1. Chapter 2 Atomic Structure Chemical Bonds Chemical Reactions
Carbohydrates – Lipids
Proteins
Amino Acids
Enzymes
DNA

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

4. 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. 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)

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)

10. Lesser and Trace Elements of the Human Body
Trace elements make up less than 0.01% of the body
They are required in minute amounts, and are found as part of enzymes

11. 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)

12. 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

14. 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

15. Identification of Elements
Isotope – atoms with same number of protons but a different number of neutrons
Radioisotopes – atoms that undergo spontaneous decay called radioactivity

16. Identification of Elements: Atomic Structure
Figure 2.2

17. Identification of Elements: Isotopes of Hydrogen
Figure 2.3

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

19. 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

20. 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

21. Colloids and Suspensions
Colloids (emulsions) – heterogeneous mixtures whose solutes do not settle out
Suspensions – heterogeneous mixtures with visible solutes that tend to settle out

22. 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

23. 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

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

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

26. Types of Chemical Bonds
Ionic
Covalent
Hydrogen

27. 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

28. 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)

29. Formation of an Ionic Bond
Figure 2.5a

30. Formation of an Ionic Bond
Figure 2.5b

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

32. Single Covalent Bonds
Figure 2.7a

33. Double Covalent Bonds
Figure 2.7b

34. Triple Covalent Bonds
Figure 2.7c

35. 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

36. Comparison of Ionic, Polar Covalent, and Nonpolar Covalent Bonds
Figure 2.9

37. 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
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Hydrogen Bonds

38. Hydrogen Bonds
Figure 2.10a

39. Chemical Reactions
Occur when chemical bonds are formed, rearranged, or broken
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

40. Examples of Chemical Reactions

41. Patterns of Chemical Reactions
Combination reactions: Synthesis reactions which always involve bond formation
A + B  AB

42. Patterns of Chemical Reactions
Decomposition reactions: Molecules are broken down into smaller molecules
AB  A + B

43. Patterns of Chemical Reactions
Exchange reactions: Bonds are both made and broken
AB + C  AC + B

44. Oxidation-Reduction (Redox) Reactions
Reactants losing electrons are electron donors and are oxidized
Reactants taking up electrons are electron acceptors and become reduced

45. Energy Flow in Chemical Reactions
Exergonic reactions – reactions that release energy
Endergonic reactions – reactions whose products contain more potential energy than did its reactants

46. 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

47. 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

48. Factors Influencing Rate of Chemical Reactions
Catalysts – increase the rate of a reaction without being chemically changed
Enzymes – biological catalysts

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

50. Properties of 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

51. Properties of Water
Reactivity – is an important part of hydrolysis and dehydration synthesis reactions
Cushioning – resilient cushion around certain body organs
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InterActive Physiology®: Fluid, Electrolyte, and Acid/Base Balance: Introduction to Body Fluids

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

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

54. 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

55. Acid-Base Concentration (pH)
Acidic: pH 0–6.99
Basic: pH 7.01–14
Neutral: pH 7.00
Figure 2.13

56. 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
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InterActive Physiology®: Fluid, Electrolyte, and Acid/Base Balance: Acid/Base Homeostasis

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

58. Carbohydrates Contain carbon, hydrogen, and oxygen
Their major function is to supply a source of cellular food
Examples:
Monosaccharides or simple sugars
Figure 2.14a

59. Carbohydrates Disaccharides or double sugars PLAY Disaccharides
Figure 2.14b

60. Carbohydrates Polysaccharides or polymers of simple sugars PLAY
Figure 2.14c

61. 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
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Fats

62. Neutral Fats (Triglycerides)
Composed of three fatty acids bonded to a glycerol molecule
Figure 2.15a

63. 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

64. Other Lipids
Phospholipids – modified triglycerides with two fatty acid groups and a phosphorus group
Figure 2.15b

65. Representative Lipids Found in the Body
Fat-soluble vitamins – vitamins A, E, and K
Eicosanoids – prostaglandins, leukotrienes, and thromboxanes
Lipoproteins – transport fatty acids and cholesterol in the bloodstream

66. Other Lipids
Steroids – flat molecules with four interlocking hydrocarbon rings
Eicosanoids – 20-carbon fatty acids found in cell membranes
Figure 2.15c

67. Amino Acids
Building blocks of protein, containing an amino group and a carboxyl group
Amino group NH2
Carboxyl groups COOH

68. Amino Acids
Figure 2.16a–c

69. Amino Acids
Figure 2.16d, e

70. Protein
Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds
Figure 2.17

71. Protein
Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds
Amino acid
Dehydration
synthesis
Hydrolysis
Dipeptide
Peptide bond + N H C R O
H2O OH
Figure 2.17

72. Protein
Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds
Amino acid + N H C R O OH
Figure 2.17

73. Protein
Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds
Amino acid
Dehydration
synthesis + N H C R O
H2O OH
Figure 2.17

74. Protein
Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds
Amino acid
Dehydration
synthesis
Dipeptide
Peptide bond + N H C R O
H2O OH
Figure 2.17

75. Protein
Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds
Dipeptide
Peptide bond N H C R O OH
Figure 2.17

76. Protein
Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds
Hydrolysis
Dipeptide
Peptide bond
H2O N H C R O OH
Figure 2.17

77. Protein
Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds
Amino acid
Hydrolysis
Dipeptide
Peptide bond + N H C R O
H2O OH
Figure 2.17

78. Protein
Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds
Amino acid
Dehydration
synthesis
Hydrolysis
Dipeptide
Peptide bond + N H C R O
H2O OH
Figure 2.17

79. Structural Levels of Proteins
Primary – amino acid sequence
Secondary – alpha helices or beta pleated sheets
Tertiary – superimposed folding of secondary structures
Quaternary – polypeptide chains linked together in a specific manner
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80. Structural Levels of Proteins
Figure 2.18a–c

81. Structural Levels of Proteins
Figure 2.18b,d,e

82. Fibrous and Globular Proteins
Fibrous proteins (a.k.a. structural proteins)
Extended and strand-like proteins – usually only secondary structure
Rope-like side by side fibers make then great “building materials”
Insoluble in water
Examples: keratin, elastin, collagen, and certain contractile fibers of muscle

83. Fibrous and Globular Proteins
Globular proteins (a.k.a. functional proteins)
Compact, spherical proteins with tertiary and quaternary structures
Examples: antibodies, hormones, and enzymes

84. Protein Denuaturation
Reversible unfolding of proteins due to drops in pH and/or increased temperature
Figure 2.19a

85. Protein Denuaturation
Irreversibly denatured proteins cannot refold and are formed by extreme pH or temperature changes
Figure 2.19b

86. Molecular Chaperones (Chaperonins)
Help other proteins to achieve their functional three-dimensional shape
Maintain folding integrity
Assist in translocation of proteins and some metal ions (Cu, Fe, Zn) across membranes
Promote the breakdown of damaged or denatured proteins

87. Characteristics of Enzymes
Most are globular proteins that act as biological catalysts – they don’t make reactions happen, they only increase the speed.
Holoenzymes consist of an apoenzyme (protein) and a cofactor (usually an ion Cu, Fe, B-Vits, etc.)
Enzymes are chemically specific

88. Characteristics of Enzymes
Frequently named for the type of reaction they catalyze (e.g. hydrolases – add water hydolysis)
Enzyme names usually end in -ase
Lower activation energy

89. Characteristics of Enzymes
Figure 2.20

90. Mechanism of Enzyme Action
Enzyme binds with substrate
Product is formed at a lower activation energy
Product is released
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How Enzymes Work

91. + Active site Amino acids Enzyme (E) Enzyme-substrate complex (E-S)
Internal rearrangements
leading to catalysis
Dipeptide product (P)
Free enzyme (E)
Substrates (S)
Peptide bond
H2O +
Figure 2.21

92. + Active site Amino acids Enzyme (E) Enzyme-substrate complex (E-S)
Substrates (S)
H2O +
Figure 2.21

93. + Active site Amino acids Enzyme (E) Enzyme-substrate complex (E-S)
Internal rearrangements
leading to catalysis
Substrates (S)
H2O +
Figure 2.21

94. + Active site Amino acids Enzyme (E) Enzyme-substrate complex (E-S)
Internal rearrangements
leading to catalysis
Dipeptide product (P)
Free enzyme (E)
Substrates (S)
Peptide bond
H2O +
Figure 2.21

95. 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

96. Nucleic Acids
Five nitrogen bases contribute to nucleotide structure – adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U)
Two major classes – DNA and RNA

97. 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

98. Complimentary Bases/Structure of DNA
Figure 2.22a

99. Structure of DNA
Figure 2.22b

100. 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
Viral RNA is unique

101. Adenosine Triphosphate (ATP)
Figure 2.23

102. Solute
Solute transported
Contracted smooth
muscle cell
Product made
Relaxed smooth
Reactants
Membrane
protein P Pi
ATP X Y +
(a) Transport work
(b) Mechanical work
(c) Chemical work
ADP
Figure 2.24

103. Solute
Membrane
protein P
ATP
(a) Transport work
Figure 2.24

104. Solute
Solute transported
Membrane
protein P Pi
ATP
(a) Transport work +
ADP
Figure 2.24

105. Relaxed smooth
muscle cell
ATP
(b) Mechanical work
Figure 2.24

106. Contracted smooth
muscle cell
Relaxed smooth
ATP
(b) Mechanical work Pi +
ADP
Figure 2.24

107. Reactants
ATP P X Y +
(c) Chemical work
Figure 2.24

108. Product made
Reactants
ATP P X Y +
(c) Chemical work Pi
ADP
Figure 2.24

109. Solute
Solute transported
Contracted smooth
muscle cell
Product made
Relaxed smooth
Reactants
Membrane
protein P Pi
ATP X Y +
(a) Transport work
(b) Mechanical work
(c) Chemical work
ADP
Figure 2.24