2. amino acids and peptide bond

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2. MONOMERS OF PROTEINS Proteins are polymers of amino acids ( the building blocks of proteins) united through peptide bonds. -amino acids There are about 300 amino acids occur in nature There are 20 commonly occurring amino acids. Most of the amino acids are alpha amino acids 3. STRUCTURE OF AMINO ACIDS 4 groups are attached to tetrahedral carbon atom 1.a carboxylic acid (- COOH) functional group 2.an amino (- NH2) functional group 3.Distinct R-groups 4. HydrogenThe amino group and the carboxyl group is attached to the same carbon atom. 4. STRUCTURE OF AMINO ACIDS Carboxyl groupCOOH Amino groupH2 NCHHydrogen atom carbonRSide chain of specific chemical group 5. Amino Acids are Optically Active Except for glycine (R = H), all AAs have 4 different groups attached to the -carbon atom. The carbon is the asymmetric carbon atom and this gives rise to 2 non-superimposable mirror image formsCOO-H3NCH .. . .. .HC .. . .. .RNH3RL-ConfigurationD-Configuration-COO- is directed up and behind plane of slide R is directed down and behind the plane of slide -H and -NH3 are directed towards you -NH3 on left = L-configuration;+ .. . .. .+COO- .. . .. .on right = D-configuration 6. At physiological pH (around 7), amino group is protonated while the carboxylic acid group is unprotonatedCOO+ H3NCRHBoth positive and negative charges are present, Electrically neutral Zwitterion or dipolar ionDegree of ionisation of both the carboxylic and amino groups depends on pH of solution 7. EFFECT OF PH The pH at which the molecule carries no net charge is known as iso-electric point or iso- electric pH.At iso-electric pH the amino acid will carry no net charge. The groups are ionized but the charges will cancel each other.There is no mobility in an electric field.Solubility and buffering capacity will be minimum at iso-electric pH .In acidic solution they behave as cations and in alkaline solutions they behave as anions. 8. CLASSIFICATION OF AMINO ACID A. Based on structure AA with aliphatic side chains, AA with hydroxyl group AA with sulphur group Acidic amino acid Basic amino acid Aromatic amino acid Imino acid B. Based on polarity Non polar amino acid Polar amino acid with no charge on R Polar amino acid with positive R charge Polar amino acid with negative R charge C. Based on nutrition Essential amino acid Non essential amino acid D. Based on metabolic fate Glycogenic Amino acid Ketogenic amino acid 9. BASED ON POLARITY 10. HYDROPHOBIC OR HYDROPHILIC CLASSES There are 2 broad classes of amino acids based upon whether the Rgroup is hydrophobic or hydrophilic. The hydrophobic amino acids tend to repel the aqueous environment , reside predominantly in the interior of proteins This class of amino acids do not ionize & do not participate in the formation of H-bonds. The hydrophilic amino acids tend to; - interact with the aqueous environment, - often involved in the formation of H-bonds and - found on the exterior surfaces proteins or in the reactive centers of enzyme 11. Amino acids differ in the R- group present. Based on R-groups, amino acids are placed into 4 groups; Group 1 Amino acids with Nonpolar Side Chains Group 2 Amino acids with Polar Side Chains (Neutral) Group 3 Amino acids with Acidic Side Chains Group 4 Amino acids with Basic Side Chains 12. GROUP 1 Aminoacids with Non-polar Side Chains (hydrophobic) Nonpolar side chains does not bind or give off protons or does not participate in H or ionic bonds, Promotes lipidlike interaction Glycine Alanine Valine Leucine Isoleucine Phenylalanine Methionine Tryptophan Proline (imino group)Total =9 13. Group 1 Amino acids with Nonpolar Side Chains 14. GROUP 2 AMINO ACIDS WITH POLAR SIDE CHAINS (Electrically Neutral = Uncharged at neutral pH) The polar OH gp of tyrosine, serine, threonine can participate in H bonds. The CO & amide gp of Aspn & Glun can form H bond Serine Threonine Tyrosine Cysteine Glutamine AsparagineTotal =6 15. Group 2 Amino acids with Polar Side ChainsNeutral (Hydrophilic) 16. Group 3 Amino acids with Acidic Side ChainsAspartateGlutamate 17. Group 4 Amino acids with Basic Side Chains 18. BASED ON STRUCTURE 19. ALIPHATIC (ALKANE) AMINO ACIDSHydrophobicityGlycine(gly, G)-only non-chiral amino acid, not hydrophobic Alanine (ala, A) R-group = methyl-group Valine (Val, V) Think V! Leucine (Leu, L) Isoleucine (Ile, I) -2 chiral carbons 20. AMINO ACIDS CONTAINING HYDROXYL GROUP SerineThreonine 21. AROMATIC AMINO ACIDS All very hydrophobic All contain aromatic group Absorb UV at 280 nm Phenylalanine (Phe, F) Tyrosine (Tyr, Y) -OH ionizable (pKa = 10.5), H-Bonding Tryptophan (Trp, W) bicyclic indole ring, H-Bonding 22. SULFUR CONTAINING AMINO ACIDS Methionine (Met, M) start amino acid, very hydrophobic Cysteine (Cys, C) sulfur in form of sulfhydroyl, important in disulfide linkages, weak acid, can form hydrogen bonds. 23. ACIDIC AMINO ACIDS Contain carboxyl groups (weaker acids than a-carboxylgroup) Negatively charged at physiological pH, present as conjugate bases (therefore ate not ic acids) Carboxyl groups function as nucleophiles in some enzymatic reactions Aspartate Glutamate 24. BASIC AMINO ACIDS Hydrophillic nitrogenous bases Contain two or more NH2 groups or nitrogen atoms that act as base i.e. can bind proton. Positively charged at physiological pH Histidine imidazole ring protonated/ionized, only amino acid that functions as buffer in physiol range. Lysine - diamino acid, protonated at pH 7.0 Arginine - guianidinium ion always protonated, most basic amino acid 25. IMINO ACID Proline (pro, P)- cyclic imino acid In proline, amino group enters in the ring formation being -imino gp so proline is an -imino acid rather than amino acid 26. ESSENTIAL/NON-ESSENTIAL AMINO ACIDS Essential histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine Non-essential alanine, arginine*, aspartate, asparagine, cysteine*, glutamate, glutamine, glycine*, proline*, serine, tyrosine* 27. Nutritional classification: 1- Essential amino acids: These amino acids cant be formed in the body and so, it is essential to be taken in diet. Their deficiency affects growth, health and protein synthesis. 2- Semiessential amino acids: These are formed in the body but not in sufficient amount for body requirements especially in children. Summary of essential and semiessential amino acids: Villa HM = Ten Thousands Pound V= valine i= isoleucine l= lysine l= leucine A = arginine* H= histidine* M= methionine T= tryptophan Th= threonine P= phenyl alanine *= arginine and histidine are semiessential 3- Non essential amino acids: These are the rest of amino acids that are formed in the body in amount enough for adults and children. They are the remaining 10 amino acids. 28. Metabolic classification: according to metabolic or degradation products of amino acids they may be: 1- Ketogenic amino acids: which give ketone bodies . Lysine and Leucine are the only pure ketogenic amino acids. 2- Mixed ketogenic and glucogenic amino acids: which give both ketonbodies and glucose.These are: isoleucine, phenyl alanine, tyrosine and tryptophan. 3- Glucogenic amino acids: Which give glucose. They include the rest of amino acids. These amino acids by catabolism yields products that enter in glycogen and glucose formation. 29. Amphoteric properties of amino acids: that is they have both basic and acidic groups and so can act as base or acid. Neutral amino acids (monobasic, monocarboxylic) exist in aqueous solution as Zwitter ion i.e. contain both positive and negative charge. Zwitter ion is electrically neutral and cant migrate into electric field. Isoelectric point (IEP) = is the pH at which the zwitter ion is formed. e.g IEP of alanine is 6 Chemical properties of amino acids: 1- Reactions due to COOH group: -Salt formation with alkalis, ester formation with alcohols, amide formation with amines and decarboxylation -2- Reactions due toNH2 group: deamination and reaction with ninhydrin reagent. -Ninhydrin reagent reacts with amino group of amino acid yielding blue colored product. The intensity of blue color indicates quantity of amino acids present. 30. Ninhydrine can react with imino acids as proline and hydroxy proline but gives yellow color. 3- Reactions due to side chain (R): 1- Millon reaction: for tyrosine gives red colored mass 2- Rosenheim reaction: for trptophan and gives violet ring. 3- Pauly reaction: for imidazole ring of histidine: gives yellow to reddish product 4- Sakagushi test: for guanido group of arginine andgives red color. 5- Lead sulfide test (sulfur test): for sulfur containing amino acids as cysteine give brown color. 31. Non-standard (Non-canonical) amino acids: These are produced by post-translational modification, and not genetically coded, except selenocystein (Sec), which is now accepted as the 21st amino acids. 32. Amino Acid useful as drug D-amino acids are found in a few small peptides, including some peptides of bacterial cell walls and certain antibiotics (such as penicillin).D-Glu D-Ala 33. Alexander Fleming discovers penicillin: 34. Penicillin binds at the active site of the transpeptidase enzyme that cleaves DAla-D-Ala and thus cross-links the peptidoglycan strands of the bacterial cell wall. Penicillin binds the enzyme by mimicking the D-Ala-D-Ala residues that would normally bind to this site. Therefore, the bacterial cell wall loses integrity and is susceptible to host defences, or simply bursts. 35. THE PEPTIDE BOND Proteins are linear polymers composed of amino acids linked together by peptide bonds.These 20 amino acids are linked together through peptide bond forming peptides and proteins (whats the difference?).- The chains containing less than 50 amino acids are called peptides, while those containing greater than 50 amino acids are called proteins.Peptide bond