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Start here_ch02_lecture

  1. 1. Chapter 2 The Chemistry of Microbiology
  2. 2. Atoms <ul><li>Matter – anything that takes up space and has mass </li></ul><ul><li>Atoms – the smallest chemical units of matter </li></ul>
  3. 3. Atoms <ul><li>Atomic Structure </li></ul><ul><ul><li>Electrons – negatively charged subatomic particles circling a nucleus </li></ul></ul><ul><ul><li>Nucleus – structure containing neutrons and protons </li></ul></ul><ul><ul><li>Neutrons – uncharged particles </li></ul></ul><ul><ul><li>Protons – positively charged particles </li></ul></ul>
  4. 4. Atoms
  5. 5. Atoms <ul><li>Atomic Structure </li></ul><ul><ul><li>Element – composed of a single type of atom </li></ul></ul><ul><ul><li>Atomic number – equal to the number of protons in the nucleus </li></ul></ul><ul><ul><li>Atomic mass (atomic weight) – sum of masses of protons, neutrons, and electrons </li></ul></ul>
  6. 6. Atoms
  7. 7. Atoms <ul><li>Isotopes </li></ul><ul><ul><li>Atoms of a given element that differ in the number of neutrons in their nuclei </li></ul></ul><ul><ul><li>Stable isotopes </li></ul></ul><ul><ul><li>Unstable isotopes </li></ul></ul><ul><ul><ul><li>Release energy during radioactive decay </li></ul></ul></ul>
  8. 8. Atoms
  9. 9. Atoms <ul><li>Electron Configurations </li></ul><ul><ul><li>Only the electrons of atoms interact, so they determine atom’s chemical behavior </li></ul></ul><ul><ul><li>Electrons occupy electron shells </li></ul></ul><ul><ul><li>Valence electrons – electrons in outermost shell that interact with other atoms </li></ul></ul>
  10. 10. Atoms
  11. 11. Atoms
  12. 12. Chemical Bonds <ul><li>Valence – combining capacity of an atom </li></ul><ul><ul><ul><li>Positive if has electrons to give up </li></ul></ul></ul><ul><ul><ul><li>Negative if has spaces to fill </li></ul></ul></ul><ul><ul><ul><li>Stable when outer electron shells contain eight electrons </li></ul></ul></ul><ul><li>Chemical bonds – attachment of atoms combined by sharing or transferring valence electrons </li></ul><ul><li>Molecule – two or more atoms held together by chemical bonds </li></ul><ul><li>Compound – a molecule composed of more than one element </li></ul>
  13. 13. Chemical Bonds <ul><li>Covalent Bond – sharing of a pair of electrons by two atoms </li></ul><ul><li>Electronegativity – attraction of atom for electrons; the more electronegative an atom, the greater the pull its nucleus exerts on electrons </li></ul>
  14. 14. Chemical Bonds <ul><li>Nonpolar Covalent Bonds </li></ul><ul><ul><li>Shared electrons spend equal amounts of time around each nucleus </li></ul></ul><ul><ul><li>Atoms with similar electronegativities </li></ul></ul><ul><ul><li>No poles exist </li></ul></ul><ul><ul><li>Carbon atoms critical to life; form four nonpolar covalent bonds with other atoms </li></ul></ul><ul><ul><ul><li>Organic compounds contain carbon and hydrogen atoms </li></ul></ul></ul>
  15. 15. Chemical Bonds
  16. 16. Chemical Bonds
  17. 17. Chemical Bonds
  18. 18. Chemical Bonds <ul><li>Polar Covalent Bonds </li></ul><ul><ul><li>Unequal sharing of electrons due to significantly different electronegativities </li></ul></ul><ul><ul><li>Most important polar covalent bonds involve hydrogen </li></ul></ul><ul><ul><ul><li>Allows for hydrogen bonding </li></ul></ul></ul>
  19. 19. Chemical Bonds
  20. 20. Chemical Bonds <ul><li>Ionic Bonds </li></ul><ul><ul><li>Occur when two atoms with vastly different electronegativities come together </li></ul></ul><ul><ul><li>Atoms have either positive (cation) or negative (anion) charges </li></ul></ul><ul><ul><li>Cations and anions attract each other and form ionic bonds (no electrons shared) </li></ul></ul><ul><ul><li>Typically form crystalline ionic compounds known as salts </li></ul></ul>
  21. 21. Chemical Bonds
  22. 22. Chemical Bonds
  23. 23. Chemical Bonds <ul><li>Hydrogen Bonds </li></ul><ul><ul><li>Weak forces that combine with polar covalent bonds </li></ul></ul><ul><ul><li>Electrical attraction between partially charged H + and full or partial negative charge on different region of same molecule or another molecule </li></ul></ul><ul><ul><li>Weaker than covalent bonds but essential for life </li></ul></ul><ul><ul><ul><li>Many help to stabilize 3-D shapes of large molecules </li></ul></ul></ul>
  24. 24. Chemical Bonds
  25. 25. Chemical Bonds
  26. 26. Chemical Reactions <ul><li>The making or breaking of chemical bonds </li></ul><ul><li>Involve reactants and products </li></ul><ul><li>Biochemistry involves chemical reactions of living things </li></ul>
  27. 27. Chemical Reactions <ul><li>Synthesis Reactions </li></ul><ul><ul><li>Involve the formation of larger, more complex molecules </li></ul></ul><ul><ul><li>Require energy (endothermic) </li></ul></ul><ul><ul><li>Most common type is dehydration synthesis </li></ul></ul><ul><ul><ul><li>Water molecule formed </li></ul></ul></ul><ul><ul><li>All the synthesis reactions in an organism are called anabolism </li></ul></ul>
  28. 28. Chemical Reactions
  29. 29. Chemical Reactions <ul><li>Decomposition Reactions </li></ul><ul><ul><li>Break bonds within larger molecules to form smaller atoms, ions, and molecules </li></ul></ul><ul><ul><li>Release energy (exothermic) </li></ul></ul><ul><ul><li>Most common type is hydrolysis </li></ul></ul><ul><ul><ul><li>Ionic components of water are added to products </li></ul></ul></ul><ul><ul><li>All the decomposition reactions in an organism are called catabolism </li></ul></ul>
  30. 30. Chemical Reactions
  31. 31. Chemical Reactions <ul><li>Exchange Reactions </li></ul><ul><ul><li>Involve breaking and forming covalent bonds, and involve endothermic and exothermic steps </li></ul></ul><ul><ul><li>Involve atoms moving from one molecule to another </li></ul></ul><ul><ul><li>Sum of all chemical reactions in an organism is called metabolism </li></ul></ul>
  32. 32. Water, Acids, Bases, and Salts <ul><li>Water </li></ul><ul><ul><li>Most abundant substance in organisms </li></ul></ul><ul><ul><li>Most of its special characteristics due to two polar covalent bonds </li></ul></ul><ul><ul><ul><li>Cohesive molecules – surface tension </li></ul></ul></ul><ul><ul><ul><li>Excellent solvent </li></ul></ul></ul><ul><ul><ul><li>Remains liquid across wide range of temperatures </li></ul></ul></ul><ul><ul><ul><li>Can absorb significant amounts of energy without changing temperature </li></ul></ul></ul><ul><ul><ul><li>Participates in many chemical reactions </li></ul></ul></ul>
  33. 33. Water, Acids, Bases, and Salts
  34. 34. Water, Acids, Bases, and Salts <ul><li>Acids and Bases </li></ul><ul><ul><li>Dissociated by water into component cations and anions </li></ul></ul><ul><ul><ul><li>Acid – dissociates into one or more H + and one or more anions </li></ul></ul></ul><ul><ul><ul><li>Base – binds with H + when dissolved into water; some dissociate into cations and OH - </li></ul></ul></ul><ul><ul><li>Metabolism requires relatively constant balance of acids and bases </li></ul></ul><ul><ul><ul><li>Concentration of H + in solution is expressed using the pH scale </li></ul></ul></ul><ul><ul><ul><li>Buffers prevent drastic changes in internal pH </li></ul></ul></ul>
  35. 35. Water, Acids, Bases, and Salts
  36. 36. Water, Acids, Bases, and Salts
  37. 37. Water, Acids, Bases, and Salts <ul><li>Salts </li></ul><ul><ul><li>Compounds that dissociate in water into cations and anions other than H + and OH - </li></ul></ul><ul><ul><li>Cations and anions of salts are electrolytes </li></ul></ul><ul><ul><ul><li>Create electrical differences between inside and outside of cell </li></ul></ul></ul><ul><ul><ul><li>Transfer electrons from one location to another </li></ul></ul></ul><ul><ul><ul><li>Form important components of many enzymes </li></ul></ul></ul>
  38. 38. Organic Macromolecules <ul><li>Functional Groups and Monomers </li></ul><ul><ul><li>Contain carbon and hydrogen atoms </li></ul></ul><ul><ul><li>Atoms often appear in certain common arrangements – functional groups </li></ul></ul><ul><ul><li>Macromolecules – large molecules used by all organisms </li></ul></ul><ul><ul><ul><li>Lipids </li></ul></ul></ul><ul><ul><ul><li>Carbohydrates </li></ul></ul></ul><ul><ul><ul><li>Proteins </li></ul></ul></ul><ul><ul><ul><li>Nucleic Acids </li></ul></ul></ul><ul><ul><li>Monomers – basic building blocks of macromolecules </li></ul></ul>
  39. 39. Organic Macromolecules
  40. 40. Organic Macromolecules <ul><li>Lipids </li></ul><ul><ul><li>Not composed of regular subunits, but are all hydrophobic </li></ul></ul><ul><ul><li>Four groups </li></ul></ul><ul><ul><ul><li>Fats </li></ul></ul></ul><ul><ul><ul><li>Phospholipids </li></ul></ul></ul><ul><ul><ul><li>Waxes </li></ul></ul></ul><ul><ul><ul><li>Steroids </li></ul></ul></ul>
  41. 41. Organic Macromolecules
  42. 42. Organic Macromolecules
  43. 43. Organic Macromolecules
  44. 44. Organic Macromolecules <ul><li>Waxes </li></ul><ul><ul><li>Contain one long-chain fatty acid covalently linked to long-chain alcohol by ester bond </li></ul></ul><ul><ul><li>Completely insoluble in water; lack hydrophilic head </li></ul></ul>
  45. 45. Organic Macromolecules
  46. 46. Organic Macromolecules <ul><li>Carbohydrates </li></ul><ul><ul><li>Organic molecules composed of carbon, hydrogen, and oxygen (CH 2 O) n </li></ul></ul><ul><ul><li>Functions </li></ul></ul><ul><ul><ul><li>Long-term storage of chemical energy </li></ul></ul></ul><ul><ul><ul><li>Ready energy source </li></ul></ul></ul><ul><ul><ul><li>Part of backbones of nucleic acids </li></ul></ul></ul><ul><ul><ul><li>Converted to amino acids </li></ul></ul></ul><ul><ul><ul><li>Form cell wall </li></ul></ul></ul><ul><ul><ul><li>Involved in intracellular interactions between animal cells </li></ul></ul></ul>
  47. 47. Organic Macromolecules <ul><li>Carbohydrates </li></ul><ul><ul><li>Types </li></ul></ul><ul><ul><ul><li>Monosaccharides </li></ul></ul></ul><ul><ul><ul><li>Disaccharides </li></ul></ul></ul><ul><ul><ul><li>Polysaccharides </li></ul></ul></ul>
  48. 48. Organic Macromolecules
  49. 49. Organic Macromolecules
  50. 50. Organic Macromolecules
  51. 51. Organic Macromolecules <ul><li>Proteins </li></ul><ul><ul><li>Mostly composed of carbon, hydrogen, oxygen, nitrogen, and sulfur </li></ul></ul><ul><ul><li>Functions </li></ul></ul><ul><ul><ul><li>Structure </li></ul></ul></ul><ul><ul><ul><li>Enzymatic catalysis </li></ul></ul></ul><ul><ul><ul><li>Regulation </li></ul></ul></ul><ul><ul><ul><li>Transportation </li></ul></ul></ul><ul><ul><ul><li>Defense and offense </li></ul></ul></ul>
  52. 52. Organic Macromolecules <ul><li>Amino Acids </li></ul><ul><ul><li>The monomers that make up proteins </li></ul></ul><ul><ul><li>Most organisms use only 21 amino acids in the synthesis of proteins </li></ul></ul><ul><ul><li>Side groups affect how amino acids interact with one another and how a protein interacts with other molecules </li></ul></ul><ul><ul><li>A covalent bond (peptide bond) is formed between amino acids by dehydration synthesis reaction </li></ul></ul>
  53. 53. Organic Macromolecules
  54. 54. Organic Macromolecules
  55. 55. Organic Macromolecules
  56. 56. Organic Macromolecules
  57. 57. Organic Macromolecules <ul><li>Nucleic Acids </li></ul><ul><ul><li>DNA and RNA: the genetic material of organisms </li></ul></ul><ul><ul><li>RNA helps form polypeptides </li></ul></ul>
  58. 58. Organic Macromolecules <ul><li>Nucleic Acids </li></ul><ul><ul><li>Nucleotides </li></ul></ul><ul><ul><ul><li>Monomers that make up nucleic acids </li></ul></ul></ul><ul><ul><ul><li>Composed of three parts </li></ul></ul></ul><ul><ul><ul><ul><li>Phosphate </li></ul></ul></ul></ul><ul><ul><ul><ul><li>Pentose sugar – deoxyribose or ribose </li></ul></ul></ul></ul><ul><ul><ul><ul><li>One of five cyclic nitrogenous bases </li></ul></ul></ul></ul>
  59. 59. Organic Macromolecules
  60. 60. Organic Macromolecules <ul><li>Nucleic Acids </li></ul><ul><ul><li>Nucleic acid structure </li></ul></ul><ul><ul><ul><li>H bonds form between C and G and between T and A in DNA </li></ul></ul></ul><ul><ul><ul><ul><li>Two H bonds form between U and A in RNA </li></ul></ul></ul></ul><ul><ul><ul><li>DNA is double stranded in most cells and viruses </li></ul></ul></ul><ul><ul><ul><ul><li>Two strands are complementary </li></ul></ul></ul></ul><ul><ul><ul><ul><li>Two strands are antiparallel </li></ul></ul></ul></ul>
  61. 61. Organic Macromolecules
  62. 62. Organic Macromolecules <ul><li>Nucleic Acids </li></ul><ul><ul><li>Nucleic acid function </li></ul></ul><ul><ul><ul><li>DNA is genetic material of all organisms and of many viruses </li></ul></ul></ul><ul><ul><ul><li>Carries instructions for synthesis of RNA and proteins; controls synthesis of all molecules in an organism </li></ul></ul></ul>
  63. 63. Organic Macromolecules
  64. 64. Organic Macromolecules