Amino Acids & Proteins Amino Acids Amino acids are organic compounds containing both amino group & carboxyl group, those occurring in human proteins are L α-amino acids having the formula RCH(NH2)COOH & with the exception of glycine all amino acids are asymmetric . D-Amino acids that occur naturally are free D-serine& D- aspartate which present in the in brain tissue. Classification of Amino acids Over 300 amino acids occur naturally, however; only 20 of them share in the formation of proteins. Classification of amino acids either according to their R-group or to their nutritional importance. 1-Classification according to R-group(side chain). 1 2 2-Classification according to their nutritional importance All 20 amino acids present in proteins are biologically essential but not all of them are nutritionally essential, therefore, they are classified into: 3 A-Nutritionally essential amino acids :they should be supplement in diet because human body can not synthesize it , there deficiencies lead to kwashiorkor (protein malnutrition) & marasmus (protein & energy malnutrition). B-Nutritionally nonessential amino acids : human body can synthesize it , therefore , it’s not essential to be supplied in the diet. R-group It determines the property of amino acid in peptide formation as: 1-Since glycine is smallest amino acid, therefore, it can accommodate in places inaccessible to other amino acids in the formation of peptide. 4 2-Hydrophobic R-group of alanine, valine, leucine, Isoleucine, & aromatic R-groups of phenylalanine , tyrosine & tryptophan make them in the interior of protein. 3-The charged R-group of basic & acidic amino acids stabilize protein conformation through ionic interaction or salt-bridge. In Vivo Synthesis of Nutritionally Nonessential Amino Acids Glutamate & Glutamine: Reductive amination of α- ketoglutarate is catalyzed by glutamate dehydrogenase enzyme forming glutamate, this reaction is reversible. Amidation of glutamate to glutamine is catalyzed by glutamine synthetase enzyme, this irreversible reaction requires ATP. Alanine: By amination of pyruvate forming alanine, the amino donor may be glutamate or aspartate, this reversible transamination reaction is catalyzed by transaminase enzyme. Aspartate & Asparagine: By amination of oxaloacetate forming aspartate, the amino donor may be alanine; this 5 reversible transamination reaction is catalyzed by transaminase enzyme. Amidation of aspartate to asparagine is catalyzed by asparagine synthetase enzyme, this irreversible reaction requires ATP and it’s resemble amidation of glutamate , however , glutamine rather than ammonium ion, provides the nitrogen for this amidation. Serine:Formed from glycolytic intermediate 3-phosphoglycerate Glycine : Formed from glyoxylate , glutamate or alanine by a reversible reaction catalyzed by glycine aminotransferases ,it can produce also from choline & serine. Proline: Formed from glutamate. Cysteine: Formed from methionine as discussed later. Tyrosine: phenylalanine converted to tyrosine by irreversible reaction catalyzed by phenylalanine hydroxylase enzyme; since this reaction is irreversible ,therefore, dietary tyrosine can not replace phenylalanine. 6 Hydroxyproline & Hydroxylysine : They are important in posttranslational processing of collagen & not necessary for protein synthesis .Formed by hydroxylation of proline & lysine in a reaction catalyzed by prolyl hydroxylase &lysyl- hydroxylase enzymes respectively, it require vitamin C as cofactor , therefore , deficiency of vitamin C lead to scurvy. Proteins Formation of peptides Link of amino acids lead to the formation of peptides. -If the chain formed from up to five amino acids the structure is called oligopeptide or called dipeptide, tripeptide, tetrapeptide & so on if consist from 2,3,4 amino acids respectively. -If the chain formed from 6-30 amino acids the structure is called polypeptide. -If the chain formed from larger than 30 amino acids the structure is called protein. Classifications of Proteins ►I-Initial classification according to their properties as: 1-Solubility : 2-Shape : 7 A-Globular proteins: roughly spherical or ovoid in shape with their axial ratios (ratio of their longest to shortest dimensions) of not more than 3 with tendency to be soluble in physiological fluids(because it is compact with hydrophilic R-group face outward ), it represent nearly all proteins of interest in clinical chemistry like hemoglobin , enzymes & plasma protein except fibrinogen. B-Fibrous proteins: their axial ratios 10 or more with tendency to be insoluble in physiological fluids e.g fibrinogen. 3-Presence of nonproteins groups (prosthetic groups): these prosthetic groups are bound to protein forming conjugated proteins , the conjugated proteins without prosthetic groups are called apoproteins. prosthetic group + apoprotein = conjugated protein example: A-lipid + protein = lipoproteins B- CHO+protein=glycoprotein(if CHO 5-15%)& mucoprotein (if CHO 15-75%) C-metal ion+ protein = metalloprotein as hemoglobin . ►II-Nowadays with the development of determination of amino acids sequences of proteins more precise classification depend on homology of sequence & structure of amino acids in protein , however , early classification still in use. Orders of Protein Structure Conformation of proteins into the following orders of structure is necessary to maintain their function & physical property. 1-Primary structure 2-Secondary structure 3-Tertiary structure 4-Quaternary structure Primary structure Represent the sequence of amino acids in polypeptide chain , its genetically determined, formed by peptide-bonds that linked amino acids together by connecting amino group of one amino 8 acid with a carboxyl group of another leaving only one free amino group & carboxyl group at both extreme of protein, the amino acids present in peptide are called aminoacyl residues & are named by replacing the ate or ine suffixes of free amino acids with yl e.g..(alanyl,aspartyl,glutamine) the ine ending of glutamine indicates that it is carboxyl group is not involved in the peptide bond formation (extreme of protein). Secondary structure Generally peptide bonds of protein restrict this secondary conformation , however , free rotation is possible only in a bond that link : a) α-carbon to the carbonyl carbon b) α-carbon to the nitrogen This secondary structure has the following conformations: 1-Alpha Helix 2- Beta Sheet 3-Loops & Bends 1-Alpha Helix: look like cylinder with R-group of each aminoacyl residue face outward. 9 2-The Beta Sheet: look like zigzag or pleated pattern with R- groups of adjacent residues point in opposite directions , unlike the compact backbone of α-helix the backbone of Beta Sheet is highly extended , most Beta Sheet are twisted & not perfectly flat forming the core of globular proteins. 3-Loops & Bends : It refer to the short segments of amino acids that joint two units of secondary structure & it represent the key of biological role of that protein. Tertiary structure Secondary structural features as alpha-helix , beta-sheet , loops & bends are assemble to form domain which represent a section of protein structure sufficient to perform a particular physical or chemical task. Some polypeptides are small consist from a single domain as myoglobin while other are large consist from many domains. The tertiary structure represents how secondary structural features are assemble to form domain & how these domains relate spatially to one another. 11 Quaternary structure Some proteins are assembled from more than one polypeptide or protomer. Quaternary structure defines the polypeptide composition of protomer & for those protein containing more than one protomer the spatial relationships between these protomers . Protein with a single protomer called monomeric protein. Protein with two protomers called dimeric protein , these two protomers either identical ((homodimeric)) or not identical ((heterodimeric)). Greek letters ((α,β,γ… )) are used to distinguish different protomers in a single protein. Pathology of Altered Protein Conformation 1-Creutzfelt-jakob disease : Its fatal neurodegenerative disease resulting from alteration of protein conformation in neural cells , the pathogenesis of disease is still not clear probably due to chromosomal changes ((chromosome 20)) . 2-Alzheimer's disease: It characterize by senile plaques in the brain with alteration in neuron protein conformation, the pathogenesis of disease is still not clear. 3-Thalassemia: caused by genetic defects that impair the synthesis of one of the polypeptide subunits (α or β) of hemoglobin. Biological Functions of Proteins 1-Enzymes: catalyze biochemical reactions. 2-Peptide hormones : regulate metabolism. 3-Antibodies & Complements : defense mechanism . 4-Albumin : maintain oncotic pressure of plasma. 5-Many plasma proteins like albumin transport vitamins, metals, hormones & drugs in the blood often serving as reservoirs . 6-Hemoglobin : carry oxygen. 7-Coagulation factors : affect haemostasis. 8-Structural proteins as keratin & collagen. 9-Contractile proteins as myosin. 10-Storage proteins as ferritin that store iron. 11 Digestion & Absorption of Proteins Few bonds are accessible to the proteolytic digestive enzymes (proteases) that catalyze hydrolysis of peptide bonds, without prior denaturation of dietary proteins (by heat in cooking & by the action of gastric acid). There are two main classes of proteases enzymes which are:- A-Endopeptidases:- hydrolyze peptide bonds between specific amino acids throughout the molecule.