Presentation on theme: "Life Chemistry and Energy"— Presentation transcript:
1 Life Chemistry and Energy 2Life Chemistry and Energy
2 Chapter 2 Life Chemistry and Energy Key Concepts2.1 Atomic Structure Is the Basis for Life’s Chemistry2.2 Atoms Interact and Form Molecules2.3 Carbohydrates Consist of Sugar Molecules2.4 Lipids Are Hydrophobic Molecules2.5 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 Knowledge2.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.
6 Like any profession, the study of biology has its own language. Word RootsLike 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 kilo - a thousand (kilocalorie: a thousand calories) Word Rootshydro - water; - philos loving; - phobos fearing (hydrophilic: having an affinity for water; hydrophobic: having an aversion to water)kilo - a thousand (kilocalorie: a thousand calories)Instructor’s Guide for Campbell/Reece Biology, Seventh Edition
8 Word Rootscarb - 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 thio - sulfur (thiol: organic compounds containing sulfhydryl groups) Word Rootsiso - 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 di - two (disaccharide: two monosaccharides joined together) Word Rootscon - 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 macro - large (macromolecule: a large molecule) Word Rootsglyco - 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 poly - many (polysaccharide: many monosaccharides joined together) Word Rootsmono - 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 Rootsbio- 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 kinet- movement (kinetic energy: the energy of motion) Word Rootskinet- 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 Rootsana - 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 Life’s Chemistry Living and nonliving matter is composed of atoms.
18 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.Dalton—mass 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 Life’s Chemistry Element—pure substance that contains only one kind of atomLiving 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 Life’s Chemistry The number of protons identifies an element.Number of protons = atomic numberFor electrical neutrality, # protons = # electrons.Mass number—total number of protons and neutrons
21 Concept 2.1 Atomic Structure Is the Basis for Life’s Chemistry A Bohr model for atomic structure—the atom is largely empty space, and the electrons occur in orbits, or electron shells.
22 Concept 2.1 Atomic Structure Is the Basis for Life’s 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 Life’s Chemistry Behavior of electronsdetermines whether a chemical bond will formand what shape the bond will have.
24 Concept 2.1 Atomic Structure Is the Basis for Life’s Chemistry Octet ruleAtoms with at least two electron shells form stable moleculesSo they have eight electrons in their outermost (valence) shells.
26 Concept 2.1 Atomic Structure Is the Basis for Life’s 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 bondAn attractive force that links atoms together to form molecules.There are several kinds of chemical bonds.ANIMATED TUTORIAL 2.1 Chemical Bond Formation
29 Concept 2.2 Atoms Interact and Form Molecules Ionic bondsIons are charged particle that form when an atom gains or loses one or more electrons.Cations—positively charged ionsAnions—negatively charged ionsIonic 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 bondsCovalent 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
36 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 movingCan 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.
39 Student Misconceptions COMMON MISCONCEPTIONThe 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.
40 Concept 2.2 Atoms Interact and Form Molecules CarbonCarbon atoms have four electrons in the outer shellCan form single covalent bonds with four other atoms.
43 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.VIDEO 2.1 Methane: A three-dimensional model
46 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 bondsSingle—sharing 1 pair of electronsDouble—sharing 2 pairs of electronsTriple—sharing 3 pairs of electronsC HC CN N
47 Concept 2.2 Atoms Interact and Form Molecules Degree of sharing electrons is not always equal.Let’s review the implications of this in terms ofElectronegativityHydrogen bondsSpecific heat capacityPolar and nonpolar covalent bondsCohesion and adhesionHeat of vaporizationSolvent
48 Concept 2.2 Atoms Interact and Form Molecules Degree of sharing electrons is not always equal.Electronegativity—the attractive force that an atomic nucleus exerts on electronsIt depends on the number of protons and the distance between the nucleus and electrons.
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 bondsAttraction 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 bondsDo 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 Concept 2.2 Atoms Interact and Form Molecules Hydrogen bonds ++H–
54 Concept 2.2 Atoms Interact and Form Molecules Hydrogen bondsCan occur between different molecules as long as there are areas of partial opposite charges.Within a cell, weak, brief bonds between molecules are important to a variety of processes.For example, signal molecules from one neuron use weak bonds to bind briefly to receptor molecules on the surface of a receiving neuron.This triggers a momentary response by the recipient.Weak interactions include ionic bonds (weak in water), hydrogen bonds, and van der Waals interactions.Hydrogen bonds form when a hydrogen atom already covalently bonded to a strongly electronegative atom is attracted to another strongly electronegative atom.These strongly electronegative atoms are typically nitrogen or oxygen.Typically, these bonds result because the polar covalent bond with hydrogen leaves the hydrogen atom with a partial positive charge and the other atom with a partial negative charge.The partially positive charged hydrogen atom is attracted to negatively charged (partial or full) molecules, atoms, or even regions of the same large molecule.For example, ammonia molecules and water molecules link together with weak hydrogen bonds.In the ammonia molecule, the hydrogen atoms have partial positive charges and the more electronegative nitrogen atom has a partial positive charge.In the water molecule, the hydrogen atoms also have partial positive charges and the oxygen atom has a partial negative charge.Areas with opposite charges are attracted.Even molecules with nonpolar covalent bonds can have partially negative and positive regions.Because electrons are constantly in motion, there can be periods when they accumulate by chance in one area of a molecule.This creates ever-changing regions of negative and positive charge within a molecule.Molecules or atoms in close proximity can be attracted by these fleeting charge differences, creating van der Waals interactions.While individual bonds (ionic, hydrogen, van der Waals) are weak, collectively they have strength.
55 Figure 2.5 Hydrogen Bonds Can Form between or within Molecules
56 Concept 2.2 Atoms Interact and Form Molecules Hydrogen bondsAre weak bonds; roughly 1/20th the strength of a typical covalent bond.Are fleeting; they form and break with slight changes in the system’s 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 Angstroms, while the hydrogen bond length is A.”
58 Hydrogen bondsAt 0oC, water becomes locked into a crystalline lattice with each molecule bonded to the maximum of four partners.
59 Hydrogen bondsRemember – bond length of hydrogen bonds is roughly twice as much as typical covalent bond
60 Hydrogen bondsResulting lattice structure finds molecules farther apart. As a result, the same amount of mass occupies more volume.
61 Hydrogen bondsWater 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 seasSo why is this oddity important to life?
63 Concept 2.2 Atoms Interact and Form Molecules 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.The invertebrates shown here are krill, photographed underneath Antarctic ice
64 Concept 2.2 Atoms Interact and Form Molecules Hydrogen bondsHydrogen bonds make possible water’s 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 Shockwave animationHydrogen bondsPolar molecules can be attracted to each other much as oppositely charged ions are. The attraction will, however, be much weaker since polarity results in only a partial charge. The weak attraction between the slightly positive hydrogen region of one polar covalent bond (usually the hydrogen is bonded to oxygen or nitrogen) and the negative region of another polar covalently bonded molecule is called a hydrogen bond. Water molecules have such polarity (see polar). The diagram shows how water molecules are linked together by hydrogen bonds. You can think of water molecules as tiny magnets with opposite poles, much like the poles of a magnet. Opposite poles attract each other. Water molecules are stuck to each other by this attracting force.Hydrogen bonds are weaker than ionic bonds and much weaker than covalent bonds. Nevertheless, they are essential in biological systems. Many weak bonds working together can result in a very strong connection. The situation is similar to a strip of Velcro where many tiny and weak links form a remarkably stable attachment. Many of the characteristics of proteins and nucleic acids (DNA and RNA) are due to hydrogen bonding, as are very important properties of water.
66 Animation – Molecular Water View animation of the rotating molecule with the charged poles.
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 MISCONCEPTIONSWeak 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 gecko’s 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 other—this 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 water—the 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 temperatureBy absorbing heat from air that is warmer and releasing the stored heat to air that is coolerWhy 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 TemperatureHeatIs a measure of the total amount of kinetic energy due to molecular motionTemperatureMeasures 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 (oC).At sea level, water freezes at Oo C and boils at 100o C.Human body temperature averages 37o 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 1oC.
81 Concept 2.2 Atoms Interact and Form Molecules 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 1oC.Another common energy unit, the joule (J), is equivalent to cal.
82 Concept 2.2 Atoms Interact and Form Molecules Water has a relatively high specific heatThe specific heat of a substanceIs the amount of heat that must be absorbed or lost for 1 gram of that substance to change its temperature by 1ºCAbsorbing heat energy will increase temperatureReleasing heat energy will decrease temperature
83 Concept 2.2 Atoms Interact and Form Molecules Water has a high specific heat compared to other substances.Example: ethyl alcohol has a specific heat of 0.6 cal/g/oCLess energy required to get a temperature increase in alcoholSpecific heat of iron is 1/10th that of water.
84 Concept 2.2 Atoms Interact and Form Molecules Due to high specific heat, water resists changes in temperatureTakes relatively more heat energy to speed up its moleculesOr, water absorbs or releases a relatively large quantity of heat for each degree of change
85 Concept 2.2 Atoms Interact and Form Molecules Water’s high specific heat is due to hydrogen bonding between each molecule of waterMust absorb heat to break the hydrogen bondsBecause 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.
86 Concept 2.2 Atoms Interact and Form Molecules When enough energy is added, enough bonds break…That’s when a liquid may change its state of matter – liquid to gas.
87 Heating Curve of WaterIt takes a lot of energy to force a change of water’s 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 heatWater’s high specific heatallows 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.
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 vaporizationMolecules 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 vaporizationQuantity 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.That’s double the heat of vaporization of alcohol or ammonia.Why?
93 So why is a high heat of vaporization important to biology? Why? I’ll tell you why!Water’s many more hydrogen bonds must be broken before it can evaporate.So why is a high heat of vaporization important to biology?
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 water’s 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 vaporization—a 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 body—as sweat evaporates from the skin, it transforms some of the adjacent body heat.LINK Evaporation is important in the physiology of both plants and animals; see Concepts 25.3 and 29.4
97 Concept 2.2 Atoms Interact and Form Molecules Hydrogen bonds also give water cohesive strength, or cohesion—water molecules resist coming apart when placed under tension.Bonding of a high percentage of the molecules to neighboring moleculesDue to hydrogen bondingPermits 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 plantsWater conducting cells100 µm
102 Water has greater surface tension that most liquids. 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 Water is a versatile solvent due to its polarity. The Solvent of LifeWater is a versatile solvent due to its polarity.It can form aqueous solutions:SolutionA liquid that is a completely homogeneous mixture of two or more substancesAqueous solutionA solution in which water is the solventSolventDissolving agent
104 The Solvent of LifeThe 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–).Cl–
105 The Solvent of LifeEach 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.
106 The Solvent of LifePolar 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.
107 Water can also interact with polar molecules such as proteins. The Solvent of LifeWater 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 protein’s Surface attract water molecules.+–
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. 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.
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) 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.
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.
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.
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 moleculesNonpolar molecules are called hydrophobic (“water-hating”); the interactions between them are hydrophobic interactions.Apply the Concept Atoms interact and form molecules
114 Water: exists in nature as three states of matter Concept 2.2 Atoms Interact and Form MoleculesWater: exists in nature as three states of matterWater pictured in the three phases of matter – gas (vapor), liquid and solid
119 Concept 2.2 Atoms Interact and Form Molecules Water: exists in nature as three states of matterConcept 2.2 Atoms Interact and Form Molecules
120 Concept 2.2 Atoms Interact and Form Molecules Water: exists in nature as three states of matterConcept 2.2 Atoms Interact and Form Molecules
121 Concept 2.2 Atoms Interact and Form Molecules Water: exists in nature as three states of matterConcept 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 OverviewConcept 2.2 Atoms Interact and Form MoleculesThree-quarters of the Earth’s surface is submerged in water. The abundance of water is the main reason the Earth is habitable.
124 Concept 2.2 Atoms Interact and Form Molecules Water is most unusualOnly 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 lifeWater 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 liquidThe best solvent – it dissolves just about everything.Helps maintain the shape of enzymes – essential catalysts of biochemistry – no shape, no chemistry.If water wasn’t the essential liquid, if another liquid could take its place, why haven’t we seen it in any life forms?
128 Concept 2.2 Atoms Interact and Form Molecules Ammonia! 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 groups—small groups of atoms with specific chemical propertiesConfer 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.CH3OHHOOEstradiolTestosteroneFemale lionMale 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.CH3OHHOOEstradiolTestosteroneFemale lionMale lion
133 Concept 2.2 Atoms Interact and Form Molecules These functional groups then interact with different targets in the body.CH3OHHOOEstradiolTestosteroneFemale lionMale lion
137 Concept 2.2 Atoms Interact and Form Molecules Six functional groups are important in the chemistry of life:HydroxylCarbonylCarboxylAminoSulfhydrylPhosphateAll are hydrophilic and increase the solubility of organic compounds in water.
138 Hydroxyl group-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.
139 Hydroxyl groupOrganic compounds with hydroxyl groups are alcohols and their names typically end in -ol.
140 Carbonyl group>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.
141 If not, then the compound is a ketone. Carbonyl groupIf not, then the compound is a ketone.Isomers with aldehydes versus ketones have different properties.
142 Compounds with carboxyl groups are carboxylic acids. -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.
143 Carboxyl groupActs as an acid because the combined electronegativities of the two adjacent oxygen atoms increase the dissociation of hydrogen as an ion (H+).
144 Organic compounds with amino groups are amines. -NH2 consists of a nitrogen atom attached to two hydrogen atoms and the carbon skeleton.Organic compounds with amino groups are amines.
145 Amino groupActs 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.
146 This group resembles a hydroxyl group in shape. Sulfhydryl group-SH consists of a sulfur atom bonded to a hydrogen atom and to the backbone.This group resembles a hydroxyl group in shape.
147 Organic molecules with sulfhydryl groups are thiols. Sulfhydryl groups help stabilize the structure of proteins.
148 Connects to the carbon backbone via one of its oxygen atoms. Phosphate group-OPO32- 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.
149 Phosphate groupAnions 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.
150 Phosphate groupATP (adenosine triphosphate) is a type of nucleotide that is the cell’s primary energy transferring molecule
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 MacromoleculesMost 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 acidsCarbohydrates—formed by linking similar sugar monomers (monosaccharides) to form polysaccharidesNucleic acids—formed from four kinds of nucleotide monomersLipids—noncovalent 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.Condensation—removal of water links monomers togetherHydrolysis—addition of water breaks a polymer into monomersANIMATED TUTORIAL 2.2 Macromolecules: Carbohydrates and Lipids
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 Source of stored energyTransport stored energy within complex organismsStructural molecules that give many organisms their shapesRecognition 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 sugarsRibose and deoxyribose are the backbones of RNA and DNA.Hexoses (C6H12O6) include glucose, fructose, mannose, and galactose.LINK For a description of the nucleic acids RNA and DNA see Concept 3.1
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.Starches—a family of polysaccharides of glucoseGlycogen—highly branched polymer of glucose; main energy storage molecule in mammalsCellulose—the most abundant carbon- containing (organic) biological compound on Earth; stable; good structural materialVIDEO 2.2 Starch: A three-dimensional modelVIDEO 2.3 Cellulose: A three-dimensional model
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 Store energy in C—C and C—H 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)Fats—solid at room temperatureOils—liquid at room temperatureThey have very little polarity and are extremely hydrophobic.
174 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 3 hydroxyl (—OH) groupsSynthesis of a triglyceride involves three condensation reactions.
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.VIDEO 2.4 Palmitic acid and linoleic acid: A three-dimensional model
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 Phospholipid—two fatty acids and a phosphate compound bound to glycerol.Phosphate group has a negative charge, making that part of the molecule hydrophilic.
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 Is a miniature factory where thousands of reactions occur OverviewThe living cellIs a miniature factory where thousands of reactions occurConverts energy in many ways
188 Convert energy to light, as in bioluminescence OverviewSome organismsConvert energy to light, as in bioluminescenceFigure 8.1
189 Graphic Organizer for Concept 2.5 OverviewGraphic 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 + H2O glucose + fructose(C12H22O11) (C6H12O6) (C6H12O6)reactants productsAPPLY THE CONCEPT Biochemical changes involve energy
191 Concept 2.5 Biochemical Changes Involve Energy Metabolism—the sum total of all chemical reactions occurring in a biological system at a given timeMetabolic reactions involve energy changes.
192 Concept 2.5 Biochemical Changes Involve Energy A metabolic pathway has many stepsThat begin with a specific molecule and end with a productThat are each catalyzed by a specific enzymeEnzyme 1Enzyme 2Enzyme 3ABCDReaction 1Reaction 2Reaction 3Starting moleculeProduct
193 Animation – Overview of Metabolic or Biochemical Pathways
194 Concept 2.5 Biochemical Changes Involve Energy Two basic types of metabolism:Anabolic reactionsCatabolic reactions
195 Catabolic pathways release energy by Metabolic PathwaysCatabolic pathways release energy bybreaking 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 Build complicated molecules from simpler ones Metabolic PathwaysAnabolic pathwaysBuild complicated molecules from simpler onesConsume 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:Potential—the energy of state or position, or stored energyKinetic—the energy of movement (the type of energy that does work) that makes things changeEnergy can be converted from one form to another.
198 Concept 2.5 Biochemical Changes Involve Energy Chemical energyis 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 (a) Exergonic reaction: energy released An exergonic reactionProceeds with a net release of free energy and is spontaneous – negative ∆GReactantsProductsEnergyProgress of the reactionAmount ofenergyreleased (∆G <0)Free energy(a) Exergonic reaction: energy released
203 Concept 2.5 Biochemical Changes Involve Energy An exergonic reactionThe greater the decrease in free energy, the greater the amount of work that can be doneReactantsProductsEnergyProgress of the reactionAmount ofenergyreleased (∆G <0)Free energy(a) Exergonic reaction: energy released
204 Concept 2.5 Biochemical Changes Involve Energy For the overall reaction of cellular respiration: C6H12O6 + 6O2 -> 6CO2 + 6H2OG = −686 kcal/molReactantsProductsEnergyProgress of the reactionAmount ofenergyreleased (∆G <0)Free energy(a) Exergonic reaction: energy released
205 Concept 2.5 Biochemical Changes Involve Energy The products have 686 kcal less free energy than the reactants.ReactantsProductsEnergyProgress of the reactionAmount ofenergyreleased (∆G <0)Free energy(a) Exergonic reaction: energy released
206 Concept 2.5 Biochemical Changes Involve Energy An endergonic reactionIs one that absorbs free energy from its surroundings and is nonspontaneousEnergyProductsAmount ofenergyreleased (∆G>0)ReactantsProgress of the reactionFree energy(b) Endergonic reaction: energy required
207 Concept 2.5 Biochemical Changes Involve Energy An endergonic reactionstores energy in molecules; G is positive.EnergyProductsAmount ofenergyreleased (∆G>0)ReactantsProgress of the reactionFree energy(b) Endergonic reaction: energy required
208 Concept 2.5 Biochemical Changes Involve Energy If cellular respiration releases 686 kcal, then photosynthesis, the reverse reaction, must require an equivalent investment of energy.EnergyProductsAmount ofenergyreleased (∆G>0)ReactantsProgress of the reactionFree energy(b) Endergonic reaction: energy required
209 Concept 2.5 Biochemical Changes Involve Energy For the conversion of carbon dioxide and water to sugar, G = +686 kcal/mol.Figure 8.6EnergyProductsAmount ofenergyreleased (∆G>0)ReactantsProgress of the reactionFree energy(b) Endergonic reaction: energy required
210 Equilibrium and Metabolism Reactions in a closed systemEventually 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 bodyExperience 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 MISCONCEPTIONLet’s 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 object’s 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 thermodynamicsEnergy can be transferred and transformed.Energy cannot be created or destroyed.
219 Concept 2.5 Biochemical Changes Involve Energy First law of thermodynamicsThe first law is also known as the principle of conservation of energyTotal 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 thermodynamicsPlants do not produce energy; they transform light energy to chemical energyAnimals eat other organisms and catabolize complex nutrient molecules into simple compounds, such as H2O and CO2Quantity of energy does not change, but the quality of energy does change
221 Concept 2.5 Biochemical Changes Involve Energy An example of energy conversionFirst law of thermodynamics: Energy can be transferred or transformed butNeither created nor destroyed. Forexample, the chemical (potential) energyin food will be converted to the kineticenergy of the cheetah’s movement in (b).(a)Chemicalenergy
222 Concept 2.5 Biochemical Changes Involve Energy No process is 100% efficient in using potential energy to do workDuring every transfer or transformation of energy, some energy is converted to heat,which is the energy associated with the random movement of atoms and moleculesEnergytotal = Energywork + Energylost as heat
223 Concept 2.5 Biochemical Changes Involve Energy
224 Concept 2.5 Biochemical Changes Involve Energy Heat can still do workA system can use heat to do work only whenthere is a temperature difference that results in heat flowing from a warmer location to a cooler one.a.k.a a temperature gradientIf 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 thermodynamicsEnergy 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 thermodynamicsEvery energy transfer or transformation increases the disorder of the universe.Second law of thermodynamics: Every energy transfer or transformation increasesthe disorder of the universe. For example, disorder is added to the cheetah’ssurroundings in the form of heat and the small molecules that are the by-productsof metabolism.(b)Heatco2H2O+
227 Concept 2.5 Biochemical Changes Involve Energy According to the second law of thermodynamicsCheetah breaks down – catabolizes – relatively more complex sugar molecules into simple CO2 and H2O.Second law of thermodynamics: Every energy transfer or transformation increasesthe disorder of the universe. For example, disorder is added to the cheetah’ssurroundings in the form of heat and the small molecules that are the by-productsof metabolism.(b)Heatco2H2O+
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 universeHence the concept of entropy
229 Concept 2.5 Biochemical Changes Involve Energy EntropyQuantity used as a measure of disorder or randomness.The more random a collection of matter, the greater its entropy.Let’s 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 increasesthe disorder (entropy) of the universe. For example, disorder is added to the cheetah’ssurroundings in the form of heat and the small molecules that are the by-productsof metabolism.(b)Heatco2H2O+
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 chemicalsSecond law of thermodynamics: Every energy transfer or transformation increasesthe disorder (entropy) of the universe. For example, disorder is added to the cheetah’ssurroundings in the form of heat and the small molecules that are the by-productsof metabolism.(b)Heatco2H2O+
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 entropyMaterialThermal
234 The Second Law of Thermodynamics Concept 2.5 Biochemical Changes Involve EnergyCombustion 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.
235 The Second Law of Thermodynamics Concept 2.5 Biochemical Changes Involve EnergyThe Second Law of ThermodynamicsC8H18 + O2 CO2 + H2O + heatThere is both an increase in disorder materially – octane to carbon dioxide and water – and thermally – the release of heat energy
236 Concept 2.5 Biochemical Changes Involve Energy Here’s another way of defining entropyEntropy is measured by the number of distinguishable arrangements by the particles of matterThe fewer the number of distinguishable arrangements, the lower the entropyThe more distinguishable arrangements, the greater the entropy
237 Concept 2.5 Biochemical Changes Involve Energy An to illustrate distinguishable arrangements ..a card trickHow 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 arrangementWhen 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 10You 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 thermodynamicsRequires increasing entropy from any closed systemIsolated from its surroundings, lacking any input of additional energy, the closed system will (eventually) increase its entropyAll 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 spontaneousSpontaneous 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 Concept 2.5 Biochemical Changes Involve Energy The Second Law of ThermodynamicsA spontaneous change is a change that has a tendency to occur without been driven by an external influencee.g. the cooling of a hot metal block to the temperature of its surroundingsA non-spontaneous change is a change that occurs only when drivene.g. forcing electric current through a metal block to heat it
244 Concept 2.5 Biochemical Changes Involve Energy So, another way to state the second law of thermodynamics isfor a process to occur spontaneously, it must increase the entropy of the universeYou will see that spontaneous processes are absolutely vital to biological processesDiffusion and facilitated diffusionOsmosis and dissolutionEvolution
245 Concept 2.5 Biochemical Changes Involve Energy Let’s describe the second law mathematicallyS = entropy∆S = change in entropyA spontaneous process will be a positive or negative ∆S?positive
246 The Second Law of Thermodynamics Enthalpy is the total potential energy of a systemH – 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 The Second Law of Thermodynamics Total entropy changeentropy change of systementropy change of surroundings=+Dissolvingdisorder of solutiondisorder of surroundingsmust be an overall increase in disorder for dissolving to occur
249 Biological Order and Disorder Now for the apparent paradox of life… Don’t living systems increase order, violating the second law of thermodynamics?50µm
250 Biological Order and Disorder Living systems are open systems that absorb energy—light or chemical energy – in the form of organic molecules50µm
251 Biological Order and Disorder and release heat and metabolic waste products such as urea or CO2 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 chainsBut living systems must use energy to maintain order.50µm
254 Biological Order and Disorder And, in using energy to maintain orderan 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.”50µmEntropy in Biology,Jayant Udgaonkar
259 Biological Order and Disorder “They gain their order at the expense of disordering the nutrient they consume.”50µmEntropy 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 entropy50µm
261 Biological Order and Disorder The entropy of a particular system, such as an organism, may decrease as long asthe total entropy of the universe—the system plus its surroundings—increases.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 entropySmall random changes in the DNA sequence is inevitable
264 Biological Order and Disorder Sometime those changes – mutations – lead to changes in a genewhich 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 thermodynamicsIndividuals and entire species are merely temporary and isolated examples of decreasing entropyEntropy drives the processes of evolution, osmosis, diffusion and other spontaneous processesNot a directed process; there is no goalEvolution is inevitable
266 Biological Order and Disorder Let’s 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 bagOsmosis 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 systemSecond, we know there will be a net flow of water into the bagThird, we know this will be spontaneousBy definition, this will increase entropy in the beaker/bag systemBut wait..there’s more!
269 Biological Order and Disorder Salt water has greater entropy than pure waterNa+ and Cl- ions are spread out through the solution, creating greater disorderPure water is just water molecules bumping into other water moleculesEntropy will seek equilibrium until ∆S = 0
270 Biological Order and Disorder Solutions have more distinguishable particlesWith a solute(s), you can see more combinations between molecules of solute(s) and solvent, than just solvent
271 Biological Order and Disorder 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)
272 Biological Order and Disorder System in Dynamic EquilibriumA B C DDynamic (coming and going), equilibrium (no net change)no overall change in disorder S 0 (zero entropy change)
273 Biological Order and Disorder 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 timeAll things must move toward a more disordered stateKnown as Time’s Arrow
274 Biological Order and Disorder Constantly increasing entropy in UniverseZero entropy13.7 billions years ago
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 Earth’s early atmosphere, including water vapor. An electric spark provided energy.Complex molecules were formed, such as amino acids. Water was essential in this experiment.ANIMATED TUTORIAL 2.3 Synthesis of Prebiotic Molecules
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 2Life Chemistry and Energy CGI Video Summation
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 mind’s eye, see the bonds, the interactions?
292 Life Chemistry and Energy Practice Questions 2Life Chemistry and Energy Practice Questions
293 Concept 2.1 Atomic Structure Is the Basis for Life’s Chemistry 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.Answers:The magnesium atom should have 12 protons and 12 neutrons in the nucleus. The first electron shell should have 2 electrons; the second shell should have 8 electrons; and the third shell should have 2 electrons.The magnesium atom is likely to bond with other atoms because it has less than the full complement of electrons in its outermost shell.293
294 Concept 2.1 Atomic Structure Is the Basis for Life’s Chemistry 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.Answer: c(The atoms of an element differ from those of other elements in number of protons.)294
295 Concept 2.2 Atoms Interact and Form Molecules Chemical bondsWorking in pairs, compare the following bonds with respect to their basis of interaction and strength:IonicCovalentHydrogenDraw an example of each type of bond.Answers:Ionic bonds are formed by the transfer of electrons whereas covalent bonds are formed by the sharing of electrons.Covalent bonds are strongest.Hydrogen bonds represent an attraction between a hydrogen atom with a slight positive charge and another atom (often oxygen) with a slight negative charge.INSTRUCTOR NOTE:Students might draw the following examples: NaCl (ionic bond); CH4 (covalent bonds); two water molecules (hydrogen bond between them).295
296 Concept 2.2 Atoms Interact and Form Molecules 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.Answer: d(During hydrolysis, not condensation, the addition of water breaks a polymer into monomers.)296
297 Concept 2.3 Carbohydrates Consist of Sugar Molecules 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.Answers:and 2. Starch is the major energy storage molecule of plants. Glycogen is an energy storage molecule in animals. Cellulose is a structural polysaccharide in plants.All are polysaccharides of glucose.The glycosidic linkages in cellulose make it a more stable molecule than either starch or glycogen. Also, whereas starch and glycogen are branched, cellulose is linear.297
298 Concept 2.3 Carbohydrates Consist of Sugar Molecules 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 cAnswer: e298
299 Concept 2.4 Lipids Are Hydrophobic Molecules TriglyceridesWorking individually, compare saturated and unsaturated fatty acids with respect to the following characteristics:1. Presence of double bonds between carbon atoms in the hydrocarbon chain2. Ability to pack tightly together3. State of lipid at room temperature4. Melting point of lipid5. Typical sourceCompare your answers with your classmates and discuss.Answers:In a saturated fatty acid, all the bonds between the carbon atoms in the hydrocarbon chain are single. In contrast, one or more double bonds is present in the hydrocarbon chain of an unsaturated fatty acid.Molecules of saturated fatty acids pack tightly together. Molecules of unsaturated fatty acids have kinks and do not pack tightly.Lipids with saturated fatty acids are usually solid at room temperature whereas those with unsaturated fatty acids are usually liquid.Lipids with saturated fatty acids tend to have high melting points whereas those with unsaturated fatty acids have low melting points.Many animal fats have saturated fatty acids. The triglycerides of plants tend to be unsaturated.299
300 Concept 2.4 Lipids Are Hydrophobic Molecules 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.Answer: a(The phosphate functional group and glycerol form the hydrophilic head.)300
301 Concept 2.5 Biochemical Changes Involve Energy Chemical reactionsWorking in pairs, consider the following chemical reaction and answer the questions below:glucose + galactose lactose + water1. 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?Answers:Condensation reactionThe reactants are glucose and galactose. The products are lactose and water.Anabolic reactionEnergy is required.301
302 Concept 2.5 Biochemical Changes Involve Energy 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 energye. Kinetic energy is the energy of movement.Answer: b(The energy released in catabolic reactions is often used to drive anabolic reactions.)302
303 Science, Technology and Society While waiting at an airport, Neil Campbell once overheard this claim:“It’s 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?
305 Practice ProblemsYou 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? *non-polarpolarelectrically chargedpolar and electrically chargedall of theseAnswer: aSource: Campbell/Reece - Biology, Sixth Edition, EOC Process of Science Question 2Discussion Notes for the InstructorThis question can be used several ways. The main discussion revolves around the non-polar nature of fatty acids. Leading to the simple choice of “non-polar” amino acids. A more involved discussion might be guided by the following questions:What is the overall polarity of a fatty acid?Is this consistent along the entire molecule?How would you structure the active site of the enzyme to hold the fatty acid in a particular orientation?In this latter case Choice E is correct as both non-polar and polar/charged amino acids would be involved.
308 Scientific InquiryLet’s begin with the condensation reaction that lead to the 1-4 glycosidic linkage
309 Scientific InquiryRepeated many times results in a polysaccharide known as starch
310 Scientific InquiryHydrolysis breaks the glycosidic linkages, leaving behind glucose monomers, reinserting a water moleculeH2ONote one hydrogen bonds with the oxygen of carbon-1; the remaining hydroxyl group OH bonds with the carbon 4
311 Scientific InquiryIf hydrochloric acid used to break glycosidic linkages..HClClThe 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