Proteins, Peptides & Amino acids

Proteins
• Proteins are polymers of amino acids produced by living
cells in all forms of life.
• A large number of proteins exist with diverse functions,
sizes, shapes and structures but each is composed of
essential and non-essential amino acids in varying numbers
and sequences.
• The number of distinct proteins within one cell is estimated
at 3,000 - 5,000
• The most abundant organic molecule in cells (50-70% of
cell dry weight)
 Composition Based Classification
1. Simple proteins:
Simple proteins are those which contain only amino acids.
Example: Egg albumin and seed globulin.

2. Conjugate proteins:
Conjugate proteins are those which contain a non-amino
acid component in addition to the amino acids. This non-
amino acid component is called the prosthetic group.
For e.g., glycoprotein (with carbohydrate as the prosthetic
group), phosphoprotein (with phosphate as the
prosthetic group), lipoprotein (with lipid as the prosthetic
group).
 Nutritional Classification
1. Complete Proteins:
These are nutritionally complete.
Sufficient/complete amino acids are present.
Human Proteins are complete
2. Incomplete Proteins:
These are nutritionally incomplete.
May not have sufficient amino acids
Plant proteins are incomplete
Mixture of plant proteins leads to completeness
 Physiological Classification
1. Catalytic (Enzymes)
Ribonuclease,Trypsin, pepsin, Renin
2. Transport Proteins(Carriers)
Haemoglobin, albumin, myoglobin
3. Nutrient or storage proteins
Gliadin, Casein, Ferritin
4. Contractile or Motile Proteins
Actin, Myosin, Tubulin
5. Structural Proteins
Keratin, Collagen, Elastin
6. Defense Proteins
Antibodies, Antifreeze, Fibrinogen
7. Regulatory proteins
Insulin, Growth hormones, Corticotropin
8. Protective proteins
Keratin
 AMINO ACIDS
Proteins are the indispensable agents of biological
function, and amino acids are the building blocks of
proteins. The stunning diversity of the thousands of
proteins found in nature arises from the intrinsic
properties of only 20 commonly occurring amino
acids.
These features include
(1) the capacity to polymerize,
(2) novel acid–base properties,
(3) varied structure and chemical functionality in the
amino acid side chains, and
Amino Acids: Building Blocks of Proteins:
Structure of a Typical Amino Acid
• Central to the structure is the tetrahedral alpha () carbon
(C), which is covalently linked to both the amino group
and the carboxyl group. Also bonded to this -carbon is a
hydrogen and a variable side chain.
• It is the side chain, the so called R group, that gives each
amino acid its identity. In neutral solution (pH 7), the
carboxyl group exists as OCOO and the amino group as
ONH3.
• Amino acids are also chiral molecules. With four different
groups attached to it, the -carbon is said to be
asymmetric.
• The two possible configurations for the -carbon constitute
• Because the resulting amino acid contains one positive and
one negative charge, it is a neutral molecule called a
zwitterion.
• In neutral solution, the COOH is ionized and the NH2 is
protonated
• The resulting structures have “+” and “-” charges (a dipolar
ion, or zwitterion)
• They are like ionic salts in solution
 Amino Acids Can Join via Peptide Bonds
• The crucial feature of amino acids that allows them to polymerize to
form peptides and proteins is the existence of their two identifying
chemical groups: the
• amino (NH3+)and carboxyl (COO-) groups,.
• The amino and carboxyl groups of amino acids can react in a head-to-
tail fashion, eliminating a water molecule and forming a covalent
amide linkage, which, in the case of peptides and proteins, is typically
referred to as a peptide bond.
• The equilibrium for this reaction in aqueous solution favors peptide
bond hydrolysis. For this reason, biological systems as well as peptide
chemists in the laboratory must carry out peptide bond formation in
an indirect manner or with energy input.
• The remarkable properties of proteins all depend in one way or
another on the unique properties and chemical diversity of the 20
common amino acids found in proteins.
 Classification of amino acids
1. Structure Based
1. Aliphatic
2. Aromatic
3. Heterocyclic

2. Composition Based
1. monoaminomonocarboxylic
2. diaminomono carboxylic
3. monoaminodicarboxylic
4. diaminodicarboxylic
 Structure Based Classification of Amino acids
• The most useful of these classifications is based on
the polarity of the side chains. Thus, they are
grouped into the following categories:
• Non Polar R chain (8 aa)
• Polar but Uncharged R Chain(7 aa)
• Polar +Ve Charged R chain(3 aa)
• Polar -Ve Charged R chain(2 aa)
Non Polar R -chain
Polar but Uncharged R Chain
Polar -Ve Charged R chain
Polar +Ve Charged R chain
 Abbreviations and Codes
Alanine A, Ala Leucine L, Leu
Arginine R, Arg Lysine K, Lys
Asparagine N, Asn Methionine M, Met
Aspartic acid D, Asp Phenylalanine F, Phe
Cysteine C, Cys Proline P, Pro
Glutamine Q, Gln Serine S, Ser
Glutamic Acid E, Glu Threonine T, Thr
Glycine G, Gly Tryptophan W, Trp
Histidine H, His Tyrosine Y, Tyr
Isoleucine I, Ile Valine V, Val
Uncommon Amino Acids
Several amino acids occur only rarely in proteins
These include
1.hydroxylysine and
2.hydroxyproline, which are found mainly in the collagen and
gelatin proteins.
3. thyroxine and 3,3,5-triiodothyronine, iodinated amino acids
that are found only in thyroglobulin, a protein produced by the
thyroid gland.
(Thyroxine and 3,3,5-triiodothyronine are produced by
iodination of tyrosine residues in thyroglobulin in the thyroid
gland.
Degradation of thyroglobulin releases these two iodinated
amino acids, which act as hormones to regulate growth and
Certain muscle proteins contain methylated amino acids,
including
4. methylhistidine,
5. -N-methyllysine, and -N,N,
6.N-trimethyllysine
7. -Carboxyglutamic acid is found in several proteins involved in
blood clotting
8. Pyroglutamic acid is found in a unique light-driven proton-
pumping protein called bacteriorhodopsin.
Certain proteins involved in cell growth and regulation are
reversibly phosphorylated on the OOH groups of serine,
threonine, and tyrosine residues.
9. Aminoadipic acid is found in proteins isolated from corn.
10.N-methylarginine
11.N-acetyllysine are found in histone proteins associated with
Amino Acids Not Found in Proteins
Certain amino acids and their derivatives, although not found
in proteins, nonetheless are biochemically important.
1. -Aminobutyric acid, or GABA, is produced by the
decarboxylation of glutamic acid and is a potent
neurotransmitter.
2.Histamine, which is synthesized by decarboxylation of
histidine, and
3. Serotonin, which is derived from tryptophan, similarly
function as neurotransmitters and regulators.
4.-Alanine is found in nature in the peptides carnosine and
anserine and
is a component of pantothenic acid (a vitamin), which is a
part of coenzyme A.
5. Epinephrine (also known as adrenaline), derived from
tyrosine, is an important hormone.
6.Penicillamine is a constituent of the penicillin antibiotics.
7.Ornithine,
8.betaine,
9.homocysteine
10.homoserine are important metabolic intermediates.
11.Citrulline is the immediate precursor of arginine.
 Essential and Non Essential Amino acids

There are two types of amino acids as per the nutritional

requirement.
They are classified into essential and non-essential amino
acids
Essential amino acids are those that are not synthesized by
the body and are needed in the diet.
Methionine, threonine, tryptophan, valine, isoleucine,
leucine and phenylalanine are the essential amino acids.
Non-essential amino acids are those that are synthesized
in the body and are not necessary in the diet.
Glycine, alanine, serine, cysteine, tyrosine, proline, aspartic
acid and glutamic acid are the non-essential amino acids.
 Physical Properties of Amino acids
D/L Configuration
D :Dexter L : Left

All amino acids exist in L isomer form so they are

α-L-aminoacids
 Optical Properties
α Carbon is asymmetric except in Glycine
Asymmetric α Carbon is optically active
It either rotate light towards right (+/d) dextorotatory
or towards left (-/l) levorotatory
Direction of light is not related to the configuration
All naturally occuring aa are L amino acids , some
being (+/d) and others (-/l)
The optical rotation of cations, anions and Zwitter ion
are different and vary according to the pH of
solution
 Cation: Zwitter ion Anion
pH < 7 pH = 7 pH > 7
• Ala +14.5 + 2.4
• Leu +15.1 -10.7
• As pH increases , +ve more
• As pH decreases , -ve more
• Acidic pH favors dextro( more +, less-)
• Basic pH favors Levo ( more -, less+)
• Rotations of aa are measured in HCl when they are
in cationic forms and considered as standards.
 Dissociation
• All Aminoacid dissociate in soln

• The α- head of all amino acids is dipolar

• As they dissociate they act both as acid /bases.
• So they amphoteric /ampholyte
• According to the pH of Soln

(Fully protonated) Dipolar Deprotinated

pH= acidic pH neutral pH = Basic
Cations Zwitterions Anion

Cathode No moment Anode

• Zwitterions containing both acidic and basic groups
and react with both acid and alkali substances to
form salts.
• Such substances are called amphoteric /
ampholytes
 Titration Curves
• In acidic pH , the aa are fully protonated and are
present as cations which dissociated in 2 steps
Pka 1 Pka 2

The amino acids cations when titrated gives a titration curves that resembles a dibasic
weak acid curve i.e dissociated twice having 2 pKa values .pka1 forming zwitterion
(conjugate base and pKa2 forming anion(salt of aa)
• The pH value between pka1 and pk2 represents Iso
electric pH at which all the aa completely exists as
Zwitterions
• Iso electric pH:pH of any amino acid/ diprotic acid
where all the aa are present in zwitterion form.
• Diprotic pI = pKa1 + pka2 (average pka)
2
• Triprotic pI = pKa1 + pka 2+pka3 for polar R_chain
3
 pH depends on side chain
• The 15 amino acids with thiol, hydroxyl groups or
pure hydrocarbon side chains have pI = 5.0 to 6.5
(average of the pKa’s)
• D and E have acidic side chains and a lower pI
• H, R, K have basic side chains and higher pI
Solubility
All amino acids are more or less soluble in water/Acids/Bases
Partially soluble in organic in organic solvents
Practically soluble in ether
Except proline
Solubility αTemp
Melting Point
Aminoa cids don’t have distinct m.ps
In some cases more than 300 ‘C
They destroy at or near their mp

Taste and Odour

Most are sweet
Some are tasteless
Few are bitter
 Synthesis of Amino Acids
• Bromination of a carboxylic acid by treatment with
Br2 and PBr3 (22.4) then use NH3 or phthalimide to
displace Br
 The Amidomalonate Synthesis
• Based on malonic ester synthesis
• Convert diethyl acetamidomalonate into enolate ion
with base, followed by alkylation with a primary
alkyl halide
• Hydrolysis of the amide protecting group and the
esters and decarboxylation yields an -amino
 Structural Organization of Proteins
The Levels of Protein Structure
• The architecture of protein molecules is quite complex. Nevertheless,
this complexity can be resolved by defining various levels of
structural organization.
Primary Structure
• The sequence of amino acid in a peptide is the primary (1°) structure
of a protein
• Primary structure contain information derived from nucleic acids
• Primary structure determine the Secondary, Tertiary, Quaternary
structures
Secondary structure is a local regularly occurring
structure in proteins and is mainly formed through
hydrogen bonds between backbone atoms.
There are four types: random coils, loops or turns,
alpha helices and beta-sheets
Random coils, loops or turns don't have a stable
secondary structure.
There are two types of stable secondary
structures: Alpha helices and beta-sheets
Alpha-helices and beta-sheets are preferably located
at the core of the protein, whereas loops prefer to
reside in outer regions.
 An alpha helix:
The backbone is formed as a helix.
An ideal alpha helix consists of 3.6
residues per complete turn.
The side chains stick out.
There are hydrogen bonds between
the carboxy group of amino acid and
the amino group of another
amino acid n+4
 Beta sheet
Beta sheets are created, when atoms of beta
strands are hydrogen bound.
Beta sheets may consist of parallel strands,
antiparallel strands or out of a mixture of
parallel and antiparallel strands
 Tertiary Structure
When the polypeptide chains of protein molecules
bend and fold in order to assume a more compact
three-dimensional shape, a tertiary (3°) level of
structure is generated .
It is by virtue of their tertiary structure that proteins
adopt a globular shape.
A globular conformation gives the lowest surface to
volume ratio, minimizing interaction of the protein
with the surrounding environment.
 Quaternary Structure
Many proteins consist of two or more interacting polypeptide chains of
characteristic tertiary structure, each of which is commonly referred to
as a subunit of the protein.
Subunit organization constitutes another level in the hierarchy of protein
structure, defined as the protein’s quaternary (4°) structure
Whereas the primary structure of a protein is determined by the
covalently linked amino acid residues in the polypeptide backbone,
secondary and higher orders of structure are determined principally by
non covalent forces such as hydrogen bonds and ionic, vander Waals,
and Hydrophobic interactions.
It is important to emphasize that all the information necessary for a
protein molecule to achieve its intricate architecture is contained
within its 1° structure, that is, within the amino acid sequence of its
polypeptide
Biological Functions of Proteins
 Protein Shape
Proteins can be assigned to one of three global classes on the basis of
shape and solubility.

1. Fibrous proteins
Tend to have relatively simple, regular linear structures. These proteins
often serve structural roles in cells. Typically, they are insoluble in water
or in dilute salt solutions.

2. Globular proteins
Are roughly spherical in shape. The polypeptide chain is compactly
folded so that hydrophobic amino acid side chains are in the interior of
the molecule and the hydrophilic side chains are on the outside exposed
to the solvent, water.Consequently, globular proteins are usually very
soluble in aqueous solutions.Most soluble proteins of the cell, such as
the cytosolic enzymes, are globular in shape.
Membrane proteins
Are found in association with the various membrane
systems of cells.
For interaction with the nonpolar phase within
membranes, membrane proteins have hydrophobic
amino acid side chains oriented outward.
As such, membrane proteins are insoluble in aqueous
solutions but can be solubilized in solutions of
detergents.
Membrane proteins characteristically have fewer
hydrophilic amino acids than cytosolic proteins.
 Some Proteins Have Chemical Groups
Other Than Amino Acids
Many proteins consist of only amino acids and contain no other
chemical groups. The enzyme ribonuclease and the contractile
protein actin are two such examples.Such proteins are called simple
proteins.
However, many other proteins contain various chemical constituents as
an integral part of their structure. These proteins are termed
conjugated proteins.
If the nonprotein part is crucial to the protein’s function, it is referred to
as a prosthetic group.
If the nonprotein moiety is not covalently linked to the protein, it can
usually be removed by denaturing the protein structure.
However, if the conjugate is covalently joined to the protein, it may be
necessary to carry out acid hydrolysis of the protein into its component
amino acids in order to release it.
Conjugated proteins are typically classified according to the chemical
nature of their non amino acid component
GLYCOPROTEINS.
• Glycoproteins are proteins that contain carbohydrate. Proteins destined
for an extracellular location are characteristically glycoproteins.
• For example, fibronectin and proteoglycans are important components
of the extracellular matrix that surrounds the cells of most tissues in
animals.
• Immunoglobulin G molecules are the principal antibody species found
circulating free in the blood plasma. Many membrane proteins are
glycosylated on their extracellular segments.
LIPOPROTEINS.
• Blood plasma lipoproteins are prominent examples of the class of
proteins conjugated with lipid. The plasma lipoproteins function
primarily in the transport of lipids to sites of active membrane synthesis.
• Serum levels of low density lipoproteins (LDLs) are often used as a
clinical index of susceptibility to vascular disease.
NUCLEOPROTEINS.
Nucleoprotein conjugates have many roles in the storage and
transmission of genetic information.
Ribosomes are the sites of protein synthesis. Virus particles and even
chromosomes are protein–nucleic acid complexes.
PHOSPHOPROTEINS.
These proteins have phosphate groups esterified to the hydroxyls of
serine,
threonine, or tyrosine residues.
Casein, the major protein of milk, contains many phosphates and
serves to bring essential phosphorus to the growing infant.
Many key steps in metabolism are regulated between states of
activity or
inactivity, depending on the presence or absence of phosphate
groups on
proteins.Glycogen phosphorylase a is one well-studied example.
METALLOPROTEINS.
Metallo-proteins are either metal storage forms, as in the case of
ferritin,or enzymes in which the metal atom participates in a
catalytically important manner.
We encounter many examples throughout this book of the vital
metabolic functions served by metallo-enzymes.
HEMOPROTEINS
These proteins are actually a subclass of metallo-proteins because
their prosthetic group is heme, the name given to iron proto-
porphyrin IX .
Because heme-containing proteins enjoy so many prominent
biological functions, they are considered a class by themselves.
FLAVOPROTEINS.
Flavin is an essential substance for the activity of a number of
important