CHEMISTRY OF AMINO ACIDS, PEPTIDES AND PROTEINS

1. CHEMISTRYOF AMINO ACIDS, PEPTIDES AND PROTEINS VinithaRamanathPai Professor, Dept of Biochemistry, Yenepoya Medical College.

2. Contents • Biological importance • Medical importance • Chemistry of amino acids • Chemistry of peptides • Chemistry of proteins

3. Biological Importance 1. of Amino acids • the basic structural units / building blocks of proteins. • Precursors of small but biologically important nitrogen containing molecules. • e.g. Heme; melanin; hormones; nitrogenous bases in nucleic acids; • bile acids and bile salts; etc.

4. Biological Importance 2. of peptides • Contain small number of amino acids - Oligomers • Mostly act as • hormones - Gastrin, oxytocin, vasopressin • neurotransmitters . encephalins

5. Biological Importance 3. of Proteins • Macromolecules / Polymers - Contain larger number of amino acids. • Distribution - abundant in living cells - about 50% of the dry weight of the cell. • Diverse functions • Catalysis (enzyme); Structure (actin, myosin), Protective (antibodies); Transport (respiratory gases by Hemoglobin)

6. Biological Importance of proteins…. • Derived from the Greek word "proteios"which means “primary” or “holding the first place”. • They are source of nitrogen to the body - • synthesis of nitrogen containing biologically important molecules. • The average N2 content of proteins is 16% (g/g).

7. Biological Importance…. • Source of proteins to the body • 1. Dietary proteins • Digestion in the GI tract • Amino acids (absorbed into blood and transported to the cells) • Protein Biologically important small N2 containing molecules • Energy (4 kCals / g protein) Translation Oxidation

8. Biological Importance…. • Proteins are synthesized in the body • DNA (contains the code for peptides / proteins). • Transcription • RNA • Translation • Protein • In humans, 30,000 proteins are known.

9. Medical Importance • Genetic disease / Hereditary disease / Inborn error of metabolism • DNA (contains the code for peptides / proteins). • Transcription • RNA • Translation • Protein Change in code of “mutation” Change in code of Change in - “Mutant / defective protein”

10. Medical Importance • Examples: diseases with defective enzymes • of amino acid metabolism. • Albinism • Phenylketonuria • Alkaptonuria • Homocysteinuria • Hereditary disease of Hemoglobin - Sickle cell anemia.

11. CHEMISTRYOF AMINO ACIDS

12. Contents • Introduction • Classification of standard amino acids • Biological function of amino acids • Role of side chains / R group of amino acid residues • Peptide bond • Biologically important peptides

13. Introduction • Amino acids - source of nitrogen to the body. • Amino acids linked by peptide bonds to form proteins. • There are 300 amino acids in nature. • 20 Amino acids in proteins. • Amino acids in proteins – “primary / standard amino acids”. • Every standard amino acid (present in protein) has a code in the Gene of the DNA.

14. An amino acid is ……. • an organic compound with two functional groups. • A carboxyl group (-COOH) • An amino group (-NH2) • Amino acids have C, H, O and N • Some amino acids have other functional groups as well OH (hydroxyl) • Some have sulphur (S). • Some have additional COOH / NH2 groups.

15. Types of Amino Acids Amino Acids Protein Amino Acids Non Protein Amino Acids Standard / Primary Amino Acids Secondary Amino Acids • Amino Acids • Not present in proteins • Not all are α – amino acids • Occur in the body 20 Amino Acids They are α – amino acids Modified primary amino acids after incorporation into proteins Present in proteins Examples : Glycine, serine, lysine, proline Examples : β – Alanine , Gama amino butyric acid (GABA), Ornithine, Citrulline Examples : Hydroxyproline; Hydroxy lysine; cystine, γcarboxy glutamate

16. L - α– Amino acid is…….. • Amino acids present in proteins are different – they are L - α-amino acids. • 20 different L, α-amino acids are present in proteins. What are L, α-amino acids ?

17. Numbering of the Carbon atoms…….. Greek alphabets α γ β δ ε * CH2 CH COOH CH3 CH2CH2CH2 NH2  - • Acid Amino

18. Basic structure of an amino acid Common to all amino acids α – Amino acid H Hydrogen atom H α COOH Carboxyl group C NH2 COOH NH2 Amino group R R Side chain ‘R’ groups is different in the 20 amino acids Monoaminomonocarboxylic amino acids

19. L, α– amino acid has asymmetric carbon atom H Hydrogen atom H α COOH Carboxyl group NH2 COOH C NH2 Amino group R R Side chain α - Carbon is an asymmetric carbon atom. Definition : An asymmetric carbon atom is attached to four different groups.

20. Amino acids are called as L,  - amino acids .

21. DL isomerism .. What are these structures ? What is the difference between these two structures ? H α NH2 group on the leftof α Carbon atom COOH C NH2 R L - isomer of amino acid H α COOH NH2 C NH2 group on the rightof α Carbon atom R D - isomer of amino acid

22. Amino acids are called as L,  - amino acids . DL Isomerism in αamino acids Based on Orientation of amino group on the αCarbon atom

23. Structure of standard amino acids Aliphatic amino acids H α Glycine (Gly, G) C H COOH NH2 H α C Alanine (Ala, A) CH3 COOH NH2

24. Aliphatic Branched chain amino acids H H CH3 CH3 α α C CH COOH C CH2 CH COOH CH3 CH3 NH2 NH2 Valine (Val, V) Leucine (Leu, L) H CH3 α C CH CH2 COOH NH2 CH3 Isoleucine(Ile, I)

25. Hydroxy amino acids Have hydroxyl group in the side chain H α C CH2OH COOH NH2 Serine (Ser, S) H α C CH3 CH COOH OH NH2 Threonine (Thr, T)

26. Sulphur containingamino acids have ‘S’ in their side chain. H α C CH2SH COOH Thiol group Labile methyl group NH2 Cystiene (Cys, C) S is between two carbon atoms. H α C CH2 S CH3 CH2 COOH NH2 Methionine (Met, M)

27. Sulphur containing amino acids Cystine H H α α COOH C C COOH SH2C CH2 S NH2 NH2 Disulphide bridge DiaminoDicarboxylic amino acid

28. Acidic amino acids have additional carboxyl group in their side chain H α C CH2COOH COOH Aspartic acid (Asp, D) NH2 H α C CH2 CH2COOH COOH NH2 Glutamic acid (Glu, E) 2 carboxylic (COOH) groups Monoamino Dicarboxylic acids

29. Amides of Acidic amino acids H α C CH2CONH2 COOH Asparagine (Asn,D) NH2 H α C CH2 CH2CONH2 COOH NH2 Glutamine (Gln, N)

30. Basic amino acids • have additional amino groups in their side chain H ε α C COOH CH2 CH2 CH2 CH2 NH2 NH2 Lysine (Lys, K) H NH2 α C CH CH2 NH C COOH NH NH2 Arginine (Arg, R) Guanidinium group 2 or more amino groups Diamino monocarboxylic acids

31. Aromatic amino acids have benzene ring in the side chain H α C CH2 COOH NH2 H α C CH2 COOH NH2 OH H α C CH2 COOH NH2 NH Benzene Phenyl alanine (Phe, F) Hydroxy phenyl Tyrosine (Tyr, Y) Indole nucleus Tryptophan (Try, W) Monoamino monocarboxylic amino acids

32. HN CH COOH H2C CH2 C H2 Heterocyclic amino acids H Histidine (His, H ) α C CH2 C CH COOH Imidazole ring NH2 N NH CH2 Iminoacids Hydroxy Proline Proline (Pro, P) HN CH COOH H2C CH2 C H OH Pyrrolidine ring

33. REVISION In the next five slides is quiz for revision MCQ’s choose the most appropriate answer

34. Quiz : The average N2 content of proteins is ______. 16 mg /DL 16 g / DL 16 g / g 16 mg /g • Answer c) 16 g / g means 16% (w/w or g/g)

35. Quiz : 2. ____________ is a sulphur containing amino acid. Glycine Valine Threonine Cystiene • Answer d) Cystiene

36. Quiz : 3. All of the following are aromatic amino acids except _________________. Phe Thr Tyr Try Answer b) Thr (threonine is a hydroxy amino acid)

37. Quiz : 4. __________ is an example for a small molecule synthesized from amino acids. Thymine Insulin keratin hemoglobin Answer a) Thymine (nitrogenous base in DNA)

38. Quiz : 5. __________ is a diaminodicarboxylic amino acid Aspartic acid Glutamic acid Cystiene Cystine Answer d) Cystine

39. Classification of amino acids 1. Based onthe structure / side chains (R group) 2. Based onchemical nature of the R group 3. Based onpolarity of the R group 4. Based onnutritional requirement 5. Based onmetabolic fate

40. 1.Classification based onstructure / side chains (R group) Aliphatic amino acids: Gly, Ala, Val, Leu, Ile Hydroxy amino acids : Ser, Thr, Tyr Sulphur containing amino acids : Cys, Met, Cystine Acidic amino acids : Asp, Glu, Asn, Gln Basic amino acids : Lys, Arg Aromatic amino acids : Phe, Tyr, Try Heterocyclic amino acids : His Iminoacids : Pro, Hydroxy Pro

41. 2. Classification based on Chemical nature / charge of the R group Neutral amino acids Monoaminomonocarboxylic amino acids Gly, Ala, Val, Leu, Iso, Ser, Thr, Cys, Met, Pro, Phe, Tyr, Try Monoaminodicarboxylic amino acids Acidic amino acids Asp, Glu Basic amino acids Diaminomonocarboxylic amino acids Lys, Arg, His

42. 3. Based on polarity of the R group Amino acids Polar Non Polar Hydrophilic Hydrophobic Uncharged Polar Charged Polar Aromatic Aliphatic Phe, Try Ala, Val, Leu, Iso, Met, Pro Ser, Thr, Tyr, Cys, Asn, Gln, Gly. Positively Charged Negatively Charged Asp, Glu Lys, Arg, His

43. 4. Classification based on Nutritional requirement Essential amino acids Cannot be synthesized in the body, have to be supplied by the diet. Met, Arg, Try, Thr, Val, Ile, Leu, Phe, His, Lys (MATT VIL PHLy) Semi essential amino acids His, Arg Synthesized in the body but not sufficient during certain phases of life i.e., growth, pregnancy. Non essential amino acids Can be synthesized in the body in adequate amounts. Gly, Ala, Ser, Tyr, Cys, Asp, Glu, Pro

44. 5. Classification based on Metabolic end products Metabolism of amino acids Amino acids Metabolism / catablism Intermediates / end products Glucose Ketone bodies Glucogenic amino acids Ketogenic amino acids Glucose + Ketone bodies Glucogenicketogenic amino acids

45. 5. Classification based on Metabolic end products Gives rise to products which can be converted to glucose Glucogenic amino acids Gly, Ala, Ser, Thr, Val, Asp, Glu, Lys, Arg, Pro Gives rise to products which can be converted to ketone bodies Ketogenic amino acids Leu Glucogenic ketogenic amino acids Phe, Tyr, Try, His Gives rise to products which can give rise to both glucose and ketone bodies

46. Quiz : ______ is an example for an acidic amino acid. Phenyl alanine Cystine Proline Aspartic acid • Answer d) Aspartic acid

47. Quiz : 2. ____________ is an example for ketogenic amino acid. Glycine Valine Threonine Leucine • Answer d) Leucine

48. Properties of Amino acids DL isomerism Optical isomerism Acid – base properties

49. DL isomerism Based on the orientation of  - NH2 group H α NH2 group on the leftof α Carbon atom COOH C NH2 R L - isomer of amino acid H α COOH NH2 C NH2 group on the rightof α Carbon atom R D - isomer of amino acid

50. Importance of DL Isomerism 1. At pH 7.0, naturally occurring amino acids are of ‘L’ configuration. 2. ‘D’ amino acids are also seen in nature. • in antibiotics • bacterial cell wall • D- Ser and D- Asp are found in the fore brain and periphery of the brain.