1. The Chemistry and Energy of Life2
The Chemistry and Energy of Life

2. Chapter 2 The Chemistry and Energy of Life
Key Concepts
2.1 Atomic Structure Is the Basis for Life’s Chemistry
2.2 Atoms Interact and Form Molecules
2.3 Carbohydrates Consist of Sugar Molecules
2.4 Lipids Are Hydrophobic Molecules
2.5 Biochemical Changes Involve Energy

3. Chapter 2 Opening Question
Why is the search for water important in the search for life?

4. Concept 2.1 Atomic Structure Is the Basis for Life’s Chemistry
Living and nonliving matter is composed of atoms.

5. Concept 2.1 Atomic Structure Is the Basis for Life’s Chemistry
Like charges repel; different charges attract. Most atoms are neutral because the number of electrons equals the number of protons.

6. Concept 2.1 Atomic Structure Is the Basis for Life’s Chemistry
Dalton—mass of one proton or neutron (1.7 × 10–24 grams) Mass of electrons is so tiny, it is usually ignored. 6

7. Concept 2.1 Atomic Structure Is the Basis for Life’s Chemistry
Element—pure substance that contains only one kind of atom Living things are mostly composed of six elements: Carbon (C) Hydrogen (H) Nitrogen (N) Oxygen (O) Phosphorus (P) Sulfur (S)

8. Concept 2.1 Atomic Structure Is the Basis for Life’s Chemistry
The number of protons identifies an element.
Number of protons = atomic number
For electrical neutrality: protons = electrons
Mass number is the number of protons plus neutrons

9. Concept 2.1 Atomic Structure Is the Basis for Life’s Chemistry
Bohr model for atomic structure: atom is largely empty space; the electrons occur in orbits, or electron shells.

10. Concept 2.1 Atomic Structure Is the Basis for Life’s Chemistry
Bohr models are simplified, but useful in understanding how atoms behave. Behavior of electrons determines whether a chemical bond will form between atoms and what shape the bond will have.

11. Figure 2.1 Electron Shells
Figure 2.1 Electron Shells Each shell can hold a specific maximum number of electrons and must be filled before electrons can occupy the next shell. The energy level of an electron is higher in a shell farther from the nucleus. An atom with fewer than eight electrons in its outermost shell (or two in the case of hydrogen) can react (bond) with other atoms.

12. Concept 2.1 Atomic Structure Is the Basis for Life’s Chemistry
Octet rule: for elements 6–20, an atom will lose, gain, or share electrons in order to achieve a stable configuration of 8 electrons in its outermost shell. When atoms share electrons, they form stable associations called molecules.

13. Concept 2.2 Atoms Interact and Form Molecules
A chemical bond is an attractive force that links atoms together in molecules. There are several kinds of chemical bonds.

14. Table 2.1

15. Concept 2.2 Atoms Interact and Form Molecules
Covalent bonds form when two atoms share pairs of electrons. The atoms attain stability by having full outer shells. Each atom contributes one member of the electron pair.

16. Figure 2.2 Electrons Are Shared in Covalent Bonds
Figure 2.2 Electrons Are Shared in Covalent Bonds Two hydrogen atoms can combine to form a hydrogen molecule. A covalent bond forms when the electron shells of the two atoms overlap in an energetically stable manner.

17. Concept 2.2 Atoms Interact and Form Molecules
Carbon atoms have 6 electrons; 4 in the outer shell. They can form covalent bonds with four other atoms.

18. Figure 2.3 Covalent Bonding
Figure 2.3 Covalent Bonding (A) Bohr models showing the formation of covalent bonds in methane, whose molecular formula is CH4. Electrons are shown in shells around the nuclei. (B) Three additional ways of representing the structure of methane. The ball-and-stick and the space-filling models show the spatial orientations of the bonds. The space-filling model indicates the overall shape and surface of the molecule. In the chapters that follow, different conventions will be used to depict molecules. Bear in mind that these are models to illustrate certain properties and are not the most accurate portrayals of reality.

19. Table 2.2

20. Concept 2.2 Atoms Interact and Form Molecules
Properties of molecules are influenced by characteristics of the covalent bonds:
Orientation—length, angle, and direction of bonds between any two elements are always the same. Example: Methane always forms a tetrahedron.

21. Concept 2.2 Atoms Interact and Form Molecules
Strength and stability—covalent bonds are very strong; it takes a lot of energy to break them.
Multiple bonds
Single—sharing 1 pair of electrons
Double—sharing 2 pairs of electrons
Triple—sharing 3 pairs of electrons
C H
C C
N N

22. Concept 2.2 Atoms Interact and Form Molecules
Two atoms of different elements do not always share electrons equally. The nucleus of one element may have greater electronegativity—the attractive force that an atomic nucleus exerts on electrons. Depends on the number of protons and the distance between the nucleus and electrons.

23. Table 2.3

24. Concept 2.2 Atoms Interact and Form Molecules
If atoms have similar electronegativities, they share electrons equally (nonpolar covalent bond). If atoms have different electronegativities, electrons tend to be near the most attractive atom, forming a polar covalent bond.

25. Concept 2.2 Atoms Interact and Form Molecules
The partial charges that result from polar covalent bonds produce polar molecules or polar regions of large molecules. Polar bonds influence interactions with other molecules. Polarity of water molecules determines many of water’s unique properties.

26. Concept 2.2 Atoms Interact and Form Molecules
Hydrogen bonds: Attraction between the δ– end of one molecule and the δ+ hydrogen end of another molecule. They form between water molecules and within larger molecules. Although much weaker than covalent bonds, they are important in the structure of DNA and proteins.

27. Figure 2.4 Hydrogen Bonds Can Form between or within Molecules
Figure 2.4 Hydrogen Bonds Can Form between or within Molecules (A) A hydrogen bond forms between two molecules because of the attraction between an atom with a partial negative charge on one molecule and a hydrogen with a partial positive charge on a second molecule. (B) Hydrogen bonds can form between different parts of the same large molecule.

28. Concept 2.2 Atoms Interact and Form Molecules
Hydrogen bonding contributes to properties of water that are significant for life:
Water is a solvent in living systems—a liquid in which other molecules dissolve.
Water molecules form multiple hydrogen bonds with each other—this contributes to high heat capacity. 28

29. In-Text Art, Chapter 2, p. 23

30. Concept 2.2 Atoms Interact and Form Molecules
A lot of heat energy is required to raise the temperature of water—the heat energy breaks the hydrogen bonds. In organisms, presence of water shields them from fluctuations in environmental temperature. Ice layer insulates water below it

31. Concept 2.2 Atoms Interact and Form Molecules
Water has a high heat of vaporization: a lot of heat energy is required to change water from the liquid to gaseous state (to break the hydrogen bonds).
Thus, evaporation has a cooling effect on the environment.
Sweating cools the body—as sweat evaporates from the skin, it absorbs some of the adjacent body heat.

32. Explain: It’s not the heat, it’s the humidity

33. Concept 2.2 Atoms Interact and Form Molecules
Hydrogen bonds give water cohesive strength, or cohesion—water molecules resist coming apart when placed under tension.
Hydrogen bonding between liquid water molecules and solid surfaces allows for adhesion between the water and the solid surface.

34. In-Text Art, Chapter 2, p. 24

35. Concept 2.2 Atoms Interact and Form Molecules
Cohesion and adhesion allow narrow columns of water to move from roots to the leaves of plants.
Surface tension: water molecules at the surface are hydrogen-bonded to other molecules below them, making the surface difficult to puncture. This allows spiders to walk on the surface of a pond. 35

37. Concept 2.2 Atoms Interact and Form Molecules
Any polar molecule can interact with any other polar molecule through hydrogen bonds.
Hydrophilic (“water-loving”): in aqueous solutions, polar molecules become separated and surrounded by water molecules.
Nonpolar molecules are called hydrophobic (“water-hating”); the interactions between them are hydrophobic interactions.

38. Figure 2.5 Hydrophilic and Hydrophobic
Figure 2.5 Hydrophilic and Hydrophobic (A) Molecules with polar covalent bonds are attracted to polar water (they are hydrophilic). (B) Molecules with nonpolar covalent bonds show greater attraction to one another than to water (they are hydrophobic). The color convention in the models shown here (gray, H; red, O; black, C; green, F) is often used.

39. High surface tension
Hydrophobic hairs on the legs of the spider
And larger surface area to spread weight

41. Concept 2.2 Atoms Interact and Form Molecules
When one atom is much more electronegative than the other, a complete transfer of electrons may occur. This makes both atoms more stable because their outer shells are full. The result is two ions—electrically charged particles that form when atoms gain or lose one or more electrons. 41

42. Figure 2.6 Ionic Attraction between Sodium and Chlorine
Figure 2.6 Ionic Attraction between Sodium and Chlorine When a sodium atom reacts with a chlorine atom, the chlorine fills its outermost shell by “stealing” an electron from the sodium. In so doing, the chlorine atom becomes a negatively charged chloride ion (Cl–). With one less electron, the sodium atom becomes a positively charged sodium ion (Na+).

43. Concept 2.2 Atoms Interact and Form Molecules
Cations—positively charged ions Anions—negatively charged ions Ionic attractions result from the electrical attraction between ions with opposite charges. The resulting molecules are called salts or ionic compounds. 43

44. Concept 2.2 Atoms Interact and Form Molecules
Ionic attractions are weak, so salts dissolve easily in water.
place text art pg 25 here

45. Concept 2.2 Atoms Interact and Form Molecules
Functional groups—small groups of atoms with specific chemical properties Functional groups confer these properties to larger molecules (e.g., polarity). One biological molecule may contain many functional groups that determine molecular shape and reactivity.

46. Figure 2.7 Functional Groups Important to Living Systems (Part 1)
Figure 2.7 Functional Groups Important to Living Systems Highlighted in yellow are the seven functional groups most commonly found in biological molecules. “R” represents the rest of the molecule.

47. Figure 2.7 Functional Groups Important to Living Systems (Part 2)
Figure 2.7 Functional Groups Important to Living Systems Highlighted in yellow are the seven functional groups most commonly found in biological molecules. “R” represents the rest of the molecule.

48. Figure 2.7 Functional Groups Important to Living Systems (Part 3)
Figure 2.7 Functional Groups Important to Living Systems Highlighted in yellow are the seven functional groups most commonly found in biological molecules. “R” represents the rest of the molecule.

49. In-Text Art, Chapter 2, p. 26

50. Concept 2.2 Atoms Interact and Form Molecules
Proteins—formed from different combinations of 20 amino acids
Carbohydrates—formed by linking sugar monomers (monosaccharides) to form polysaccharides
Nucleic acids—formed from four kinds of nucleotide monomers
Lipids—noncovalent forces maintain the interactions between the lipid monomers

51. Concept 2.2 Atoms Interact and Form Molecules
Polymers are formed and broken apart in reactions involving water.
Condensation—removal of water links monomers together
Hydrolysis—addition of water breaks a polymer into monomers

52. Figure 2.8 Condensation and Hydrolysis of Polymers (Part 1)
Figure 2.8 Condensation and Hydrolysis of Polymers (A) Condensation reactions link monomers into polymers and produce water. (B) Hydrolysis reactions break polymers into individual monomers and consume water.

53. Figure 2.8 Condensation and Hydrolysis of Polymers (Part 2)
Figure 2.8 Condensation and Hydrolysis of Polymers (A) Condensation reactions link monomers into polymers and produce water. (B) Hydrolysis reactions break polymers into individual monomers and consume water.

54. Concept 2.3 Carbohydrates Consist of Sugar Molecules
Source of stored energy
Transport stored energy within organisms
Structural molecules give many organisms their shapes
Recognition or signaling molecules can trigger specific biological responses

55. Concept 2.3 Carbohydrates Consist of Sugar Molecules
Monosaccharides are simple sugars.
Pentoses are 5-carbon sugars.
Ribose and deoxyribose are the backbones of RNA and DNA.
Hexoses (C6H12O6) include glucose, fructose, mannose, and galactose.

56. Figure 2.9 Monosaccharides
Figure 2.9 Monosaccharides Monosaccharides are made up of varying numbers of carbons. Many have the same kind and number of atoms, but the atoms are arranged differently.

57. Concept 2.3 Carbohydrates Consist of Sugar Molecules
Monosaccharides are covalently bonded by condensation reactions that form glycosidic linkages to form disaccharides.
place text art pg 27 here

58. Concept 2.3 Carbohydrates Consist of Sugar Molecules
Oligosaccharides contain several monosaccharides.
Many have additional functional groups.
They are often bonded to proteins and lipids on cell surfaces, where they serve as recognition signals.
The human blood groups (ABO) get their specificity from oligosaccharide chains.

59. Concept 2.3 Carbohydrates Consist of Sugar Molecules
Polysaccharides are large polymers; the chains can be branching.
Starches—polymers of glucose
Glycogen—highly branched polymer of glucose; main energy storage molecule in mammals

60. Figure 2.10 Polysaccharides (Part 1)
Figure Polysaccharides Cellulose, starch, and glycogen are all composed of long chains of glucose but with different levels of branching and compaction.

61. Concept 2.3 Carbohydrates Consist of Sugar Molecules61

62. Concept 2.3 Carbohydrates Consist of Sugar Molecules
Cellulose—the main component of plant cell walls.
It is the most abundant carbon- containing (organic) biological compound on Earth.
Very stable; good structural material 62

63. Concept 2.3 Carbohydrates Consist of Sugar Molecules63

64. Concept 2.4 Lipids Are Hydrophobic Molecules
Lipids Hydrocarbons (composed of C and H atoms) that are insoluble in water because of many nonpolar covalent bonds. When close together, weak but additive van der Waals interactions hold them together.

65. Concept 2.4 Lipids Are Hydrophobic Molecules
Store energy in C—C and C—H bonds
Play structural roles in cell membranes
Fat in animal bodies serves as thermal insulation

66. Concept 2.4 Lipids Are Hydrophobic Molecules
Triglycerides (simple lipids)
Fats—solid at room temperature
Oils—liquid at room temperature
Have very little polarity and are extremely hydrophobic.

67. Concept 2.4 Lipids Are Hydrophobic Molecules
Triglycerides consist of:
Three fatty acids—nonpolar hydrocarbon chain attached to a polar carboxyl group (—COOH) (carboxylic acid)
One glycerol—an alcohol with three hydroxyl (—OH) groups
Synthesis of a triglyceride involves three condensation reactions.

68. Figure 2.11 Synthesis of a Triglyceride
Figure Synthesis of a Triglyceride In living things, the reaction that forms a triglyceride is more complex than the single step shown here.

69. Concept 2.4 Lipids Are Hydrophobic Molecules
The fatty acid chains can vary in length and structure. In saturated fatty acids, all bonds between carbon atoms are single; they are saturated with hydrogens. In unsaturated fatty acids, hydrocarbon chains have one or more double bonds. This causes kinks in the chain and prevents molecules from packing together tightly.

70. Concept 2.4 Lipids Are Hydrophobic Molecules
Because the unsaturated fatty acids do not pack tightly, they have low melting points and are usually liquid at room temperature.
place text art pg 30 here 70

71. Figure 2.12 Saturated and Unsaturated Fatty Acids (Part 1)
Figure Saturated and Unsaturated Fatty Acids (A) The straight hydrocarbon chain of a saturated fatty acid allows the molecule to pack tightly with other, similar molecules. (B) In unsaturated fatty acids, kinks in the chain prevent close packing.

72. Figure 2.12 Saturated and Unsaturated Fatty Acids (Part 2)
Figure Saturated and Unsaturated Fatty Acids (A) The straight hydrocarbon chain of a saturated fatty acid allows the molecule to pack tightly with other, similar molecules. (B) In unsaturated fatty acids, kinks in the chain prevent close packing.

73. Concept 2.4 Lipids Are Hydrophobic Molecules
Fatty acids are amphipathic; they have a hydrophilic end and a hydrophobic tail. Phospholipid—two fatty acids and a phosphate group bound to glycerol; The phosphate group has a negative charge, making that part of the molecule hydrophilic.

74. Figure 2.13 Phospholipids (Part 1)
Figure Phospholipids (A) Phosphatidylcholine (lecithin) is an example of a phospholipid molecule. In other phospholipids, the amino acid serine, the sugar alcohol inositol, or another compound replaces choline. (B) In an aqueous environment, hydrophobic interactions bring the “tails” of phospholipids together in the interior of a bilayer. The hydrophilic “heads” face outward on both sides of the bilayer, where they interact with the surrounding water molecules.

75. Concept 2.4 Lipids Are Hydrophobic Molecules
In an aqueous environment, phospholipids form a bilayer. The nonpolar, hydrophobic “tails” pack together and the phosphate-containing “heads” face outward, where they interact with water. Biological membranes have this kind of phospholipid bilayer structure.

76. Figure 2.13 Phospholipids (Part 2)
Figure Phospholipids (A) Phosphatidylcholine (lecithin) is an example of a phospholipid molecule. In other phospholipids, the amino acid serine, the sugar alcohol inositol, or another compound replaces choline. (B) In an aqueous environment, hydrophobic interactions bring the “tails” of phospholipids together in the interior of a bilayer. The hydrophilic “heads” face outward on both sides of the bilayer, where they interact with the surrounding water molecules.

77. Concept 2.5 Biochemical Changes Involve Energy
Chemical reactions occur when atoms have enough energy to combine or change bonding partners.
sucrose + H2O glucose + fructose
(C12H22O11) (C6H12O6) (C6H12O6)
reactants products

78. Concept 2.5 Biochemical Changes Involve Energy
Chemical reactions involve changes in energy. Energy can be defined as the capacity to do work, or the capacity for change. In biochemical reactions, energy changes are usually associated with changes in the chemical composition and properties of molecules.

79. Concept 2.5 Biochemical Changes Involve Energy
All forms of energy can be considered as either:
Potential—the energy of state or position, or stored energy
Kinetic—the energy of movement; the type of energy that does work; that makes things change
Energy can be converted from one form to another. 79

80. Concept 2.5 Biochemical Changes Involve Energy
Metabolism—sum total of all chemical reactions occurring in a biological system at a given time Metabolic reactions involve energy changes. Energy is either stored in, or released from, chemical bonds. A chemical reaction will occur spontaneously if the total energy consumed by breaking bonds in the reactants is less than the total energy released by forming bonds in the products.

81. Concept 2.5 Biochemical Changes Involve Energy
Two basic types of metabolism:
Anabolic reactions link simple molecules to form complex ones.
They require energy inputs (endergonic or endothermic; energy is captured in the chemical bonds that form.

82. Figure 2.14 Energy Changes in Reactions
Figure Energy Changes in Reactions (A) In an endergonic (anabolic) reaction, rolling the ball uphill requires an input of energy. (B) In an exergonic (catabolic) reaction, the reactants behave like a ball rolling down a hill, and energy is released.

83. Concept 2.5 Biochemical Changes Involve Energy
Catabolic reactions: energy is released (exergonic or exothermic)
Complex molecules are broken down into simpler ones.
Energy stored in the chemical bonds is released. 83

84. Concept 2.5 Biochemical Changes Involve Energy
Catabolic and anabolic reactions are often linked. The energy released in catabolic reactions is often used to drive anabolic reactions— to do biological work. 84

85. Concept 2.5 Biochemical Changes Involve Energy
The laws of thermodynamics apply to all matter and energy transformations in the universe.
First law: Energy is neither created nor destroyed.
Second law: Useful energy tends to decrease.
When energy is converted from one form to another, some of that energy becomes unavailable for doing work.

86. Figure 2.15 The Laws of Thermodynamics (Part 1)
Figure The Laws of Thermodynamics (A) The first law states that energy cannot be created or destroyed. (B) The second law states that after energy transformations, some energy becomes unavailable to do work.

87. Figure 2.15 The Laws of Thermodynamics (Part 2)
Figure The Laws of Thermodynamics (A) The first law states that energy cannot be created or destroyed. (B) The second law states that after energy transformations, some energy becomes unavailable to do work.

88. Figure 2.15 The Laws of Thermodynamics (Part 3)
Figure The Laws of Thermodynamics (A) The first law states that energy cannot be created or destroyed. (B) The second law states that after energy transformations, some energy becomes unavailable to do work.

89. Concept 2.5 Biochemical Changes Involve Energy
No physical process or chemical reaction is 100% efficient—some of the released energy is lost in a form associated with disorder. This energy is so dispersed that it is unusable. Entropy is a measure of the disorder in a system. As a result of energy transformations, disorder tends to increase.

90. Concept 2.5 Biochemical Changes Involve Energy
If a chemical reaction increases entropy, its products are more disordered or random than its reactants. If there are fewer products than reactants, the disorder is reduced; this requires energy to achieve. 90

91. Concept 2.5 Biochemical Changes Involve Energy
Metabolism creates more disorder (more energy is lost to entropy) than the amount of order that is stored.
Example:
The anabolic reactions needed to construct 1 kg of animal body require the catabolism of about 10 kg of food.
Life requires a constant input of energy to maintain order.

92. Answer to Opening Question
Water is essential for life. One way to investigate the possibility of life on other planets is to study how life may have originated on Earth. Experiments in the 1950s combined gases thought to be present in Earth’s early atmosphere, including water vapor. An electric spark provided energy. Complex molecules formed, such as amino acids. Water was essential in this experiment.

93. Figure 2.16 Miller and Urey Synthesized Prebiotic Molecules in an Experimental Atmosphere (Part 1)
Figure Miller and Urey Synthesized Prebiotic Molecules in an Experimental Atmosphere With an increased understanding of the atmospheric conditions that existed on primitive Earth, the researchers devised an experiment to see if these conditions could lead to the formation of organic molecules.a [a S. L. Miller and H. C. Urey Science 130: 245–251.]

94. Figure 2.16 Miller and Urey Synthesized Prebiotic Molecules in an Experimental Atmosphere (Part 2)
Figure Miller and Urey Synthesized Prebiotic Molecules in an Experimental Atmosphere With an increased understanding of the atmospheric conditions that existed on primitive Earth, the researchers devised an experiment to see if these conditions could lead to the formation of organic molecules.a [a S. L. Miller and H. C. Urey Science 130: 245–251.]