chpt 2 of a biology book - chemistry

Overview: A Chemical Connection to BiologyBiology is a multidisciplinary scienceLiving organisms are subject to basic laws of physics and chemistryOne example is the use of formic acid by ants to maintain devils gardens, stands of Duroia trees

2011 Pearson Education, Inc.

Figure 2.1Who tends this garden?

Figure 2.2aDuroiatreeDevils gardenCedrelasaplingInside,unprotectedInside,protectedInsectbarrierOutside,protectedOutside,unprotectedEXPERIMENTWhat creates devils gardens in the rain forest?

Figure 2.2bRESULTSInside,unprotectedInside,protectedOutside,unprotectedOutside,protectedCedrela saplings, inside and outside devils gardens1612840Dead leaf tissue (cm2)after one day

Concept 2.1: Matter consists of chemical elements in pure form and in combinations called compoundsOrganisms are composed of __________Matter is anything that takes up space and has mass 2011 Pearson Education, Inc.

Elements and CompoundsMatter is made up of elements An __________ is a substance that cannot be broken down to other substances by chemical reactionsA __________ is a substance consisting of two or more elements in a fixed ratioA compound has characteristics different from those of its elements


Figure 2.3SodiumChlorineSodium chlorideThe emergent properties of a compound

The Elements of LifeAbout 2025% 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 sulfur________ _______are those required by an organism in minute quantities


Table 2.1

Case 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


Figure 2.4Serpentine plant community

Concept 2.2: An elements propertiesdepend on the structure of its atomsEach element consists of unique atomsAn __________ is the smallest unit of matter that still retains the properties of an element


Subatomic ParticlesAtoms are composed of subatomic particlesRelevant subatomic particles include__________ (no electrical charge)__________(positive charge)__________ (negative charge) 2011 Pearson Education, Inc.

Neutrons and protons form the __________ __________Electrons form a cloud around the nucleusNeutron mass and proton mass are almost identical and are measured in __________


Figure 2.5Cloud of negativecharge (2 electrons)ElectronsNucleus(a)(b)Simplified models of a helium (He) atom.

Atomic Number and Atomic MassAtoms of the various elements differ in number of subatomic particlesAn elements ______ _________ is the number of protons in its nucleusAn elements _____ _______is the sum of protons plus neutrons in the nucleus _______ ______, the atoms total mass, can be approximated by the mass number


Atomic NumbersInsert new figure 2.3

IsotopesAll atoms of an element have the same number of protons but may differ in number of neutrons__________ are two atoms of an element that differ in number of neutrons__________ __________ decay spontaneously, giving off particles and energy


Isotopesinsert new fig 2.4

Some applications of radioactive isotopes in biological research areDating fossilsTracing atoms through metabolic processesDiagnosing medical disorders


Figure 2.7CancerousthroattissueA PET scan, a medical use for radioactive isotopes.

The Energy Levels of Electrons__________ is the capacity to cause change__________ ________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 ________ _______


Figure 2.8Energy levels of an atoms electrons.

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


Figure 2.9First shellSecond shellThird shellHydrogen1HLithium3LiSodium11NaBeryllium4BeMagnesium12MgBoron5BAluminum13AlCarbon6CSilicon14SiNitrogen7NPhosphorus15POxygen8OSulfur16SFluorine9FChlorine17ClNeon10NeArgon18ArHelium2He2He4.00Mass numberAtomic numberElement symbolElectrondistributiondiagramElectron distribution diagrams for the first 18 elements in the periodic table.

__________ __________ are those in the outermost shell, or __________ _______The chemical behavior of an atom is mostly determined by the valence electronsElements with a full valence shell are chemically inert


Electron OrbitalsAn __________ is the three-dimensional space where an electron is found 90% of the timeEach electron shell consists of a specific number of orbitals


Figure 2.10aNeon, with two filledShells (10 electrons)First shellSecond shell(a) Electron distribution diagram

Figure 2.10bFirst shellSecond shell1s orbital2s orbitalThree 2p orbitals(b) Separate electron orbitalsxyz

Figure 2.10c(c) Superimposed electron orbitals1s, 2s, and2p orbitals

Concept 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 __________ __________


Covalent BondsA _________ _________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


Figure 2.11-1Hydrogen atoms (2 H)

Figure 2.11-2Hydrogen atoms (2 H)

Figure 2.11-3Hydrogen atoms (2 H)Hydrogen molecule (H2)Formation of a covalent bond

A __________ consists of two or more atoms held together by covalent bondsA single covalent bond, or _______ _______, is the sharing of one pair of valence electronsA double covalent bond, or ________ ________, is the sharing of two pairs of valence electrons


The notation used to represent atoms and bonding is called a __________ __________For example, HH This can be abbreviated further with a __________ __________For example, H2

2011 Pearson Education, Inc.Animation: Covalent Bonds

Figure 2.12(a) Hydrogen (H2)(b) Oxygen (O2)(c) Water (H2O)Name andMolecularFormulaElectronDistributionDiagramLewis DotStructure and StructuralFormula

Space-FillingModel(d) Methane (CH4)

Figure 2.12a(a) Hydrogen (H2)Name andMolecularFormulaElectronDistributionDiagramLewis DotStructure and StructuralFormula

Space-FillingModel

Figure 2.12b(b) Oxygen (O2)Name andMolecularFormulaElectronDistributionDiagramLewis DotStructure and StructuralFormula

Space-FillingModel

Figure 2.12cName andMolecularFormulaElectronDistributionDiagramLewis DotStructure and StructuralFormula

Space-FillingModel(c) Water (H2O)

Figure 2.12d(d) Methane (CH4)Name andMolecularFormulaElectronDistributionDiagramLewis DotStructure and StructuralFormula

Space-FillingModel

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 __________


Atoms in a molecule attract electrons to varying degrees_______________ is an atoms attraction for the electrons in a covalent bondThe more electronegative an atom, the more strongly it pulls shared electrons toward itself


In a __________ __________ ______, the atoms share the electron equallyIn a __________ __________ _______, 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


Figure 2.13HHH2O++OPolar covalent bonds in a water molecule.

Ionic 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 __________


Figure 2.14-1NaSodium atomClChlorine atomElectron transfer and ionic bonding.

Figure 2.14-2+NaSodium atomClChlorine atomNa+Sodium ion(a cation)ClChloride ion(an anion)Sodium chloride (NaCl)Electron transfer and ionic bonding.

A __________ is a positively charged ionAn __________ is a negatively charged ionAn __________ is an attraction between an anion and a cation

2011 Pearson Education, Inc.Animation: Ionic Bonds

Compounds formed by ionic bonds are called _____ __________, or __________Salts, such as sodium chloride (table salt), are often found in nature as crystals


Figure 2.15Na+ClA sodium chloride (NaCl) crystal.

Weak Chemical BondsMost of the strongest bonds in organisms are covalent bonds that form a cells 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


Hydrogen BondsA __________ __________ 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 charge_____ ____ ________ __________ are attractions between molecules that are close together as a result of these charges


Collectively, such interactions can be strong, as between molecules of a geckos toe hairs and a wall surface


Molecular Shape and FunctionA molecules shape is usually very important to its functionA molecules 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


Figure 2.17as orbitalThree p orbitalsFour hybrid orbitalsTetrahedron(a) Hybridization of orbitalszxyMolecular shapes due to hybrid orbitals

Figure 2.17bMolecular shapes due to hybrid orbitals

Biological molecules recognize and interact with each other with a specificity based on molecular shapeMolecules with similar shapes can have similar biological effects


Figure 2.18aNatural endorphinMorphineCarbonHydrogenNitrogenSulfurOxygen(a) Structures of endorphin and morphineA molecular mimic

Figure 2.18b(b) Binding to endorphin receptorsBrain cellMorphineNaturalendorphinEndorphinreceptorsA molecular mimic

Concept 2.4: Chemical reactions make and break chemical bonds__________ __________ are the making and breaking of chemical bondsThe starting molecules of a chemical reaction are called __________The final molecules of a chemical reaction are called __________


Figure 2.UN02ReactantsReactionProducts2 H22 H2OO2+

Photosynthesis is an important chemical reaction Sunlight powers the conversion of carbon dioxide and water to glucose and oxygen6 CO2 + 6 H20 C6H12O6 + 6 O2


All chemical reactions are reversible: products of the forward reaction become reactants for the reverse reaction__________ __________ is reached when the forward and reverse reaction rates are equal


Figure 2.UN03NucleusProtons (+ charge)determine elementNeutrons (no charge)determine isotopeElectrons ( charge)form negative cloudand determinechemical behaviorAtom

Figure 2.UN05Singlecovalent bondDoublecovalent bond

Figure 2.UN06+NaSodium atomClChlorine atomNa+Sodium ion(a cation)ClChloride ion(an anion)Ionic bondElectronictransferforms ions

***Figure 2.1 Who tends this garden?*Figure 2.2 INQUIRY: What creates devils gardens in the rain forest?*Figure 2.2 INQUIRY: What creates devils gardens in the rain forest?***Figure 2.3 The emergent properties of a compound.**Table 2.1 Elements in the Human Body**Figure 2.4 Serpentine plant community.****Figure 2.5 Simplified models of a helium (He) atom.**What distinguishes one element, such as chlorine, from another such as neon or oxygen? Atoms of different elements have a different number of protons in the nucleus. A chlorine atom has 17 protons, a neon atom has 10 protons, and an oxygen atom has 8 protons. Each element is given a name (and an abbreviation, such as O for oxygen and C for carbon) and an atomic number that corresponds to how many protons it has.So far, about 90 elements have been discovered that are present in nature and about 25 others can be made in the laboratory. Everything you see around you is made up of some combination of those naturally occurring elements.

Figure 2-3 The vital statistics of atoms.*Atoms dont always have the exact same number of protons and neutrons in their nucleus and electrons circling around it. They sometimes acquire or lose components. An atom that has extra neutrons or fewer neutrons than the number of protons is called an isotope. An atoms charge doesnt change in an isotope because neutrons have no electrical charge, but the atoms mass changes with the loss or addition of another particle in the nucleus (Fig. 2-4). Carbon, for example, has six protons and so usually has a mass of 12. Occasionally, though, carbon has an extra neutron or two and an atomic mass of 13 or 14. This is rare in nature, but it does occur. These isotopes are called carbon-13 (13C) and carbon-14 (14C) and are referred to as heavy carbon. In nature, we frequently see mixtures of several isotopes for a given element. So although a sample of pure carbon is predominantly 12C atoms (with 6 protons and 6 neutrons), there are some 13C and 14C atoms in the sample, too.***Figure 2.7 A PET scan, a medical use for radioactive isotopes.**Figure 2.8 Energy levels of an atoms electrons.**Figure 2.9 Electron distribution diagrams for the first 18 elements in the periodic table.***Figure 2.10 Electron orbitals.

*Figure 2.10 Electron orbitals.

*Figure 2.10 Electron orbitals.

***Figure 2.11 Formation of a covalent bond.*Figure 2.11 Formation of a covalent bond.*Figure 2.11 Formation of a covalent bond.***Figure 2.12 Covalent bonding in four molecules.*Figure 2.12 Covalent bonding in four molecules.*Figure 2.12 Covalent bonding in four molecules.*Figure 2.12 Covalent bonding in four molecules.*Figure 2.12 Covalent bonding in four molecules.****Figure 2.13 Polar covalent bonds in a water molecule.**Figure 2.14 Electron transfer and ionic bonding.*Figure 2.14 Electron transfer and ionic bonding.***Figure 2.15 A sodium chloride (NaCl) crystal.***Figure 2.16 A hydrogen bond.****Figure 2.17 Molecular shapes due to hybrid orbitals.*Figure 2.17 Molecular shapes due to hybrid orbitals.**Figure 2.18 A molecular mimic.*Figure 2.18 A molecular mimic.**Figure 2. UN02 In-text figure, p. 42 ***Figure 2.UN03 Summary figure, Concept 2.2 *Figure 2.UN05 Summary figure, Concept 2.3 *Figure 2.UN06 Summary figure, Concept 2.3

chpt 2 of a biology book - chemistry

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