Lecture 3: Amino Acids

1. Lecture 3: Amino Acids • Bonus seminar today at 3PM 148 Baker (bonus point assignment due on Wed. in class or electronically by email) • Quiz next Wed. (9/7) • Introduction to amino acid structure • Amino acid chemistry

2. + + + + COO- COO- COO- COO- H3N H3N H3N H3N C C H H C C H H H C OH H CH2 CH2 CH3 Glycine Gly G OH Serine Ser S Threonine Thr T OH Tyrosine Tyr Y Uncharged polar side chains

3. + H3N Uncharged polar side chains COO- C H R-S- + H+ R-SH CH2 SH R-O- + H+ R-OH Cysteine Cys C

4. Formation of cystine

5. + + COO- COO- H3N H3N C C H H CH2 CH2 C CH2 O NH2 C Asparagine Asn N O NH2 Glutamine Gln Q Uncharged polar side chains

6. Amino acids • Polar, uncharged amino acids • Contain R-groups that can form hydrogen bonds with water • Includes amino acids with alcohols in R-groups (Ser, Thr, Tyr) • Amide groups: Asn and Gln • Usually more soluble in water • Exception is Tyr (most insoluble at 0.453 g/L at 25 C) • Sulfhydryl group: Cys • Cys can form a disulfide bond (2 cysteines can make one cystine)

7. + + COO- COO- H3N H3N C C H H Charged polar (acidic) side chains CH2 CH2 CH2 C C O O- O O- Aspartic acid Asp D Glutamic acid Glu E

8. Amino acids • Acidic amino acids • Amino acids in which R-group contains a carboxyl group • Asp and Glu • Have a net negative charge at pH 7 (negatively charged pH > 3) • Negative charges play important roles • Metal-binding sites • Carboxyl groups may act as nucleophiles in enzymatic interactions • Electrostatic bonding interactions

9. + + + COO- COO- H3N H3N H3N C C H H Charged polar (basic) side chains COO- C H CH2 CH2 CH2 CH2 CH2 CH2 CH2 C HC NH CH2 NH H+N C NH3+ CH NH2 NH2+ Lysine Lys K Histidine His H Arginine Arg R

10. Amino acids • Basic amino acids • Amino acids in which R-group have net positive charges at pH 7 • His, Lys, and Arg • Lys and Arg are fully protonated at pH 7 • Participate in electrostatic interactions • His has a side chain pKa of 6.0 and is only 10% protonated at pH 7 • Because His has a pKa near neutral, it plays important roles as a proton donor or acceptor in many enzymes. • His containing peptides are important biological buffers

11. Nonstandard amino acids • 20 common amino acids programmed by genetic code • Nature often needs more variation • Nonstandard amino acids play a variety of roles: structural, antibiotics, signals, hormones, neurotransmitters, intermediates in metabolic cycles, etc. • Nonstandard amino acids are usually the result of modification of a standard amino acid after a polypeptide has been synthesized. • If you see the structure, could you tell where these nonstandard amino acids were derived from?

12. Nonstandard amino acids

13. Nonstandard amino acids

14. + + O R2 O R1 H H3N H3N O- C C OH C C H N H H O R2 O R1 O- C C C N C H H H + H2O Peptide bonds • Proteins are sometimes called polypeptides since they contain many peptide bonds +

15. Structural character of amide groups • Understanding the chemical character of the amide is important since the peptide bond is an amide bond. • These characteristics are true for the amide containing amino acids as well (Asn, Gln) • Amides will not ionize: O O NH2 R C NH2 R C

16. Acid-base properties of amino acids The dissociation of first proton from the -carboxyl group is The dissociation of the second proton from the -amino group Gly0 + H2O Gly- + H3O+ Gly+ + H2O Gly0 + H3O+ [Gly0][H3O+] [Gly-][H3O+] K1= K2= [Gly+] [Gly0] The pKa’s of these two groups are far enough apart that they can be approximated by Henderson-Hasselbalch [Gly0] [Gly-] pK1 + log pK2 + log pH = pH = [Gly+] [Gly0]

17. + H3N COO- Neutral form C H H Titration curve of glycine

18. + + H3N H2N H3N COO- COOH COO- C H C C H H pK1 pK2 H H H Gly+ Gly- Gly0 Titration of Gly pH 2.3 pH 9.6 From the pK values we can calculate the pI (isoelectric point) where the amino acid is neutral. pI ≈ average of (pK below neutral+ pKabove neutral) So, for Gly, pI = (pK1 + pK2)/2 = (2.3 + 9.6)/2 ≈ 6

19. General rules for amino acid ionization • Alpha carboxylic acids ionize at acidic pH and have pKs less than 6; So in titrating a fully protonated amino acid, alpha carboxylic acids lose the proton first. • Alpha amino groups ionize at basic pH and have pKs greater than 8; So after acids lose their protons, amino groups lose their proton. • Most of the 20 amino acids are similar to Gly in their ionization properties because their side chains do not ionize at biological pHs. • However, there are 5 exceptions worth noting (the amino acids with polar charged side chains) • Glu, Asp, Lys, Arg, His • Each has 3 ionizible groups and thus, 3 pKs.

20. + + COOH COOH H3N H3N C C H H CH2 CH2 CH2 C C O OH O OH Aspartic acid Asp D Glutamic acid Glu E Charged polar (acidic) side chains 2.1 2.0 9.5 9.8 3.9 4.1

21. How to calculate the pI of a compound with more than 2 pKs • Find the amino acid form with no net charge (total charge = 0). • Take the pK of the amino acid form going towards +1 form as the lower pK. • Next find the amino acid form going towards the -1 form. • Finally, average these two pKs to get the pI.

22. Titration curve of aspartic acid The neutral form of Asp is close to pH 2.8 Take the pKs for +1 and -1 from this point and average to get approximate pI, pI = (pK3 + pK1)/2 = (2.0 + 3.9)/2 = 2.95

23. + + + COOH COOH H3N H3N H3N C C H H Charged polar (basic) side chains 1.8 2.2 1.8 COOH 9.2 9.3 C H 9.0 CH2 CH2 CH2 CH2 CH2 CH2 CH2 C HC 6.0 NH CH2 NH H+N C NH3+ CH NH2 NH2+ Lysine Lys K 10.8 Histidine His H Arginine Arg R 12.5

24. Titration curve of arginine The neutral form of Asp is close to pH 10.8 Take the pKs for +1 and -1 from this point and average to get approximate pI, pI = (pK2 + pK3)/2 = (9.0 + 13.0)/2 = 11.0

25. Acid-base properties of amino acids

26. More rules for amino acid ionization • Carboxylic acid groups near an amino group in a molecule have a more acidic pK than isolated carboxylic groups. • Amino groups near a carboxylic acid group also have a more acidic pK than isolated amines. • Aromatic amines like His have a pK about pH 6. • When titrating an amino acid that is fully protonated (ie starting at pH = 1), the alpha carboxylic acids lose their proton first (all free amino acids have this group), then side chain carboxylic acids, then aromatic amine side chains (His), then alpha amino groups, then side chain amino groups. • These rules apply to small peptides too.

27. Amino acids are optically active • All amino acids are optically active (exception Gly). • Optically active molecules have asymmetry; not superimposable (mirror images) • Central atoms are chiral centers or asymmetric centers. • Enantiomers -molecules that are nonsuperimposable mirror images

28. Asymmetry • Molecules are classified as Dextrorotatory (right handed), D or Levrotatory (left handed) L depending on whether they rotate the plane of plane-polarized light clockwise or counterclockwise determined by a polarimeter

29. Asymmetry • Fischer projections are a shorthand way to write molecules with chiral centers

30. Asymmetry • For -amino acids the arrangement of the amino, carboxyl, R, and H groups about the C atom is related to glyceraldehyde

31. Asymmetry • All -amino acids from proteins have the L-stereochemical configuration

32. Diastereomers • Stereoisomers or optical isomers are molecules with different configurations about at least one of their chiral centers but are otherwise identical • Since each asymmetric center in a chiral molecule can have two possible configurations, a molecule with n chiral centers has 2n different possible stereoisomers and 2n-1enantiomeric pairs • Ex. Threonine and Isoleucine both have two chiral centers, and thus 4 possible stereoisomers.

33. Diastereomers * *

34. Diastereomers • Special case: 2 asymmetric centers are chemically identical (2 asymmetric centers are mirror images of one another) • A molecule that is superimposable on its mirror image is optically inactive (meso form)

35. Cahn-Ingold-Prelog or (RS) System • The 4 groups surrounding a chiral center a ranked as follows: Atoms of higher atomic number bonded to a chiral center are ranked above those of lower atomic number. • Priorities of some common functional groups SH > OH > NH2 > COOH > CHO > CH2OH > C6H5 > CH3 > 2H > 1H • Prioritized groups are assigned letters W, X, Y, Z, so that W > X > Y > Z • Z group has the lowest priority (usually H) and is used to establish the chiral center. • If the order of the groups W X Y is clockwise, as viewed from the direction of Z, the configuration is (R from the latin rectus, right) • If the order of the groups W X Y is counterclockwise, as viewed from the direction of Z, the configuration is (S from the latin sinister, left)

36. Cahn-Ingold-Prelog or (RS) System

37. Cahn-Ingold-Prelog or (RS) System

38. Cahn-Ingold-Prelog or (RS) System

39. Prochiral centers have distinguishable substituents • Prochiral molecules can be converted from an achiral to chrial molecule by a single substitution • Molecules can be assigned a right side and left side for two chemically identical substituents. • True for tetrahedral centered molecules • Example is ethanol

40. Prochiral centers

41. Planar objects can also be prochiral • Stereospecific additions in enzymatic reactions • If a trigonal carbon is facing the viewer so that the substituents decrease in a clockwise manner it is the re face • If a trigonal carbon is facing the viewer so that the substituents decrease in a counterclockwise manner it is the si face • Acetaldehyde example

42. Nomenclature • Glx can be Glu or Gln • Asx can be Asp or Asn • Polypeptide chains are always described from the N-terminus to the C-terminus

43. Nomenclature • Nonhydrogen atoms of the amino acid side chain are named in sequence with the Greek alphabet