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CHAPTER2 THE CHEMICAL CONTEXT OF LIFE OUTLINE L ChemicalElementsandCompounds called A. Matter consistsof chemicalelementsin pure form and in combinations comPounds B. Life requiresabout25 chemicalelements II. Atoms andMolecules the behaviorof an element A. Atomic structuredetermines B.Atomscombinebychemicalbondingtoformmolecules c. weak chemicalbondsplay importantroles in the chemistryof life D'Amolecule'sbiologicalfunctionisrelatedtoitsshape E. Chemicalreactionsmakeandbreakchemicalbonds OBJECTTVES be able to: After reading this chapter and attending lecture, the student should Define element and comPound' 1. State four elements essential to lif'e that make up 96Yoof living matter' 2. 3. 4. 5. Describe the structureof an atom' weight' and Define and distinguish among atomic number, mass number, atomic valence' the number of Given the atomic number and mass number of an atom, determine neutrons. 6'Explainwhyradioisotopesareimportanttobiologists. of an atom' Explain how electron configuration influencesthe chemical behavior 7. form' Explain the octet rule and predict how many bonds an atom might 8. g. Explain why the noble gasesare so unreactive' the formation of chemical 10. Define electronegativity and explain how it influences bonds. and ionic bonds' I 1. Distinguish among nonpolar covalent, polar covalent how it differs from a covalent lZ. Describe the formation of a hydrogen bond and explain or ionic bond. 13. Explain why weak bonds are important to living organisms. products affect a chemical 14, Describe how the relative concentrations of reactants and reaction. L2 Unit I TheChemisrryof Life KEYTERMS matter atomic weight isotope element trace element atom neutron proton radioactive isotope energy potential energy energy level valence electron valenceshell chemical bond cation covalent bond molecule anion ionic bond structural formula molecular formula polar covalent bond ion atomic nucleus dalton energy potential energy energy level double covalent bond hydrogen bond chemical reactions reactants valence products atomic number massnumber electron shell orbital electronegativity nonpolar covalent bond chemicalequilibrium electron LECTT]RENOTES I. Chemical Elements and Compounds A. Matter consists of chemical elements in pure form and in combinations called compounds Chemistry is fundamental to an understandingof life, becauseliving organisms are made of matter. Matter: Anything that takes up spaceand has mass. Mass : A measure of the amount of matter an obiect contains. You might want to distinguish between mass and weight for your students. Mass is the measure of the amount of matter an object contains, and it stays the same regardless of _changes in the object's position. Weight is the measureof how strongly an object is pulled by earth's gravity, and it varies with distance from the earth's center. Thi key point is that the mass of a body does not vary with its position, whereasweight does. So, for all practical purposes-as long as we are earthbound-weight can be used as a measureof mass. B. Life requires about 25 chemical elements Element = A substancethat cannot be broken down into other substancesbv chemical reactions. . All matter is made of elements. . There are 92 naturally occurring elements. . They are designatedby a symbol of one or two letters. About 25 of the 92 naturally occurring elementsare essentialto tife. Biologically important elements include: C = O H : N = _l carbon oxygen I makeup 96Yoof living matter hydrogen I nitrogen J Chapter2 TheChernicalContextof Life 13 calcium Ca : phosphorus P = potassium K : sulfur $ = = sodium Na = chlorine Cl magnesium Mg: Trace elements make up remaining 4%oof an organism'sweight Traceelement= Elementrequiredby an organismin extremelyminutequantities. for life . Thoughrequiredby organismsin smallquantity,they are indispensable . Examples:B, Cr, Co, Cu, F, I, Fe,Mn, Mo, Se,Si, Sn,V andZn calledcompounds. Elementscan exist in combinations . Compound: A puresubstance of two or more elementscombinedin composed a fixed ratio. . Example:NaCl (sodiumchloride) . Has uniqueemergentpropertiesbeyondthoseof its combinedelements(Na and Cl havevery differentpropertiesfrom NaCl). SeeCampbell,Figure2.2. Since a compound is the next structural level above element or atom, this is an excellent place to emphasizethe concept of emergentproperties, an integral theme found throughout the text and course. tr. Atoms and Molecules A. Atomic structure determinesthe behavior of an element Atom : Smallestpossibleunit of matterthat retainsthe physicaland chemical propertiesof its element. . Atoms of the sameelementsharesimilarchemicalproperties. . Atoms are madeup of subatomicparticles. 1. Subatomic Particles The threemoststablesubatomicparticlesare: 1. Neutrons[no charge(neutral)]. charge]. 2. Protons [+l electrostatic charge]. 3. Electrons[-l electrostatic IYEUTRON No charge PROTON *l charge ELECTRON -l charge Found together in a dense core called the nucleus Orbits around nucleus (held by electrostatic attraction (positivel! chargedbecauseof protons) charged positivelY to nucleus) 1.009dalton 1.007dalton Massesof both areaboutthe same(aboutI dalton) 112000dalton Mass is so small, usually not used to calculate atomicmass NOTE: Thedalton is a unit usedto expressmassat the atomiclevel.One dalton(d) is equalto 1.67x lo-'og. If an atom is electricallyneutral,the numberof protonsequalsthe numberof electrons, balancedcharge. which yieldsan electrostatically 14 Unit I The Chemistrvof Life 2. Atomic number and atomic uight Atomic number: Numberof protonsin an atomof a particularelement. . All atomsof an elementhavethe sameatomic number. ' written as a subscriptto the left of the element'ssymbol(e.g., 11Na) . In a neutral atom, # protons: # electrons. Mass number: Number of protonsand neutronsin an atom. . Writtenas a superscript to left of an element'ssymbol1e.g.,23Na; ' Is approximatemassof the whole atom,sincethe massof a proton and the massof a neutronare both about I dalton ' Can deducethe number of neutrons by subtractingotomic number from mossnumber ' Number of neutrons can vary in an element, but number of protons is constant ' Is notthe same as an element'satomic weight, which is the weighted mean of the massesof an element'sconstituent isbtopes In a large classroomwith up to 300 students,it can be diflicult to interact. Trv putting exampleson an overheadtransparencyand soliciting student input to complete the information. It is a quick way to check for understandineand to actively involve students. Examples: (Mass #) 23 (Atomic #) I I Na # of electrons # of protons # of neutrons t2 6 C #ofelectrons # of protons # of neutrons 3. fsotopes Isotopes: Atoms of an elementthat have the sameatomic numberbut different massnumber. ' They have the samenumberof protons,but a different numberof neutrons. ' under naturalconditions,elementsoccur as mixturesof isotopes. ' Different ieotopesof the sameelementreactchemicallyin sameway. . Someisotopesare radioactive. Radioactiveisotope: Unstableisotopein which the nucleusspontaneously decays, emitting subatomlcparticlesand/orenergyas radioactivity. ' . Loss of nuclearparticlesmay transforrnone elementto another ( " . g . ,t l c + t l N ) . Has a fixed half life. ' Half life : Time for 50Yoof radioactiveatomsin a sampleto decay. Biologicalapplicationsof radioactiveisotopesinclude: a. Dating geologicalstrataand fossils Contextof Life 15 2 TheChemical Chapter . Hasa fixed half life' . Hatf life = Time for 50Yoof radioactiveatomsin a sampleto decay. of radioactiveisotopesinclude: Biologicalapplications a. Datinggeologicalstrataandfossils . Radioactivedecayis at a fixed rate. . By comparingthe ratio of radioactiveand stableisotopesin a fossil with the-ratiJof isotopesin living organisms,one can estimatethe age of a fossil' . The ratio of toc to 'tC is frequentlyusedto datefossilslessthan 50,000 yearsold. b. Radioactivetracers . Chemicals labelledwith radioactiveisotopesare usedto trace the steps of a biochemicalreactionor to determinethe location of a particular within an organism(seecampbell,p. XX, Methods:The use substance of RadioactiveTracersin Biology). . Radioactiveisotopesare usefulas biochemicaltracers becausethey chemicallyreact iike the stableisotopesand are easilydetectedat low concentrations. . Isotopesof P, N, andH wereusedto determineDNA structure. . Usedto diagnosedisease(e.g.,PET scanner) . Becauseradioactivitycan damagecell molecules,radioactiveisotopes canalsobe hazardous c. Treatmentof cancer ' €.g.,radioactive cobalt 4 . The energy levels of electrons Electrons= Light negativelychargedparticlesthat orbit aroundnucleus' . o Equalin massandcharge Are the only stablesubatomicparticlesdirectlyinvolvedin chemicalreactions r Have potential energ/ becauseof their position relative to the positively chargednucleus Energy: Ability to do work potential energ/ = Energy that matter storesbecauseof its position or location. . There is a natural tendency for matter to move to the lowest state of potential energy. potential energy of electrons is not infinitely divisible, but exists only in . discreteamountscalled quanto. . Different fixed potential energy states for electrons are called energt levels or electronshells (see Campbell,Figure 2'7)' . Electrons with lowest potential energy are in energy levels closest to the nucleus. . Electronswith greaterenergy are in energy levels further from nucleus. gain or Electrons may move from one energy level to another.In the process,they new and the old between tor" .n.tgy equal to the difference in potential energy energy level. 16 Unit I TheChemistrvof Life Third energy lewl Second energy lewl First energy lewl 5. Electron orbitals Orbital = Three-dimensional spacewherean electronwill mostlikely be found90% of the time (seeCampbell,Figure2.8). ' Viewedas a three-dimensional probabilitycloud(a statisticalconcept) . No more thantwo electronscan occupysameorbital. First energylevel: . Has one sphericals orbital(ls orbital) . Holds a maximumof two electrons Secondenergylevel . Holds a maximumof eightelectrons . One sphericals orbital(2s orbital) ' Threedumbbell-shaped p orbitalseachorientedat right anglesto the other two (2p*,Zpr,2p. orbitals) Higherenergylevels: . Contains andp orbitals . Containadditionalorbitalswith morecomplexshapes 6. Electron configuration and chemical properties An atom's electronconfigurationdeterminesits chemicalbehavior. ' Electron conJiguration= Distributionof electronsin an atom's electron shells The first l8 elementsof a periodicchartare arrangedsequentially by atomic numberinto threerows (periods).In referenceto theserepresentotive elements, note the following: ' Outermostshell of theseatomsnever have more than four orbitals(one s and threep) or eight electrons. ' Electronsmust first occupy lower electron shellsbeforethe higher shells canbe occupied.(This is a reflectionof the naturaltendencyfor matter to move to the lowestpossiblestate of potential energy-the most stable state.) ' Electronsare addedto each of the p orbitalssingly, beforethey can be paired. ' If an atomdoesnot have enoughelectronsto fill all shells,the outer shell will be the only one partially filled. Example: 02 with a total of eight electrons: Chapter2 TheChemicalContextof Life 17 OXYGEN 8o Two electronshavethe ls orbitalof the first electronshell. First two electronsin the secondshell are both in the 2s orbital. Next three electronseach have a p orbital (2p,,ZPr,2P,). Eighthelectronis pairedin the 2p, orbital. ls 2 2s p1 2pt P, 2 2 1 I Chemical propertiesof an atom depend upon the number of valence electrons. . Valenceelectrons: Electrons in the outermostenergy shell (valence shell). Octet rule: Rule that a valence shell is completewhen it contains eight electrons (except H and He). . An atom with a complete valence shell is unreactiveor inert' . Noble elements (e.g., helium, argon, and neon) have filled outer shells in their elemental state and are thus inert' . An atom with an incomplete valence shell is chemically reactive (tends to form chemical bonds uniil it has eight electronsto fill the valence shell). . Atoms with the same number of valence electrons show similar chemical behavior. NOTE: The consequenceof this unifiing chemical principle is th-atthe.valence to most electronsur. ,.rponrible for the atom's bonding capacity. This rule applies of the representativeelements,but not all' B. Atoms combine by chemical bonding to form molecules with other Atoms with incomplete valence shells tend to fill those shells by interacting form atoms. These interactionsof electronsamong atoms may allow atoms to chemical bonds. , chemical bonds: Attractions that hold molecules together Molecules = Two or more atoms held togetherby chemical bonds. 1. Covalent bonds pair of valence Covalent bond = Chemical bond betweenatoms formed by sharing a electrons. ' Strong chemical bond . Example: molecular hydrogen (Hz); when two hydrogen atoms come close H2 18 Unit I TheChemistryof Life structuralformula: Formulawhich represents the atomsandbondingwithin a molecule(e.g.,H-H). The line represents a sharedpair of electrons. Molecularformula: Formulawhich indicatesthe numberandtype of atoms(e.g., Hz). st sl" covalentbond = Bond betweenatomsformedby sharinga singlepair of valenceelectrons. . Atoms may freely rotatearoundthe axis of the bond. Double covalentbond : Bond formedwhen atomssharetwo pairs of valence electrons(e.9.,Oz). @@ o2 O=O Molecules: Two or moreatomsheldtogetherby chemicalbonds. Triple covalentbond = Bond formedwhen atomssharethreepairs of valence electrons(e.g.,Nz or N1{). NorE: Doubleandtriple covalentbondsare rigid and do not allow rotation. Valence= Bondingcapacityof an atomwhich is the numberof covalentbondsthat must be formedto completethe outerelectronshell. . Valencesof somecommonelements: hydrogen: l, oxygen:2, nitrogen: 3, carbon: 4, phosphorus: 3 (sometimes5 as in biologicallyimportant compounds, e.g.,ATP), sulfur= 2. = Compound A puresubstance composed of two or moreelementscombinedin a fixed ratio. . Example:water (HzO),methane(CH4) ' Note that two hydrogensare necessaryto completethe valenceshell of oxygenin water,and four hydrogensare necessary for carbonto complete the valenceshell in methane. @ @ @ @ H Hzo @ o-H I H CHa @ H - c-H I H t,, Chapter2 TheChemicalContextof Life 19 2. Nonpolar and polar covalent bonds Electronegativity -- Atom's ability to attract and hold electrons. . The more electronegative an atom, the more strongly it attracts shared electrons. . Scale determined by Linus Pauling: o:3.5 N:3.0 SandC=2.5 P a n dH : 2 . 1 Nonpolar covalent bond : Covalent bond formed by an equal sharing of electrons between atoms. o Occurs when electronegativityof both atoms is about the same (e.g., CHa) o Molecules made of one element usually have nonpolar covalent bonds (e.g., H} Oz,Cl2,N2). Polar covalent bond : Covalent bond formed by an unequal sharing of electrons between atoms. . Occurs when the atoms involved have different electronegativities. . Shared electrons spend more time around the more electronegative atom. . In H2O, for example, the oxygen is strongly electronegative, so negatively charged electrons spend more time around the oxygen than the hydrogens. This causesthe oxygen atom to have a slight negative charge and the hydrogens to have a slight positive charge(seealso Campbell,Figure 2.11). 3. Ionic bonds Ion: Chargedatom or molecule. Anion: An atom that has gained one or more electronsfrom another atom and has become negatively charged; a negatively charged ion. Cation: An atom that has lost one or more electronsand has become positively charged;a positively chargedion. Ionic bond: Bond formed by the electrostaticattraction after the complete transfer of an electron from a donor atom to an acceptor. . The acceptor atom attracts the electrons because it is much more electronegativethan the donor atom. Are strong bonds in crystals, but are fragile bonds in water; salt crystals will readily dissolve in water and dissociateinto ions. Ionic compounds are called salts (e.g., NaCl or table salt) (see Campbell, Figure 2.13). NOTE: The dffirence in electronegativity between interacting atoms determines ifelectrons are shared equally (nonpolar covalent), shared unequally (polar covalent), gained or lost (ionic bond). Nonpolar covalent bonds and ionic bonds are two extremes of a continuum from interacting atoms with similar electronegativitiesto interacting atoms with very different electronegativities. 20 Unit I TheChemistryof Life c. weak chemical bonds play important roles in the chemistry of life Biologicallyimportantweakbondsincludethe following: ' Hydrogenbonds,ionic bondsin aqueous solutions,andotherweakforcessuchas Van der Waalsand hydrophobicinteractions ' Make chemicalsignalingpossiblein living organismsbecausethey are only temporary associations.Signalmoleculescan briefly and reversiblybind tb receptormoleculeson a cell, causinga short-livedresponse. ' Can form betweenmoleculesor betweendifferent parts of a single large molecule. ' Help stabilizethe three-dimensional shapeof largemolecules(e.g., DNA and proteins). l. Hydrogen bonds Hydrogen bond : Bond formedby the chargeattractionwhen a hydrogenatom covalentlybondedto one electronegative atom is attractedto another electronegative atom. o Weak affractive force that is about 20 times easier to break than a covalent bond o Is a charge attraction between oppositely chargedportions of polar molecules o Can occur between a hydrogen that has a slight positive charge when covalently bonded to an atom with high electronegativity (usually O and N) r Example: NH3 in H2O (see Campbell, Figure 2.14) 2. Van der Waals interactions Weak interactions that occurbetweenatomsand moleculesthat are very close togetherand resultfrom chargeasymetryin electronclouds. D. A molecule'sbiological function is related to its shape A moleculehasa charasteric sizeandshape. The functionof manymoleculesdependsupontheir shape Insulin causesglucoseuptake into liver and musclecells of veterbratesbecausethe shapeof the insulinmoleculeis recognized by specificreceptors on the targetcell. . . Molecules with only two atoms are linear. Molecules with more than two atoms have more complex shapes. When an atom forms covalent bonds, orbitals in the valence shell realrange into the most stable configuration. To illustrate, consider atoms with valence electronsin the s and threep orbitals: . The s and three p orbitals hybridize into four new orbitals. ' The new orbitals are teardrop shaped,extend from the nucleus and spread out as far apart as possible. ' Example: If outer tips of orbitals in methane(CH+) are connectedby imaginary lines, the new molecule has a tetrahedral shape with C at the center (see Campbell,Figure 2.15). 2 TheChemical Contextof Life 2l Chapter E Chemical reactionsmake and break chemical bonds Chemicalreactions= processof makingandbreakingchemicalbondsleadingto changesin the compositionof matter. . Processwherereactantsundergochangesintoproducts. . Matter is conserved, to form products. so all reactantatomsare only rearranged . Somereactionsgo to completion(all reactantsconvertedto products),but mostreactionsarereversible.For example: 3H2+N2 + 2NH3 . of reactantsand productsaffectsreactionrate (the The relativeconcentration the greaterprobabilityof reaction). higherthe concentration, whenthe rateof forwardreactionequals Chemicalequilibrium: Equilibriumestablished the rate of the reversereaction. . Is a dynamicequilibriumwith reactionscontinuingin both directions . Relativeconcentrations of reactantsand productsstopchanging. Point out to students that chemical equilibrium does NOT mean that the of reactantsand productsare equal. concentrations REFERENCES Atkins, P.W.Atoms,Electronsand Change.W.H. Freemanand Company,1991. 1998. N., et al.Biologt.5th ed. MenloPark,Califomia:Benjamin/Cummings, Campbell, Weinberg,S. TheDiscoveryof SubatomicParticles.New York, SanFrancisco:W.H. Freemanand Company,1983. Brown,T.L., H. E. Le May, Jr., and B. Bursten.Chemistry:The CentralScience.Tth ed. Upper SaddleRiver,New Jersey:PrenticeHall, 1997.