Proteins

By
Dr. Abid Ullah
What are Proteins?

• Protein derived from Greek word proteious meaning first

• Most important compound after DNA
• They Large biomolecules or macromolecules
• Are found in every cell in the body
• Are involved in most of the body’s functions and life processes
• The sequence of amino acids is determined by DNA
• It has been estimated that average-sized bacteria contain about 2
million proteins per cell
• By contrast, eukaryotic cells are larger and thus contain much more
protein (human cells on the order of 1 to 3 billion)
Amino Acids
• Amino acids are the building blocks of proteins.
• contain a carboxylic acid group and an amino group on the alpha ()
carbon.
The Peptide Bond
A peptide bond is an amide bond.
• forms between the carboxyl group of one amino acid and the amino
group of the next amino acid.
• contains an N (free H3N+) terminal written on the left.
• contains a C (free COO–) terminal written on the right.
Peptide bonds link Amino Acids

• Form when the acid group

(COOH) of one amino acid
joins with the amine group
(NH2) of a second amino
acid
• Formed through
condensation
• Broken through hydrolysis
Essential, Nonessential, and
Conditional

• Essential – must be consumed in the diet

• Nonessential – can be synthesized in the body
• Conditionally essential – cannot be synthesized due to
illness or lack of necessary precursors
Properties of Proteins
• Denaturation and Renaturation
• Proteins can be denatured by agents such as heat and urea that
cause unfolding of polypeptide chains without causing
hydrolysis of peptide bonds.
• The denaturing agents destroy secondary and tertiary
structures, without affecting the primary structure.
• If a denatured protein returns to its native state after the
denaturing agent is removed, the process is called renaturation.
• Some of the denaturing agents include
• Physical agents: Heat, radiation, pH
• Chemical agents: Urea solution which forms new hydrogen
bonds in the protein, organic solvents, detergents.
Coagulation
• When proteins are denatured by heat, they form insoluble
aggregates known as coagulum.
• All the proteins are not heat coagulable, only a few like the
albumins, globulins are heat coagulable.
Solubility in water
• The relationship of proteins with water is complex.
• Proteins are buid up out of amino acids.
• All amino acids have a similar backbone structure, but differ
in their side chains.
• These side chains have different properties, some are
hydrophobic (not water soluble) whereas others are
hydrophylic (water soluble)
Chemical Properties
• 1. Biuret test:
• When 2 ml of test solution is added to an equal volume of
10% NaOH and one drop of 10% CuSO4 solution, a violet col­
our formation indicates the presence of peptide linkage.
• 2. Ninhydrin test:
• When 1 ml of Ninhydrin solu­tion is added to 1 ml protein
solution and heated, formation of a violet colour indicates
the presence of α-amino acids.
Structure of the Protein

• Four levels of structure

• Primary structure
• Secondary structure
• Tertiary structure
• Quaternary structure

Any alteration in the structure or sequencing changes the

shape and function of the protein
Primary Structure of Proteins
 The primary structure of a protein refers to the sequence
of amino acids in the polypeptide chain.
 The primary structure is held together by peptide
bonds that are made during the process of protein
biosynthesis.
 The two ends of the polypeptide chain are referred to as
the carboxyl terminus (C-terminus) and the amino
terminus (N-terminus) based on the nature of the free group
on each extremity.
 A specific sequence of nucleotides in DNA is transcribed into
mRNA, which is read by the ribosome in a process
called translation
 Example of Primary Structure

 Insulin (Frederick Banting)

 It was the first protein to have
its primary structure
determined.
 It has a primary structure of
two polypeptide chains linked
by disulfide bonds.
 It has an A chain with 21 amino
acids and a B chain with 30
amino acids.

© 2013 Pearson Education, Inc. Chapter 19, Section 1 14

 Secondary Structure

The secondary structures of proteins describe the

type of structure that forms when amino acids form
hydrogen bonds within a single polypeptide chain or
between polypeptide chains

Alpha helix (α-helix)

• a coiled shape held in place by hydrogen bonds between
the amide groups and the carbonyl groups of the amino
acids along the chain.
• hydrogen bonds between the H of an —NH group and
the O of C═O of the fourth amino acid down the chain.

© 2013 Pearson Education, Inc. Chapter 19, Section 1 15

 pulls the polypeptide
chain into a helical
structure that resembles a
curled ribbon, with each
turn of the helix
containing 3.6 amino
acids.

The R groups of the amino

acids stick outward from
the α helix, where they
are free to interact.

© 2013 Pearson Education, Inc. Chapter 19, Section 1 16

 Secondary Structure: Beta-
Pleated Sheet
A beta-pleated sheet (β-pleated sheet) is a
secondary structure that

• two or more segments of a polypeptide chain

line up next to each other, forming a sheet-
like structure held together by hydrogen
bonds.
• has hydrogen bonds between chains.
• has R groups above and below the sheet.
• The strands of a β pleated sheet may
be parallel, pointing in the same direction
or antiparallel, pointing in opposite directions
• Example: Silk Fibroin

© 2013 Pearson Education, Inc. Chapter 19, Section 1 17

 Secondary Structure: Triple
Helix
A triple helix
• consists of three alpha helix chains
woven together.
• contains large amounts of glycine,
proline, hydroxyproline, and
hydroxylysine that contain
–OH groups for hydrogen bonding.
• is found in collagen, connective
tissue, skin, tendons, and cartilage.

© 2013 Pearson Education, Inc. Chapter 19, Section 1 19

Tertiary Structure
• The overall three-dimensional structure of a polypeptide is
called its tertiary structure.
• The tertiary structure is primarily due to interactions
between the R groups of the amino acids that make up the
protein.
• is stabilized by:
hydrophobic and hydrophilic interactions,
salt bridges,
hydrogen bonds, and
disulfide bonds.
Tertiary Structure (continued)
• The interactions of
the R groups give a
protein its specific
three-dimensional
tertiary structure.
 Myoglobin
• Myoglobin is a tertiary
structure protein, also
called hemoprotein
• Myoglobin store and
transport oxygen in
muscle.
 Quaternary Structure
The quaternary structure Hemoglobin
• is the combination of two or
more polypeptide chains.
• is stabilized by the same
interactions found in tertiary
structures.
• Haemoglobin consists of two
alpha chains and two beta chains
with heme groups in each
subunit that pick up oxygen for
transport in the blood to the
tissues.

© 2013 Pearson Education, Inc. Chapter 19, Section 1 23

Can you do a quick review?
Protein classification based on
chemical composition
• On the basis of their chemical composition, proteins are
divided into two major classes: simple and complex
(conjugated).
• Simple proteins
• Also known as homoproteins, they are made up of only kind
of amino acids. Examples are albumin, collagen, and keratin.
• Conjugated proteins
• Sometimes also called heteroproteins, they contain in their
structure a non-protein portion. Examples are glycoproteins,
chromoproteins, phosphoproteins etc.,
Types of conjugated proteins
• Glycoproteins
They are proteins that covalently bind one or
more carbohydrate units to the polypeptide backbone.
• Typically, the branches consist of not more than 15-
20 carbohydrate units, where you can find arabinose, galactose,
glucose, mannose, N-acetylglucosamine and N-acetylneuraminic
acid.

• Example
blood proteins (fibrinogen, prothrombin, and the gamma
globulins)
• Chromoproteins
They are proteins that contain colored prosthetic groups
(non protein).

• Typical examples are:

• hemoglobin and myoglobin
• Chlorophylls
• rhodopsins
• Phosphoproteins
They are proteins that bind phosphoric acid to serine and
threonine residues.

• Generally, they have a structural function, such as tooth

dentin, or reserve function, such as milk caseins (the main
protein present in egg and milk).
• Metalloproteins.
• These are the proteins linked with various metals.
• These may be of stable nature or may be more or less labile
(easily change).
• Example: hemoglobin containing iron

• Lipoproteins.
• Proteins forming complexes with lipids (cephalin, lecithin,
cholesterol)

• Nucleoproteins.
• These are compounds containing nucleic acid and protein,
esp., histones.
Protein classification based on
shape
• On the basis of their shape, proteins may be divided into
two classes: fibrous and globular.

• Fibrous proteins
• They are generally composed of long chains
• They have primarily mechanical and structural functions,
providing support to the cells as well as the whole organism.

• These proteins are insoluble in water as they contain, both

internally and on their surface, many hydrophobic amino
acids.
• Here are some examples.
• Fibroin
It is produced by spiders and insects. An example is that produced by
the silkworm
• Collagen
The term “collagen” indicates not a single protein but a family of
structurally related proteins (at least 29 different types), which
constitute the main protein component of connective tissue, and more
generally, the extracellular scaffolding of multicellular organisms.
• In vertebrates, they represent about 25-30% of all proteins.
• α-Keratins
They constitute almost the entire dry weight of nails, claws, beak,
hooves, horns, hair, wool, and a large part of the outer layer of the skin.
Globular proteins

• Most of the proteins belong to this class.

• They have a compact and more or less spherical
structure, more complex than fibrous proteins.
• In this regard, motifs, domains, tertiary and quaternary
structures are found, in addition to the secondary structures.
• They are generally soluble in water but can also be found
inserted into biological membranes (transmembrane
proteins), thus in a hydrophobic environment.
• Unlike fibrous proteins, they act as a functional
protiens:
• enzymes;
• hormones;
• membrane transporters and receptors;
• transporters of triglycerides, fatty acids and oxygen in the blood;
• immunoglobulins or antibodies;
• grain and legume storage proteins.
• Examples of globular proteins are myoglobin, hemoglobin, and
cytochrome c.
At the intestinal level, most of the globular proteins of animal
origin are hydrolyzed almost entirely to amino acids.
Protein classification based
on biological functions
From the functional point of view, they may be divided into
several groups.
•Enzymes (biochemical catalysts).
In living organisms, almost all reactions are catalyzed by
specific proteins called enzymes.
•They have a high catalytic power, increasing the rate of the
reaction.
•Therefore, life as we know could not exist without their
“facilitating action”.
•Almost all known enzymes, and in the human body they are
thousand, are proteins (except some catalytic RNA molecules
called ribozymes, that is, ribonucleic acid enzymes).
• Transport proteins
Many small molecules, organic and inorganic, are
transported in the bloodstream and extracellular fluids,
across the cell membranes, and inside the cells from one
compartment to another, by specific proteins.

• Examples are:
• hemoglobin, that carries oxygen from the alveolar blood
vessels to tissue capillaries;
• transferrin, which carries iron in the blood;
• Storage proteins

• Examples are:
• ferritin, that stores iron intracellularly in a non-toxic form;
• milk caseins, that act as a reserve of amino acids for the
milk;
• egg yolk phosvitin, that contains high amounts of
phosphorus; Phosphoprotein
• Prolamins and glutelins, the storage proteins of cereals.
• Mechanical support
• Proteins have a pivotal role in the stabilization of many structures.
• Examples are α-keratins, collagen and elastin.
• The same cytoskeletal system, the scaffold of the cell, is made
of proteins.
• They generate movement.
They are responsible, for:
• the contraction of the muscle fibers (of which myosin is the main
component);
• the propulsion of spermatozoa and microorganisms with flagella;

• the separation of chromosomes during mitosis.

• They are involved in nerve transmission.
An example is the receptor for acetylcholine at synapses.
• Acetylcholine is the neurotransmitter used at the
neuromuscular junction

• They control development and differentiation.

Some proteins are involved in the regulation of gene
expression.
• An example is the nerve growth factor (NGF), that plays a
leading role in the formation of neural networks.
• Hormones

• Many hormones are proteins.

• They are regulatory molecules involved in the control of
many cellular functions, from metabolism to reproduction.
Examples are abscisic acid, Jasmonic acid etc.
• Protection against harmful agents.
• The antibodies or immunoglobulins are glycoproteins that
recognize antigens expressed on the surface of viruses,
bacteria and other infectious agents.
• fibrinogen, and factors of blood coagulation are other
members of this group.
• Storage of energy.
Proteins, and in particular the amino acids that constitute
them, act as energy storage, second in size only to the
adipose tissue, that in particular conditions, such as
prolonged fasting, may become essential for survival.
• However, their reduction of more than 30% leads to a
decrease of the contraction capacity of respiratory muscle,
immune function, and organ function, that are not
compatible with life.
• Therefore, proteins are an extremely valuable fuel.
•Thank You