins, protamines, scleroproteins, lectins.
Conjugated proteins: They are combined with non-protein moiety. e. g.
Nucleoprotein, Phosphoprotein, Lipoprotein, Metalloprotein,
Glycoproteins etc.
Derived proteins: They are derivatives or degraded products of simple
and conjugated proteins. They may be :
Primary derived protein: Proteans, Metaproteins, Coagulated proteins
Secondary derived proteins: Proteoses or albunoses, peptones,
peptides.
Classification based on Shape
Fibrous proteins: The molecules are elongated or needle shaped. Their
solubility is minimum. They resist digestion. Collagen, elastin and
keratins.
Globular proteins: These proteins are more or else spherical or oval in
shape in nature. They are easily soluble in aqueous solution, e.g.
albumins, globulins and protamines.
 Proteins are vital for the growth and repair, and their functions are endless. They also have
enormous diversity of biological function and are the most important final products of the
information pathways.
A. Classification based on functions
1. Catalytic proteins: Biochemical catalysts (except some catalytic RNA molecules) e.g. enzymes
2. Structural proteins: Coverings and support such as keratin of hair and nail e.g. collagen, the most
abundant protein in mammals and is the main fibrous component of skin, bone, tendon, cartilage
and teeth. Other example is elastin
3. Contractile proteins, e.g. myosin, actin.
4. Transport proteins: Move small molecules in blood e.g. hemoglobin, transferrin, myoglobin
5. Regulatory proteins or hormones As hormones, they control metabolism. e.g. ACTH, insulin,
6. Genetic proteins, e.g. histones
7. Protective proteins, e.g. immunoglobulins, interferons, clotting factors.
8. Storage proteins: Ferritin, Ovalbumine, zein, glutelin etc.

Biologically Important Peptides

When 10 or less number of amino acids are joined together, it is called an oligopeptide. Some of
them are biologically active.
Examples:
i. Thyrotropin releasing hormone (TRH) is a tripeptide with the sequence of Glu-His-Pro; but the
Glu and Pro are modified.
ii. Glutathione is a tripeptide. It is gamma glutamyl cysteinyl glycine. It is involved in erythrocyte
membrane integrity and is important in keeping enzymes in active state.
iii. Oxytocin and vasopressin (ADH) are nonapeptides; with 9 amino acids. They are secreted by
posterior pituitary.
Denaturation of Proteins involves disruption of bonds in the secondary, tertiary and
quaternary structures.
1. Mild heating, treating with urea, salicylate, X-ray, ultraviolet rays, high pressure,
vigorous shaking and similar physicochemical agents produce denaturation.
2. There will be nonspecific alterations in secondary, tertiary and quaternary structures of
protein molecules. Primary structure is not altered during denaturation.
3. In general, during the process the solubility is decreased while precipitability of the
protein is increased. It often causes loss of biological activity.
4. Native proteins are often resistant to proteolytic enzymes, but denatured proteins will
have more exposed sites for enzyme action. Since cooking leads to denaturation of
proteins, cooked foods are more easily digested.
5. Denatured proteins are sometimes re-natured when the physical agent is removed.
Ribonuclease is a good example for such reversible denaturation. Immunoglobulin
chains are dissociated when treated with urea. When the urea is removed by dialysis,
the subunits are reassociated and biological activity of immunoglobulin is regained.
6. But many proteins undergo irreversible denaturation. For example, albumin cannot be
renatured by removing the physical agent
• Amino acids are critical to life. They have
particularly important functions like being the
building blocks of proteins and being the
intermediates in metabolism.
• Generally, amino acids have the following
structural properties:
A carbon (the alpha carbon)
A hydrogen atom (H)
A Carboxyl group (-COOH)
An Amino group (-NH2)
A "variable" group or "R" group called the side
chains and have different chemistries.

• Thus amino acids are molecules containing an

amine group, a carboxylic acid group and a side
chain that varies between different amino acids.
• Amino acids
have the general formula
RCH(NH2)COOH each of which has a unique side
chain.
Classification of Amino Acids.
Amino acids can be classified according to the location of the
amino group.

There are 20 genetically encoded -amino acids found in peptides

and proteins. All proteins are composed of the 20 standard amino
acids.

19 are primary amines, 1 (proline) is a secondary amine

19 are “chiral”, 1 (glycine) is achiral; the natural configuration of
the -carbon is L.
CLASSIFICATION OF AMINO • Glucogenic amino acids: These
ACIDS BASED ON amino acids serve as
METABOLISM precursors gluconeogenesis for
glucose formation. Glycine,
alanine, serine, aspartic acid,
asparagine, glutamic acid,
glutamine, proline, valine,
methionine, cysteine,
histidine, and arginine.
• Ketogenic amino acids: These
amino acids breakdown to
form ketone bodies. Leucine
and Lysine.
• Bothglucogenic and ketogenic
amino acids: These amino
acids breakdown to form
precursors for both ketone
bodies and glucose. Isoleucine,
Phenylalanine, Tryptophan,
and tyrosine.
CLASSIFICATION OF AMINO ACIDS BASED ON NUTRITIONAL
REQUIREMENT
Essential/Indispensable amino acids
The amino acids may further be classified according to their essentiality for
growth. Thus Isoleucine, Leucine, Threonine, Lysine, Methionine,
Phenylalanine, Tryptophan, Valine, Arginine* and histidine* are essential
amino acids.
• Theircarbon skeleton cannot be synthesized by human beings and so
preformed amino acids are to be taken in food for normal growth. They cannot
be synthesized in the body. They have to be supplied in the diet.
Histidine and arginine are semi-indispensable amino acids. Growing children
require them in food.

Non-essential amino acids

The other ten amino acids can be synthesized in the body – hence they are
called Non-essential amino acids.
e. g. glycine, alanine, serine, tyrosine, cysteine, glutamic acid, aspartic acid,
asparagine, glutamine and proline.
CLASSIFICATION BASED ON NUTRITIONAL VALUE
1. Nutritionally Rich Proteins
They are also called as complete proteins or first class proteins. They
contain all the essential amino acids in the required proportion. On
supplying these proteins in the diet, children will grow satisfactorily. A good
example is casein of milk.
2. Incomplete Proteins
They lack one essential amino acid. They cannot promote body growth in
children; but may
be able to sustain the body weight in adults. Proteins from pulses are
deficient in methionine,
while proteins of cereals lack in lysine. If both of them are combined in the
diet, adequate growth
may be obtained.
3. Poor Proteins
They lack in many essential amino acids and a diet based on these proteins
will not even sustain the original body weight. Zein from corn lacks
tryptophan and lysine.
 PROPERTIES OF ➢At iso-electric point the amino acid will
AMINO ACIDS carry no net charge; all the groups are
•Some amino acids (Glycine, alanine,
valine, serine, tryptophan, ionized but the charges will cancel each
histidine and proline) are sweet in taste; other. Therefore at isoelectric point, there
leucine is tasteless;
while isoleucine and arginine are bitter. is no mobility in an electrical field.
•All amino acids have high melting points Solubility and buffering capacity will be
(more than 200°C).
minimum at iso-electric pH.
•All amino acids are soluble in water and
alcohol (polar solvents); but insoluble in ➢Since the amino acids at their isoelectric
non-polar solvents (benzene). points have both negative and positive
➢Amino acids can exist as ampholytes or charges, they are known as zwitterions.
zwitterions (German word "zwitter" =
hybrid) in solution, depending on the pH •Ampholytes are compounds that when
of the medium. dissolved in water (which is itsef an
➢The pH at which the molecule carries amphoteric compound) can act either as acid
no net charge is known as iso-electric or as a base.
point or isoelectric pH (pI).

➢In acidicsolution they are cationic in

form and in alkaline solution they
behave as anions.
Optical Activity ➢D-amino acids are seen in small amounts
➢Amino acids having an in microorganisms and as constituents of
asymmetric carbon atom certain antibiotics such as Gramicidin-S.
exhibit optical activity.
Asymmetry arises when 4
different groups are attached to
the same carbon atom.
➢Glycine is the simplest amino
acid and has no asymmetric
carbon atom and therefore
shows no optical activity. All
others are optically active.
➢The mirror image forms
produced with reference to the
alpha carbon atom, are called D
and L isomers.
➢The L-amino acids occur in
nature and are therefore called
natural amino acids.
PEPTIDE BOND FORMATION
Peptide bonds have a
planar trans configuration and
undergo very little rotation or
twisting around the amide bond that
links the α-amino nitrogen of one
amino acid to the carbonyl carbon of
the next amino acid . It is therefore
noted that the Alpha carboxyl group
of one amino acid reacts with alpha
amino group of another amino acid
to form a peptide bond or CO-NH
bridge.
Proteins are made by polymerization
of amino acids through peptide
bonds.
Digestion:
In one end
and out the
other.
Protein Structure and Function
Primary Structure
The amino acid sequence is known as the primary structure of the protein. The linear
sequence of amino acids are simply held together by peptide bonds. The higher orders
of structure, including any disulfide bonds, are determined in part by the primary
structure.
Stretches of polypeptide chain that form α helices and β sheets constitute the
protein’s secondary structure. It is formed by a regular repeating pattern of hydrogen
bond formation between backbone atoms.
The overall three-dimensional organization of a polypeptide chain is sometimes referred
to as the protein’s tertiary structure, and if a particular protein molecule is formed as
a complex of more than one polypeptide chain, the complete structure is designated
as the quaternary structure. It refers to the interaction of one or more subunits to form
a functional protein, using the same forces that stabilize the tertiary structure.
Protein conformation may be defined as the arrangement in space of its constituent
atoms which determine the overall shape of the molecule. Conformation means the
spatial relationship of every atom in a molecule, e.g. rotation of a portion of the
molecule.
Configuration of a compound denotes the spatial relationship between particular atoms,
e.g. L- and D-amino acids. In protein structure, a domain is a substructure produced by
any part of a polypeptide chain that can fold independently into a compact, stable
structure. They are frequently described as protein regions with assigned experimental
functions, irrespective of their three-dimensional (3D) structures. It is the modular unit
from which many larger proteins are constructed.
PLASMA PROTEINS
• Plasma proteins can be broadly classified into two groups: those, including albumin,
that are synthesized by the liver, and the immunoglobulins, which are produced by
plasma cells of the bone marrow, usually as part of the immune response.
• The clinical laboratory performs a large number of biochemical analyses on body
fluids, which can give answers to specific clinical questions about an individual
patient. Such analyses are usually requested to aid in the diagnosis or treatment of
specific conditions. The majority of specimens received by the laboratory are blood
and urine samples.
• Whereas some measurements are performed on whole blood, serum or plasma are
preferred for most analyses of molecules and ions.
• A number of plasma proteins have the ability to bind certain ligands with a high
affinity and answers
specificity. These proteins can then act as a reservoir for the ligand and
The clinical laboratory performs a large number of biochemical analyses on body fluids, which can give
to specific clinical questions about an individual patient. Such analyses are usually requested to aid
The role of the AND
PLASMA clinical laboratory
SERUM
help controlinits distribution and availability
the diagnosis or treatment of specific conditions.
by
The majority
blood and urine samples.
transporting it to tissues throughout
of specimens received by the laboratory are

the body. Binding to a protein can also render a toxic substance less harmful to the
tissues. Major binding proteins and their ligands are shown below
• Almost all plasma proteins bind ligands, and this is a major function of many
proteins. Albumin can bind many molecules weakly and nonspecifically, but other
proteins bind tightly to specific molecules - for example, transferrin is specific for
ferric iron (Fe3+)
Plasma is the natural environment of blood cells but most chemical measurements
are done in serum
The formed elements of blood are suspended in an aqueous solution that is termed
plasma.
Plasma is the supernatant obtained by centrifuging a blood sample that has been
treated with an anticoagulant to prevent clotting of red cells.
Serum is the supernatant obtained if a blood sample is allowed to clot (usually
requires 30-45 minutes) and then centrifuged.
In laboratory practice, the most common anticoagulants are lithium heparinate and
ethylenediamine tetraacetic acid (EDTA). Heparinate prevents clotting by binding
to thrombin. EDTA and citrate bind Ca++ and Mg++ thus interfering with the action of
calcium/magnesium-dependent enzymes (prothrombin-converting complex,
thromboplastin andenvironment
Plasma is the natural thrombin) involved
of blood cells in measurements
but most chemical the clotting
are donecascade.
in serum When blood is
collected for transfusion, citrate is used as an anticoagulant, as this preserves
procoagulants and its effects are readily reversible by calcium. During clotting,
fibrinogen is converted to fibrin as a result of proteolytic cleavage by thrombin, and
so a major difference between plasma and serum is the absence of fibrinogen in
serum.
Hemoproteins are a group of specialized proteins that
contain heme as a tightly bound prosthetic group. Heme
is the non-protein part mainly present in that mean
which is one of the constituents of Hemoglobin,
Chlorophyll, Myoglobin, and Cytochromes.
Heme is a porphyrin nucleus which has a tetrapyrrole
ring.
In the structure of heme.
It contains 4 pyrrole nucleus is connected by methylene
bridges
It is a planner molecule. The ring contains Vinyl
groups(-CH=CH2), Methyl group (-CH3), Propionic
acid groups (-CH2-CH2-COOH).
PORPHYRINS
Porphyrins are highly coloured cyclic tetrapyrrolic pigments formed by the linkage of
four pyrrole rings through methene (–HC=) bridges (as shown below). The
basic structure of a tetrapyrroleis four pyrrole rings surrounding a central metal atom.
The porphyrins represent the most widespread of all the prosthetic groups found in
nature. They mediate a spectrum of critical functions in a variety of biological systems
ranging from electron transfer, oxygen transport, photosynthetic energy transduction and
conversion of carbon dioxide into fuel.
References
DM Vasudevan, Sreekumari S., and Kannan Vaidyanathan. Textbook of Biochemistryfor Medical
Students 6th Edition Ch 3 -4, pp 19-39