1. 1 Amino Acids & Peptides

2. 2 Chapter Outline Amino Acids 5.1 Amino Acids 5.1 –Amino acid classes (G1) –Stereoisomers (G2) –Bioactive AA –Titration of AA (G3) –Modified AA –AA reactions Peptides 5.2 Peptides 5.2

3. General Properties There are 20 standard amino acids. With exception of proline, all have primary amino group and a carboxylic acid bonded to same carbon. There are 20 standard amino acids. With exception of proline, all have primary amino group and a carboxylic acid bonded to same carbon. Carboxyl group and amino group all have pKa values around 2.2 and 9.4 respectively Carboxyl group and amino group all have pKa values around 2.2 and 9.4 respectively 3

4. Note that at physiological pH of 7, amino acids are charged as shown to right. They can act as either acid or base. Note that at physiological pH of 7, amino acids are charged as shown to right. They can act as either acid or base. Also referred to as zwitterions Also referred to as zwitterions This imparts special properties e.g. some have melting points of 300 C, just like salts. Also very soluble in water and not organics. This imparts special properties e.g. some have melting points of 300 C, just like salts. Also very soluble in water and not organics. 4

5. AMINO ACIDS Overview The general structure of an amino acid molecule, with the amine group on the right and the carboxylic acid group on the left. The R group is dependent on the amino acid. The general structure of an amino acid molecule, with the amine group on the right and the carboxylic acid group on the left. The R group is dependent on the amino acid. 5

6. AAs overview cont.. In chemistry, an amino acid is any molecule that contains both amine and carboxylic acid functional groups. In biochemistry, this shorter and more general term is frequently used to refer to alpha amino acids: those amino acids in which the amino and carboxylate functionalities are attached to the same carbon, the so-called α–carbon. In chemistry, an amino acid is any molecule that contains both amine and carboxylic acid functional groups. In biochemistry, this shorter and more general term is frequently used to refer to alpha amino acids: those amino acids in which the amino and carboxylate functionalities are attached to the same carbon, the so-called α–carbon.α–carbon 6

7. AAs overview cont.. An amino acid residue is what is left of an amino acid once a molecule of water has been lost (an H+ from the nitrogenous side and an OH- from the carboxylic side) in the formation of a peptide bond. An amino acid residue is what is left of an amino acid once a molecule of water has been lost (an H+ from the nitrogenous side and an OH- from the carboxylic side) in the formation of a peptide bond.H+OH-H+OH- 7

8. AAs overview cont.. Amino acids are the basic structural building units of proteins. They form short polymer chains called peptides or polypeptides which in turn form structures called proteins. The process of such formation from an mRNA template is known as translation, which is part of protein synthesis. Amino acids are the basic structural building units of proteins. They form short polymer chains called peptides or polypeptides which in turn form structures called proteins. The process of such formation from an mRNA template is known as translation, which is part of protein synthesis.peptidespolypeptidesproteinsmRNAtranslationprotein synthesispeptidespolypeptidesproteinsmRNAtranslationprotein synthesis Phenylalanine is one of the standard Phenylalanine is one of the standard Phenylalanine amino acids. 8

9. Twenty amino acids are encoded by the standard genetic code and are called proteinogenic or standard amino acids. Combinations of these amino acids produce every single essential protein for the homeostasis of the human body. At least two others are also coded by DNA in a non-standard manner Twenty amino acids are encoded by the standard genetic code and are called proteinogenic or standard amino acids. Combinations of these amino acids produce every single essential protein for the homeostasis of the human body. At least two others are also coded by DNA in a non-standard mannergenetic code proteinogenicgenetic code proteinogenic 9 AAs overview cont..

10. 19 standard AAs have the same general str. 19 standard AAs have the same general str. These molecules contain a central C atom (the α-C) to amino group, carboxylate group, H atom and R group are attached. These molecules contain a central C atom (the α-C) to amino group, carboxylate group, H atom and R group are attached. 10 AAs overview cont..

11. Proline is the only proteinogenic amino acid whose side group cyclizes onto the backbone: it links to the α-amino group, and thus is also the only proteinogenic amino acid containing a secondary amine at this position. Proline is the only proteinogenic amino acid whose side group cyclizes onto the backbone: it links to the α-amino group, and thus is also the only proteinogenic amino acid containing a secondary amine at this position. Prolineproteinogenic Prolineproteinogenic 11 AAs overview cont..

12. 12 Amino Acid: Definition An alpha amino acid is a carboxylic acid with an amino group on the carbon alpha to the carboxylic acid. An alpha amino acid is a carboxylic acid with an amino group on the carbon alpha to the carboxylic acid. The alpha carbon also has an R group side chain except for glycine which has two Hs. The alpha carbon also has an R group side chain except for glycine which has two Hs. Generic amino acid at physiological pH: zwitterion form  C C

13. 13 Definition, cont. If the R group is not H, the AA can exist in two enantiomeric forms (nonsuperimposable mirror image) forms.) If the R group is not H, the AA can exist in two enantiomeric forms (nonsuperimposable mirror image) forms.) Mirror plane  carbon

14. 14 Amino Acids General form: 1. an amino acid (AA); 2. two AA linked to form the peptide bond. General form: 1. an amino acid (AA); 2. two AA linked to form the peptide bond. L-form

15. 15 Amino Acids-2 Only the L form of amino acids is commonly found in proteins. Only the L form of amino acids is commonly found in proteins. Depending on the nature of the R group, AA are classified into four groups. Depending on the nature of the R group, AA are classified into four groups.nonpolarpolaracidicbasic

16. 16 Hydrophobic Amino Acids 1

17. 17

18. 18 AA with nonpolar side chains-2

19. Hydrophobic Amino Acids 2 19

20. Neutral Nonpolar AA Contain mostly HC R groups Contain mostly HC R groups Neutral = R groups ≠ ± charges Neutral = R groups ≠ ± charges They interact poorly with water, nonpolar (hydrophobic) They interact poorly with water, nonpolar (hydrophobic) Important role maintaining the 3-D protein str Important role maintaining the 3-D protein str 20

21. 21 AA with polar side chains-1

22. Polar Amino Acids 1 22

23. 23 AA with polar side chains-2

24. Polar Amino Acids 2 24

25. Polar AA Have functional groups capable of H bonding; easily interact with water Have functional groups capable of H bonding; easily interact with water Give significant effect on protein stability Give significant effect on protein stability 25

26. 26 AA: acidic and basic

27. Charged Amino Acids 27

28. 28 The side chains of aspartic acid and glutamic acid are negatively charged above pH 3. The side chains of aspartic acid and glutamic acid are negatively charged above pH 3. The side chains of basic amino acids are positively charged at physiological pH values: The side chains of basic amino acids are positively charged at physiological pH values: Lysine – has butylammonium side chain Arginine – bears a guanidino group Histidine – carries a imidazolium moeity

29. Can form ionic bonds with acidic AA Can form ionic bonds with acidic AA Play an important role in the catalytic activity of numerous enzymes Play an important role in the catalytic activity of numerous enzymes 29

30. 30

31. Bioactive AAs 31 In addition to protein synthesis, amino acids have other biologically-important roles. Glycine and glutamate are neurotransmitters as well as standard amino acids in proteins. Many amino acids are used to synthesize other molecules, for example: In addition to protein synthesis, amino acids have other biologically-important roles. Glycine and glutamate are neurotransmitters as well as standard amino acids in proteins. Many amino acids are used to synthesize other molecules, for example: Glycineglutamate neurotransmitters Glycineglutamate neurotransmitters  Tryptophan is a precursor of the neurotransmitter serotonin.  Glycine is one of the reactants in the synthesis of porphyrins such as heme.  Arginine is used to synthesize the hormone nitric oxide.

32. Bioactive AAs cont…. Numerous non-standard amino acids are also biologically-important: Gamma- aminobutyric acid is another neurotransmitter, carnitine is used in lipid transport within a cell, ornithine, citrulline, homocysteine, hydroxyproline, hydroxylysine, and sarcosine. Numerous non-standard amino acids are also biologically-important: Gamma- aminobutyric acid is another neurotransmitter, carnitine is used in lipid transport within a cell, ornithine, citrulline, homocysteine, hydroxyproline, hydroxylysine, and sarcosine.Gamma- aminobutyric acidcarnitinelipidcellornithinecitrulline homocysteinehydroxyproline hydroxylysinesarcosineGamma- aminobutyric acidcarnitinelipidcellornithinecitrulline homocysteinehydroxyproline hydroxylysinesarcosine 32

33. Bioactive AAs cont…. The 20 standard amino acids undergo a bewildering number of chemical transformations to other amino acids and related compounds as part of their normal cellular synthesis and degradation. The 20 standard amino acids undergo a bewildering number of chemical transformations to other amino acids and related compounds as part of their normal cellular synthesis and degradation. Many organisms use certain amino acids to transport nitrogen in the form of amino groups. Many organisms use certain amino acids to transport nitrogen in the form of amino groups. Amino acids may also be oxidized as metabolic fuels to provide energy. Amino acids may also be oxidized as metabolic fuels to provide energy. 33

34. Bioactive AAs cont…. Amino acids often function as chemical messengers for communication between cells. Amino acids often function as chemical messengers for communication between cells. Alpha-aminobutric acid and dopamine are neuro transmitters. Alpha-aminobutric acid and dopamine are neuro transmitters. Histamine is a mediator of allergic reactions. Histamine is a mediator of allergic reactions. 34

35. Bioactive AAs cont…. Thyroxine stimulates vertebrate metabolism. Thyroxine stimulates vertebrate metabolism. Many peptides (e.g. glutathione) have physiological functions as hormones or regulatory molecules. Many peptides (e.g. glutathione) have physiological functions as hormones or regulatory molecules. 35

36. Modified AAs in Proteins The ‘universal’ genetic code specifies only the 20 essential amino acids. The ‘universal’ genetic code specifies only the 20 essential amino acids. Other amino acids are components of certain proteins resulting from the specific modification of an amino acid residue after the polypeptide chain has been synthesized. Other amino acids are components of certain proteins resulting from the specific modification of an amino acid residue after the polypeptide chain has been synthesized. 36

37. Modified AAs in Proteins cont… These modifications include the simple addition of small chemical groups to certain amino acid chains: hydroxylation, methylation, acetylation, and phosphorylation. These modifications include the simple addition of small chemical groups to certain amino acid chains: hydroxylation, methylation, acetylation, and phosphorylation. Larger groups, including lipids and carbohydrate polymers, are attached to particular amino acid residues of certain proteins Larger groups, including lipids and carbohydrate polymers, are attached to particular amino acid residues of certain proteins Examples: γγ-carboxyglutamate, 4- hydroxyproline Examples: γγ-carboxyglutamate, 4- hydroxyproline 37

38. AA Stereoisomer Most amino acids occur in two possible optical isomers, called D and L. The L amino acids represent the vast majority of amino acids found in proteins. Most amino acids occur in two possible optical isomers, called D and L. The L amino acids represent the vast majority of amino acids found in proteins. optical isomersproteins optical isomersproteins D amino acids are found in some proteins produced by exotic sea-dwelling organisms, such as cone snails. They are also abundant components of the proteoglycan cell walls of bacteria. D amino acids are found in some proteins produced by exotic sea-dwelling organisms, such as cone snails. They are also abundant components of the proteoglycan cell walls of bacteria.cone snails proteoglycancell wallsbacteriacone snails proteoglycancell wallsbacteria 38

39. The D-isomer of aspartic acid is found in some proteins as the result of a spontaneous post-translational modification associated with protein aging or as the by-product of enzymatic modification catalyzed by protein L- isoaspartyl methyltransferase. The D-isomer of aspartic acid is found in some proteins as the result of a spontaneous post-translational modification associated with protein aging or as the by-product of enzymatic modification catalyzed by protein L- isoaspartyl methyltransferase. 39

40. All amino acids (except glycine) recovered from polypeptides are optically active and direction of angle of rotation is measured by polarimeter. All amino acids (except glycine) recovered from polypeptides are optically active and direction of angle of rotation is measured by polarimeter. Optically active molecules are asymmetric and the central atoms (C-alpha atoms of amino acids) in such molecules are chiral centers with property of chirality. Optically active molecules are asymmetric and the central atoms (C-alpha atoms of amino acids) in such molecules are chiral centers with property of chirality. 40

41. These asymmetric centers give rise to enantiomers (nonsuperimposable mirror images of one another) or are stereoisomers (chiral molecules with different configurations about at least one of their asymmetric centers but which are otherwise identical). These asymmetric centers give rise to enantiomers (nonsuperimposable mirror images of one another) or are stereoisomers (chiral molecules with different configurations about at least one of their asymmetric centers but which are otherwise identical). Life is based on chiral molecules as biosynthetic processes almost invariably produce pure stereoisomers. Life is based on chiral molecules as biosynthetic processes almost invariably produce pure stereoisomers. 41

42. Acid-Base Properties of AAs Titration curve for glycine Titration curve for glycine Note that one starts with all groups in acid form. Note that one starts with all groups in acid form. Note how many equivalents are added Note how many equivalents are added Note that at 0.5 and 1.5 equivalents, pH is equal to pK of group being titrated. Note that at 0.5 and 1.5 equivalents, pH is equal to pK of group being titrated. Note pH which gives zero charge is the isoelectric point. Calculated as (pK1+pK2)/2 Note pH which gives zero charge is the isoelectric point. Calculated as (pK1+pK2)/2 Note where the buffering capacity is best Note where the buffering capacity is best 42

43. 43 Amino Acid Titration At physiological pH, the carboxyl group of the AA is negatively charged and the amino group is positively charged. At physiological pH, the carboxyl group of the AA is negatively charged and the amino group is positively charged. Amino acids without charged side chains are zwitterions and have no net charge. H 3 + N-CHR-COO -. Amino acids without charged side chains are zwitterions and have no net charge. H 3 + N-CHR-COO -. A titration curve shows how the amine and carboxyl groups react with hydrogen ion. A titration curve shows how the amine and carboxyl groups react with hydrogen ion.

44. 44 Amino Acid Titration At low pH a nonacidic/nonbasic amino acid is protonated and has the structure below. At low pH a nonacidic/nonbasic amino acid is protonated and has the structure below. H 3 N + CHRCOOH H 3 N + CHRCOOH The charge behavior of acidic and basic AAs is more complex. The charge behavior of acidic and basic AAs is more complex.

45. 45 Titration of Alanine 1 A A=B pK 1 =2.3 B, pI=pH=6.0 B=C pK 2 =9.73 C

46. 46 Isoelectric point The isoelectric point (pI) for an AA occurs when there is no net charge. The isoelectric point (pI) for an AA occurs when there is no net charge. For a neutral AA, the pI is calculated using the equation pK 1 + pK 2 /2 For a neutral AA, the pI is calculated using the equation pK 1 + pK 2 /2 Eg.: alanine: 2.34 + 9.7 / 2 = 6.0 Eg.: alanine: 2.34 + 9.7 / 2 = 6.0 For acidic or basic AAs, the pI is the average of the two pK a values bracketing the isoelectric structure. For acidic or basic AAs, the pI is the average of the two pK a values bracketing the isoelectric structure.

47. 47 More Titration Curves AA with ionizable side chains hv complex titration curve AA with ionizable side chains hv complex titration curve Eg. Glutamic acid has a carboxyl side chain group Eg. Glutamic acid has a carboxyl side chain group At low pH it has net charge +1. As base is added, the α-carboxyl group loses a proton to become carboxylate group. At low pH it has net charge +1. As base is added, the α-carboxyl group loses a proton to become carboxylate group. Glutamate now has no net charge. As more base is added Glutamate now has no net charge. As more base is added

48. 48 More Titration Curves cont… As more base is added, the second carboxyl group loses a proton and the molecule has a -1 charge. As more base is added, the second carboxyl group loses a proton and the molecule has a -1 charge. Adding additional base results in the NH 3 ion lossing its proton. Adding additional base results in the NH 3 ion lossing its proton. At this point glutamate has a net charge of -2. the pI value for glutamate is the halfway btw the pKa values for the 2 carboxyl group At this point glutamate has a net charge of -2. the pI value for glutamate is the halfway btw the pKa values for the 2 carboxyl group pI = 3.22 pI = 3.22

49. Peptide Bonds Peptide bond formed from elimination of water from 2 amino acids resulting in CO- NH linkage. Peptide bond formed from elimination of water from 2 amino acids resulting in CO- NH linkage. Can have di-, tri-, oligo- and poly- peptides. Can have di-, tri-, oligo- and poly- peptides. Proteins composed of linear polymer of amino acids. Proteins composed of linear polymer of amino acids. 49

50. Large number of proteins can exist. A small protein of 100 amino acids can have 20 100 or 1.27x10 130 possible unique polypeptide chains. Large number of proteins can exist. A small protein of 100 amino acids can have 20 100 or 1.27x10 130 possible unique polypeptide chains. 50

51. Peptides Peptide: a polymer of about 2-100 AAs linked by the peptide(amide) bond. As the amino group and the carboxyl group link, water is lost. Peptide: a polymer of about 2-100 AAs linked by the peptide(amide) bond. As the amino group and the carboxyl group link, water is lost. 51

52. Peptides A peptide is written with the N-terminal end to the left and the C-terminal end to the right. A peptide is written with the N-terminal end to the left and the C-terminal end to the right. H 2 N-Tyr-Ala-Cys-Gly-COOH H 2 N-Tyr-Ala-Cys-Gly-COOH Name = Tyrosylalanylcysteinylglycine Name = Tyrosylalanylcysteinylglycine The peptide bond is rigid and planar due to the resonance contribution shown below. The peptide bond is rigid and planar due to the resonance contribution shown below. 52

53. Peptides The peptide bond angles force specific conformations of proteins and, on extended chains, successive R groups are on opposite sides. The peptide bond angles force specific conformations of proteins and, on extended chains, successive R groups are on opposite sides. 53

54. Physiologically Interesting Peptides 54  carbon Common name: carnosine found in muscle tissue

55. Physiologically Interesting Peptides 55 Glutathione: the reduced form reduces oxidizing agents by dimerizing to form the disulfide bond with release of 2 H.

56. Physiologically Interesting Peptides 56 Tyr-Gly-Gly-Phe-Leu N-terminal AA C-terminal AA Short form description for a peptide. Leucine enkephalin: a natural analgesic found in the brain

57. Physiologically Interesting Peptides 57 Oxytocin Induces labor and aids in forcing milk from the mammary glands. Vassopressin has a Phe at position 3 instead of Ile and an Arg at position 8 instead of a Leu. Its role is in regulating blood pressure. 3 8

58. 58 Amino Acids & Peptides THE END