Amino Acid and Protein Chemistry

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Lecture 1, 2nd semester Amino acid and protein chemistry
Amino acid and protein chemistry

Part 1
Medical biochemistry
by
Dr Yasmine Sami Nassir
2023-2024
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Learning outcomes:
1. Describe the major chemical components of the human body.

2. Discuss the properties of amino acid.
3. Describe the general structure of an amino acid
4. State the different classifications of amino acids and recognize them
based on the characteristics of their side chains
Biochemistry, sometimes called biological chemistry, is the study of

chemistry processes within and related to living organisms. It focuses
heavily on the role, function and structure of biomolecules, such as
carbohydrates, lipids, proteins and nucleic acids, which provide the
structure of cells and perform many functions associated with life.
The principle types of biological molecules or biomolecules are,

carbohydrates, lipids, proteins and nucleic acids.
Many of these molecules are complex molecules called polymers, which

are constructed from monomer subunits. Most polymerization reactions
involving the building of small organic biomolecules into larger more
complex ones occur by the formation of water. This is called a
condensation reaction in which water is removed from the reacting
monomer unites to form the biopolymers.
Introduction to amino acids and proteins chemistry
Proteins are the most abundant and functionally diverse molecules in living
systems. They are about 50% of the dry weight of most cells, and are the
most structurally complex molecules known. Proteins are organic

nitrogenous compounds consisted of carbon (C), hydrogen (H), oxygen (O)

and nitrogen (N). They may also contain sulfur (S).
Proteins are biopolymers built from monomeric units called amino acids.
More than 700 amino acids occur naturally, but only 20 of them are
commonly found as constituents of mammalian proteins. These are the
only amino acids that are coded for by DNA, the genetic material in the cell.
Protein function depends on both:
1. Amino acid content
2. Amino acid sequence.
To understand protein function, we must first understand the nature of

amino acids.
Structure of the amino acids
Amino acids are the building blocks (structural units) of proteins. Proteins
are polymers of amino acids monomers linked together by peptide
linkages.
Each amino acid (except for proline, which has a secondary amino group)
has a carboxyl group, a primary amino group, and a distinctive side chain
(R- group) bonded to the α-carbon atom as shown below.
All the natural 20 amino acids contain alpha α- amino and α- carboxylic
groups.

Each amino acid is formed of:
- An amino group (-NH2).

- A carboxylic group(-COOH)
- A hydrogen atom (-H).
- A side chain radical (-R).
All these groups are attached to a carbon atom called α carbon atom,
which is the first carbon attached to the COOH group. At physiologic pH
(approximately pH 7.4), the carboxyl group is dissociated, forming the
negatively charged carboxylate ion (–COO –), and the amino group is
protonated (–NH3+). In proteins, almost all of these carboxyl and amino
groups are combined through peptide linkage. Amino acids differ from each
other in the structure of their side chains (radical or R groups).
Each amino acid name can be abbreviated into either three letters or one
letter. Table 1 displays the abbreviations for the amino acids.

Table 1. α-Amino Acid Abbreviations
Properties of amino acids
1. Soluble in polar solvent

2. Colorless
3. Stereoisomerism (optical activities)
4. Amphoteric property

5. Isoelectric point
6. Buffering activity
1. Amino acids solubility
Amino acids are soluble in polar solvents like water and alcohol due to
presence of charged groups, and they are insoluble in non-polar solvents
2. Amino acids are colorless
Amino acids do not absorb visible light. Aromatic amino acids absorb
ultraviolet light at wave length 280nm.
3. The stereoisomers of amino acids
The α-carbon of an amino acid is attached to four different chemical groups

and is, therefore, a chiral or optically active carbon atom. Glycine is the
exception because its α-carbon has two hydrogen substituents and,
therefore, is optically inactive. Amino acids that have an asymmetric center
at the α-carbon can exist in two forms, designated D and L, that are mirror
images of each other.
D and L forms of alanine are mirror images

The two forms in each pair are termed stereoisomers, optical isomers, or
enantiomers. All amino acids found in proteins are of the L-configuration.
However, D-amino acids are found in some antibiotics and in plant and
bacterial cell walls.
By stereoisomerism, molecules have the same molecular formula and

same structural group but differ in orientation of the groups in space. The
form of the enantiomer can be determined from the location of the NH2
group on the chiral carbon. If the NH2 group is on the left side, this is the L-
enantiomer, and if the NH2 group is on the right, this is the D-enantiomers.
4. Amphoteric properties
The property of amino acid to behave as an acid (proton donor) or as a

base (proton accepter). In the alkaline media (low H+ concentration),
carboxyl group donates a proton and the aa becomes negatively charged.
Amino acid migrates to the anode in an electric field.
In the acidic media (high H+ concentration), amino group accepts a proton

and the aa becomes positively charged. Amino acid migrates to cathode in
an electric field.
5. Isoelectric point
The generic structure of an amino acid at pH 7 is shown below.
Isoelectric points can be defined according to specific pH range. The net

electric charge is found to have zero value at characteristic pH value. Such

a point is defined as an isoelectric point. At specific pH, the aa will carry

zero net charge (number of positive charge = number of negative charge).
The aa is electrically neutral and it does not move in an electrical field.
Each amino acid has an isoelectric point, (pI) numerically equal to the pH at
which the zwitterion concentration is at a maximum. The amino acid has no
NET charge at its pI; it has one positive and one negative charge.
At a pH less than the value of the isoelectric point, the amino acid is
protonated and has a POSITIVE charge; at a pH greater than the pI the
amino acid is deprotonated and has a NEGATIVE charge.
At pH 7, the amino acid is a zwitterion, or dipolar ion. A unique side chain,

or R group, characterizes each amino acid.
The (neutral) zwitterion is the usual form amino acids exist in solution.
Depending on the pH, there are two other forms, an anion and a cation:

The titration curve of glycine
6. Buffering activity
The structure of an amino acid allows it to act as both an acid and a base.
An amino acid has this ability because at a certain pH value (different for
each amino acid) nearly all the amino acid molecules exist as zwitterions. If
acid is added to a solution containing the zwitterion, the carboxylate group
captures a hydrogen (H+) ion, and the amino acid becomes positively
charged. If base is added, ion removal of the H+ ion from the amino group
of the zwitterion produces a negatively charged amino acid. In both
circumstances, the amino acid acts to maintain the pH of the system—that
is, to remove the added acid (H+) or base (OH−) from solution.

α- Amino acids can be described as amphoteric as they can react with both
acid and alkali. They are effective buffers in biological systems. At very low
pH all α-amino acids exist as ions with overall positive charge, while at high
pH they exist as ions with an overall negative charge.
Classification of amino acids
1. Chemical classification of amino acids: based on the structure of the

side chain (R group).
 Aliphatic amino acids

- Aliphatic: Glycine (the smallest amino acid) and Alanine, branched
chain amino acid include: Valine, Leucine, Isoleucine.

- Side chain containing OH group: Serine, Threonine

- Side chain containing SH group: Cysteine, Methionine (methyl donor)
- Side chain containing acidic groups: Aspartic acid and Glutamic acid
- Side chain containing amide groups: Asparagine and Glutamine
- Side chain containing basic groups: Arginine (contains guanidino
group) and Lysine.
 Cyclic amino acids
- Aromatic ring: Phenylalanine, Tyrosine, Tryptophan (contain indole
ring)
- Heterocyclic: Histidine (contain imidazole ring), (basic amino acid)
- Imino group: Proline
2. Classification according to polarity
Amino acids are classified according to the polarity of their R groups or

their tendency to interact with water at physiological pH (7.4) into:
- Amino acid with non-polar side chains (Do not interact with water):
Glycine, Alanine, Valine, Leucine, Isoleucine, Phenylalanine,
Methionine Proline and Tryptophan
- Amino acid with polar side chains (interact with water)
a. Polar with uncharged side chains: Cysteine, Serine, Threonine,
Tyrosine, Asparagine and Glutamine
b. Polar with charged R group:
1. Negatively charged radicals: Aspartic acid and Glutamic acid
2. Positively charged radicals: Lysine, Arginine and histidine.


3. Biological (Nutritional) classification of amino acids
According to the biological (Nutritional) importance, amino acids are

classified into essential (indispensable or must be provided by diet) and
non-essential (dispensable or can be synthesized by body) amino acids.

a. Essential amino acids (10 amino acids): valine, leucine, isoleucine,

phenylalanine, methionine, tryptophan, threonine, histidine, lysine,
and arginine.
- They cannot be synthesized in the body, they have to be taken in diet
- They are essential for protein biosynthesis
- They are essential for normal health and normal metabolism
- Their absence may result in development of deficiency diseases
b. Nonessential amino acids:
- can be synthesized in the body from essential amino acids
- Not essential to be taken in diet
- They are important for protein synthesis
c. Semi essential amino acids: Arginine and Histidine, they are
synthesized in the body in quantities less than the requirement so
they must be taken in diet. They are required in quantities greater
than that formed inside the body especially for growing children.
 Protein of high biological value contain 10 essential amino acids, for

example animal proteins, while proteins of low biological value, such
as vegetable proteins which lack one or more of essential amino
acids.
 Proteins that contain all the essential amino acids are called
complete proteins.
 Soybeans and most proteins found in animal products are complete
proteins.
 Some plant proteins are incomplete proteins because they lack one
or more essential amino acid.

 Complete proteins (high biological value) can be obtained by

combining foods like rice and beans.
4. Metabolic classification of amino acid: based on the metabolic fate of

amino acids in the body.

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Lecture 1, 2nd semester Amino acid and protein chemistry

Flexcil - The Smart Study Toolkit & PDF, Annotate, Note

Lecture 1, 2nd semester Amino acid and protein chemistry

1. Describe the major chemical components of the human body.

Biochemistry, sometimes called biological chemistry, is the study of

The principle types of biological molecules or biomolecules are,

Many of these molecules are complex molecules called polymers, which

Introduction to amino acids and proteins chemistry

Flexcil - The Smart Study Toolkit & PDF, Annotate, Note

Lecture 1, 2nd semester Amino acid and protein chemistry

nitrogenous compounds consisted of carbon (C), hydrogen (H), oxygen (O)

1. Amino acid content

2. Amino acid sequence.

To understand protein function, we must first understand the nature of

Structure of the amino acids

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Lecture 1, 2nd semester Amino acid and protein chemistry

Each amino acid is formed of:

- An amino group (-NH2).

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Lecture 1, 2nd semester Amino acid and protein chemistry

Table 1. α-Amino Acid Abbreviations

Properties of amino acids

1. Soluble in polar solvent

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Lecture 1, 2nd semester Amino acid and protein chemistry

1. Amino acids solubility

2. Amino acids are colorless

3. The stereoisomers of amino acids

The α-carbon of an amino acid is attached to four different chemical groups

D and L forms of alanine are mirror images

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Lecture 1, 2nd semester Amino acid and protein chemistry

By stereoisomerism, molecules have the same molecular formula and

The property of amino acid to behave as an acid (proton donor) or as a

In the acidic media (high H+ concentration), amino group accepts a proton

The generic structure of an amino acid at pH 7 is shown below.

Isoelectric points can be defined according to specific pH range. The net

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Lecture 1, 2nd semester Amino acid and protein chemistry

a point is defined as an isoelectric point. At specific pH, the aa will carry

At pH 7, the amino acid is a zwitterion, or dipolar ion. A unique side chain,

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Lecture 1, 2nd semester Amino acid and protein chemistry

The titration curve of glycine

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Lecture 1, 2nd semester Amino acid and protein chemistry

Classification of amino acids

1. Chemical classification of amino acids: based on the structure of the

 Aliphatic amino acids

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Lecture 1, 2nd semester Amino acid and protein chemistry

- Side chain containing OH group: Serine, Threonine

2. Classification according to polarity

Amino acids are classified according to the polarity of their R groups or

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