PROTEIN CHEMISTRY

Proteins
Proteins are complex organic nitrogenous compounds of high molecular weight Proteins are the most complex materials produced in nature They are consisting largely or entirely of -amino acids linked together by peptide linkages

Proteins
The name protein is derived from the Greek word proteios of prime importance this is because proteins are the basis of the cytoplasm of cells and are present in all living organisms Without proteins life would NOT be possible Proteins are the most abundant macromolecules in living cells and constitute 50 % or more of their dry weight

Proteins
Proteins are polymers of -Amino Acids. Proteins are synthesized from only 20 amino acids, known as the common amino acids Amino acids are formed mainly of carbon, hydrogen, oxygen and nitrogen Nitrogen is a characteristic component of proteins forming about 16% of their weight i.e. 100 g of protein contains 16 g of nitrogen Proteins perform many essential functions

BIOLOGICAL IMPORTANCE OF PROTEINS

1- Plasma membrane proteins (channel, carrier, pump proteins) regulate the transfer of various substances across the cell membrane 2- All receptors are protein in nature 3- All enzymes are proteins in nature 4- All antibodies (Immunogobulins) are proteins in nature

BIOLOGICAL IMPORTANCE OF PROTEINS

5- Some hormones are proteins in nature e.g. Insulin, Glucagon, Growth hormone, FSH, LH. 6- Some proteins are protective e.g. Keratins (skin, hair, nails) make the skin resistant to chemicals 7- Some proteins have supportive functions e.g. Collagen; the most abundant protein in animals. 8- Hemoglobin is a protein carries O2 in the blood

BIOLOGICAL IMPORTANCE OF PROTEINS

9- Actin and Myosin are contractile proteins found in muscle cells and are responsible for muscular contraction 10- Amino acids are converted to other nitrogenous substances of great physiologic importance e.g. Creatine,

Histamine, Serotonin, Pyrimidines.

Heme, Purines,

AMINO ACIDS
- Amino acids are the building units of proteins. Each - amino acid consists of an amino group (-NH2), a carboxylic acid group ( -COOH ), a hydrogen atom (-H ) and a side chain group (-R), all connected to a carbon atom called carbon atom.

AMINO ACIDS
The -carbon is the first carbon adjacent to the COOH group. The side chain group ( R ) is specific and unique for each amino acid. The R may be a hydrogen, a straight or branched- chain aliphatic group, an aromatic ring or a heterocyclic ring.

AMINO ACID
Hydrogen atom

H
side chain radicle carboxylic group

R
- carbon atom

C NH2

COOH
amino group

Representation of Amino Acid

Basic Amino Acid Structure

-Carbon is chiral in all amino acids except for glycine. At pH 7.0 amino acids have both +ve and-ve charges so called dipolar ion or zwitterions Amino acids have a tetrahedral structure (3D shape).

Natural Amino Acid are in the L-configuration

L and D forms are called Optical isomers (= Stereoisomers = Enantiomers) Biological system in all organisms synthesize and use only L-amino-acids

The R group determines the amino acid

R group
-H - CH3 - CH2OH - CH2SH - CH2COOH -CH2CH2CH2CH2NH2

Amino acid
Glycine Alanine Serine Cysteine Aspartic acid Lysine

Side chain
Non-polar Non-polar Uncharged polar Uncharged polar Acidic (-ve) Charged polar Basic (+ve) Charged polar

Table: Abbreviations for the 20 Amino Acids

Amino Acid
Abbreviation Three letter Alanine Arginine Asparagine Aspartic acid Cysteine Glycine Glutamine Glutamic acid Histidine Isoleucine One letter

Amino Acid

Abbreviation Three letter One letter

Ala Arg Asn Asp Cys Gly Gln Glu His Ile

A R N D C G Q E H I

Leucine Lysine Methionine Phenylalanine Proline Serine Threonine Tryptophan Tyrosine Valine

Leu Lys Met Phe Pro Ser Thr Trp Tyr Val

L K M F P S T W Y V

CHEMICAL CLASSIFICATION
1. 2. 3. 4. 5. 6. 7. The 20 amino acids are classified according to the chemical structure of the side chain ( R ) into: Aliphatic Hydroxy Sulfur containing Aromatic Acidic Basic Imino acids

All aliphatic AA are nonpolar (Hydrophobic) Valine, Leucine and Isoleucine are branched-chain AA

Hydroxy Amino Acids

Hydroxy AA (Serine and Threonine) are Polar (Hydrophilic) They Can form hydrogen bonds with their OH groups

Sulfur Containing Amino Acids

Cysteine: Important in disulfide linkages polar, Can form hydrogen bonds Methionine: Methyl donor Non-polar (hydrophobic)

Aromatic Amino Acids

Phenylalanine and Tryptophan are nonpolar (hydrophobic) Tyrosine is polar (hydrophilic): H-Bonding with its (OH).

Acidic Amino Acids and their amides

Aspartate and glutamate are polar and negatively charged (-ve) at physiologic pH Asparagine and glutamine are polar but non charged

Basic Amino Acids

Arginine, Lysine and Histidine are polar and positively charged (+ve) at physiologic pH

Imino Acids

Proline is imino acid because it contains imino group (-NH) not amino group (-NH2) Proline is heterocyclic and non-polar AA.

NUTRITIONAL CLASSIFICATION of AA
On nutritional basis amino acids are classified into essential or non-essential A.A.

(A)- ESSENTIAL AMINO ACIDS:

Can NOT be synthesized in the body and must be taken in the diet. They are 10 AA: Phenylalanine Valine Tryptophan (PVT) Threonine - Isoleucine Methionine (TIM) Histidine Arginine Lysine Leucine (HALL)

NUTRITIONAL CLASSIFICATION of AA
(B)- NON-ESSENTIAL AMINO ACIDS: Can be synthesized inside the body, so they must not be taken in the diet. They include the other 10 amino acids N.B. The essential amino acids are not more important to our body than the non-essential amino acids. Both (all 20 AA) are equally needed and equally essential for the normal growth and good health

Table: Nutritionally Essential and non-Essential Amino Acids

Essential Amino Acids Non-Essential Amino Acids

1- Arginine 2- Histidine 3- Isoleucine 4- Leucine 5- Lysine 6- Methionine 7- Phenylalanine 8- Threonine 9- Tryptophan 10- Valine

1- Alanine 2- Asparagine 3- Aspartic acid 4- Cysteine 5- Glutamine 6- Glutamic acid 7- Glycine 8- Proline 9- Serine 10- Tyrosine

Amino Acid deficiency in Selected Vegetables and Grains

Food Source Amino Acid Missing Eggs, Milk, Meat, Fish, Poultry None Wheat, Rice, Oats Corn Beans Peas Almonds, Walnuts Soy Lysine Lysine, Tryptophan Methionine, Tryptophan Methionine Lysine, Tryptophan Low in Methionine

PROPERTIES OF AMINO ACIDS

All amino acids are optically active except Glycine, this is because all AA contain asymmetric carbon atom but in Glycine the R group is a hydrogen atom so it has no asymmetric carbon atom

Linking of amino acids: Peptide Bond Formation

Amino acids are linked together by condensation reaction between carboxylic and amino groups from two different amino acids (with elimination of water). The amide bond formed is called peptide bond The product is called a peptide, and named according to the number of amino acids involved: e.g. dipeptide (2), tripeptide (3), decapeptide (10) Big peptides (> 50 amino acids) are called polypeptides

Peptide Linkage Formation

PROTEIN STRUCTURE

PROTEIN STRUCTURE
A protein molecule may consist of one or more polypeptide chains, which are usually folded in regular manner that gives the molecule a specific shape A polypeptide chain is formed of L-amino acids linked together by peptide bonds At one end of the polypeptide chain there is a free -amino group, the N-terminal amino acid residue

PROTEIN STRUCTURE
At the other end there is a free carboxyl group, the C- terminal amino acid residue The peptide structure are written with the N-terminal residue at the left and with the C-terminal residue at the right

Protein structure: conformation and assembly

Primary Structure: The order of amino acids: Amino acid sequence Secondary Structure: H-bonding between amino acids: twisting and folding Tertiary Structure Ionic-covalent- bonds: Overall folding: spherical OR fibrous shape Quaternary Structure Organization of multiple protein units together

Secondary Structures
AAs are arranged to minimize collision and to form H-bonds

Alpha Helix

Pleated Sheets

Tertiary Structures
Cross links and bonds in 3ry structure:

S-S bond, Ionic,Hydrophobic interactions and H-bonding Examples of tertiary structure types (shapes): I- Globular proteins (enzymes, molecular machines) Approximately spherical shape- Water Soluble.

II- Fibrous Proteins (structural proteins) Rod-like shape - Poor water solubility.

Tertiary Structure

Intermolecular Forces in Proteins

Hydrogen bonding Ionic bonds Disulfide linkages Dispersion forces

Quaternary Structures
Organization of multiple proteins (units) together Example: hemoglobin: 2 units - 2 units.

DENATURATION OF PROTEINS It is the destruction of the organization (internal structure) of the protein molecule (2ry, 3ry and 4ry structures) but the primary structure remains intact So the polypeptide chains become unfolded and irregularly arranged

DENATURATION OF PROTEINS
CAUSES: a- Physical agents: Heat, UV rays, X-ray, wave, high pressure or shaking b- Chemical Agents: acids, alkalis or urea

ultrasound excessive

Effects of Denaturation
Denaturation destroys the biologic activity of a protein, there is loss of hormonal, enzymatic and antibody activity. The biologic activity of a protein depends on their native conformation. Denaturation destroys the native conformation of protein.

Applications of protein denaturing

1- Boiling eggs: Change in albumin shape and solubility. 2- Cooking meat: Easily chewable,digestible. 3- swabbing skin with alcohol (disinfectant): Denatures/kills bacteria and viruses. 4- HCl in our stomach: denatures proteins, making it easily digestible by enzymes
So, eating cooked eggs, meat and liver is more useful to humans than eating them raw