BIOCHEMISTRY Amino Acids

1. BIOCHEMISTRYAmino Acids Credit to PnSyazniZainul Kamal School of Bioprocess

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

4. 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 Amino Acids structure

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 • 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. Standard amino acid (primary amino group) Proline (secondary amino group)

8. The amino and carboxylic groups of amino acids readily ionized • 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 (+NH3) • Thus, each amino acid can behave as an acid or base • referred as amphoteric (substance that can act as acid or base) Amino acid structure

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

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

12. 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 • Contain hydrocarbon R groups • 2 types of hydrocarbon R groups: a) aromatic (contain cyclic structure) eg. Phenylalanine, tryptophan a) Neutral nonpolar amino acids

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

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

17. 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 (effect on protein stability)

18. 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 c) Acidic amino acids

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

22. 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. • Besides being components of protein, amino acids have several biological roles : • Chemical messengers • Precursors • Metabolite intermediates Biologically active amino acids

23. 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 - 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 - 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 • Molecule with chiral carbon, can exist as 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 • 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)

30. Amino acids contain ionizable group, the predominant ionic form of amino acids in solution depends on pH • 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 Titration of amino acids

31. 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 acid, it act as a base (accept proton)

32. Glycine has two titratable (ionizable) groups : carboxyl group & ammonium group +NH3-CH2-COO- • Upon titration with base, glycine loses two protons • At pH0 (acidic) – glycine is present in the form which carboxyl group is uncharged +NH3-CH2-COOH • At this point, glycine net charge = +1, because ammonium group is protonated eg. titration of glycine with NaOH (base)

33. Gly 0 Gly - Gly +

34. As the pH increase, carboxyl group losing its proton to become a negatively charged carboxylate group +NH3-CH2-COO- • At this point, glycine has no net charge and is electrically neutral. • The pH at which this occurs is called the isoelectric point (pI). • Isoelectric point of glycine may be calculated as pI = pK1 + pK2 2

35. pK1 and pK2 of glycine are 2.34 and 9.6. • 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 NH2-CH2-COO- 2

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

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

39. The pI value for glutamate is the pH halfway between the pKa values for the two carboxyl group pI = pK1 + pK2 2

40. Note: • pI is the pH at which amino acid has a net charge zero. • For acidic amino acids pI = pK1 + pK2 • For basic amino acids : pI = pK2 + pK3 2 2

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

43. 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 bond formation

45. This reaction is a dehydration (mol. water is removed) • 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. • 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 • 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 free carboxyl group is called C-terminal residue and is written to the right

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

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

50. Summary