1. Chemistry Comes Alive Part A2

2. The “stuff” of the universe Anything that has mass and takes up space
Matter
The “stuff” of the universe
Anything that has mass and takes up space
States of matter
Solid – has definite shape and volume
Liquid – has definite volume, changeable shape
Gas – has changeable shape and volume

3. The capacity to do work (put matter into motion) Types of energy
Kinetic – energy in action
Potential – energy of position; stored (inactive) energy

4. Chemical – stored in the bonds of chemical substances
Forms of Energy
Chemical – stored in the bonds of chemical substances
Electrical – results from the movement of charged particles
Mechanical – directly involved in moving matter
Radiant or electromagnetic – energy traveling in waves (i.e., visible light, ultraviolet light, and X rays)

5. Energy Form Conversions
Energy is easily converted from one form to another
During conversion, some energy is “lost” as heat

6. Atoms – more-or-less identical building blocks for each element
Composition of Matter
Elements – unique substances that cannot be broken down by ordinary chemical means
Atoms – more-or-less identical building blocks for each element
Atomic symbol – one- or two-letter chemical shorthand for each element

7. Properties of Elements
Each element has unique physical and chemical properties
Physical properties – those detected with our senses
Chemical properties – pertain to the way atoms interact with one another

8. Major Elements of the Human Body
Oxygen (O)
Carbon (C)
Hydrogen (H)
Nitrogen (N)
96% of body matter

9. Lesser and Trace Elements of the Human Body
Lesser elements make up 3.9% of the body and include:
Calcium (Ca), phosphorus (P), potassium (K), sulfur (S), sodium (Na), chlorine (Cl), magnesium (Mg), iodine (I), and iron (Fe)
Trace elements make up less than 0.01% of the body
They are required in minute amounts, and are found as part of enzymes

10. The nucleus consists of neutrons and protons
Atomic Structure
The nucleus consists of neutrons and protons
Neutrons – have no charge and a mass of one atomic mass unit (amu)
Protons – have a positive charge and a mass of 1 amu
Electrons are found orbiting the nucleus
Electrons – have a negative charge and 1/2000 the mass of a proton (0 amu)

11. Models of the Atom
Planetary Model – electrons move around the nucleus in fixed, circular orbits
Orbital Model – regions around the nucleus in which electrons are most likely to be found

12. Models of the Atom
Figure 2.1

13. Identification of Elements
Atomic number – equal to the number of protons
Mass number – equal to the mass of the protons and neutrons
Atomic weight – average of the mass numbers of all isotopes
Isotope – atoms with same number of protons but a different number of neutrons
Radioisotopes – atoms that undergo spontaneous decay called radioactivity

14. Identification of Elements
Figure 2.2

15. Identification of Elements
Figure 2.3

16. Molecules and Compounds
Molecule – two or more atoms held together by chemical bonds
Compound – two or more different kinds of atoms chemically bonded together

17. Mixtures and Solutions
Mixtures – two or more components physically intermixed (not chemically bonded)
Solutions – homogeneous mixtures of components
Solvent – substance present in greatest amount
Solute – substance(s) present in smaller amounts

18. Concentration of Solutions
Percent, or parts per 100 parts
Molarity, or moles per liter (M)
A mole of an element or compound is equal to its atomic or molecular weight (sum of atomic weights) in grams

19. Colloids and Suspensions
Colloids, or emulsions, are heterogeneous mixtures whose solutes do not settle out
Example: Jello and Cytosol
Suspensions are heterogeneous mixtures with visible solutes that tend to settle out
Example: Blood

20. Mixtures Compared with Compounds
No chemical bonding takes place in mixtures
Most mixtures can be separated by physical means
Mixtures can be heterogeneous or homogeneous
Compounds cannot be separated by physical means
All compounds are homogeneous

21. Electron shells, or energy levels, surround the nucleus of an atom
Chemical Bonds
Electron shells, or energy levels, surround the nucleus of an atom
Bonds are formed using the electrons in the outermost energy level
Valence shell – outermost energy level containing chemically active electrons
Octet rule – except for the first shell which is full with two electrons, atoms interact in a manner to have eight electrons in their valence shell

22. Chemically Inert Elements
Inert elements have their outermost energy level fully occupied by electrons
Figure 2.4a

23. Chemically Reactive Elements
Reactive elements do not have their outermost energy level fully occupied by electrons
Figure 2.4b

24. Types of Chemical Bonds
Ionic
Covalent
Hydrogen

25. Ions are charged atoms resulting from the gain or loss of electrons
Ionic Bonds
Ions are charged atoms resulting from the gain or loss of electrons
Anions have gained one or more electrons
Cations have lost one or more electrons

26. Formation of an Ionic Bond
Ionic bonds form between atoms by the transfer of one or more electrons
Ionic compounds form crystals instead of individual molecules
Example: NaCl (sodium chloride)

27. Formation of an Ionic Bond
Figure 2.5a

28. Formation of an Ionic Bond
Figure 2.5b

29. Covalent bonds are formed by the sharing of two or more electrons
Electron sharing produces molecules

30. Single Covalent Bonds
Figure 2.6a

31. Double Covalent Bonds
Figure 2.6b

32. Triple Covalent Bonds
Figure 2.6c

33. Polar and Nonpolar Molecules
Electrons shared equally between atoms produce nonpolar molecules
Unequal sharing of electrons produces polar molecules
Atoms with six or seven valence shell electrons are electronegative
Atoms with one or two valence shell electrons are electropositive

34. Comparison of Ionic, Polar Covalent, and Nonpolar Covalent Bonds
Figure 2.8

35. Too weak to bind atoms together Common in dipoles such as water
Hydrogen Bonds
Too weak to bind atoms together
Common in dipoles such as water
Responsible for surface tension in water
Important as intramolecular bonds, giving the molecule a three-dimensional shape

36. Hydrogen Bonds
Figure 2.9

37. Occur when chemical bonds are formed, rearranged, or broken
Chemical Reactions
Occur when chemical bonds are formed, rearranged, or broken
Are written in symbolic form using chemical equations
Chemical equations contain:
Number and type of reacting substances, and products produced
Relative amounts of reactants and products

38. Examples of Chemical Reactions

39. Patterns of Chemical Reactions
Combination reactions: Synthesis reactions which always involve bond formation
A + B  AB
Decomposition reactions: Molecules are broken down into smaller molecules
AB  A + B
Exchange reactions: Bonds are both made and broken
AB + C  AC + B

40. Oxidation-Reduction (Redox) Reactions
Reactants losing electrons are electron donors and are oxidized
Reactants taking up electrons are electron acceptors and become reduced
Therefore, both decomposition and electron exchange occur.

41. Energy Flow in Chemical Reactions
Exergonic reactions – reactions that release energy
Usually when a bond is broken.
Endergonic reactions – reactions whose products contain more potential energy than did its reactants

42. Reversibility in Chemical Reactions
All chemical reactions are theoretically reversible
A + B  AB
AB  A + B
If neither a forward nor reverse reaction is dominant, chemical equilibrium is reached

43. Factors Influencing Rate of Chemical Reactions
Temperature – chemical reactions proceed quicker at higher temperatures
Particle size – the smaller the particle the faster the chemical reaction
Concentration – higher reacting particle concentrations produce faster reactions
Catalysts – increase the rate of a reaction without being chemically changed
Enzymes – biological catalysts

44. Chemistry Comes Alive: Biochemistry Part B2

45. Inorganic compounds Organic compounds Biochemistry
Do not contain carbon
Water, salts, and many acids and bases
Organic compounds
Contain carbon, are covalently bonded, and are often large

46. Inorganic: Water
High heat capacity – absorbs and releases large amounts of heat before changing temperature
High heat of vaporization – changing from a liquid to a gas requires large amounts of heat
Polar solvent properties – dissolves ionic substances, forms hydration layers around large charged molecules, and serves as the body’s major transport medium

47. Inorganic: Water
Reactivity – is an important part of hydrolysis and dehydration synthesis reactions
Cushioning – resilient cushion around certain body organs

48. Contain cations other than H+ and anions other than OH–
Inorganic: Salts
Inorganic compounds
Contain cations other than H+ and anions other than OH–
Are electrolytes; they conduct electrical currents

49. Inorganic: Acids and Bases
Acids release H+ and are therefore proton donors
HCl  H+ + Cl –
Bases release OH– and are proton acceptors
NaOH  Na+ + OH–

50. Inorganic: Acid-Base Concentration (pH)
Acidic solutions have higher H+ concentration and therefore a lower pH
Alkaline solutions have lower H+ concentration and therefore a higher pH
Neutral solutions have equal H+ and OH– concentrations

51. Inorganic: Acid-Base Concentration (pH)
Acidic: pH 0–6.99
Basic: pH 7.01–14
Neutral: pH 7.00
Figure 2.12

52. Systems that resist abrupt and large swings in the pH of body fluids
Inorganic: Buffers
Systems that resist abrupt and large swings in the pH of body fluids
Carbonic acid-bicarbonate system
Carbonic acid dissociates, reversibly releasing bicarbonate ions and protons
The chemical equilibrium between carbonic acid and bicarbonate resists pH changes in the blood

53. Organic Compounds
Molecules unique to living systems contain carbon and hence are organic compounds
They include:
Carbohydrates
Lipids
Proteins
Nucleic Acids

54. Organic: Carbohydrates
Contain carbon, hydrogen, and oxygen
Their major function is to supply a source of cellular food
Examples:
Monosaccharides or simple sugars
Figure 2.13a

55. Organic: Carbohydrates
Disaccharides or double sugars
Figure 2.13b

56. Organic: Carbohydrates
Polysaccharides or polymers of simple sugars
Figure 2.13c

57. Organic: Lipids
Contain C, H, and O, but the proportion of oxygen in lipids is less than in carbohydrates
Examples:
Neutral fats or triglycerides
Phospholipids
Steroids
Eicosanoids

58. Organic: Neutral Fats (Triglycerides)
Composed of three fatty acids bonded to a glycerol molecule
Figure 2.14a

59. Organic: Other Lipids
Phospholipids – modified triglycerides with two fatty acid groups and a phosphorus group
Figure 2.14b

60. Organic: Other Lipids
Steroids – flat molecules with four interlocking hydrocarbon rings
Eicosanoids – 20-carbon fatty acids found in cell membranes
Figure 2.14c

61. Organic: Representative Lipids Found in the Body
Neutral fats – found in subcutaneous tissue and around organs
Phospholipids – chief component of cell membranes
Steroids – cholesterol, bile salts, vitamin D, sex hormones, and adrenal cortical hormones
Fat-soluble vitamins – vitamins A, E, and K
Eicosanoids – prostaglandins, leukotriens, and thromboxanes
Lipoproteins – transport fatty acids and cholesterol in the bloodstream

62. Organic: Amino Acids
Building blocks of protein, containing an amino group and a carboxyl group
Amino acid structure

63. Organic: Amino Acids
Figure 2.15a-c

64. Organic: Amino Acids
Figure 2.15d, e

65. Organic: Protein
Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds
Figure 2.16

66. Organic: Structural Levels of Proteins
Primary – amino acid sequence
Secondary – alpha helices or beta pleated sheets

67. Organic: Structural Levels of Proteins
Tertiary – superimposed folding of secondary structures
Quaternary – polypeptide chains linked together in a specific manner

68. Organic: Structural Levels of Proteins
Figure 2.17a-c

69. Organic: Structural Levels of Proteins
Figure 2.17d, e

70. Organic: Fibrous and Globular Proteins
Fibrous proteins
Extended and strandlike proteins
Examples: keratin, elastin, collagen, and certain contractile fibers
Globular proteins
Compact, spherical proteins with tertiary and quaternary structures
Examples: antibodies, hormones, and enzymes

71. Organic: Protein Denuaturation
Reversible unfolding of proteins due to drops in pH and/or increased temperature
Figure 2.18a

72. Organic: Protein Denuaturation
Irreversibly denatured proteins cannot refold and are formed by extreme pH or temperature changes
Figure 2.18b

73. Organic: Molecular Chaperones (Chaperonins)
Help other proteins to achieve their functional three-dimensional shape
Maintain folding integrity
Assist in translocation of proteins across membranes
Promote the breakdown of damaged or denatured proteins

74. Organic: Characteristics of Enzymes
Most are globular proteins that act as biological catalysts
Holoenzymes consist of an apoenzyme (protein) and a cofactor (usually an ion)
Enzymes are chemically specific
Frequently named for the type of reaction they catalyze
Enzyme names usually end in -ase
Lower activation energy

75. Organic: Characteristics of Enzymes
Figure 2.19

76. Organic: Mechanism of Enzyme Action
Enzyme binds with substrate
Product is formed at a lower activation energy
Product is released

77. Organic: Mechanism of Enzyme Action
Active site
Amino acids 1
Enzyme (E)
Substrates (s)
Enzyme-substrate complex (E–S)
H20
Free enzyme (E) 2 3
Peptide bond
Internal rearrangements leading to catalysis
Dipeptide product (P)
Figure 2.20

78. Organic: Nucleic Acids
Composed of carbon, oxygen, hydrogen, nitrogen, and phosphorus
Their structural unit, the nucleotide, is composed of N-containing base, a pentose sugar, and a phosphate group
Five nitrogen bases contribute to nucleotide structure – adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U)
Two major classes – DNA and RNA

79. Organic: Deoxyribonucleic Acid (DNA)
Double-stranded helical molecule found in the nucleus of the cell
Replicates itself before the cell divides, ensuring genetic continuity
Provides instructions for protein synthesis

80. Organic: Structure of DNA
Figure 2.21a

81. Organic: Structure of DNA
Figure 2.21b

82. Organic: Ribonucleic Acid (RNA)
Single-stranded molecule found in both the nucleus and the cytoplasm of a cell
Uses the nitrogenous base uracil instead of thymine
Three varieties of RNA: messenger RNA, transfer RNA, and ribosomal RNA

83. Organic: Adenosine Triphosphate (ATP)
Source of immediately usable energy for the cell
Adenine-containing RNA nucleotide with three phosphate groups

84. Organic: Adenosine Triphosphate (ATP)
Figure 2.22

85. Organic: How ATP Drives Cellular Work
Figure 2.23