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WELCOME ON THE BIOCHEMISTRY LECTURES

WELCOME ON THE BIOCHEMISTRY LECTURES. 2 nd semester An Introduction to Biochemistry. Bioorganic Chemistry 1. Amino acids, Protein and Enzymes 2. Other b iomolecules: Carbohydrates Lipids Nucleotides and Nucleic Acids Vitamins and Coenzymes. Biochemistry - Bioenergetics

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WELCOME ON THE BIOCHEMISTRY LECTURES

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  1. WELCOME ON THE BIOCHEMISTRY LECTURES 32

  2. 2nd semester An Introduction to Biochemistry • Bioorganic Chemistry • 1. Amino acids, Protein and Enzymes • 2. Other biomolecules: • Carbohydrates • Lipids • Nucleotides and Nucleic Acids • Vitamins and Coenzymes • Biochemistry - Bioenergetics • 1. High energy phosphate compounds • 2. Metabolic Pathways: • Glycolysis • Citrate cycle • Mitochondrial respiration 32

  3. Books and Notes Lehninger: Biochemistry (selected chapters) Calculation book (previous semester) Practice book (previous semester) Collected STUCTURES You can download the lecture material from our website www.biokemia.sote.hu Username:file Password:open2 32

  4. 2 Midterms during the semester Assay questions (topics), calculations, structures Chemistry Final 2nd semester:30 multiplichoice questions 1st semester:20 multiplichoice questions 10 structures 32

  5. DR. M. Sasvári Biochemistry Lectures Amino Acids, Proteins, Enzymes • Amino Acids • The Building Blocks of Proteins • Neutral amino acids • (one amino- and one carboxyl group) 32

  6. a-ketoacid derivatives of amino acids COO- COO- O C H +H3N C R R Amino Acids Grouping of amino acids is based on the side chains: Nonpolar (hydrophobic) – aliphatic and aromatic side chains (only C,H) Polar, uncharged (hydrophylic) – other atoms (O,N,S) than C and H Polar, charged (ionic) – weak acids or bases 32

  7. Main metabolic intermediers: Reduction: a-hydroxy-acid Transamination: a-ketoacid COO- O COO- COO- H +H3N C red HO H C C CH3 ox CH3 CH3 pyruvate lactate Nonpolar (hydrophobic), aliphatic side chains L-Alanine (3C) Ala, A 32

  8. COO- COO- COO- H H H CH3 CH +H3N +H3N +H3N C C C CH2 CH CH2 CH CH3 CH3 CH3 CH3 CH3 Transaminated forms: Nonpolar (hydrophobic), aliphatic side chains BRANCHED CHAIN AMINO ACIDS Val, V Valine Leu, L Leucine Ile, I Isoleucine keto  isovalerate keto  isocapronate keto  isocapronate Metabolic disorder in the catabolism of branched chain amino acids: a-hydroxy-isovalerate and a-hydroxy-isocapronate in the urine 32

  9. Val Leu Ile 32

  10. Neutral Amino Acids: Acid-base character 32

  11. Protonated forms Deprotonated forms - H A-+ H+ H+ B+ H+ a-carboxyl group is an ACID: HA pKa1 a-amino group is a base: B+ pKa2 pH < pKa pKa <pH 32

  12. Neutral Amino Acids: Protonic equilibria 32

  13. H H H+ Form I. Fully protonated form C +H3N COOH R pKa1= 2.3 - Form 2. Isoelectric form H H+ COO- C +H3N R pKa2 = 9.6 - Form 3. Fully deprotonated form H COO- C H2N R pH < pKa1 pH =(pKa1+pKa2)/2 pH > pKa2 32

  14. H C +H3N COOH R H COO- C +H3N R H COO- C H2N R BUFFERS pH around pKa1 Form 2./ Form 1. BUFFER pKa1= 2.3 NO Buffer at Isoelectric pH! pH around pKa2 Form 3./ Form 2. BUFFER pKa2 = 9.6 32

  15. Neutral Amino Acids: pH dependence of different forms 32

  16. Different forms of Ala 10 mmol 5 pH 2 4 6 8 10 12 H H H C +H3N COOH COO- COO- C C +H3N H2N R R R + + - - 32

  17. pH Ip meqv NaOH added Buffer 1. Buffer 2. 1st Eqv.Point 2nd Eqv.Point Neutral amino acids: Titration curve START: 10 mmol completely protonated neutral amino acid 32

  18. 10 ml of 0.1 M glycine solution (completely protonated) +4 ml0.1 N NaOH, pH=? pH = 2.3 + lg (deprot./prot.) pH = 2.3 + lg 4/6 = 2.1 10 ml of 0.1 M completely protonated glycine solution +x ml0.1 N NaOH, pH=2.6 pH = 2.3 + lg x/(10-x) = 2.6 x= 6.66 ml See also: Selected Calc. CHAPTER 8. AMINO ACIDS AS BUFFER 32

  19. COO- COO- +H2N H H +H3N C Aliphatic secondary amine Aliphatic primary amine Glycine and Proline: Two extremities Gly, G Glycine Pro, P Proline No side chain Alicyclic side chain (nonpolar) maximal flexibility rigid 32

  20. Gly Pro 32

  21. AROMATIC AMINO ACIDS hydrophobic interactions between stacking aromatic rings COO- COO- CH2 Phe hydroxylase CH2 H H +H3N +H3N C C (deficiency: phenylketonuria) polar Transaminated forms: phenyl-pyruvate p-hydroxyphenyl-pyruvate Phe, F Phenylalanine Tyr, Y Tyrosine nonpolar Phenolic -OH (very weak acid) 32 Phenylketonuria: phenyl-pyruvate, phenyl-lactate and phenyl-acetate in the urine

  22. COO- CH2 H +H3N C AROMATIC AMINO ACIDS hydrophobic interactions between stacking aromatic rings Trp, W Tryptophan polar Aromatic secondary amine in the indol ring Very weak base 32

  23. Aromatic amino acids have a characteristic absorbance at 280 nm Characteristic absorbance of proteins. 32

  24. CH2 COO- CH2 H +H3N C NH HN + NH+ HN delocalized structure AROMATIC AMINO ACIDS with positively charged side chain His, H Histidine aromatic imine (weak base) in the imidasol ring 32

  25. Ile Phe Tyr 32

  26. Amino Acids: Optical Activity Assymetrical (chiral) C atom (4 different substituents) Enantiomer pairs (mirror images, not imposable on each other) Optical activity 32

  27. CHO OH C H CH2OH CHO H C OH CH2OH Amino Acids: Optical Activity Proteins Consist of L-Amino Acids D-Glyceraldehyde L-Glyceraldehyde 32

  28. COO- COO- H NH2 H2N C C H CH3 CH3 Amino Acids: Optical Activity Proteins Consist of L-Amino Acids D-Alanine L-Alanine 32

  29. 32

  30. D- Alanine L- Alanine 32

  31. H H OH C C H OH C C C C COO- +H3N C H COO- COO- COO- +H3N NH3+ NH3+ H C OH H H CH3 CH3 CH3 CH3 L-Thr D-Thr Diastereomers Diastereomers Enantiomer pairs H OH Amino Acids: Optical activity Some amino acids have 2 chiral centers 32 L-allothreonine D-allothreonine

  32. COO- COO- H H +H3N +H3N C C CH OH CH2 OH CH3 Amino Acids: Polar side chains -OH containing side chains Thr, T Threonine Ser, S Serine Secondary alcohol Primary alcohol 32

  33. Chemical reaction: O R1 C OH P C + Carboxylic acid Alcohol O O H+ R2 R2 OH OH Biochemical reaction: R2 R2 R1 R1 O O heat O + H2O R1 P OH + enzyme OH OH Phosphate group of ATP Ser –OH of a protein Phosphate ester on a protein Reactions of the Ser OH group An ALCOHOL reacting with CARBOXYLIC ACID forms ESTERS + H2O Ester 32

  34. COO- H +H3N C CH OH CH3 Thr 32

  35. COO- COO- CH2 H H +H3N +H3N C C CH2 CH2 SH S CH3 Amino Acids: Grouping principles -S containing side chains S: low electronnegativity slight polarity Met, M Methionine Cys, C Cysteine Thioalcohol 32 Thioether

  36. Reactions of Amino Acids Formation of disulfide bridge 32

  37. A schematic diagram of two disulfides from the protein structure of bovine insulin 32

  38. COO- COO- COO- H H H +H3N C +H3N C +H3N C CH2 CH2 CH2 SH CH2 SH Cystein (3C) CH2 Homocystein (4C) S Methionin (5C) CH3 Role of Methionin in the metabolism Its activated form is a methyl group donor 32

  39. Homoserine (4C and -OH) Cystein (3C and -SH) COO- COO- H +H3N C H +H3N C CH2 CH2 CH2 S Homocystein (4C and -SH) Serine (3C and -OH) Exchange of the sulfur in the metabolism Cystathionine 32

  40. COO- COO- H H CH2 +H3N +H3N C C b CH2 g CH2 COO - COO - Amino Acids: Polar side chains Negatively charged (ACIDIC) side chains. Asp, D Aspartate Glu, E Glutamate b-carboxyl g-carboxyl Transamination: a-keto-glutarate oxaloacetate 32

  41. COO- COO- H H CH2 +H3N +H3N C C b CH2 g CH2 CONH2 CONH2 Amino Acids:Polar side chains Amides Asn, N Asparagine Gln, Q Glutamine amide amide Amide of Aspartate Amide of Glumatate 32

  42. COO- COO- H H CH2 CH2 +H3N +H3N C C g g CH2 CH2 COO - CONH2 Gln Glu 32

  43. Side chain Side chain CH2 CH2 Side chain C NH2 C NH2 N H O O H H O NH O C O - C O CH2 CH2 Side chain Side chain Side chain Hydrogen bonds between side chains Hydrogen donors: Trp, Ser,Thr,Tyr,Asn, Gln, His Hydrogen acceptors: Asp, Glu, Asn, Gln 32

  44. Glu Tyr 32

  45. Gln Tyr 32

  46. Gln Asn 32

  47. CO2 H2 decarboxylation +H3N C R R Biogen amine Biogen amines Biochemical reaction: Decarboxylation of amino acids COO- H +H3N C specific decarboxylases (enzymes) Amino acid 32

  48. CO2 O2 H2O + + H2 H H N N C C 3 3 CH CH 2 2 decarboxylation hydroxylation OH OH OH OH OH Dopa Dopamine Tyrosine Biogen amine Biogen amines Synthesis of dopamine from Tyr Aromatic amino acid decarboxylase Tyr hydroxylase Dopamine: neurotransmitter Parkinson’s disease - low dopamine production 32

  49. CH3 + + H2 H H N N C C + + 3 3 H2 H H N N C C 2 HO O2 H2O CH CH HO CH CH methyl group donor + + H2 H H N N C C 3 3 methylation CH CH hydroxylation 2 2 OH OH OH OH OH OH OH OH OH Norepinephrine (noradrenaline) Biogen amine OH Epinephrine (adrenaline) Biogen amine OH OH dopamine Neurotransmitter Stress hormone Biogen amines Synthesis of norepinephrine and epinephrine Dopamine b hydroxylase vitamin C phenylethanol amine N-methyl transferase 32

  50. CO2 H H - - + + H H N N - - C C - - COO COO 3 3 CH CH decarboxylation 2 2 CH CH 2 2 - - COO COO Gamma-amino butirate (GABA) biogen amine Glu neurotransmitter Biogen amines Synthesis of GABA from Glu Glu decarboxylase 32

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