Peptides and Proteins

20 amino acids are commonly found in protein.

These 20 amino acids are linked together through peptide bonds forming
peptides and proteins.
- The chains containing less than 50 amino acids are called “peptides”, while
those containing greater than 50 amino acids are called “proteins”.

Peptide bond formation:

α-carboxyl group of one amino acid (with side chain R1) forms a covalent
peptide bond with α-amino group of another amino acid ( with the side chain
R2) by removal of a molecule of water. The result is : Dipeptide ( i.e. Two
amino acids linked by one peptide bond). By the same way, the dipeptide can
then form a second peptide bond with a third amino acid to give Tripeptide.
Repetition of this process generates a polypeptide or protein of specific amino
acid sequence.

1
 Peptide bond formation:

- Each polypeptide chain starts on the left side by free amino group of the first
amino acid to enter in chain formation . It is termed (N- terminus).
- Each polypeptide chain ends on the right side by free COOH group of the last
amino acid and termed (C-terminus).

2
Examples on Peptides:
1- Dipeptide ( two amino acids joined by one peptide bond):

2- Tripeptides ( 3 amino acids linked by two peptide bonds).

3- octapeptides: (8 amino acids)

4- polypeptides: 10- 50 amino acids: e.g. Insulin hormone

3
Proteins have four levels of structure:
1. Primary (1o)
2. Secondary (2o)
3. Tertiary (3o)
4. Quaternary (4o)
Each level of protein structure is a result of interactions between the
amino acids of the protein.

4
Primary structure:
• The primary structure is the order in
which the amino acids are joined together
by peptide bonds that forms the backbone
from N-terminus to C-terminus.
• The order or sequence of amino acids in
a protein chain are important in
determining its structure and function.
• Arranging amino acids in a different order
creates a polypeptide or protein that no
longer has the same function as the initial
sequence of amino acids.
5
 High orders of Protein structure

• A functional protein is not just a polypeptide chain, but one or more

polypeptides precisely twisted, folded and coiled into a molecule of
unique shape (conformation). This conformation is essential for some
protein function e.g. Enables a protein to recognize and bind specifically
to another molecule e.g. hormone/receptor; enzyme/substrate and
antibody/antigen.

6
 2- Secondary structure:
Results from hydrogen bond formation between hydrogen of
–NH group of peptide bond and the carbonyl oxygen of
another peptide bond. According to H-bonding there are two
main forms of secondary structure:

α-helix: The  helix is a coiled structure, and much like the

coil of a telephone cord, it is a right-handed coil.

This coil is stabilized by hydrogen bonds between the

carbonyl oxygen of one amino acid and the
N—H hydrogen atom of another amino acid located four
amino acids from it in the primary structure.
.
β-sheets: is another form of secondary structure in which
two or more polypeptides (or segments of the same peptide
chain) are linked together by hydrogen bond between H- of
NH- of one chain and carbonyl oxygen of adjacent chain (or
segment).
7
Hydrogen bonding in α-helix: In the α-helix
CO of the one amino acid residue forms H-
bond with NH of the forth one.

8
The tertiary structure is the three-
dimensional structure of the protein.

It involves twisting and folding of the

polypeptide chain caused by hydrophobic
and hydrophilic interactions between the
side chains of the amino acids.

The nonpolar amino side chains end up in

the interior of the protein away from the
aqueous environment.

The polar side chains appear on the surface

of the protein since they are attracted to the
aqueous surroundings.
9
10
Proteins are classified into groups based on their three-
dimensional shape.
• Globular proteins are compact, spherical structures
that are soluble in an aqueous environment.
Myoglobin, which stores oxygen in muscle, is an
example.
• Fibrous proteins are long, threadlike structures.
Keratins, found in hair, nails, the scales of reptiles,
and collagen, are examples.

11
Quaternary structure:
• The quaternary structure is two or more polypeptide chains interacting to form a
biologically active protein.
• Hemoglobin, an oxygen transport protein, is an example of a protein with a quaternary
structure.
It consists of four polypeptide chains or subunits.
It has two identical alpha subunits and two identical beta subunits.
All four subunits must be present for the protein to function as an oxygen carrier.

Not all proteins have a quaternary structure

12
13
Classification of proteins based on chemical constituents

1- Simple proteins:
These are proteins which on hydrolysis give only amino acids
e.g Albumin and globulins:

14
2. Conjugated proteins

These are proteins which on hydrolysis, give protein part and non protein
part and subclassified into:
•Lipoproteins:
proteins conjugated with lipids.
• Glycoproteins:
proteins conjugated with sugar (carbohydrate)
•Nucleoproteins: These are basic proteins ( e.g. histones) conjugated
with nucleic acid (DNA or RNA).

15
• Metalloproteins: These are proteins conjugated with metal like iron,
copper, zinc, ……

a- Iron-containing proteins:
Iron may present in heme such as in
- hemoglobin (Hb)
- myoglobin ( protein of skeletal muscles and cardiacmuscle),
- cytochromes
- catalase, peroxidases (destroy H2O2)

Iron may be present in free state ( not in heme) as in:

- Ferritin: Main store of iron in the body. ferritin is present in liver, spleen
and bone marrow.
- Hemosidrin: another iron store.
- Transferrin: is the iron carrier protein in plasma.

16
b- Copper containing proteins:
e.g. - Ceruloplasmin
- Oxidase enzymes

c- Zn containing proteins: e.g. Insulin

d- Mg containing proteins:e.g. Kinases

In conjugated proteins the nonprotein part is the prosthetic

group and the protein shell is the apoprotein

17
3. Derived proteins

Produced from hydrolysis of simple proteins.

e.g. - Gelatin: from hydrolysis of collagen
- Peptone: from hydrolysis of albumin
Protein Denaturation
• Is a process that disrupts secondary, tertiary, and quaternary structures.
• The primary structure is not destroyed during denaturation.
• Protein becomes insoluble and looses biological activity
• Denaturation can be caused by
• Heat
• Changes in pH
• Organic compounds
• Heavy metals eg mercury, lead etc.
• The process of denaturation is used as an antidote for lead or mercury poisoning.
• Egg whites can be given to an individual who has ingested a heavy metal. Egg
whites are denaturated by the heavy metals and a precipitate is formed.
• Vomiting is induced to eliminate the metal-protein precipitate.

19
Functions of proteins
1. Repair and Maintenance. Protein is termed the building block of the body. It is called this because protein is vital in the
maintenance of body tissue, including development and repair.
2. Protein is a major source of energy
3. Hormones. Many hormones are proteins e.g. insulin
4. Biological catalysts (Enzymes) Nearly all known enzymes are proteins
5. Transportation and Storage of Molecules
• Protein is a major element in transportation of certain molecules. For example, hemoglobin is a protein that
transports oxygen throughout the body. Protein is also sometimes used to store certain molecules. Ferritin is an
example of a protein that combines with iron for storage in the liver.
6. Immune response. Protein forms antibodies that help prevent infection, illness and disease.
7. Coordination and motion. Proteins are a major component in muscle contraction. Muscle contraction occurs when two
fibrous protein filament glide across each other.
8. Mechanical support
Collagen, the most abundant protein found in the human body is a type of structural protein that is fibrous in nature.
Collagen is responsible for giving strength and support to tissues such as skin and bone that undergo continual wear and
tear.
9. Nerve generation and impulses. These receptor sites are made of protein complexes and are responsible for
transmitting nerve messages from cell to cell

20
1.What is a simple protein?
2.What is a conjugated protein?
3.What is a prosthetic group?
4.How many subunits are in hemoglobin?
5.What are the main functions of amino acids?
6.What are the main functions of proteins?
7.How may peptide bonds are in a tripeptide?
8.What is meant by a protein primary structure?
9.What is a quaternary protein structure?
10.In which proteins is iron found in free state?