Dr.

Firas Shawqi Algburi Amino acids and Peptides

Amino Acids

Amino acids are organic compounds that contain amine (–NH2) and carboxyl (–
COOH) functional groups, along with a side chain (R group) specific to each amino acid.

The key elements of an amino acid are carbon (C), hydrogen (H), oxygen (O),
and nitrogen (N), although other elements are found in the side chains of certain amino
acids.

Amino acids can be classified according to the core structural functional groups' locations
as alpha- (α-), beta- (β-), gamma- (γ-) or delta- (δ-) amino acids; other categories relate to
polarity, pH level, and side chain group type (aliphatic, acyclic, aromatic, containing
hydroxyl or sulfur, etc.). In the form of proteins, amino acid residues form the second-
largest component (water is the largest) of human muscles and other tissues. Beyond their
role as residues in proteins, amino acids participate in a number of processes such as
neurotransmitter transport and biosynthesis.

In biochemistry, amino acids which have the amine group attached to the (alpha-) carbon
atom next to the carboxyl group have particular importance. They are known as α-amino
acids (generic formula H2NCHRCOOH in most cases, where R is an organic substituent
known as a "side chain").

General Structure
In the structure shown at the top of the page, R represents a side chain specific to each
amino acid. The carbon atom next to the carboxyl group is called the α–carbon. Amino
acids containing an amino group bonded directly to the alpha carbon are referred to
as alpha amino acids. These include amino acids such as proline which contain secondary
amines, which used to be often referred to as "imino acids”.

General structure of α-Amino acid

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Dr.Firas Shawqi Algburi Amino acids and Peptides

Isomerism
Alpha-amino acids are the common natural forms of amino acids. With the exception
of glycine, other natural amino acids adopt the L configuration. While L-amino acids
represent all of the amino acids found in proteins during translation in the ribosome.

Side chains
Amino acids are usually classified by the properties of their side chain twenty of the
proteinogenic amino acids are encoded directly by triplet codons in the genetic code and
are known as "standard" amino acids. Their structures have shown in the scheme below

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Dr.Firas Shawqi Algburi Amino acids and Peptides

Occurrence and functions in biochemistry

1-Proteinogenic amino acids
Amino acids are the structural units (monomers) that make up proteins. They join together
to form short polymer chains called peptides or longer chains called either polypeptides or
proteins. These chains are linear and unbranched, with each amino acid residue within the
chain attached to two neighboring amino acids. The process of making proteins encoded
by DNA/RNA genetic material is called translation and involves the step-by-step addition
of amino acids to a growing protein chain by a ribozyme that is called a ribosome. The
order in which the amino acids are added is read through the genetic code from
an mRNA template, which is an RNA copy of one of the organism's genes.

Twenty-two amino acids are naturally incorporated into polypeptides and are
called proteinogenic or natural amino acids. Of these, 20 are encoded by the
universal genetic code. The remaining 2, selenocysteine and pyrrolysine, are incorporated
into proteins by unique synthetic mechanisms.

2-Non-proteinogenic amino acids

Aside from the 22 proteinogenic amino acids, many non-proteinogenic amino acids are
known. Those either are not found in proteins (for
example carnitine, GABA, levothyroxine) or are not produced directly and in isolation by
standard cellular machinery(i.e., 4-hydroxyproline, 5-hydroxylysin and selenomethionine).

In humans, non-protein amino acids also have important roles as metabolic intermediates,
such as in the biosynthesis of the neurotransmitter gamma-aminobutyric acid (GABA).
Many amino acids are used to synthesize other molecules, for example:

-Tryptophan is a precursor of the neurotransmitter serotonin.

-Tyrosine is precursors of the catecholamine neurotransmitters dopamine, epinephrine and

norepinephrine and various trace amines.

-Phenylalanine is a precursor of phenethylamine and tyrosine in humans. In plants, it is a

precursor of various phenylpropanoids, which are important in plant metabolism.

-Glycine is a precursor of porphyrins such as heme.

-Arginine is a precursor of nitric oxide.

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Dr.Firas Shawqi Algburi Amino acids and Peptides
-Ornithine and S-adenosylmethionine are precursors of polyamines.

-Aspartate, glycine, and glutamine are precursors of nucleotides. However, not all of the
functions of other abundant nonstandard amino acids are known.

3-Non-standard amino acids

The 20 amino acids that are encoded directly by the codons of the universal genetic
code are called standard or canonical amino acids. A modified form of methionine (N-
formylmethionine) is often incorporated in place of methionine as the initial amino acid of
proteins in bacteria, mitochondria and chloroplasts. Other amino acids are
called nonstandard or non-canonical. Most of the nonstandard amino acids are also non-
proteinogenic (i.e. they cannot be incorporated into proteins during translation), but two of
them are proteinogenic, as they can be incorporated translationally into proteins by
exploiting information not encoded in the universal genetic code.

ESSENTIAL AMINO ACIDS

Essential amino acids cannot be made by the body. As a result, they must come from food.
NONESSENTIAL AMINO ACIDS

Nonessential means that our bodies produce an amino acid, even if we do not get it from
the food we eat.

Zwitterions
In aqueous solution amino acids exist in two forms (as illustrated at the right), the
molecular form and the zwitterion form in equilibrium with each other.

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Dr.Firas Shawqi Algburi Amino acids and Peptides
Because all amino acids contain amine and carboxylic acid functional groups, they are
amphiprotic. The amino acid in the acidic medium carries a positive charge, while in the
basic medium it carries a negative charge, while in the neutral medium it carries two
charges, and that also depends on the nature of the amino acid.

Zwitterion
Isoelectric point(pI)
The isoelectric point (pI) is the pH at which a particular molecule carries no net electrical
charge. The net charge on the molecule is affected by the pH of its surrounding
environment and can become more positive or negative due to the gain or loss of protons,
respectively. A net charge of 0 may result in protein Aggregation. It is important to note
that the calculation of the pI for a protein purely based on its amino acid sequence is often
imprecise, since protein folding, modification and also labeling can influence the pI.

Calculating pI values
For an amino acid with only one amine and one carboxyl group, the pI can be calculated
from the mean of the pKas of this molecule.

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Dr.Firas Shawqi Algburi Amino acids and Peptides

Peptides

Peptides: are short chains of between two and fifty amino acids, linked by peptide bonds.
Peptide bond: A bonding force formed between two amino acids (between the carboxyl
group of the first amino acid and the amine group of the second amino acid) after drawing
a water molecule between them

The peptide is written from the free amine terminal (left side) and ending with the free
carboxylate (right side).

Polypeptide: is a longer, continuous, unbranched peptide chain of up to approximately

fifty amino acids.

A polypeptide that contains more than approximately fifty amino acids is known as a
protein.

Example families
The peptide families in this section are ribosomal peptides, usually with hormonal activity.
All of these peptides are synthesized by cells as longer "propeptides" or "proproteins" and
truncated prior to exiting the cell. They are released into the bloodstream where they
perform their signaling functions.

Antimicrobial peptides
• Magainin family

• Cecropin family

• Cathelicidin family

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Dr.Firas Shawqi Algburi Amino acids and Peptides
• Defensin family

Vasoactive intestinal peptides

• VIP (Vasoactive Intestinal Peptide; The endogenous peptide PHM27)

• GHRH (Growth Hormone Releasing Hormone)

• Glucagon

• Secretin

Calcitonin peptides
• Calcitonin

• Amylin

Other peptides
Glutathione (GSH): is an antioxidant in plants, animals, fungi, and some bacteria and
archaea. Glutathione is capable of preventing damage to important cellular components
caused by reactive oxygen species such as free radicals, peroxides, lipid peroxides, and
heavy metals. It is a tripeptide with a gamma peptide linkage between the carboxyl group
of the glutamate side chain and cysteine. The carboxyl group of the cysteine residue is
attached by normal peptide linkage to glycine.

Oxytocin (Oxt): is a peptide hormone and neuropeptide. It is normally produced in the

hypothalamus and released by the posterior pituitary. It plays a role in social bonding,
reproduction, childbirth, and the period after childbirth.

The deduced structure of the active nonapeptide is:

Cys – Tyr – Ile – Gln – Asn – Cys – Pro – Leu – Gly – NH2

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Dr.Firas Shawqi Algburi Amino acids and Peptides

Angiotensin: is a peptide hormone that causes vasoconstriction and an increase in blood

pressure. It is part of the renin–angiotensin system, which regulates blood pressure.
Angiotensin also stimulates the release of aldosterone from the adrenal cortex to promote
sodium retention by the kidneys.

The sequence of peptide

To detect the amino acid sequence in peptides, it is used for this assignment. Some of them
reveal the amino side and others reveal the carboxylate side.

Sanger's reagent (DNB): 1-Fluoro-2,4-dinitrobenzene is a chemical that reacts with

the N-terminal amino acid of peptides.

1-Fluoro-2,4-dinitrobenzene

Edman reagent (Phenyl isothiocyanate): is a method of sequencing amino acids

in a peptide. In this method, the amino-terminal residue is labeled and cleaved from the
peptide without disrupting the peptide bonds between other amino acid residues.

Phenyl isothiocyanate

Carboxypeptidase: It reveals the amino acid sequence of the carboxylic terminal.

EX: Penta peptide contain the following amino acids (Ala., Leu., Gly., Tyr., Ser), treated
with sanger reagent gave DNB-Ser. Gly was isolated when treated with carboxypeptidase,
and the partial hydrolysis of the peptide gave the following fragment(Ser.-Leu.),(Tyr.-
Gly.) and (Ala.). Write the sequence of the peptide.