1. Chapter 2
Chemical Principles

2. Q&A
A Salmonella bacterium releases a regulatory molecule containing amino acids and phosphate that causes a human cell’s cytoskeleton to change shape, thereby allowing the bacterium to enter the cell. What type of chemical is this regulatory molecule?

3. The Structure of Atoms
2-1 Describe the structure of an atom and its relation to the physical properties of elements.

4. The Structure of Atoms
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

5. The Structure of Atoms Atoms are composed of
Electrons: Negatively charged particles
Protons: Positively charged particles
Neutrons: Uncharged particles

6. The Structure of Atoms Protons and neutrons are in the nucleus
Electrons move around the nucleus
Figure 2.1

7. Chemical Elements
Each chemical element has a different number of protons
Isotopes of an element are atoms with different numbers of neutrons. Isotopes of oxygen:

8. The Elements of Life
Table 2.1

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

10. Electronic Configurations
Table 2.2

11. Electronic Configurations
Table 2.2

12. How does C differ from C? What is the atomic number of each carbon atom? The atomic weight? 2-1

13. How Atoms Form Molecules
2-2 Define ionic bond, covalent bond, hydrogen bond, molecular weight, and mole.

14. How Atoms Form Molecules
Atoms combine to complete the outermost shell
The number of missing or extra electrons in this shell is known as the valence
Molecules hold together because the valence electrons of the combining atoms form attractive forces, called chemical bonds, between the atomic nuclei

15. Chemical Bonds
A compound contains different kinds of atoms H2O

16. Ionic Bonds The number of protons and electrons is equal in an atom
Ions are charged atoms that have gained or lost electrons

17. Ionic Bonds
Figure 2.2a

18. Ionic Bonds
Ionic bonds are attractions between ions of opposite charge. One atom loses electrons, and another gains electrons.

19. Ionic Bonds
Figure 2.2b

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

21. Covalent Bonds
Figure 2.3b

22. Hydrogen Bonds
Hydrogen bonds form when a hydrogen atom that is covalently bonded to an O or N atom is attracted to another N or O atom in another molecule
Figure 2.4

23. Molecular Weight and Moles
The sum of the atomic weights in a molecule is the molecular weight
One mole of a substance is its molecular weight in grams
H2O
2H = 2  1 = 2
O = 16
MW = 18
1 mole weighs 18g

24. Differentiate an ionic bond from a covalent bond. 2-2

25. Chemical Reactions
2-3 Diagram three basic types of chemical reactions.

26. Chemical Reactions
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

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

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

29. Exchange Reactions NaCl + H2O NaOH HCl 
Are part synthesis and part decomposition
NaCl +
H2O
NaOH
HCl 

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

31. This chemical reaction below is used to remove chlorine from water.
What type of reaction is it? 2-3
HClO + Na2SO3  Na2SO4 + HCl

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

33. Inorganic Compounds
2-4 List several properties of water that are important to living systems.
2-5 Define acid, base, salt, and pH.

34. Water Inorganic Polar molecule Solvent
Polar substances dissociate,forming solutes
Figure 2.4a

35. Water
Figure 2.5

36. Water H+ and OH participate in chemical reactions
R—R + H2O  R—OH + H—R
Maltose + H2O  Glucose + Glucose

37. Water Maltose + H2O  Glucose + Glucose Glucose C6H12O6
Total C12H24O12
Maltose C12H22O11
The difference is:

38. Water
H bonds absorb heat
Makes water a temperature buffer
Figure 2.4b

39. Acids, Bases, and Salts
Figure 2.6

40. Acids Substances that dissociate into one or more H+ HCl  H+ + Cl
Figure 2.6a

41. Bases Substances that dissociate into one or more OH NaOH  Na+ + OH
Figure 2.6b

42. Salts
Substances that dissociate into cations and anions, neither of which is H+ or OH NaCl  Na+ + Cl
Figure 2.6c

43. Acid-Base Balance 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

44. The pH Scale
Figure 2.7

45. Why is the polarity of a water molecule important? 2-4
Antacids neutralize acid by the following reaction Identify the acid, base, and salt. 2-5
Mg(OH)2 + 2HCl  MgCl2 + H2O

46. Organic Compounds 2-6 Distinguish organic and inorganic compounds.
2-7 Define functional group.

47. Structure and Chemistry
The chain of carbon atoms in an organic molecule is the carbon skeleton

48. Structure and Chemistry
Functional groups are responsible for most of the chemical properties of a particular organic compound.

49. Functional Groups
Table 2.3

50. Functional Groups
Table 2.3

51. Functional Groups
Identify the functional groups in an amino acid:

52. Define organic. 2-6
Add the appropriate functional group(s) to the ethyl group below to produce each of the following compounds: ethanol, acetic acid, acetaldehyde, ethanolamine, diethyl ether. 2-7

53. Organic Compounds 2-8 Identify the building blocks of carbohydrates.
2-9 Differentiate simple lipids, complex lipids, and steroids.
2-10 Identify the building blocks and structure of proteins.
2-11 Identify the building blocks of nucleic acids.
2-12 Describe the role of ATP in cellular activities.

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

55. Polymers
Monomers join by dehydration synthesis or condensation reactions

56. Carbohydrates Cell structures and energy sources
Consist of C, H, and O with the formula (CH2O)n
Monosaccharides are simple sugars with 3 to 7 carbon atoms

57. Carbohydrates
Disaccharides are formed when 2 monosaccharides are joined in a dehydration synthesis
Disaccharides can be broken down by hydrolysis

58. Dehydration Synthesis and Hydrololysis
Figure 2.8

59. Carbohydrates 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 2 sugars repeating many times

60. Give an example of a monosaccharide, a disaccharide, and a polysaccharide. 2-8

61. Lipids Primary components of cell membranes Consist of C, H, and O
Are nonpolar and insoluble in water

62. Simple Lipids Fats or triglycerides
Contain glycerol and fatty acids; formed by dehydration synthesis

63. Structural Formulas of Simple Lipids
Figure 2.9c

64. Simple Lipids Saturated fat: No double bonds
Unsaturated fat: One or more double bonds in the fatty acids
cis: H atoms on the same side of the double bond
trans: H atoms on opposite sides of the double bond

65. Simple Lipids
Figure 2.9c

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

67. Steroids 4 carbon rings with an –OH group attached to one ring
Part of membranes
Figure 2.11

68. How do simple lipids differ from complex lipids? 2-9

69. Proteins 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

70. Amino Acids Proteins consist of subunits called amino acids
Figure 2.12

71. Amino Acids Exist in either of two stereoisomers: D or L.
L-forms are most often found in nature.

72. Amino Acids
Figure 2.13

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

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

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

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

77. Levels of Protein Structure
Figure 2.15c

78. Levels of Protein Structure
The quaternary structure consists of 2 or more polypeptides.
Figure 2.15d

79. Protein Structure
Figure 2.15

80. Levels of Protein Structure
Conjugated proteins consist of amino acids and other organic molecules
Glycoproteins
Nucleoproteins
Lipoproteins

81. Q&A
A Salmonella bacterium releases a regulatory molecule containing amino acids and phosphate that causes a human cell’s cytoskeleton to change shape, thereby allowing the bacterium to enter the cell. What type of chemical is this regulatory molecule?

82. What two functional groups are in all amino acids? 2-10

83. Nucleic Acids Consist of nucleotides Nucleotides consist of a
Pentose
Phosphate group
Nitrogen-containing (purine or pyrimidine) base
Nucleosides consist of a
Nitrogen-containing base

84. Nucleic Acids
Figure 2.16

85. DNA Deoxyribonucleic acid Has deoxyribose Exists as a double helix
A hydrogen bonds with T
C hydrogen bonds with G

86. DNA
Figure 2.16

87. RNA Ribonucleic acid Has ribose Is single-stranded
A hydrogen bonds with U
C hydrogen bonds with G

88. RNA
Figure 2.17

89. ATP Adenosine triphosphate
Has ribose, adenine, and 3 phosphate groups.

90. The Structure of ATP
Figure 2.18

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

92. Which can provide more energy for a cell and why: ATP or ADP? 2-12