Bài giảng Biology - Chapter 2: The Chemical Context of Life

Chapter 2The Chemical Context of LifeOverview: Chemical Foundations of BiologyThe bombardier beetle uses chemistry to defend itselfFigure 2.1Concept 2.1: Matter consists of chemicalelements in pure form and in combinationscalled compoundsElements and CompoundsOrganisms are composed of matter, whichis anything that takes up space and hasmassMatter is made up of elements, substancesthat cannot be broken down to other substances by chemical reactionsSodiumChlorideSodium Chloride+A compoundIs a substance consisting of two or more elements combined in a fixed ratioHas characteristics different from those of its elementsFigure 2.2Essential Elements of LifeEssential elementsInclude carbon, hydrogen, oxygen, and nitrogenMake up 96% of living matterA few other elementsMake up the remaining 4% of living matterTable 2.1(a) Nitrogen deficiency(b) Iodine deficiencyThe effects of essential element deficienciesFigure 2.3Trace elementsAre required by an organism in only minute quantitiesConcept 2.2: An element’s propertiesdepend on the structure of its atomsEach elementConsists of a certain kind of atom that is different from those of other elementsAn atomIs the smallest unit of matter that still retains the properties of an elementSubatomic ParticlesAtoms of each elementAre composed of even smaller parts called subatomic particlesRelevant subatomic particles includeNeutrons, which have no electrical chargeProtons, which are positively chargedElectrons, which are negatively chargedProtons and neutronsAre found in the atomic nucleusElectronsSurround the nucleus in a “cloud”Nucleus(a)(b)In this even more simplifiedmodel, the electrons areshown as two small bluespheres on a circle around thenucleus.Cloud of negativecharge (2 electrons)ElectronsThis model represents theelectrons as a cloud ofnegative charge, as if we hadtaken many snapshots of the 2electrons over time, with eachdot representing an electron‘sposition at one point in time.Simplified models of an atomFigure 2.4Atomic Number and Atomic MassAtoms of the various elementsDiffer in their number of subatomic particlesThe atomic number of an elementIs the number of protonsIs unique to each elementThe mass number of an elementIs the sum of protons plus neutrons in the nucleus of an atomIs an approximation of the atomic mass of an atomIsotopesAtoms of a given elementMay occur in different formsIsotopes of a given elementDiffer in the number of neutrons in the atomic nucleusHave the same number of protonsRadioactive isotopesSpontaneously give off particles and energyCan be used in biologyAPPLICATION Scientists use radioactive isotopes to label certain chemical substances, creating tracers that can be used to follow a metabolic process or locate the substance within an organism. In this example, radioactive tracers are being used to determine the effect of temperature on the rate at which cells make copies of their DNA.DNA (old and new)Ingredients includingRadioactive tracer (bright blue)Human cellsIncubators12345698710°C15°C20°C25°C30°C35°C40°C45°C50°CTECHNIQUE21The cells are placed in test tubes, their DNA is isolated, and unused ingredients are removed.12 3 4 5 6 7 8 9Ingredients for making DNA are added to human cells. One ingredient is labeled with 3H, a radioactive isotope of hydrogen. Nine dishes of cells are incubated at different temperatures. The cells make new DNA, incorporating the radioactive tracer with 3H.Temperature (°C) The frequency of flashes, which is recorded as counts per minute, is proportional to the amount of the radioactive tracer present, indicating the amount of new DNA. In this experiment, when the counts per minute are plotted against temperature, it is clear that temperature affects the rate of DNA synthesis—the most DNA was made at 35°C.1020304050Optimumtemperaturefor DNAsynthesis3020100Counts per minute(x 1,000)RESULTS3RESULTSA solution called scintillation fluid is added to the test tubes and they are placed in a scintillation counter. As the 3H in the newly made DNA decays, it emits radiation that excites chemicals in the scintillation fluid, causing them to give off light. Flashes of light are recorded by the scintillation counter.Figure 2.5Can be used in biologyCancerous throat tissueFigure 2.6The Energy Levels of ElectronsAn atom’s electronsVary in the amount of energy they possessEnergyIs defined as the capacity to cause changePotential energyIs the energy that matter possesses because of its location or structureThe electrons of an atomDiffer in the amounts of potential energy they possessA ball bouncing down a flightof stairs provides an analogyfor energy levels of electrons,because the ball can only reston each step, not betweensteps.(a) Figure 2.7AEnergy levelsAre represented by electron shellsThird energy level (shell)Second energy level (shell)First energy level (shell)EnergyabsorbedEnergylostAn electron can move from one level to another only if the energyit gains or loses is exactly equal to the difference in energy betweenthe two levels. Arrows indicate some of the step-wise changes inpotential energy that are possible.(b) Atomic nucleusFigure 2.7BElectron Configuration and Chemical PropertiesThe chemical behavior of an atomIs defined by its electron configuration and distributionThe periodic table of the elementsShows the electron distribution for all the elementsSecondshellHelium2HeFirstshellThirdshellHydrogen1H2He4.00Atomic massAtomic numberElement symbolElectron-shelldiagramLithium3LiBeryllium4BeBoron3BCarbon6CNitrogen7NOxygen8OFluorine9FNeon10NeSodium11NaMagnesium12MgAluminum13AlSilicon14SiPhosphorus15PSulfur16SChlorine17ClArgon18ArFigure 2.8Valence electronsAre those in the outermost, or valence shellDetermine the chemical behavior of an atomElectron OrbitalsAn orbitalIs the three-dimensional space where an electron is found 90% of the timeEach electron shellConsists of a specific number of orbitalsElectron orbitals.Each orbital holdsup to two electrons.1s orbital2s orbitalThree 2p orbitals1s, 2s, and 2p orbitals(a) First shell (maximum 2 electrons)(b) Second shell (maximum 8 electrons)(c) Neon, with two filled shells (10 electrons)Electron-shell diagrams.Each shell is shown withits maximum number of electrons, grouped in pairs.xZYFigure 2.9Concept 2.3: The formation and function of molecules depend on chemical bonding between atomsCovalent Bonds A covalent bondIs the sharing of a pair of valence electronsFigure 2.10Formation of a covalent bondHydrogen atoms (2 H)Hydrogenmolecule (H2)++++++In each hydrogenatom, the single electronis held in its orbital byits attraction to theproton in the nucleus.1When two hydrogenatoms approach eachother, the electron ofeach atom is alsoattracted to the protonin the other nucleus.2The two electronsbecome shared in a covalent bond,forming an H2molecule.3A moleculeConsists of two or more atoms held together by covalent bondsA single bondIs the sharing of one pair of valence electronsA double bondIs the sharing of two pairs of valence electrons(a)(b)Name(molecularformula)Electron-shelldiagramStructuralformulaSpace-fillingmodelHydrogen (H2). Two hydrogen atoms can form a single bond.Oxygen (O2). Two oxygen atoms share two pairs of electrons to form a double bond.HHOOFigure 2.11 A, BSingle and double covalent bondsName(molecularformula)Electron-shelldiagramStructuralformulaSpace-fillingmodel(c)Methane (CH4). Four hydrogen atoms can satisfy the valence ofone carbonatom, formingmethane.Water (H2O). Two hydrogenatoms and one oxygen atom arejoined by covalent bonds to produce a molecule of water.(d)HOHHHHHCFigure 2.11 C, DCovalent bonding in compoundsElectronegativityIs the attraction of a particular kind of atom for the electrons in a covalent bondThe more electronegative an atomThe more strongly it pulls shared electrons toward itselfIn a nonpolar covalent bondThe atoms have similar electronegativities Share the electron equallyFigure 2.12This results in a partial negative charge on theoxygen and apartial positivecharge onthe hydrogens.H2Od–OHHd+d+Because oxygen (O) is more electronegative than hydrogen (H), shared electrons are pulled more toward oxygen.In a polar covalent bondThe atoms have differing electronegativitiesShare the electrons unequallyIonic BondsIn some cases, atoms strip electrons away from their bonding partnersElectron transfer between two atoms creates ionsIonsAre atoms with more or fewer electrons than usualAre charged atomsAn anionIs negatively charged ionsA cationIs positively chargedCl–Chloride ion(an anion)– The lone valence electron of a sodiumatom is transferred to join the 7 valenceelectrons of a chlorine atom.1 Each resulting ion has a completedvalence shell. An ionic bond can formbetween the oppositely charged ions.2NaNaClCl+NaSodium atom(an unchargedatom)ClChlorine atom(an unchargedatom)Na+Sodium on(a cation)Sodium chloride (NaCl)Figure 2.13An ionic bondIs an attraction between anions and cationsNa+Cl–Figure 2.14Ionic compoundsAre often called salts, which may form crystalsWeak Chemical BondsSeveral types of weak chemical bonds are important in living systemsHydrogen Bonds – + +Water(H2O)Ammonia(NH3)OHH + –NHHHA hydrogenbond results from the attraction between thepartial positive charge on the hydrogen atom of water and the partial negative charge on the nitrogen atom of ammonia.+d+Figure 2.15A hydrogen bondForms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atomVan der Waals InteractionsVan der Waals interactionsOccur when transiently positive and negative regions of molecules attract each otherWeak chemical bondsReinforce the shapes of large moleculesHelp molecules adhere to each otherMolecular Shape and FunctionThe precise shape of a moleculeIs usually very important to its function in the living cellIs determined by the positions of its atoms’ valence orbitalss orbitalZThree p orbitalsXYFour hybrid orbitals(a) Hybridization of orbitals. The single s and three p orbitals of a valence shell involved in covalent bonding combine to form four teardrop-shaped hybrid orbitals. These orbitals extend to the four corners of an imaginary tetrahedron (outlined in pink).TetrahedronFigure 2.16 (a)In a covalent bondThe s and p orbitals may hybridize, creating specific molecular shapesSpace-fillingmodelHybrid-orbital model(with ball-and-stickmodel superimposed)UnbondedElectron pair104.5°OHWater (H2O) Methane (CH4)HHHHCOHHHCBall-and-stickmodelHHHH(b) Molecular shape models. Three models representing molecular shape are shown for two examples; water and methane. The positions of the hybrid orbital determine the shapes of the moleculesFigure 2.16 (b)Molecular shapeDetermines how biological molecules recognize and respond to one another with specificityMorphineCarbonHydrogenNitrogenSulfurOxygenNaturalendorphin(a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds toreceptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close match.(b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell recognize and can bind to both endorphin and morphine.NaturalendorphinEndorphinreceptorsMorphineBrain cellFigure 2.17Concept 2.4: Chemical reactions make and break chemical bondsA Chemical reactionIs the making and breaking of chemical bondsLeads to changes in the composition of matterReactantsReactionProduct2 H2O22 H2O++Chemical reactionsConvert reactants to productsPhotosynthesisIs an example of a chemical reactionFigure 2.18Chemical equilibriumIs reached when the forward and reverse reaction rates are equal