AMINO ACIDS & PEPTIDE BONDS STRUCTURE, CLASSIFICATION & METABOLISM

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1 AMINO ACIDS & PEPTIDE BONDS STRUCTURE, CLASSIFICATION & METABOLISM

2 OBJECTIVES At the end of this session the student should be able to, recognize the structures of the protein amino acid and state their short forms classify amino acids according to the four systems define pi and calculate it for any amino acid given the structure and pka value draw a dipeptide and a tripeptide write the equations for the deamination and transamination of glutamate outline the fate of the carbon skeleton of amino acids on oxidation outline the biosynthesis of non-essential amino acids outline haeme biosynthesis outline the conversion of haeme to bilirubin recognize the defects in enzymes cause genetic disease

3 Structure of Amino Acids An asymmetric C-atom contains 4 different groups attached to it At physiological ph the NH 2 group is NH 3+ and the carboxyl group COO - An amino acid is therefore a zwitter ion

4 Glycine is the only amino acid that is not optically active Proline is the only imino acid (NH not NH 2 group) Threonine has two asymmetric C atoms Cysteine can dimerise to give cystine

5 Classification of Amino Acids Classification based on structure Aliphatic Aromatic Hydroxy Sulpho Acidic Amides Basic Imino Gly, Ala, Val, Ile Phe, Tyr, Trp Ser, Thr Cys, Met Glu, Asp Gln, Asn Lys, Arg, His Proline

6 Cont., Classification based on polarity and charge Non polar Uncharged polar Acidic Polar Basic Polar Gly, Ala, Val, Leu, Ile, Phe, Trp, Met, Pro Ser, Thr, Tyr, Asn, Gln, Cys Asp, Glu His, Lys, Arg

7 Cont., Classification based on biosynthesis in human Essential amino acids: amino acid that cannot be synthesized in adequate amount in the human body and therefore must be taken it with the diet Arg, His, Met, Thr, Val, Ile, Phe, Trp, Leu, Lys Non-essential amino acids: Ala, Asp, Asn, Cys, Glu, Gly, Pro, Ser, Tyr

8 Cont., Classification based on metabolism Glucogenic Glucogenic and ketogenic Ketogenic

9 Isoelectric Point (pi) of Amino Acids The ph at which an amino acid has no net charge is called the isoelectric point What is no net charge? When the positive charge on α NH 3+ equal to the negative charge on α COO -, the total charge is zero. The amino acid will now not move in an electric field

10 Calculation of Isoelectric Point Amino acid with no charge on the R group. That is amino acids that are not acidic or basic Take into account the pka values of the group: e.g. If pka α NH3 + /NH 2 = 9 (pka 1 ) α COO - /COOH = 2 (pka 2 ) pi = pka 1 + pka 2 2 pi = pi = 5.5

11 Cont., For acidic amino acids, the R group has a third ionizing group e.g. The γ carboxyl of glutamic acid If pka values are: α-coo - = 2 (pka 1 ) γ-coo - = 4 (pka 2 ) NH + 3 = 9 (pka 3 ) For acidic amino acids the basic group is ignored pi = pka 1 + pka 2 2 pi = 2+4 pi = 3 2

12 For basic amino acids, Cont., e.g. lysine there are two NH + groups α-nh 2 = 9 pka 2 ε-nh 2 = 8 pka 3 α-coo = 2 pka 1 Here the acidic pka value is ignored in the calculation pi = pka 2 + pka 3 2 = pi = 8.5

13 Peptides & Peptide Bond When two amino acids are joined together with the loss of one H 2 O molecule a dipeptide is formed

14 No: of amino acids Peptide No: of peptide bonds 4 Tetra 3 5 Penta 4 6 Hexa Oligo (8-12) Polypeptide

15 The arrangement of the R groups in the peptide chain gives rise to different peptides e.g. A dipeptide with one Gly and one Ala can be Ala.Gly or Gly.Ala i.e. If N is the number of different amino acids total number of possible dipeptide = N! (Factorial N) = 2 1=2 Tripeptide: e.g. Gly, Ala and Ser N! = 3! = = 6 That is: Gly, Ala, Ser Gly, Ser, Ala Ala, Gly, Ser Ala, Ser, Gly Ser, Ala, Gly Ser, Gly, Ala

16 Cont., If there is one each of 20 amino acids. Then N! = 20! 20! = A very large number

17 Biosynthesis of Non-essential Amino Acids The overall aim is to obtain the carbon skeleton in the form of an α-keto acid then add on the NH 2 group The primary carbon skeleton comes from either the glycolytic pathway or the TCA cycle The NH 2 group is transferred mainly from 3 amino acids to be attached to these carbon skeletons Alanine, aspartate & glutamate which acts under the influence of enzymes transaminases/aminotransferases

18 Overview of Biosynthesis of Non-essential Amino Acids

19 Degradation of Amino Acids This involves the removal of the amino group and oxidation of the carbon skeleton The oxidation of the carbon skeleton converges to: Oxaloacetate Ketoglutarate Pyruvate Fumerate Acetyl coenzyme A Acetoacetyl coenzyme A Succinyl coenzyme A The product depends on the amino acid

20 Removal of NH 2 Group (Deamination) The NH 2 group of most amino acids are transaminated to give keto acids by using α-ketogluterate (α-keto glu) as amino acceptor The C-skeleton is now ready for oxidation Glutamate is converted to α-ketogluterate by glutamate dehydrogenases

21 Oxidation of Carbon Skeleton of Amino Acids The entry points of the C-skeleton to catabolic oxidation is as follows

22 Metabolic Classification of Amino Acids TYPE A: Glucogenic Those amino acids that yield pyruvate and intermediates of the TCA cycle only, namely, Ala, Asp, Asn, Cys, Glu, Gln, Gly, Pro, Ser, Arg, His, Met, Thr, Val TYPE B: Ketogenic Those amino acids that yield only acetyl CoA or acetoacetoacely CoA namely, Leu, Lys. TYPE C: Glucogenic and ketogenic (amphibolic) Tyr, His, Phe, Trp

23 Defects in Amino Acid Metabolism Enzyme Amino Acid Disease Phenylalanine hydroxylase Phe Phenylketonuria Homogenistic oxidase Any enzyme in conversion of Tyr to melanin Branch chain aminoacyl CoA synthetase Propionyl CoA carboxylase Cystathionase Cystathione synthetase Histidase Tyr Tyr Ile, Val, Leu Thr, Met Met Met His Alcaptanuria Albinism Maple syrup urine disease Propionyl CoA carboxylase deficiency Cystathionuria Homocystenuria Histidinaemia

24 Biosynthesis of heme Metabolism of Haemins Heam

25 Degradation of haem

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