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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
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Figure 2.1Who tends this garden?
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Figure 2.2aDuroiatreeDevils
gardenCedrelasaplingInside,unprotectedInside,protectedInsectbarrierOutside,protectedOutside,unprotectedEXPERIMENTWhat
creates devils gardens in the rain forest?
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Figure
2.2bRESULTSInside,unprotectedInside,protectedOutside,unprotectedOutside,protectedCedrela
saplings, inside and outside devils gardens1612840Dead leaf tissue
(cm2)after one day
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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
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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
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Figure 2.3SodiumChlorineSodium chlorideThe emergent properties
of a compound
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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
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Table 2.1
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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
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Figure 2.4Serpentine plant community
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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
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Subatomic ParticlesAtoms are composed of subatomic
particlesRelevant subatomic particles include__________ (no
electrical charge)__________(positive charge)__________ (negative
charge) 2011 Pearson Education, Inc.
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Neutrons and protons form the __________ __________Electrons
form a cloud around the nucleusNeutron mass and proton mass are
almost identical and are measured in __________
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Figure 2.5Cloud of negativecharge (2
electrons)ElectronsNucleus(a)(b)Simplified models of a helium (He)
atom.
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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
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Atomic NumbersInsert new figure 2.3
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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
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Isotopesinsert new fig 2.4
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Some applications of radioactive isotopes in biological research
areDating fossilsTracing atoms through metabolic
processesDiagnosing medical disorders
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Figure 2.7CancerousthroattissueA PET scan, a medical use for
radioactive isotopes.
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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 ________ _______
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Figure 2.8Energy levels of an atoms electrons.
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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
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Figure 2.9First shellSecond shellThird
shellHydrogen1HLithium3LiSodium11NaBeryllium4BeMagnesium12MgBoron5BAluminum13AlCarbon6CSilicon14SiNitrogen7NPhosphorus15POxygen8OSulfur16SFluorine9FChlorine17ClNeon10NeArgon18ArHelium2He2He4.00Mass
numberAtomic numberElement
symbolElectrondistributiondiagramElectron distribution diagrams for
the first 18 elements in the periodic table.
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__________ __________ 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
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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
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Figure 2.10aNeon, with two filledShells (10 electrons)First
shellSecond shell(a) Electron distribution diagram
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Figure 2.10bFirst shellSecond shell1s orbital2s orbitalThree 2p
orbitals(b) Separate electron orbitalsxyz
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Figure 2.10c(c) Superimposed electron orbitals1s, 2s, and2p
orbitals
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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 __________ __________
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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
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Figure 2.11-1Hydrogen atoms (2 H)
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Figure 2.11-2Hydrogen atoms (2 H)
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Figure 2.11-3Hydrogen atoms (2 H)Hydrogen molecule (H2)Formation
of a covalent bond
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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
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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
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Figure 2.12(a) Hydrogen (H2)(b) Oxygen (O2)(c) Water (H2O)Name
andMolecularFormulaElectronDistributionDiagramLewis DotStructure
and StructuralFormula
Space-FillingModel(d) Methane (CH4)
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Figure 2.12a(a) Hydrogen (H2)Name
andMolecularFormulaElectronDistributionDiagramLewis DotStructure
and StructuralFormula
Space-FillingModel
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Figure 2.12b(b) Oxygen (O2)Name
andMolecularFormulaElectronDistributionDiagramLewis DotStructure
and StructuralFormula
Space-FillingModel
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Figure 2.12cName
andMolecularFormulaElectronDistributionDiagramLewis DotStructure
and StructuralFormula
Space-FillingModel(c) Water (H2O)
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Figure 2.12d(d) Methane (CH4)Name
andMolecularFormulaElectronDistributionDiagramLewis DotStructure
and StructuralFormula
Space-FillingModel
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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
__________
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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
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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
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Figure 2.13HHH2O++OPolar covalent bonds in a water molecule.
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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 __________
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Figure 2.14-1NaSodium atomClChlorine atomElectron transfer and
ionic bonding.
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Figure 2.14-2+NaSodium atomClChlorine atomNa+Sodium ion(a
cation)ClChloride ion(an anion)Sodium chloride (NaCl)Electron
transfer and ionic bonding.
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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
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Compounds formed by ionic bonds are called _____ __________, or
__________Salts, such as sodium chloride (table salt), are often
found in nature as crystals
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Figure 2.15Na+ClA sodium chloride (NaCl) crystal.
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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
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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
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Figure 2.16Water (H2O)Ammonia (NH3)Hydrogen bond+++++
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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
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Collectively, such interactions can be strong, as between
molecules of a geckos toe hairs and a wall surface
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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
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Figure 2.17as orbitalThree p orbitalsFour hybrid
orbitalsTetrahedron(a) Hybridization of orbitalszxyMolecular shapes
due to hybrid orbitals
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Figure 2.17bMolecular shapes due to hybrid orbitals
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Biological molecules recognize and interact with each other with
a specificity based on molecular shapeMolecules with similar shapes
can have similar biological effects
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Figure 2.18aNatural
endorphinMorphineCarbonHydrogenNitrogenSulfurOxygen(a) Structures
of endorphin and morphineA molecular mimic
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Figure 2.18b(b) Binding to endorphin receptorsBrain
cellMorphineNaturalendorphinEndorphinreceptorsA molecular mimic
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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
__________
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Figure 2.UN02ReactantsReactionProducts2 H22 H2OO2+
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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
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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
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Figure 2.UN03NucleusProtons (+ charge)determine elementNeutrons
(no charge)determine isotopeElectrons ( charge)form negative
cloudand determinechemical behaviorAtom
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Figure 2.UN05Singlecovalent bondDoublecovalent bond
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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