Sinh học - Chapter 02: The chemical context of life

The Chemical Context of LifeChapter 2Concept 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© 2011 Pearson Education, Inc.Elements 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© 2011 Pearson Education, Inc.Figure 2.3SodiumChlorineSodium chlorideThe Elements of LifeAbout 20–25% of the 92 elements are essential to lifeCarbon, 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 minute quantities© 2011 Pearson Education, Inc.Table 2.1Concept 2.2: An element’s propertiesdepend 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© 2011 Pearson Education, Inc.Subatomic ParticlesAtoms are composed of subatomic particlesRelevant subatomic particles includeNeutrons (no electrical charge)Protons (positive charge)Electrons (negative charge)© 2011 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© 2011 Pearson Education, Inc.Figure 2.5Cloud of negativecharge (2 electrons)ElectronsNucleus(a)(b)Atomic Number and Atomic MassAtoms of the various elements differ in number of subatomic particlesAn element’s atomic number is the number of protons in its nucleusAn element’s mass number is the sum of protons plus neutrons in the nucleus Atomic mass, the atom’s total mass, can be approximated by the mass number© 2011 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© 2011 Pearson Education, Inc.Some applications of radioactive isotopes in biological research areDating fossilsTracing atoms through metabolic processesDiagnosing medical disorders© 2011 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 electron’s state of potential energy is called its energy level, or electron shell© 2011 Pearson Education, Inc.Figure 2.8A ball bouncing down a flightof stairs provides an analogyfor energy levels of electrons.Third shell (highest energylevel in this model) Second shell (higherenergy level)First shell (lowest energylevel)Atomic nucleusEnergyabsorbedEnergy lost(b)(a)Electron 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© 2011 Pearson Education, Inc.Figure 2.9First shellSecond shellThird shellHydrogen1HLithium3LiSodium11NaBeryllium4BeMagnesium12MgBoron5BAluminum13AlCarbon6CSilicon14SiNitrogen7NPhosphorus15POxygen8OSulfur16SFluorine9FChlorine17ClNeon10NeArgon18ArHelium2He2He4.00Mass numberAtomic numberElement symbolElectrondistributiondiagramValence 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 are chemically inert© 2011 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© 2011 Pearson Education, Inc.Figure 2.10Neon, with two filledShells (10 electrons)First shellSecond shellFirst shellSecond shell1s orbital2s orbitalThree 2p orbitals(a) Electron distribution diagram(b) Separate electron orbitals(c) Superimposed electron orbitals1s, 2s, and2p orbitalsxyzConcept 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 called chemical bonds © 2011 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 atom’s valence shell© 2011 Pearson Education, Inc.Figure 2.11-3Hydrogen atoms (2 H)Hydrogen molecule (H2)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© 2011 Pearson Education, Inc.The notation used to represent atoms and bonding is called a structural formulaFor example, H—H This can be abbreviated further with a molecular formula For example, H2© 2011 Pearson Education, Inc.Figure 2.12(a) Hydrogen (H2)(b) Oxygen (O2)(c) Water (H2O)Name andMolecularFormulaElectronDistributionDiagramLewis DotStructure and StructuralFormulaSpace-FillingModel(d) Methane (CH4)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 atom’s valence© 2011 Pearson Education, Inc.Atoms in a molecule attract electrons to varying degreesElectronegativity is an atom’s attraction for the electrons in a covalent bondThe more electronegative an atom, the more strongly it pulls shared electrons toward itself© 2011 Pearson Education, Inc.Elements with Electronegativity Values: a nonpolar covalent bond, the atoms share the electron equallyIn a polar covalent bond, one atom is more electronegative, and the atoms do not share the electron equallyUnequal sharing of electrons causes a partial positive or negative charge for each atom or molecule© 2011 Pearson Education, Inc.Figure 2.13HHH2O++–OIonic 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© 2011 Pearson Education, Inc.Figure 2.14-2+–NaSodium atomClChlorine atomNa+Sodium ion(a cation)Cl–Chloride ion(an anion)Sodium chloride (NaCl)A cation is a positively charged ionAn anion is a negatively charged ionAn ionic bond is an attraction between an anion and a cation© 2011 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 © 2011 Pearson Education, Inc.Figure 2.15Na+Cl–Weak Chemical BondsMost of the strongest bonds in organisms are covalent bonds that form a cell’s moleculesWeak chemical bonds, such as ionic bonds and hydrogen bonds, are also importantWeak chemical bonds reinforce shapes of large molecules and help molecules adhere to each other© 2011 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© 2011 Pearson Education, Inc.Figure 2.16Water (H2O)Ammonia (NH3)Hydrogen bond––+++++Van der Waals InteractionsIf electrons are distributed asymmetrically in molecules or atoms, they can result in “hot spots” of positive or negative chargeVan der Waals interactions are attractions between molecules that are close together as a result of these chargesCollectively, such interactions can be strong, as between molecules of a gecko’s toe hairs and a wall surface© 2011 Pearson Education, Inc.Molecular Shape and FunctionA molecule’s shape is usually very important to its functionA molecule’s shape is determined by the positions of its atoms’ valence orbitalsIn a covalent bond, the s and p orbitals may hybridize, creating specific molecular shapes© 2011 Pearson Education, Inc.Figure 2.17s orbitalThree p orbitalsFour hybrid orbitalsTetrahedron(a) Hybridization of orbitalszxySpace-FillingModelBall-and-StickModelHybrid-Orbital Model(with ball-and-stickmodel superimposed)UnbondedElectronpairWater (H2O)Methane (CH4)(b) Molecular-shape modelsBiological molecules recognize and interact with each other with a specificity based on molecular shapeMolecules with similar shapes can have similar biological effects© 2011 Pearson Education, Inc.Figure 2.18Natural endorphinMorphineCarbonHydrogenNitrogenSulfurOxygen(a) Structures of endorphin and morphine(b) Binding to endorphin receptorsBrain cellMorphineNaturalendorphinEndorphinreceptorsConcept 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© 2011 Pearson Education, Inc.Figure 2.UN02ReactantsReactionProducts2 H22 H2OO2+Photosynthesis is an important chemical reaction Sunlight powers the conversion of carbon dioxide and water to glucose and oxygen 6 CO2 + 6 H20 → C6H12O6 + 6 O2© 2011 Pearson Education, Inc.Figure 2.19All chemical reactions are reversible: products of the forward reaction become reactants for the reverse reactionChemical equilibrium is reached when the forward and reverse reaction rates are equal. It is NOT when all reactions cease to occur.© 2011 Pearson Education, Inc.Figure 2.UN05Singlecovalent bondDoublecovalent bondFigure 2.UN09Figure 2.UN11Figure 2.UN07Figure 2.UN12