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• Second level

BASIC PROTEIN
• Third level
• Fourth level

STRUCTURE
• Fifth level

Dr. Magda Ibrahim

Medical Biochemistry and Molecular Biology
Intended Learning Outcomes (ILOs)

• By the end of this lecture, the student should be able to:

• Identify the monomeric units and basic structure of proteins.
• Define the peptide bond and illustrate how a peptide bond is
formed.
• Describe the properties of the peptide bond
• Describe other bond that stabilize protein structure.
 Protein Structure

• Amino acids are the structural units of proteins.

• Amino acids are bonded together in a specific

sequence, number and type to form different proteins
in our body.
 Peptide Bonds
• Peptide Bond is a covalent bond
• Peptide bond formation is a
condensation (dehydration) reaction
between an -carboxyl group of an
amino acid and an -amino group
of another amino acid.

• Proteins are made of many -amino

acids linked together by peptide
linkages (bonds).
Two amino acids 3 amino acids

Di-peptide Tri-peptide

One peptide bond Two peptide bond

 +
3

N-terminal C-terminal
 Protein Structure

Peptides will have only one free -amino group, called

the N-terminal amino group, and one free -carboxyl
group termed the C-terminal carboxyl.

• Amino acid residues of peptides are numbered from the N-

terminal towards the C-terminal.
 Properties of Peptide Bonds

Rigid

Polar un-charged

Trans peptide bond

Resist denaturation
 +
3

N-terminal C-terminal
 Properties of Peptide Bonds

• Rigid
There is NO freedom of rotation of groups around the bond.

• Polar Uncharged
- CO and NH groups of peptide bond are uncharged at physiological
pH.
- Polar: Its groups can form hydrogen bonds
- The charge on the peptide comes from N-terminal, C-terminal and
any ionized groups present in the side chain.
Properties of Peptide Bonds

Cis/ Trans configuration

Cis peptide bond

Trans peptide bond
Properties of Peptide Bonds

• Double bonds restrict rotation of the alkyl chains.

• It depends on the orientation (arrangement) of groups around

the axis of the double bond.

• Cis-configuration: When the two bulky groups on the same side

of the bond.

• Trans-configuration: When the two bulky groups on the opposite

sides of the bond.
Test yourself

• Which one is a predominant form Cis peptide bond or

Trans peptide bond in proteins?

• Because of steric repulsive forces between side chains of amino

acids, trans peptide bonds are the predominant
conformation found in proteins.
 Properties of Peptide Bonds

Resistant to denaturation

• We need strong acid or base + high temperature to

break peptide bond in vitro.

• However, in vivo, it can be cleaved by peptidase

enzymes
Test your-self

• Mention (List) the properties of peptide bond

 Biologically Active Peptides

• A protein consists of one or more large peptides and has a

specific biological function.

• Although shorter peptide chains (less than about 50 amino acid

residues) have specific biological functions, they are generally
not classified as proteins.

• Short peptide chains function as chemical signaling compounds;

over one hundred of them have been identified.
List biologically active peptides

Glutathione (GSH)

Endorphins

Oxytocin
Biologically Active Peptides

• Glutathione is a biologically active tripeptide that is

formed of glutamate, cysteine, and glycine.

Glutathione is an important tripeptide acting as reducing

agent.

- Reduce toxic H2O2 into H2O in RBCs (red blood cells);

protect the wall of RBCs against toxic H2O2
Endorphins

• Endorphins (5 amino acids) 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
 Oxytocin
• Oxytocin contains nine amino
acid residues.

• It is produced by the pituitary

gland, and stimulates uterine
contractions in labor.
Test yourself

Complete

Glutathione Endorphins Oxytocin

Number of AA

Function
 Forces that stabilize protein
structure

Non- covalent bonds Covalent bonds

Hydrogen bonds Peptide bond

Electrostatic bonds Disulfide bond

Hydrophobic
interaction
Van der Waal
forces
Student’s activity

Complete the following table

Peptide Disulfide Hydrogen Hydrophobic Electrostatic

bond bond bonds interaction bonds

Formation

Types

Importance
 Disulfide bond
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- Itlevel
• Second is a covalent bond
•
between
Third level
• Fourth level
two molecules
of cysteine
• Fifth level to form
cystine.
Click to edit Master title style
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• Second level
• Third level
• Fourth level REDUCTION
• Fifth level

OXIDATION Cystine

2H
 Disulfide bond
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• Second level
• What is the difference between intra-chain
• Third level
• Fourth level
disulfide bond and inter-chain disulfide
• Fifth level

bond?????????
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• Intra-chain
• Edit Master text disulfide
styles bond:
It formslevel
• Second between two residues
in• the
Third same
level polypeptide chain.
• Fourth level
• Fifth level
• Inter-chain disulfide bond:

It forms between two residues

to link two polypeptide
chains.
 Forces that stabilize protein
structure
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Non- covalent bonds Covalent bonds
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• Second level
Hydrogen
• Third level bonds Peptide bond
• Fourth level
• Fifth level
Electrostatic bonds Disulfide bond

Hydrophobic
interaction
Van der Waal
forces
 Non covalent bonds
Hydrogen bond
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• Second level
It is the attraction between polar
• Third level
groups that occurs when
• Fourth level
• Fifth level (H) atom bound to a
a hydrogen
highly electronegative atom such
as nitrogen (N), oxygen(O)
 Non covalent bonds

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Hydrogen bonds
• are weak in comparison to covalent bond but their presence
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in large styles in protein contribute to stability of folded
number
• Second level
protein.
• Third level
• Fourth level
• Fifth level
• So hydrogen bond increases the solubility of a protein
when they are formed between polar groups on the surface
of proteins & the aqueous solvent.

• It is the main determinant of secondary structure of

protein.
 Non covalent bonds

Hydrogen bond
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It occurs
• Edit•Master between:
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- Two
• Second amino
level acids.
• Third level
- Two polypeptide
• Fourth level chains.
• Fifth level
- Amino acid and water in the surrounding
environment.
 Test your self

Choose the correct answer

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A- Hydrogen bonds are covalent bond
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B- Hydrogen
• Second level bond don’t affect the stability of protein
C-• Third
Hydrogen
level bond could be formed between two amino acids
• Fourth level
D- Hydrogen• Fifth levelbond is the main determinant of primary
structure
E- The presence of hydrogen bonds decrease the solubility of
the protein
 Test your self

Choose the correct answer

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- Disulfide bond
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A- is non
• Second level covalent bond
B-• Third
Only interchain disulfide bond is present in proteins
level
• Fourth level
C- It is •formed
Fifth level between two cystine with formation of
cysteine.
D- No intra-chain or inter-chain disulfide bond
E- It is formed between two cysteine with formation of
cystine
 Non covalent bonds

Electrostatic bonds
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• Also called; ionic bonds, ionic pairs, salt bridges
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• Second level
• •Interactions
Third level between charged groups in side chains of
• Fourth level
amino acids affected by pH of the surrounding medium.
• Fifth level

• It includes:
- Electrostatic attractive forces: between different charges
- Electrostatic repulsive forces: between same charges
 Non covalent bonds

Click to edit Hydrophobic interactions

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Non-polar
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water
• Second molecules and tend to cluster together because they
level
•are insoluble
Third level in water.
• Fourth level
• Fifth level
• Bury hydrophobic amino acids in the interior of proteins.

• The most important non covalent bond that drives the

process of protein folding.
 Non covalent bonds

Van der Waals forces

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• Is the
• Second sum of attractive or repulsive forces between atoms.
level
• Third level
• Fourth level
• At shorter distance,
• Fifth level a strong repulsive force between
positively charged nuclei are predominant

• They are very weak forces, but they are important to

stabilize atoms in their positions
 Forces that stabilize protein
structure
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Non- covalent bonds Covalent bonds
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• Second level
Hydrogen
• Third level bonds Peptide bond
• Fourth level
• Fifth level
Electrostatic bonds Disulfide bond

Hydrophobic
interaction
Van der Waal
forces
 Complete the following table
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Peptide titleHydrogen
Disulfide style Hydrophobic Electrostatic
bond bond bonds interactions Forces
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By dehydration between two between polar Non polar molecules between charged
Formation
• Second levelreaction molecules of groups that cannot form hydrogen groups in side chains
between an - cysteine to form occurs when bonds with water of amino acids
• Third levelcarboxyl group cystine. a hydrogen (H) molecules and tend to
• Fourthoflevel
an amino acid atom bound to a cluster together
and an -amino highly electroneg because they are
• Fifth
grouplevel
of ative atom such insoluble in water.
another amino as nitrogen (N), o
acid xygen(O) It bury hydrophobic
amino acids in the
interior of proteins.

Types Cis/Trans Intar/ inter Intra/inter -------- Repulsive/

peptide chain chain attractive
bond disulfide
bond
Importance Primary Tertiary Secondary Protein folding In protein
structure structure structure structure
 Reference
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• Harvey, Richard A. "Lippincottt’s illustrated review
• Edit Master text stylesth
biochemistry 7 edition." (2017).
• Second level
• Third level
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