GBME,SKKUMolecular&CellBiology

H.F.K.

ChemicalFoundationsI

Chapter2– ChemicalFoundations

2.1CovalentBondsandNoncovalentInteractions2.2ChemicalBuildingBlocksofCells2.3ChemicalReactionsandChemicalEquilibrium2.4BiochemicalEnergetics

Knowledgefrombiochemistry

Whyisitimportant?

Drawyourowncell!

AfterlearningMCB!

Allaremolecules!!!Well-organizedandwell-structured…

Structuresareinformativeitself!

Chemistryoflife:fourkeyconcepts.• Molecularcomplementarityenablesproteinswithcomplementaryshapesandchemicalpropertiestoformbiomolecularinteractions.

• SmallmoleculebuildingblocksformlargercellularstructuresandpolymerssuchasDNA.• Chemicalreactionsarereversible.Keq,theratioofforward(kf)andreverse(kr)reactionrateconstants,reflectstherelativeamountsofproductsandreactantsatequilibrium.

• Energydrivingmanycellularactivitiesreactionsisderivedfromhydrolysisofthehigh-energyphosphoanhydride bondlinkingtheb andg phosphatesintheATPmolecule.

Chemistryoflife:fourkeyconcepts.• Molecularcomplementarityenablesproteinswithcomplementaryshapesandchemicalpropertiestoformbiomolecularinteractions.

• SmallmoleculebuildingblocksformlargercellularstructuresandpolymerssuchasDNA.• Chemicalreactionsarereversible.Keq,theratioofforward(kf)andreverse(kr)reactionrateconstants,reflectstherelativeamountsofproductsandreactantsatequilibrium.

• Energydrivingmanycellularactivitiesreactionsisderivedfromhydrolysisofthehigh-energyphosphoanhydride bondlinkingtheb andg phosphatesintheATPmolecule.

Chemistryoflife:fourkeyconcepts.• Molecularcomplementarityenablesproteinswithcomplementaryshapesandchemicalpropertiestoformbiomolecularinteractions.

• SmallmoleculebuildingblocksformlargercellularstructuresandpolymerssuchasDNA.• Chemicalreactionsarereversible.Keq,theratioofforward(kf)andreverse(kr)reactionrateconstants,reflectstherelativeamountsofproductsandreactantsatequilibrium.

• Energydrivingmanycellularactivitiesreactionsisderivedfromhydrolysisofthehigh-energyphosphoanhydride bondlinkingtheb andg phosphatesintheATPmolecule.

Youcanseetheseveralstatesofmolecules.

Chemistryoflife:fourkeyconcepts.• Molecularcomplementarityenablesproteinswithcomplementaryshapesandchemicalpropertiestoformbiomolecularinteractions.

• SmallmoleculebuildingblocksformlargercellularstructuresandpolymerssuchasDNA.• Chemicalreactionsarereversible.Keq,theratioofforward(kf)andreverse(kr)reactionrateconstants,reflectstherelativeamountsofproductsandreactantsatequilibrium.

• Energydrivingmanycellularactivitiesreactionsisderivedfromhydrolysisofthehigh-energyphosphoanhydride bondlinkingtheb andg phosphatesintheATPmolecule.

YoucanusethemoleculesbasedonknowledgeofMCB!

<ex>Self-assemblyproteinsViralcapsidprotein

https://www.youtube.com/watch?v=X-8MP7g8XOE

ViralcapsidproteinUnderstandingthemechanism&environment(Basicscience)

Application(Engineering)

Howisitpossible?

Chapter2– ChemicalFoundations• 2.1CovalentBondsandNoncovalentInteractions

– Molecules:hydrophilic,hydrophobic,andamphipathic– Covalentbonds:sharedelectronpairsarrangespecificmoleculargeometriessuchasstereoisomersaroundasymmetriccarbons;unequalelectronsharingyieldspolarcovalentbondswithpartialcharges;morestablethanweakernoncovalentinteractions

– Fourtypesofbiologicalnoncovalentinteractions:ionicbonds(electrostaticinteractions),hydrogenbonds(nonbondingelectronhydrogenattraction),vanderWaalsinteractions(transientdipoleinteractions),andhydrophobiceffectinteractions(reducescontactwithwater)

– Molecularcomplementarity:fitbetweenmolecularshapes,charges,andotherphysicalproperties

Covalentinteraction

A covalent bond, also called a molecular bond, is a chemical bond that involves the sharing of electron pairs between atoms

Strongcovalentbondsformbyatomssharingpairsofelectronsintheiroutermostelectronorbitals

Geometryofbondswhencarboniscovalentlylinkedtothreeorfourotheratoms

Moststable!

Stereoisomers

Organicreaction?!

• AlthoughL- andD-stereoisomersofaminoacidsarechemicallyidentical,onlyLaminoacidsarefoundinproteins.

Configuration•The source of the D and L labels was the Latin words dexter (on the right) and laevus (on the left)•R comes from rectus (right-handed) and S from sinister (left-handed)

http://chemistry.umeche.maine.edu/CHY251/dlwrong.html

As shown, the assignments in modern notation are R and S, respectively. (Note: it will not always work out that D = R and L=S; this is an accident here.)

D&Lform

Seetherealmodel!

D:Deter– right

L:Levo - left

Non-covalentinteraction

What’stheforce?

Water

forcebetweenpermanent dipoles (Keesom force)forcebetweenapermanent dipole andacorrespondinginduceddipole(Debyeforce)forcebetweeninstantaneouslyinduced dipoles (Londondispersionforce).

Van der Waals forceare the residual attractive or repulsive forces between molecules or atomic groups that do not arise from covalent bonds, nor ionic bonds.

HydrogenbondA hydrogenbond isthe electrostatic attractionbetweentwopolargroupsthatoccurswhena hydrogen (H)atomcovalentlyboundtoahighly electronegative atomsuchas nitrogen (N), oxygen (O),or fluorine (F) experiencestheelectrostaticfieldofanotherhighlyelectronegativeatomnearby.

AretheVan der Waals force & H-bond weak?

Gecko’sfoot

https://www.youtube.com/watch?v=YeSuQm7KfaE

Gecko’sfoot&WanderWaalsforce

http://www.pnas.org/content/103/51/19320.figures-only

WanderWaalsforce&Robotics

Biomimics!

Ionicbond

• ThepolarityoftheO=PdoublebondcausesoneoftheP=OdoublebondelectronstoaccumulatearoundtheOatom,givingitanegativecharge,leavingthePatomwithapositivecharge.

• TheactualH3PO4 structureisaresonancehybrid intermediatebetweenthetworepresentations.

Electrostaticinteractionsoftheoppositelychargedionsofsalt(NaCl)incrystalsandinaqueoussolution

Whereisthecovalentbonding?

1

2

3

• Red(negative)andblue(positive)linesrepresentcontoursanddensityofcharge.

Electronsarenotshared.Electronsareshared.

HydrophobicinteractionWhat’sthemeaning?

Example?

Schematicdepictionofthehydrophobiceffect

Complementarybinding

Molecularcomplementaritypermitstightproteinbonding viamultiplenoncovalent interactions

2.1CovalentBondsandNoncovalentInteractions2.2ChemicalBuildingBlocksofCells2.3ChemicalReactionsandChemicalEquilibrium2.4BiochemicalEnergetics

– Macromoleculepolymersofmonomersubunits:proteins-aminoacids;nucleicacids-nucleotides;polysaccharides-monosaccharides

– Proteins:differencesinsize,shape,charge,hydrophobicity,andreactivityofthe20commonaminoacidsidechainsdetermineproteinchemicalandstructuralproperties

– Nucleicacids:purineAandG,andpyrimidineC,T(DNA),andU(RNA)nucleotidebasescompriseDNAandRNA

– Polysaccharides:hexoses (glucoseandothers)linkedbytwotypesofbonds

– Membranes:amphipathicphospholipidswithsaturatedorunsaturatedtailsassociatenoncovalentlytoformbilayermembranestructure

Overviewofthecell’sprincipalchemicalbuildingblocks

Whatkindofbond?

Whatkindofbond?

Aminoacids

The20commonaminoacidsusedtobuildproteins

HistidineRgroupcharge

• HistidineRgroupimadazole shiftsfrompositivelychargedtounchargedinresponsetosmallchangesinacidityofitsenvironment.

• Activitiesofmanyproteinsaremodulatedbyshiftsinenvironmentalacidity(pH)throughprotonationordeprotonationofhistidinesidechains.

Whatisthisbond?

Commonmodificationsofaminoacidsidechainsinproteins.• AminoacidRgroupscanbemodifiedbyadditionofvariouschemicalgroups(red)duringoraftersynthesisofapolypeptidechain.

Nucleotides

Commonstructureofnucleotides.• (a)Adenosine5ʹ-monophosphate(AMP),anucleotidepresentinRNA.• AllfivenucleotidesusedtomakenucleicacidsDNAandRNAhaveacommonstructure:aphosphategroup

linkedbyaphosphoester bondtothe5’Cinapentose(five-carbon)sugar,whichalsoislinkedthroughits1’Ctoabase.

• (b)Pentoses:riboseinRNAanddeoxyriboseinDNA.• Bases:purinesadenine andguanine,andpyrimidinescytosineinbothDNAandRNA;thymineonlyinDNAor

uracilonlyinRNA

Thismakeshugedifferenceinstability!

Chemicalstructuresoftheprincipalbasesinnucleicacids.• Bases:purines(pairoffusedrings)adenine andguanine,andpyrimidines(singlering)cytosineinbothDNAandRNA;thymineonlyinDNAoruracilonlyinRNA

TerminologyofNucleosidesandNucleotides

Pyrophosphategroup

ATP

Whereisthepyrophosphate?

Energy!!!!

Monosaccharides

Monosaccharides are the simplest form of carbohydrates. They consist of one sugar and are usually colorless, water-soluble, crystalline solids.

Chemicalgroupsinmonosaccharides

Chemicalstructuresofhexoses.• Allhexoseshavethesamechemicalformula

(C6H12O6)andcontainanaldehydeoraketogroup.

• (a)D-glucoselinearandringformsareinterconvertiblebyreactionofthealdehydeatcarbon1withthehydroxylonC5orC4–thesix-memberringpyranoseform(right)predominatesinbiologicalsystems.

• (b)InD-mannoseandD-galactose,theconfigurationoftheH(green)andOH(blue)boundtoC2orC4differsfromthatinglucose.D-mannoseandD-galactoseexistprimarilyaspyranoses(six-memberrings).

Whereisthealdehyde?

WhereistheKeto?

Simplequestion!HowdoestheL-glucoselooklike?

Pleasedrawonyournotebook.

RealmodelofGlucose

Complexstructure…

WhyandHow?

2’attack!

Pyranoseringconformation• Moststableconformationischairlike withnonring HandObondsnearlyperpendiculartothering(a,axial)ornearlyintheplaneofthering(e,equatorial).

Formationofthedisaccharideslactoseandsucrose.• Glycosidic linkageformswhentheanomericcarbonofonesugarmolecule(ineithertheαorβconformation)

islinkedtoahydroxyloxygenonanothersugarmolecule.• Lactose(milksugar)containsaβ(1→4)glycosidic bond,whichisnotdigestedinlactose-intolerantindividuals

missingthelactaseenzyme.• Sucrose(tablesugarmadebyplants)containsanα(1→2)bond.• Glucoseisstoredinlargerpolysaccahrides – glycogeninanimalsandstarchinplants.• Humandigestiveenzymescanhydrolyzetheαglycosidic bondsinstarchbutnottheβglycosidic bondsin

cellulose.Bacteriaincowandtermitegutscan.

Lipid

Discusswithfriends1.Duringmuchofthe"AgeofEnlightenment"ineighteenth-centuryEurope,scientiststoiledunderthebeliefthatlivingthingsandtheinanimateworldwerefundamentally

distinctformsofmatter.Thenin1828,FriedrichWohlershowedthathecouldsynthesizeurea,awell-knownwasteproductofanimals,fromthemineralssilver

isocyanateandammoniumchloride."Icanmakeureawithoutkidneys!"heissaidtohaveremarked.OfWohler'sdiscoverythepreeminentchemistJustusvonLiebigwrotein1837thatthe"productionofureawithouttheassistanceofvitalfunctions...must

beconsideredoneofthediscoverieswithwhichanewerainsciencehascommenced."Slightlymorethan100yearslater,StanleyMillerdischargedsparksintoamixtureofH20,CH4,NH1,andH2inanefforttosimulatethechemicalconditionsof

anancientreducingearthatmosphere(thesparksmimickedlightningstrikingaprimordialseaor"soup")andidentifiedmanybiomoleculesintheresultingmixture,includingaminoacidsandcarbohydrates.Whatdotheseexperimentssuggestabout

thenatureofbiomoleculesandtherelationshipbetweenorganic(living)andinorganic(nonliving)matter? Whatdotheysuggestabouttheevolutionoflife?

Whatdotheyindicateaboutthevalueofchemistryinunderstandinglivingthings?

2.RNAislessstablethanDNA.ExplaintworeasonsinaspectsofchemicalreactionandenzymeanddiscusshowtosafelyhandletheRNAinlab.

GBME,SKKUMolecular&CellBiology

H.F.K.

ChemicalFoundationsII

2.1CovalentBondsandNoncovalentInteractions2.2ChemicalBuildingBlocksofCells2.3ChemicalReactionsandChemicalEquilibrium2.4BiochemicalEnergetics

Atanyonetime,severalhundreddifferentkindsofchemicalreactionsareoccurringsimultaneouslyineverycell,andmanychemicalscan,inprinciple,undergomultiplechemicalreactions.

– Chemicalreactions:Keq=product/reactantratiowhenforwardandreverseratesareequal

– Celllinkedreactionsareatsteadystatenotequilibrium– Dissociationconstant(Kd) ismeasureofnoncovalentinteractions– pH(-log[H+]):cytoplasm(pH7.2-7.4) butlowerinsomeorganelles(lysosome,pH4.5)

– Acidsreleaseprotons(H+);basebindprotons– Biologicalsystemusesweakacid/basebufferstomaintainpHinnarrowranges.

Timedependenceoftheratesofachemicalreaction.• Theextentandrateatwhichchemicalreactionsproceeddeterminethechemical

compositionofcells.• Chemicalreactionsarereversible.• Initialforwardandreversereactionratesdependontheinitialconcentrationsofreactants

andproducts.Thenetforwardreactionrateslowsastheconcentrationofreactantsdecreases;thenetreversereactionrateincreasesastheconcentrationofproductsincreases.

• Equilibrium:ratesoftheforwardandreversereactionsareequal,andtheconcentrationsofreactantsandproductsremainconstant.

• Equilibriumconstant(Keq):ratioofproducttoreactantconcentrationsatequilibriumandratioofforwardtoreverserateconstants;dependsontemperatureandpressure[standardconditionsare25°Cand1atm].

• AcatalystcanincreasereactionratebuthasnoeffectonKeq.

Keq isfixedvalue!

Comparisonofreactionsatequilibriumandatsteadystate.• Reactionsincellsmaybelinkedinpathwaysinwhichaproductofonereactionisnotsimplyreconvertedviaareversereactiontothereactants,soreactionneverreachesequilibrium.

• (a)Testtubereaction(A→B)eventuallyreachesequilibrium,atwhichtheratesoftheforwardandreversereactionsareequal(reactionarrowsofequallength).

• (b)Inasteadystatepathway, theproductBismadefromAandconvertedtoCatequalrates,buttheindividualreversiblereactionsneverreachequilibrium(unequalarrowlengths)andBconcentrationcanbedifferentfromthatatequilibrium.

Whichfactors?

Dissociationconstant

Receptor– Ligandbinding

FIGURE 2-24 Macromolecules can have distinct binding sites for multiple ligands. A large macromolecule (e.g., a protein, blue) with three distinct binding sites (A-C) is shown; each binding site exhibits molecular complementarity to three different binding partners (ligands A-C) with distinct dissociation constants (KdA-cl·

predil:tc:u. To illustrate the general approach for determining the concentration of noncovalently associated complexes, we will calculate the extent to which a protein (P) is bound to DNA (D), forming a protein-DNA complex (PD):

P + D PD

Most commonly, binding reactions are described in terms of the dissociation constan t Kd, which is the reciprocal of the equilibrium constant. For this binding reaction, the dissocia-tion constant is given by

[P][DJ K -d- [PO ] (2-4)

It is worth noting that in such a binding reaction, when half of the DNA is bound to the protein ([PO] = [D]), the concen-tration of Pis equal to the Kd. The lower the K0, the lower the concentration of P needed to bind to half of D. In other words, the lower the Kd, the tighter the binding (the higher the affinity) of P for D. Typical reactions in which a protein binds to a specific DNA sequence have a Kd of 10 10 M, where M symbolizes molarity, or moles per liter (moi/L). To relate the magnitude of this dissociation constant to the in-tracellular ratio of bound to unbound DNA, let's consider the simple example of a bacterial cell having a volume of 1.5 X 10 15 Land containing 1 molecule of DNA and 10 molecules of the DNA-binding protein P. In this case, given a Kd of 10 10 M and the total concentration of the Pin the cell ( - 111 X 10- 10 M, 1 00-fold higher than the Kd), 99 percent of the time this specific DNA sequence will have a molecule of protein bound to it and 1 percent of the time it will not, even though the cell contains only 10 molecules of the pro-tein! Clearly, P and D have a high affinity for each other and bind tightly, as reflected by the low value of the dissociation constant for their bindillg reaction. For protein-protein and protein-DNA bind ing, Kd values of ::510 9 M (nanomolar) are considered to be tight, -10 6 M (micromolar) modestly tight, and - 10 3 M (millimolar) relatively weak.

A large biological macromolecule, such as a protein, can have multiple binding surfaces for binding several molecules simultaneously (Figure 2-24). In some cases, these binding reactions are independent, with their own distinct K..1 values that are constant. In other cases, binding of a molecule at om: :,itc: on a macromolecu le can change the three-dimen-sional shape of a distant site, thus altering the binding inter-actions of that distant site with some other molecule. This is an important mechanism by which one molecule can alter, and thus regu late, the binding activity of another. We examine this regulatory mechanism in more detail in Chapter 3.

Multiligand binding macromolecule (e.g., protein)

Ligand B (e.g., small molecule)

Biological Fluids Have Characteristic pH Values The solvent inside cells and in all extracellular fluids is water. An important characteristic of anr aqueous solution is the con-centration of positively charged hydrogen ions (H+) and nega-tively charged hydroxyl ions (OH ). Because these ions are the dissociation products of H 20, they arc constituents of all living systems, and they arc liberated by many reactions that take place between organic molecules within cells. These ions also can be transported into or out of celh., as when highly acidic gastric juice is secreted by cells lining the walls of the stomach.

When a water molecule dissociates, one of its polar H-0 bonds breaks. The resulting hydrogen ion, often referred to as a proton, has a short lifetime as a free ion and quickly combines with a water molecule to form a hydronium ion (H 30 convenience, we refer to the concentration of hydrogen ions in a solution, [H +I, even though this really represents the concentration of hydronium ions, [H10 ]. Dissociation of H20 generates one OH ion along with each H.._. The dissociation of water is a reversible reaction:

H20 H + OH

At 25 °C, [H+][OH l = 10 14 M2 , so that in pure water, IH. ] = [OH-] = 10 M.

The concentration of hydrogen ions in a solution is ex-pressed conventionally as its pH, defined as the negative log of the hydrogen ion concentration. The pH of pure water at 25 oc is 7:

1 1 pH= - log[H ] = log[ :;-= log 7 = 7

H ] 10

It is important to keep in mind that a I unit difference in pH represents a tenfold difference in the concentration of pro-tons. On the pH scale, 7.0 is considered neutral: pH values

2.3 Chemical React1ons and Chemical Equilibrium 45

FIGURE 2-24 Macromolecules can have distinct binding sites for multiple ligands. A large macromolecule (e.g., a protein, blue) with three distinct binding sites (A-C) is shown; each binding site exhibits molecular complementarity to three different binding partners (ligands A-C) with distinct dissociation constants (KdA-cl·

predil:tc:u. To illustrate the general approach for determining the concentration of noncovalently associated complexes, we will calculate the extent to which a protein (P) is bound to DNA (D), forming a protein-DNA complex (PD):

P + D PD

Most commonly, binding reactions are described in terms of the dissociation constan t Kd, which is the reciprocal of the equilibrium constant. For this binding reaction, the dissocia-tion constant is given by

[P][DJ K -d- [PO ] (2-4)

It is worth noting that in such a binding reaction, when half of the DNA is bound to the protein ([PO] = [D]), the concen-tration of Pis equal to the Kd. The lower the K0, the lower the concentration of P needed to bind to half of D. In other words, the lower the Kd, the tighter the binding (the higher the affinity) of P for D. Typical reactions in which a protein binds to a specific DNA sequence have a Kd of 10 10 M, where M symbolizes molarity, or moles per liter (moi/L). To relate the magnitude of this dissociation constant to the in-tracellular ratio of bound to unbound DNA, let's consider the simple example of a bacterial cell having a volume of 1.5 X 10 15 Land containing 1 molecule of DNA and 10 molecules of the DNA-binding protein P. In this case, given a Kd of 10 10 M and the total concentration of the Pin the cell ( - 111 X 10- 10 M, 1 00-fold higher than the Kd), 99 percent of the time this specific DNA sequence will have a molecule of protein bound to it and 1 percent of the time it will not, even though the cell contains only 10 molecules of the pro-tein! Clearly, P and D have a high affinity for each other and bind tightly, as reflected by the low value of the dissociation constant for their bindillg reaction. For protein-protein and protein-DNA bind ing, Kd values of ::510 9 M (nanomolar) are considered to be tight, -10 6 M (micromolar) modestly tight, and - 10 3 M (millimolar) relatively weak.

A large biological macromolecule, such as a protein, can have multiple binding surfaces for binding several molecules simultaneously (Figure 2-24). In some cases, these binding reactions are independent, with their own distinct K..1 values that are constant. In other cases, binding of a molecule at om: :,itc: on a macromolecu le can change the three-dimen-sional shape of a distant site, thus altering the binding inter-actions of that distant site with some other molecule. This is an important mechanism by which one molecule can alter, and thus regu late, the binding activity of another. We examine this regulatory mechanism in more detail in Chapter 3.

Multiligand binding macromolecule (e.g., protein)

Ligand B (e.g., small molecule)

Biological Fluids Have Characteristic pH Values The solvent inside cells and in all extracellular fluids is water. An important characteristic of anr aqueous solution is the con-centration of positively charged hydrogen ions (H+) and nega-tively charged hydroxyl ions (OH ). Because these ions are the dissociation products of H 20, they arc constituents of all living systems, and they arc liberated by many reactions that take place between organic molecules within cells. These ions also can be transported into or out of celh., as when highly acidic gastric juice is secreted by cells lining the walls of the stomach.

When a water molecule dissociates, one of its polar H-0 bonds breaks. The resulting hydrogen ion, often referred to as a proton, has a short lifetime as a free ion and quickly combines with a water molecule to form a hydronium ion (H 30 convenience, we refer to the concentration of hydrogen ions in a solution, [H +I, even though this really represents the concentration of hydronium ions, [H10 ]. Dissociation of H20 generates one OH ion along with each H.._. The dissociation of water is a reversible reaction:

H20 H + OH

At 25 °C, [H+][OH l = 10 14 M2 , so that in pure water, IH. ] = [OH-] = 10 M.

The concentration of hydrogen ions in a solution is ex-pressed conventionally as its pH, defined as the negative log of the hydrogen ion concentration. The pH of pure water at 25 oc is 7:

1 1 pH= - log[H ] = log[ :;-= log 7 = 7

H ] 10

It is important to keep in mind that a I unit difference in pH represents a tenfold difference in the concentration of pro-tons. On the pH scale, 7.0 is considered neutral: pH values

2.3 Chemical React1ons and Chemical Equilibrium 45

Lowerorhigher,whichmeansthetighterforbinding?

What’sthismean?Biotin and avidin bindwithadissociationconstantofroughly10^−15 M=1fM =0.000001nM.

Macromoleculescanhavedistinctbindingsitesformultipleligands.• Alargemacromolecule(e.g.,aprotein,blue)canhavemultipledistinctindependentorinterdependentbindingsites(A–C)asshown;eachwithdistinctdissociationconstants(KdA–C)forbindingthreedifferentbindingpartners(ligandsA–C).

Notsosimple…

pH

FIGURE 2-24 Macromolecules can have distinct binding sites for multiple ligands. A large macromolecule (e.g., a protein, blue) with three distinct binding sites (A-C) is shown; each binding site exhibits molecular complementarity to three different binding partners (ligands A-C) with distinct dissociation constants (KdA-cl·

predil:tc:u. To illustrate the general approach for determining the concentration of noncovalently associated complexes, we will calculate the extent to which a protein (P) is bound to DNA (D), forming a protein-DNA complex (PD):

P + D PD

Most commonly, binding reactions are described in terms of the dissociation constan t Kd, which is the reciprocal of the equilibrium constant. For this binding reaction, the dissocia-tion constant is given by

[P][DJ K -d- [PO ] (2-4)

It is worth noting that in such a binding reaction, when half of the DNA is bound to the protein ([PO] = [D]), the concen-tration of Pis equal to the Kd. The lower the K0, the lower the concentration of P needed to bind to half of D. In other words, the lower the Kd, the tighter the binding (the higher the affinity) of P for D. Typical reactions in which a protein binds to a specific DNA sequence have a Kd of 10 10 M, where M symbolizes molarity, or moles per liter (moi/L). To relate the magnitude of this dissociation constant to the in-tracellular ratio of bound to unbound DNA, let's consider the simple example of a bacterial cell having a volume of 1.5 X 10 15 Land containing 1 molecule of DNA and 10 molecules of the DNA-binding protein P. In this case, given a Kd of 10 10 M and the total concentration of the Pin the cell ( - 111 X 10- 10 M, 1 00-fold higher than the Kd), 99 percent of the time this specific DNA sequence will have a molecule of protein bound to it and 1 percent of the time it will not, even though the cell contains only 10 molecules of the pro-tein! Clearly, P and D have a high affinity for each other and bind tightly, as reflected by the low value of the dissociation constant for their bindillg reaction. For protein-protein and protein-DNA bind ing, Kd values of ::510 9 M (nanomolar) are considered to be tight, -10 6 M (micromolar) modestly tight, and - 10 3 M (millimolar) relatively weak.

A large biological macromolecule, such as a protein, can have multiple binding surfaces for binding several molecules simultaneously (Figure 2-24). In some cases, these binding reactions are independent, with their own distinct K..1 values that are constant. In other cases, binding of a molecule at om: :,itc: on a macromolecu le can change the three-dimen-sional shape of a distant site, thus altering the binding inter-actions of that distant site with some other molecule. This is an important mechanism by which one molecule can alter, and thus regu late, the binding activity of another. We examine this regulatory mechanism in more detail in Chapter 3.

Multiligand binding macromolecule (e.g., protein)

Ligand B (e.g., small molecule)

Biological Fluids Have Characteristic pH Values The solvent inside cells and in all extracellular fluids is water. An important characteristic of anr aqueous solution is the con-centration of positively charged hydrogen ions (H+) and nega-tively charged hydroxyl ions (OH ). Because these ions are the dissociation products of H 20, they arc constituents of all living systems, and they arc liberated by many reactions that take place between organic molecules within cells. These ions also can be transported into or out of celh., as when highly acidic gastric juice is secreted by cells lining the walls of the stomach.

When a water molecule dissociates, one of its polar H-0 bonds breaks. The resulting hydrogen ion, often referred to as a proton, has a short lifetime as a free ion and quickly combines with a water molecule to form a hydronium ion (H 30 convenience, we refer to the concentration of hydrogen ions in a solution, [H +I, even though this really represents the concentration of hydronium ions, [H10 ]. Dissociation of H20 generates one OH ion along with each H.._. The dissociation of water is a reversible reaction:

H20 H + OH

At 25 °C, [H+][OH l = 10 14 M2 , so that in pure water, IH. ] = [OH-] = 10 M.

The concentration of hydrogen ions in a solution is ex-pressed conventionally as its pH, defined as the negative log of the hydrogen ion concentration. The pH of pure water at 25 oc is 7:

1 1 pH= - log[H ] = log[ :;-= log 7 = 7

H ] 10

It is important to keep in mind that a I unit difference in pH represents a tenfold difference in the concentration of pro-tons. On the pH scale, 7.0 is considered neutral: pH values

2.3 Chemical React1ons and Chemical Equilibrium 45

FIGURE 2-24 Macromolecules can have distinct binding sites for multiple ligands. A large macromolecule (e.g., a protein, blue) with three distinct binding sites (A-C) is shown; each binding site exhibits molecular complementarity to three different binding partners (ligands A-C) with distinct dissociation constants (KdA-cl·

predil:tc:u. To illustrate the general approach for determining the concentration of noncovalently associated complexes, we will calculate the extent to which a protein (P) is bound to DNA (D), forming a protein-DNA complex (PD):

P + D PD

Most commonly, binding reactions are described in terms of the dissociation constan t Kd, which is the reciprocal of the equilibrium constant. For this binding reaction, the dissocia-tion constant is given by

[P][DJ K -d- [PO ] (2-4)

It is worth noting that in such a binding reaction, when half of the DNA is bound to the protein ([PO] = [D]), the concen-tration of Pis equal to the Kd. The lower the K0, the lower the concentration of P needed to bind to half of D. In other words, the lower the Kd, the tighter the binding (the higher the affinity) of P for D. Typical reactions in which a protein binds to a specific DNA sequence have a Kd of 10 10 M, where M symbolizes molarity, or moles per liter (moi/L). To relate the magnitude of this dissociation constant to the in-tracellular ratio of bound to unbound DNA, let's consider the simple example of a bacterial cell having a volume of 1.5 X 10 15 Land containing 1 molecule of DNA and 10 molecules of the DNA-binding protein P. In this case, given a Kd of 10 10 M and the total concentration of the Pin the cell ( - 111 X 10- 10 M, 1 00-fold higher than the Kd), 99 percent of the time this specific DNA sequence will have a molecule of protein bound to it and 1 percent of the time it will not, even though the cell contains only 10 molecules of the pro-tein! Clearly, P and D have a high affinity for each other and bind tightly, as reflected by the low value of the dissociation constant for their bindillg reaction. For protein-protein and protein-DNA bind ing, Kd values of ::510 9 M (nanomolar) are considered to be tight, -10 6 M (micromolar) modestly tight, and - 10 3 M (millimolar) relatively weak.

A large biological macromolecule, such as a protein, can have multiple binding surfaces for binding several molecules simultaneously (Figure 2-24). In some cases, these binding reactions are independent, with their own distinct K..1 values that are constant. In other cases, binding of a molecule at om: :,itc: on a macromolecu le can change the three-dimen-sional shape of a distant site, thus altering the binding inter-actions of that distant site with some other molecule. This is an important mechanism by which one molecule can alter, and thus regu late, the binding activity of another. We examine this regulatory mechanism in more detail in Chapter 3.

Multiligand binding macromolecule (e.g., protein)

Ligand B (e.g., small molecule)

Biological Fluids Have Characteristic pH Values The solvent inside cells and in all extracellular fluids is water. An important characteristic of anr aqueous solution is the con-centration of positively charged hydrogen ions (H+) and nega-tively charged hydroxyl ions (OH ). Because these ions are the dissociation products of H 20, they arc constituents of all living systems, and they arc liberated by many reactions that take place between organic molecules within cells. These ions also can be transported into or out of celh., as when highly acidic gastric juice is secreted by cells lining the walls of the stomach.

When a water molecule dissociates, one of its polar H-0 bonds breaks. The resulting hydrogen ion, often referred to as a proton, has a short lifetime as a free ion and quickly combines with a water molecule to form a hydronium ion (H 30 convenience, we refer to the concentration of hydrogen ions in a solution, [H +I, even though this really represents the concentration of hydronium ions, [H10 ]. Dissociation of H20 generates one OH ion along with each H.._. The dissociation of water is a reversible reaction:

H20 H + OH

At 25 °C, [H+][OH l = 10 14 M2 , so that in pure water, IH. ] = [OH-] = 10 M.

The concentration of hydrogen ions in a solution is ex-pressed conventionally as its pH, defined as the negative log of the hydrogen ion concentration. The pH of pure water at 25 oc is 7:

1 1 pH= - log[H ] = log[ :;-= log 7 = 7

H ] 10

It is important to keep in mind that a I unit difference in pH represents a tenfold difference in the concentration of pro-tons. On the pH scale, 7.0 is considered neutral: pH values

2.3 Chemical React1ons and Chemical Equilibrium 45

FIGURE 2-24 Macromolecules can have distinct binding sites for multiple ligands. A large macromolecule (e.g., a protein, blue) with three distinct binding sites (A-C) is shown; each binding site exhibits molecular complementarity to three different binding partners (ligands A-C) with distinct dissociation constants (KdA-cl·

predil:tc:u. To illustrate the general approach for determining the concentration of noncovalently associated complexes, we will calculate the extent to which a protein (P) is bound to DNA (D), forming a protein-DNA complex (PD):

P + D PD

Most commonly, binding reactions are described in terms of the dissociation constan t Kd, which is the reciprocal of the equilibrium constant. For this binding reaction, the dissocia-tion constant is given by

[P][DJ K -d- [PO ] (2-4)

It is worth noting that in such a binding reaction, when half of the DNA is bound to the protein ([PO] = [D]), the concen-tration of Pis equal to the Kd. The lower the K0, the lower the concentration of P needed to bind to half of D. In other words, the lower the Kd, the tighter the binding (the higher the affinity) of P for D. Typical reactions in which a protein binds to a specific DNA sequence have a Kd of 10 10 M, where M symbolizes molarity, or moles per liter (moi/L). To relate the magnitude of this dissociation constant to the in-tracellular ratio of bound to unbound DNA, let's consider the simple example of a bacterial cell having a volume of 1.5 X 10 15 Land containing 1 molecule of DNA and 10 molecules of the DNA-binding protein P. In this case, given a Kd of 10 10 M and the total concentration of the Pin the cell ( - 111 X 10- 10 M, 1 00-fold higher than the Kd), 99 percent of the time this specific DNA sequence will have a molecule of protein bound to it and 1 percent of the time it will not, even though the cell contains only 10 molecules of the pro-tein! Clearly, P and D have a high affinity for each other and bind tightly, as reflected by the low value of the dissociation constant for their bindillg reaction. For protein-protein and protein-DNA bind ing, Kd values of ::510 9 M (nanomolar) are considered to be tight, -10 6 M (micromolar) modestly tight, and - 10 3 M (millimolar) relatively weak.

A large biological macromolecule, such as a protein, can have multiple binding surfaces for binding several molecules simultaneously (Figure 2-24). In some cases, these binding reactions are independent, with their own distinct K..1 values that are constant. In other cases, binding of a molecule at om: :,itc: on a macromolecu le can change the three-dimen-sional shape of a distant site, thus altering the binding inter-actions of that distant site with some other molecule. This is an important mechanism by which one molecule can alter, and thus regu late, the binding activity of another. We examine this regulatory mechanism in more detail in Chapter 3.

Multiligand binding macromolecule (e.g., protein)

Ligand B (e.g., small molecule)

Biological Fluids Have Characteristic pH Values The solvent inside cells and in all extracellular fluids is water. An important characteristic of anr aqueous solution is the con-centration of positively charged hydrogen ions (H+) and nega-tively charged hydroxyl ions (OH ). Because these ions are the dissociation products of H 20, they arc constituents of all living systems, and they arc liberated by many reactions that take place between organic molecules within cells. These ions also can be transported into or out of celh., as when highly acidic gastric juice is secreted by cells lining the walls of the stomach.

When a water molecule dissociates, one of its polar H-0 bonds breaks. The resulting hydrogen ion, often referred to as a proton, has a short lifetime as a free ion and quickly combines with a water molecule to form a hydronium ion (H 30 convenience, we refer to the concentration of hydrogen ions in a solution, [H +I, even though this really represents the concentration of hydronium ions, [H10 ]. Dissociation of H20 generates one OH ion along with each H.._. The dissociation of water is a reversible reaction:

H20 H + OH

At 25 °C, [H+][OH l = 10 14 M2 , so that in pure water, IH. ] = [OH-] = 10 M.

The concentration of hydrogen ions in a solution is ex-pressed conventionally as its pH, defined as the negative log of the hydrogen ion concentration. The pH of pure water at 25 oc is 7:

1 1 pH= - log[H ] = log[ :;-= log 7 = 7

H ] 10

It is important to keep in mind that a I unit difference in pH represents a tenfold difference in the concentration of pro-tons. On the pH scale, 7.0 is considered neutral: pH values

2.3 Chemical React1ons and Chemical Equilibrium 45

WhydoweknowthepH?

Allorganisms,organsandorganellesareworkingintheirproperpHconditions.

SomepHvaluesforcommonsolutions.• H+ andOH- aredissociationproductsofH2Oandpresentinallaqueoussolutions(purewater,pH7).

• ThepHofanaqueoussolutionisthenegativelogofthehydrogenionconcentration.

• pHvaluesformostintracellular(cytoplasm6.6-7.2)andextracellularbiologicalfluidsarenear7andarecarefullyregulatedtopermittheproperfunctioningofcells,organelles,andcellularsecretions.

• pHvaluesofintracellularorganellesmaybe4.5(lysosome).StomachpHis1-2.

• ChangesinpHcanregulatecellularactivities.Higherprotonion?

Acid&BaseAnacidisanymolecule,ion,orchemicalgroupthattendstoreleaseahydrogenion(H),suchashydrochloricacid(HCI)

Abaseisanymolecule,ion,orchemicalgroupthatreadilycombineswithaH,suchasthehydroxylion(OH-)

IfAcidisaddedtothesolution,howisthepHchanged?

IfBaseisaddedtothesolution,howisthepHchanged?

Aciddissociationconstant

pKa

Molecules’characters.Constantvalue

pH&pKa

Increasingly basic (lower H concentration)

pH scale

f------+---14 Sodium hydroxide (1 N)

f------+---12 Household bleach Ammonia (1 N)

Seawater

Increasingly acidic (greater H concentration)

8 ____/ Interior of cell

7 Fertilized egg ---- Unfertilized egg

6 Urine

5

4

3 2

Interior of the lysosome

Grapefruit juice

Gastric juice

0 Hydrochloric acid (1 N)

FIGURE 2-25 pH values of common solutions. The pH of an aqueous solution is the negative log ofthe hydrogen ion concentra· tion. The pH values for most intracellular and extracellular biological fluids are near 7 and are carefully regulated to permit the proper functioning of cells •. organelles, and cellular secretions.

below 7.0 indicate acidic solutions (higher [H ' ]),and values above 7.0 indicate basic, or alkaline, solutions (Figure 2-25). For instance, gastric juice, which is rich in hydrochloric acid (HCI), has a pH of about 1. Its [H+] is roughly a millionfold greater than that of cytoplasm, with a pH of about 7.2.

Although the cytosol of cells normally has a pH of about 7.2, the interior of certain organelles in eukaryotic cells (see Chapter 9 ) can have a much lower pH. Lysosomes, for ex-ample, have a pH of about 4.5. The many degradative en-zymes withm lysosomes function optimally in an acidic environment, whereas their action is inhibited in the near neutral environment of the cytoplasm. As this example illustrates, maintenance of a specific pH is essential for proper functioning of some cellular structures. On the other hand, dramatic shifts in cellular pH may play an important role in controlling cellular activity. For example, the pH of the cytoplasm of an unfertilized egg of the sea urchin, an aquatic animal, is 6.6. Within 1 minute of fertilization, how-ever, the pH rises to 7.2; that is, the [H+] decreases to about one-fourth its original value, a change necessary for subse-quent growth and division of the egg.

46 CHAPTER 2 • Chemical Foundations

Hydrogen Ions Are Released by Acids and Taken Up by Bases In general, an acid is any molecule, ion, or chemical group that tends to release a hydrogen ion (H ), such as hydrochlo-ric acid (HCI ) or the carboxyl group (-COOH ), which tends to dissociate to form the negatively charged carboxyl-ate ion (-COO- ). Likewise, a base is any molecule, ion, or chemical group that readily combines with a H , such as the hydroxyl ion (OH-); ammonia (NH 3), which forms an am-monium ion (NH 4 the amino group (-NH1 ).

When acid is added to an aqueous solution, the [H +l in-creases and the pH goes down. Conversely, when a base is added to a solution, the IH+] decreases and the pH goes up. Because ] = 10 14 M 2, any increase in fH j is cou-pled with a commensurate decrease in [OH- ] and vice versa.

Many biological molecules contain both acidic and basic groups. For example, in neutral solutions (pH = 7.0), many amino acids exist predominantly in the doubly ionized form, in which the carboxyl group has lost a proton and the amino group has accepted one:

NH + I 3 H-c-coo-

R

where R represents the uncharged side chain. Such a mol-ecule, containing an equal number of positive and nega-tive ions, is called a zwitterion. Zwitterions, having no net charge, are neutral. At extreme pH values, only one of these two ionizable groups of an amino acid will be charged.

The dissociation reaction for an acid (or acid group in a larger molecule) HA can be written as HA H + + A . The equilibrium constant for this reaction, denoted Ka (the subscript a stands for "acid"), is defined as Ka = [H+lfA ]/ [HA]. Taking the logarithm of both sides and rearranging the result yields a very useful relation between the equilib-rium constant and pH:

[A ] pH= pK. + log [HA]

where pK3 equals - log K,.

(2-5)

From this expression, commonly known as the Henderson-Hasselbalch equation, it can be seen that the pK, of any acid is equal to the pH at which half the molecules are dissoci-ated and half are neutral (undissociated). This is because when fA ] = fHAj, then log ([A ]/[HA]) = 0, and thus

= pH. The Henderson-Hasselbalch equation allows us to calculate the degree of dissociation of an acid if both the pH of the solution and the pKa of the acid are known. Ex-perimentally, by measuring the fA J and fHA] as a function of the solution's pH, one can calculate the pK" of the acid and thus the equilibrium constant K, for the dissociation reaction (figure 2-26). Knowing the pK, of a molecule not only provides an important description of its properties but

Increasingly basic (lower H concentration)

pH scale

f------+---14 Sodium hydroxide (1 N)

f------+---12 Household bleach Ammonia (1 N)

Seawater

Increasingly acidic (greater H concentration)

8 ____/ Interior of cell

7 Fertilized egg ---- Unfertilized egg

6 Urine

5

4

3 2

Interior of the lysosome

Grapefruit juice

Gastric juice

0 Hydrochloric acid (1 N)

FIGURE 2-25 pH values of common solutions. The pH of an aqueous solution is the negative log ofthe hydrogen ion concentra· tion. The pH values for most intracellular and extracellular biological fluids are near 7 and are carefully regulated to permit the proper functioning of cells •. organelles, and cellular secretions.

below 7.0 indicate acidic solutions (higher [H ' ]),and values above 7.0 indicate basic, or alkaline, solutions (Figure 2-25). For instance, gastric juice, which is rich in hydrochloric acid (HCI), has a pH of about 1. Its [H+] is roughly a millionfold greater than that of cytoplasm, with a pH of about 7.2.

Although the cytosol of cells normally has a pH of about 7.2, the interior of certain organelles in eukaryotic cells (see Chapter 9 ) can have a much lower pH. Lysosomes, for ex-ample, have a pH of about 4.5. The many degradative en-zymes withm lysosomes function optimally in an acidic environment, whereas their action is inhibited in the near neutral environment of the cytoplasm. As this example illustrates, maintenance of a specific pH is essential for proper functioning of some cellular structures. On the other hand, dramatic shifts in cellular pH may play an important role in controlling cellular activity. For example, the pH of the cytoplasm of an unfertilized egg of the sea urchin, an aquatic animal, is 6.6. Within 1 minute of fertilization, how-ever, the pH rises to 7.2; that is, the [H+] decreases to about one-fourth its original value, a change necessary for subse-quent growth and division of the egg.

46 CHAPTER 2 • Chemical Foundations

Hydrogen Ions Are Released by Acids and Taken Up by Bases In general, an acid is any molecule, ion, or chemical group that tends to release a hydrogen ion (H ), such as hydrochlo-ric acid (HCI ) or the carboxyl group (-COOH ), which tends to dissociate to form the negatively charged carboxyl-ate ion (-COO- ). Likewise, a base is any molecule, ion, or chemical group that readily combines with a H , such as the hydroxyl ion (OH-); ammonia (NH 3), which forms an am-monium ion (NH 4 the amino group (-NH1 ).

When acid is added to an aqueous solution, the [H +l in-creases and the pH goes down. Conversely, when a base is added to a solution, the IH+] decreases and the pH goes up. Because ] = 10 14 M 2, any increase in fH j is cou-pled with a commensurate decrease in [OH- ] and vice versa.

Many biological molecules contain both acidic and basic groups. For example, in neutral solutions (pH = 7.0), many amino acids exist predominantly in the doubly ionized form, in which the carboxyl group has lost a proton and the amino group has accepted one:

NH + I 3 H-c-coo-

R

where R represents the uncharged side chain. Such a mol-ecule, containing an equal number of positive and nega-tive ions, is called a zwitterion. Zwitterions, having no net charge, are neutral. At extreme pH values, only one of these two ionizable groups of an amino acid will be charged.

The dissociation reaction for an acid (or acid group in a larger molecule) HA can be written as HA H + + A . The equilibrium constant for this reaction, denoted Ka (the subscript a stands for "acid"), is defined as Ka = [H+lfA ]/ [HA]. Taking the logarithm of both sides and rearranging the result yields a very useful relation between the equilib-rium constant and pH:

[A ] pH= pK. + log [HA]

where pK3 equals - log K,.

(2-5)

From this expression, commonly known as the Henderson-Hasselbalch equation, it can be seen that the pK, of any acid is equal to the pH at which half the molecules are dissoci-ated and half are neutral (undissociated). This is because when fA ] = fHAj, then log ([A ]/[HA]) = 0, and thus

= pH. The Henderson-Hasselbalch equation allows us to calculate the degree of dissociation of an acid if both the pH of the solution and the pKa of the acid are known. Ex-perimentally, by measuring the fA J and fHA] as a function of the solution's pH, one can calculate the pK" of the acid and thus the equilibrium constant K, for the dissociation reaction (figure 2-26). Knowing the pK, of a molecule not only provides an important description of its properties but

Increasingly basic (lower H concentration)

pH scale

f------+---14 Sodium hydroxide (1 N)

f------+---12 Household bleach Ammonia (1 N)

Seawater

Increasingly acidic (greater H concentration)

8 ____/ Interior of cell

7 Fertilized egg ---- Unfertilized egg

6 Urine

5

4

3 2

Interior of the lysosome

Grapefruit juice

Gastric juice

0 Hydrochloric acid (1 N)

FIGURE 2-25 pH values of common solutions. The pH of an aqueous solution is the negative log ofthe hydrogen ion concentra· tion. The pH values for most intracellular and extracellular biological fluids are near 7 and are carefully regulated to permit the proper functioning of cells •. organelles, and cellular secretions.

below 7.0 indicate acidic solutions (higher [H ' ]),and values above 7.0 indicate basic, or alkaline, solutions (Figure 2-25). For instance, gastric juice, which is rich in hydrochloric acid (HCI), has a pH of about 1. Its [H+] is roughly a millionfold greater than that of cytoplasm, with a pH of about 7.2.

Although the cytosol of cells normally has a pH of about 7.2, the interior of certain organelles in eukaryotic cells (see Chapter 9 ) can have a much lower pH. Lysosomes, for ex-ample, have a pH of about 4.5. The many degradative en-zymes withm lysosomes function optimally in an acidic environment, whereas their action is inhibited in the near neutral environment of the cytoplasm. As this example illustrates, maintenance of a specific pH is essential for proper functioning of some cellular structures. On the other hand, dramatic shifts in cellular pH may play an important role in controlling cellular activity. For example, the pH of the cytoplasm of an unfertilized egg of the sea urchin, an aquatic animal, is 6.6. Within 1 minute of fertilization, how-ever, the pH rises to 7.2; that is, the [H+] decreases to about one-fourth its original value, a change necessary for subse-quent growth and division of the egg.

46 CHAPTER 2 • Chemical Foundations

Hydrogen Ions Are Released by Acids and Taken Up by Bases In general, an acid is any molecule, ion, or chemical group that tends to release a hydrogen ion (H ), such as hydrochlo-ric acid (HCI ) or the carboxyl group (-COOH ), which tends to dissociate to form the negatively charged carboxyl-ate ion (-COO- ). Likewise, a base is any molecule, ion, or chemical group that readily combines with a H , such as the hydroxyl ion (OH-); ammonia (NH 3), which forms an am-monium ion (NH 4 the amino group (-NH1 ).

When acid is added to an aqueous solution, the [H +l in-creases and the pH goes down. Conversely, when a base is added to a solution, the IH+] decreases and the pH goes up. Because ] = 10 14 M 2, any increase in fH j is cou-pled with a commensurate decrease in [OH- ] and vice versa.

Many biological molecules contain both acidic and basic groups. For example, in neutral solutions (pH = 7.0), many amino acids exist predominantly in the doubly ionized form, in which the carboxyl group has lost a proton and the amino group has accepted one:

NH + I 3 H-c-coo-

R

where R represents the uncharged side chain. Such a mol-ecule, containing an equal number of positive and nega-tive ions, is called a zwitterion. Zwitterions, having no net charge, are neutral. At extreme pH values, only one of these two ionizable groups of an amino acid will be charged.

The dissociation reaction for an acid (or acid group in a larger molecule) HA can be written as HA H + + A . The equilibrium constant for this reaction, denoted Ka (the subscript a stands for "acid"), is defined as Ka = [H+lfA ]/ [HA]. Taking the logarithm of both sides and rearranging the result yields a very useful relation between the equilib-rium constant and pH:

[A ] pH= pK. + log [HA]

where pK3 equals - log K,.

(2-5)

From this expression, commonly known as the Henderson-Hasselbalch equation, it can be seen that the pK, of any acid is equal to the pH at which half the molecules are dissoci-ated and half are neutral (undissociated). This is because when fA ] = fHAj, then log ([A ]/[HA]) = 0, and thus

= pH. The Henderson-Hasselbalch equation allows us to calculate the degree of dissociation of an acid if both the pH of the solution and the pKa of the acid are known. Ex-perimentally, by measuring the fA J and fHA] as a function of the solution's pH, one can calculate the pK" of the acid and thus the equilibrium constant K, for the dissociation reaction (figure 2-26). Knowing the pK, of a molecule not only provides an important description of its properties but

Increasingly basic (lower H concentration)

pH scale

f------+---14 Sodium hydroxide (1 N)

f------+---12 Household bleach Ammonia (1 N)

Seawater

Increasingly acidic (greater H concentration)

8 ____/ Interior of cell

7 Fertilized egg ---- Unfertilized egg

6 Urine

5

4

3 2

Interior of the lysosome

Grapefruit juice

Gastric juice

0 Hydrochloric acid (1 N)

FIGURE 2-25 pH values of common solutions. The pH of an aqueous solution is the negative log ofthe hydrogen ion concentra· tion. The pH values for most intracellular and extracellular biological fluids are near 7 and are carefully regulated to permit the proper functioning of cells •. organelles, and cellular secretions.

below 7.0 indicate acidic solutions (higher [H ' ]),and values above 7.0 indicate basic, or alkaline, solutions (Figure 2-25). For instance, gastric juice, which is rich in hydrochloric acid (HCI), has a pH of about 1. Its [H+] is roughly a millionfold greater than that of cytoplasm, with a pH of about 7.2.

Although the cytosol of cells normally has a pH of about 7.2, the interior of certain organelles in eukaryotic cells (see Chapter 9 ) can have a much lower pH. Lysosomes, for ex-ample, have a pH of about 4.5. The many degradative en-zymes withm lysosomes function optimally in an acidic environment, whereas their action is inhibited in the near neutral environment of the cytoplasm. As this example illustrates, maintenance of a specific pH is essential for proper functioning of some cellular structures. On the other hand, dramatic shifts in cellular pH may play an important role in controlling cellular activity. For example, the pH of the cytoplasm of an unfertilized egg of the sea urchin, an aquatic animal, is 6.6. Within 1 minute of fertilization, how-ever, the pH rises to 7.2; that is, the [H+] decreases to about one-fourth its original value, a change necessary for subse-quent growth and division of the egg.

46 CHAPTER 2 • Chemical Foundations

Hydrogen Ions Are Released by Acids and Taken Up by Bases In general, an acid is any molecule, ion, or chemical group that tends to release a hydrogen ion (H ), such as hydrochlo-ric acid (HCI ) or the carboxyl group (-COOH ), which tends to dissociate to form the negatively charged carboxyl-ate ion (-COO- ). Likewise, a base is any molecule, ion, or chemical group that readily combines with a H , such as the hydroxyl ion (OH-); ammonia (NH 3), which forms an am-monium ion (NH 4 the amino group (-NH1 ).

When acid is added to an aqueous solution, the [H +l in-creases and the pH goes down. Conversely, when a base is added to a solution, the IH+] decreases and the pH goes up. Because ] = 10 14 M 2, any increase in fH j is cou-pled with a commensurate decrease in [OH- ] and vice versa.

Many biological molecules contain both acidic and basic groups. For example, in neutral solutions (pH = 7.0), many amino acids exist predominantly in the doubly ionized form, in which the carboxyl group has lost a proton and the amino group has accepted one:

NH + I 3 H-c-coo-

R

where R represents the uncharged side chain. Such a mol-ecule, containing an equal number of positive and nega-tive ions, is called a zwitterion. Zwitterions, having no net charge, are neutral. At extreme pH values, only one of these two ionizable groups of an amino acid will be charged.

The dissociation reaction for an acid (or acid group in a larger molecule) HA can be written as HA H + + A . The equilibrium constant for this reaction, denoted Ka (the subscript a stands for "acid"), is defined as Ka = [H+lfA ]/ [HA]. Taking the logarithm of both sides and rearranging the result yields a very useful relation between the equilib-rium constant and pH:

[A ] pH= pK. + log [HA]

where pK3 equals - log K,.

(2-5)

From this expression, commonly known as the Henderson-Hasselbalch equation, it can be seen that the pK, of any acid is equal to the pH at which half the molecules are dissoci-ated and half are neutral (undissociated). This is because when fA ] = fHAj, then log ([A ]/[HA]) = 0, and thus

= pH. The Henderson-Hasselbalch equation allows us to calculate the degree of dissociation of an acid if both the pH of the solution and the pKa of the acid are known. Ex-perimentally, by measuring the fA J and fHA] as a function of the solution's pH, one can calculate the pK" of the acid and thus the equilibrium constant K, for the dissociation reaction (figure 2-26). Knowing the pK, of a molecule not only provides an important description of its properties but

Increasingly basic (lower H concentration)

pH scale

f------+---14 Sodium hydroxide (1 N)

f------+---12 Household bleach Ammonia (1 N)

Seawater

Increasingly acidic (greater H concentration)

8 ____/ Interior of cell

7 Fertilized egg ---- Unfertilized egg

6 Urine

5

4

3 2

Interior of the lysosome

Grapefruit juice

Gastric juice

0 Hydrochloric acid (1 N)

FIGURE 2-25 pH values of common solutions. The pH of an aqueous solution is the negative log ofthe hydrogen ion concentra· tion. The pH values for most intracellular and extracellular biological fluids are near 7 and are carefully regulated to permit the proper functioning of cells •. organelles, and cellular secretions.

below 7.0 indicate acidic solutions (higher [H ' ]),and values above 7.0 indicate basic, or alkaline, solutions (Figure 2-25). For instance, gastric juice, which is rich in hydrochloric acid (HCI), has a pH of about 1. Its [H+] is roughly a millionfold greater than that of cytoplasm, with a pH of about 7.2.

Although the cytosol of cells normally has a pH of about 7.2, the interior of certain organelles in eukaryotic cells (see Chapter 9 ) can have a much lower pH. Lysosomes, for ex-ample, have a pH of about 4.5. The many degradative en-zymes withm lysosomes function optimally in an acidic environment, whereas their action is inhibited in the near neutral environment of the cytoplasm. As this example illustrates, maintenance of a specific pH is essential for proper functioning of some cellular structures. On the other hand, dramatic shifts in cellular pH may play an important role in controlling cellular activity. For example, the pH of the cytoplasm of an unfertilized egg of the sea urchin, an aquatic animal, is 6.6. Within 1 minute of fertilization, how-ever, the pH rises to 7.2; that is, the [H+] decreases to about one-fourth its original value, a change necessary for subse-quent growth and division of the egg.

46 CHAPTER 2 • Chemical Foundations

Hydrogen Ions Are Released by Acids and Taken Up by Bases In general, an acid is any molecule, ion, or chemical group that tends to release a hydrogen ion (H ), such as hydrochlo-ric acid (HCI ) or the carboxyl group (-COOH ), which tends to dissociate to form the negatively charged carboxyl-ate ion (-COO- ). Likewise, a base is any molecule, ion, or chemical group that readily combines with a H , such as the hydroxyl ion (OH-); ammonia (NH 3), which forms an am-monium ion (NH 4 the amino group (-NH1 ).

When acid is added to an aqueous solution, the [H +l in-creases and the pH goes down. Conversely, when a base is added to a solution, the IH+] decreases and the pH goes up. Because ] = 10 14 M 2, any increase in fH j is cou-pled with a commensurate decrease in [OH- ] and vice versa.

Many biological molecules contain both acidic and basic groups. For example, in neutral solutions (pH = 7.0), many amino acids exist predominantly in the doubly ionized form, in which the carboxyl group has lost a proton and the amino group has accepted one:

NH + I 3 H-c-coo-

R

where R represents the uncharged side chain. Such a mol-ecule, containing an equal number of positive and nega-tive ions, is called a zwitterion. Zwitterions, having no net charge, are neutral. At extreme pH values, only one of these two ionizable groups of an amino acid will be charged.

The dissociation reaction for an acid (or acid group in a larger molecule) HA can be written as HA H + + A . The equilibrium constant for this reaction, denoted Ka (the subscript a stands for "acid"), is defined as Ka = [H+lfA ]/ [HA]. Taking the logarithm of both sides and rearranging the result yields a very useful relation between the equilib-rium constant and pH:

[A ] pH= pK. + log [HA]

where pK3 equals - log K,.

(2-5)

From this expression, commonly known as the Henderson-Hasselbalch equation, it can be seen that the pK, of any acid is equal to the pH at which half the molecules are dissoci-ated and half are neutral (undissociated). This is because when fA ] = fHAj, then log ([A ]/[HA]) = 0, and thus

= pH. The Henderson-Hasselbalch equation allows us to calculate the degree of dissociation of an acid if both the pH of the solution and the pKa of the acid are known. Ex-perimentally, by measuring the fA J and fHA] as a function of the solution's pH, one can calculate the pK" of the acid and thus the equilibrium constant K, for the dissociation reaction (figure 2-26). Knowing the pK, of a molecule not only provides an important description of its properties but

‘A’standsforacid.

Henderson-Hasselbalchequation

pK,ofanyacidisequaltothepHatwhichhalfthemoleculesaredissociatedandhalfareneutral.

IfHA=A-

TherelationshipbetweenpH,pKa,andthedissociationofanacid.• AcidsreleaseH+;basescombinewithH+.• pKa ofanyacidisthepHatwhichhalfthemoleculesaredissociatedandhalfareneutral(undissociated).

HowabouttheconcentrationsatpH6.4?

Increasingly basic (lower H concentration)

pH scale

f------+---14 Sodium hydroxide (1 N)

f------+---12 Household bleach Ammonia (1 N)

Seawater

Increasingly acidic (greater H concentration)

8 ____/ Interior of cell

7 Fertilized egg ---- Unfertilized egg

6 Urine

5

4

3 2

Interior of the lysosome

Grapefruit juice

Gastric juice

0 Hydrochloric acid (1 N)

FIGURE 2-25 pH values of common solutions. The pH of an aqueous solution is the negative log ofthe hydrogen ion concentra· tion. The pH values for most intracellular and extracellular biological fluids are near 7 and are carefully regulated to permit the proper functioning of cells •. organelles, and cellular secretions.

below 7.0 indicate acidic solutions (higher [H ' ]),and values above 7.0 indicate basic, or alkaline, solutions (Figure 2-25). For instance, gastric juice, which is rich in hydrochloric acid (HCI), has a pH of about 1. Its [H+] is roughly a millionfold greater than that of cytoplasm, with a pH of about 7.2.

Although the cytosol of cells normally has a pH of about 7.2, the interior of certain organelles in eukaryotic cells (see Chapter 9 ) can have a much lower pH. Lysosomes, for ex-ample, have a pH of about 4.5. The many degradative en-zymes withm lysosomes function optimally in an acidic environment, whereas their action is inhibited in the near neutral environment of the cytoplasm. As this example illustrates, maintenance of a specific pH is essential for proper functioning of some cellular structures. On the other hand, dramatic shifts in cellular pH may play an important role in controlling cellular activity. For example, the pH of the cytoplasm of an unfertilized egg of the sea urchin, an aquatic animal, is 6.6. Within 1 minute of fertilization, how-ever, the pH rises to 7.2; that is, the [H+] decreases to about one-fourth its original value, a change necessary for subse-quent growth and division of the egg.

46 CHAPTER 2 • Chemical Foundations

Hydrogen Ions Are Released by Acids and Taken Up by Bases In general, an acid is any molecule, ion, or chemical group that tends to release a hydrogen ion (H ), such as hydrochlo-ric acid (HCI ) or the carboxyl group (-COOH ), which tends to dissociate to form the negatively charged carboxyl-ate ion (-COO- ). Likewise, a base is any molecule, ion, or chemical group that readily combines with a H , such as the hydroxyl ion (OH-); ammonia (NH 3), which forms an am-monium ion (NH 4 the amino group (-NH1 ).

When acid is added to an aqueous solution, the [H +l in-creases and the pH goes down. Conversely, when a base is added to a solution, the IH+] decreases and the pH goes up. Because ] = 10 14 M 2, any increase in fH j is cou-pled with a commensurate decrease in [OH- ] and vice versa.

Many biological molecules contain both acidic and basic groups. For example, in neutral solutions (pH = 7.0), many amino acids exist predominantly in the doubly ionized form, in which the carboxyl group has lost a proton and the amino group has accepted one:

NH + I 3 H-c-coo-

R

where R represents the uncharged side chain. Such a mol-ecule, containing an equal number of positive and nega-tive ions, is called a zwitterion. Zwitterions, having no net charge, are neutral. At extreme pH values, only one of these two ionizable groups of an amino acid will be charged.

The dissociation reaction for an acid (or acid group in a larger molecule) HA can be written as HA H + + A . The equilibrium constant for this reaction, denoted Ka (the subscript a stands for "acid"), is defined as Ka = [H+lfA ]/ [HA]. Taking the logarithm of both sides and rearranging the result yields a very useful relation between the equilib-rium constant and pH:

[A ] pH= pK. + log [HA]

where pK3 equals - log K,.

(2-5)

From this expression, commonly known as the Henderson-Hasselbalch equation, it can be seen that the pK, of any acid is equal to the pH at which half the molecules are dissoci-ated and half are neutral (undissociated). This is because when fA ] = fHAj, then log ([A ]/[HA]) = 0, and thus

= pH. The Henderson-Hasselbalch equation allows us to calculate the degree of dissociation of an acid if both the pH of the solution and the pKa of the acid are known. Ex-perimentally, by measuring the fA J and fHA] as a function of the solution's pH, one can calculate the pK" of the acid and thus the equilibrium constant K, for the dissociation reaction (figure 2-26). Knowing the pK, of a molecule not only provides an important description of its properties but

Increasingly basic (lower H concentration)

pH scale

f------+---14 Sodium hydroxide (1 N)

f------+---12 Household bleach Ammonia (1 N)

Seawater

Increasingly acidic (greater H concentration)

8 ____/ Interior of cell

7 Fertilized egg ---- Unfertilized egg

6 Urine

5

4

3 2

Interior of the lysosome

Grapefruit juice

Gastric juice

0 Hydrochloric acid (1 N)

FIGURE 2-25 pH values of common solutions. The pH of an aqueous solution is the negative log ofthe hydrogen ion concentra· tion. The pH values for most intracellular and extracellular biological fluids are near 7 and are carefully regulated to permit the proper functioning of cells •. organelles, and cellular secretions.

below 7.0 indicate acidic solutions (higher [H ' ]),and values above 7.0 indicate basic, or alkaline, solutions (Figure 2-25). For instance, gastric juice, which is rich in hydrochloric acid (HCI), has a pH of about 1. Its [H+] is roughly a millionfold greater than that of cytoplasm, with a pH of about 7.2.

Although the cytosol of cells normally has a pH of about 7.2, the interior of certain organelles in eukaryotic cells (see Chapter 9 ) can have a much lower pH. Lysosomes, for ex-ample, have a pH of about 4.5. The many degradative en-zymes withm lysosomes function optimally in an acidic environment, whereas their action is inhibited in the near neutral environment of the cytoplasm. As this example illustrates, maintenance of a specific pH is essential for proper functioning of some cellular structures. On the other hand, dramatic shifts in cellular pH may play an important role in controlling cellular activity. For example, the pH of the cytoplasm of an unfertilized egg of the sea urchin, an aquatic animal, is 6.6. Within 1 minute of fertilization, how-ever, the pH rises to 7.2; that is, the [H+] decreases to about one-fourth its original value, a change necessary for subse-quent growth and division of the egg.

46 CHAPTER 2 • Chemical Foundations

Hydrogen Ions Are Released by Acids and Taken Up by Bases In general, an acid is any molecule, ion, or chemical group that tends to release a hydrogen ion (H ), such as hydrochlo-ric acid (HCI ) or the carboxyl group (-COOH ), which tends to dissociate to form the negatively charged carboxyl-ate ion (-COO- ). Likewise, a base is any molecule, ion, or chemical group that readily combines with a H , such as the hydroxyl ion (OH-); ammonia (NH 3), which forms an am-monium ion (NH 4 the amino group (-NH1 ).

When acid is added to an aqueous solution, the [H +l in-creases and the pH goes down. Conversely, when a base is added to a solution, the IH+] decreases and the pH goes up. Because ] = 10 14 M 2, any increase in fH j is cou-pled with a commensurate decrease in [OH- ] and vice versa.

Many biological molecules contain both acidic and basic groups. For example, in neutral solutions (pH = 7.0), many amino acids exist predominantly in the doubly ionized form, in which the carboxyl group has lost a proton and the amino group has accepted one:

NH + I 3 H-c-coo-

R

where R represents the uncharged side chain. Such a mol-ecule, containing an equal number of positive and nega-tive ions, is called a zwitterion. Zwitterions, having no net charge, are neutral. At extreme pH values, only one of these two ionizable groups of an amino acid will be charged.

The dissociation reaction for an acid (or acid group in a larger molecule) HA can be written as HA H + + A . The equilibrium constant for this reaction, denoted Ka (the subscript a stands for "acid"), is defined as Ka = [H+lfA ]/ [HA]. Taking the logarithm of both sides and rearranging the result yields a very useful relation between the equilib-rium constant and pH:

[A ] pH= pK. + log [HA]

where pK3 equals - log K,.

(2-5)

From this expression, commonly known as the Henderson-Hasselbalch equation, it can be seen that the pK, of any acid is equal to the pH at which half the molecules are dissoci-ated and half are neutral (undissociated). This is because when fA ] = fHAj, then log ([A ]/[HA]) = 0, and thus

= pH. The Henderson-Hasselbalch equation allows us to calculate the degree of dissociation of an acid if both the pH of the solution and the pKa of the acid are known. Ex-perimentally, by measuring the fA J and fHA] as a function of the solution's pH, one can calculate the pK" of the acid and thus the equilibrium constant K, for the dissociation reaction (figure 2-26). Knowing the pK, of a molecule not only provides an important description of its properties but

pKa

KnowingthepKa,ofamoleculenotonlyprovidesanimportantdescriptionofitspropertiesbutalsoallowsustoexploitthesepropertiestomanipulatetheacidityofanaqueoussolutionandtounderstandhowbiologicalsystemscontrolthiscriticalcharacteristic oftheiraqueousfluids.

Buffer

(ex)Aliving,activelymetabolizingcellmustmaintainaconstantpHinthecytoplasmofabout7.2-7.4

BUT!

Cellshaveareservoirofweakbasesandweakacids,calledbuffers!

Agoodexampleis…

Buffer

If additional acid (or base) is added to a buffered solution whose pH is equal to the pKa of the buffer, the pH of the solution changes, but it changes less than it would if the buffer had not been present.

Increasingly basic (lower H concentration)

pH scale

f------+---14 Sodium hydroxide (1 N)

f------+---12 Household bleach Ammonia (1 N)

Seawater

Increasingly acidic (greater H concentration)

8 ____/ Interior of cell

7 Fertilized egg ---- Unfertilized egg

6 Urine

5

4

3 2

Interior of the lysosome

Grapefruit juice

Gastric juice

0 Hydrochloric acid (1 N)

FIGURE 2-25 pH values of common solutions. The pH of an aqueous solution is the negative log ofthe hydrogen ion concentra· tion. The pH values for most intracellular and extracellular biological fluids are near 7 and are carefully regulated to permit the proper functioning of cells •. organelles, and cellular secretions.

below 7.0 indicate acidic solutions (higher [H ' ]),and values above 7.0 indicate basic, or alkaline, solutions (Figure 2-25). For instance, gastric juice, which is rich in hydrochloric acid (HCI), has a pH of about 1. Its [H+] is roughly a millionfold greater than that of cytoplasm, with a pH of about 7.2.

Although the cytosol of cells normally has a pH of about 7.2, the interior of certain organelles in eukaryotic cells (see Chapter 9 ) can have a much lower pH. Lysosomes, for ex-ample, have a pH of about 4.5. The many degradative en-zymes withm lysosomes function optimally in an acidic environment, whereas their action is inhibited in the near neutral environment of the cytoplasm. As this example illustrates, maintenance of a specific pH is essential for proper functioning of some cellular structures. On the other hand, dramatic shifts in cellular pH may play an important role in controlling cellular activity. For example, the pH of the cytoplasm of an unfertilized egg of the sea urchin, an aquatic animal, is 6.6. Within 1 minute of fertilization, how-ever, the pH rises to 7.2; that is, the [H+] decreases to about one-fourth its original value, a change necessary for subse-quent growth and division of the egg.

46 CHAPTER 2 • Chemical Foundations

Hydrogen Ions Are Released by Acids and Taken Up by Bases In general, an acid is any molecule, ion, or chemical group that tends to release a hydrogen ion (H ), such as hydrochlo-ric acid (HCI ) or the carboxyl group (-COOH ), which tends to dissociate to form the negatively charged carboxyl-ate ion (-COO- ). Likewise, a base is any molecule, ion, or chemical group that readily combines with a H , such as the hydroxyl ion (OH-); ammonia (NH 3), which forms an am-monium ion (NH 4 the amino group (-NH1 ).

When acid is added to an aqueous solution, the [H +l in-creases and the pH goes down. Conversely, when a base is added to a solution, the IH+] decreases and the pH goes up. Because ] = 10 14 M 2, any increase in fH j is cou-pled with a commensurate decrease in [OH- ] and vice versa.

Many biological molecules contain both acidic and basic groups. For example, in neutral solutions (pH = 7.0), many amino acids exist predominantly in the doubly ionized form, in which the carboxyl group has lost a proton and the amino group has accepted one:

NH + I 3 H-c-coo-

R

where R represents the uncharged side chain. Such a mol-ecule, containing an equal number of positive and nega-tive ions, is called a zwitterion. Zwitterions, having no net charge, are neutral. At extreme pH values, only one of these two ionizable groups of an amino acid will be charged.

The dissociation reaction for an acid (or acid group in a larger molecule) HA can be written as HA H + + A . The equilibrium constant for this reaction, denoted Ka (the subscript a stands for "acid"), is defined as Ka = [H+lfA ]/ [HA]. Taking the logarithm of both sides and rearranging the result yields a very useful relation between the equilib-rium constant and pH:

[A ] pH= pK. + log [HA]

where pK3 equals - log K,.

(2-5)

From this expression, commonly known as the Henderson-Hasselbalch equation, it can be seen that the pK, of any acid is equal to the pH at which half the molecules are dissoci-ated and half are neutral (undissociated). This is because when fA ] = fHAj, then log ([A ]/[HA]) = 0, and thus

= pH. The Henderson-Hasselbalch equation allows us to calculate the degree of dissociation of an acid if both the pH of the solution and the pKa of the acid are known. Ex-perimentally, by measuring the fA J and fHA] as a function of the solution's pH, one can calculate the pK" of the acid and thus the equilibrium constant K, for the dissociation reaction (figure 2-26). Knowing the pK, of a molecule not only provides an important description of its properties but

Increasingly basic (lower H concentration)

pH scale

f------+---14 Sodium hydroxide (1 N)

f------+---12 Household bleach Ammonia (1 N)

Seawater

Increasingly acidic (greater H concentration)

8 ____/ Interior of cell

7 Fertilized egg ---- Unfertilized egg

6 Urine

5

4

3 2

Interior of the lysosome

Grapefruit juice

Gastric juice

0 Hydrochloric acid (1 N)

FIGURE 2-25 pH values of common solutions. The pH of an aqueous solution is the negative log ofthe hydrogen ion concentra· tion. The pH values for most intracellular and extracellular biological fluids are near 7 and are carefully regulated to permit the proper functioning of cells •. organelles, and cellular secretions.

below 7.0 indicate acidic solutions (higher [H ' ]),and values above 7.0 indicate basic, or alkaline, solutions (Figure 2-25). For instance, gastric juice, which is rich in hydrochloric acid (HCI), has a pH of about 1. Its [H+] is roughly a millionfold greater than that of cytoplasm, with a pH of about 7.2.

Although the cytosol of cells normally has a pH of about 7.2, the interior of certain organelles in eukaryotic cells (see Chapter 9 ) can have a much lower pH. Lysosomes, for ex-ample, have a pH of about 4.5. The many degradative en-zymes withm lysosomes function optimally in an acidic environment, whereas their action is inhibited in the near neutral environment of the cytoplasm. As this example illustrates, maintenance of a specific pH is essential for proper functioning of some cellular structures. On the other hand, dramatic shifts in cellular pH may play an important role in controlling cellular activity. For example, the pH of the cytoplasm of an unfertilized egg of the sea urchin, an aquatic animal, is 6.6. Within 1 minute of fertilization, how-ever, the pH rises to 7.2; that is, the [H+] decreases to about one-fourth its original value, a change necessary for subse-quent growth and division of the egg.

46 CHAPTER 2 • Chemical Foundations

Hydrogen Ions Are Released by Acids and Taken Up by Bases In general, an acid is any molecule, ion, or chemical group that tends to release a hydrogen ion (H ), such as hydrochlo-ric acid (HCI ) or the carboxyl group (-COOH ), which tends to dissociate to form the negatively charged carboxyl-ate ion (-COO- ). Likewise, a base is any molecule, ion, or chemical group that readily combines with a H , such as the hydroxyl ion (OH-); ammonia (NH 3), which forms an am-monium ion (NH 4 the amino group (-NH1 ).

When acid is added to an aqueous solution, the [H +l in-creases and the pH goes down. Conversely, when a base is added to a solution, the IH+] decreases and the pH goes up. Because ] = 10 14 M 2, any increase in fH j is cou-pled with a commensurate decrease in [OH- ] and vice versa.

Many biological molecules contain both acidic and basic groups. For example, in neutral solutions (pH = 7.0), many amino acids exist predominantly in the doubly ionized form, in which the carboxyl group has lost a proton and the amino group has accepted one:

NH + I 3 H-c-coo-

R

where R represents the uncharged side chain. Such a mol-ecule, containing an equal number of positive and nega-tive ions, is called a zwitterion. Zwitterions, having no net charge, are neutral. At extreme pH values, only one of these two ionizable groups of an amino acid will be charged.

The dissociation reaction for an acid (or acid group in a larger molecule) HA can be written as HA H + + A . The equilibrium constant for this reaction, denoted Ka (the subscript a stands for "acid"), is defined as Ka = [H+lfA ]/ [HA]. Taking the logarithm of both sides and rearranging the result yields a very useful relation between the equilib-rium constant and pH:

[A ] pH= pK. + log [HA]

where pK3 equals - log K,.

(2-5)

From this expression, commonly known as the Henderson-Hasselbalch equation, it can be seen that the pK, of any acid is equal to the pH at which half the molecules are dissoci-ated and half are neutral (undissociated). This is because when fA ] = fHAj, then log ([A ]/[HA]) = 0, and thus

= pH. The Henderson-Hasselbalch equation allows us to calculate the degree of dissociation of an acid if both the pH of the solution and the pKa of the acid are known. Ex-perimentally, by measuring the fA J and fHA] as a function of the solution's pH, one can calculate the pK" of the acid and thus the equilibrium constant K, for the dissociation reaction (figure 2-26). Knowing the pK, of a molecule not only provides an important description of its properties but

Thetitrationcurveofthebufferaceticacid(CH3COOH).• ManycellsmaintaincytosolicpHat7.2-7.4despitemetabolismproducingacidsbybufferingpHwithareservoirofweakacidandbasebuffersthatbondandreleaseH+.

• Bufferingcapacity dependsonconcentrationofthebufferandtherelationshipbetweenitspKa valueandthepH.

• Buffersbestinrange1pHunitabovetobelowpKa:Aceticacid4.75(pKa)is91percentCH3COOHatpH3.75and9percentCH3COOHatpH5.75.

Baseadded&bindtoH+

Whathappens?

Allbiologicalsystemscontainoneormorebuffers.

Thetitrationcurveofphosphoricacid(H3PO4),acommonbufferinbiologicalsystems.• ThisbiologicallyubiquitousandabundantmoleculehasthreehydrogenatomsthatdissociatewithdifferentpKa valuesthatbufferinthreepHranges.

Threeprotons!

2.1CovalentBondsandNoncovalentInteractions2.2ChemicalBuildingBlocksofCells2.3ChemicalReactionsandChemicalEquilibrium2.4BiochemicalEnergetics

Whichoneiseasier?

– DG:measureofreactionchangeinfreeenergy;-DG reactionsarethermodynamicallyfavorable;+DG reactionsarenot

– freeenergychangeDG0’(-2.3RTlogKeq):calculatedfromreactants/productsatequilibrium

– rateofreaction:dependsonactivationenergy;loweredbyacatalystEx.Enzymes!!!

Enzymesinthecell

– DG:measureofreactionchangeinfreeenergy;-DG reactionsarethermodynamicallyfavorable;+DG reactionsarenot

– freeenergychangeDG0’(-2.3RTlogKeq):calculatedfromreactants/productsatequilibrium

– rateofreaction:dependsonactivationenergy;loweredbyacatalyst

– -DG reactionsuchasATPhydrolysistoADP+Pi candrivecoupled+DG reaction.

ATP!

Phosphoanhydride bond• Eachofthetwophosphoanhydride bonds-phosphodiester(red)inATP(top)hasa“high-energy”ΔG°ʹofabout−7.3kcal/mol forhydrolysis,becauseofthehighamountofenergynecessarytoformthecovalentbondholding twonegativelycharged(repellant)phosphategroupstogether.

ATP!

Stableorunstableinsenseofenergy?

Hydrolysisofadenosinetriphosphate(ATP).• CellsuseenergyderivedfromexergonicreactionssuchashydrolysisofATPtoADP+Pi todrivecoupledendergonicreactions.

• Eachofthetwophosphoanhydridebonds-phosphodiester(red)inATP(top)hasa“high-energy”ΔG°ʹofabout−7.3kcal/mol forhydrolysis,becauseofthehighamountofenergynecessarytoformthecovalentbondholdingtwonegativelycharged(repellant)phosphategroupstogether.

• Energyderivedfromhydrolysisoftheterminalphosphoanhydride bond isusedbyproteinstodrivemanyenergy-requiringreactionsinbiologicalsystems.

But!

https://www.khanacademy.org/science/biology/energy-and-enzymes/atp-reaction-coupling/a/atp-and-reaction-coupling

Wheredoestheenergycomefrom?

Howtomakethehighenergy-containingmolecules?

– DG:measureofreactionchangeinfreeenergy;-DG reactionsarethermodynamicallyfavorable;+DG reactionsarenot

– freeenergychangeDG0’(-2.3RTlogKeq):calculatedfromreactants/productsatequilibrium

– rateofreaction:dependsonactivationenergy;loweredbyacatalyst

– -DG reactionsuchasATPhydrolysistoADP+Pi candrivecoupled+DG reaction.

– sunlightenergycapturedbyphotosynthesisisultimatesourceofallcellenergy

– coenzyme(NAD+,FAD)oxidation(lossofe-)andreduction(gainofe-)electrontransferstoresandtransferscellenergy

Youcanlearnthisinbiochemistryclass…

Glycolysis

Topyruvate

Kreb cycle

Theelectron-carryingcoenzymesNAD+ andFAD.• (a)NAD+ (nicotinamideadeninedinucleotide)isreducedtoNADHbytheadditionoftwoelectronsandoneprotonsimultaneously.Theotherprotonisreleasedintosolution.

• (b)FAD(flavin adeninedinucleotide)isreducedtoFADH2 bytheadditionoftwoelectronsandtwoprotons.

• Inaredoxreaction,electronsmovespontaneouslytowardatomsormoleculeshavingmorepositivereductionpotentials(measuredinvolts,V).

Kreb cycleproducts

Electrontransportchain

Totalinputsandouputs

https://www.youtube.com/watch?v=VER6xW_r1vc

Discussionwithfriends…

3.IfthePHisnotpropertolivingorganisms(ex.toohighortoolow),whathappensinmoleculessuchasprotein,lipidandnucleotide?Pleaseexplainwithanexample.4. DerivetheHenderson-Hasselbalchequationanddiscussthemeaningofequation.

Discusswithfriends1.Duringmuchofthe"AgeofEnlightenment"ineighteenth-centuryEurope,scientiststoiledunderthebeliefthatlivingthingsandtheinanimateworldwerefundamentally

distinctformsofmatter.Thenin1828,FriedrichWohlershowedthathecouldsynthesizeurea,awell-knownwasteproductofanimals,fromthemineralssilver

isocyanateandammoniumchloride."Icanmakeureawithoutkidneys!"heissaidtohaveremarked.OfWohler'sdiscoverythepreeminentchemistJustusvonLiebigwrotein1837thatthe"productionofureawithouttheassistanceofvitalfunctions...must

beconsideredoneofthediscoverieswithwhichanewerainsciencehascommenced."Slightlymorethan100yearslater,StanleyMillerdischargedsparksintoamixtureofH20,CH4,NH1,andH2inanefforttosimulatethechemicalconditionsof

anancientreducingearthatmosphere(thesparksmimickedlightningstrikingaprimordialseaor"soup")andidentifiedmanybiomoleculesintheresultingmixture,includingaminoacidsandcarbohydrates.Whatdotheseexperimentssuggestabout

thenatureofbiomoleculesandtherelationshipbetweenorganic(living)andinorganic(nonliving)matter? Whatdotheysuggestabouttheevolutionoflife?

Whatdotheyindicateaboutthevalueofchemistryinunderstandinglivingthings?

2.RNAislessstablethanDNA.ExplaintworeasonsinaspectsofchemicalreactionandenzymeanddiscusshowtosafelyhandletheRNAinlab.3.IfthePHisnotpropertolivingorganisms(ex.toohighortoolow),whathappensinmoleculessuchasprotein,lipidandnucleotide?Pleaseexplainwithanexample.4. DerivetheHenderson-Hasselbalchequationanddiscussthemeaningofequation.