Amino acids chemistrymanhalacademy.edu.sd/new_site/wp-content/uploads/2020/04/...Protein chemistry...

Amino acids chemistry

Dr. Almoeiz Yousif

MS.c.,Ph.D.,MEE

Thursday, April 23, 2020 1

Introduction:

• Amino acids are the building unit of proteins.

• There are than 300 amino acids found in nature.

• only 20 are usually found in proteins.


Structure

• The general structure of amino acids includes an amino

group and a carboxyl group, both of which are bonded to

the α-carbon (the one next to the carboxyl group).


• The α -carbon is also bonded to a hydrogen and to the side

chain group, which is represented by the letter R. The R

group determines the identity of the

• particular amino acid


Physical and chemical properties

• 1- Most amino acids are soluble in water , have a sweet

taste and some are widely used in food industry .

• 2- they are optically active .


• 3- Amino acids are considered as amphpolytes (bipolar), this

is due to presence of both amino and acidic groups

• 4- In aqueous or physiological conditions . Thy are found in the

form of zwitter ion (di polar).

• 5- they can act as buffers


D& L amino acids:


Classification of amino acid • We have four systemic classification of amino acid

according to:

• 1.Side chain.

• 2.solubilty .

• 3. Nutritional classification .

• 4. Metabolic classification.


Amino Acids with Aliphatic R-Groups

Glycine Alanine Valine

Leucine Isoleucine Thursday, April 23, 2020 10

Non-Aromatic Amino Acids with Hydroxyl R-Groups

Sulfur containing Amino acids

Serine Threonine

Cysteine Methionine Thursday, April 23, 2020 11

Acidic Amino Acids and Their Amides

Aspartic Acid Asparagine

Glutamic Acid Glutamine Thursday, April 23, 2020 12

Basic Amino Acids

Arginine Lysine

Histidine Thursday, April 23, 2020 13

Aromatic Amino Acids

Phenylalanine Tyrosine

Tryptophan Thursday, April 23, 2020 14

Proline

Imino Acid


Classification by solubility

•There are two broad classes of amino acids

based upon whether the R-group is

1. Hydrophobic

2. Hydrophilic.


The hydrophobic amino acids

The hydrophobic amino acids tend to repel the

aqueous environment and, therefore, reside

predominantly in the interior of proteins.

The side chain of this class of amino acids does not

ionize nor participate in the formation of H-bonds.


The hydrophilic amino acids

The hydrophilic amino acids tend to interact with the

aqueous environment; polar or charged side chain.

They are often involved in the formation of H-bonds

They are predominantly found on the exterior surfaces of

proteins or in the reactive centers of enzymes


Dietary Classification of Amino Acids

Some amino acids can be formed from metabolic

intermediates in the mammalian cells, thus are not

necessary taken in food (Dietary non-essential) .

Other amino acids must be obtained from diet, thus they

are termed (Dietary essential)


peptide pond

• 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.

For example, valine and alanine can form the dipeptide

valylalanine through the formation of a peptide bond


• Peptide bonds are not broken by conditions that denature

proteins, such as heating or high concentrations of urea.

Prolonged exposure to a strong acid or base at elevated

temperatures is required to hydrolyze these bonds

nonenzymically.


peptide pond

• Peptide bond formation is a condensation reaction leading

to the polymerization of amino acids into peptides and

proteins.

• Peptides are small consisting of few amino acids.


Important of peptides

• Enzymes, many hormones, antibodies, antitumor agents

and neurotransmitters are peptides.

• Proteins are polypeptides of greatly divergent length and

amino acid composition.


Formation of peptide bond


Protein chemistry

• Definition

• Proteins are polymers of amino acids linked by peptide bond.

Proteins are formed of a set of 20 amino acids.

They are called standard amino acids.

There are more than 300 amino acid in nature, only these 20 amino acids

are found in protein from all living sources (bacteria, animal and plant).


Importance of protein:

• 1- enzymes

• hormones

• 3- structural

• 4- transport

• 5- immunoglobulin's

• 6- clotting factors

• 7- complements

• 8- buffers


Protein Structure

• Primary : linear sequence of amino acids

• Secondary: localized folding

• Tertiary: overall 3-D structure

• Quaternary: association of 2 or more protein subunits into a

protein


Levels of structure in proteins


1.Primary structure

no non-covalent bonds. Only peptide bonds


2.Secondary Structures

• The two very important secondary structures of proteins

are:

• a-helix

• b-pleated sheet

• Both depend on hydrogen bonding between the amide H

and the carbonyl O further down the chain or on a parallel

chain.


Secondary Structure – Alpha Helix

• 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”


b-Pleated Sheet

• All of the carbonyl O and amide H are involved in the H bonds with the chain nearly completely extended.


Two possible orientations

Parallel

Antiparallel


3.Tertiary Structure

• • 3D folding of the protein

• Non-covalent bonds found

• • Non-polar residues are buried inside, polar

residues are exposed outwards to aqueous

environment


Interactions Involved in Tertiary Structure


4.Quaternary Structure

• • Association of more than

• one polypeptides

• • Each unit of this protein is called as a subunit


Level of Proteins structure


Protein Denaturation

• is the breakdown of all non-covalent bonds in a protein, causing loss of function.

• Disruption of secondary, tertiary and quaternary protein structure. Does not alter primary structure

-caused by changes in:

-pH

-temperature

-salt concentration

-heavy metal ions


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