Department of

Biochemistry
Faculty of Medicine – Umm Alqura University

Basics of Biochemistry
First Year – MBBS & Dentistry
program
 Biochemical Aspects of
Amino Acids and Proteins I
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Amino Acids and Proteins
Proteins are organic compounds of high molecular weight formed
by a number of Amino acids

Amino acids are the building blocks (units) of proteins.

About 300 amino acids occur in nature. Only 20 of them enter in

protein synthesis. They called L, α-amino acids
Structures of Amino Acids
Tetrahedral carbon atom (α- carbon) attached to:
.


α α
Note: Allamino acids in protein
have chiral carbon except glycine.
I. Chemical classification:
A. Amino Acids with Hydrophobic (Nonpolar) side chain (R Group).
B. Amino Acids with Hydrophilic (Polar) side chain (R Groups).
II. Nutritional classification:
A- Essential amino acid:
B- Non essential amino acid:
III. Biological or metabolic classification:
A. Glucogenic amino acids:
B. Ketogenic amino acid:
C. Both glucogenic and ketogenic amino acids:
 • The hydrophobic amino acids tend to avoid the aqueous environment
• Their side chain (R) cannot give H+ ions (protons) or receive it (non
polar).
• They do not enter in the formation of hydrogen or ionic bonds.
They include:

Glycine- Alanine – Valine

Leucine – Isoleucine
Methionine – Proline
Phenylalanine -Tryptophan
2. Hydrophilic; polar, amino acids:
 Hydrophilic amino acids tend to interact with the aqueous
environment

 Hydrophilic amino acids tend to the formation of H-bonds.

 Hydrophilic amino acids tend to predominantly found on the

exterior surfaces proteins or in the reactive centers of enzymes

Acidic amino acids

Basic amino acids
(Mono amino dicarboxylic)
(Diamino mono carboxylic)
 Nonpolar

Glycine Alanine Valine Leucine Isoleucine

(Gly or G) (Ala or A) (Val or V) (Leu or L) (Ile or I)

The 20 amino acids

Methionine Phenylalanine Tryptophan Proline
of proteins (Met or M) (Phe or F) (Trp or W) (Pro or P)
Asparagine
Polar (Asn or N)

Serine Threonine Cysteine Tyrosine Glutamine

(Ser or S) (Thr or T) (Cys or C) (Tyr or Y) (Gln or Q)

Electrically
charged
Acidic Basic

Aspartic acid Glutamic acid Lysine Arginine Histidine

(Asp or D) (Glu or E) (Lys or K) (Arg or R) (His or H)
• A. Essential Amino Acids
They are not synthesized in the body.
Should be taken in diet.
Their deficiency in diet leads to various nutritional
deficiency diseases
B. Non Essential Amino Acid
 These Amino Acid are synthesized in the body
from suitable precursors
 not necessarily to be present in the proteins of
diet.
 However they are also required for the normal
protein synthesis.
Semi- essential Amino Acid
Histidine and arginine are essential for the growing
children, but not essential for the adult individual.
III. Biological or metabolic classification:
• It is based upon the metabolic fate of amino acid, in the body whether it
gives glucose, ketone bodies or both.
1.Glucogenic amino acids:
• All amino acid, are glucogenic except leucine and lysine.
• They are converted in the body to carbohydrate only

2.Ketogenic amino acid:

• Leucine (pure ketogenic) and lysine.
• It is converted in the body to ketone bodies only.
3.Both glucogenic and ketogenic amino acids:
• Tyrosine - phenylalanine - tryptophan - isoleucine.
• They are converted in the body to carbohydrate and ketone bodies.
1- Amino acids stereoisomers
• All amino acids except glycine are optically active
• They contain an asymmetric carbon atom.
• Amino acids have stereoisomers.
• In biological systems, only L-amino acids are used in proteins
COOH COOH COOH COOH
H2N H H NH2 H2N H H NH2
CH3 CH3 CH2SH CH2SH

L-Alanine D-Alanine L-Cysteine D-Cysteine

2- Amphoterism (Acid-Base Properties)
The amphoteric substance is that:
 act as an acid when a base added to it and as a base when an acid is
added to it.
 Amphoteric properties of amino acids are due to the presence basic
group (NH2) and acidic group (COOH)
3-Zwitter ion or Dipolar ion formation
• The form of amino acid that carrying equal number of (+) and (-) charges
is electrically neutral and called Zwitter ion or Dipolar ion.
•

• Zwitterion = double ion – when both NH3+ and COO- are ionized
• (pI)
• α α

• Proteins are formed by a number of amino acids united together by

peptide link
 The molecule of protein that contains one peptide bond and 2 amino
acid, called Dipeptide.

 The molecule which contains two peptide bond and 3 amino acids,
called Tripeptides.

 The molecule which contains from 20-50 amino acids is called

polypeptides.

 A protein consists of one or more polypeptides

Protein Structure
Biological Importance Of Proteins
• Proteins are organic compounds of high molecular weight, that contain C, H, O, S, N

1. They provide the body with nitrogen, sulfur, and some vitamins.
2. Formation of enzymes and protein hormones.
3. Formation of supporting structures in the body as bone, cartilage, skin, nails, hair and
muscles.
4. They enter in the formation of buffer system of the blood.
5. They share in the formation of haemoglobin which carries O2 from the lung to tissues.
6. They include plasma proteins which carry hormones, minerals and lipids.
7. They enter in formation of antibodies which play an important role in the defensive mechanism
of the body.
Biological value of proteins
(Complete protein)

• Proteins in diet comes from both animal and vegetable sources.

• Most animal sources (meat, milk, eggs) provide complete protein,
They contain all of the essential amino acids, thus, these
proteins are of high Biological value
• Vegetable sources usually missing some essential amino acids, thus
proteins of low Biological value
Protein Structure

• The protein molecule has Four Levels of Protein Structure:

1.Primary structure
2.Secondary structure
3.Tertiary structure
4.Quaternary structures
1- Primary Structure
Primary structure is the number and linear sequence
of amino acids in the polypeptide chain
The bond responsible for primary structure is peptide
bond
The amino acids are linked in a head-to-tail
fashion
 The amino acid that has the amino group free is N-
terminal end, and the amino acid that has the carboxyl
group free is the C-terminal end.
 2-Secondary structure
•

• Types of protein folding for Secondary structure

 Helix and β- pleated sheet are composed of one or two
polypeptide chains .
 α-structure (α-helix) in which the twisting of a molecule
in opposite peptide bonds in the right direction
 β-structure (β- pleated sheet) in which the peptide chains
exist in a zigzag shape

 The bond responsible for α-helix and β-structure are

hydrogen bonds and peptide bond.
 3-Tertiary Structure
• It is the final arrangement of single polypeptide chain, where its coiled structure is
further twisted into specific layers.
• Tertiary structure is responsible for many of the physical and chemical properties
of the protein
• Is stabilized by
• Hydrophobic and hydrophilic interactions
• Ionic bonds (Salt bridges)
• Disulfide bonds
• Hydrogen bonds
4- Quaternary structure

Many proteins consist of a single polypeptide chain, and are defined

as monomeric proteins.
However, others may consist of two or more polypeptide chains that
may be structurally identical or totally unrelated.
The arrangement of these polypeptide subunits is called the quaternary
structure of the protein.
• Protein having quaternary structure including
1.Insulin (2 subunits),
2.Globin of hemoglobin (4 subunits).
Summary of Protein Structure

Primary structure is the amino acid sequence

Secondary structure is how the amino acids in sequence fold up

locally. Examples are a-helixes and b-strands.

Tertiary structure is the 3-dimensional folding of the secondary

structural elements in space.

Quaternary structure is the association of multiple subunits, each

with a tertiary structure and each a unique gene product.
Thank
you