Amino Acids and Proteins

1. Amino Acids and Proteins Amino Acids as Acids and Bases

2. Functions of Proteins • Proteins perform many different functions in the body. TABLE 19.1

3. Amino Acids Amino acids • Are the building blocks of proteins. • Contain a carboxylic acid group and an amino group on the alpha () carbon. • Are ionized in solution. • Each contain a different side group (R). R R │ + │ H2N—C —COOH H3N—C —COO− │ │ H H ionized form

4. Examples of Amino Acids H + │ H3N—C—COO− │ H glycine CH3 + │ H3N—C—COO− │ H alanine

5. Types of Amino Acids Amino acids are classified as • Nonpolar (hydrophobic) with hydrocarbon side chains. • Polar (hydrophilic) with polar or ionic side chains. • Acidic (hydrophilic) with acidic side chains. • Basic (hydrophilic) with –NH2 side chains. Nonpolar Polar Acidic Basic

6. Nonpolar Amino Acids A nonpolar amino acid has • An R group that is H, an alkyl group, or aromatic.

7. Polar Amino Acids A polar amino acid has • An R group that is an alcohol, thiol, or amide.

8. Acidic and Basic Amino Acids An amino acid is • Acidic with a carboxyl R group (COO−). • Basic with an amino R group (NH3+). Basic Amino Acids

9. Learning Check Identify each as (P) polar or (NP) nonpolar. + A. H3N–CH2–COO− (Glycine) CH3 | CH–OH + │ B. H3N–CH–COO− (Threonine)

10. Solution Identify each as (P) polar or (NP) nonpolar. + A. H3N–CH2–COO− (Glycine) (NP) nonpolar CH3 | CH–OH + │ B. H3N–CH–COO− (Threonine) (P) polar

11. Fischer Projections of Amino Acids Amino acids • Are chiral except for glycine. • Have Fischer projections that are stereoisomers. • That areL are used in proteins. L-alanine D-alanine L-cysteine D-cysteine

12. Zwitterions and Isoelectric Points A zwitterion • Has charged—NH3+ and COO- groups. • Forms when both the —NH2 and the —COOH groups in an amino acid ionize in water. • Has equal + and − charges at the isoelectric point (pI). O O ║+║ NH2—CH2—C—OH H3N—CH2—C—O– Glycine Zwitterion of glycine

13. Amino Acids as Acids In solutions more basic than the pI, • The —NH3+ in the amino acid donates a proton. + OH– H3N—CH2—COO–H2N—CH2—COO– Zwitterion Negative ion at pI pH > pI Charge: 0 Charge: 1−

14. Amino Acids as Bases In solutions more acidic than the pI, • The COO− in the amino acid accepts a proton. + H+ + H3N—CH2—COO–H3N—CH2—COOH Zwitterion Positive ion at pI pH< pI Charge: 0 Charge: 1+

15. pH and Ionization H+OH− + + H3N–CH2–COOHH3N–CH2–COO–H2N–CH2–COO– positive ionzwitterion negative ion (at low pH)(at pI)(at high pH)

16. Electrophoresis: Separation of Amino Acids In electrophoresis, an electric current is used to separate a mixture of amino acids, and • The positively charged amino acids move toward the negative electrode. • The negatively charged amino acids move toward the positive electrode. • An amino acid at its pI does not migrate. • The amino acids are identified as separate bands on the filter paper or thin­layer plate.

17. Electrophoresis With an electric current, a mixture of lysine, aspartate, and valine are separated.

18. Learning Check CH3 CH3 +|| H3N—CH—COOH H2N—CH—COO– (1) (2) Which structure represents: A. Alanine at a pH above its pI? B. Alanine at a pH below its pI?

19. Solution CH3 CH3 +|| H3N—CH—COOH H2N—CH—COO– (1) (2) Which structure represents: A. Alanine at a pH above its pI? (2) B. Alanine at a pH below its pI? (1)

20. Essential Amino Acids Essential amino acids • Must be obtained from the diet. • Are the ten amino acids not synthesized by the body. • Are in meat and diary products. • Are missing (one or more) in grains and vegetables. TABLE 19.3

21. Amino Acids and Proteins Formation of Peptides

22. The Peptide Bond A peptide bond • Is an amide bond. • Forms between the carboxyl group of one amino acid and the amino group of the next amino acid. O CH3 O + || + | || H3N—CH2—C—O– + H3N—CH—C—O– O H CH3 O + || | | || H3N—CH2—C—N—CH—C—O– + H2O peptide bond

23. Formation of A Dipeptide

24. Learning Check Write the dipeptide Ser-Thr. OH CH3 | | CH2O HCOHO + | ║ +| ║ H3N─CH─C─O – + H3N─CH─C─O– Ser Thr

25. Solution Write the dipeptide Ser-Thr. OH CH3 | | CH2O HCOHO + | ║+| ║ H3N─CH─C─O– + H3N─CH─C─O– Ser peptideThr OH bond CH3 | | CH2O H HCOHO + | ║|| ║ NH3─CH─C─N─CH─C─O– + H2O Ser-Thr

26. Naming Dipeptides A dipeptide is named with • A -yl ending for the N-terminal amino acid. • The full amino acid name of the free carboxyl group (COO-) at the C-terminal end.

27. Learning Check Write the three-letter abbreviations and names of the tripeptides that could form from two glycine and one alanine.

28. Solution Write the names and three-letter abbreviations of the tripeptides that could form from two glycine and one alanine. Glycylglycylalanine Gly-Gly-Ala Glycylalanylglycine Gly-Ala-Gly Alanylglycylglycine Ala-Gly-Gly

29. Learning Check What are the possible tripeptides formed from one each of leucine, glycine, and alanine?

30. Solution Tripeptides possible from one each of leucine, glycine, and alanine Leu-Gly-Ala Leu-Ala-Gly Ala-Leu-Gly Ala-Gly-Leu Gly-Ala-Leu Gly-Leu-Ala

31. Learning Check Write the three-letter abbreviation and name for the following tetrapeptide: CH3 │ CH3 S │ │ CH–CH3 SH CH2 │ │ │ CH3 O H CH2 O H CH2O H CH2 O + │ ║ │ │ ║ │ │ ║ │ │ ║ H3N–CH–C–N–CH–C–N–CH–C–N–CH–CO–

32. Solution Ala-Leu-Cys-Met Alanylleucylcysteylmethionine CH3 │ CH3 S │ │ CH–CH3 SH CH2 │ │ │ CH3 O H CH O H CH2O H CH2 O + │ ║ │ │ ║ │ │ ║ │ │ ║ H3N–CH–C–N–CH–C–N–CH–C–N–CH–CO– Ala Leu Cys Met

33. Amino Acids and Proteins Protein Structure: Primary and Secondary Levels

34. Primary Structure of Proteins The primary structure of a protein is • The particular sequence of amino acids. • The backbone of a peptide chain or protein. Ala─Leu─Cys─Met

35. Primary Structures The nonapeptides oxytocin and vasopressin • Have similar primary structures. • Differ only in the amino acids at positions 3 and 8.

36. Primary Structureof Insulin Insulin • Was the first protein to have its primary structure determined. • Has a primary structure of two polypeptide chains linked by disulfide bonds. • Has a chain A with 21 amino acids and a chain B with 30 amino acids.

37. Secondary Structure – Alpha Helix The secondary structures of proteins indicate the three-dimensional spatial arrangements of the polypeptide chains. An alpha helix has • A coiled shape held in place by hydrogen bonds between the amide groups and the carbonyl groups of the amino acids along the chain. • Hydrogen bonds between the H of a –N-H group and the O of C=O of the fourth amino acid down the chain.

38. Secondary Structure – Alpha Helix

39. Secondary Structure – Beta Pleated Sheet A beta-pleated sheet is a secondary structure that • Consists of polypeptide chains arranged side by side. • Has hydrogen bonds between chains. • Has R groups above and below the sheet. • Is typical of fibrous proteins such as silk.

40. Secondary Structure: β-Pleated Sheet

41. Secondary Structure: Triple Helix A triple helix • Consists of three alpha helix chains woven together. • Contains large amounts glycine, proline, hydroxy proline, and hydroxylysine that contain –OH groups for hydrogen bonding. • Is found in collagen, connective tissue, skin, tendons, and cartilage.

42. Learning Check Indicate the type of protein structure as 1) primary 2) alpha helix 3) beta-pleated sheet 4) triple helix A. Polypeptide chains held side by side by H bonds. B. Sequence of amino acids in a polypeptide chain. C. Corkscrew shape with H bonds between amino acids. D. Three peptide chains woven like a rope.

43. Solution Indicate the type of protein structure as: 1) primary 2) alpha helix 3) beta-pleated sheet 4) triple helix A. 3 Polypeptide chains held side by side by H bonds. B. 1 Sequence of amino acids in a polypeptide chain. C. 2 Corkscrew shape with H bonds between amino acids. D. 4 Three peptide chains woven like a rope.

44. Amino Acids and Proteins Protein Structure: Tertiary and Quaternary Levels

45. Tertiary Structure The tertiary structure of a protein • Gives a specific three dimensional shape to the polypeptide chain. • Involves interactions and cross links between different parts of the peptide chain. • Is stabilized by Hydrophobic and hydrophilic interactions. Salt bridges. Hydrogen bonds. Disulfide bonds.

46. Tertiary Structure • The interactions of the R groups give a protein its specific three-dimensional tertiary structure.

47. Tertiary Structure TABLE 19.5

48. Globular Proteins Globular proteins • Have compact, spherical shapes. • Carry out synthesis, transport, and metabolism in the cells. • Such as myoglobin store and transport oxygen in muscle. Myoglobin

49. Fibrous Proteins Fibrous proteins • Consist of long, fiber-like shapes. • Such as alpha keratins make up hair, wool, skin, and nails. • Such as feathers contain beta keratins with large amounts of beta-pleated sheet structures.

50. Learning Check Select the type of tertiary interaction 1) disulfide 2) ionic 3) H bonds 4) hydrophobic A. Leucine and valine B. Two cysteines C. Aspartic acid and lysine D. Serine and threonine