1. Chemistry of microbiology Chapter 2

2. Atoms Matter – anything that takes up space and has mass
Atoms – the smallest chemical units of matter

3. Atomic Structure
Electrons – negatively charged subatomic particles circling a nucleus
Nucleus – contains neutrons and protons
Neutrons – uncharged particles
Protons – positively charged particles

4. Atomic Structure
Figure 2.1

5. Atomic Structure Element – composed of a single type of atom
Atomic number – equals the number of protons in the nucleus
Atomic mass (atomic weight) – sum of masses of protons, neutrons, and electrons 12 C 6 23 Na 11

6. Isotopes
Elements that differ in number of neutrons in their nuclei are isotopes
Stable isotopes
Unstable isotopes
Release energy during radioactive decay

7. 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

8. Electron Configurations
Figure 2.3b

9. Figure 2.4

10. Chemical Bonds
Outer electron shells are stable when contain eight electrons
Valence – combining capacity of an atom
Positive if has electrons to give up
Negative if has spaces to fill
Chemical bonds – when 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

11. Chemical Bonds Principal types of chemical bonds Covalent
Nonpolar covalent bonds
Polar covalent bonds
Ionic bonds
Hydrogen bonds – weak forces that combine with polar covalent bonds

12. Covalent 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

13. Nonpolar Covalent Bonds
Atoms with similar electronegativities
Shared electrons spend equal amount of time around each nucleus
No poles exist
Carbon atoms critical to life; forms four nonpolar covalent bonds with other atoms
Organic compounds contain carbon and hydrogen atoms

14. Nonpolar Covalent Bonds
Figure 2.5a-b

15. Nonpolar Covalent Bonds
Figure 2.5c-d

16. Polar Covalent Bonds
Unequal sharing of electrons due to significantly different electronegativities
Most important polar covalent bonds involve hydrogen
Allows for hydrogen bonding

17. Polar Covalent Bonds
Water
Figure 2.7a

18. Ionic Bonds Formed by a transfer of electrons
Creating ions: positive (cation) and negative (anion)
Cations and anions attract each other and form ionic bonds (no electrons shared)
Typically form crystalline ionic compounds known as salts

19. Hydrogen Bonds
Electrical attraction between partially charged H+ and full or partial negative charge on different region of same molecule or another molecule
Weaker than covalent bonds but essential for life
Many help to stabilize 3-D shapes of large molecules

20. Chemical Reactions The making or breaking of chemical bonds
Involve reactant(s) and product(s)
A + B  C + D Q + R  S T U + V
Three categories of chemical reactions
Synthesis reactions
Decomposition reactions
Exchange reactions

21. Synthesis Reactions
Involve the formation of larger, more complex molecules
Important type – dehydration synthesis
Water molecule formed
Require energy (endothermic)
All the synthesis reactions in an organism are called anabolism

22. Decomposition Reactions
Break bonds within larger molecules to form smaller atoms, ions, and molecules
Release energy (exothermic)
Common type – hydrolysis
Bond broken as the ionic components of water are added to products
All the decomposition reactions in an organism are called catabolism

23. Exchange Reactions
Involve breaking and forming covalent bonds, and involve endothermic and exothermic steps
Atoms moved from one molecule to another
Sum of all chemical reactions in an organism is called metabolism

24. Water Most abundant substance in organisms
Most of its special characteristics due to two polar covalent bonds
Water molecules are cohesive – surface tension
Excellent solvent
Remains liquid across wide range of temperatures
Can absorb significant amounts of energy without changing temperature
Participates in many chemical reactions

26. Acids and Bases Dissociated by water into component cations and anions
Acid – dissociates into one or more H+ and one or more anions
Base – binds with H+ when dissolved into water; some dissociate into cations and OH-
Metabolism requires relatively constant balance of acids and bases
Concentration of H+ in solution is expressed using the pH scale
Buffers prevent drastic changes in internal pH

27. Salts
Compounds that dissociate in water into cations and anions other than H+ and OH- (NaCl -----Na+ + Cl- )
Cations and anions of salts are electrolytes
Create electrical differences between inside and outside of cell
Transfer electrons from one location to another
Important components of many enzymes

28. Organic Macromolecules
Contain carbon and hydrogen atoms
Atoms often appear in certain common arrangements – functional groups
Macromolecules
Lipids
Carbohydrates
Proteins
Nucleic Acids
Monomers – basic building blocks of macromolecules

29. Lipids Not composed of regular subunits, but are all hydrophobic Types
Fats and oils (triglycerides)
Phospholipids
Steroids

30. Fats
Figure 2.15a

31. Fats
Figure 2.15b

32. Phospholipids
Figure 2.16a

33. Phospholipids
Figure 2.16b-c

34. Steroids
Figure 2.17a-b

35. Carbohydrates
Organic molecules composed of carbon, hydrogen, and oxygen (CH2O)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 intercellular interactions between animal cells

36. Carbohydrates
Types
Monosaccharides
Disaccharides
Polysaccharides

37. Monosaccharides

38. Disaccharides

39. Polysaccharides
Cellulose
Amylose (starch)
Glycogen

40. Proteins
Mostly composed of carbon, hydrogen, oxygen, nitrogen, and sulfur
Functions
Structure
Enzymatic catalysis
Regulation
Transportation
Defense and offense

41. Amino Acids The monomers that make up proteins
Most organisms use only amino acids in the synthesis of proteins
Side groups affect how amino acids interact with one another and how a protein interacts with other molecules
A covalent bond (peptide bond) formed between amino acids by dehydration synthesis reaction

42. Amino Acids and the Peptide Bond

43. Protein Structure

44. Another Look at Protein Structure

45. Primary structure

46. Secondary structure

47. Tertiary structure

48. Quaternary structure

50. Nucleic Acids DNA and RNA: the genetic material of organisms
RNA helps form polypeptides

51. Nucleotides The monomers that make up nucleic acids
Composed of three parts
Phosphate
Pentose sugar – deoxyribose or ribose
One of five cyclic nitrogenous bases
Adenine (A)
Guanine (G)
Cytosine (C)
Thymine (T)
Uracil (U)

52. Figure 2.25a-b

53. Nucleic Acid Structure
Figure 2.26a-b

54. Nucleic Acid Structure
H bonds form between C and G and between T and A in DNA
U and A in RNA
DNA is double stranded in most cells and viruses
Two strands are complementary
Two strands are antiparallel

55. 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

56. Table 2.5

57. ATP
Figure 2.27