1. 22 22-1 © 2006 Thomson Learning, Inc. All rights reserved General, Organic, and Biochemistry, 8e Bettelheim, Brown CAmpbell, and Farrell

2. 22 22-2 © 2006 Thomson Learning, Inc. All rights reserved Chapter 22 Proteins Proteins

3. 22 22-3 © 2006 Thomson Learning, Inc. All rights reserved Proteins Proteins serve many functions, including the following. Given are examples of each. 1.Structure:1.Structure: collagen and keratin are the chief constituents of skin, bone, hair, and nails. 2. Catalysts:2. Catalysts: virtually all reactions in living systems are catalyzed by proteins called enzymes. 3. Movement:3. Movement: muscles are made up of proteins called myosin and actin. 4. Transport4. Transport: hemoglobin transports oxygen from the lungs to cells; other proteins transport molecules across cell membranes. 5. Hormones:5. Hormones: many hormones are proteins, among them insulin, oxytocin, and human growth hormone.

4. 22 22-4 © 2006 Thomson Learning, Inc. All rights reserved Proteins 6. Protection:6. Protection: blood clotting involves the protein fibrinogen; the body used proteins called antibodies to fight disease. 7. Storage:7. Storage: casein in milk and ovalbumin in eggs store nutrients for newborn infants and birds; ferritin, a protein in the liver, stores iron. 8. Regulation:8. Regulation: certain proteins not only control the expression of genes, but also control when gene expression takes place. Proteins are divided into two types: fibrous proteins globular proteins

5. 22 22-5 © 2006 Thomson Learning, Inc. All rights reserved Amino Acids Amino acid: Amino acid: a compound that contains both an amino group and a carboxyl group.  -Amino acid:  -Amino acid: an amino acid in which the amino group is on the carbon adjacent to the carboxyl group. zwitterionAlthough  -amino acids are commonly written in the un-ionized form, they are more properly written in the zwitterion (internal salt) form.

6. 22 22-6 © 2006 Thomson Learning, Inc. All rights reserved Chirality of Amino Acids With the exception of glycine, all protein-derived amino acids have at least one stereocenter (the  - carbon) and are chiral. The vast majority of protein-derived  -amino acids have the L-configuration at the  -carbon.

7. 22 22-7 © 2006 Thomson Learning, Inc. All rights reserved Chirality of Amino Acids A comparison of the stereochemistry of L-alanine and D-glyceraldehyde (as Fischer projections):

8. 22 22-8 © 2006 Thomson Learning, Inc. All rights reserved 20 Protein-Derived AA Nonpolar side chains (at pH 7.0)

9. 22 22-9 © 2006 Thomson Learning, Inc. All rights reserved 20 Protein-Derived AA Polar side chains (at pH 7.0)

10. 22 22-10 © 2006 Thomson Learning, Inc. All rights reserved 20 Protein-Derived AA Acidic and basic side chains (at pH 7.0)

11. 22 22-11 © 2006 Thomson Learning, Inc. All rights reserved 20 Protein-Derived AA 1. All 20 are  -amino acids. 2. For 19 of the 20, the  -amino group is primary; for proline, it is secondary. 3. With the exception of glycine, the  -carbon of each is a stereocenter. 4. Isoleucine and threonine each contain a second stereocenter.

12. 22 22-12 © 2006 Thomson Learning, Inc. All rights reserved Ionization vs pH The net charge on an amino acid depends on the pH of the solution in which it is dissolved. If we dissolve an amino acid in water, it is present in the aqueous solution as its zwitterion. If we now add a strong acid such as HCl to bring the pH of the solution to 2.0 or lower, the strong acid donates a proton to the -COO - of the amino acid turning the zwitterion into a positive ion.

13. 22 22-13 © 2006 Thomson Learning, Inc. All rights reserved Ionization vs pH If we add a strong base such as NaOH to the solution and bring its pH to 10.0 or higher, a proton is transferred from the NH 3 + group to the base turning the zwitterion into a negative ion. to summarize:

14. 22 22-14 © 2006 Thomson Learning, Inc. All rights reserved Isoelectric Point Isoelectric point, pI: Isoelectric point, pI: The pH at which the majority of molecules of a compound in solution have no net charge.

15. 22 22-15 © 2006 Thomson Learning, Inc. All rights reserved Cysteine SH -S-S- The -SH (sulfhydryl) group of cysteine is easily oxidized to an -S-S- (disulfide).

16. 22 22-16 © 2006 Thomson Learning, Inc. All rights reserved Other Amino Acids Hydroxylation (oxidation) of proline, lysine, and tyrosine, and iodination for tyrosine, give these nonstandard amino acids.

17. 22 22-17 © 2006 Thomson Learning, Inc. All rights reserved Peptides In 1902, Emil Fischer proposed that proteins are long chains of amino acids joined by amide bonds. peptide bond:peptide bond: The special name given to the amide bond between the  -carboxyl group of one amino acid and the  -amino group of another.

18. 22 22-18 © 2006 Thomson Learning, Inc. All rights reserved Peptides PeptidePeptide: A short polymer of amino acids joined by peptide bonds; they are classified by the number of amino acids in the chain. DipeptideDipeptide: A molecule containing two amino acids joined by a peptide bond. TripeptideTripeptide: A molecule containing three amino acids joined by peptide bonds. PolypeptidePolypeptide: A macromolecule containing many amino acids joined by peptide bonds. ProteinProtein: A biological macromolecule containing at least 30 to 50 amino acids joined by peptide bonds.

19. 22 22-19 © 2006 Thomson Learning, Inc. All rights reserved Writing Peptides By convention, peptides are written from the left, beginning with the free -NH 3 + group and ending with the free -COO - group on the right. C-terminal amino acid:C-terminal amino acid: the amino acid at the end of the chain having the free -COO - group. N-terminal amino acid:N-terminal amino acid: the amino acid at the end of the chain having the free -NH 3 + group.

20. 22 22-20 © 2006 Thomson Learning, Inc. All rights reserved Peptides and Proteins Proteins behave as zwitterions. isoelectric point, pI Proteins also have an isoelectric point, pI. At its isoelectric point, the protein has no net charge. At any pH above (more basic than) its pI, it has a net negative charge. At any pH below (more acidic than) its pI, it has a net positive charge. Hemoglobin, for example, has an almost equal number of acidic and basic side chains; its pI is 6.8. Serum albumin has more acidic side chains; its pI is 4.9. Proteins are least soluble in water at their isoelectric points and can be precipitated from solution at this pH.

21. 22 22-21 © 2006 Thomson Learning, Inc. All rights reserved Levels of Structure Primary structure: Primary structure: the sequence of amino acids in a polypeptide chain; read from the N-terminal amino acid to the C-terminal amino acid. Secondary structure: Secondary structure: conformations of amino acids in localized regions of a polypeptide chain; examples are  -helix,  -pleated sheet, and random coil. Tertiary structure: Tertiary structure: the complete three- dimensional arrangement of atoms of a polypeptide chain. Quaternary structure: Quaternary structure: the spatial relationship and interactions between subunits in a protein that has more than one polypeptide chain.

22. 22 22-22 © 2006 Thomson Learning, Inc. All rights reserved Primary Structure Primary structure: Primary structure: the sequence of amino acids in a polypeptide chain. The number peptides possible from the 20 protein-derived amino acids is enormous. there are 20 x 20 = 400 dipeptides possible. there are 20 x 20 x 20 = 8000 tripeptides possible. n 20 nthe number of peptides possible for a chain of n amino acids is 20 n. for a small protein of 60 amino acids, the number of proteins possible is 20 60 = 10 78, which is possibly greater than the number of atoms in the universe!

23. 22 22-23 © 2006 Thomson Learning, Inc. All rights reserved Primary Structure Figure 22.6 The hormone insulin consists of two polypeptide chains held together by two interchain disulfide bonds.

24. 22 22-24 © 2006 Thomson Learning, Inc. All rights reserved Primary Structure Just how important is the exact amino acid sequence? Human insulin consists of two polypeptide chains having a total of 51 amino acids; the two chains are connected by two interchain disulfide bonds. In the table are differences between four types of insulin.

25. 22 22-25 © 2006 Thomson Learning, Inc. All rights reserved Primary Structure Vasopressin and oxytocin are both nonapeptides but have quite different biological functions. Vasopressin is an antidiuretic hormone. Oxytocin affects contractions of the uterus in childbirth and the muscles of the breast that aid in the secretion of milk.

26. 22 22-26 © 2006 Thomson Learning, Inc. All rights reserved Secondary Structure Secondary structure: Secondary structure: conformations of amino acids in localized regions of a polypeptide chain. The most common types of secondary structure are  - helix and  -pleated sheet.  -Helix:  -Helix: a type of secondary structure in which a section of polypeptide chain coils into a spiral, most commonly a right-handed spiral.  -Pleated sheet:  -Pleated sheet: a type of secondary structure in which two polypeptide chains or sections of the same polypeptide chain align parallel to each other; the chains may be parallel or antiparallel.

27. 22 22-27 © 2006 Thomson Learning, Inc. All rights reserved  -Helix Figure 22.8(a) The  -helix structure.

28. 22 22-28 © 2006 Thomson Learning, Inc. All rights reserved  -Helix In a section of  -helix; There are 3.6 amino acids per turn of the helix. The six atoms of each peptide bond lie in the same plane. N-H groups of peptide bonds point in the same direction, roughly parallel to the axis of the helix. C=O groups of peptide bonds point in the opposite direction, also roughly parallel to the axis of the helix. The C=O group of each peptide bond is hydrogen bonded to the N-H group of the peptide bond four amino acid units away from it. All R- groups point outward from the helix.

29. 22 22-29 © 2006 Thomson Learning, Inc. All rights reserved  -Pleated Sheet Figure 22.8(b). The  -pleated sheet structure.

30. 22 22-30 © 2006 Thomson Learning, Inc. All rights reserved  -Pleated Sheet In a section of  -pleated sheet; The six atoms of each peptide bond lie in the same plane. The C=O and N-H groups of peptide bonds from adjacent chains point toward each other and are in the same plane so that hydrogen bonding is possible between them. All R- groups on any one chain alternate, first above, then below the plane of the sheet, etc.

31. 22 22-31 © 2006 Thomson Learning, Inc. All rights reserved Collagen Triple Helix Figure 22.11 The collagen triple helix.

32. 22 22-32 © 2006 Thomson Learning, Inc. All rights reserved Collagen Triple Helix Consists of three polypeptide chains wrapped around each other in a ropelike twist to form a triple helix called tropocollagen. 30% of amino acids in each chain are Pro and L- hydroxyproline (Hyp); L-hydroxylysine (Hyl) also occurs. Every third position is Gly and repeating sequences are X-Pro-Gly and X-Hyp-Gly. Each polypeptide chain is a helix but not an  -helix. The three strands are held together by hydrogen bonding involving hydroxyproline and hydroxylysine. With age, collagen helices become cross linked by covalent bonds formed between side chains of Lys residues.

33. 22 22-33 © 2006 Thomson Learning, Inc. All rights reserved Tertiary Structure Tertiary structure: Tertiary structure: the overall conformation of an entire polypeptide chain. Tertiary structure is stabilized in four ways: Covalent bondsCovalent bonds, as for example, the formation of disulfide bonds between cysteine side chains. Hydrogen bondingHydrogen bonding between polar groups of side chains, as for example between the -OH groups of serine and threonine. Salt bridgesSalt bridges, as for example, the attraction of the -NH 3 + group of lysine and the -COO - group of aspartic acid. Hydrophobic interactionsHydrophobic interactions, as for example, between the nonpolar side chains of phenylalanine and isoleucine.

34. 22 22-34 © 2006 Thomson Learning, Inc. All rights reserved Tertiary Structure Figure 22.13 Forces that stabilize 3° structure of proteins

35. 22 22-35 © 2006 Thomson Learning, Inc. All rights reserved Quaternary Structure Quaternary structure: Quaternary structure: the arrangement of polypeptide chains into a noncovalently bonded aggregation. The individual chains are held in together by hydrogen bonds, salt bridges, and hydrophobic interactions. Hemoglobin Adult hemoglobin:Adult hemoglobin: two alpha chains of 141 amino acids each, and two beta chains of 146 amino acids each. Each chain surrounds an iron-containing heme unit. Fetal hemoglobin:Fetal hemoglobin: two alpha chains and two gamma chains; fetal hemoglobin has a greater affinity for oxygen than does adult hemoglobin.

36. 22 22-36 © 2006 Thomson Learning, Inc. All rights reserved Hemoglobin Figure 22.15 The 4° structure of hemoglobin.

37. 22 22-37 © 2006 Thomson Learning, Inc. All rights reserved Hemoglobin Figure 22.16 The structure of heme.

38. 22 22-38 © 2006 Thomson Learning, Inc. All rights reserved Quaternary Structure Figure 22.17 Integral membrane protein of rhodopsin made of  -helices.

39. 22 22-39 © 2006 Thomson Learning, Inc. All rights reserved Quaternary Structure Figure 22.18 The  -barrel of an integral membrane protein of the outer membrane of a mitochondrion is made of eight  -pleated sheets.

40. 22 22-40 © 2006 Thomson Learning, Inc. All rights reserved Denaturation Denaturation Denaturation: the process of destroying the native conformation of a protein by chemical or physical means. Some denaturations are reversible, while others permanently damage the protein. Denaturing agents include: Heat:Heat: heat can disrupt hydrogen bonding; in globular proteins, it can cause unfolding of polypeptide chains with the result that coagulation and precipitation may take place.

41. 22 22-41 © 2006 Thomson Learning, Inc. All rights reserved Denaturation 6 M aqueous urea:6 M aqueous urea: disrupts hydrogen bonding. Surface-active agents:Surface-active agents: detergents such as sodium dodecylbenzenesulfate (SDS) disrupt hydrogen bonding. Reducing agents:Reducing agents: 2-mercaptoethanol (HOCH 2 CH 2 SH) cleaves disulfide bonds by reducing -S-S- groups to - SH groups. Heavy metal ions:Heavy metal ions: transition metal ions such as Pb 2+, Hg 2+, and Cd 2+ form water-insoluble salts with -SH groups; Hg 2+ for example forms -S-Hg-S-. Alcohols:Alcohols: 70% ethanol, for example, which denatures proteins, is used to sterilize skin before injections.

42. 22 22-42 © 2006 Thomson Learning, Inc. All rights reserved End Chapter 22 Proteins