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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.