BIOCHEMISTRY OF PEPTIDE

AND PROTEIN

Dr. Rehab Omer

Faculty of Medicine
U of D
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Peptides
a peptide consists of 2 or more amino acids residues
linked by peptide bond.
peptide more than 10 amino acids are called
polypeptides including protein.
Structure of Peptides
 Structure of Peptides

§ The free amino end (N-terminal) of the peptide chain is

written to the left and the free carboxyl end (C-terminal) to
the right.

§ All amino acid sequences are read from the N- to the C-

terminal end of the peptide
Glu- Ala - Lys - Gly - Tyr - Ala
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BIOMEDICAL IMPORANCE

e.g, oxytocin (9 amino acid ) hormone,

glutathione (tripeptide

Antibiotics & a few antitumor agents

Structure of Peptides

• In peptides and proteins, only the amino

acid side chains and the amino group at
the amino terminal and carboxyl group at
the carboxyl terminal have dissociable
protons.
• All of the other carboxylic acid and amino
groups on the α-carbons are joined in
peptide bonds that have no dissociable
protons. .
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Proteins
Protein are high molecular weight polypeptides.
Polymer of amino acids with 50 or more amino acid residues.
• No universal system for classification,
1) on the basis of solubility: albumin, globulin depending on
their solubility in aquous salt solutions.
2) on the basis of the shape ( Axial ratio) : fibrous, globular

3) On the basis of biologic function : enzymes, hormones, etc

4)On the bases of structure :Simple proteins contain only amino

acids.
Complex proteins contain ; heme, vitamin derivatives, lipids,
or carbohydrate.
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ASPECTS OF PROTEIN STRUCTURE ARE

CONSIDERAD IN TERMS OF FOUR DIVISIONS,
OR ORDERDERS
. Primary structure.
. Secondary structure.
. Tertiary structure.
. Quaternary structure.
 Structure of Proteins
Primary Structure
§ The sequence of amino acids in a protein is called the
primary structure of the protein

§ Understanding the primary structure of proteins is important

because many genetic diseases result in proteins with
abnormal amino acid sequences

§ In proteins, amino acids are joined covalently by peptide

bonds, which are amide linkages between the α-carboxyl
group of one amino acid and the α-amino group of another

§ primary structure also includes the location of any

disulfide bonds.
 Structure of Proteins
Primary Structure
§ The free amino end (N-terminal) of the peptide chain is
written to the left and the free carboxyl end (C-terminal) to
the right.

§ All amino acid sequences are read from the N- to the C-

terminal end of the peptide
Glu- Ala - Lys - Gly - Tyr - Ala
peptide bond has partial double-bond character.
Structure of Proteins
Primary Structure
• The primary structures of all of the diverse
human proteins are synthesized from 20 amino
acids arranged in a linear sequence determined
by the genetic code.
• Each three-base (nucleotide) sequence (codon)
within the coding region of a gene (the genetic
code) specifies which amino acid should be
present in a protein.
 Structure of Proteins
Secondary Structure
§ This is a region of the spatial arrangement with
regular repeating units of the polypeptide it describe
the relation between the adjacent amino acid
§ There are many types of secondary structure,
1. the α-helix and
2. the β-sheet
3. the β -turn
A. alpha-helix
right-handed helical structure in which there is
3.6 residues/turn
• the helix is stabilized by hydrogen bonds
N----H----O between the N atom of amino acid and
O of the 4th amino acid in the primary structure.
• Proline can not fit because it can not form the
proper H bonds and lead to break in the helix.
 Structure of Proteins
Secondary Structure (α-helix)
§ A complete turn of the helix
contains an average of 3.6
aminoacyl residues
§ The R groups of each aminoacyl
residue in an α helix face outward
§ The stability of an α helix arises
primarily from hydrogen bonds
formed between the oxygen of the
peptide bond carbonyl and the
hydrogen atom of the peptide
bond nitrogen of the fourth
residue down the polypeptide
chain
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Secondary Structure – Alpha Helix

• arrangement of amino
acids with the
polypeptide chain in a
corkscrew shape
• Held by H bonds
between the H of –N-H
group and the –O of C=O
of the fourth amino acid
along the chain
• Looks like a coiled
“telephone cord”
 Structure of Proteins
Secondary Structure (β-sheet)
§ all of the peptide bond components are
involved in hydrogen bonding
forming zigzag shape
§ are composed of two or more peptide
chains (β-strands)
§ are almost fully extended
§ antiparallel to each other (with the
N-terminal and C-terminal ends
of the β-strands alternating)
§ parallel to each other (with all the
N-termini of the β-strands together
B) B-Sheets
• These are regular regions contain 5-10 from different
regions in the primary structure lie fully extended
and parallel or antiparallel to each other and it is
stabilized by H bonds.

Schematic representation
of protein structure
Cylinder for alpha helix
Arrows for B-sheets
3) Tertiary structure
• Specific overall shape of a protein
• the tertiary structure describe the 3-dimensional
structure of a protein stabilized by

disulfide –S–S– +
ionic –COO– H3N–
H bonds C=O HO–
hydrophobic –CH3 H3C–
 Structure of Proteins
Tertiary Structure
§ The three-dimensional
structure of proteins
vary for
protein to other
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Quaternary Structure
• Proteins with two or more chains
• Example is hemoglobin
Carries oxygen in blood
Four polypeptide chains
Each chain has a heme group to
bind oxygen
 Structure of Proteins
Quaternary Structure
§ Define the relation between subunits in polymeric proteins
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Denaturation
Protein denaturants rupture non covalent bond in
proteins with loss of biologic activity.
Disruption of secondary, tertiary and quaternary
protein structure by
Heat (Break H bonds )
organics solvent (disrupt hydrophobic interaction)
acids/ bases
Break H bonds between polar R groups and
ionic bonds
heavy metal ions (react with SH group)
The result of denutration is
Loss of function of protein( e,g
enzymes ,hormones)
Decrease solubility
Decrease viscisity
Increase digestability