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02The Chemical Context of LifeLecture Presentation by Nicole Tunbridge andKathleen FitzpatrickCAMPBELLBIOLOGYReece Urry Cain Wasserman Minorsky Jackson 2014 Pearson Education, Inc.TENTHEDITIONCAMPBELLBIOLOGYReece Urry Cain Wasserman Minorsky JacksonTENTHEDITION 2014 Pearson Education, Inc.1A Chemical Connection to BiologyBiology is the study of lifeLiving organisms and their environments are subject to basic laws of physics and chemistryOne example is the use of formic acid by ants to protect themselves against predators and microbial parasites 2014 Pearson Education, Inc.2

Figure 2.1 2014 Pearson Education, Inc.Figure 2.1 What weapon are these wood ants shooting into the air?3

Figure 2.1a 2014 Pearson Education, Inc.Figure 2.1a What weapon are these wood ants shooting into the air? (part 1: detail)4Concept 2.1: Matter consists of chemical elements in pure form and in combinations called compoundsOrganisms are composed of matterMatter is anything that takes up space and has mass 2014 Pearson Education, Inc.5Elements and CompoundsMatter is made up of elements An element is a substance that cannot be broken down to other substances by chemical reactionsA compound is a substance consisting of two or more elements in a fixed ratioA compound has characteristics different from those of its elements 2014 Pearson Education, Inc.6

Figure 2.2SodiumChlorineSodium chloride 2014 Pearson Education, Inc.Figure 2.2 The emergent properties of a compound7

Figure 2.2aSodium 2014 Pearson Education, Inc.Figure 2.2a The emergent properties of a compound (part 1: sodium)8

Figure 2.2bChlorine 2014 Pearson Education, Inc.Figure 2.2b The emergent properties of a compound (part 2: chlorine)9

Figure 2.2cSodium chloride 2014 Pearson Education, Inc.Figure 2.2c The emergent properties of a compound (part 3: sodium chloride)10The Elements of LifeAbout 2025% of the 92 elements are essential to life (essential elements)Carbon, hydrogen, oxygen, and nitrogen make up 96% of living matterMost of the remaining 4% consists of calcium, phosphorus, potassium, and sulfurTrace elements are those required by an organism in only minute quantities 2014 Pearson Education, Inc.

Table 2.1 2014 Pearson Education, Inc.Table 2.1 Elements in the human body12Case Study: Evolution of Tolerance to Toxic ElementsSome elements can be toxic, for example, arsenicSome species can become adapted to environments containing toxic elementsFor example, some plant communities are adapted to serpentine 2014 Pearson Education, Inc.Figure 2.3

2014 Pearson Education, Inc.Figure 2.3 Serpentine plant community14Figure 2.3a

2014 Pearson Education, Inc.Figure 2.3a Serpentine plant community (part 1: serpentine landscape)15Figure 2.3b

2014 Pearson Education, Inc.Figure 2.3b Serpentine plant community (part 2: Tiburon mariposa lily)16

Figure 2.3c 2014 Pearson Education, Inc.Figure 2.3c Serpentine plant community (part 3: serpentine rock)17Concept 2.2: An elements properties depend on the structure of its atomsEach element consists of unique atomsAn atom is the smallest unit of matter that still retains the properties of an element 2014 Pearson Education, Inc.Subatomic ParticlesAtoms are composed of subatomic particlesRelevant subatomic particles includeNeutrons (no electrical charge)Protons (positive charge)Electrons (negative charge) 2014 Pearson Education, Inc. Neutrons and protons form the atomic nucleusElectrons form a cloud around the nucleusNeutron mass and proton mass are almost identical and are measured in daltons 2014 Pearson Education, Inc.

Figure 2.4(b)++++(a)Electrons--NucleusCloud of negativecharge (2 electrons) 2014 Pearson Education, Inc.Figure 2.4 Simplified models of a helium (He) atom21Atomic Number and Atomic MassAtoms of the various elements differ in number of subatomic particlesAn elements atomic number is the number of protons in its nucleusAn elements mass number is the sum of protons plus neutrons in the nucleus Atomic mass, the atoms total mass, can be approximated by the mass number 2014 Pearson Education, Inc.IsotopesAll atoms of an element have the same number of protons but may differ in number of neutronsIsotopes are two atoms of an element that differ in number of neutronsRadioactive isotopes decay spontaneously, giving off particles and energy 2014 Pearson Education, Inc.Radioactive TracersRadioactive isotopes are often used as diagnostic tools in medicineRadioactive tracers can be used to track atoms through metabolismThey can also be used in combination with sophisticated imaging instruments 2014 Pearson Education, Inc.

Figure 2.5Cancerousthroattissue 2014 Pearson Education, Inc.Figure 2.5 A PET scan, a medical use for radioactive isotopes25Radiometric DatingA parent isotope decays into its daughter isotope at a fixed rate, expressed as the half-lifeIn radiometric dating, scientists measure the ratio of different isotopes and calculate how many half-lives have passed since the fossil or rock was formed Half-life values vary from seconds or days to billions of years 2014 Pearson Education, Inc.The Energy Levels of ElectronsEnergy is the capacity to cause changePotential energy is the energy that matter has because of its location or structureThe electrons of an atom differ in their amounts of potential energyAn electrons state of potential energy is called its energy level, or electron shell 2014 Pearson Education, Inc.

Figure 2.6(a)A ball bouncing down a flightof stairs provides an analogyfor energy levels of electrons.Third shell (highest energylevel in this model)Second shell (next highestenergy level)First shell (lowest energylevel)AtomicnucleusEnergylostEnergyabsorbed(b) 2014 Pearson Education, Inc.Figure 2.6 Energy levels of an atoms electrons28Electron Distribution and Chemical PropertiesThe chemical behavior of an atom is determined by the distribution of electrons in electron shellsThe periodic table of the elements shows the electron distribution for each element 2014 Pearson Education, Inc.

Figure 2.7Atomic massAtomic numberElement symbolElectrondistributiondiagram24.003HeHelium2HeNeon10NeFluorine9FOxygen8ONitrogen7NCarbon6CBoron5BBeryllium4BeLithium3LiSecondshellFirstshellHydrogen1HArgon18ArChlorine17ClSulfur16SPhosphorus15PSilicon14SiAluminum13AlMagnesium12MgSodium11NaThirdshell 2014 Pearson Education, Inc.Figure 2.7 Electron distribution diagrams for the first 18 elements in the periodic table30

Figure 2.7aAtomic massAtomic numberElectrondistributiondiagram24.003HeHelium5HeElement symbol 2014 Pearson Education, Inc.Figure 2.7a Electron distribution diagrams for the first 18 elements in the periodic table (part 1)31

Figure 2.7bHelium2HeHydrogen1HFirstshell 2014 Pearson Education, Inc.Figure 2.7b Electron distribution diagrams for the first 18 elements in the periodic table (part 2)32

Figure 2.7cBoron5BCarbon6CBeryllium4BeLithium1LiSecondshellThirdshellAluminum13AlSilicon13SiMagnesium12MgSodium11Na 2014 Pearson Education, Inc.Figure 2.7c Electron distribution diagrams for the first 18 elements in the periodic table (part 3)33

Figure 2.7dFluorine9FNeon10NeOxygen8ONitrogen7NSecondshellThirdshellChlorine17ClArgon18ArSulfur16SPhosphorus15P 2014 Pearson Education, Inc.Figure 2.7d Electron distribution diagrams for the first 18 elements in the periodic table (part 4)34 Valence electrons are those in the outermost shell, or valence shellThe chemical behavior of an atom is mostly determined by the valence electronsElements with a full valence shell arechemically inert 2014 Pearson Education, Inc.Electron OrbitalsAn orbital is the three-dimensional space where an electron is found 90% of the timeEach electron shell consists of a specific number of orbitals 2014 Pearson Education, Inc.

Figure 2.8Second shellFirst shellFirstshellSecondshell1s orbital2s orbitalThree 2p orbitalsxyzNeon,with twofilled shells(10 electrons)(a)Electron distributiondiagram(b)Separate electron orbitals1s, 2s, and2p orbitals(c)Superimposed electron orbitals 2014 Pearson Education, Inc.Figure 2.8 Electron orbitals37

Figure 2.8aFirstshellSecondshellNeon,with twofilled shells(10 electrons)(a) Electron distributiondiagram 2014 Pearson Education, Inc.Figure 2.8a Electron orbitals (part 1: distribution diagram)38

Figure 2.8bSecond shellFirst shell1s orbital2s orbitalThree 2p orbitalsxyz(b) Separate electron orbitals 2014 Pearson Education, Inc.Figure 2.8b Electron orbitals (part 2: separate orbitals)39

Figure 2.8c1s, 2s, and2p orbitals(c) Superimposed electron orbitals 2014 Pearson Education, Inc.Figure 2.8c Electron orbitals (part 3: superimposed orbitals)40Concept 2.3: The formation and function of molecules depend on chemical bonding between atomsAtoms with incomplete valence shells can share or transfer valence electrons with certain other atomsThese interactions usually result in atoms staying close together, held by attractions calledchemical bonds 2014 Pearson Education, Inc.Covalent BondsA covalent bond is the sharing of a pair of valence electrons by two atomsIn a covalent bond, the shared electrons count as part of each atoms valence shell 2014 Pearson Education, Inc.

Figure 2.9-1Hydrogen atoms (2 H)++ 2014 Pearson Education, Inc.Figure 2.9-1 Formation of a covalent bond (step 1)43

Figure 2.9-2Hydrogen atoms (2 H)++++ 2014 Pearson Education, Inc.Figure 2.9-2 Formation of a covalent bond (step 2)44

Figure 2.9-3Hydrogen atoms (2 H)Hydrogenmolecule (H2)++++++ 2014 Pearson Education, Inc.Figure 2.9-3 Formation of a covalent bond (step 3)45 A molecule consists of two or more atoms held together by covalent bondsA single covalent bond, or single bond, is the sharing of one pair of valence electronsA double covalent bond, or double bond, is the sharing of two pairs of valence electrons 2014 Pearson Education, Inc. The notation used to represent atoms and bonding is called a structural formulaFor example, HH This can be abbreviated further with a molecular formula For example, H2 2014 Pearson Education, Inc.

Figure 2.10Name andMolecularFormulaElectronDistributionDiagramLewis DotStructure andStructuralFormulaSpace-FillingModel(d) Methane (CH4)(c) Water (H2O)(b) Oxygen (O2)(a) Hydrogen (H2)HHOOOHHCHHHH 2014 Pearson Education, Inc.Figure 2.10 Covalent bonding in four molecules48

Figure 2.10aName andMolecularFormulaElectronDistributionDiagramLewis DotStructure andStructuralFormulaSpace-FillingModel(a) Hydrogen (H2)HH 2014 Pearson Education, Inc.Figure 2.10a Covalent bonding in four molecules (part 1: hydrogen)49

Figure 2.10bName andMolecularFormulaElectronDistributionDiagramLewis DotStructure andStructuralFormulaSpace-FillingModel(b) Oxygen (O2)OO 2014 Pearson Education, Inc.Figure 2.10b Covalent bonding in four molecules (part 2: oxygen)50

Figure 2.10cName andMolecularFormulaElectronDistributionDiagramLewis DotStructure andStructuralFormulaSpace-FillingModel(c) Water (H2O)OHH 2014 Pearson Education, Inc.Figure 2.10c Covalent bonding in four molecules (part 3: water)51

Figure 2.10dName andMolecularFormulaElectronDistributionDiagramLewis DotStructure andStructuralFormulaSpace-FillingModel(d) Methane (CH4)CHHHH 2014 Pearson Education, Inc.Figure 2.10d Covalent bonding in four molecules (part 4: methane)52

Animation: Covalent Bonds 2014 Pearson Education, Inc. Covalent bonds can form between atoms of the same element or atoms of different elements A compound is a combination of two or more different elementsBonding capacity is called the atoms valence 2014 Pearson Education, Inc. Atoms in a molecule attract electrons to varying degreesElectronegativity is an atoms attraction for the electrons in a covalent bondThe more electronegative an atom, the more strongly it pulls shared electrons toward itself 2014 Pearson Education, Inc. In a nonpolar covalent bond, the atoms share the electron equallyIn a polar covalent bond, one atom is more electronegative, and the atoms do not sharethe electron equallyUnequal sharing of electrons causes a partial positive or negative charge for each atomor molecule 2014 Pearson Education, Inc.

Figure 2.11HHOH2Od+d+d- 2014 Pearson Education, Inc.Figure 2.11 Polar covalent bonds in a water molecule57Ionic BondsAtoms sometimes strip electrons from their bonding partnersAn example is the transfer of an electron from sodium to chlorineAfter the transfer of an electron, both atoms have chargesA charged atom (or molecule) is called an ion 2014 Pearson Education, Inc.

Figure 2.12-1NaClNaSodium atomClChlorine atom 2014 Pearson Education, Inc.Figure 2.12-1 Electron transfer and ionic bonding (step 1)59

Figure 2.12-2+-NaClNa+Sodium ion(a cation)Cl-Chloride ion(an anion)Sodium chloride (NaCl)NaClNaSodium atomClChlorine atom 2014 Pearson Education, Inc.Figure 2.12-2 Electron transfer and ionic bonding (step 2)60

Animation: Ionic Bonds 2014 Pearson Education, Inc. A cation is a positively charged ionAn anion is a negatively charged ionAn ionic bond is an attraction between an anion and a cation 2014 Pearson Education, Inc. Compounds formed by ionic bonds are called ionic compounds, or saltsSalts, such as sodium chloride (table salt), are often found in nature as crystals 2014 Pearson Education, Inc.

Figure 2.13Na+Cl- 2014 Pearson Education, Inc.Figure 2.13 A sodium chloride (NaCl) crystal64

Figure 2.13a 2014 Pearson Education, Inc.Figure 2.13a A sodium chloride (NaCl) crystal (part 1: photo)65Weak Chemical BondsMost of the strongest bonds in organisms are covalent bonds that form a cells moleculesWeak chemical bonds are also indispensableMany large biological molecules are held in their functional form by weak bondsThe reversibility of weak bonds can be an advantage 2014 Pearson Education, Inc.Hydrogen BondsA hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atomIn living cells, the electronegative partners are usually oxygen or nitrogen atoms 2014 Pearson Education, Inc.

Figure 2.14Water (H2O)Ammonia (NH3)Hydrogen bondd+d-d+d+d+d+d- 2014 Pearson Education, Inc.Figure 2.14 A hydrogen bond68Van der Waals InteractionsIf electrons are distributed asymmetrically in molecules or atoms, they may accumulate by chance in one part of a moleculeVan der Waals interactions are attractions between molecules that are close together as a result of these charges 2014 Pearson Education, Inc. Collectively, such interactions can be strong, as between molecules of a geckos toe hairs and a wall surface 2014 Pearson Education, Inc.

Figure 2.UN02 2014 Pearson Education, Inc.Figure 2.UN02 In-text figure, gecko, p. 3971Molecular Shape and FunctionA molecules shape is usually very important to its functionA molecules shape is determined by the positions of its atoms orbitalsIn a covalent bond, the s and p orbitals may hybridize, creating specific molecular shapes 2014 Pearson Education, Inc.

Figure 2.15s orbitalzyx(a) Hybridization of orbitalsFour hybrid orbitalsTetrahedronThreep orbitals(b) Molecular-shape modelsMethane (CH4)Water (H2O)Space-FillingModelBall-and-StickModelHybrid-Orbital Model(with ball-and-stickmodel superimposed)UnbondedelectronpairHHHHCHHHHCHHOHHO104.5 2014 Pearson Education, Inc.Figure 2.15 Molecular shapes due to hybrid orbitals73

Figure 2.15as orbitalzyx(a) Hybridization of orbitalsFour hybrid orbitalsTetrahedronThreep orbitals 2014 Pearson Education, Inc.Figure 2.15a Molecular shapes due to hybrid orbitals (part 1: hybridization)74

Figure 2.15b(b) Molecular-shape modelsMethane (CH4)Water (H2O)Space-FillingModelBall-and-StickModelHybrid-Orbital Model(with ball-and-stickmodel superimposed)UnbondedelectronpairHHHHCHHHHCHHOHHO104.5 2014 Pearson Education, Inc.Figure 2.15b Molecular shapes due to hybrid orbitals (part 2: models)75 Molecular shape is crucial in biology because it determines how biological molecules specifically recognize and respond to one another Opiates, such as morphine, and naturally produced endorphins have similar effects because their shapes are similar and they bind the same receptors in the brain 2014 Pearson Education, Inc.

Figure 2.16Natural endorphin(a) Structures of endorphin and morphineMorphineKeyCarbonHydrogenOxygenSulfurNitrogenMorphineNatural endorphinEndorphinreceptorsBrain cell(b) Binding to endorphin receptors 2014 Pearson Education, Inc.Figure 2.16 A molecular mimic77Concept 2.4: Chemical reactions make and break chemical bondsChemical reactions are the making and breaking of chemical bondsThe starting molecules of a chemical reaction are called reactantsThe final molecules of a chemical reaction are called products 2014 Pearson Education, Inc.

Figure 2.UN03ReactantsReactionProducts2 H2O22 H2O 2014 Pearson Education, Inc.Figure 2.UN03 In-text figure, water formation, p. 4079 Photosynthesis is an important chemical reaction Sunlight powers the conversion of carbon dioxide and water to glucose and oxygen6 CO2 + 6 H2O C6H12O6 + 6 O2 2014 Pearson Education, Inc.

Figure 2.17 2014 Pearson Education, Inc.Figure 2.17 Photosynthesis: a solar-powered rearrangement of matter81 All chemical reactions are reversible: products of the forward reaction become reactants for the reverse reactionChemical equilibrium is reached when the forward and reverse reactions occur at the same rate At equilibrium the relative concentrations of reactants and products do not change 2014 Pearson Education, Inc.

Figure 2.UN01a1.00.90.80.70.60.50.40.30.20.10012345678910Time before present (half-lives)Fraction of isotope remaining in fossil 2014 Pearson Education, Inc.Figure 2.UN01a Skills exercise: calibrating a standard radioactive isotope decay curve and interpreting data (part 1)83

Figure 2.UN01bNeanderthal fossils 2014 Pearson Education, Inc.Figure 2.UN01b Skills exercise: calibrating a standard radioactive isotope decay curve and interpreting data (part 2)84

Figure 2.UN04NucleusProtons (+ charge)determine elementNeutrons (no charge)determine isotopeAtomElectrons ( chargeform negative cloudand determinechemical behavior++ 2014 Pearson Education, Inc.Figure 2.UN04 Summary of key concepts: atom components85

Figure 2.UN05Singlecovalent bondDoublecovalent bond 2014 Pearson Education, Inc.Figure 2.UN05 Summary of key concepts: covalent bonds86

Figure 2.UN06Ionic bondElectrontransferforms ionsNa+Sodium ion(a cation)ClChloride ion(a anion)ClNaClNaClChlorine atomNaSodium atom+ 2014 Pearson Education, Inc.Figure 2.UN06 Summary of key concepts: ionic bonds87

Figure 2.UN07(a)(b) 2014 Pearson Education, Inc.Figure 2.UN07 Test your understanding, question 9 (Lewis dot structures)88

Figure 2.UN08 2014 Pearson Education, Inc.Figure 2.UN08 Test your understanding, question 11 (silkworm moth, Bombyx mori)89

Figure 2.UN09 2014 Pearson Education, Inc.Figure 2.UN09 Test your understanding, question 13 (bombardier beetle)90