Biomolecules: Amino Acids, Peptides, and Proteins

1. Biomolecules: Amino Acids, Peptides, and Proteins Based on McMurry’s Organic Chemistry, 6th edition

2. Proteins – Amides from Amino Acids • Amino acids contain a basic amino group and an acidic carboxyl group • Joined as amidesbetween the NH2 of one amino acid and the CO2H the next • Chains with fewer than 50 units are called peptides • Proteins: large chains that have structural or catalytic functions in biology

3. Structures of Amino Acids • In neutral solution, the COOH is ionized and the NH2 is protonated • The resulting structures have “+” and “-” charges (a dipolar ion, or zwitterion) • They are like ionic salts in solution

4. The Common Amino Acids • 20 amino acids form amides in proteins • All are -amino acids - the amino and carboxyl are connected to the same C • They differ by the other substituent attached to the  carbon, called the side chain, with H as the fourth substituent except for proline • Proline, is a five-membered secondary amine, with N and the  C part of a five-membered ring

5. The Structure of Amino Acids R – can be a series of functional groups

6. Leucine L, Leu Lysine K, Lys Methionine M, Met Phenylalanine F, Phe Proline P, Pro Serine S, Ser Threonine T, Thr Tryptophan W, Trp Tyrosine Y, Tyr Valine V, Val Abbreviations and Codes Alanine A, Ala Arginine R, Arg Asparagine N, Asn Aspartic acid D, Asp Cysteine C, Cys Glutamine Q, Gln Glutamic Acid E, Glu Glycine G, Gly Histidine H, His Isoleucine I, Ile

7. Learning the Names and Codes • The names are not systematic so you learn them by using them (They become your friends) • One letter codes – learn them too • If only one amino acid begins with that letter, use it (Cys, His, Ile, Met, Ser, Val) • If more than one begins with that letter, the more common one uses the letter (Ala, Gly, Leu, Pro, Thr) • For the others, some are phonetic: Fenylalanine, aRginine, tYrosine • Tryp has a double ring, hence W • Amides have letters from the middle of the alphabet (Q – Think of “Qtamine” for glutamine; asparagine -contains N • “Acid” ends in D and E follows (smallest is first: aspartic aciD, Glutamic acid E)

8. Neutral Hydrocarbon Side Chains

9. -OH, SH (Nucleophiles) and -S-CH3 Cysteine C, Cys Methionine M, Met Serine S, Ser Threonine T, Thr Tyrosine Y, Tyr

10. Acids and Amides Aspartic acid D, Asp Glutamic Acid E, Glu Asparagine N, Asn Glutamine Q, Gln

11. Amines Arginine R, Arg Histidine H, His Lysine K, Lys Tryptophan W, Trp

12. Chirality of Amino Acids • Glycine, 2-amino-acetic acid, is achiral • In all the others, the  carbons of the amino acids are centers of chirality • The stereochemical reference for amino acids is the Fischer projection of L-serine • Proteins are derived exclusively from L-amino acids

13. Types of side chains • Neutral: Fifteen of the twenty have neutral side chains • Acidic Amino Acids: Asp and Glu have a second COOH and are acidic • Basic Amino Acids: Lys, Arg, His have additional basic amino groups side chains (the N in tryptophan is a very weak base) • Polar Amino Acids: Cys, Ser, Tyr (OH and SH) are weak acids that are good nucleophiles

14. Notes on Histidine • Contains an imidazole ring that is partially protonated in neutral solution • Only the pyridine-like, doubly bonded nitrogen in histidine is basic. The pyrrole-like singly bonded nitrogen is nonbasic because its lone pair of electrons is part of the 6  electron aromatic imidazole ring (see Section 24.4).

15. Essential Amino Acids • All 20 of the amino acids are necessary for protein synthesis • Humans can synthesize only 10 of the 20 • The other 10 must be obtained from food

16. Isoelectric Points • In acidic solution, the carboxylate and amine are in their conjugate acid forms, an overall cation • In basic solution, the groups are in their base forms, an overall anion • In neutral solution cation and anion forms are present • This pH where the overall charge is 0 is the isoelectric point, pI

17. pI Depends on Side Chain • The 15 amino acids thiol, hydroxyl groups or pure hydrocarbon side chains have pI = 5.0 to 6.5 (average of the pKa’s) • D and E have acidic side chains and a lower pI • H, R, K have basic side chains and higher pI

18. Electrophoresis • Proteins have an overall pI that depends on the net acidity/basicity of the side chains • The differences in pI can be used for separating proteins on a solid phase permeated with liquid • Different amino acids migrate at different rates, depending on their isoelectric points and on the pH of the aqueous buffer

19. Titration Curves of Amino Acids • If pKa values for an amino acid are known the fractions of each protonation state can be calculated (Henderson-Hasselbach Equation) • pH = pKa – log [A-]/[HA] • This permits a titration curve to be calculated or pKa to be determined from a titration curve

20. Titration Curves

21. Synthesis of Amino Acids • Bromination of a carboxylic acid by treatment with Br2 and PBr3 (Section 22.4) then use NH3 or phthalimide (24.6) to displace Br

22. The Amidomalonate Synthesis • Based on malonic ester synthesis (see 22.8). • Convert diethyl acetamidomalonate into enolate ion with base, followed by alkylation with a primary alkyl halide • Hydrolysis of the amide protecting group and the esters and decarboxylation yields an -amino

23. Reductive Amination of -Keto Acids • Reaction of an -keto acid with NH3 and a reducing agent produces an -amino acid

24. Enantioselective Synthesis of Amino Acids • Amino acids (except glycine) are chiral and pure enantiomers are required for any protein or peptide synthesis • Resolution of racemic mixtures is inherently ineffecient since at least half the material is discarded • An efficient alternative is enantioselective synthesis

25. Chemical Resolution of R,S Amino Acids • Convert the amino group into an amide and react with a chiral amine to form diastereomeric salts • Salts are separated and converted back to the amino acid by hydrolysis of the amide

26. Enzymic Resolution • Enzymes selectively catalyze the hydrolysis of amides formed from an L amino acid (S chirality center)

27. Enantioselective Synthesis of Amino Acids • Chiral reaction catalyst creates diastereomeric transition states that lead to an excess of one enantiomeric product • Hydrogenation of a Z enamido acid with a chiral hydrogenation catalyst produces S enantiomer selectively

28. Peptides and Proteins • Proteins and peptides are amino acid polymers in which the individual amino acid units, called residues, are linked together by amide bonds, or peptide bonds • An amino group from one residue forms an amide bond with the carboxyl of a second residue

29. Peptide Linkages • Two dipeptides can result from reaction between A and S,depending on which COOH reacts with which NH2 we get AS or SA • The long, repetitive sequence of NCHCO atoms that make up a continuous chain is called the protein’s backbone • Peptides are always written with the N-terminal amino acid (the one with the free NH2 group) on the left and the C-terminal amino acid (the one with the free CO2H group) on the right • Alanylserine is abbreviated Ala-Ser (or A-S), and serylalanine is abbreviated Ser-Ala (or S-A)

30. Covalent Bonding in Peptides • The amide bond that links different amino acids together in peptides is no different from any other amide bond (see Section 24.4). Amide nitrogens are nonbasic because their unshared electron pair is delocalized by interaction with the carbonyl group. This overlap of the nitrogen p orbital with the π orbitals of the carbonyl group imparts a certain amount of double-bond character to the C–N bond and restricts rotation around it. The amide bond is therefore planar, and the N–H is oriented 180° to the C=O.

31. Covalent Bonding in Peptides

32. Disulfides • Thiols in adjacent chains can form a disulfide RS–SR through spontaneous oxidation • A disulfide bond between cysteine residues in different peptide chains links the otherwise separate chains together, while a disulfide bond between cysteine residues in the same chain forms a loop

33. Structure Determination of Peptides: Amino Acid Analysis • The sequence of amino acids in a pure protein is specified genetically • If a protein is isolated it can be analyzed for its sequence • The composition of amino acids can be obtained by automated chromatography and quantitative measurement of eluted materials using a reaction with ninhydrin that produces an intense purple color

34. Amino Acid Analysis Chromatogram

35. Peptide Sequencing: The Edman Degradation • The Edman degradation cleaves amino acids one at a time from the N-terminus and forms a detectable, separable derivative for each amino acid

36. Peptide Sequencing: C-Terminal Residue Determination • Carboxypeptidase enzymes cleave the C-terminal amide bond • Analysis determines the appearance of the first free amino acid, which must be at the carboxy terminus of the peptide

37. Peptide Synthesis • Peptide synthesis requires that different amide bonds must be formed in a desired sequence • The growing chain is protected at the carboxyl terminal and added amino acids are N-protected • After peptide bond formation, N-protection is removed

38. Carboxyl Protecting Groups • Usually converted into methyl or benzyl esters • Removed by mild hydrolysis with aqueous NaOH • Benzyl esters are cleaved by catalytic hydrogenolysis of the weak benzylic C–O bond

39. Amino Group Protection • An amide that is less stable than the protein amide is formed and then removed • The tert-butoxycarbonyl amide (BOC) protecting group is introduced with di-tert-butyl dicarbonate • Removed by brief treatment with trifluoroacetic acid

40. Peptide Coupling • Amides are formed by treating a mixture of an acid and amine with dicyclohexylcarbodiimide (DCC)

41. Overall Steps in Peptide Synthesis

42. Automated Peptide Synthesis: The Merrifield Solid-Phase Technique • Peptides are connected to beads of polystyrene, reacted, cycled and cleaved at the end

43. Automated Synthesis • The solid-phase technique has been automated, and computer-controlled peptide synthesizers are available for automatically repeating the coupling and deprotection steps with different amino acids Applied Biosystems® Synthesizer

44. Protein Classification • Simple proteins yield only amino acids on hydrolysis • Conjugated proteins, which are much more common than simple proteins, yield other compounds such as carbohydrates, fats, or nucleic acids in addition to amino acids on hydrolysis. • Fibrous proteins consist of polypeptide chains arranged side by side in long filaments • Globular proteins are coiled into compact, roughly spherical shapes • Most enzymes are globular proteins

45. Some Common Fibrous and Globular Proteins

46. Protein Structure • The primary structure of a protein is simply the amino acid sequence. • The secondary structure of a protein describes how segments of the peptide backbone orient into a regular pattern. • The tertiary structure describes how the entire protein molecule coils into an overall three-dimensional shape. • The quaternary structure describes how different protein molecules come together to yield large aggregate structures

47. -Keratin • A fibrous structural protein coiled into a right-handed helical secondary structure, -helix stabilized by H-bondsb between amide N–H groups and C=O groups four residues away a-helical segments in their chains

48. Fibroin • Fibroin has a secondary structure called a b-pleated sheet in which polypeptide chains line up in a parallel arrangement held together by hydrogen bonds between chains

49. Myoglobin • Myoglobin is a small globular protein containing 153 amino acid residues in a single chain • 8 helical segments connected by bends to form a compact, nearly spherical, tertiary structure

50. Internal and External Forces • Acidic or basic amino acids with charged side chains congregate on the exterior of the protein where they can be solvated by water • Amino acids with neutral, nonpolar side chains congregate on the hydrocarbon-like interior of a protein molecule • Also important for stabilizing a protein's tertiary structure are the formation of disulfide bridges between cysteine residues, the formation of hydrogen bonds between nearby amino acid residues, and the development of ionic attractions, called salt bridges, between positively and negatively charged sites on various amino acid side chains within the protein