1. ERT 106 BIOCHEMISTRY Amino Acids Pn Syazni Zainul Kamal

2. Introduction Proteins - the most structural, sophisticated molecules known Proteins - the most structural, sophisticated molecules known - vary extensively in structure - are polymer constructed from the same set of 20 amino acids - are polymer constructed from the same set of 20 amino acids Polymer of amino acids = polypetides Polymer of amino acids = polypetides Proteins consists of 1 or more polypeptides folded and coiled into specific conformations Proteins consists of 1 or more polypeptides folded and coiled into specific conformations

4. Amino Acids structure Amino Acids contain a central carbon atom (α-carbon) to which an amino group, a carboxylate group, a hydrogen atom and an R (side chain) group are attached

5. Structure of amino acids commonly found in protein Amino acids shown in their prevailing ionic forms at pH7, approx pH within a cell

6. Name and three-letter abbreviation of amino acid

7. The exception : proline differ from other standard amino acid The exception : proline differ from other standard amino acid R group makes up part of a ring which also includes the amino group and the α-carbon atom. R group makes up part of a ring which also includes the amino group and the α-carbon atom. Since the amino group in proline is involved in two carbon-nitrogen bonds, it is a secondary amino group. Since the amino group in proline is involved in two carbon-nitrogen bonds, it is a secondary amino group. Proline (secondary amino group) Standard amino acid (primary amino group)

8. Amino acid structure The amino and carboxylic groups of amino acids readily ionized The amino and carboxylic groups of amino acids readily ionized At physiological pH (7) At physiological pH (7) - carboxyl group of an amino acid is unprotonated. conjugate base form (-COO - ) - amino group of an amino acid is protonated. in its conjugate acid form ( + NH 3 ) Thus, each amino acid can behave as an acid or base Thus, each amino acid can behave as an acid or base referred as amphoteric (substance that can act as acid or base) referred as amphoteric (substance that can act as acid or base)

9. Neutral molecules which bear an equal umber of positive and negative charges simultaneously are called zwitterions Neutral molecules which bear an equal umber of positive and negative charges simultaneously are called zwitterions The R group give each amino acid its unique properties The R group give each amino acid its unique properties Structure of amino acid at pH7

10. Amino acid classes Sequence of amino acids determines the three- dimensional configuration of each protein Sequence of amino acids determines the three- dimensional configuration of each protein Amino acids classified based on their capacity to interact with water Amino acids classified based on their capacity to interact with water 4 classes of amino acids : 4 classes of amino acids : a) neutral nonpolar b) neutral polar c) acidic d) basic

12. a) Neutral nonpolar amino acids Term‘Neutral’ – R groups do not bear +ve or Term‘Neutral’ – R groups do not bear +ve or –ve charge So they interact poorly with water and play important role in maintaining the three- dimensional structure of protein So they interact poorly with water and play important role in maintaining the three- dimensional structure of protein Contain hydrocarbon R groups Contain hydrocarbon R groups 2 types of hydrocarbon R groups: 2 types of hydrocarbon R groups: a) aromatic (contain cyclic structure) eg. Phenylalanine, tryptophan

14. b) aliphatic (nonaromatic hydrocarbon) eg. Glycine, alanine, valine, leucine, isoleucine, proline, methionine, cysteine Methionine & cysteine contain sulfur atom in the aliphatic side chain Methionine & cysteine contain sulfur atom in the aliphatic side chain

15. b) Neutral polar amino acids Polar amino acids = hydrophilic (water loving) Polar amino acids = hydrophilic (water loving) Have functional group capable of forming hydrogen bonding, so easily interact with water Have functional group capable of forming hydrogen bonding, so easily interact with water Serine, threonine, tyrosine, asparagine, glutamine Serine, threonine, tyrosine, asparagine, glutamine Serine, threonine, tyrosine Serine, threonine, tyrosine - contain polar hydroxyl group (-OH) - Thus enable them to from hydrogen bonding (important factor in protein structure)

17. Asparagine & glutamine Asparagine & glutamine - are amide derivatives of aspartic acid and glutamic acid (acidic amino acids) - amide funtional group are highly polar, so can form hydrogen bonding (effet on protein stability)

18. c) Acidic amino acids Contain carboxylate R group Contain carboxylate R group The side chains of aspartic acid & glutamic acid are polar and negatively charged at physiological pH, so they often referred as aspartate and glutamate The side chains of aspartic acid & glutamic acid are polar and negatively charged at physiological pH, so they often referred as aspartate and glutamate

20. d) Basic amino acids Lysine, Arginine, Histidine Lysine, Arginine, Histidine Contain amine R group Contain amine R group Are polar and positively charge at physiological pH Are polar and positively charge at physiological pH Can form ionic bond with acidic amino acids Can form ionic bond with acidic amino acids Very hydrophilic Very hydrophilic

22. Biologically active amino acids The 20 standard amino acids undergo a bewildering number of chemical transformations. The 20 standard amino acids undergo a bewildering number of chemical transformations. Many amino acids are synthesizes not to be residues of polypeptides but to function independently. Many amino acids are synthesizes not to be residues of polypeptides but to function independently. Besides being components of protein, amino acids have several biological roles : Besides being components of protein, amino acids have several biological roles : 1) Chemical messengers 2) Precursors 3) Metabolite intermediates

23. Chemical messengers Chemical messengers - Neurotransmitters = substances released from one nerve cell that influence the function of a second nerve cell or a muscle cell - Glycine - γ-amino butyric acids (GABA) (derivative of glutamate), - serotonin & melatonin (derivative of tryptophan)

24. - Hormones = chemical signal molecules produced in one cell that regulate the function of other cells - Thyroxine (tyrosine derivative), thyroid hormon secreted by thyroid gland - Indole acetic acid (tryptophan derivative), is an auxin plant hormones. Stimulate growth of the root and shoot

25. Precursors Precursors - a compound that participate in the chemical reaction to produces another compound - amino acids are precursors of variety of complex nitrogen-containing molecules - eg. Nucleotides, nucleic acids, chlorophyll

26. Metabolic intermediates Metabolic intermediates - several amino acids act as metabolic intermediates - eg. Arginine, citrulline, ornithine (components of urea cycle)

27. Amino acid stereoisomers α-carbon of 19 amino acids attached to 4 diff. groups, referred as asymmetric/chiral carbons α-carbon of 19 amino acids attached to 4 diff. groups, referred as asymmetric/chiral carbons Molecule with chiral carbon, can exist as stereoisomers Molecule with chiral carbon, can exist as stereoisomers Stereoisomers Stereoisomers - isomeric molecule that have the same molecular formula - but differ only in the three- dimensional orientations of their atoms in space.

28. Molecules with chiral carbon are not superimposable on their mirror image in the same way that a left hand is not superimposable on its mirror image, a right hand Molecules with chiral carbon are not superimposable on their mirror image in the same way that a left hand is not superimposable on its mirror image, a right hand They are known as enantiomers of one another They are known as enantiomers of one another L-Alanine and D-Alanine are mirror image to one another

29. Glyceraldehyde is the reference compound for optical isomers (to differ between L and D) Glyceraldehyde is the reference compound for optical isomers (to differ between L and D)

30. Titration of amino acids Amino acids contain ionizable group, the predominant ionic form of amino acids in solution depends on pH Amino acids contain ionizable group, the predominant ionic form of amino acids in solution depends on pH Titration of amino acid : Titration of amino acid : - illustrate the effect of pH on amino acids structure - a useful tool in determining the reactivity of amino acid side chains

31. when amino acid is dissolved in water, it exist predominantly in the isoelectric form when amino acid is dissolved in water, it exist predominantly in the isoelectric form Upon titration with base, it act as an acid (donate proton) Upon titration with base, it act as an acid (donate proton) Upon titration with acid, it act as a base (accept proton) Upon titration with acid, it act as a base (accept proton)

32. eg. titration of glycine with NaOH (base) Glycine has two titratable (ionizable) groups : Glycine has two titratable (ionizable) groups : carboxyl group & ammonium group + NH 3 -CH 2 -COO - + NH 3 -CH 2 -COO - Upon titration with base, glycine loses two protons Upon titration with base, glycine loses two protons At pH0 (acidic) – glycine is present in the form which carboxyl group is uncharged At pH0 (acidic) – glycine is present in the form which carboxyl group is uncharged + NH 3 -CH 2 -COOH At this point, glycine net charge = +1, because ammonium group is protonated At this point, glycine net charge = +1, because ammonium group is protonated

33. Gly 0 Gly + Gly -

34. As the pH increase, carboxyl group losing its proton to become a negatively charged carboxylate group As the pH increase, carboxyl group losing its proton to become a negatively charged carboxylate group + NH 3 -CH 2 -COO - + NH 3 -CH 2 -COO - At this point, glycine has no net charge and is electrically neutral. At this point, glycine has no net charge and is electrically neutral. The pH at which this occurs is called the isoelectric point (pI). The pH at which this occurs is called the isoelectric point (pI). Isoelectric point of glycine may be calculated as Isoelectric point of glycine may be calculated as pI = pK 1 + pK 2 pI = pK 1 + pK 2 2

35. pK 1 and pK 2 of glycine are 2.34 and 9.6. pK 1 and pK 2 of glycine are 2.34 and 9.6. The pI value for glycine : The pI value for glycine : pI = 2.34 + 9.6 = 5.97 As the titration continues, the ammonium group will lose its proton, leaving an uncharged amino group As the titration continues, the ammonium group will lose its proton, leaving an uncharged amino group NH 2 -CH 2 -COO - NH 2 -CH 2 -COO - 2

36. eg. Titration of glutamic acid with NaOH Amino acids with ionizable side chains (acidic & basic a.a) have more complex titration curve. Amino acids with ionizable side chains (acidic & basic a.a) have more complex titration curve. eg. Glutamic acid has a carboxyl side chain group eg. Glutamic acid has a carboxyl side chain group At acidic pH (eg. pH0), carboxyl groups are uncharged At acidic pH (eg. pH0), carboxyl groups are uncharged Glutamic acid net charge = +1 Glutamic acid net charge = +1

38. As base is added, α-carboxyl group loses a proton to become a carboxylate group As base is added, α-carboxyl group loses a proton to become a carboxylate group Glutamate now, has no net charge Glutamate now, has no net charge As more base added, the 2 nd carboxyl group (side chain) loses a proton As more base added, the 2 nd carboxyl group (side chain) loses a proton The molecule now has a net charge of -1 The molecule now has a net charge of -1 Adding more base, ammonium ion loses its proton Adding more base, ammonium ion loses its proton At this point, glutamate has a net charge of -2 At this point, glutamate has a net charge of -2

39. The pI value for glutamate is the pH halfway between the pK a values for the two carboxyl group The pI value for glutamate is the pH halfway between the pK a values for the two carboxyl group pI = pK 1 + pK 2 2

40. Note: pI is the pH at which amino acid has a net charge zero. pI is the pH at which amino acid has a net charge zero. For acidic amino acids For acidic amino acids pI = pK 1 + pK 2 For basic amino acids : For basic amino acids : pI = pK 2 + pK 3 pI = pK 2 + pK 3 2 2

42. Amino acid reactions Amino acids with their carboxyl group, amino group and various R group can undergo numerous chemical reaction Amino acids with their carboxyl group, amino group and various R group can undergo numerous chemical reaction i.e peptide bond & disulfide bridge formation (effect protein structure) i.e peptide bond & disulfide bridge formation (effect protein structure)

43. Peptide bond formation Polypeptides are linear polymers composed of amino acids linked together by peptide bonds Polypeptides are linear polymers composed of amino acids linked together by peptide bonds Peptide bonds are amide linkage (CO-NH) formed when the carboxyl group of one amino acid react with amino group of another amino acid Peptide bonds are amide linkage (CO-NH) formed when the carboxyl group of one amino acid react with amino group of another amino acid

45. This reaction is a dehydration (mol. water is removed) This reaction is a dehydration (mol. water is removed) So, the linked amino acids are referred to as amino acid residues. So, the linked amino acids are referred to as amino acid residues. When two amino acid molecules are linked, the product is called a dipeptide. When two amino acid molecules are linked, the product is called a dipeptide. eg. Serine and glycine can form dipeptides glycylserine or serylglycine eg. Serine and glycine can form dipeptides glycylserine or serylglycine

46. As amino acids are added and the chain lengthens, the prefix reflect the number of residues As amino acids are added and the chain lengthens, the prefix reflect the number of residues eg. Tripeptides contain three amino acid residues eg. Tripeptides contain three amino acid residues Amino acid residue with the free amino group is called the N-terminal residue and is written to the left Amino acid residue with the free amino group is called the N-terminal residue and is written to the left Amino acid residue with free carboxyl group is called C-terminal residue and is written to the right Amino acid residue with free carboxyl group is called C-terminal residue and is written to the right

47. eg. eg. Peptides are named by using their amino acid sequence, start from their N-terminal residue eg. Alanylglycylphenilalanine

48. Cysteine oxidation The sulfhydryl group of cysteine is highly reactive The sulfhydryl group of cysteine is highly reactive Common reaction = reversible oxidation that form disulfide Common reaction = reversible oxidation that form disulfide Two molecules of cysteine oxidized to form a cystine (molecule that contain disulfide bond) Two molecules of cysteine oxidized to form a cystine (molecule that contain disulfide bond)