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MCB 3020, Spring 2005 1-10-2004

MCB 3020, Spring 2005 1-10-2004. Chapter 3: The Building Blocks of Life I. Chapter 3. I. The chemistry of life II. Macromolecules of the cell A. polysaccharides B. lipids C. nucleic acids D. proteins. O-. CH 2 -CH 2 CH 2 - O-P=O. O O OR C=O C=O

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MCB 3020, Spring 2005 1-10-2004

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  1. MCB 3020, Spring 20051-10-2004 Chapter 3: The Building Blocks of Life I

  2. Chapter 3 I. The chemistry of life II. Macromolecules of the cell A. polysaccharides B. lipids C. nucleic acids D. proteins

  3. O- CH2-CH2 CH2-O-P=O O O OR C=O C=O CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH3 CH3 membrane lipids The Chemistry of Life All cells are made of organic molecules.

  4. I. The Chemistry of Life: a review A. the 6 major bioelements B. charge distribution in molecules C. attractive forces D. important functional groups

  5. A. The 6 Major Bioelements C Carbon H Hydrogen O Oxygen N Nitrogen P Phosphorus S Sulfur

  6. B. Charge distribution in molecules 1. electronegativity 2. hydrophilic (polar) 3. hydrophobic (nonpolar) 4. amphipathic

  7. 1. Electronegativity Among the major bioelements oxygen and nitrogen have the highest electronegativity A measure of the degree of attraction of valence electrons TB

  8. 2. Polar (hydrophilic) - + asymmetric charge distribution in a molecule d+ d- H - O - CH2 CH3 TB

  9. d- d+ d- d+ O H - O - H H - C - O- d+ Polar molecules Polar molecules result from the bonding of atoms with very different electronegativities TB

  10. 3. Nonpolar (hydrophobic) little charge asymmetry TB

  11. Nonpolar molecules hydrocarbon chain aromatic rings Nonpolar molecules result from the bonding of atoms with similar electronegativities. TB

  12. - 4. Amphipathic partly polar, partly nonpolar phospholipid molecule negatively charged head nonpolar hydrocarbon tail TB

  13. C. Attractive forces 1. ionic bonds 2. covalent bonds 3. hydrogen bonds 4. van der Waals forces 5. hydrophobic interactions 6. comparison of bond strengths

  14. 1. Ionic bonds NaCl Na+ Cl- • • • • H H– C – H 2. Covalent bonds electron sharing between atoms H • • H C H H • • • • • • H attraction between charged particles

  15. 3. Hydrogen bonds (H-bonds) 1. A highly electronegative atom (usually O or N) 2. A hydrogen atom bonded to a highly electronegative atom (usually O or N) noncovalent bonds formed between the following: TB

  16. Hydrogen bonding of water molecules H H H H O O O O H H H H H-bonding of hydroxyl groups R O H O R H

  17. H-bonding of amino groups R R R — N H N R R Keto groups R O H O R H-bonds will form with various combinations of hydroxyl, amino and keto groups that meet the H-bonding criteria. TB

  18. Hydrogen bonding between amino acids in a protein | H-C-R1 | C=O | N-H | H-C-R2 | C=O | N-H | H-C-R3 | | R4-C-H | H –N | O=C | R5-C-H | H –N | O=C | Rc- C-H |

  19. Hydrogen bonding between bases in DNA H-N-H O N N NH N N H N-H H O N H cytosine guanine Three H-bonds between G and C

  20. 4. van der Waals forces nucleus - - + + electrons induced dipoles (polar) Attraction between molecules that are very close together van der Waals attractions result from attractions between induced dipoles TB

  21. 5. Hydrophobic forces (interactions) Attraction between hydrophobic molecules or hydrophobic portions of molecules • driven by an increase in entropy (disorder) due to water exclusion TB

  22. Water is the biological solvent of life as we know it. • cells are 70 to 90% water • water is polar • many polar biological molecules dissolve in water • nonpolar (hydrophobic) molecules tend to aggregate together in water • water can H-bond with polar molecules

  23. 6. Comparison of bond strength strength (kcal/mol) type of bond 1. Covalent bonds 2. ionic bonds 3. hydrogen bonds 4. van der waals forces 5. hydrophobic forces -50 to -100 -80 or -1 -3 to -6 -0.5 to -1 -0.5 to -3

  24. Biological importance carboxylic acid organic acids, amino and fatty acids reducing sugars, like glucose aldehyde lipids and carbohydrates alcohol D. Important functional groups

  25. Important functional groups (contd.) pyruvate, citric acid cyle intermediates keto lipids of Bacteria and Eukarya ester DNA, RNA, ATP phosphoester

  26. amino amino acids, nucleotides -NH2 Important functional groups (contd.) ether lipids (archaea)

  27. OH C  O H2N – C – H CH2OH O- C  O +H3N – C – H CH2OH serine at pH 7 What functional groups are present in the amino acid serine?

  28. II. Macromolecules of the cell A. polysaccharides B. lipids C. nucleic acids D. proteins

  29. Monomers and polymers macromolecules arepolymers of covalently linked monomers monomer (eg. amino acid) covalent bond polymer (eg. protein)

  30. Macromolecules are large molecules made of repeating units (monomers). s s s s DNA a nucleic acid: a chain (polymer) of nucleotides a protein a polymer of amino acids

  31. Macromolecules make up 96% of the dry weight of cells. polysaccharides proteins lipids nucleic acids

  32. The 4 major cellular macromolecules*: chains (polymers) of repeating units polymer monomer example covalent bond (see notes for other examples) polysaccharide sugars cell wall glycosidic lipid fatty acids or membranes ester or ether isoprenoids nucleic acid nucleotides DNA, RNA phosphodiester protein amino acids enzymes peptide *Important recurring theme

  33. B. Polysaccharides polymers of sugarslinked by glycosidic bonds starch glycogen cellulose peptidoglycan 1. common sugar monomers 2. glycosidic bonds 3. cellular polysaccharides

  34. CH2OH O OH OH HO OH 1. common sugar monomers a. glucose (ring form) O b. fructose (ring form) HOH2C CH2OH HO OH HO TB

  35. O HOH2C c. ribose OH HO HO O HOH2C d. deoxyribose OH HO TB

  36. CH2OH O OH e. glucosamine OH HO NH2 CH2OH O OH f. muramic acid HO NH2 -OOCCHCH3 TB

  37. 2. Glycosidic bonds: a. -1,4-glycosidic bond CH2OH O OH HO OH CH2OH O OH H H OH O OH

  38. CH2OH CH2OH O O OH H O OH H OH HO OH OH b. -1,4-glycosidic bond

  39. 3. cellular polysaccharides a. starch a-1,4 glycosidic bonds large polymer of glucose mostly a-1,4 glycosidic bonds glucose storage molecule of plants TB

  40. large branched polymer of glucose mostly a-1,4 glycosidic bonds b. glycogen a-1,6 a-1,6 a-1,6 glycosidic bonds produce branching glucose storage molecule of animals and some microorganisms TB

  41. c. cellulose large glucose polymer major structural polysaccharide of plants mostly b-1,4 glycosidic bonds only microbes can break the b-1,4 bond TB

  42. d. peptidoglycan large polymer of N-acetyl glucosamine and N-acetyl muramic acid the main structural component of most Bacterial cell walls -1,4-glycosidic bonds *Penicillin inhibits Bacterial cell wall synthesis by inhibiting the formation of peptidoglycan. TB

  43. Study objectives 1. Memorize the 6 major bioelements. 2. Understand the terms electronegativity, hydrophilic, hydrophobic, polar, nonpolar, amphipathic. Know how these properties are important in chemical bonds and interactions. 3. Very important recurring theme: Understand the attractive forces (ionic, covalent, hydrogen bonds, van der Waals forces, and hydrophobic interactions), the examples presented in class, where they might occur. Which are strong bonds? Which are weaker? 4. Understand the role of water as the solvent of life. 5. Know the functional groups. Be able to recognize their structures. Know their biological importance and where they occur in cellular molecules. 6. Recurring theme: Know the four important cellular macromolecules (polymers), the monomers that comprise them, the bonds that connect the monomers, and the specific example presented in class. These macromolecules are the building blocks of cells. 7. In what parts of cells are the four macromolecules found?

  44. Study objectives 8. Describe the structure and functions of the four cellular macromolecules, the monomers, connecting bonds. Memorize the specific examples of monomers, polymers, and bonds presented in class. 9. Be able to recognize the structures of glucose, ribose, and deoxyribose. 10. Know the difference between -1,4 glycosidic bonds and -1,4-glycosidic bonds and where they can be found. Know the features of the cellular polysaccharides presented. How does penicillin inhibit microbial growth? 8.

  45. MCB 3020, Spring 20041-14-2004 Chapter 2 The Building Blocks of Life II:

  46. Chapter 2 (contd.) II. Macromolecules of the cell A. polysaccharides B. lipids C. nucleic acids D. proteins

  47. B. Lipids 1. fatty acids (glycerol) 2. membrane lipids a. bacterial and eukaryal b. archaeal

  48. B. Lipids CH2OH CHOH CH2OH O HO - C glycerol glycerol bonded to fatty acids (or isoprenoid units) and other groups by ester or ether linkages

  49. oleic (C18) COO- a monounsaturated fatty acid 1. Fatty acids a. common fatty acids palmitic (C16) COO- stearic (C18) COO- TB

  50. b. saturated and unsaturated fatty acids monounsaturated: 1 double bond COO- polyunsaturated: > 1 double bond COO- saturated: no double bonds COO-

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