PROTEIN
proteins.
 one of the four macromolecules.
 major structural and functional
components of all cells in the body.
 act to facilitate biochemical reactions
among the most abundant biological
macromolecules.
 play a crucial role in a healthy,
balanced diet.
 twenty percent of the human body is
made up of proteins.
 the large, complex molecules that are
critical for normal functioning of cells.
 a typical human cell contains about
9000 different kinds of proteins.
 the human body contains about
100,000 different proteins.
 Proteins are needed for the synthesis
of enzymes, certain hormones, and
some blood components; for the
maintenance and repair of existing
tissues.
 A Protein is a naturally occurring,
extremely complex substance that
consists of amino acid residues joined
by peptide bonds
 The more specific definition of
proteins.
 A protein is a peptide in which at least
40 amino acid residues are present.
Characteristics of Proteins
 All proteins contain the elements
carbon ( 50-55 %) , hydrogen ( 6-7.3
% ), oxygen (19-24 % ) , and nitrogen (
13-19 % ) ; most also contain sulfur
( 0-4 % ). The presence of nitrogen in
proteins sets them apart from
carbohydrates and lipids.
 The average nitrogen content of
proteins is 15.4% by mass.
 Other elements, such as phosphorus
and iron, are essential constituents of
certain specialized proteins.
Amino Acids: The building blocks for
Proteins
 More than 700 different naturally
occurring amino acid are known, but
only 20 of them, called standard
amino acids, are normally present in
 These 20 Amino acids are the only
amino acids that are coded for by
DNA, the genetic material in the cell.
 The general structure of amino acid
includes an amino group and a
carboxyl group, both of which are
bonded to the α-carbon (the one next
to the carboxyl group). The α-carbon is
also bonded to α- hydrogen and to the
side chain group, which is represented
by the letter R. The R group
determines the identity of the particular
amino acid.
Chemical Properties
 A zwitterion is a molecule that has both
negative and positive charges
 Since amino acids have chiral center,
optical activity is observed
 Except for glycine which is achiral
 Amino acids are amphoteric (able to
react both as a base and as an acid.)
 There are 20 known amino acids
 Amino acids naturally occur in L form
Acid–Base Properties of Amino Acids
 A zwitterion is a molecule that has a
positive charge on one atom and a
negative charge on another atom, but
which has no net charge.
 Note that the net charge on a
zwitterion is zero even though parts of
the molecule carry charges.
 Zwitterion structure changes when the
pH of a solution containing an amino
acid is changed from neutral either to
acidic (low pH) by adding an acid such
as HCl or to basic (high pH) by adding
a base such as NaOH.
 In an acidic solution, the zwitterion
accepts a proton (H+) to form a
positively charged ion.
 In basic solution, the -NH3 of the
zwitterion loses a proton, and a
negatively charged species is formed.
 Classification of Amino Acids based on
Side Chain (R groups)
Zwitterionic Property  There are 20 amino acids. Based on
the nature of their ‘R’ group, they are
 a molecule with functional groups, of
classified based on their polarity as:
which at least one has a positive and
one has a negative electrical charge.
 the net charge of the entire molecule is
zero. Amino acids are the best-known
examples of zwitterions.
 They contain an amine group (basic)
and a carboxylic group (acidic). The -
NH2 group is the stronger base, and
so it picks up H+ from the -COOH
group to leave a zwitterion.
 The (neutral) zwitterion is the usual
form amino acids exist in solution.
Amphoteric property
 Amino acids are amphoteric in nature
that is they act as both acids and base
since due to the amine and carboxylic Classification of Amino Acids based on
group present. Side Chain (R groups)
 Non polar aliphatic amino acids
 Amino acids with Uncharged (neutral)
side chain
 Acidic amino acids
 Amino acids with basic side chain
Classification of Amino Acids based on
Capacity of the Body to Synthesize Them
 Essential Amino acids
 Non-essential amino acids
Essential Amino Acids (Nine)
 Nine amino acids cannot be
synthesized in the body and, therefore,
must be present in the diet in order for
protein synthesis to occur.
 These essential amino acids are
histidine, isoleucine, leucine, lysine,
 methionine, phenylalanine threonine,
tryptophan, and valine.
 Phe, Thr, Val, Met Trp, His, Ile, Lys and
Leu
Non-essential Amino Acids (Eleven)
 These amino acids can be synthesized
in the body itself and hence not
necessarily needed to be acquired
through diet.
 Nonessential amino acids include:
alanine, arginine, asparagine, aspartic
acid, cysteine, glutamic acid,
glutamine, glycine, proline, serine, and
tyrosine.
Peptides
 Under proper conditions, amino acids
can bond together to produce an
unbranched chain of amino acids.
 The length of the amino acid chain can
vary from a few amino acids to many
amino acids. Representative of such
chains is the following five-amino-acid
chain.
Peptides Bonds
 Amino acids are linked together in
proteins by a special kind of bond, the
Peptide Bond
 During protein synthesis, the carboxyl
group of amino acid at the end of the
growing polypeptide chain reacts with
the amino group of an incoming amino
acid, releasing a molecule of water.
 The resulting bond between the amino
acids is a peptide bond.
Biologically-Relevant Peptides
 Many relatively small peptides have
been shown to be biochemically
active. Functions for them include
hormonal action, neurotransmission,
and antioxidant activity.
Small Peptide Hormones
Vasopressin
 regulates the excretion of water by the
kidneys; it also affects blood pressure.
 Another name for vasopressin is
antidiuretic hormone (ADH).
 This name relates to vasopressin’s
function in the kidneys, which is to
decrease urine output in order to
decrease water elimination from the
body.
 Such action is necessary when the
bod becomes dehydrated.
Oxytocin
 It is produced by the pituitary gland,
and stimulates uterine contractions in
labor.
 Oxytocin was the first naturally-
occurring hormone to be produced in a
laboratory.
 Oxytocin contains nine amino acid
residue, which are connected in the
sequence shown: Cys-Tyr-Ile-Gln-Asn-
Cys-Pro-Leu-Gly
Small Peptide Neurotransmitters
Enkephalins
 Pentapeptide neutrotransmitters
produced by the brain itself that bind at
the receptor sites in the brain to
reduce pain.
2 best known:
 Met-enkephalin – Tyr-Gly-Gly-Phe-Met
 Leu-enkephalin – Tyr-Gly-Gly-Phe-Leu
Small Peptide Antioxidants
Glutathione
 Is present in significant concentrations
  in most cells and have physiological
importance as a regulator of oxidation-
reduction reactions. As anti- oxidants.
 Protecting cells contents form the
oxidizing agents such as peroxides
and superoxides. Glu-Cys-Gly
Other example of Biologically-Relevant
Peptides
Endorphins
 are examples of chemical signaling
peptides.
 They are natural painkillers that are
produced in the body.
 They interact with receptors in the
brain to inhibit the transmission of pain
signals.
 An example of an endorphin peptide is
α-endorphin.
 It contains sixteen amino acid
residues, which are connected in the
sequence (N-terminus to C-terminus)
shown below: Tyr-Gly-Phe-Met-Thr-
Ser-Glu-Lys-Ser-Gln-Thr-Pro-Leu-Val-
Thr
4 PROTEIN STRUCTURAL LEVELS
PRIMARY STRUCTURE
 Is the order in which amino acids are
linked together in a protein.
 Insulin, the hormone that regulates
blood glucose levels.
 51 amino acid sequence by biologist
Frederick Sanger.(1953)
 153 amino acid sequence a human
myoglobin
SECONDARY STRUCTURE
 Is the arrangement in a space adopted
by the backbone portion of protein.
 Has 2 types of folding: alpha (α) helix
and the beta (β) pleated sheets
Alpha Helix
 alpha helix, the polypeptide chain is
coiled tightly in the fashion of a spring.
 The "backbone" of the peptide forms
the inner part of the coil while the side
chains extend outward from the coil.
 The helix is stabilized by hydrogen
bonds between the >N-H of one amino
acid and the >C=O on the 4th
Beta (β) pleated sheets
 In this structure, individual protein
chains are aligned side-by-side with
every other protein chain aligned in an
opposite direction.
 The protein chains are held together
by intermolecular hydrogen bonding,
that is hydrogen bonding between
amide groups of two separate chains.
TERTIARY STRUCTURE
 Is the overall three dimensional
structure shape of the protein that
result from the interaction between
amino acid side chains (R Groups).
Four types of interactions contribute to
the tertiary structure of a protein.
Covalent disulfide
 it is the strongest of the tertiary
structure interactions resulting from the
–SH groups. Of two cysteine residues
interacting with each other
Electrostatic interactions called salt Bridges
 Involves the interactions between the
acidic side Groups and basic R group.
 The acidic being negative –COOH
becomes –COO-
 The basic being positive –NH2
becomes NH3 +
Hydrogen Bonds
 This can occur between amino acids
with polar R groups.
Hydrophobic Interactions
 Results when 2 non polar amino acids
are close with each other.
QUATERNARY STRUCTURE
 Highest level of protein organization.
 It is only found in multimeric proteins.
 Describes the interactions of the
subunits in an oligomeric protein
 Present also The electrostatic
interactions

Protein Classification Based on Shape

 Based on molecular shape, which is
determined primarily by tertiary and
quaternary structural features,
 there are three main types of proteins:
Fibrous, Globular
 A fibrous protein is a protein whose
molecules have an elongated shape
with one dimension much longer than
the others. Fibrous proteins tend to
have simple, regular, linear structures.
 A globular protein is a protein whose
molecules have peptide chains that
are folded into spherical or globular
shapes.
 Conjugated proteins. These are simple
proteins combined with some non-
protein material in the body.
 They are classified according their
prosthetic group.
Denaturation of a Protein
 Denaturation is a structural change in
a protein that results in the loss
(usually permanent) of its biological
properties
 Because the way a protein folds
determines its function, any change or
abrogation of the tertiary structure will
alter its activity
 Temperature
 High levels of thermal energy may
disrupt the hydrogen bonds that hold
the protein together
 As these bonds are broken, the protein
will begin to unfold and lose its
capacity to function as intended
 Temperatures at which proteins
denature may vary, but most human
proteins function optimally at body
temperature (~37ºC).