1. The Chemical & Physical Basis of Life Chapter 2

2. Life is a series of complex chemical reactions. Chemical reactions are the basis of physiology. Chemistry follows the laws of Physics. Physics is, fundamentally, the study of matter & energy.

3. Matter Matter is “stuff”. It occupies space and has mass. Mass is measured in grams. Mass and “weight” are often used interchangeably but are really two different things Weight is a measure of the effect of force on an object. It changes. Mass does not change. Example: The Moon’s gravitational force is 1/6th that of Earth’s. If you weigh 155 pounds on Earth (70 kg), you will only weigh 26 pounds on the Moon. But you will still have 70 kilograms of mass! (The BE or British Engineering unit of mass is the “slug”.)

4. Energy Potential = stored energy. The amount energy contained in an object of a given mass that can be used to do work. Kinetic Energy = energy of work. This is energy that is actually being released and doing work.

5. Other Forms of Energy 1.Electrical 2.Mechanical 3.Chemical 4.Radiant 5.Nuclear

6. Energy is governed by the Laws of Thermodynamics

7. The 1st Law of Thermodynamics: Energy cannot be created nor can it be destroyed. Also known as “the Conservation Statement”

8. The 2nd law of Thermodynamics: Energy flows from an area of high density to an area of low density. This is also referred to as “the Entropy Statement”. The 2nd LTD is perhaps the most relevant concept to us for our understanding biological systems, chemistry and physiology.

9. Another way to look at the 2nd LTD: Since energy is what holds matter together, or maintains “order”, then the 2nd LTD dictates that systems go from order to disorder.

10. Example of Entropy

11. The 3rd Law of Thermodynamics: You cannot reach absolute zero in a finite number of steps. This is implied from the first two LTDs.

12. Absolute zero That’s really cold!

13. The Zeroth Law: There is no net flow of energy between to systems that are in equilibrium. (The “well duh!” statement.)

14. Atoms, Ions, and Molecules Expected Learning Outcomes –Name the chemical elements of the body from their chemical symbols. –Distinguish between chemical elements and compounds. –State the functions of minerals in the body. –Explain the basis for radioactivity and the types of hazards of ionizing radiation. –Distinguish between ions, electrolytes, and free radials. –Define the types of chemical bonds. 2-14

15. 2-15 The Chemical Elements Element—simplest form of matter to have unique chemical properties Atomic number of an element—number of protons in its nucleus –Periodic table Elements arranged by atomic number Elements represented by one- or two-letter symbols –24 elements have biological role 6 elements = 98.5% of body weight –Oxygen, carbon, hydrogen, nitrogen, calcium, and phosphorus Trace elements in minute amounts, but play vital roles

16. 2-16 The Chemical Elements

17. 2-17 The Chemical Elements Minerals—inorganic elements extracted from soil by plants and passed up the food chain to humans –Ca, P, Cl, Mg, K, Na, Fe, Zn, and S Constitute about 4% of body weight –Structure (teeth, bones, etc.) –Enzymes Electrolytes needed for nerve and muscle function are mineral salts

18. Atomic Structure Nucleus—center of atom –Protons: single + charge, mass = 1 atomic mass unit (amu) –Neutrons: no charge, mass = 1 amu –Atomic mass of an element is approximately equal to its total number of protons and neutrons Electrons—in concentric clouds that surround the nucleus –Electrons: single negative charge, very low mass Determine the chemical properties of an atom The atom is electrically neutral because the number of electrons is equal to the number of protons –Valence electrons in the outermost shell Determine chemical bonding properties of an atom 2-18

19. Atomic structure Atomic number = the number of protons Mass number = protons + neutrons Atomic mass = mass of protons (1.008 amu) + mass of neutrons (1.007 amu) + mass of electrons (0.0005 amu)

20. 2-20 Bohr Planetary Models of Elements p + represents protons, n 0 represents neutrons Figure 2.1 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. First energy level Nitrogen (N) 7p +, 7e -, 7n 0 Atomic number = 7 Atomic mass = 14 Second energy level Third energy level Fourth energy level Nitrogen (N) 7p +, 7e -, 7n 0 Atomic number = 7 Atomic mass = 14 Sodium (Na) 11p +, 11e -, 12n 0 Atomic number = 11 Atomic mass = 23 Potassium (K) 19p +, 19e -, 20n 0 Atomic number = 19 Atomic mass = 39

21. 2-21 Isotopes and Radioactivity Isotopes—varieties of an element that differ from one another only in the number of neutrons and therefore in atomic mass –Extra neutrons increase atomic weight –Isotopes of an element are chemically similar Have same valence electrons Atomic weight (relative atomic mass) of an element accounts for the fact that an element is a mixture of isotopes

22. There are 3 basic types of atomic radiation   particles = a He nucleus (2 protons + 2 neutrons)  Easily stopped. Dangerous if ingested or inhaled. Produced by the decay of Polonium, Radon, Radium and Uranium   particles = are electrons and are negatively charged  More energetic and therefore, more dangerous. Given off in the opposite direction of  particle. Produced by Krypton, Strontium, Carbon and Indium.   rays = high energy electromagnetic radiation  Most deadly, mutagenic and toxic. Produced by Polonium, Krypton, Radon, Radium, and Uranium

23. 2-23 Isotopes of Hydrogen Figure 2.2 Key Deuterium ( 2 H) (1p 2, 1n 0, 1e – ) Hydrogen ( 1 H) (1p +, 0n 0, 1e – ) = Proton (p + ) = Electron (e 0 ) = Neutron (n – ) Tritium ( 3 H) (1p +, 2n 0, 1e – ) Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

24. 2-24 Isotopes and Radioactivity Radioisotopes –Unstable isotopes that give off radiation –Every element has at least one radioisotope Radioactivity –Radioisotopes decay to stable isotopes releasing radiation –We are all mildly radioactive

25. 2-25 Physical half-life of radioisotopes –Time needed for 50% to decay into a stable state –Nuclear power plants create radioisotopes Biological half-life of radioisotopes –Time required for 50% to disappear from the body –Decay and physiological clearance Isotopes and Radioactivity

26. Chemical reactivity: It’s all about electrons

27. Unfilled valence shells lead to reactivity

28. 2-28 Ions—charged particles with unequal number of protons and electron Elements with one to three valence electrons tend to give up, and those with four to seven electrons tend to gain Ionization—transfer of electrons from one atom to another (  stability of valence shell) Ions, Electrolytes, and Free Radicals Figure 2.4 (1) Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Chlorine atom (Cl) Sodium atom (Na) 17 protons 18 neutrons 17 electrons 11 protons 12 neutrons 11 electrons Transfer of an electron from a sodium atom to a chlorine atom 1

29. 2-29 Anion—atom that gains electrons (net negative charge) Cation—atom that loses an electron (net positive charge) Ions with opposite charges are attracted to each other Ions, Electrolytes, and Free Radicals Figure 2.4 (2) +– Sodium chloride Chloride ion (Cl – ) Sodium ion (Na + ) 11 protons 12 neutrons 10 electrons 17 protons 18 neutrons 18 electrons The charged sodium ion (Na + ) and chloride ion (Cl – ) that result 2 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

30. 2-30 Ions, Electrolytes, and Free Radicals Electrolytes—salts that ionize in water and form solutions capable of conducting an electric current Electrolyte importance –Chemical reactivity –Osmotic effects (influence water movement) –Electrical effects on nerve and muscle tissue

31. 2-31 Ions, Electrolytes, and Free Radicals Electrolyte balance is one of the most important considerations in patient care Imbalances have ranging effects from muscle cramps, brittle bones, to coma and cardiac arrest

32. 2-32 Ions, Electrolytes, and Free Radicals

33. 2-33 Ions, Electrolytes, and Free Radicals Free radicals—chemical particles with an odd number of electrons Produced by –Normal metabolic reactions, radiation, chemicals Causes tissue damage –Reactions that destroy molecules –Causes cancer, death of heart tissue, and aging Antioxidants –Neutralize free radicals –In body, superoxide dismutase (SOD) converts superoxides into water and oxygen –In diet (selenium, vitamin E, vitamin C, carotenoids)

34. The Octet Rule Atoms with eight electrons in their valance shell are most stable. When a reaction between two atoms leads to full valance shells then the two are more likely to interact. Atoms or molecules with partially filled valance shells are more reactive.

35. 2-35 Molecules and Chemical Bonds Molecules—chemical particles composed of two or more atoms united by a chemical bond Compounds—molecules composed of two or more different elements Molecular formula—identifies constituent elements and how many atoms of each are present Structural formula –Location of each atom –Structural isomers revealed

36. 2-36 Isomers—molecules with identical molecular formulae but different arrangement of their atoms Molecules and Chemical Bonds Figure 2.5 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Structural formulae Condensed structural formulae Molecular formulae C2H6OC2H6O C2H6OC2H6O CH 3 CH 2 OH Ethyl ether Ethanol HCC HH H H OH HCO H H C H H H

37. 2-37 Molecules and Chemical Bonds The molecular weight of a compound is the sum of atomic weights of atoms Calculate: MW of glucose (C 6 H 12 O 6 ) 6 C atoms x 12 amu each = 72 amu 12 H atoms x 1 amu each = 12 amu 6 O atoms x 16 amu each = 96 amu Molecular weight (MW) = 180 amu

38. 2-38 Molecules and Chemical Bonds Chemical bonds—forces that hold molecules together, or attract one molecule to another Types of chemical bonds –Ionic bonds –Covalent bonds –Hydrogen bonds –Van der Waals forces TABLE 2.3 Types of Chemical Bonds

39. Molecules and Chemical Bonds 2-39

40. 2-40 Molecules and Chemical Bonds Single covalent bond—one pair of electrons are shared Figure 2.6a Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. + HH Hydrogen molecule (H 2 ) Hydrogen atom (a) P+P+ P+P+ P+P+ P+P+

41. 2-41 Figure 2.6b Double covalent bonds—two pairs of electrons are shared; each C=O bond Molecules and Chemical Bonds Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. COO Oxygen atomCarbon atomOxygen atom Carbon dioxide molecule (CO 2 ) (b) 8p + 8n 0 8p + 8n 0 6p + 6n 0

42. 2-42 Molecules and Chemical Bonds Electrons shared equally Electrons shared unequally Figure 2.7 Nonpolar and polar covalent bonds—the strongest of all chemical bonds Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Polar covalent O — H bond Nonpolar covalent C — C bond (a) (b) __ ++ C C C C O O HH

43. 2-43 Molecules and Chemical Bonds Hydrogen bond—a weak attraction between a slightly positive hydrogen atom in one molecule and a slightly negative oxygen or nitrogen atom in another Water molecules are weakly attracted to each other by hydrogen bonds Relatively weak bonds Very important to physiology –Protein structure –DNA structure

44. 2-44 Molecules and Chemical Bonds Figure 2.8 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ –– –– –– –– –– H Hydrogen bond Covalent bond Water molecule H H H H H H H H H H H H H H H H H H H H o o o o o o o o o o

45. 2-45 Molecules and Chemical Bonds Van der Waals forces—weak, brief attractions between neutral atoms Fluctuations in electron density in electron cloud of a molecule creates polarity for a moment, and can attract adjacent molecules in the region for a very short instant in time Only 1% as strong as a covalent bond

46. 2-46 Molecules and Chemical Bonds When two surfaces or large molecules meet, the attraction between large numbers of atoms can create a very strong attraction –Important in protein folding –Important with protein binding with hormones –Association of lipid molecules with each other

47. Water and Mixtures Expected Learning Outcomes –Define mixture and distinguish between mixtures and compounds. –Describe the biologically important properties of water. –Show how three kinds of mixtures differ from each other. –Discuss some ways in which the concentration of a solution can be expressed, and explain why different expressions of concentration are used for different purposes. –Define acid and base and interpret the pH scale. 2-47

48. 2-48 Water and Mixtures Mixtures—consist of substances physically blended, but not chemically combined Body fluids are complex mixtures of chemicals –Each substance maintains its own chemical properties Most mixtures in our bodies consist of chemicals dissolved or suspended in water Water 50% to 75% of body weight –Depends on age, sex, fat content, etc.

49. 2-49 Water Polar covalent bonds and V-shaped molecule give water a set of properties that account for its ability to support life –Solvency –Cohesion –Adhesion –Chemical reactivity –Thermal stability

50. 2-50 Water Solvency—ability to dissolve other chemicals Water is called the universal solvent –Hydrophilic—substances that dissolve in water Molecules must be polarized or charged –Hydrophobic—substances that do not dissolve in water Molecules are nonpolar or neutral (fat) Virtually all metabolic reactions depend on the solvency of water

51. Water Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. ++ –– ++ Oxygen Hydrogen 105˚ (a) (b) Na + Cl – 2-51 Polar water molecules overpower the ionic bond in Na + and Cl - –Forming hydration spheres around each ion –Water molecules: negative pole faces Na +, positive pole faces Cl - Figure 2.9

52. 2-52 Water Adhesion—tendency of one substance to cling to another Cohesion—tendency of like molecules to cling to each other –Water is very cohesive due to its hydrogen bonds –Surface film on surface of water is due to molecules being held together by a force called surface tension

53. 2-53 Water Chemical reactivity is the ability to participate in chemical reactions –Water ionizes into H + and OH - –Water ionizes other chemicals (acids and salts) –Water is involved in hydrolysis and dehydration synthesis reactions

54. 2-54 Water Water helps stabilize the internal temperature of the body –Has high heat capacity—the amount of heat required to raise the temperature of 1 g of a substance by 1°C –Calorie (cal)—the amount of heat that raises the temperature of 1 g of water 1°C Hydrogen bonds inhibit temperature increases by inhibiting molecular motion Water absorbs heat without changing temperature very much –Effective coolant 1 mL of perspiration removes 500 calories

55. Solutions, Colloids, and Suspensions Solution—consists of particles of matter called the solute mixed with a more abundant substance (usually water) called the solvent Solute can be gas, solid, or liquid Solutions are defined by the following properties: –Solute particles under 1 nm –Solute particles do not scatter light –Will pass through most membranes –Will not separate on standing 2-55

56. 2-56 Solutions, Colloids, and Suspensions Figure 2.10 SuspensionSolutionColloid a–d: © Ken Saladin. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

57. 2-57 Solutions, Colloids, and Suspensions Most common colloids in the body are mixtures of protein and water Many can change from liquid to gel state within and between cells Colloids are defined by the following physical properties: –Particles range from 1–100 nm in size –Scatter light and are usually cloudy –Particles too large to pass through semipermeable membrane –Particles remain permanently mixed with the solvent when mixture stands

58. 2-58 Solutions, Colloids, and Suspensions Suspension –Defined by the following physical properties: Particles exceed 100 nm Too large to penetrate selectively permeable membranes Cloudy or opaque in appearance Separates on standing Emulsion –Suspension of one liquid in another Fat in breast milk

59. 2-59

60. 2-60 Measures of Concentration How much solute in a given volume of solution? Weight per volume –Weight of solute in given volume of solution IV saline: 8.5 g NaCl per liter of solution Biological purposes: milligrams per deciliter –mg/dL (deciliter = 100 mL)

61. 2-61 Measures of Concentration Percentages –Weight/volume of solute in solution IV D 5 W (5% w/v dextrose in distilled water) –5 g dextrose and fill to 100 mL water Molarity—known number of molecules per volume –Moles of solute/liter of solution –Physiologic effects based on number of molecules in solution not on weight

62. 2-62 Measures of Concentration 1 mole of a substance is its molecular weight in grams 1 mole of a substance is equal to Avogadro’s number of molecules, 6.023 x 10 23

63. 2-63 Measures of Concentration Molarity (M) is the number of moles of solute/ liter of solution –MW of glucose is 180 –One-molar (1.0 M) glucose solution contains 180 g/L

64. 2-64 Molar –# of molecules equal –Weight of solute unequal Percentage –# of molecules unequal – Weight of solute equal Measures of Concentration Figure 2.11 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. (a) Solutions of equal percentage concentration 5% sucrose (w/v) (50 g/L) 5% glucose (w/v) (50 g/L) 0.1 M sucrose (34 g/L) 0.1 M glucose (18 g/L) (b) Solutions of equal molar concentration

65. 2-65 Measures of Concentration Electrolytes are important for their chemical, physical, and electrical effects on the body –Electrical effects determine nerve, heart, and muscle actions

66. 2-66 Measures of Concentration Measured in equivalents (Eq) –1 equivalent is the amount of electrolyte that will electrically neutralize 1 mole of H + or OH - ions –In the body, expressed as milliequivalents (mEq/L) –Multiply molar concentration x valence of the ion –1 mM Na + = 1 Eq/L –1 mM Ca 2+ = 2 Eq/L

67. 2-67 Acids, Bases, and pH An acid is a proton donor (releases H + ions in water) A base is a proton acceptor (accepts H + ions) –Releases OH - ions in water pH is a measure derived from the molarity of H+ –a pH of 7.0 is neutral pH (H + = OH - ) –a pH of less than 7 is acidic solution (H + > OH - ) –a pH of greater than 7 is basic solution (OH - > H + )

68. 2-68 Acids, Bases, and pH pH—measurement of molarity of H + [H+] on a logarithmic scale –pH scale invented by Sören Sörensen in 1909 to measure acidity of beer –pH = -log [H + ] thus pH = -log [10 -3 ] = 3 A change of one number on the pH scale represents a 10-fold change in H + concentration –A solution with pH of 4.0 is 10 times as acidic as one with pH of 5.0

69. 2-69 Acids, Bases, and pH Our body uses buffers to resist changes in pH –Slight pH disturbances can disrupt physiological functions and alter drug actions –pH of blood ranges from 7.35 to 7.45 –Deviations from this range cause tremors, paralysis, or even death

70. 2-70 Acids, Bases, and pH Figure 2.12 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 0 9 8 76 5 4 3 2 1 1M hydrochloric acid(0) Gastric juice (0.9–3.0) Lemon juice (2.3) Wine, vinegar (2.4–3.5) Bananas, tomatoes (4.7) Bread, black coffee (5.0) Milk, saliva (6.3–6.6) Pure water (7.0) Egg white (8.0) Household bleach (9.5) Household ammonia (10.5–11.0) Oven cleaner, lye (13.4) 1 M sodium hydroxide (14) 14 13 12 11 10 Neutral

71. Energy and Chemical Reactions Expected Learning Outcomes –Define energy and work, and describe some types of energy. –Understand how chemical reactions are symbolized by chemical equations. –List and define the fundamental types of chemical reactions. –Identify the factors that govern the speed and direction of a reaction. –Define metabolism and its two subdivisions. –Define oxidation and reduction and relate these to changes in the energy content of a molecule. 2-71

72. 2-72 Energy and Work Energy—capacity to do work –To do work means to move something –All body activities are a form of work Potential energy—energy contained in an object because of its position or internal state –Not doing work at the time –Water behind a dam –Chemical energy—potential energy stored in the bonds of molecules –Free energy—potential energy available in a system to do useful work

73. 2-73 Energy and Work Kinetic energy—energy of motion; energy that is actively doing work –Moving water flowing through a dam –Heat—kinetic energy of molecular motion –Electromagnetic energy—the kinetic energy of moving “packets” of radiation called photons

74. 2-74 Classes of Chemical Reactions Chemical reaction—a process in which a covalent or ionic bond is formed or broken Chemical equation—symbolizes the course of a chemical reaction –Reactants (on left)  products (on right) Classes of chemical reactions –Decomposition reactions –Synthesis reactions –Exchange reactions

75. 2-75 Classes of Chemical Reactions Decomposition reactions— large molecule breaks down into two or more smaller ones AB  A + B Figure 2.13a Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Glucose molecules (a) Decomposition reaction Starch molecule

76. 2-76 Classes of Chemical Reactions Synthesis reactions—two or more small molecules combine to form a larger one A + B  AB Figure 2.13b Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. (b) Synthesis reaction Protein molecule Amino acids

77. 2-77 Classes of Chemical Reactions Exchange reactions—two molecules exchange atoms or group of atoms AB+CD  ABCD  AC + BD Stomach acid (HCl) and sodium bicarbonate (NaHCO 3 ) from the pancreas combine to form NaCl and H 2 CO 3 Figure 2.13c Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. + BD (c) Exchange reaction AB + CD AC AA C C BBDD C C C C AA AA BB BBDD DD

78. 2-78 Classes of Chemical Reactions Reversible reactions –Can go in either direction under different circumstances Symbolized with double-headed arrow CO 2 + H 2 O H 2 CO 3 HCO 3- + H + –Most common equation discussed in this book –Respiratory, urinary, and digestive physiology

79. 2-79 Classes of Chemical Reactions Law of mass action determines direction –Proceeds from the side of equation with greater quantity of reactants to the side with the lesser quantity Equilibrium exists in reversible reactions when the ratio of products to reactants is stable

80. 2-80 Reaction Rates Basis for chemical reactions is molecular motion and collisions –Reactions occur when molecules collide with enough force and the correct orientation

81. Reaction Rates Reaction rates affected by: –Concentration Reaction rates increase when the reactants are more concentrated –Temperature Reaction rates increase when the temperature rises 2-81

82. Reaction Rates –Catalysts—substances that temporarily bond to reactants, hold them in favorable position to react with each other, and may change the shapes of reactants in ways that make them more likely to react Speed up reactions without permanent change to itself Hold reactant molecules in correct orientation Catalyst not permanently consumed or changed by the reaction Enzymes—most important biological catalysts 2-82

83. 2-83 Metabolism, Oxidation, and Reduction All the chemical reactions of the body Catabolism –Energy-releasing (exergonic) decomposition reactions Breaks covalent bonds Produces smaller molecules Releases useful energy Anabolism –Energy-storing (endergonic) synthesis reactions Requires energy input Production of protein or fat Driven by energy that catabolism releases Catabolism and anabolism are inseparably linked

84. 2-84 Metabolism, Oxidation, and Reduction Oxidation –Any chemical reaction in which a molecule gives up electrons and releases energy –Molecule oxidized in this process –Electron acceptor molecule is the oxidizing agent Oxygen is often involved as the electron acceptor

85. Metabolism, Oxidation, and Reduction Reduction –Any chemical reaction in which a molecule gains electrons and energy –Molecule is reduced when it accepts electrons –Molecule that donates electrons is the reducing agent 2-85

86. Metabolism, Oxidation, and Reduction Oxidation-reduction (redox) reactions –Oxidation of one molecule is always accompanied by the reduction of another –Electrons are often transferred as hydrogen atoms 2-86

87. 2-87 Metabolism, Oxidation, and Reduction

88. Organic Compounds Expected Learning Outcomes –Explain why carbon is especially well suited to serve as the structural foundation of many biological molecules. –Identify some common functional groups of organic molecules from their formulae. –Discuss the relevance of polymers to biology and explain how they are formed and broken by dehydration synthesis and hydrolysis. –Discuss the types and functions of carbohydrates, lipids, and proteins. –Explain how enzymes function. –Describe the structure, production, and function of ATP. –Identify other nucleotide types and their functions; and the principal types of nucleic acids. 2-88

89. 2-89 Carbon Compounds and Functional Groups Organic chemistry—the study of compounds containing carbon Four categories of carbon compounds –Carbohydrates –Lipids –Proteins –Nucleotides and nucleic acids

90. 2-90 Carbon Compounds and Functional Groups Four valence electrons –Binds with other atoms that can provide it with four more electrons to fill its valence shell Carbon atoms bind readily with each other to form carbon backbones –Form long chains, branched molecules, and rings –Form covalent bonds with hydrogen, oxygen, nitrogen, sulfur, and other elements Carbon backbone carries a variety of functional groups

91. 2-91 Small clusters of atoms attached to carbon backbone Determines many of the properties of organic molecules Hydroxyl, methyl, carboxyl, amino, phosphate Carbon Compounds and Functional Groups Figure 2.14 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. CC NN PP H H O O H H Hydroxyl ( — OH) Name and Symbol StructureOccurs in Sugars, alcohols Fats, oils, steroids, amino acids Amino acids, sugars, proteins Amino acids, proteins Nucleic acids, ATP Methyl (—CH 3 ) Carboxyl (—COOH) Amino (—NH 2 ) Phosphate (—H2PO 4 ) H H H H O O O O H H CC O O O O O O O O H H H H H H H H

92. 2-92 Monomers and Polymers Macromolecules—very large organic molecules –Very high molecular weights Proteins, DNA Polymers—molecules made of a repetitive series of identical or similar subunits (monomers) –Starch is a polymer of about 3,000 glucose monomers Monomers—identical or similar subunits

93. 2-93 Monomers and Polymers Polymerization—joining monomers to form a polymer Dehydration synthesis (condensation) is how living cells form polymers –A hydroxyl (-OH) group is removed from one monomer, and a hydrogen (-H) from another Producing water as a by-product Hydrolysis—opposite of dehydration synthesis –A water molecule ionizes into –OH and -H –The covalent bond linking one monomer to the other is broken –The -OH is added to one monomer –The -H is added to the other

94. 2-94 Monomers and Polymers Monomers covalently bond together to form a polymer with the removal of a water molecule –A hydroxyl group is removed from one monomer and a hydrogen from the next Figure 2.15a Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. + O H+H+ Monomer 1Monomer 2 (a) Dehydration synthesis OHHO Dimer H2OH2OOH —

95. 2-95 Monomers and Polymers Splitting a polymer (lysis) by the addition of a water molecule (hydro) –A covalent bond is broken All digestion reactions consist of hydrolysis reactions Figure 2.15b Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. O +H+H+ Monomer 2Monomer 1 (b) Hydrolysis Dimer OH — HOOH H2OH2O

96. 2-96 Carbohydrates Hydrophilic organic molecule General formula –(CH 2 O) n, n = number of carbon atoms –Glucose, n = 6, so formula is C 6 H 12 O 6 – 2:1 ratio of hydrogen to oxygen Names of carbohydrates often built from: –Word root sacchar- –Suffix -ose –Both mean “sugar” or “sweet” Monosaccharide or glucose

97. 2-97 Carbohydrates Three important monosaccharides –Glucose, galactose, and fructose –Same molecular formula: C 6 H 12 O 6 All isomers of each other –Produced by digestion of complex carbohydrates Glucose is blood sugar Figure 2.16 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H H H H H O H H H H H O H H O H Glucose CH 2 OH OH HO OH Galactose CH 2 OH OH HO OH Fructose HOCH 2 CH 2 OH OH HO

98. 2-98 Carbohydrates Disaccharide—sugar molecule composed of two monosaccharides Three important disaccharides –Sucrose—table sugar Glucose + fructose –Lactose—sugar in milk Glucose + galactose –Maltose—grain products Glucose + glucose Figure 2.17 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H H H H H H H H H HH H H H H H H HH H H H H H H H H H O O O O OO O O O CH 2 OH Sucrose CH 2 OH OH HO OH Lactose CH 2 OH OH CH 2 OH HO OH Maltose CH 2 OH OH HO OH

99. 2-99 Carbohydrates Oligosaccharides—short chains of 3 or more monosaccharides (at least 10) Polysaccharides—long chains of monosaccharides (at least 50)

100. 2-100 Carbohydrates Three polysaccharides of interest in humans –Glycogen: energy storage polysaccharide in animals Made by cells of liver, muscles, brain, uterus, and vagina Liver produces glycogen after a meal when glucose level is high, then breaks it down between meals to maintain blood glucose levels Muscles store glycogen for own energy needs Uterus uses glycogen to nourish embryo

101. 2-101 Carbohydrates Three polysaccharides of interest in humans (cont) –Starch: energy storage polysaccharide in plants Only significant digestible polysaccharide in the human diet –Cellulose: structural molecule of plant cell walls Fiber in our diet

102. 2-102 Glycogen Figure 2.18 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O OO O O O O O O O OO O O CH 2 OH CH 2 (b)(a)

103. 2-103 Carbohydrates Quickly mobilized source of energy –All digested carbohydrates converted to glucose –Oxidized to make ATP Conjugated carbohydrate—covalently bound to lipid or protein –Glycolipids External surface of cell membrane –Glycoproteins External surface of cell membrane Mucus of respiratory and digestive tracts –Proteoglycans (mucopolysaccharides) Gels that hold cells and tissues together Forms gelatinous filler in umbilical cord and eye Joint lubrication Tough, rubbery texture of cartilage

104. 2-104 Carbohydrates

105. 2-105 Lipids Hydrophobic organic molecule –Composed of carbon, hydrogen, and oxygen –With high ratio of hydrogen to oxygen Less oxidized than carbohydrates, and thus has more calories/gram Five primary types in humans –Fatty acids –Triglycerides –Phospholipids –Eicosanoids –Steroids

106. 2-106 Lipids Triglycerides (Neutral Fats) –Three fatty acids covalently bonded to three-carbon alcohol called glycerol –Each bond formed by dehydration synthesis –Once joined to glycerol, fatty acids can no longer donate protons— neutral fats –Broken down by hydrolysis Triglycerides at room temperature –When liquid, called oils Often polyunsaturated fats from plants –When solid, called fat Saturated fats from animals Primary function: energy storage, insulation, and shock absorption (adipose tissue)

107. 2-107 Lipids Chain of 4 to 24 carbon atoms –Carboxyl (acid) group on one end, methyl group on the other, and hydrogen bonded along the sides Classified –Saturated—carbon atoms saturated with hydrogen –Unsaturated—contains C=C bonds without hydrogen –Polyunsaturated—contains many C=C bonds –Essential fatty acids—obtained from diet, body cannot synthesize Figure 2.19 CC HHHHHHHHHHHHH O HHHHHHHHHHHHH CCCCCCCCCCCCC H H CH H H Palmitic acid (saturated) CH 3 (CH 2 ) 14 COOH HO Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

108. 2-108 Lipids Similar to neutral fat except that one fatty acid is replaced by a phosphate group Structural foundation of cell membrane Amphiphilic –Fatty acid “tails” are hydrophobic –Phosphate “head” is hydrophilic Figure 2.21a,b N+N+ O PO O C O O O CO Hydrophobic region (tails) Hydrophilic region (head) (a) (b) Nitrogen- containing group (choline) CH 3 CH 2 Phosphate group OO CH 2 CHCH 2 Glycerol (CH 2 ) 5 CH CH 3 (CH 2 ) 5 CH 3 (CH 2 ) 12 Fatty acid tails Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

109. Trans Fats and Cardiovascular Health Trans-fatty acids –Two covalent single C-C bonds angle in opposites (trans, “across from each other”) on each side of the C=C double bond –Resist enzymatic breakdown in the human body, remain in circulation longer, deposits in the arteries; thus, raises the risk of heart disease Cis-fatty acids –Two covalent single C-C bonds angle in the same direction adjacent to the C=C double bond 2-109 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. (a) A trans-fatty acid (elaidic acid) (b) A cis-fatty acid (oleic acid) OH O O

110. 2-110 Lipids Eicosanoids –20 carbon compounds derived from a fatty acid called arachidonic acid Hormonelike chemical signals between cells Includes prostaglandins—produced in all tissues –Role in inflammation, blood clotting, hormone action, labor contractions, blood vessel diameter Figure 2.22 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. O OH COOH

111. 2-111 Lipids Steroid—a lipid with 17 of its carbon atoms in four rings Cholesterol—the “parent” steroid from which the other steroids are synthesized –Cortisol, progesterone, estrogens, testosterone, and bile acids –Synthesized only by animals Especially liver cells 15% from diet, 85% internally synthesized –Important component of cell membranes –Required for proper nervous system function

112. “Good” and “Bad” Cholesterol One kind of cholesterol –Does far more good than harm “Good” and “bad” cholesterol actually refers to droplets of lipoprotein in the blood –Complexes of cholesterol, fat, phospholipid, and protein HDL (high-density lipoprotein): “good” cholesterol –Lower ratio of lipid to protein –May help to prevent cardiovascular disease LDL (low-density lipoprotein): “bad” cholesterol –High ratio of lipid to protein –Contributes to cardiovascular disease 2-112

113. 2-113 Cholesterol Figure 2.23 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. CH 3 H3CH3C HO

114. Lipids and Functions 2-114

115. 2-115 Proteins Greek word meaning “of first importance” – Most versatile molecules in the body Protein—a polymer of amino acids Amino acid—central carbon with three attachments –Amino group (NH 2 ), carboxyl group (—COOH), and radical group (R group) 20 amino acids used to make the proteins are identical except for the radical (R) group –Properties of amino acid determined by R group

116. 2-116 Proteins Amino acids differ only in the R group Figure 2.24a Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Some polar amino acidsSome nonpolar amino acids Methionine Cysteine ArginineTyrosine H N C C H O H OH SHCH 2 CH 3 H N C C H S O H CH 2 OH H N C C C H O H NH 2 + NH 2 NH OH (CH 2 ) 3 CH 2 H N C C H O H OH (a)

117. 2-117 Proteins Peptide—any molecule composed of two or more amino acids joined by peptide bonds Peptide bond—joins the amino group of one amino acid to the carboxyl group of the next –Formed by dehydration synthesis Peptides named for the number of amino acids –Dipeptides have 2 –Tripeptides have 3 –Oligopeptides have fewer than 10 to 15 –Polypeptides have more than 15 –Proteins have more than 50

118. 2-118 Proteins Dehydration synthesis creates a peptide bond that joins the amino acid of one group to the carboxyl group of the next Figure 2.24b Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H H O + + OH H NCC H H O H R2R2 NCC H H OH R1R1 NCC O H R2R2 H NCC Amino acid1 R1R1 Amino acid2 A dipeptide H2OH2O (b) Peptide bond

119. 2-119 Protein Structure Conformation—unique, three-dimensional shape of protein crucial to function –Ability to reversibly change their conformation Enzyme function Muscle contraction Opening and closing of cell membrane pores Denaturation –Extreme conformational change that destroys function Extreme heat or pH Example: when you cook an egg

120. 2-120 Protein Structure Primary structure –Protein’s sequence amino acid which is encoded in the genes Secondary structure –Coiled or folded shape held together by hydrogen bonds –Hydrogen bonds between slightly negative C=O and slightly positive N-H groups –Most common secondary structures are: Alpha helix—springlike shape Beta helix—pleated, ribbonlike shape

121. 2-121 Protein Structure Tertiary structure –Further bending and folding of proteins into globular and fibrous shapes Globular proteins—compact tertiary structure well suited for proteins embedded in cell membrane and proteins that must move about freely in body fluid Fibrous proteins—slender filaments better suited for roles as in muscle contraction and strengthening the skin Quaternary structure –Associations of two or more separate polypeptide chains –Functional conformation: three-dimensional shape

122. 2-122 Protein Structure C C=O HN NH O=C C C C CC C C C C C O=C C NH O=C NH C=O HN C H NC C O O O O C C O C N H C C N H N H C Amino acids Peptide bonds Primary structure Sequence of amino acids joined by peptide bonds Secondary structure Alpha helix or beta sheet formed by hydrogen bonding Beta sheet Chain 1 Chain 2 Alpha helix Quaternary structure Association of two or more polypeptide chains with each other Beta chain Heme groups Alpha chain Alpha chain Tertiary structure Folding and coiling due to interactions among R groups and between R groups and surrounding water Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Figure 2.25

123. 2-123 Conjugated proteins contain a non–amino acid moiety called a prosthetic group Hemoglobin contains four complex iron- containing rings called a heme moiety Proteins Quaternary structure Association of two or more polypeptide chains with each other Beta chain Heme groups Alpha chain Alpha chain Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Figure 2.25 (4)

124. 2-124 Primary Structure of Insulin Figure 2.26 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Thr Lys Pro Thr Tyr Phe Gly Arg Glu Gly Cys Val Leu Tyr Leu Ala Glu Val Leu His Cys Gly Ser Leu His Gln Asn Val Phe Thr Ser lle Ser Leu Tyr Gln Leu Glu Asn Tyr Asn Gly lle Val Glu Gln

125. 2-125 Proteins Structure –Keratin—tough structural protein Gives strength to hair, nails, and skin surface –Collagen—durable protein contained in deeper layers of skin, bones, cartilage, and teeth Communication –Some hormones and other cell-to-cell signals –Receptors to which signal molecules bind Ligand—any hormone or molecule that reversibly binds to a protein Membrane transport –Channels in cell membranes that govern what passes through –Carrier proteins—transports solute particles to other side of membrane –Turn nerve and muscle activity on and off

126. 2-126 Proteins Catalysis –Enzymes Recognition and protection –Immune recognition –Antibodies –Clotting proteins Movement –Motor proteins—molecules with the ability to change shape repeatedly Cell adhesion –Proteins bind cells together –Immune cells to bind to cancer cells –Keeps tissues from falling apart

127. 2-127 Enzymes and Metabolism Enzymes—proteins that function as biological catalysts –Permit reactions to occur rapidly at normal body temperature Substrate—substance an enzyme acts upon Naming convention –Named for substrate with -ase as the suffix Amylase enzyme digests starch (amylose) Lowers activation energy—energy needed to get reaction started –Enzymes facilitate molecular interaction

128. 2-128 Enzymes and Metabolism Time Free energy content Time Energy level of products Energy level of reactants Activation energy Net energy released by reaction Activation energy Net energy released by reaction (a) Reaction occurring without a catalyst(b) Reaction occurring with a catalyst Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Figure 2.27a, b

129. 2-129 Enzyme Structure and Action Substrate approaches active site on enzyme molecule Substrate binds to active site forming enzyme– substrate complex –Highly specific fit— ‟ lock and key” Enzyme–substrate specificity Enzyme breaks covalent bonds between monomers in substrate

130. 2-130 Enzyme Structure and Action Adding H + and OH - from water—hydrolysis Reaction products released—glucose and fructose Enzyme remains unchanged and is ready to repeat the process

131. 2-131 Enzyme Structure and Action Sucrase (enzyme) 1 Enzyme and substrate Sucrose (substrate) Enzyme–substrate complex 2 Enzyme and reaction products 3 GlucoseFructose O O Active site Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Figure 2.28

132. 2-132 Reusability of enzymes –Enzymes are not consumed by the reactions Astonishing speed –One enzyme molecule can consume millions of substrate molecules per minute Enzyme Structure and Action

133. 2-133 Factors that change enzyme shape –pH and temperature –Alters or destroys the ability of the enzyme to bind to substrate –Enzymes vary in optimum pH Salivary amylase works best at pH 7.0 Pepsin works best at pH 2.0 –Temperature optimum for human enzymes—body temperature (37°C) Enzyme Structure and Action

134. 2-134 Cofactors –About two-thirds of human enzymes require a nonprotein cofactor – Inorganic partners (iron, copper, zinc, magnesium, and calcium ions) –Some bind to enzyme and induce a change in its shape, which activates the active site –Essential to function

135. 2-135 Cofactors Coenzymes –Organic cofactors derived from water-soluble vitamins (niacin, riboflavin) –They accept electrons from an enzyme in one metabolic pathway and transfer them to an enzyme in another

136. 2-136 Action of a Coenzyme NAD + transports electrons from one metabolic pathway to another PiPi +ADP Glycolysis Aerobic respiration Glucose Pyruvic acid CO 2 + H 2 O ATP Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Figure 2.29

137. 2-137 Metabolic Pathways Chain of reactions, with each step usually catalyzed by a different enzyme    A  B  C  D A is the initial reactant, B and C are intermediates, and D is the end product Regulation of metabolic pathways –Activation or deactivation of the enzymes –Cells can turn on or off pathways when end products are needed and shut them down when the end products are not needed

138. 2-138 ATP, Other Nucleotides, and Nucleic Acids Three components of nucleotides –Nitrogenous base (single or double carbon– nitrogen ring) –Sugar (monosaccharide) –One or more phosphate groups ATP—best-known nucleotide –Adenine (nitrogenous base) –Ribose (sugar) –Phosphate groups (3)

139. 2-139 Adenosine Triphosphate ATP contains adenine, ribose, and three phosphate groups C NH 2 N N N H Adenosine Adenine Ribose Adenine Ribose Triphosphate Monophosphate (a) Adenosine triphosphate (ATP) N CH HC C C H HH OH O OH CH 2 – OPO – O O – O O – O O POOP C NH 2 N N N H N CH HC C C H HH HO (b) Cyclic adenosine monophosphate (cAMP) O OH CH 2 O OP O Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Figure 2.30a, b

140. 2-140 Adenosine Triphosphate Body’s most important energy-transfer molecule Briefly stores energy gained from exergonic reactions Releases it within seconds for physiological work Holds energy in covalent bonds –Second and third phosphate groups have high energy bonds (~) –Most energy transfers to and from ATP involve adding or removing the third phosphate

141. 2-141 Adenosine Triphosphate Adenosine triphosphatases (ATPases) hydrolyze the third high-energy phosphate bond –Separates into ADP + P i + energy Phosphorylation –Addition of free phosphate group to another molecule –Carried out by enzymes called kinases (phosphokinases)

142. 2-142 Sources and Uses of ATP Glucose + 6 O 2 6 CO 2 + 6 H 2 O are converted to which releases energy which is used for which is then available for Muscle contraction Ciliary beating Active transport Synthesis reactions etc. PiPi +ADP ATP Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Figure 2.31

143. 2-143 ATP Production ATP consumed within 60 seconds of formation Entire amount of ATP in the body would support life for less than 1 minute if it were not continually replenished Cyanide halts ATP synthesis Stages of glucose oxidation 2 + Glycolysis Anaerobic fermentation Aerobic respiration Glucose Pyruvic acid Lactic acid No oxygen available 2 2 CO 2 + H 2 O 36 + 36 Oxygen available PiPi ADP PiPi ATP Mitochondrion ATP Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Figure 2.32

144. 2-144 Other Nucleotides Guanosine triphosphate (GTP) –Another nucleotide involved in energy transfer –Donates phosphate group to other molecules Cyclic adenosine monophosphate (cAMP) –Nucleotide formed by removal of both second and third phosphate groups from ATP –Formation triggered by hormone binding to cell surface –cAMP becomes “second messenger” within cell –Ativates metabolic effects inside cell

145. 2-145 Nucleic Acids Polymers of nucleotides DNA (deoxyribonucleic acid) –100 million to 1 billion nucleotides long –Constitutes genes Instructions for synthesizing all of the body’s proteins Transfers hereditary information from cell to cell and generation to generation RNA (ribonucleic acid)—three types –Messenger RNA, ribosomal RNA, transfer RNA –70 to 10,000 nucleotides long –Carries out genetic instruction for synthesizing proteins –Assembles amino acids in the right order to produce proteins

146. Summary This is all considered review from Bi 112 or whatever prerequisite you took to get into A & P. I expect you to know it well.

147. Next More review! Cells and their basic structure and funtion