Proteins

Lecture 10Proteins

Introduction Proteins are the most abundant organic molecules of the living systemThey occur in every part of the cell and constitute about 50% of the cellular dry weightThey form the fundamental basis of structure and function of life

Origin The term protein is derived from a Greek word Proteios, meaning holding the first placeMulder (Dutch chemist) in 1983 used the term proteins for the higher molecular weight nitrogen-rich and most abundant substances present in animals and plants

Functions of proteinsStatic (structural) functions:e.g. Elastin, collagen, -KertainDynamic functions:As enzymes, hormones, blood clotting factors, immunoglobulin, membrane receptors, storage proteins, muscle contraction, respiration (working horses of cell)

Elemental composition of proteinsProteins are predominantly constituted by five major elements in the following proportionCarbon 50-55%Hydrogen 6-7.3%Oxygen 19-24%Nitrogen 13-19%Sulfur 0-4%Beside these proteins also contain other elements as P, Fe, Cu, I, Mg, Mn, Zn etc

Proteins are polymers of amino acids and yield L--amino acids on complete hydrolysis with concentrated HCL for several hours

Standard amino acids As many as 300 amino acids occur in nature- of these only 20-known as standard amino acids are repeatedly found in the structure of proteins isolated from different forms of life animal, plant and microbialThis is because of the universal nature of the genetic code available for the incorporation of only 20 amino acids

Amino acids Amino acids are a group of organic compounds containing two functional groupAmino (-NH2)-basicCarboxyl (-C00H)-acidic

General structure The amino acids are termed as -amino acids if both the carboxyl and amino groups are attached to the same carbon atom

The Alpha carbon atom binds to side chain represented by R which is different for each of the 20 amino acids

Classification of amino acids A. Classification based on the structure

B. Classification based on polarity Four groupsNon-amino acidsThese are also referred to as hydrophobic. They have no charge on the R groupe.g. alanine, leucine, isoleucine2. Polar amino acids with no charge on R groupThey posses groups such as hydroxyl, sulfhydryl and amide and participate in hydrogen bonding of protein structureGlycine, serine, threonine, cysteine,

3. Polar amino acids with positive R groupe.g. lysine, arginine and histidine are included in this group

4. Polar amino acids with negative R groupe.g. Aspartic acid and glutamic acid

c. Nutritional classification of amino acidsEssential or indispensible amino acidsThe amino acids that cannot be synthesized by the body and therefore need to be supplied through the dietThey are required for proper growth and maintenance of individualse.g. PVT TIM HALL

2. Non-essential or dispensable amino acidsThe body can synthesize about 10 amino acids to meet the biological needs hence they cannot be consumed in the diete.g. Glycine, alanine, serine serine, cysteine, aspartate, asparagine, glutamate, glutamine, tyrosine, proline

D. Classification based on their metabolic fateThe carbon skeleton of amino acids can serve as a precursor for the synthesis of glucose (glucogenic) or fat (ketogenic) or bothThree groups:Glycogenic amino acids (alanine, aspartate, glycine, methionine)Ketogenic amino acids (leucine, lysine)Glycogenic and ketogenic (isoleucine, phenyl alanine, tryptophan, tyrosine)

Selenocysteine-the 21st amino acidIt is found at the active site of various enzymes/proteins (selenoproteins) eg Glutathione peroxidase, glycine reductaseIt contain the trace element selenium in place of the sulfur atom of cysteineCodon UGA

Physical properties of amino acidsSolubility:Most of the amino acids are usually soluble in water and insoluble in organic solvents2. Melting point:Generally melt at higher temperature often above 200oC3. Taste:They may be sweet , tasteless or bitter

4. Optical properties: All the amino acids except glycine posses optical isomers due to the presence o asymmetric carbon atom5. Amino acids as ampholytesAmino acids contain both acidic (-COOH) and basic (-NH2) groups. The can donate and accept a protonZwitterion or dipolar ion

Chemical propertiesThe general reactions of amino acids are mostly due to the presence of two functional groupsCarboxyl groupAmino group

Reactions due to COOH groupAmino acids form salts with bases and esters with alcoholAmino acids undergo decarboxylation producing corresponding amines (histamine, tyramine)The carboxyl group of dicarboxylic amino acids reacts with ammonia to form amideAspartic acid + NH3 AsparagineGlutamic acid + NH3 glutamine

Reactions due to NH2 groupThe amino groups behave as bases and combine with acids to form saltThe amino acids react with ninhydrin to form a purple, blue or pink colour complex (Ruhemanns purple)Colour reaction of amino acids: amino acids can be identified by specific colour reactionsTransaminationOxidative deamination

Non-standard amino acidsAmino acid derivatives in proteinse.g. Collagen, Histone, cystine Non-protein amino acidsThey may be either alpha or non alpha amino acidse.g. Ornithine, Citrulline, thyroxine D-amino acidsThe vast majority of aa isolated from animals and plants are of L-category. Certain D-amino acids are found in the antibiotics. D-alanine and D-glutamic acid are found in bacterial cell wallD-serine and D-aspartate are found in brain tissues

Structure of ProteinsThe structure of proteins can be divided into four levels of organizationPrimary structureSecondary structureTertiary structureQuaternary structure

Primary structure of proteinsEach protein has a unique sequence of amino acids which is determined by the genes contained in a DNA.The primary structure is largely responsible for its functionA vast majority of genetic disorders are due to abnormalities in the primary structure of proteinsPeptide bondCharacteristics of peptide bondsThe peptide bond is rigid and planar with partial double bond in character. Both C=O and NH groups of peptide bonds are polar and are involved in hydrogen bon formation

Writing of peptide structures:Conventionally the peptide chains are written with the free amino end (N-terminal) at the left and the free carboxyl end (C-terminal) at the right.

The amino acid sequence is read from N-terminal end to C-terminal end

The protein synthesis also starts from the N-terminal amino acid

Shorthand to read peptides:The amino acids in a peptide or proteins are represented by the 3-letter or one letter abbreviation. This is chemical shorthand to write proteinsNaming of peptides:The suffixes ine, -an, -ate are changed to yl with the exception of C-terminal amino acidH3N-glutamate-cysteine-glycine-COO- E C G Glu Cys Gly Glutamyl Cysteinyl Glycine

Secondary structure of Protein