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Life Chemistry and Energy 2. Chapter 2 Life Chemistry and Energy Key Concepts 2.1 Atomic Structure Is the Basis for Lifes Chemistry 2.2 Atoms Interact.

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Presentation on theme: "Life Chemistry and Energy 2. Chapter 2 Life Chemistry and Energy Key Concepts 2.1 Atomic Structure Is the Basis for Lifes Chemistry 2.2 Atoms Interact."— Presentation transcript:

1 Life Chemistry and Energy 2

2 Chapter 2 Life Chemistry and Energy Key Concepts 2.1 Atomic Structure Is the Basis for Lifes 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 Enduring Understanding 2.A. Growth, reproduction, and maintenance of the organization of living systems require free energy and matter. (The concept of free energy will be discussed in detail during Chapter 6)

4 Essential Knowledge 2.A.1. All living systems require constant input of energy. 2.A.3. Organisms must exchange matter with the environment to grow, reproduce, and maintain organization.

5 Assessment Test of Chapter 2

6 Word Roots Like any profession, the study of biology has its own language. Nouns constructed with components – prefixes and suffixes – of definite purpose and meaning. What follows may be useful to you in understanding the construction and meaning of scientific vocabulary.

7 Word Roots hydro - water; - philos loving; - phobos fearing (hydrophilic: having an affinity for water; hydrophobic: having an aversion to water) kilo - a thousand (kilocalorie: a thousand calories) Instructors Guide for Campbell/Reece Biology, Seventh Edition

8 Word Roots carb - coal (carboxyl group: a functional group present in organic acids, consisting of a carbon atom double-bonded to an oxygen atom and a hydroxyl group) enanti - opposite (enantiomer: molecules that are mirror images of each other) hydro - water (hydrocarbon: an organic molecule consisting only of carbon and hydrogen)

9 Word Roots iso - equal (isomer: one of several organic compounds with the same molecular formula but different structures and, therefore, different properties) sulf - sulfur (sulfhydryl group: a functional group that consists of a sulfur atom bonded to an atom of hydrogen) thio - sulfur (thiol: organic compounds containing sulfhydryl groups)

10 Word Roots con - together (condensation reaction: a reaction in which two molecules become covalently bonded to each other through the loss of a small molecule, usually water) di - two (disaccharide: two monosaccharides joined together)

11 Word Roots glyco - sweet (glycogen: a polysaccharide sugar used to store energy in animals) hydro - water; - lyse break (hydrolysis: breaking chemical bonds by adding water) macro - large (macromolecule: a large molecule) meros - part (polymer: a chain made from smaller organic molecules)

12 Word Roots mono - single; - sacchar sugar (monosaccharide: simplest type of sugar) poly - many (polysaccharide: many monosaccharides joined together) tri - three (triacylglycerol: three fatty acids linked to one glycerol molecule)

13 Word Roots bio- life (bioenergetics: the study of how organisms manage their energy resources) endo- within (endergonic reaction: a reaction that absorbs free energy from its surroundings) ex- out (exergonic reaction: a reaction that proceeds with a net release of free energy)

14 Word Roots kinet- movement (kinetic energy: the energy of motion) therm- heat (thermodynamics: the study of the energy transformations that occur in a collection of matter)

15 Word Roots ana - up (anabolic pathway: a metabolic pathway that consumes energy to build complex molecules from simpler ones) cata- down (catabolic pathway: a metabolic pathway that releases energy by breaking down complex molecules into simpler ones)

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

17 Concept 2.1 Atomic Structure Is the Basis for Lifes Chemistry Living and nonliving matter is composed of atoms.

18 Concept 2.1 Atomic Structure Is the Basis for Lifes Chemistry Like charges repel; different charges attract. Most atoms are neutral because the number of electrons equals the number of protons. Daltonmass of one proton or neutron (1.7 × 10 –24 grams) Mass of electrons is so tiny, it is usually ignored.

19 Concept 2.1 Atomic Structure Is the Basis for Lifes Chemistry Elementpure substance that contains only one kind of atom Living things are mostly composed of 6 elements: Carbon (C) Hydrogen (H) Nitrogen (N) Oxygen (O) Phosphorus (P) Sulfur (S)

20 Concept 2.1 Atomic Structure Is the Basis for Lifes Chemistry The number of protons identifies an element. Number of protons = atomic number For electrical neutrality, # protons = # electrons. Mass numbertotal number of protons and neutrons

21 Concept 2.1 Atomic Structure Is the Basis for Lifes Chemistry A Bohr model for atomic structurethe atom is largely empty space, and the electrons occur in orbits, or electron shells.

22 Concept 2.1 Atomic Structure Is the Basis for Lifes Chemistry Actual atomic structure is far more complicated than the Bohr model - electron clouds, quantum mechanics, electron configurations, etc.

23 Concept 2.1 Atomic Structure Is the Basis for Lifes Chemistry Behavior of electrons determines whether a chemical bond will form and what shape the bond will have.

24 Concept 2.1 Atomic Structure Is the Basis for Lifes Chemistry Octet rule Atoms with at least two electron shells form stable molecules So they have eight electrons in their outermost (valence) shells.

25 Figure 2.1 Electron Shells

26 Concept 2.1 Atomic Structure Is the Basis for Lifes Chemistry Atoms with unfilled outer shells tend to undergo chemical reactions to fill their outer shells. Stability attained by sharing electrons with other atoms or by losing or gaining electrons. The atoms are then bonded together into molecules.

27 Concept 2.2 Atoms Interact and Form Molecules Chemical bond An attractive force that links atoms together to form molecules. There are several kinds of chemical bonds.

28 Table 2.1 Chemical Bonds and Interactions

29 Concept 2.2 Atoms Interact and Form Molecules Ionic bonds Ions are charged particle that form when an atom gains or loses one or more electrons. Cationspositively charged ions Anionsnegatively charged ions Ionic bonds result from the electrical attraction between ions with opposite charges. The resulting molecules are called salts.

30 Figure 2.2 Ionic Bond between Sodium and Chlorine

31 Concept 2.2 Atoms Interact and Form Molecules Ionic attractions are weak, so salts dissolve easily in water. More about dissolving later…

32 Concept 2.2 Atoms Interact and Form Molecules Covalent bonds 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.

33 Figure 2.3 Electrons Are Shared in Covalent Bonds

34 Covalent Bonds

35 Animation – Ionic and Covalent Bonds

36 Van der Waals Interactions Van der Waals interactions Occur when transiently positive and negative regions of molecules attract each other

37 Van der Waals interactions Molecules with partially negative and positive regions: Their electrons are constantly moving Can be moments when electrons accumulate by chance in one area of a molecule. At that moment, a regions of negative charge is created, and positive region opposite. Van der Waals Interactions

38 Van der Waals interactions

39 COMMON MISCONCEPTION The simplified models of the atom electron shells, and covalent bonding can be confusing if you take them too literally. Please understand that: Atoms do not have defined surfaces. Electrons do not travel in planetary orbits around the nucleus of the atom. Shared electron pairs are not paired spatially in covalent bonds. Electron shells represent energy levels rather than the position of electrons. Student Misconceptions

40 Concept 2.2 Atoms Interact and Form Molecules Carbon Carbon atoms have four electrons in the outer shell Can form single covalent bonds with four other atoms.

41 Figure 2.4 Covalent Bonding (Part 1)

42 Figure 2.4 Covalent Bonding (Part 2)

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

44 Video 2.1 Methane: A three-dimensional model

45 Video 2.2 Starch: A three-dimensional model

46 Concept 2.2 Atoms Interact and Form Molecules Strength and stabilitycovalent bonds are very strong; it takes a lot of energy to break them. Multiple bonds Singlesharing 1 pair of electrons Doublesharing 2 pairs of electrons Triplesharing 3 pairs of electrons C H C N

47 Concept 2.2 Atoms Interact and Form Molecules Degree of sharing electrons is not always equal. Lets review the implications of this in terms of Electronegativity Hydrogen bonds Specific heat capacity Polar and nonpolar covalent bonds Cohesion and adhesion Heat of vaporization Solvent

48 Concept 2.2 Atoms Interact and Form Molecules Degree of sharing electrons is not always equal. Electronegativitythe attractive force that an atomic nucleus exerts on electrons It depends on the number of protons and the distance between the nucleus and electrons.

49 Table 2.2 Some Electronegativities

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

51 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 forms hydrogen bonds. Special kind of interactive force of attraction between a hydrogen atom, H, and the nonbonding electrons of a second, very electronegative F, O, or N

52 Concept 2.2 Atoms Interact and Form Molecules Hydrogen bonds Do not involve the sharing or transfer of electrons. Relies on the attraction of partial opposite charges. Important in the structure of DNA and proteins.

53 Hydrogen bonds + + H H + + – – – – Concept 2.2 Atoms Interact and Form Molecules

54 Hydrogen bonds Can occur between different molecules as long as there are areas of partial opposite charges.

55 Figure 2.5 Hydrogen Bonds Can Form between or within Molecules

56 Concept 2.2 Atoms Interact and Form Molecules Hydrogen bonds Are weak bonds; roughly 1/20 th the strength of a typical covalent bond. Are fleeting; they form and break with slight changes in the systems energy. Have a collective strength, as you see in the formation of water ice.

57 Hydrogen bonds The bond lengths give some indication of the bond strength. A normal covalent bond is 0.96 Angstroms, while the hydrogen bond length is 1.97 A. Ahydrogenbond.html

58 Hydrogen bonds At 0 o C, water becomes locked into a crystalline lattice with each molecule bonded to the maximum of four partners.

59 Hydrogen bonds Remember – bond length of hydrogen bonds is roughly twice as much as typical covalent bond

60 Hydrogen bonds Resulting lattice structure finds molecules farther apart. As a result, the same amount of mass occupies more volume.

61 Hydrogen bonds Water ice is approximately 10% less dense that liquid water.

62 Concept 2.2 Atoms Interact and Form Molecules Since ice floats in water, Life can exist under the frozen surfaces of lakes and polar seas So why is this oddity important to life? Concept 2.2 Atoms Interact and Form Molecules

63 If ice sank, eventually all ponds, lakes, and even the ocean would freeze solid from bottom up. During the summer, only the upper few inches of the ocean would thaw. Instead, the surface layer of ice insulates liquid water below, preventing it from freezing and allowing life to exist under the frozen surface.

64 Concept 2.2 Atoms Interact and Form Molecules Hydrogen bonds Hydrogen bonds make possible waters properties: freezing point, cohesion and adhesion, plus its ability to dissolve many substances. Weak bonds like the hydrogen bond are vital in many biological processes

65 Animation – Hydrogen Bonds

66 Animation – Molecular Water

67 Video- Hydrogen Bonds

68 Animation – Hydrogen Bonds

69 Animation – Basilisk Lizard

70 Student Misconceptions COMMON MISCONCEPTION Students often believe that a hydrogen bond can occur between atoms in the same manner as ionic or covalent bonds instead of as a strong, yet transient attraction.

71 Student Misconceptions COMMON MISCONCEPTIONS Weak bonds play important roles in the chemistry of life, despite the transient nature of each individual bond. The compelling example of the gecko, able to walk on ceilings because of the van der Waals interactions between the ceiling and the hairs on the geckos toes. Strong and weak bonds are both important in the chemistry of life. Can you think of any examples?

72 Concept 2.2 Atoms Interact and Form Molecules Water molecules form multiple hydrogen bonds with each otherthis contributes to high specific heat capacity.

73 Concept 2.2 Atoms Interact and Form Molecules A lot of heat is required to raise the temperature of waterthe heat energy breaks the hydrogen bonds. In organisms, presence of water shields them from fluctuations in environmental temperature.

74 Concept 2.2 Atoms Interact and Form Molecules Water moderates air temperature By absorbing heat from air that is warmer and releasing the stored heat to air that is cooler Why can water absorb or release relatively large amounts of heat with only a slight change in its own temperature?

75 Concept 2.2 Atoms Interact and Form Molecules Distinguish Between Heat and Temperature Heat Is a measure of the total amount of kinetic energy due to molecular motion Temperature Measures the intensity of heat due to the average kinetic energy of molecules.

76 Concept 2.2 Atoms Interact and Form Molecules Atoms and molecules have kinetic energy, the energy of motion, because they are always moving. Faster that a molecule moves, the more kinetic energy that it has. As the average speed of molecules increases, a thermometer will record an increase in temperature. Heat and temperature are related, but not identical.

77 Concept 2.2 Atoms Interact and Form Molecules FYI: There is no measure of cold in science – all objects have heat energy until the object is at absolute zero. Heat passes from the warmer object to the cooler until the two are the same temperature. Molecules in the cooler object speed up at the expense of kinetic energy of the warmer object. Ice cubes cool a drink by absorbing heat as the ice melts.

78 Concept 2.2 Atoms Interact and Form Molecules Biology measure temperature on the Celsius scale ( o C). At sea level, water freezes at O o C and boils at 100 o C. Human body temperature averages 37 o C.

79 Concept 2.2 Atoms Interact and Form Molecules Convenient unit of measurement of heat energy is the calorie (cal). One calorie is the amount of heat energy necessary to raise the temperature of one g of water by 1 o C.

80 Concept 2.2 Atoms Interact and Form Molecules

81 In biology, the kilocalorie (kcal), is even more convenient. A kilocalorie is the amount of heat energy necessary to raise the temperature of 1000g (1 kilogram or kg) of water by 1 o C. Another common energy unit, the joule (J), is equivalent to cal.

82 Water has a relatively high specific heat The specific heat of a substance Is the amount of heat that must be absorbed or lost for 1 gram of that substance to change its temperature by 1ºC Absorbing heat energy will increase temperature Releasing heat energy will decrease temperature Concept 2.2 Atoms Interact and Form Molecules

83 Water has a high specific heat compared to other substances. Example: ethyl alcohol has a specific heat of 0.6 cal/g/ o C Less energy required to get a temperature increase in alcohol Specific heat of iron is 1/10th that of water. Concept 2.2 Atoms Interact and Form Molecules

84 Due to high specific heat, water resists changes in temperature Takes relatively more heat energy to speed up its molecules Or, water absorbs or releases a relatively large quantity of heat for each degree of change Concept 2.2 Atoms Interact and Form Molecules

85 Waters high specific heat is due to hydrogen bonding between each molecule of water Must absorb heat to break the hydrogen bonds Because so much energy must first be used to break hydrogen bonds… Less energy is actually available to move the molecules faster – to increase its kinetic energy and therefore its temperature. Concept 2.2 Atoms Interact and Form Molecules

86 When enough energy is added, enough bonds break… Thats when a liquid may change its state of matter – liquid to gas. Concept 2.2 Atoms Interact and Form Molecules

87 Heating Curve of Water It takes a lot of energy to force a change of waters state of matter – solid to liquid to gas. Why? Goes back to hydrogen bonds – added energy goes first to breaking hydrogen bonds before water can be evaporated.

88 Concept 2.2 Atoms Interact and Form Molecules Environmental significance of high specific heat Waters high specific heat allows water to minimize temperature fluctuations to within limits that permit life. Ever notice how it is cooler near at a beach?

89 Environmental significance of high specific heat Large bodies of water can absorb a large amount of heat from the sun in daytime and during the summer, while warming only a few degrees. At night and during the winter, the warm water will warm cooler air. Therefore, ocean temperatures and coastal land areas have more stable temperatures than inland areas. Environmental significance of high specific heat

90 High specific heat impact individual organisms Organisms are mostly water. Water moderates changes in temperature better than if composed of a liquid with a lower specific heat.

91 Concept 2.2 Atoms Interact and Form Molecules Transformation of a substance from a liquid to a gas known as vaporization Molecules now move fast enough to overcome the attraction of other molecules in the liquid. Even in a low temperature liquid (low average kinetic energy), some molecules are moving fast enough to evaporate. Heating a liquid increases the average kinetic energy and increases the rate of evaporation.

92 Concept 2.2 Atoms Interact and Form Molecules Heat of vaporization Quantity of heat a liquid must absorb for 1 gram of it to be converted from a liquid to a gas. Water has a relatively high heat of vaporization. About 580 cal of heat to evaporate 1g of water at room temperature. Thats double the heat of vaporization of alcohol or ammonia. Why?

93 Why? Ill tell you why! Waters many more hydrogen bonds must be broken before it can evaporate. So why is a high heat of vaporization important to biology? Heat of Vaporization

94 Concept 2.2 Atoms Interact and Form Molecules Observe same quantities of water and isopropyl alcohol poured onto tables as a thin film. What did you see? The alcohol evaporated much faster than the water. What does this say about alcohols heat of vaporization?

95 Concept 2.2 Atoms Interact and Form Molecules As a liquid evaporates, the surface of the liquid that remains behind cools - evaporative cooling. Is due to waters high heat of vaporization. Allows water to cool a surface. Cooling happens because the most energetic molecules are the most likely to evaporate, leaving the lower kinetic energy molecules behind. So why is evaporative cooling important to biology?

96 Concept 2.2 Atoms Interact and Form Molecules Remember, water has a high heat of vaporizationa lot of heat is required to change water from liquid to gaseous state. Thus, evaporation has a cooling effect on the environment. Sweating cools the bodyas sweat evaporates from the skin, it transforms some of the adjacent body heat.

97 Concept 2.2 Atoms Interact and Form Molecules Hydrogen bonds also give water cohesive strength, or cohesionwater molecules resist coming apart when placed under tension. Bonding of a high percentage of the molecules to neighboring molecules Due to hydrogen bonding Permits narrow columns of water to move from roots to leaves of plants.

98 Concept 2.2 Atoms Interact and Form Molecules Helps pull water up through the microscopic vessels of plants Water conducting cells 100 µm

99 Concept 2.2 Atoms Interact and Form Molecules

100 Cohesion and formation of a meniscus

101 Animation - Cohesion Transport

102 Surface tension Related to cohesion, it is a measure of the force necessary to break the surface of a liquid. Water has greater surface tension that most liquids.

103 The Solvent of Life Water is a versatile solvent due to its polarity. It can form aqueous solutions: Solution A liquid that is a completely homogeneous mixture of two or more substances Aqueous solution A solution in which water is the solvent Solvent Dissolving agent

104 The different regions of the polar water molecule can interact with ionic compounds called solutes and dissolve them. Negative oxygen regions of polar water molecules are attracted to sodium cations (Na + ) Cl – – – – – Na + Positive hydrogen regions of water molecules cling to chloride anions (Cl – ) – – – – – – Na + Cl – The Solvent of Life

105 Each dissolved ion is surrounded by a sphere of water molecules, a hydration shell. Eventually, water dissolves all the ions, resulting in a solution with two solutes, sodium and chloride. The Solvent of Life

106 Polar molecules are water soluble because they can form hydrogen bonds with water. Even large molecules, like proteins, can dissolve in water if they have ionic and polar regions. The Solvent of Life

107 Water can also interact with polar molecules such as proteins. This oxygen is attracted to a slight positive charge on the lysozyme molecule. This oxygen is attracted to a slight negative charge on the lysozyme molecule. (a) Lysozyme molecule in a nonaqueous environment (b) Lysozyme molecule (purple) in an aqueous environment such as tears or saliva (c) Ionic and polar regions on the proteins Surface attract water molecules. + – The Solvent of Life

108 Glucose molecules have polar hydroxyl (OH) groups in them and these attract the water to them. When sugar is in a crystal the molecules are attracted to the water and go into solution. Once in solution the molecules stay in solution at least in part because they become surrounded by water molecules. This layer of water molecules surrounding another molecule is called a hydration shell. hydrophilic.html

109 Dissolving leads to a hydration shell which bounds up water molecules – fewer free water molecules, less osmotic potential (more on osmosis in later chapter) hydrophilic.html

110 When a sucrose molecule is in water, it is immediately surrounded by water molecules. The sucrose has hydroxyl groups that have a slight negative charge. The positive charge of the oxygen found in the water molecule binds with the sugar. As the hydration shell forms around the sucrose molecule, the molecule is shielded from other sugar molecules so the sugar crystal does not reform. quiry/water/waterpaid/waterhtmls/ chem8.html

111 Assuming two solutions of the same molar concentration, one of glucose, the other of sucrose Glucose, being a smaller molecule with therefore relatively greater surface area than sucrose, will bound up more water molecules. quiry/water/waterpaid/waterhtmls/ chem8.html

112 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.

113 Figure 2.6 Hydrophilic and Hydrophobic

114 Water: exists in nature as three states of matter Concept 2.2 Atoms Interact and Form Molecules

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119 Water: exists in nature as three states of matter Concept 2.2 Atoms Interact and Form Molecules

120 Water: exists in nature as three states of matter Concept 2.2 Atoms Interact and Form Molecules

121 Water: exists in nature as three states of matter Concept 2.2 Atoms Interact and Form Molecules

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

123 Overview Three-quarters of the Earths surface is submerged in water. The abundance of water is the main reason the Earth is habitable. Concept 2.2 Atoms Interact and Form Molecules

124 Water is most unusual Only pure substance that exists naturally as a gas, liquid and solid. Less dense as a solid than a liquid, unlike almost all other chemicals. Explains why ice floats.

125 Concept 2.2 Atoms Interact and Form Molecules Water is the molecule that supports all of life Water is the biological medium here on Earth. All living organisms require water more than any other substance.

126 Concept 2.2 Atoms Interact and Form Molecules Liquids essential to biochemistry because… Biochemical reactions need a liquid medium. In a liquid, molecules can dissolve and chemical reactions can occur. Liquid not stable; it can transport chemical from place to place within a cell, organism, or ecosystem. Imagine trying to transport vital nutrients within a solid or a gas.

127 Concept 2.2 Atoms Interact and Form Molecules Water is the best liquid The best solvent – it dissolves just about everything. Helps maintain the shape of enzymes – essential catalysts of biochemistry – no shape, no chemistry. If water wasnt the essential liquid, if another liquid could take its place, why havent we seen it in any life forms?

128 Concept 2.2 Atoms Interact and Form Molecules Ammonia!

129 Concept 2.2 Atoms Interact and Form Molecules AP TIP You should be able to describe the properties of water and why these properties are important to life.

130 Concept 2.2 Atoms Interact and Form Molecules Functional groupssmall groups of atoms with specific chemical properties Confer these properties to larger molecules, e.g., polarity. One biological molecule may contain many functional groups. Attachments that replace one or more hydrogen atoms to the carbon skeleton. Behave consistently from one organic molecule to another.

131 Concept 2.2 Atoms Interact and Form Molecules Basic structure of testosterone (male hormone) and estradiol (female hormone) is identical. CH 3 OH HO O CH 3 OH Estradiol Testosterone Female lion Male lion

132 Concept 2.2 Atoms Interact and Form Molecules Both are steroids with four fused carbon rings, but have different functional groups attached to the rings. CH 3 OH HO O CH 3 OH Estradiol Testosterone Female lion Male lion

133 Concept 2.2 Atoms Interact and Form Molecules These functional groups then interact with different targets in the body. CH 3 OH HO O CH 3 OH Estradiol Testosterone Female lion Male lion

134 Male and female mallards

135 Male and female peacocks

136 Male and female sage grouse

137 Concept 2.2 Atoms Interact and Form Molecules Six functional groups are important in the chemistry of life: Hydroxyl Carbonyl Carboxyl Amino Sulfhydryl Phosphate All are hydrophilic and increase the solubility of organic compounds in water.

138 -OH, a hydrogen atom forms a polar covalent bond with an oxygen atom, which forms a polar covalent bond to the carbon skeleton. Because of these polar covalent bonds, hydroxyl groups improve the solubility of organic molecules. Hydroxyl group

139 Organic compounds with hydroxyl groups are alcohols and their names typically end in -ol. Hydroxyl group

140 >Carbonyl consists of an oxygen atom joined to the carbon skeleton by a double bond. If the carbonyl group is on the end of the skeleton, the compound is an aldelhyde. Carbonyl group

141 If not, then the compound is a ketone. Isomers with aldehydes versus ketones have different properties. Carbonyl group

142 -Carboxyl COOH consists of a carbon atom with a double bond to an oxygen atom and a single bond to a hydroxyl group. Compounds with carboxyl groups are carboxylic acids. Carboxyl group

143 Acts as an acid because the combined electronegativities of the two adjacent oxygen atoms increase the dissociation of hydrogen as an ion (H + ). Carboxyl group

144 -NH 2 consists of a nitrogen atom attached to two hydrogen atoms and the carbon skeleton. Organic compounds with amino groups are amines. Amino group

145 Acts as a base because ammonia can pick up a hydrogen ion (H + ) from the solution. Amino acids, the building blocks of proteins, have amino and carboxyl groups. Amino group

146 -SH consists of a sulfur atom bonded to a hydrogen atom and to the backbone. This group resembles a hydroxyl group in shape. Sulfhydryl group

147 Organic molecules with sulfhydryl groups are thiols. Sulfhydryl groups help stabilize the structure of proteins. Sulfhydryl group

148 -OPO 3 2- consists of phosphorus bound to four oxygen atoms (three with single bonds and one with a double bond). Connects to the carbon backbone via one of its oxygen atoms. Phosphate group

149 Anions with two negative charges as two protons have dissociated from the oxygen atoms. One function of phosphate groups is to transfer energy between organic molecules. Phosphate group

150 ATP (adenosine triphosphate) is a type of nucleotide that is the cells primary energy transferring molecule Phosphate group

151 Figure 2.7 Functional Groups Important to Living Systems (Part 1)

152 Figure 2.7 Functional Groups Important to Living Systems (Part 2)

153 Concept 2.2 Atoms Interact and Form Molecules AP TIP You should be able to identify the functional groups most common in biological molecules and explain the characteristics that each functional group confers on molecules.

154 Concept 2.2 Atoms Interact and Form Molecules Macromolecules Most biological molecules are polymers (poly, many; mer, unit), made by covalent bonding of smaller molecules called monomers.

155 Concept 2.2 Atoms Interact and Form Molecules Proteins: Formed from different combinations of 20 amino acids Carbohydratesformed by linking similar sugar monomers (monosaccharides) to form polysaccharides Nucleic acidsformed from four kinds of nucleotide monomers Lipidsnoncovalent forces maintain the interactions between the lipid monomers

156 Concept 2.2 Atoms Interact and Form Molecules Polymers are formed and broken apart in reactions involving water. Condensationremoval of water links monomers together Hydrolysisaddition of water breaks a polymer into monomers

157 Figure 2.8 Condensation and Hydrolysis of Polymers (Part 1)

158 Figure 2.8 Condensation and Hydrolysis of Polymers (Part 2)

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

160 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 (C 6 H 12 O 6 ) include glucose, fructose, mannose, and galactose.

161 Figure 2.9 Monosaccharides (Part 1)

162 Figure 2.9 Monosaccharides (Part 2)

163 Concept 2.3 Carbohydrates Consist of Sugar Molecules Monosaccharides are covalently bonded by condensation reactions that form glycosidic linkages. Sucrose is a disaccharide.

164 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.

165 Concept 2.3 Carbohydrates Consist of Sugar Molecules Polysaccharides are large polymers of monosaccharides; the chains can be branching. Starchesa family of polysaccharides of glucose Glycogenhighly branched polymer of glucose; main energy storage molecule in mammals Cellulosethe most abundant carbon- containing (organic) biological compound on Earth; stable; good structural material

166 Figure 2.10 Polysaccharides (Part 1)

167 Figure 2.10 Polysaccharides (Part 2)

168 Figure 2.10 Polysaccharides (Part 3)

169 Video 2.3 Cellulose: A three-dimensional model

170 Concept 2.3 Carbohydrates Consist of Sugar Molecules AP TIP You should be able to describe structure and function of carbohydrates. You should be able to explain how polysaccharides for energy storage differ from structural polysaccharides.

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

172 Concept 2.4 Lipids Are Hydrophobic Molecules Lipids Store energy in CC and CH bonds Play structural role in cell membranes Fat in animal bodies serves as thermal insulation

173 Concept 2.4 Lipids Are Hydrophobic Molecules Triglycerides (simple lipids) Fatssolid at room temperature Oilsliquid at room temperature They have very little polarity and are extremely hydrophobic.

174 Concept 2.4 Lipids Are Hydrophobic Molecules Triglycerides consist of: Three fatty acidsnonpolar hydrocarbon chain attached to a polar carboxyl group ( COOH) (carboxylic acid) One glycerolan alcohol with 3 hydroxyl (OH) groups Synthesis of a triglyceride involves three condensation reactions.

175 Figure 2.11 Synthesis of a Triglyceride

176 Concept 2.4 Lipids Are Hydrophobic Molecules Fatty acid chains can vary in length and structure. Saturated fatty acids – hydrocarbon chains contain only single carbon-carbon bonds; they have the maximum number of hydrogen atoms (hence saturated). Unsaturated fatty acids – hydrocarbon chains contain one or more double bonds. Results in kinks in the chain and prevents molecules from packing together tightly.

177 Figure 2.12 Saturated and Unsaturated Fatty Acids (Part 1)

178 Figure 2.12 Saturated and Unsaturated Fatty Acids (Part 2)

179 Video 2.4 Palmitic acid and linoleic acid: A three-dimensional model

180 Concept 2.4 Lipids Are Hydrophobic Molecules Fatty acids are amphipathic; they have a hydrophilic end and a hydrophobic tail.

181 Concept 2.4 Lipids Are Hydrophobic Molecules Phospholipidtwo fatty acids and a phosphate compound bound to glycerol. Phosphate group has a negative charge, making that part of the molecule hydrophilic.

182 Figure 2.13 A Phospholipids

183 Figure 2.13 B Phospholipids In an aqueous environment, phospholipids form a bilayer.

184 Figure 2.13 B Phospholipids The nonpolar, hydrophobic tails pack together and the phosphate- containing heads face outward, where they interact with water.

185 Figure 2.13 B Phospholipids Biological membranes have this kind of phospholipid bilayer structure.

186 Concept 2.4 Lipids are Hydrophobic Molecules AP TIP You should be able to describe structure and function of lipids. You should be able to explain how lipids form biological membranes and describe why the degree of saturation in the fatty acid tail affects the structure of lipids.

187 Overview The living cell Is a miniature factory where thousands of reactions occur Converts energy in many ways

188 Overview Some organisms Convert energy to light, as in bioluminescence Figure 8.1

189 Overview Graphic Organizer for Concept 2.5

190 Concept 2.5 Biochemical Changes Involve Energy Chemical reactions occur when atoms have enough energy to combine, or change, bonding partners. sucrose + H 2 O glucose + fructose (C 12 H 22 O 11 ) (C 6 H 12 O 6 ) (C 6 H 12 O 6 ) reactants products

191 Concept 2.5 Biochemical Changes Involve Energy Metabolismthe sum total of all chemical reactions occurring in a biological system at a given time Metabolic reactions involve energy changes.

192 A metabolic pathway has many steps That begin with a specific molecule and end with a product That are each catalyzed by a specific enzyme Enzyme 1Enzyme 2Enzyme 3 A B C D Reaction 1Reaction 2Reaction 3 Starting molecule Product Concept 2.5 Biochemical Changes Involve Energy

193 Animation – Overview of Metabolic or Biochemical Pathways

194 Concept 2.5 Biochemical Changes Involve Energy Two basic types of metabolism: Anabolic reactions Catabolic reactions

195 Metabolic Pathways Catabolic pathways release energy by breaking down complex molecules into simpler compounds. Energy stored in the chemical bonds is released. A major pathway of catabolism is cellular respiration, in which the sugar glucose is broken down in the presence of oxygen to carbon dioxide and water.

196 Metabolic Pathways Anabolic pathways Build complicated molecules from simpler ones Consume energy; require energy input and capturing of some of that energy in newly formed chemical bonds. Also called biosynthetic pathways. The synthesis of protein from amino acids is an example of anabolism. The energy released by catabolic pathways can be stored and then used to drive anabolic pathways.

197 Concept 2.5 Biochemical Changes Involve Energy All forms of energy can be considered as either: Potentialthe energy of state or position, or stored energy Kineticthe energy of movement (the type of energy that does work) that makes things change Energy can be converted from one form to another.

198 Concept 2.5 Biochemical Changes Involve Energy Chemical energy is a form of potential energy stored in molecules because of the arrangement of their atoms. Breaking or making chemical bonds – covalent or ionic – requires the release or absorption of energy during a chemical reaction

199 Chemical reactions can be classified as either exergonic or endergonic based on free energy.

200 Figure 2.14 Energy Changes in Reactions (Part 1)

201 Figure 2.14 Energy Changes in Reactions (Part 2)

202 An exergonic reaction Proceeds with a net release of free energy and is spontaneous – n egative G Reactants Products Energy Progress of the reaction Amount of energy released (G <0) Free energy (a) Exergonic reaction: energy released

203 An exergonic reaction The greater the decrease in free energy, the greater the amount of work that can be done Reactants Products Energy Progress of the reaction Amount of energy released (G <0) Free energy (a) Exergonic reaction: energy released Concept 2.5 Biochemical Changes Involve Energy

204 For the overall reaction of cellular respiration: C 6 H 12 O 6 + 6O 2 -> 6CO 2 + 6H 2 O G = 686 kcal/mol Reactants Products Energy Progress of the reaction Amount of energy released (G <0) Free energy (a) Exergonic reaction: energy released Concept 2.5 Biochemical Changes Involve Energy

205 The products have 686 kcal less free energy than the reactants. Reactants Products Energy Progress of the reaction Amount of energy released (G <0) Free energy (a) Exergonic reaction: energy released Concept 2.5 Biochemical Changes Involve Energy

206 An endergonic reaction Is one that absorbs free energy from its surroundings and is nonspontaneous Energy Products Amount of energy released (G>0) Reactants Progress of the reaction Free energy (b) Endergonic reaction: energy required Concept 2.5 Biochemical Changes Involve Energy

207 An endergonic reaction stores energy in molecules; G is positive. Energy Products Amount of energy released (G>0) Reactants Progress of the reaction Free energy (b) Endergonic reaction: energy required Concept 2.5 Biochemical Changes Involve Energy

208 If cellular respiration releases 686 kcal, then photosynthesis, the reverse reaction, must require an equivalent investment of energy. Energy Products Amount of energy released (G>0) Reactants Progress of the reaction Free energy (b) Endergonic reaction: energy required Concept 2.5 Biochemical Changes Involve Energy

209 For the conversion of carbon dioxide and water to sugar, G = +686 kcal/mol. Figure 8.6 Energy Products Amount of energy released (G>0) Reactants Progress of the reaction Free energy (b) Endergonic reaction: energy required Concept 2.5 Biochemical Changes Involve Energy

210 Equilibrium and Metabolism Reactions in a closed system Eventually reach equilibrium and can do no work (a) A closed hydroelectric system. Water flowing downhill turns a turbine that drives a generator providing electricity to a light bulb, but only until the system reaches equilibrium. G < 0 G = 0

211 Equilibrium and Metabolism Should a cell reach equilibrium, when G = 0, THAT CELL IS DEAD! (a) A closed hydroelectric system. Water flowing downhill turns a turbine that drives a generator providing electricity to a light bulb, but only until the system reaches equilibrium. G < 0 G = 0

212 Equilibrium and Metabolism Cells in our body Experience a constant flow of materials in and out, preventing metabolic pathways from reaching equilibrium. (b) An open hydroelectric system. Flowing water keeps driving the generator because intake and outflow of water keep the system from reaching equlibrium. G < 0

213 Equilibrium and Metabolism Metabolic disequilibrium is one of the defining features of life. Cells maintain disequilibrium because they are open systems. The constant flow of materials into and out of the cell keeps metabolic pathways from ever reaching equilibrium. A cell continues to do work throughout its life.

214 Equilibrium and Metabolism An analogy for cellular respiration ( c) A multistep open hydroelectric system. Cellular respiration is analogous to this system: Glucoce is brocken down in a series of exergonic reactions that power the work of the cell. The product of each reaction becomes the reactant for the next, so no reaction reaches equilibrium. G < 0

215 Equilibrium and Metabolism Some reversible reactions of respiration are constantly pulled in one direction, as the product of one reaction does not accumulate but… becomes the reactant in the next step. Sunlight provides a daily source of free energy for photosynthetic organisms. Nonphotosynthetic organisms depend on a transfer of free energy from photosynthetic organisms in the form of organic molecules.

216 Student Misconceptions COMMON MISCONCEPTION Lets double check if you fully grasp the concept of energy, and especially potential energy. Potential energy is not a substance or fuel that is somehow stored in matter. Potential energy is associated with an objects ability to move to a lower-energy state, thus releasing some of the potential energy.

217 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: Disorder (entropy) tends to increase. When energy is converted from one form to another, some of that energy becomes unavailable for doing work. That lost energy contributes to disorder or entropy.

218 Concept 2.5 Biochemical Changes Involve Energy First law of thermodynamics Energy can be transferred and transformed. Energy cannot be created or destroyed.

219 Concept 2.5 Biochemical Changes Involve Energy First law of thermodynamics The first law is also known as the principle of conservation of energy Total energy in a system before a transformation must equal the total energy in the system after the transformation

220 Concept 2.5 Biochemical Changes Involve Energy First law of thermodynamics Plants do not produce energy; they transform light energy to chemical energy Animals eat other organisms and catabolize complex nutrient molecules into simple compounds, such as H 2 O and CO 2 Quantity of energy does not change, but the quality of energy does change

221 Concept 2.5 Biochemical Changes Involve Energy An example of energy conversion First law of thermodynamics: Energy can be transferred or transformed but Neither created nor destroyed. For example, the chemical (potential) energy in food will be converted to the kinetic energy of the cheetahs movement in (b). (a) Chemical energy

222 Concept 2.5 Biochemical Changes Involve Energy No process is 100% efficient in using potential energy to do work During every transfer or transformation of energy, some energy is converted to heat, which is the energy associated with the random movement of atoms and molecules Energy total = Energy work + Energy lost as heat

223 Concept 2.5 Biochemical Changes Involve Energy

224 Heat can still do work A system can use heat to do work only when there is a temperature difference that results in heat flowing from a warmer location to a cooler one. a.k.a a temperature gradient If temperature is uniform, as in a living cell, heat can only be used to warm the organism.

225 Concept 2.5 Biochemical Changes Involve Energy Inherent inefficiency in energy transformations leads us to the second law of thermodynamics Energy transfers and transformations make the universe more disordered due to this loss of usable energy. Cue the cheetah

226 Concept 2.5 Biochemical Changes Involve Energy According to the second law of thermodynamics Every energy transfer or transformation increases the disorder of the universe. Second law of thermodynamics: Every energy transfer or transformation increases the disorder of the universe. For example, disorder is added to the cheetahs surroundings in the form of heat and the small molecules that are the by-products of metabolism. (b) Heat co 2 H2OH2O +

227 Concept 2.5 Biochemical Changes Involve Energy According to the second law of thermodynamics Cheetah breaks down – catabolizes – relatively more complex sugar molecules into simple CO 2 and H 2 O. Second law of thermodynamics: Every energy transfer or transformation increases the disorder of the universe. For example, disorder is added to the cheetahs surroundings in the form of heat and the small molecules that are the by-products of metabolism. (b) Heat co 2 H2OH2O +

228 Concept 2.5 Biochemical Changes Involve Energy We needed a better way to conceptualize the second law of thermodynamics and the disorder of the universe Hence the concept of entropy

229 Concept 2.5 Biochemical Changes Involve Energy Entropy Quantity used as a measure of disorder or randomness. The more random a collection of matter, the greater its entropy. Lets update the cheetah

230 Concept 2.5 Biochemical Changes Involve Energy Every energy transfer or transformation increases the disorder (entropy) of the universe. Second law of thermodynamics: Every energy transfer or transformation increases the disorder (entropy) of the universe. For example, disorder is added to the cheetahs surroundings in the form of heat and the small molecules that are the by-products of metabolism. (b) Heat co 2 H2OH2O +

231 Concept 2.5 Biochemical Changes Involve Energy Entropy increases because as the cheetah runs, it adds heat to its surroundings and releases simple by-products from the breakdown of complex chemicals Second law of thermodynamics: Every energy transfer or transformation increases the disorder (entropy) of the universe. For example, disorder is added to the cheetahs surroundings in the form of heat and the small molecules that are the by-products of metabolism. (b) Heat co 2 H2OH2O +

232 Concept 2.5 Biochemical Changes Involve Energy The universe the cheetah lives in is a closed system (so far as we know). Second law requires that the disorder or entropy of any closed system always increases. Therefore, if there is at one point a decrease in entropy, there must also be somewhere an increase in entropy.

233 Concept 2.5 Biochemical Changes Involve Energy If the second law of thermodynamics requires an increase in disorder, what form may that disorder take? Catabolism breaks complex molecules into simpler ones, increasing disorder (entropy) Each catabolic reaction will also release heat energy, increasing disorder (entropy) So there are two types of entropy Material Thermal

234 The Second Law of Thermodynamics Combustion of the fuel releases heat, thereby increasing entropy. Automobiles convert only 25% of the energy in gasoline into motion; the rest is lost as heat. Concept 2.5 Biochemical Changes Involve Energy

235 The Second Law of Thermodynamics C 8 H 18 + O 2 CO 2 + H 2 O + heat There is both an increase in disorder materially – octane to carbon dioxide and water – and thermally – the release of heat energy Concept 2.5 Biochemical Changes Involve Energy

236 Heres another way of defining entropy Entropy is measured by the number of distinguishable arrangements by the particles of matter The fewer the number of distinguishable arrangements, the lower the entropy The more distinguishable arrangements, the greater the entropy

237 Concept 2.5 Biochemical Changes Involve Energy An to illustrate distinguishable arrangements..a card trick How many possible five card hands can be dealt in poker?

238 Concept 2.5 Biochemical Changes Involve Energy Each of the 2,598,960 five-card hands are a distinguishable arrangement When happens when the number of cards is halved to 26?

239 Concept 2.5 Biochemical Changes Involve Energy With 26 cards, only 65,780 five card arrangements can be made. Now suppose those cards are atoms?

240 Concept 2.5 Biochemical Changes Involve Energy With fewer atoms, few distinguishable arrangements can be made, the lower the entropy. But then of course, if you increased the number of atoms in each arrangement, from 5 to 10 You get 5,311,735 distinguishable arrangements – fewer atoms but larger molecules – entropy is increased!

241 Concept 2.5 Biochemical Changes Involve Energy Second law of thermodynamics Requires increasing entropy from any closed system Isolated from its surroundings, lacking any input of additional energy, the closed system will (eventually) increase its entropy All things will fall apart

242 Concept 2.5 Biochemical Changes Involve Energy For a process to occur on its own, without outside help in the form of energy input, it must increase the entropy of the universe. In other words, the process must be spontaneous Spontaneous processes need not occur quickly. Some spontaneous processes are instantaneous, such as an explosion. Some are very slow, such as the rusting of an old car.

243 A spontaneous change is a change that has a tendency to occur without been driven by an external influence e.g. the cooling of a hot metal block to the temperature of its surroundings A non-spontaneous change is a change that occurs only when driven e.g. forcing electric current through a metal block to heat it The Second Law of Thermodynamics Concept 2.5 Biochemical Changes Involve Energy

244 So, another way to state the second law of thermodynamics is for a process to occur spontaneously, it must increase the entropy of the universe You will see that spontaneous processes are absolutely vital to biological processes Diffusion and facilitated diffusion Osmosis and dissolution Evolution

245 Concept 2.5 Biochemical Changes Involve Energy Lets describe the second law mathematically S = entropy S = change in entropy A spontaneous process will be a positive or negative S? positive

246 The Second Law of Thermodynamics Enthalpy is the total potential energy of a system H – the total enthalpy (in biological systems, equivalent to energy) Enthalpy – the energy and matter within a system that may be exchanged with its surroundings.

247 The Second Law of Thermodynamics Entropy is that fraction of enthalpy that cannot be used to do work – it is always lost to increasing disorder So the amount of energy in any system that can do work is approximately the difference between the two

248 Total entropy change entropy change of system entropy change of surroundings + = Dissolving disorder of solution disorder of surroundings must be an overall increase in disorder for dissolving to occur The Second Law of Thermodynamics

249 Biological Order and Disorder Now for the apparent paradox of life… Dont living systems increase order, violating the second law of thermodynamics? 50µm

250 Biological Order and Disorder Living systems are open systems that absorb energylight or chemical energy – in the form of organic molecules 50µm

251 Biological Order and Disorder and release heat and metabolic waste products such as urea or CO 2 to their surroundings. 50µm

252 Biological Order and Disorder Living systems create ordered structures from less ordered starting materials. The structure of a multicellular body is organized and complex. 50µm

253 Biological Order and Disorder Example: amino acids are ordered into polypeptide chains But living systems must use energy to maintain order. 50µm

254 Biological Order and Disorder And, in using energy to maintain order an organism takes in organized forms of matter and energy from its surroundings and replaces them with less ordered forms. 50µm

255 Biological Order and Disorder Example: an animal consumes organic molecules as food and catabolizes them to low-energy carbon dioxide and water. 50µm

256 Biological Order and Disorder So what is the answer to the paradox? 50µm

257 Biological Order and Disorder While they can increase order locally and temporarily, there is an unstoppable trend toward randomization of the entire universe. 50µm

258 Biological Order and Disorder Living things preserve their low levels of entropy throughout time, because they receive energy from their surroundings in the form of food. 50µm Entropy in Biology, Jayant Udgaonkar

259 Biological Order and Disorder They gain their order at the expense of disordering the nutrient they consume. 50µm Entropy in Biology, Jayant Udgaonkar

260 Biological Order and Disorder Dust thou art, and unto dust thou shalt return" (Genesis 3:19) Death is the inevitable result of increasing molecular entropy 50µm

261 Biological Order and Disorder The entropy of a particular system, such as an organism, may decrease as long as the total entropy of the universethe system plus its surroundingsincreases. Think of organisms as islands of low entropy in an increasingly random universe. The evolution of biological order is perfectly consistent with the laws of thermodynamics.

262 Biological Order and Disorder Now how does entropy relate to evolution? Over evolutionary time, complex organisms have evolved from simpler ones. How does this happen?

263 Biological Order and Disorder Second law of thermodynamics makes certain that a sequence of DNA cannot be maintained forever. Eventually it must fall to disorder and increase its entropy Small random changes in the DNA sequence is inevitable

264 Biological Order and Disorder Sometime those changes – mutations – lead to changes in a gene which leads to different proteins being produced, which leads to different traits, which allows natural selection to determine the advantageous traits, and so on and so on.

265 Biological Order and Disorder Evolution therefore does not violate the second law of thermodynamics Individuals and entire species are merely temporary and isolated examples of decreasing entropy Entropy drives the processes of evolution, osmosis, diffusion and other spontaneous processes Not a directed process; there is no goal Evolution is inevitable

266 Biological Order and Disorder Lets check your understanding of entropy using this model of osmosis. Assume the dialysis bag contains a saline solution. It is surrounded by pure water. Which direction will the water tend – into or out of the bag?

267 Biological Order and Disorder Water will tend to go into the bag Osmosis requires water move from an area of high concentration – outside – to an area of low concentration until equilibrium is reached. Now explain what happens in terms of entropy.

268 Biological Order and Disorder First, we recognize the bag is an open system Second, we know there will be a net flow of water into the bag Third, we know this will be spontaneous By definition, this will increase entropy in the beaker/bag system But wait..theres more!

269 Biological Order and Disorder Salt water has greater entropy than pure water Na+ and Cl- ions are spread out through the solution, creating greater disorder Pure water is just water molecules bumping into other water molecules Entropy will seek equilibrium until S = 0

270 Biological Order and Disorder Solutions have more distinguishable particles With a solute(s), you can see more combinations between molecules of solute(s) and solvent, than just solvent

271 1. If we freeze water, disorder of the water molecules decreases, entropy decreases ( -ve S, -ve H) 2. If we boil water, disorder of the water molecules increases, entropy increases (vapour is highly disordered state) ( +ve S, +ve H) Biological Order and Disorder

272 System in Dynamic Equilibrium A + B C + D Dynamic (coming and going), equilibrium (no net change) no overall change in disorder S 0 (zero entropy change) Biological Order and Disorder

273 Is the second law of thermodynamics responsible for time? Well, not really. Second law and entropy do not require time in the equations, however… Second does imply a direction of time All things must move toward a more disordered state Known as Times Arrow

274 Biological Order and Disorder Zero entropy 13.7 billions years ago Constantly increasing entropy in Universe Biological Order and Disorder

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281 Figure 2.15 The Laws of Thermodynamics (Part 2)

282 Figure 2.15 The Laws of Thermodynamics (Part 3)

283 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.

284 Concept 2.5 Biochemical Changes Involve Energy As a result of energy transformations, disorder tends to increase. Some energy is always lost to random thermal motion (entropy).

285 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.

286 Concept 2.5 Biochemical Changes Involve Energy AP TIP You should be able to predict the outcome of endergonic and exergonic reactions You should be able to discuss the significance of the second law of thermodynamics.

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

288 Figure 2.16 Synthesis of Prebiotic Molecules in an Experimental Atmosphere (Part 1)

289 Figure 2.16 Synthesis of Prebiotic Molecules in an Experimental Atmosphere (Part 2)

290 Life Chemistry and Energy CGI Video Summation 2

291 Inner Lives of a Cell – Full version with musical score We have reviewed the basics of biological molecules. This video shows those biological molecules in action. Can you, in your minds eye, see the bonds, the interactions?

292 Life Chemistry and Energy Practice Questions 2

293 Atomic structure The element magnesium has an atomic number of 12 and a mass number of 24. Working in pairs, and using the Bohr model for atomic structure, draw a magnesium atom. Once you have drawn your magnesium atom, answer the following questions: 1. How many protons and neutrons are in the nucleus? How many electrons are in this atom? 2. Is the magnesium atom likely to bond with other atoms? Why or why not? Take a few minutes to discuss, and then present your drawing and answers to the class. Concept 2.1 Atomic Structure Is the Basis for Lifes Chemistry

294 Select the false statement about elements: a. An element contains only one kind of atom. b. Isotopes are variants of an element with additional neutrons in the nucleus. c. Atoms of different elements can have the same number of protons. d. All the atoms of a particular element contain the same number of protons. e. Carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur are the main elements found in living organisms. Concept 2.1 Atomic Structure Is the Basis for Lifes Chemistry

295 Chemical bonds Working in pairs, compare the following bonds with respect to their basis of interaction and strength: Ionic Covalent Hydrogen Draw an example of each type of bond. Concept 2.2 Atoms Interact and Form Molecules

296 Which of the following statements about water is false? a. Water helps to prevent dramatic changes in body temperature because it has a high heat capacity. b. Sweating cools the body because water has a high heat of vaporization. c. Not counting bones, water makes up about 70% of the weight of your body. d. During condensation, the addition of water breaks a polymer into monomers. e. Molecules with polar covalent bonds are attracted to water. Concept 2.2 Atoms Interact and Form Molecules

297 Carbohydrates Working in pairs or small groups, discuss the polysaccharides starch, glycogen, and cellulose. In your discussion, consider the following questions: 1. Where are these polysaccharides found? 2. What biological role does each polysaccharide play? 3. What do these molecules have in common? 4. How do these molecules differ? Present your answers to the class. Concept 2.3 Carbohydrates Consist of Sugar Molecules

298 Carbohydrates a. can have the same chemical formula, but distinct chemical properties and different biological roles. b. such as polysaccharides are formed when monosaccharides are ionically bonded by condensation reactions. c. are made of carbon, hydrogen, and oxygen. d. are always linear, unbranched molecules. e. Both a and c Concept 2.3 Carbohydrates Consist of Sugar Molecules

299 Triglycerides Working individually, compare saturated and unsaturated fatty acids with respect to the following characteristics: 1.Presence of double bonds between carbon atoms in the hydrocarbon chain 2. Ability to pack tightly together 3. State of lipid at room temperature 4. Melting point of lipid 5. Typical source Compare your answers with your classmates and discuss. Concept 2.4 Lipids Are Hydrophobic Molecules

300 Which of the following statements about phospholipids is false? a. The phosphate functional group and glycerol form the hydrophobic head of a phospholipid. b. A phospholipid has two fatty acids whereas a triglyceride has three fatty acids. c. Phospholipids are amphipathic (i.e., they have two opposing chemical properties). d. The phosphate functional group and glycerol form the hydrophilic head of a phospholipid. e. Biological membranes are characterized by a phospholipid bilayer structure. Concept 2.4 Lipids Are Hydrophobic Molecules

301 Chemical reactions Working in pairs, consider the following chemical reaction and answer the questions below: glucose + galactose lactose + water 1. Is this a condensation or hydrolysis reaction? 2. What are the reactants? What are the products? 3. Is this an anabolic or catabolic reaction? 4. Is energy required or released? Concept 2.5 Biochemical Changes Involve Energy

302 Which of the following statements about energy is false? a. Exergonic reactions release energy. b. The energy released in anabolic reactions is often used to drive catabolic reactions. c. Potential energy is stored energy. d. Endergonic reactions require energy e. Kinetic energy is the energy of movement. Concept 2.5 Biochemical Changes Involve Energy

303 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Science, Technology and Society While waiting at an airport, Neil Campbell once overheard this claim: – Its paranoid and ignorant to worry about industry or agriculture contaminating the environment with their chemical wastes. After all, this stuff is just made of the same atoms that were already present in our environment. How would you counter this argument?

304 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Review – Online Quiz by Campell/Reece

305 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 2.You are studying a cellular enzyme involved in breaking down fatty acids for energy. Looking at the R groups of the amino acids in the following figures, what amino acids would you predict to occur in the parts of the enzyme that interact with the fatty acids? * a.non-polar b.polar c.electrically charged d.polar and electrically charged e.all of these Practice Problems

306 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The 20 Amino Acids of Proteins

307 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The 20 Amino Acids of Proteins (cont.)

308 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Lets begin with the condensation reaction that lead to the 1-4 glycosidic linkage Scientific Inquiry

309 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Repeated many times results in a polysaccharide known as starch Scientific Inquiry

310 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings H2OH2O Scientific Inquiry Hydrolysis breaks the glycosidic linkages, leaving behind glucose monomers, reinserting a water molecule Note one hydrogen bonds with the oxygen of carbon-1; the remaining hydroxyl group OH bonds with the carbon 4

311 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings HCl Scientific Inquiry If hydrochloric acid used to break glycosidic linkages.. The hydrogen will bond with carbon-1, as before, but the chlorine Cl - will bond with the carbon-4, resulting in only one glucose monomer, not two Cl

312 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Scientific Inquiry


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