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Chapter 25 Amino Acids, Peptides, and Proteins

Chapter 25 Amino Acids, Peptides, and Proteins. 25.1 Classification of Amino Acids. Fundamentals. While their name implies that amino acids are compounds that contain an —NH 2 group and a —CO 2 H group, these groups are actually present as —NH 3 + and —CO 2 – respectively.

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Chapter 25 Amino Acids, Peptides, and Proteins

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  1. Chapter 25Amino Acids, Peptides, and Proteins

  2. 25.1Classification of Amino Acids

  3. Fundamentals • While their name implies that amino acids are compounds that contain an —NH2 group and a —CO2H group, these groups are actually present as —NH3+ and —CO2– respectively. • They are classified as , , , etc. amino acids according the carbon that bears the nitrogen.

  4. + NH3 – CO2 + – H3NCH2CH2CO2 + – H3NCH2CH2CH2CO2 Amino Acids an -amino acid that is anintermediate in the biosynthesisof ethylene  a -amino acid that is one ofthe structural units present incoenzyme A  a -amino acid involved inthe transmission of nerveimpulses 

  5. The 20 Key Amino Acids • More than 700 amino acids occur naturally, but 20 of them are especially important. • These 20 amino acids are the building blocks of proteins. All are -amino acids. • They differ in respect to the group attached to the  carbon. • These 20 are listed in Table 25.1.

  6. O H + – H3N O C C R Table 25.1 • The amino acids obtained by hydrolysis of proteins differ in respect to R (the side chain). • The properties of the amino acid vary as the structure of R varies.

  7. O H + – H3N O C C R Table 25.1 • The major differences among the side chains concern: • Size and shape Electronic characteristics

  8. Table 25.1 • General categories of a-amino acids • nonpolar side chains polar but nonionized side chains acidic side chains basic side chains

  9. O H + – H3N O C C H Table 25.1 • Glycine is the simplest amino acid. It is the only one in the table that is achiral. • In all of the other amino acids in the table the  carbon is a chirality center. Glycine (Gly or G)

  10. Table 25.1 O H • Alanine, valine, leucine, and isoleucine have alkyl groups as side chains, which are nonpolar and hydrophobic. + – H3N O C C CH3 Alanine (Ala or A)

  11. Table 25.1 O H + – H3N O C C CH(CH3)2 Valine (Val or V)

  12. Table 25.1 O H + – H3N O C C CH2CH(CH3)2 Leucine (Leu or L)

  13. O H + – H3N O C C CH3CHCH2CH3 Isoleucine (Ile or I) Table 25.1

  14. Table 25.1 O H • The side chain in methionine is nonpolar, but the presence of sulfur makes it somewhat polarizable. + – H3N O C C CH3SCH2CH2 Methionine (Met or M)

  15. O H + – H2N O C C CH2 H2C CH2 Table 25.1 • Proline is the only amino acid that contains a secondary amine function. Its side chain is nonpolar and cyclic. Proline (Pro or P)

  16. O H + – H3N O C C CH2 Table 25.1 • The side chain in phenylalanine (a nonpolar amino acid) is a benzyl group. Phenylalanine (Phe or F)

  17. O H + – H3N O C C CH2 Tryptophan (Trp or W) N H Table 25.1 • The side chain in tryptophan (a nonpolar amino acid) is larger and more polarizable than the benzyl group of phenylalanine.

  18. Table 25.1 • General categories of a-amino acids • nonpolar side chains polar but nonionized side chains acidic side chains basic side chains

  19. Table 25.1 O H • The —CH2OH side chain in serine can be involved in hydrogen bonding. + – H3N O C C CH2OH Serine (Ser or S)

  20. Table 25.1 O H • The side chain in threonine can be involved in hydrogen bonding, but is somewhat more crowded than in serine. + – H3N O C C CH3CHOH Threonine (Thr or T)

  21. Table 25.1 O H • The side chains of two remote cysteines can be joined by forming a covalent S—S bond. + – H3N O C C CH2SH Cysteine (Cys or C)

  22. O H + – H3N O C C CH2 OH Table 25.1 • The side chain of tyrosine is similar to that of phenylalanine but can participate in hydrogen bonding. Tyrosine (Tyr or Y)

  23. O H + – H3N O C C H2NCCH2 O Table 25.1 • The side chains of asparagine and glutamine (next slide) terminate in amide functions that are polar and can engage in hydrogen bonding. Asparagine (Asn or N)

  24. O H + – H3N O C C H2NCCH2CH2 O Table 25.1 Glutamine (Gln or Q)

  25. Table 25.1 • General categories of a-amino acids • nonpolar side chains polar but nonionized side chains acidic side chains basic side chains

  26. O H + – H3N O C C – OCCH2 O Table 25.1 • Aspartic acid and glutamic acid (next slide) exist as their conjugate bases at biological pH. They are negatively charged and can form ionic bonds with positively charged species. Aspartic Acid (Asp or D)

  27. O H + – H3N O C C – OCCH2CH2 O Table 25.1 Glutamic Acid (Glu or E)

  28. Table 25.1 • General categories of a-amino acids • nonpolar side chains polar but nonionized side chains acidic side chains basic side chains

  29. Table 25.1 O H • Lysine and arginine (next slide) exist as their conjugate acids at biological pH. They are positively charged and can form ionic bonds with negatively charged species. + – H3N O C C Lysine + (Lys or K) CH2CH2CH2CH2NH3

  30. Table 25.1 O H + – Arginine H3N O C C (Arg or R) CH2CH2CH2NHCNH2 + NH2

  31. CH2 N NH Table 25.1 O H • Histidine is a basic amino acid, but less basic than lysine and arginine. Histidine can interact with metal ions and can help move protons from one site to another. + – H3N O C C Histidine (His or H)

  32. 25.2Stereochemistry of Amino Acids

  33. – CO2 + H3N H R Configuration of -Amino Acids • Glycine is achiral. All of the other amino acids in proteins have the L-configuration at their carbon.

  34. 25.3Acid-Base Behavior of Amino Acids

  35. Recall • While their name implies that amino acids are compounds that contain an —NH2 group and a —CO2H group, these groups are actually present as —NH3+ and —CO2– respectively. How do we know this?

  36. more consistent with this than this O O •• •• •• •• + – •• •• •• H3NCH2C O H2NCH2C OH •• •• •• Properties of Glycine • The properties of glycine: • high melting point: (when heated to 233°C it decomposes before it melts)solubility: soluble in water; not soluble in nonpolar solvent

  37. O •• •• + – •• H3NCH2C O •• •• Properties of Glycine • The properties of glycine: • high melting point: (when heated to 233°C it decomposes before it melts)solubility: soluble in water; not soluble in nonpolar solvent more consistent with this called a zwitterion or dipolar ion

  38. O •• •• + •• H3NCH2C OH •• Acid-Base Properties of Glycine • The zwitterionic structure of glycine also follows from considering its acid-base properties. • A good way to think about this is to start with the structure of glycine in strongly acidic solution, say pH = 1. • At pH = 1, glycine exists in its protonated form (a monocation).

  39. typical ammonium ion: pKa ~9 typical carboxylic acid: pKa ~5 O •• •• + •• H3NCH2C OH •• Acid-Base Properties of Glycine • Now ask yourself "As the pH is raised, which is the first proton to be removed? Is it the proton attached to the positively charged nitrogen, or is it the proton of the carboxyl group?" • You can choose between them by estimating their respective pKas.

  40. O •• •• + •• H3NCH2C OH •• Acid-Base Properties of Glycine • The more acidic proton belongs to the CO2H group. It is the first one removed as the pH is raised. typical carboxylic acid: pKa ~5

  41. O •• •• + – •• H3NCH2C O •• •• O •• •• + •• H3NCH2C OH •• Acid-Base Properties of Glycine • Therefore, the more stable neutral form of glycine is the zwitterion. typical carboxylic acid: pKa ~5

  42. O •• •• + •• H3NCH2C OH •• Acid-Base Properties of Glycine • The measured pKa of glycine is 2.34. • Glycine is stronger than a typical carboxylic acid because the positively charged N acts as an electron-withdrawing, acid-strengthening substituent on the  carbon. typical carboxylic acid: pKa ~5

  43. O O •• •• •• •• – + HO – – •• •• •• H3NCH2C O H2NCH2C O •• •• •• •• Acid-Base Properties of Glycine A proton attached to N in the zwitterionic form of nitrogen can be removed as the pH is increased further. • The pKa for removal of this proton is 9.60.This value is about the same as that for NH4+ (9.3).

  44. O O •• •• •• •• + – – •• •• •• H3NCH2C O H2NCH2C O •• •• •• •• O •• •• + •• H3NCH2C OH •• Isoelectric Point (pI) • The pH at which the concentration of the zwitterion is a maximum is called the isoelectric point. Its numerical value is the average of the two pKas. • The pI of glycine is 5.97. pKa = 2.34 pKa = 9.60

  45. Acid-Base Properties of Amino Acids • One way in which amino acids differ is in respect to their acid-base properties. This is the basis for certain experimental methods for separating and identifying them. • Just as important, the difference in acid-base properties among various side chains affects the properties of the proteins that contain them. • Table 25.2 gives pKa and pI values for amino acids with neutral side chains.

  46. H O + – H3N O C C H Table 25.2Amino Acids with Neutral Side Chains pKa1 = 2.34pKa2 = 9.60pI = 5.97 Glycine

  47. Table 25.2Amino Acids with Neutral Side Chains O H + – H3N O C C pKa1 = 2.34pKa2 = 9.69pI = 6.00 Alanine CH3

  48. Table 25.2Amino Acids with Neutral Side Chains O H + – H3N O C C pKa1 = 2.32pKa2 = 9.62pI = 5.96 Valine CH(CH3)2

  49. Table 25.2Amino Acids with Neutral Side Chains O H pKa1 = 2.36pKa2 = 9.60pI = 5.98 + – H3N O C C Leucine CH2CH(CH3)2

  50. O H + – H3N O C C CH3CHCH2CH3 Table 25.2Amino Acids with Neutral Side Chains pKa1 = 2.36pKa2 = 9.60pI = 6.02 Isoleucine

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