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TheChemistryofMicrobiology

Matter&Atoms

Matter anythingthattakesupspaceandhasmass

Atoms the

smallest

chemical

units

of

matterWps.prenhall.com

Atoms&AtomicStructure

Nucleus structurecontainingneutronsandprotons

Neutrons unchargedparticles

Protons positivelychargedparticles

Electrons negativelychargedsubatomicparticles

circlinganucleus

Electronshells

Nucleus Proton(pNeutron(n

+0

))

Electron(e)

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Atomic Number and Atomic Mass

Anelementsatomic

numberis

the

number

ofprotonsinitsnucleus

Elementalsymbol Anelementsmass

numberisthesumofprotonsplusneutronsinthenucleus

Electronsanegligible Atomicmass,the

atomstotalmass,canbeapproximated bythemassnumber

96 3

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AtomsElectronsConfigurations

ElectronConfigurations

Onlytheelectronsofatomsinteract,sotheydetermineatom'schemicalbehavior

Electronsoccupyelectronshells

Valenceelectrons electronsinoutermostshellthatinteractwithotheratoms

Neon,

with

two

filledShells(10electrons)

Firstshell

Secondshell

++x

z

y

=

SecondshellFirstshell

Electron shells of neon: three-dimensional view

+ =

Firstshell Secondshell

Electron shells of neon: two-dimensional view

Figure2.3 Electronconfigurations.

Figure2.4 Bohrdiagramsofthefirst20elementsandtheirplaceswithinthechartknownastheperiodictableoftheelements.

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ChemicalBonds

Valence combiningcapacityofanatom

Positive ifatomhaselectronstogiveup

Negativeifatomhasspacestofill

Stablewhenouterelectronshellscontaineightelectrons

Chemicalbonds atomscombinebysharingortransferringvalence

electrons

Molecule twoormoreatomsheldtogetherbychemicalbonds

Compound amoleculecomposedofmorethanoneelement

ChemicalBonds

Covalentbond sharingofapairofelectronsbytwoatoms

Nonpolarcovalentbonds

Polarcovalentbonds

Electronegativity attractionofatomforelectrons

Themore

electronegative

an

atom,

the

greater

the

pull

its

nucleus

exertsonelectronsFigure2.5ab Fourmoleculesformedbycovalentbonds.

ChemicalBonds

Nonpolarcovalentbonds

Sharedelectronsspendequalamountsoftime

aroundeachnucleus

Atomswithsimilarelectronegativities

Nopoles

exist

Carbonatomsformfournonpolarcovalentbonds

withotheratoms

Organiccompoundscontaincarbonandhydrogen

atoms

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Figure2.5cd Fourmoleculesformedbycovalentbonds.

ChemicalBonds

PolarCovalentBonds

Unequal sharingofelectronsduetosignificantly

differentelectronegativities

Mostimportantpolarcovalentbondsinvolve

hydrogen

Allow

for

hydrogen

bondingFigure2.7 Polarcovalentbondinginawatermolecule.

Figure2.6 Electronegativityvaluesofselectedelements.

Electronegativityvaluesofselectedelements.

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ChemicalBonds

IonicBonds

Occurwhentwoatomswithvastlydifferent

electronegativitiescometogether

Atoms:eitherpositive(cation)ornegative(anion)charges

Cations andanionsattracteachotherandformionic

bonds(noelectrons shared)

Typicallyformcrystallineioniccompoundsknownassalts

Figure2.8 Theinteractionofsodiumandchlorinetoformanionicbond.

Figure2.9 DissociationofNaCI inwater.

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ChemicalBonds

HydrogenBonds

ElectricalattractionbetweenpartiallychargedH+

andfullorpartialnegativechargeonsameor

differentmolecule

Weakerthancovalentbondsbutessentialforlife

Helptostabilize3Dshapesoflargemolecules

Figure2.10 Hydrogenbonds.

Water(H2O)

Ammonia(NH3)

Hydrogenbond

++

+++

ChemicalReactions

Chemicalreactionsarethemakingandbreaking

ofchemicalbonds

Thestartingmoleculesofachemicalreactionare

calledreactants

Thefinalmoleculesofachemicalreactionare

calledproducts

Reactants Reaction Products

2H2 2H2OO2+

Chemical

SeeFigure2.11a Twotypesofchemicalreactionsinlivingthings.

ChemicalReactions

SynthesisReactions

Involvethe

formation

of

larger,

more

complex

molecules

Requireenergy(endothermic)

Commontypeisdehydrationsynthesis

Watermoleculeformed

All thesynthesis reactionsinanorganismarecalled

anabolism

Figure2.11a Twotypesofchemicalreactionsinlivingthings.

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ChemicalReactions

DecompositionReactions

Breakbondswithinlargermoleculestoformsmalleratoms,ions,andmolecules

Releaseenergy(exothermic)

Commontypeishydrolysis

Ioniccomponentsofwaterareaddedtoproducts

Allthedecompositionreactionsinanorganismarecalledcatabolism

Figure2.11b Twotypesofchemicalreactionsinlivingthings.

ChemicalReactions

ExchangeReactions

Involvebreakingandformingcovalentbonds

Haveendothermicandexothermicsteps

Involveatomsmovingfromonemoleculeto

another

Sumofallchemicalreactionsinanorganismis

calledmetabolism

Water,Acids,Bases,andSalts

Water

Mostabundant

substance

in

organisms

Specialcharacteristicsduetotwopolarcovalentbonds

Cohesivemolecules surfacetension

Excellentsolvent

Remainsliquidacrosswiderangeoftemperatures

Canabsorbsignificantamountsofenergywithoutchanging

temperature

Participatesinmanychemicalreactions

Figure2.12 Thecohesivenessofliquidwater.

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Water,Acids,Bases,andSalts

AcidsandBases

Dissociatedbywaterintocations andanions

Acid dissociatesintooneormoreH+ andoneor

moreanions

Base bindswithH+ whendissolvedintowater;

somedissociateintocations andOH

Figure2.13 Acidsandbases.

Figure2.14 ThepHscale.

ConcentrationofH+ in

solutionexpressed

usingthepHscale

Metabolismrequires

relativelyconstant

balanceofacidsand

bases

Buffersprevent

drasticchangesin

internalpH

Water,Acids,Bases,andSalts

Salts

Compoundsthat

dissociate

in

water

into

cationsand

anionsotherthanH+ andOH

Cations andanionsofsaltsareelectrolytes

Createelectricaldifferences betweeninsideandoutsideof

cell

Transferelectronsfromonelocationtoanother

Formimportantcomponentsofmanyenzymes

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OrganicMacromolecules

Containcarbonandhydrogenatoms

Atomsoftenappearinarrangements calledfunctionalgroups

Macromolecules largemoleculesusedbyallorganisms

Lipids

Carbohydrates

Proteins

Nucleicacids

Monomers basicbuildingblocksofmacromolecules

OrganicMacromolecules

Lipids

Notcomposedofregularsubunits

Areallhydrophobic

Fourgroups

Fats

Phospholipids

Waxes

Steroids

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Figure2.15 Fats(triglycerides).

3

Dehydrationsynthesis

3fattyacids+Glycerol Fat(triglyceride)

Esterbond

Saturatedfattyacid

Monounsaturatedfattyacid

Figure2.16 Phospholipids.

Organicgroup

Phosphategroup

Glycerol

Saturatedfattyacid

Unsaturatedfattyacid

Doublebond

Hydrophilic(polar)head

Hydrophobic(nonpolar)tails

Symbol Phospholipid bilayer

Unsaturatedfattyacid

Cell

Phospholipid

OrganicMacromolecules

Lipids

Waxes

Containonelongchainfattyacidcovalentlylinkedto

longchainalcoholbyesterbond

Lackhydrophilichead

Completelyinsolubleinwater

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Phospholipids

Cholesterol

Cellmembrane

Figure2.17 Steroids.

OrganicMacromolecules

Carbohydrates

Organicmoleculescomposedofcarbon,hydrogen,andoxygen(CH2O)n

Functions

Longtermstorageofchemicalenergy

Readyenergysource

Partofbackbonesofnucleicacids

Convertedtoaminoacids

Formcellwall

Involvedinintracellularinteractionsbetweenanimalcells

OrganicMacromolecules

Carbohydrates

Types

Monosaccharides

Disaccharides

Polysaccharides

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Figure2.18 Monosaccharides(simplesugars).

Glucose

configuration configuration

N-acetylglucosamine

Acetyl

group

Figure2.19 Disaccharides.

1,6bond

Hydrogen

bondsHydrogen

bond

1,6bond

Cellulose

Amylose

(unbranched)

1,4bonds

1,4bonds

1,4bond

1,4bond

Glycogen

Figure2.20 Polysaccharides.

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OrganicMacromolecules

Proteins

Mostlycomposed

of

carbon,

hydrogen,

oxygen,

nitrogen,andsulfur

Functions

Structure

Enzymaticcatalysis

Regulation

Transportation

Defenseandoffense

OrganicMacromolecules

Proteins

Aminoacids

Themonomersthatmakeupproteins

Mostorganisms useonly21aminoacidsinprotein

synthesis

Sidegroupsaffecthowaminoacidsinteractwithone

anotherandhowaproteininteracts withother

molecules

Acovalentpeptidebondisformedbetweenamino

acids

Figure2.21 Aminoacids.

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Figure2.22 Stereoisomers,moleculesthataremirrorimagesofoneanother.

Figure2.23 Thelinkageofaminoacidsbypeptidebondsviaadehydrationreaction.

Carboxylgroup

Aminogroup

Dehydrationsynthesis

Peptidebond

DipeptideAminoacid2Aminoacid1

Figure2.24 Levelsofproteinstructure.

Peptide

bond

Primary structure

Amino

acid1

Amino

acid2

Amino

acid3

Aminoacid4

helix

Secondary structure

pleatedsheet

Hydrogenbond

pleatedsheets

helix

T er ti ar y st ru ct ur e Q ua te rn ar y st ru ct ur e

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OrganicMacromolecules

NucleicAcids

DNAandRNAarethegeneticmaterialof

organismsandviruses

RNAalsoactsasenzyme,bindsaminoacids,and

helpsformpolypeptides

OrganicMacromolecules

Nucleic Acids

Nucleotidesandnucleosides

Nucleotides

Monomersthatmakeupnucleicacids

Composedofthreeparts

Phosphate

Pentosesugar deoxyriboseorribose

Oneoffivecyclicnitrogenousbases

Nucleosidesarenucleotideslackingphosphate

Phosphategroup

Purineorpyrimidinenitrogenousbase

Pentosesugar

Deoxyribose Ribose

Purines Pyrimidines

Adenine(A)(UsedinDNAandRNA)

Thymine(T)(UsedinDNA)

Guanine(G)(UsedinDNAandRNA)

Cytosine (C)(UsedinDNAandRNA)

Uracil(U)(UsedinRNA)

Figure2.25 Nucleotides.

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OrganicMacromolecules

NucleicAcids

Nucleicacidstructure

ThreeHbondsformbetweenCandG

TwoHbondsformbetweenTandA(DNA)orUandA

(RNA)

DNAisdoublestrandedinmostcellsandviruses

The twostrandsarecomplementary

The twostrandsareantiparallel

Figure2.26 Generalnucleicacidstructure.

5'end

Deoxyribose

Phosphate

Adeninebase

Guaninebase

Thymine base

Cytosinebase

Twohydrogenbonds

Threehydrogenbonds

Sugarphosphatebackbones

5' C

4'

3' 2'

1'

O

3'end

5' 3'

5' 3'

A

G

T

C

C

A

G

G

A

C

T

OrganicMacromolecules

NucleicAcids

Nucleicacidfunction

DNAisgeneticmaterialofallorganismsandofmany

viruses

Carriesinstructions forsynthesisofRNAandproteins

Controlssynthesisofallmoleculesinanorganism

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Figure2.27 ATP.