1. © 2012 Pearson Education Inc. Lecture prepared by Mindy Miller-Kittrell North Carolina State University Chapter 2 The Chemistry of Microbiology

2. Atoms Matter – anything that takes up space and has mass Atoms – the smallest chemical units of matter © 2012 Pearson Education Inc.

3. Atoms Atomic Structure –Electrons – negatively charged subatomic particles circling a nucleus –Nucleus – structure containing neutrons and protons –Neutrons – uncharged particles –Protons – positively charged particles © 2012 Pearson Education Inc.

4. Figure 2.1 Bohr model of atomic structure Electron shells Nucleus Proton (p  ) Neutron (n 0 ) Electron (e  )

5. Atoms Atomic Structure –Element – composed of a single type of atom –Atomic number – equal to the number of protons in the nucleus –Atomic mass (atomic weight) – sum of masses of protons, neutrons, and electrons © 2012 Pearson Education Inc.

6. Atoms Isotopes –Atoms of a given element that differ in the number of neutrons in their nuclei –Stable isotopes –Unstable isotopes –Release energy during radioactive decay © 2012 Pearson Education Inc.

7. Figure 2.2 Nuclei of the three naturally occurring isotopes of carbon-overview

8. Atoms Electron Configurations –Only the electrons of atoms interact, so they determine atom’s chemical behavior –Electrons occupy electron shells –Valence electrons – electrons in outermost shell that interact with other atoms © 2012 Pearson Education Inc.

9. Figure 2.3 Electron configurations-overview

10. Figure 2.4 Bohr diagrams of the first 20 elements Hydrogen H Lithium Li Beryllium Be Sodium Na Magnesium Mg Calcium Ca Potassium K Boron B Carbon C Nitrogen N Oxygen O Fluorine F Neon Ne Helium He Aluminum Al Silicon Si Phosphorus P Sulfur S Chlorine Cl Argon Ar Periodic table of elements H Li Be Na Mg K Ca B CNOF He Ne Al SiP S Cl Ar

11. Chemical Bonds © 2012 Pearson Education Inc. Valence – combining capacity of an atom –Positive if has electrons to give up –Negative if has spaces to fill –Stable when outer electron shells contain eight electrons Chemical Bonds – atoms combine by sharing or transferring valence electrons Molecule – two or more atoms held together by chemical bonds Compound – a molecule composed of more than one element

12. Chemical Bonds Covalent Bond – sharing of a pair of electrons by two atoms Electronegativity – attraction of atom for electrons –The more electronegative an atom, the greater the pull its nucleus exerts on electrons © 2012 Pearson Education Inc.

13. Chemical Bonds Nonpolar Covalent Bonds –Shared electrons spend equal amounts of time around each nucleus –Atoms with similar electronegativities –No poles exist –Carbon atoms form four nonpolar covalent bonds with other atoms –Organic compounds contain carbon and hydrogen atoms © 2012 Pearson Education Inc.

14. Figure 2.5a-b Hydrogen and Oxygen Hydrogen (H) Hydrogen molecule (H 2 ) Oxygen molecule (O 2 ) Oxygen (O)

15. Figure 2.5c-d Methane and Formaldehyde Hydrogen (H) Carbon (C) Oxygen (O) 4 2 Methane (CH 4 ) or Formaldehyde (CH 2 O) or

16. Figure 2.6 Electronegativity values of selected elements H 2.1 Li 1.0 Be 1.5 Na 0.9 Mg 1.2 K 0.8 Ca 1.0 Sc 1.3 Ti 1.5 V 1.6 Cr 1.6 Mn 1.5 Fe 1.8 Co 1.8 Ni 1.8 Cu 1.9 Zn 1.6 Ga 1.6 Ge 1.8 As 2.0 Se 2.4 Br 2.8 Kr 0.0 Al 1.5 Si 1.8 P 2.1 S 2.5 Cl 3.0 Ar 0.0 B 2.0 C 2.5 N 3.0 O 3.5 F 4.0 Ne 0.0 He 0.0 Inert gases VII VI V IV III II I

17. Chemical Bonds Polar Covalent Bonds –Unequal sharing of electrons due to significantly different electronegativities –Most important polar covalent bonds involve hydrogen –Allow for hydrogen bonding © 2012 Pearson Education Inc.

18. Figure 2.7 Polar covalent bonding in a water molecule-overview

19. Chemical Bonds Ionic Bonds –Occur when two atoms with vastly different electronegativities come together –Atoms have either positive (cation) or negative (anion) charges –Cations and anions attract each other and form ionic bonds (no electrons shared) –Typically form crystalline ionic compounds known as salts © 2012 Pearson Education Inc.

20. Figure 2.8 The interaction of sodium and chlorine to form an ionic bond Electron lost Sodium atom Chlorine atom Attraction of opposite charges Sodium ion (Na  ) Chlorine ion (Cl  ) Formation of an ionic bond Sodium chloride (NaCl)

21. Figure 2.9 Dissociation of NaCI in water Hydrated sodium ion Hydrated chlorine ion When water surrounds ions in salt crystal, individual Na  and Cl  ions break away.

22. Chemical Bonds Hydrogen Bonds –Weak forces that combine with polar covalent bonds –Electrical attraction between partially charged H + and full or partial negative charge on same or different molecule –Weaker than covalent bonds but essential for life –Many help to stabilize 3-D shapes of large molecules © 2012 Pearson Education Inc.

23. Figure 2.10 Hydrogen bonds Cytosine Guanine Hydrogen bond

24. Table 2.2 Characteristics of Chemical Bonds

25. Chemical Reactions The making or breaking of chemical bonds Involve reactants and products Biochemistry involves chemical reactions of living things © 2012 Pearson Education Inc.

26. Chemical Reactions Synthesis Reactions –Involve the formation of larger, more complex molecules –Require energy (endothermic) –Most common type is dehydration synthesis –Water molecule formed –All the synthesis reactions in an organism are called anabolism © 2012 Pearson Education Inc.

27. Figure 2.11a Dehydration synthesis Dehydration synthesis Small molecule Energy Larger molecule

28. Chemical Reactions Decomposition Reactions –Break bonds within larger molecules to form smaller atoms, ions, and molecules –Release energy (exothermic) –Most common type is hydrolysis –Ionic components of water are added to products –The decomposition reactions in an organism are called catabolism © 2012 Pearson Education Inc.

29. Figure 2.11b Hydrolysis Hydrolysis Small molecule Energy Large molecule

30. Chemical Reactions Exchange Reactions –Involve breaking and forming covalent bonds, and involve endothermic and exothermic steps –Involve atoms moving from one molecule to another –Sum of all chemical reactions in an organism is called metabolism © 2012 Pearson Education Inc.

31. Water, Acids, Bases, and Salts Water –Most abundant substance in organisms –Most special characteristics due to two polar covalent bonds –Cohesive molecules – surface tension –Excellent solvent –Remains liquid across wide range of temperatures –Absorbs significant amounts of energy without changing temperature –Participates in many chemical reactions © 2012 Pearson Education Inc.

32. Figure 2.12 The cohesiveness of water-overview

33. Water, Acids, Bases, and Salts Acids and Bases –Dissociated by water into component cations and anions –Acid – dissociates into H + and one or more anions –Base – binds with H + when dissolved into water; some dissociate into cations and OH – –Metabolism requires balance of acids and bases –Concentration of H + in solution expressed using the pH scale –Buffers prevent drastic changes in internal pH © 2012 Pearson Education Inc.

34. Figure 2.13 Acids and bases-overview

35. Figure 2.14 The pH scale Extremely Acidic Extremely Basic Increasing concentration of H  Increasing concentration of OH  Battery acid Hydrochloric acid Lemon juice Beer, vinegar Wine, tomatoes Black coffee Urine, milk Pure water Seawater Baking soda Milk of magnesia Household ammonia Household bleach Oven cleaner Sodium hydroxide

36. Water, Acids, Bases, and Salts Salts –Compounds that dissociate in water into cations and anions other than H + and OH – –Cations and anions of salts are electrolytes –Create electrical differences between inside/outside of cell –Transfer electrons from one location to another –Form important components of many enzymes © 2012 Pearson Education Inc.

37. Organic Macromolecules Functional Groups –Contain carbon and hydrogen atoms –Functional groups of common arrangements –Macromolecules – large molecules used by all organisms –Lipids –Carbohydrates –Proteins –Nucleic acids –Monomers – basic building blocks of macromolecules © 2012 Pearson Education Inc.

38. Organic Macromolecules Lipids –Not composed of regular subunits, but are all hydrophobic –Four groups –Fats –Phospholipids –Waxes –Steroids © 2012 Pearson Education Inc.

39. Figure 2.15 Fats (triglycerides)-overview

40. Figure 2.16 Phospholipids-overview

41. Organic Macromolecules Waxes –Contain one long-chain fatty acid covalently linked to long-chain alcohol by ester bond –Completely insoluble in water; lack hydrophilic head © 2012 Pearson Education Inc.

42. Figure 2.17 Steroids-overview

43. Organic Macromolecules Carbohydrates –Organic molecules composed of carbon, hydrogen, and oxygen (CH 2 O) n –Functions –Long-term storage of chemical energy –Ready energy source –Part of backbones of nucleic acids –Converted to amino acids –Form cell wall –Involved in intracellular interactions between animal cells © 2012 Pearson Education Inc.

44. Organic Macromolecules Carbohydrates –Types –Monosaccharides –Disaccharides –Polysaccharides © 2012 Pearson Education Inc.

45. Figure 2.18 Monosaccharides-overview

46. Figure 2.19 Disaccharides-overview

47. Figure 2.20 Polysaccharides-overview

48. Organic Macromolecules Proteins –Mostly composed of carbon, hydrogen, oxygen, nitrogen, and sulfur –Functions –Structure –Enzymatic catalysis –Regulation –Transportation –Defense and offense © 2012 Pearson Education Inc.

49. Organic Macromolecules Amino Acids –The monomers that make up proteins –Most organisms use 21 amino acids in the synthesis of proteins –Side groups affect how amino acids interact and how a protein interacts with other molecules –A covalent bond (peptide bond) is formed between amino acids by dehydration synthesis reaction © 2012 Pearson Education Inc.

50. Figure 2.21 Amino acids-overview

51. Figure 2.22 Stereoisomers Mirror Left Right L -Serine (Ser) D -Serine (Ser)

52. Figure 2.23 Linkage of amino acids by peptide bonds Amino acid 1 Amino acid 2Dipeptide Peptide bond Carboxyl group Amino group Dehydration synthesis

53. Figure 2.24 Levels of protein structure-overview

54. Organic Macromolecules Nucleic Acids –DNA and RNA: the genetic material of organisms –RNA also acts as enzyme, binds amino acids, and helps form polypeptides © 2012 Pearson Education Inc.

55. Organic Macromolecules Nucleic Acids –Nucleotides and nucleosides –Nucleotides are monomers that make up nucleic acids –Composed of three parts –Phosphate –Pentose sugar – deoxyribose or ribose –One of five cyclic nitrogenous bases –Nucleosides are nucleotides lacking the phosphate © 2012 Pearson Education Inc.

56. Figure 2.25 Nucleotides-overview

57. Organic Macromolecules Nucleic Acids –Nucleic acid structure –Three H bonds form between C and G –Two H bonds form between T and A in DNA or between U and A in RNA –DNA is double stranded in most cells and viruses –Two strands are complementary –Two strands are antiparallel © 2012 Pearson Education Inc.

58. Figure 2.26 General nucleic acid structure-overview

59. Organic Macromolecules Nucleic Acids –Nucleic acid function –DNA is genetic material of all organisms and of many viruses –Carries instructions for synthesis of RNA and proteins; controls synthesis of all molecules in an organism © 2012 Pearson Education Inc.

60. Organic Macromolecules Nucleic Acids –Adenosine triphosphate (ATP) –Short-term, recyclable energy supply for cells –Phosphate-phosphate bonds of ATP are high- energy bonds © 2012 Pearson Education Inc.

61. Figure 2.27 ATP Adenine Ribose Adenosine (nucleoside) Adenosine monophosphate (AMP) Adenosine diphosphate Adenosine triphosphate