1. Medical Technology Department, Faculty of Science, Islamic University-Gaza MB M ICRO B IOLOGY Dr. Abdelraouf A. Elmanama Ph. D Microbiology 2008 Chapter 2 Chemical Principles

2. 2008 Chemistry Chemistry is the study of interactions between atoms and molecules. The atom is the smallest unit of matter that enters into chemical reactions. Atoms interact to form molecules.

3. 2008 Atoms are composed of Electrons: negatively charged particles Protons: positively charged particles Neutrons: uncharged particles The Study of Atoms

4. 2008 Protons and neutrons are in the nucleus. Electrons move around the nucleus. The Study of Atoms Figure 2.1

5. 2008 Each chemical element has a different number of protons. Isotopes of an element are atoms with different numbers of neutrons. Isotopes of oxygen are: Chemical Elements 16 8 O 17 8 O 18 8 O

6. 2008 Table 2.1

7. 2008 Electrons are arranged in electron shells corresponding to different energy levels. Electronic Configurations

8. 2008 Electronic Configurations Table 2.2.1

9. 2008 Electronic Configurations Table 2.2.2

10. 2008 Atoms combine to complete the outermost shell. The number of missing or extra electrons in this shell is the valence. How Atoms Form Molecules: Chemical Bonds

11. 2008 A compound contains different kinds of atoms. H 2 O The forces holding atoms in a compound are chemical bonds. How Atoms Form Molecules: Chemical Bonds

12. 2008 The number of protons and electrons is equal in an atom. Ions are atoms that have gained or lost electrons and are charged. How Atoms Form Molecules: Chemical Bonds Figure 2.2a

13. 2008 Ionic bonds are attractions between ions of opposite charge. One atom loses electrons and another gains electrons. Ionic Bonds Figure 2.2b

14. 2008 Covalent bonds form when two atoms share one or more pairs of electrons. Covalent Bonds Figure 2.3a

15. 2008 Hydrogen bonds form when a hydrogen atom covalently bonded to an O or N atom in another molecule. Hydrogen Bonds Figure 2.4

16. 2008 The sum of the atomic weights in a molecule is the molecular weight. One mole of a substance is its molecular weight in grams. Molecular Weight and Moles H 2 O 2H = 2  1 = 2 O = 16 MW= 18 1 mole weighs 18 g

17. 2008 Chemical reactions involve the making or breaking of bonds between atoms. A change in chemical energy occurs during a chemical reaction. Endergonic reactions absorb energy. Exergonic reactions release energy. Chemical Reactions

18. 2008 Occur when atoms, ions, or molecules combine to form new, larger molecules Anabolism is the synthesis of molecules in a cell. Synthesis Reactions A+BAB Atom, ion, or molecule A  Atom, ion, or molecule B New molecule AB

19. 2008 Occur when a molecule is split into smaller molecules, ions, or atoms. Catabolism is the decomposition reactions in a cell. Decomposition Reactions A+B AB Atom, ion, or molecule A  Atom, ion, or molecule B New molecule AB Breaks down into

20. 2008 Are part synthesis and part decomposition. Exchange Reactions NaCl+H2OH2O  NaOH+HCl

21. 2008 Can readily go in either direction. Each direction may need special conditions. Reversible Reactions A+B Water  AB Heat

22. 2008 Important Biological Molecules Organic compounds always contain carbon and hydrogen. Inorganic compounds typically lack carbon.

23. 2008 Polar molecule Inorganic Compounds: Water Figure 2.4a

24. 2008 Solvent Polar substances dissociate, forming solutes Inorganic Compounds: Water Figure 2.5

25. 2008 H + and OH  participate in chemical reactions Inorganic Compounds: Water

26. 2008 Hydrogen bonding between water molecules makes water a temperature buffer. Inorganic Compounds: Water Figure 2.4b

27. 2008 An acid is a substance that dissociates into one or more H +. HCl  H + + Cl  Acids, Bases, and Salts Figure 2.6a

28. 2008 A base is a substance that dissociates into one or more OH . NaOH  Na + + OH  Acids, Bases, and Salts Figure 2.6b

29. 2008 A salt is a substance that dissociates into cations and anions, neither of which is H + or OH . NaCl  Na + + Cl  Acids, Bases, and Salts Figure 2.6c

30. 2008 The amount of H + in a solution is expressed as pH. pH =  log[H + ] Increasing [H + ], increases acidity. Increasing [OH  ] increases alkalinity. Most organisms grow best between pH 6.5 and 8.5. Acid-Base Balance

31. 2008 Acid-Base Balance Figure 2.7

32. 2008 The chain of carbon atoms in an organic molecule is the carbon skeleton. Functional groups are responsible for most of the chemical properties of a particular organic compound. Organic Compounds

33. 2008 Table 2.3.1

34. 2008 Small organic molecules can combine into large macromolecules. Macromolecules are polymers consisting of many small repeating molecules. The smaller molecules are called monomers. Organic Compounds

35. 2008 Monomers join by dehydration synthesis or condensation reactions. Organic Compounds Figure 2.8

36. 2008 Are important for structure and as energy sources. Consist of C, H, and O with the formula (CH 2 O) n Carbohydrates Figure 2.8

37. 2008 Monosaccharides are simple sugars with 3 to 7 carbon atoms. Carbohydrates Figure 2.8

38. 2008 Disaccharides are formed when two monosaccharides are joined in a dehydration synthesis. Disaccharides can be broken down by hydrolysis. Carbohydrates Figure 2.8

39. 2008 Oligosaccharides consist of 2 to 20 monosaccharides. Polysaccharides consist of tens or hundreds of monosaccharides joined through dehydration synthesis. Starch, glycogen, dextran, and cellulose are polymers of glucose that are covalently bonded differently. Chitin is a polymer of two sugars repeating many times. Carbohydrates

40. 2008 Are the primary components of cell membranes. Consist of C, H, and O. Are nonpolar and insoluble in water. Lipids

41. 2008 Called fats or triglycerides contain glycerol and fatty acids; formed by dehydration synthesis. Unsaturated fats have one or more double bonds in the fatty acids. Simple lipids Figure 2.9c

42. 2008 Contain C, H, and O + P, N, or S. Membranes are made of phospholipids Complex lipids Figure 2.10a

43. 2008 Consist of four carbon rings, with an –OH group attached to one ring. Are part of membranes. Steroids Figure 2.11

44. 2008 Are essential in cell structure and function. Enzymes are proteins that speed chemical reactions. Transporter proteins move chemicals across membranes. Flagella are made of proteins. Some bacterial toxins are proteins. Proteins

45. 2008 Consist of subunits called amino acids. Proteins Table 2.4.1

46. 2008 Proteins Table 2.4.2

47. 2008 Exist in either of two stereoisomers, D or L. L -forms are most often found in nature. Amino Acids Figure 2.13

48. 2008 Peptide bonds between amino acids are formed by dehydration synthesis. Peptide Bonds Figure 2.14

49. 2008 The primary structure is a polypeptide chain Levels of Protein Structure Figure 2.15a

50. 2008 The secondary structure occurs when the amino acid chain folds and coils in a regular helix or pleats. Levels of Protein Structure Figure 2.15b

51. 2008 The tertiary structure occurs when the helix folds irregularly, forming disulfide bonds, hydrogen bonds, and ionic bonds between amino acids in the chain. Levels of Protein Structure Figure 2.15c

52. 2008 The quaternary structure consists of two or more polypeptides. Levels of Protein Structure Figure 2.15d

53. 2008 Conjugated proteins consist of amino acids and other organic molecules: Glycoproteins Nucleoproteins Lipoproteins Level of Protein Structure

54. 2008 Consist of nucleotides. Nucleotides consist of a: Pentose Phosphate group Nitrogen-containing (purine or pyrimidine) base Nucleic Acids Figure 2.16

55. 2008 Has deoxyribose Exists as a double helix A hydrogen bonds with T C hydrogen bonds with G DNA Figure 2.16

56. 2008 Has ribose Is single-stranded A hydrogen bonds with U C hydrogen bonds with G RNA Figure 2.17

57. 2008 Has ribose, adenine, and 3 phosphate groups ATP Figure 2.18

58. 2008 Is made by dehydration synthesis. Is broken by hydrolysis to liberate useful energy for the cell. ATP