1. Chapter 5 The Structure and Function of Large Biological Molecules

2. I. Monomers - Polymers polymer = long molecule of many similar building blocks monomers = small building-block molecules Three of the four classes of life’s organic molecules are polymers: – Carbohydrates – Proteins – Nucleic acids

3. Condensation / dehydration reaction = two monomers bond together through the loss of a water molecule Enzymes = macromolecules that speed up the dehydration process Polymers are disassembled to monomers by hydrolysis (reverse of dehydration reaction) II. Synthesis and Breakdown of Polymers

4. Fig. 5-2a Dehydration removes a water molecule, forming a new bond Short polymerUnlinked monomer Longer polymer Dehydration reaction in the synthesis of a polymer HO H2OH2O H H H 4 3 2 1 1 2 3 (a)

5. Fig. 5-2b Hydrolysis adds a water molecule, breaking a bond Hydrolysis of a polymer HO H2OH2O H H H 3 2 1 1 23 4 (b)

6. III: Carbohydrates Carbohydrates = sugars and the polymers of sugars Monosaccharides = single sugars Polysaccharides = polymers made of many sugar building blocks

7. A. Monosaccharides Monosaccharides = formulas are usually multiples of CH 2 O Glucose (C 6 H 12 O 6 ) = most common Classified by – The location of the carbonyl group (as aldose or ketose) – The number of carbons in the skeleton

8. Fig. 5-3 Dihydroxyacetone Ribulose Ketoses Aldoses Fructose Glyceraldehyde Ribose Glucose Galactose Hexoses (C 6 H 12 O 6 ) Pentoses (C 5 H 10 O 5 ) Trioses (C 3 H 6 O 3 )

9. Fig. 5-4a (a) Linear and ring forms

10. disaccharide - dehydration reaction joins two monosaccharides Covalent bond is called a glycosidic linkage

11. Fig. 5-5 (b) Dehydration reaction in the synthesis of sucrose GlucoseFructose Sucrose MaltoseGlucose (a) Dehydration reaction in the synthesis of maltose 1–4 glycosidic linkage 1–2 glycosidic linkage

12. B. Polysaccharides Polysaccharides (polymers of sugars) have storage and structural roles Str and fnct of polys are determined by its sugar monomers and positions of glycosidic linkages

13. 1. Storage Polysaccharides Starch = storage poly of plants, consists entirely of glucose monomers Plants store surplus starch as granules within chloroplasts Glycogen = storage poly in animals, found in liver and muscles

14. Fig. 5-6 (b) Glycogen: an animal polysaccharide Starch Glycogen Amylose Chloroplast (a) Starch: a plant polysaccharide Amylopectin Mitochondria Glycogen granules 0.5 µm 1 µm

15. 2. Structural Polysaccharides cellulose = major component of plant cell walls Cellulose (like starch) is a polymer of glucose, but the glycosidic linkages differ The difference is based on two ring forms for glucose: alpha (  ) and beta (  )

16. Fig. 5-7a (a) α and β glucose ring structures α Glucoseβ Glucose

17. Fig. 5-7bc (b) Starch: 1–4 linkage of α glucose monomers (c) Cellulose: 1–4 linkage of β glucose monomers

18.  glucose are helical  glucose are straight In straight structures, H atoms can bond with OH groups on other strands, making microfibrils

19. Fig. 5-8 b Glucose monomer Cellulose molecules Microfibril Cellulose microfibrils in a plant cell wall 0.5 µm 10 µm Cell walls

20. Enzymes that digest starch by hydrolyzing  linkages can’t hydrolyze  linkages in cellulose Cellulose in food passes through the digestive tract as insoluble fiber Some microbes use enzymes to digest cellulose Many herbivores, cows to termites, have symbiotic relationships with these microbes

21. Chitin, another structural polysaccharide, is found in the exoskeleton of arthropods and cell walls of fungi

22. IV: Lipids Lipids do not form polymers Little or no affinity for water Lipids are hydrophobic b/c  they consist mostly of hydrocarbons, which form nonpolar covalent bonds

23. A. Fats Fats – made from glycerol and fatty acids Glycerol – 3 carbon alcohol with a hydroxyl group on each carbon fatty acid = carboxyl group attached to a long carbon chain Three fatty acids are joined to glycerol by an ester linkage

24. Fig. 5-11 Fatty acid (palmitic acid) Glycerol (a) Dehydration reaction in the synthesis of a fat Ester linkage (b) Fat molecule (triacylglycerol)

25. Saturated fatty acids = max # of H atoms and no double bonds, most animal fats, solid @ room temp Unsaturated fatty acids have one or more double bonds, most plant and fish oils, liquid @ room temp

26. Fig. 5-12a (a) Saturated fat Structural formula of a saturated fat molecule Stearic acid, a saturated fatty acid

27. Fig. 5-12b (b) Unsaturated fat Structural formula of an unsaturated fat molecule Oleic acid, an unsaturated fatty acid cis double bond causes bending

28. saturated fats may contribute to cardio disease Hydrogenation = converting unsaturated fats to saturated fats by adding H Hydrogenating vegetable oils also creates unsaturated fats with trans double bonds trans fats may contribute more than saturated fats to cardio disease

29. The major function of fats is energy storage Mammals store their fat in adipose cells (cushions vital organs and insulates the body)

30. B. Phospholipids phospholipid, two fatty acids and a phosphate are attached to glycerol Two fatty acid tails are hydrophobic, but phosphate group forms a hydrophilic head

31. Fig. 5-13ab (b) Space-filling model(a) Structural formula Fatty acids Choline Phosphate Glycerol Hydrophobic tails Hydrophilic head

32. Phospholipids form a bilayer in water, hydrophobic tails pointing toward interior Structure results in a bilayer found in cell membranes

33. Fig. 5-14 Hydrophilic head Hydrophobic tail WATER

34. C. Steroids Steroids = lipids characterized by a carbon skeleton consisting of four fused rings Cholesterol = a component in animal cell membranes, can give cardio disease

35. Fig. 5-15

36. V: Proteins

37. Enzymes = protein acts as a catalyst to speed up chemical reactions Enzymes do not get used up and are specific

38. Fig. 5-16 Enzyme (sucrase) Substrate (sucrose) Fructose Glucose OH H O H2OH2O

39. A. Polypeptides Polypeptides are polymers built from set of 20 amino acids A protein = one or more polypeptides

40. 1. Amino Acid Monomers Amino acids = org molecules with carboxyl and amino groups Amino acids differ in their properties due to differing side chains (R groups)

41. Fig. 5-UN1 Amino group Carboxyl group α carbon

42. Fig. 5-17a Nonpolar Glycine (Gly or G) Alanine (Ala or A) Valine (Val or V) Leucine (Leu or L) Isoleucine (Ile or I) Methionine (Met or M) Phenylalanine (Phe or F) Tryptophan (Trp or W) Proline (Pro or P)

43. Fig. 5-17b Polar Asparagine (Asn or N) Glutamine (Gln or Q) Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) Tyrosine (Tyr or Y)

44. Fig. 5-17c Acidic Arginine (Arg or R) Histidine (His or H) Aspartic acid (Asp or D) Glutamic acid (Glu or E) Lysine (Lys or K) Basic Electrically charged

45. 2. Amino Acid Polymers Amino acids are linked by peptide bonds Range in length from a few to more than 1000 monomers Each polypeptide has a unique linear sequence of amino acids

46. Peptide bond Fig. 5-18 Amino end (N-terminus) Peptide bond Side chains Backbone Carboxyl end (C-terminus) (a) (b)

47. B. Protein Structure and Function A functional protein consists of one or more polypeptides twisted, folded, and coiled into a unique shape Sequence of amino acids determines a protein’s 3-D structure, which determines the function

48. Fig. 5-19 A ribbon model of lysozyme (a)(b) A space-filling model of lysozyme Groove

49. Fig. 5-20 Antibody protein Protein from flu virus

50. 1. Four Levels of Protein Structure Primary structure = its unique sequence of amino acids Primary Structure

51. Secondary structure = folds and twists result from H bonds between amino acid backbone Examples are a coil (  helix) and a folded structure (  pleated sheet) Secondary Structure β pleated sheet Examples of amino acid subunits α helix

52. Tertiary structure = interactions between R groups Include H bonds, ionic bonds, hydrophobic interactions, and van der Waals forces Strong covalent bonds called disulfide bridges may reinforce the protein’s structure

53. Fig. 5-21e Tertiary StructureQuaternary Structure

54. Fig. 5-21f Polypeptide backbone Hydrophobic interactions and van der Waals interactions Disulfide bridge Ionic bond Hydrogen bond

55. Quaternary structure = two or more polypeptide chains form a protein Collagen = fibrous protein of three polypeptides coiled like a rope Hemoglobin = globular protein consisting of four polypeptides: two alpha and two beta chains Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

56. Fig. 5-21g Polypeptide chain  Chains Heme Iron  Chains Collagen Hemoglobin

57. 2. Sickle-Cell Disease: Change in primary structure can affect a protein’s ability to function Sickle-cell disease (inherited blood disorder) results from a single amino acid substitution in the protein hemoglobin

58. Fig. 5-22 Primary structure Secondary and tertiary structures Quaternary structure Normal hemoglobin (top view) Primary structure Secondary and tertiary structures Quaternary structure Function  subunit Molecules do not associate with one another; each carries oxygen. Red blood cell shape Normal red blood cells are full of individual hemoglobin moledules, each carrying oxygen. 10 µm Normal hemoglobin     1234567 Val His Leu ThrPro Glu Red blood cell shape  subunit Exposed hydrophobic region Sickle-cell hemoglobin   Molecules interact with one another and crystallize into a fiber; capacity to carry oxygen is greatly reduced.   Fibers of abnormal hemoglobin deform red blood cell into sickle shape. 10 µm Sickle-cell hemoglobin GluPro Thr Leu His Val 1234567

59. 3. Other factors Physical and chemical conditions can affect structure Changes in pH, [salt], temperature or other factors can cause a protein to unravel (denaturation) Normal protein Denatured protein Denaturation Renaturation

60. 4. Protein Folding in the Cell Chaperonins are protein molecules that assist the proper folding of other proteins Correctly folded protein Polypeptide Steps of Chaperonin Action: 1 An unfolded poly- peptide enters the cylinder from one end. The cap attaches, causing the cylinder to change shape in such a way that it creates a hydrophilic environment for the folding of the polypeptide. The cap comes off, and the properly folded protein is released.

61. VI. Nucleic acids Amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene Genes are made of DNA, a nucleic acid

62. A. Roles of Nucleic Acids Two types: – Deoxyribonucleic acid (DNA) – Ribonucleic acid (RNA) DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis Protein synthesis occurs in ribosomes

63. Fig. 5-26-3 mRNA Synthesis of mRNA in the nucleus DNA NUCLEUS mRNA CYTOPLASM Movement of mRNA into cytoplasm via nuclear pore Ribosome Amino acids Polypeptide Synthesis of protein 1 2 3

64. B. The Structure of Nucleic Acids Nucleic acids are polymers called polynucleotides (monomers called nucleotides) Each nucleotide consists of a nitrogenous base, a pentose sugar, and a phosphate group

65. Fig. 5-27 5 end Nucleoside Nitrogenous base Phosphate group Sugar (pentose) (b) Nucleotide (a) Polynucleotide, or nucleic acid 3 end 3C3C 3C3C 5C5C 5C5C Nitrogenous bases Pyrimidines Cytosine (C) Thymine (T, in DNA)Uracil (U, in RNA) Purines Adenine (A)Guanine (G) Sugars Deoxyribose (in DNA) Ribose (in RNA) (c) Nucleoside components: sugars

66. Fig. 5-27ab 5' end 5'C 3'C 5'C 3'C 3' end (a) Polynucleotide, or nucleic acid (b) Nucleotide Nucleoside Nitrogenous base 3'C 5'C Phosphate group Sugar (pentose)

67. 1. Nucleotide Monomers Two families of nitrogenous bases: – Pyrimidines (cytosine, thymine, and uracil) have a single six-membered ring – Purines (adenine and guanine) have a six- membered ring fused to a five-membered ring DNA, sugar = deoxyribose; RNA, sugar = ribose Nucleotide = nucleoside (sugar + N base) + phosphate group

68. Fig. 5-27c-1 (c) Nucleoside components: nitrogenous bases Purines Guanine (G) Adenine (A) Cytosine (C) Thymine (T, in DNA)Uracil (U, in RNA) Nitrogenous bases Pyrimidines

69. Fig. 5-27c-2 Ribose (in RNA)Deoxyribose (in DNA) Sugars (c) Nucleoside components: sugars

70. 2. Nucleotide Polymers Nucleotides are joined by covalent bonds that form between the –OH group on the 3 carbon of one nucleotide and the phosphate on the 5 carbon on the next Creates a backbone of sugar-phosphate units with nitrogenous bases as appendages Sequence of bases along DNA or mRNA is unique for each gene

71. The DNA Double Helix A DNA molecule has two polynucleotides spiraling around an imaginary axis, forming a double helix In the DNA double helix, the two backbones run in opposite 5 → 3 directions from each other, an arrangement referred to as antiparallel One DNA molecule includes many genes The nitrogenous bases in DNA pair up and form hydrogen bonds: adenine (A) to thymine (T), and guanine (G) to cytosine (C)

72. Fig. 5-28 Sugar-phosphate backbones 3' end 5' end Base pair (joined by hydrogen bonding) Old strands New strands Nucleotide about to be added to a new strand