PROTEINS AMINO ACID

PART 1 >building blocks of proteins

A highly complex substance that is present in >an organic compound that contains both an
all living organisms. amino (-NH2) group and a carboxyl (-COOH)
They account for about 15% of a cell’s overall group
mass. Amino Group
Carboxyl Group
NH2 COOH
History

Gerardus Johannes Mulder

– Dutch chemist found that egg and milk can
be coagulated on heating and were
nitrogenous substances

JJ Berzelius – suggested to Mulder that

these substances should be called proteins

from GreeK word “proteios” which means

“primary”, or “holding first place” or
“preeminent”

Proteins are fundamental structural >alpha amino acids are always found in
components of the body; nitrogeneous proteins
macromolecules composed of many amino
acids >alpha amino acid is an amino acid in which
the amino group and the carboxyl group are
PROTEIN SUBUNITS attached to the alpha carbon

The proteins in the body are made up of >All amino acids isolated from proteins, with
some combination of 20 different subunits the exception of proline, have the same
called amino acids. general structure

>side chains vary in size, shape, charge,

acidity, functional group present, hydrogen-
bonding ability, and chemical reactivity

What are the functional group present in the

molecules of amino acid?

Proline Amino Acid

General Formula of Amino Acids
>The carboxyl group attach to alpha carbon with one another and remain isolated from
can either be unprotonated (COO-) which has water
-1 net charge or neutral (COOH) which has 0
charge.

>The amino group attach to attach to alpha Non polar Amino Acids
carbon can either be protonated (NH3+)
which has +1 net charge or neutral (NH2)
which has 0 charge.

>Theres no such cases that carboxyl will

have +1 charge nor Amino group charge
becomes -1.

Polar Group
-They are attracted to polar water molecules,
they are said to be “hydrophilic Amino acids”
–water loving.
The hydrophilic side chains are often found
on the surface of proteins.
20 Important amino acid
3 Classes of Polar Amino Group

Polar, neutral amino acids

They have R groups that have a high affinity
for water but that are not ionic pH7.
Most of these amino acids associate with one
another by hydrogen bonding: but cystein
molecules form disulfide bonds with one
another.

Zwitterion
>Any neutral molecule with equal number of
positive and negative charges.
>Dipolar ions
>Amino acids in the presence of water
becomes Zwitter ions

Classes of Amino Acids

>Non Polar Groups

-These group of amino acid prefer to contact
with one another rather than water and are
said to be “hydrophobic amino acids”- water
fearing. Negatively charge Amino Acids
-They are generally found buried in the >Have ionized carboxyl groups in their side
interior of proteins, where they can associate chains. At pH7 these amino acids have a net
charge of -1.
>They are acidic amino acids because >Glycine and cysteine help in synthesis of
ionization of the carboxylic acid releases a bile salts
proton.
>Glutamate, cysteine, and glycine synthesize
glutathione

>Histidine changes to histamine

>In addition to tripeptide formation, glycine is

used for the synthesis of heme

>Pyrimidines and purines use several amino

acid for their synthesis such as aspartate and
glutamine for pyrimidines and glycine,
aspartic acid, glutamine and serine for purine
synthesis.
Positively charged Amino Acids
>Some amino acids such as glycine and
>At pH 7 these amino acids have a net cysteine, are used as detoxicants of specific
positive charge because their side chains substances.
contain positive groups.
>These amino groups are basic because the >Methionine acts as “active” methionine (S-
side chain reacts with water, picking up a adenosylmethionine) transfers methyl group
proton and releasing a hydroxide anion to various substances by transmethylation.

>Cystine and methionine are sources of

sulfur.

Special Amino Acids Present in

Some Proteins
>Hydroxyproline and hydroxylysine – Found
in collagen of connective tissue

>N-Methyllysine –Found in myosin, a muscle

protein functioning in contraction.

>Gamma-carboxyglutamic acid- Found in the

blood-clotting protein prothrombin.
Functions of Amino Acids
>Desmosine- A derivative of lysine, found
>Monomeric constituents of proteins and
only in the fibrous protein elastin
peptides

>Some amino acids are converted to ESSENTIALS OF AMINO ACIDS

carbohydrates and are called glucogenic
amino acids >Essential Amino Acids: not synthesized by
the body and must be taken in the diet (valine,
>Specific amino acids give rise to specialized leucine, isoleucine, phenylalanine, threonine,
products e.g. tyrosine forms hormones such tryptophan, histidine, arginine methionine and
as thyroid hormones (T3, T4), epinephrine lysine)
and norepinephrine and a pigment called
melanin >Non-essential amino acids: These can be
synthesized by the body and may not be the
>Tryptophan can synthesize a vitamin called requisite components of the diet.
niacin
>Semi-essential amino acids: These are
>Glycine, arginine, and methionine growth promoting factors since they are not
synthesize creatinine synthesized insufficient quantity during
growth. They include arginine and histidine
(for infants only and not for adult). They
become essential in growing children, -Amino group exhibits a wide range of
pregnancy, and lactating women. solubilities. In general, amino acids are
minimally soluble at their isoelectric points.
>Conditional amino acids: are usually not
essential, except in times of illness and stress. -Those amino acids with longer alipathic side
chains are less soluble than those with
shorter chain 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(Gly, Ala, Val, Ser), tasteless
(Leu), or bitter (Iso).

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 W, Y
and F absorb ultraviolet light. Most of the UV
absorption of proteins is due to their W
content

6. Optical Properties of Amino Acid

- The alpha carbon of all amino acids except
glycine are asymmetric, so they show optical
activity. The rotation of the amino acid 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 acid or bases.
Amino acid having single amino and carboxyl
group crystallize from neutral aqueous
solutions in a fully ionized species called
dipolar ion or zwitterion.

Online Discussion

Vitamin B3 is also known as Niacin. It can be

synthesize in our body from amino acid
Tryptophan. Why there are such instances
that a physician will prescribe Vit B3 to a
patient given that our body could synthesize
Niacin?

Amphoteric Nature and Isoelectric pH

PROPERTIES OF AMINO ACIDS >NH2 and COOH groups are ionizable,

charged polar side chain of amino acids.
1.Solubility
>Depending on the pH of the solution, these which the amino group attach in alpha carbon
groups act as proton donors (acids) or proton is on the left side.
acceptors (bases). This property is called
amphoteric and therefor amino acids are
called ampholytes.

>At a specific pH, amino acid carries both the

charges in equal number and exists as
dipolar ion or zwitterion. At this point, the net
charge is zero (+ and – charges on the
protein amino acid molecule equalises)
Chemical Reactions of Amino Acids
>pI or Isoelectric pH – the pH at which it 3 important components which give the different
occurs without any charge on it . On the amino acids their characteristic reactivities:
acidic side of its pI, amino acid exist as a >The amino or NH2 group
cation by accepting a proton and on alkaline >The carboxyl or COOH group
side as anion by donating a proton. >The various R group

Important Chemical Reaction Use in

Amino Acid

A. Ninhydrin Reaction
-When an alpha amino acid is boiled with
ninhydrin, a powerful oxidizing agent forming
a purple product (ruhemann’s purple)
-Proline and hydroxyproline will give a yellow
color.
-Use as quantitative and qualitative test for
protein

B. Reaction with Sanger’s reagent

-Sanger’s reagent is 1-fluoro-2,4-
dinitrobenzene (FDNM).
-It is useful in the identification of individual
amino acids.
-Gives colored bright yellow
-Important in determining the amino acid
sequence of peptides.

The Peptide Bond

-Proteins are linear polymers of L-α-amino

acids in which the carboxyl group of one
amino acid is linked to the amino group of
another amino acid.

-The Peptide bond is an amide bond formed

between the –COO- group of one amino acid
and α-N+H3 group of another amino acids.

Stereoisomers of Amino Acids

The configuration of alpha-amino acids

isolated from proteins is in L configuration, in The molecules formed by condensing 2
amino acids is called dipeptide. The amino
acid free α-N+H3 group is know as N-terminal exoskeletal structures which makes a
amino acid (amino terminal), and the amino supportive tissues.
acid with –COO- group is carboxyl, or C- Ex: Keratin and Collagen. Gelatin is a
terminal amino acid. degenerated
albuminoid
Peptides with Biologic Activity
F. Histones – high content of amino acids,
>Insulin- a hormone secreted by B cells of they appear to occur in the combination with
pancreas which stimulates the capacity of the nucleic acid in the nuclei of the somatic
cells to use glucose as a metabolic fuel. cells of organisms. Ex: Histones and globin

>Oxytocin- A hormone with 9 amino acid G. Protamines- They are the simplest of the
residue secreted by the posterior pituitary proteins and may be regarded as large
gland which stimulates uterine contractions. polypeptides. They are strongly basic and
yield chiefly basic amino acids upon
>Bradykin- A substance that inhibits hydrolysis, such as arginine. Ex: Salmine of
inflammation of tissues salmon sperm

>Enkephalins- a short peptide formed in the II. Conjugated Protein

central nervous system; it binds to specific
receptors in certain cells of the brain and They are composed of simple proteins
induces analgesia, deadening of pain combined with some non protein substance.
sensations. The non-protein group is referred to as the
prosthetic group.
>Corticotropin – A hormone of the pituitary
gland stimulates the adrenal cortex. A. Nucleoproteins – The prosthetic group is a
nucleic acid. It is the protein of nuclei and
apparently are the chief constituent of
CLASSIFICATION OF PROTEIN
chromatin. Ex. Nucleohistone
Based on the composition, physical and
B. Glycoprotein and Mucoproteins- These are
chemical properties of the proteins:
compounds with carbohydrate prosthetic
group (Mucopolysaccharides). Glycoprotein
-Simple Protein
contain less 4% of carbohydrates while
-Conjugated Protein
Mucoproteins contains more than 4%.
-Derived Protein
C. Phosphoteins – The prosthetic group is
I. Simple Protein
phosphoric acid. Ex: Casein
-Protein which upon hydrolysis yield only
D. Chromoproteins – composed of simple
amino acids or their derivatives.
united with colored prosthetic group which is
believed to be pigment. Ex: Heme of
A. Albumin – soluble in water, coagulated by
hemoglobin
heat; deficient in glycine. Ex: lactoalbumin,
ovalbumin.
E. Lipoproteins- simple conjugated to lipids
such as phospholipids and cholesterol.
B. Globulins- insoluble in water, coagulated
by heat; contain glycine. Ex. Ovoglubulin,
F. Metalloproteins – proteins plus metallic
serum globulin
elements such as Fe, Cu, Mn.
Ex: Copper of ceruloplasmin
C. Glutelins- soluble in diluted acids and
alkali, insoluble in neutral solvents;
III. Derived Proteins
coagulated by heat. Ex: Glutamine of wheat,
oryzenin of rice
These proteins includes the artificially
synthesized protein-like compounds and
D. Prolamines of gliadins – soluble proteins;
those resulting from decomposition of
plant proteins found principally in seeds.
proteins.
Ex: zein in corn, gliadin of wheat.
A. Primary derived proteins
E. Scleroproteins of Albuminoids – least
B. Secondary derived proteins
soluble of all proteins. Entirely animal
proteins and are the chief constituents of
A. Primary Derived Proteins

Those proteins 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 actions of

acids and alkalies upon proteins.

3. Coagulate proteins- They are insoluble PROTEINS PART2

products formed by the action of heat or
alcohol upon natural protein
Cellular Function of Proteins
B. Secondary derived proteins • Enzymes are biological catalyst –ex:
They are formed in the progressive hydrolytic Pepsin, Trypsin
cleavage of the peptide union of protein • Defense Proteins include antibodies
molecules. (Immunoglobulins) which are specific
protein molecules produced by
1. Proteases – they are hydrolytic products of specialized cells of the immune system
protein which are soluble in water, not in response to foreign antigens.
coagulated by heat.
2. Peptones- a product of further hydrolytic
decompositions. They are simpler structure
than the proteases.
3. Peptides – a compound of 2 or more amino
acids, either synthesized or resulting from the
hydrolysis of proteins

Proteins can also be classified on the

basis of their shape:

1. Globular proteins • Transport Protein carry material from place

-Peptide chain is tightly folded into compact, to another in the body. Ex: transferrin,
spherical or globular shape. Hemoglobin and Myoglobin.
-Usually soluble in aqueous systems and • Regulatory Protein controls many aspects of
diffuse readily. cell function, including metabolism and
-Nearly all enzymes are globular proteins, as reproduction. Ex: Insulin and Glucagon•
are blood transport proteins, antibodies and Structural proteins provide mechanical
nutrient storage proteins support to large animals and provide them
with their outer coverings. Ex: Keratin
• Movement Proteins are necessary for all
forms of movement. Ex. Actin and Myosin,
2. Fibrous proteins Flagella of sperm cell.
-Consist of polypeptide chains arranged in a • Nutrient Protein serves as source of Amino
parallel fashion along a single axis, to yield acids for embroyos or infants. Ex: Albumin
long fibers or sheets. and Casein
-Physically tough and are soluble in water or
dilute salt solutions.
-The basic structural elements in the
connective tissue of higher animals. Ex:
Keratin of hair, skin and nails
Structural Property of a-helix
- It has great mechanical strength and is
applied very efficiently in both the fibrous
protein of skin and those of muscle.
PROTEIN DIGESTION
• Is the degradation of protein by cellular
enzymes in a process called hydrolysis.
• The macromolecules are the proteins or
polypeptides themselves, and the subunits
are the amino acids.

• It takes place in two different phases:

- In the stomach
- In the small intestine.
Both of these phases of digestion are based on
several types of enzymes that are called
Proteinases and Proteases.
What will be the impact of protein
denaturation?
ENZYMES
PART 1
ENZYMES PART 2