CHAPTER 4 Protein and Amino Acid

Chemistry
LEARNING TARGETS:
At the end of the lesson, the students can:
✓ Enumerate the general characteristics of proteins.
✓ Diagram the general structure of amino add.
✓ Describe the physical properties of amino acids.
✓ identify and characterize the different classification of amino acids.

What are PROTEINS?

An extraordinary number of different proteins, each with a different
function, exist in the human body. A typical human cell contains about 9,000
different kinds of proteins, and the human body contains about 100,000 different
proteins. Proteins are important for the synthesis of enzymes, certain hormones,
and some blood component; for the maintenance and repair of existing tissues;
for the synthesis of new tissue, and sometimes for energy.

GENERAL CHARACTERISTICS OF PROTEINS

Proteins are the most abundant substances in nearly all cells next to water. They account for about
15% of cell’s overall mass. All protein contains the elements carbon, hydrogen, oxygen, and nitrogen. The
presence of nitrogen in proteins set them apart from carbohydrates and lipids, which most often do not
contain nitrogen. Other elements such as sulfur, phosphorus, and iron are essential constituents of
certain specialized proteins.
Casein, the main protein of milk, contains phosphorus, an element which is very important in the
diet of infants and children. Hemoglobin, the oxygen -transporting protein of blood, contains iron.

AMINO ACIDS: THE BUILDING BLOCKS OF PROTEINS

An amino acid is an organic compound that contains both an amino (-NH2)
group and a carboxyl (-COOH) group. The amino acids found in proteins are
always alpha-amino acids. An alpha-amino acid is an amino acid in which the
amino group and the carboxyl group are attached to the alpha carbon atom. As
with carbohydrates, it is traditional to use the D and L nomenclature with amino
acids based on the configuration of glyceraldehyde.
The structure of an alpha amino
acid in its un-ionized form

CHO CO2H

L - glyceraldehyde L - alanine
Naturally occurring amino acids generally have the same configuration as L – glyceraldehyde
configuration at the alpha-carbon.

GENERAL STRUCTURE OF AMINO ACIDS

The general formula for alpha-amino acid is shown below:

R<--- side chain

Amino group NH 2 — C — COOH ca rb ox yl gr ou p

H alpha carbon atom

It is called an alpha-amino add because both amino and carboxyl groups are attached to the alpha carbon
atom. All of the 20 amino adds found in proteins have a common denominator: a carbon and an amino
group bonded to the same carbon atom. The amino acids differ from each other in their side chains, or R groups,
which vary in structure, size, electric charge, and solubility in water.

Examination of the above formula discloses the fact that

the alpha carbon atoms have 4 different groups attached to
it (except for the case where R is H like glycine), so this carbon
is asymmetric, and because of the presence of this asymmetric
carbon atom, amino acids are capable of optical rotation, except
glycine, because the phenomena of optical rotation is due to
asymmetry.

Amino acids are optically active molecules and

asymmetry of their mirror images is not superimposable (except
in the case of glycine where the R-group is hydrogen).

GENERAL CHARACTERISTICS OF AMINO ACIDS

Amino acids are colorless crystalline substances soluble in water and insoluble in organic solvents with a
high melting point.
Various ways of classifying the amino acids on the basis of their R groups have been proposed. The most
meaningful is based on their polarity, i.e., their tendency to interact with water at biological pH (near pH
7.0). There are 5 main families of amino acids based on the polarity of their R-groups or side chains. Amino
acids are classified on the basis of the structure of R.

1. Aliphatic side chains – hydrophobic

ALIPHATIC SIDE CHAINS – HYDROPHOBIC

2. Polar side chains - text classifies as HO-, S-, and amide containing - hydrophilic

POLAR SIDE CHAINS HYDROPHILIC

3. Acidic – hydrophilic

ACIDIC – HYDROPHILIC
 4. Basic – hydrophilic

BASIC – HYDROPHILIC

5. Heterocyclic/Aromatic —hydrophilic or hydrophobic

Heterocyclic/Aromatic

ANOTHER WAYOF CLASSIFYING AMINO ACIDS

A. Neutral amino acids- they are monoamine-monocarboxylic (with one as well as other
substituents distinguish these amino acids from each other).
1. Straight-chain
a. Glycine
b. Alanine
c. Serine
d. Threonine
2. Branched-chain amino acids
a. Valine
b . Leucine
c . Isoleucine
B. Aromatic amino acids- these consists of amino acids with phenyl hydroxyphenyl, or indole
rings substituted on alanine.

1. Phenylalanine - contains the phenyl ring

2. Tyrosin- contains the hydroxyphenyl ring
3. Tryptophan- contains the indole ring

C. Essentials and Non-essentials amino acids

1. Cysteine
2. Homocysteine
3. M e t h i o n i n e

D. Basic amino acid

1. Lysine
2. A r ginin e
3. H is ti dine

E. Acidic amino acids

1. Aspartic acid
2. Glutamic acid

F. Amino acids - a molecule that contains both imine (>C=NH) and carboxyl ( -C(=0)-0H)
functional groups.
1. Proline
2. Hydroxy proline

PHYSICAL PROPERTIES OF AMINO ACIDS

1. Solubility - amino acids exhibit a wide range of solubilities. In general, amino acids are
minimally soluble at their isoelectric points. Those amino acids with longer aliphatic side chains
are less soluble (e.g., leu, lie, Val) than those with shorter chains (e.g., Gly, Ala.) polar groups
such as carboxyl and hydroxyl, tend increase solubility.
2. Melting point - amino acids possess' high melting points, usually above 200°C.
3. Tastes of amino acids - amino acids are usually sweet, tasteless, or bitter. Glycine, alanine,
valine, and serine are sweet. Leucine is tasteless; isoleucine is bitter.
4. Appearance - the amino acids are white crystalline substance; the crystal from being
characteristic for each one.
5. Ultraviolet absorption spectrum of aromatic amino acids - the aromatic amino acids
tryptophan, tyrosine, and phenylalanine absorb ultraviolet light. Most of the UV absorption of
proteins is due to their tryptophan content.
6. Optical properties of amino acids - the alpha carbon atoms of all the amino acids except glycine
are asymmetric, so they show optical activity. The rotations of the amino acids vary according
to the pH of the solution, which determines the ionic state of the amino acid.
7. Acid-base properties of amino acids- amino acids in aqueous solution are ionized and can
act as acids or bases. Those amino acids having a single amino group and a single carboxyl group
crystallize from neutral aqueous solutions in a fully ionized species called dipolar ion or
zwitterion. These dipolar and negative charges. Below is the formula of zwitterion :
 NH3+

R C COO

H
Zwitterion

Since the amino acids have both amino and carboxyl groups; they are amphoteric which me ans
that they can react act either as an acid (proton donor) or a base (proton acceptor). Substances
with amphoteric properties are called ampholytes. Amino acids may be e ither positively or
negatively charged depending on the pH or hydrogen ion concentration of the environment.

Isoelectric pH (pl or 1pH)

It is that characteristic pH which the amino acids have no net charge and is not attached to
either electrode of the electrophoretic system. If the dipolar or zwitterions from an amino acid
is titrated with an acid such as HCI, the following reaction takes place.

The addition of an acid depresses the ionization of the carboxyl group, and the dipolar ion
accepts a proton, thus placing a net positive charge on the amino acid molecule.
 CHEMICAL REACTIONS OF AMINO ACIDS

The chemical reactions of the amino acids are relatively numerous because the different
reactive groups that are present in the same molecule. The 3 important components which
give the different amino acids their characteristic reactivities are the following:
1. The amino or NH2 group
2. The carboxyl or COOH group
3. The various R groups which identify them from one another

Although we shall not examine all such organic reactions of amino acids, here are two
important reactions that are widely used for the detection, measurement, and identification
of amino acids:

A. Ninhydrin reaction
If a solution of an alpha amino acid is boiled with ninhydrin (triketohydrindene hydrate) a
powerful oxidizing agent, carbon dioxide+ dioxide+ ammonia+ aldehyde is formed together
with reduced ninhydrin. The reduced ninhydrin then reacts with the liberated ammonia, forming
a purple product color (ruhemann's purple). Proline and hydroxyproline will give a yellow color.
The purple to blue color forms the basis of a quantitative test for &-amino acids. The intensity
of color produced can be used to measure amino acid concentration colorimetrically. The
visualization of amino acids on paper chromatography and the quantitative determination of
amino acids after ion-exchange chromatography usually involves the ninhydrin reaction.

B. Reaction with Sanger's reagent

Sanger's reagent is 1-fluoro-2, 4-dinitrobenzene (FDNB). In mildly alkaline solution FDNB
reacts with & amino acids to yields 2, 4-dinitrophenyl derivatives, useful in the identification
of individual amino acids. Most of the DNP-amino acids are colored bright yellow. This reaction
is important in determining the amino acids sequence of peptides.

SPECIAL AMINO ACIDS PRESENT IN SOME PROTEINS

1. Hydroxyproline and hydroxylysine - found in the collagen of connective tissue
2. N-Methyllysine- found in myosin, a muscle protein functioning in contraction
3. Gamma-carboxyglutamic acid- found in the blood-clotting protein prothrombin.
4. Desmosine - a derivative of lysine, found only in the fibrous protein elastin

PEPTIDES
Peptides are chains of amino acids. Two amino acid molecules can be covalently joined
through a peptide bond, to yield a dipeptide. Such linkage is formed by removal of the elements
of water from the carboxyl group of one amino acid and the alpha -amino group of the other
by the action of strong condensing agents.
 Three amino acids can be joined by two peptide bonds in a similar manner to form a
tripeptide; similarity, we have tetrapeptides and pentapeptides. When there are more than 10
amino acids joined in this fashion, the structure is called polypeptide.
The amino acid units in a peptide are usually called residues. The amino acids residue at
the end of the peptide having a free alpha amino group is the amino-terminal (also called
N-terminal) residue; at the opposite end, the residue which has a f ree carboxyl group is the
carboxyl-terminal (also C-terminal) residue. Peptides are named from the sequence of their
constituent amino acids beginning from the N-terminal residue as amino acid number 1.

Ser-gly-tyr-ala-leu
(seryglycity rosin alanyl leucine)
The above structure is a pentapeptide. The N -terminal amino acid residue is serine; the C-
terminal residue is leucine; the 3rd amino acid residue is tyrosine.

Some Peptides with Biological Activity

1. Insulin- a hormone secreted by the B cells of the pancreas stimulates the capacity
of cells to use glucose as a metabolic fuel.
2. Oxytocin- a hormone with 9 amino acid residues secreted by the posterior pituitary
gland which stimulates uterine contractions.
3. Brakdykin- a substance that inhibits inflammation of tissues.
4. Enkephalins- a short peptide formed in the central nervous system; it binds to
specific receptor in certain cells of the brain and induces analgesia, deadening of pain
sensations.
5. Corticotrophin- a hormone of the Pituitary gland that stimulates the adrenal cortex.

Biological Functions of Proteins

1. Enkephalins catalysis - all known enzymes are proteins.

2. Transport proteins - hemoglobin of red blood cells bind oxygen as the blood
Passes through the lungs and carries it to the peripheral tissue.
3. Nutrient proteins - examples are ovalbumin, the major protein of egg white
and casein major protein of milk.
4. Storage proteins - ferritin of animal tissues stories iron.
5. Contractile proteins - actin and myosin are filamentous proteins function i n
the contractile system of skeletal muscle.
6. Structural proteins - examples are:
a. Collagen- the major component of tendons and cartilage; this
fibrous protein has very tensile strength.
b. Elastin- found in ligaments in a structural protein capable of
stretching in two dimensions.
c. Keratin- a tough, insoluble protein found in hair, fingernails, and
features.
d. Fibrin- the major component of silk fibers and spider webs.
 7. Defense proteins - examples are:
a. Immunoglobulins or antibodies - are specialized proteins by
lymphocytes which can recognize and precipitate or neutralize invading
bacteria, viruses, and other pathogenic, microorganisms.
b. Prothrombin and fibrinogen - are blood-clotting proteins that
prevent loss of blood when the vascular is injured.
8. Regulatory proteins - examples are polypeptides or peptide hormones that
help regulate cellular or physiological activity.

From the foregoing items, it is clear that proteins are among the most important substances
which make up the human body, carrying out the regulation of almost every aspect of biological
activity.

Classification of Proteins

This classification is based on the composition, physical and chemical p roperties of the
proteins:
I. Simple proteins - defined as those proteins which upon hydrolysis yield only amino
acids or their derivatives.
A. Albumin - soluble in water, coagulated by heat; deficient in glycine
Examples: lactalbumin from milk, ovalbumin from the egg white.
B. Globulins- insoluble in water, coagulated by heat; contain glycine
Examples: ovoglobulin of egg yolk, serum globulin of blood.
C. Glutelins soluble in dilute acids and alkali, insoluble in neutral solvents;
coagulated by heat
Examples: glutamine of wheat, oryzenin of rice.
D. Prolamines of gliadins - they are soluble proteins; plant proteins found
principally in seeds.
Examples: zein of corn, gliadin of wheat
E. Scleroproteins of Albumniods - the least soluble of all the proteins;
insoluble in water' salt solutions, dilute acids and alkalies and alcohol. They
are entirely animal proteins and the chief constituents of exoskeletal structures
such as hair, horn, hoofs and nails, and of th e organic materials of cartilage
and bones. They are the protein of supportive tissues. The two principal
classes are collagens and keratins. Gelatin is a degenerated albuminoid.
F. Histones - characterized by a high content of basic amino acids, they appear
to occur in combination with the nucleic acid in the nuclei of the somatic cells
of many organisms,
Examples: histories of nucleoproteins, globin of hemoglobin.
G. Protamines - they are the simplest of the proteins and may be regarded as
large polypeptides. They are strongly basic and yield chiefly basic amino acids
upon hydrolysis, particularly arginine.
H. Example: salmine of salmon sperm.
II. Conjugated proteins- they are composed of simple proteins combined with some
non-protein substance. The non-protein group is referred to as the prosthetic
group.
A. Nucleoproteins - the prosthetic group is a nucleic acid; they are the
proteins of cell nuclei and apparently are the chief constituent of chromatin
Example: nucleohistone
B. Glycoproteins and mucoproteins - these are compounds with
carbohydrate prosthetic group (mucopolysaccharides). The distinction
between glycoproteins and mucoproteins is based on the amount of
carbohydrates glycoproteins contain less 4% of carbohydrates in the molecule
and mucoproteins contain more than 4%.
C. Phosphoteins - the prosthetic group is phosphoric acid.
Example: casein of milk
D. Chromoproteins - composed of simple united with a colored prosthetic
group, which is believed to be a pigment.
Example: heme of hemoglobin
E. Lipoproteins - simple conjugated to lipids such as phospholipids and
cholesterol.
F. Metalloproteins - protein plus metallic elements such as Fe, Cu, Mn
Example: copper of ceruloplasmin.
Ill. Derived proteins- these proteins include those substances formed from simple
and conjugated proteins. This category includes the artificially synthesized
protein-like compounds and those resulting from the decomposition of
proteins.
a. Primary derived proteins - those protein derivatives are formed by a
process which causes only slight changes in the protein molecule and its
properties. There is no hydrolytic cleavage of peptide bonds. They are
synonymous with denatured proteins.
1. Proteins - they are insoluble products formed by the incipient
action of water, very dilute acids and enzymes.
2. Metaproteins - formed by further action of acids and alkalies
upon proteins.
3. Coagulate proteins- they are insoluble products formed by the
action of heat or alcohol upon natural proteins.
b. Secondarily derived proteins - they are formed in the progressive
hydrolytic cleavage of the peptide union of proteins molecules.
1. Proteases - they are hydrolytic products of protein which are
soluble in water, not coagulated by heat.
2. Peptones - a product of further hydrolytic decompositions. They
are of simpler structure than the proteases.
3. Peptides - a compound of 2 or more amino acids, either
synthesized or resulting from the hydrolysis of proteins.
Protein can also be classified on the basis of their shape:
1. Lobular protein - is the kind of proteins wherein the peptide chains is tightly folded into
compact spherical or globular shape. They are usually soluble in aqueous systems and
diffuse readily; most have a mobile or dynamic function. Nearly all enzymes are globular
proteins, as are blood transport proteins, antibodies and nutrient storage proteins.
2. Fibrous protein – consist of polypeptide arranged in a parallel fashion along a single axis
to yield long fibers or sheets. They are physically tough and are soluble in water or dilute
salt solution. They are basic structure elements in the connectives tissue of higher animals
Examples: are the collagen tendons of bone matrix, & - keratin of hair skin, nails, and
features and elastin of elastin connective tissues.

Bonds Responsible for Protein Structure

Protein structures are established by 2 classes of strong bonds (peptide and disulfide) and
2 classes of weak bonds (hydrogen and hydrophobic)
1. Peptide bonds – the primary structure of proteins derives ultimately from the linkage
of alphamino acids by peptide bonds.
2. Disulfide bonds – the disulfides bond may interconnect 2 parallel peptide chains
through cysteine residues within each polypeptide. This is relatively stable and is not
really broken under the usual condition or denaturation.
3. Hydrogen bonds - the hydrogen bond results from the sharing of hydrogen atoms
between the nitrogen and the carbonyl oxygen or different peptide bonds. These may be
contributed by amino acid residues in the name or different polypeptide chains.
4. Hydrophobic bonds - the non-polar side chains of neutral amino acids tend to
nonstoichiometric hence no true bond may be said to exist so that it is better called
hydrophobic interaction.
5. Electrostatic or ionic bonds - these are salt bonds formed between oppositely charged
groups in the side chains of amino acids.
Levels of Structural Organizations of Proteins

A. Primary structure of proteins

This is concerned with the quantitative amino acid composition (i.e., the number of amino
acid residue) of the protein and the sequence of the constituents in the peptide chain.

Secondary structure
Chain and this gives to the following or twisting of the
primary structure.
 Alpha-helix

Beta-sheets
The Alpha-helix, the Beta - pleated sheets, and collagen helixes are examples of
secondary structure.

B. The tertiary structure of proteins

It so called the 3-dimensional or conformational

structure of proteins. This structure results when
attractive forces between amino acid residues cause a
linking or winding attractive of the secondary
structure. This structure refers to the manner in which
the polypeptide chain is bent or folded to for m the
compact, tightly folded structure of globular proteins.
It is maintained by an interaction between the
different R groups of the amino acids com posing the
peptide chain.

Tertian/ Structure
 C. Quaternary structure of proteins

It denotes the manner in which the polypeptide

chains of a protein having more than one peptide
chain are arranged or clustered in space. This level
of structural organization is exhibited only by
proteins that contain more than one polypeptide
chain and this structure refers to the way in which
the chains are packed together or how the chains are
arranged in relation to each other.

Quaternary structure

Oligomeric protein- these are protein with or more polypeptide chain; their component
chains subunits or Promoter. An example of an oligomeric protein is hemoglobin consist
of 4 polypeptide chain.

1. Pure protein are odorless – they turn brown and char upon heating and give an odor
of burning hair.
2. 2. Protein are vicious and their viscosity is dependent upon the kind of protein and
concentration, long, molecules are higher viscosity then these that are major or less
globular.
3. Proteins are very large molecules; hence, they are colloidal in nature. They
polypeptides of different proteins may have been anywhere from about 100 to as
many as 1800 or more amino acid residues.
4. Amphoteric behavior- since proteins contain both acidic and basic amino acids, they
are amphoteric and are capable of donating and accepting. In an acid environment,
containing excess protons the protein molecules have a net positive charge , whereas
in alkaline medium proteins molecules have a net negative charge is zero, the
isoelectric point. A protein is least soluble at its isoelectric pH an d consequently, it is
most easily precipitated.
5. Ion bonding of proteins - since proteins are either positive or negative in charge on
either side of their isoelectric point, they may form salts its various anions and
cations.
6. Solubility - each homogenous protein has a definite and characteristic solubility in a
solution on fixed salt concentration and pH. The solubility of proteins is at a minimum
at the isoelectric point and increase with increasing acidity and alkalinity.
 Denaturation of Proteins

It is defined as a disruption of the secondary, tertiary and quaternary

organization of protein, due to the cleavage of non-covalent bonds. This
disorganization results in alterations of the chemical, physical and biological
characteristics of the protein.

Denaturing agents:

a. Physical agents b. chemical agents

1. Heat 1. Organic solvent
2. Surface action a. acids and alkaline
3. Ultraviolet light b. urea and guanidine
4. High pressure 2. Detergents

Chemical alterations brought about by denaturation

1. Decreased solubility at the protein's isoelectric point.
2. As a result of the unfolding process in denaturation many chemical groups
which were rather inactive awing be shielding of the native state become exposed
and more readily detectable.

The change in a protein that is produced by several agents is known as their

natural state are called native proteins; after the change, they are denatured
proteins.

Physical alterations brought about by denaturation

1. Incr eases in the viscosity of the solution, so the r ate of diff usion of the pr otei n
molecules decrease.
2. Increased levorotation
3. Denatured proteins cannot be crystallized since the formation of a crystal depends upon a high
degree of organization of the molecules.

cal alterations brought about by denaturation

Biological alterations brought about by denaturation
Increased digestibility by proteolytic enzymes
1. Increased digestibility by proteolytic enzymes
2. Enzymatic or hormonal activity is usually destroyed by denaturation.
Enzymatic or hormonal activity is usually destroyed
3. The antigenic or antibody functions of proteins are frequently altered as well.

The antigenic or antibody functions of proteins are