Chemistry, Water, and Buffers

BB 450 / 550

Dr. Kevin Ahern

BasicChemistry

GeometryofCarbon

GeometryofCarbon

GeometryofCarbon

Tetrahedral

GeometryofCarbon

TetrahedralHandedness & Stereochemistry

GeometryofCarbon

TetrahedralHandedness & Stereochemistry

BasicChemistry

BasicChemistry

Electronegativity

BasicChemistry

ElectronegativityRelative “pull” of nuclei for outer shell electrons

BasicChemistry

ElectronegativityRelative “pull” of nuclei for outer shell electrons

HydrogenBonds

Partial Negative & Partial Positive Charges Arise From Different Electronegativities

Reduction/Oxidation

Reduction/Oxidation

Reduction - Gain of electrons

Reduction/Oxidation

Reduction - Gain of electronsOxidation - Loss of electrons

Reduction/Oxidation

Reduction - Gain of electronsOxidation - Loss of electrons

H3CHC=O + NADH + H+<=> H3CH2COH + NAD+

GibbsFreeEnergy

ΔG = ΔH - TΔS

aA + bB <=> cC + dD Keq = {[C]ceq[D]deq]} / {[A]aeq[B]beq}

ΔG = ΔG°’ + RTln {[C]ceq[D]deq]} / {[A]aeq[B]beq}

ΔG°’ = -RTlnKeq

GibbsFreeEnergy

Water&Buffers

Water&Buffers

Uneven Charge Distribution

Water&Buffers

Uneven Charge DistributionDipolar

Water&Buffers

Uneven Charge DistributionDipolarHydrogen Bonds

Water&Buffers

Uneven Charge DistributionDipolarHydrogen Bonds

HydrophilicvsHydrophobic

HydrophilicvsHydrophobic

HydrophilicvsHydrophobic

Amphiphilic

Amphiphilic

Amphiphilic

OtherAmphiphilicSubstances

OtherAmphiphilicSubstances

Membrane Lipids

OtherAmphiphilicSubstances

Membrane Lipids

OtherAmphiphilicSubstances

Membrane Lipids

OtherAmphiphilicSubstances

Membrane LipidsGlycerophospholipids

OtherAmphiphilicSubstances

Membrane LipidsGlycerophospholipidsSphingolipids

OtherAmphiphilicSubstances

Membrane Lipids Glycerophospholipids Sphingolipids

OtherAmphiphilicSubstances

Membrane Lipids Glycerophospholipids Sphingolipids

LipidBilayers

ProteinFolding

ProteinFolding

UNFOLDED

ProteinFolding

UNFOLDED FOLDED

ProteinFolding

Hydrophobic

UNFOLDED FOLDED

ProteinFolding

HydrophobicHydrophilic

UNFOLDED FOLDED

ProteinFolding

HydrophobicHydrophilic

Outside

UNFOLDED FOLDED

ProteinFolding

HydrophobicHydrophilic

Outside Inside

UNFOLDED FOLDED

ProteinFolding

HydrophobicHydrophilic

Outside Inside

UNFOLDED FOLDED

Water’s Chemistry Affects Molecules

HydrogenBondingBetweenWaterMolecules

HydrogenBondingBetweenWaterandOtherMolecules

HydrogenBondingBetweenWaterandOtherMolecules

HydrogenBondingBetweenWaterandOtherMolecules

HydrogenBondingintheCell

BondStrength

BondStrength

IonizationandAcidStrength

AcidMeasurement

AcidMeasurement

pH = -Log[H+]

AcidMeasurement

pH = -Log[H+]

pOH = -Log[OH-]

AcidMeasurement

pH = -Log[H+]

pOH = -Log[OH-]

pKevinAhern = -Log[KevinAhern]

AcidMeasurement

pH = -Log[H+]

pOH = -Log[OH-]

pKevinAhern = -Log[KevinAhern]

pH + pOH = 14

WeakAcidDissociation

WeakAcidDissociation

WeakAcidDissociation

HendersonHasselbalchEquation

HendersonHasselbalchEquation

pH = pKa + log ([HCO3-]/[H2CO3])

HendersonHasselbalchEquation

pH = pKa + log ([HCO3-]/[H2CO3])

pH = pKa + log ([Ac-]/[HAc])

HendersonHasselbalchEquation

pH = pKa + log ([HCO3-]/[H2CO3])

pH = pKa + log ([Ac-]/[HAc])

In General,

HendersonHasselbalchEquation

pH = pKa + log ([HCO3-]/[H2CO3])

pH = pKa + log ([Ac-]/[HAc])

In General,

pH = pKa + Log([Salt]/[Acid])

pKaandAcidStrength

StrongAcids,likeHCl,essentiallyhavenopKavalue

pKaandAcidStrength

StrongAcids,likeHCl,essentiallyhavenopKavalueLowpKa-StrongerWeakAcid

pKaandAcidStrength

StrongAcids,likeHCl,essentiallyhavenopKavalueLowpKa-StrongerWeakAcidHighpKa-WeakerWeakAcid

pKaandAcidStrength

StrongAcids,likeHCl,essentiallyhavenopKavalueLowpKa-StrongerWeakAcidHighpKa-WeakerWeakAcid

FormicAcid(pKa=3.75)vsAceticAcid(pKa=4.76)

pKaandAcidStrength

Buffers

Buffers

Resist Changes in pH

Buffers

Resist Changes in pH

Weak Acid Systems

Buffers

Resist Changes in pH

Weak Acid Systems

Buffering Capacity

Buffers

Resist Changes in pH

Weak Acid Systems

Buffering Capacity

Buffers

Resist Changes in pH

Weak Acid Systems

Buffering Capacity

Rapid pH Change

Rapid pH Change

Buffers

Resist Changes in pH

Weak Acid Systems

Buffering Capacity

Rapid pH Change

Rapid pH Change

Limited pH Change

AcidsWithMultiplepKaValues

AcidsWithMultiplepKaValues

AcidsWithMultiplepKaValues

AcidsWithMultiplepKaValues

AcidsWithMultiplepKaValues

AcidsWithMultiplepKaValues

AcidsWithMultiplepKaValues

AcidsWithMultiplepKaValues

AcidsWithMultiplepKaValues

EstimatingWeakAcidCharge

1.IfpH>pKabyoneormorepHunits-ProtonOFF

EstimatingWeakAcidCharge

1.IfpH>pKabyoneormorepHunits-ProtonOFF2.IfpH<pKabyoneormorepHunits-ProtonON

EstimatingWeakAcidCharge

1.IfpH>pKabyoneormorepHunits-ProtonOFF2.IfpH<pKabyoneormorepHunits-ProtonON

-COOHvs-COO-

EstimatingWeakAcidCharge

1.IfpH>pKabyoneormorepHunits-ProtonOFF2.IfpH<pKabyoneormorepHunits-ProtonON

-COOHvs-COO-

-NH3+vs-NH2

EstimatingWeakAcidCharge

MetabolicMelody

Henderson Hasselbalch(To the tune of "My Country 'Tis of Thee")

Copyright © Kevin Ahern

Henderson HasselbalchYou put my brain in shock

Oh woe is meThe pKa’s can makeMe lie in bed awake

They give me really bad headachesOh hear my plea

Salt - acid RA-ti-os

Help keep the pH frozeBy buf-fer-ING

They show tenacityComplete audacity

If used within capacityTo maintain things

Henderson Hasselbalch(To the tune of "My Country 'Tis of Thee")

Copyright © Kevin Ahern

Henderson HasselbalchYou put my brain in shock

Oh woe is meThe pKa’s can makeMe lie in bed awake

They give me really bad headachesOh hear my plea

Salt - acid RA-ti-os

Help keep the pH frozeBy buf-fer-ING

They show tenacityComplete audacity

If used within capacityTo maintain things

I know when H’s flyA buffer will defy

Them activelyThose protons cannot waltz

When they get bound to saltsWith this the change in pH halts

All praise to thee

Thus now that I’ve addressedThis topic for the testI’ve got know-howThe pH I can sayEquals the pKA

In sum with log of S o’er AI know it now

Henderson Hasselbalch(To the tune of "My Country 'Tis of Thee")

Copyright © Kevin Ahern

MetabolicMelody

The Number Song(to the tune of “Everybody Loves Somebody Sometime”)

Copyright © Kevin Ahern

Avogadro’s number is a huge oneBoltzmann's constant's rather miniscule

Values differing enormouslyAs WE learned in school

Science numbers need to have dimensions

Size is not the most important thingUnits give the yardsticks needed

For under-STAN-ding

BridgeIt’s taught in the ivory towers

By professors it's so ballyhooedValues can have such diff’rent powers

That to know them we must have their magnitudes

The Number Song(to the tune of “Everybody Loves Somebody Sometime”)

Copyright © Kevin Ahern

Avogadro’s number is a huge oneBoltzmann's constant's rather miniscule

Values differing enormouslyAs WE learned in school

Science numbers need to have dimensions

Size is not the most important thingUnits give the yardsticks needed

For under-STAN-ding

BridgeIt’s taught in the ivory towers

By professors it's so ballyhooedValues can have such diff’rent powers

That to know them we must have their magnitudes

One light year’s a really lengthy distanceGrams define the masses high and lowThe ohm can measure the resistance

If current should flow

BridgeOne set of factors you SHOULD know

The roots of seven and of three et alCannot be expressed as a ratio

Oh these numbers all are quite irration-al

Three point one four one five nine two six fiveNo end to Pi’s digits it’s absurd

Endlessly reminding me that I’veBEEN SO OUT-num-bered

The Number Song(to the tune of “Everybody Loves Somebody Sometime”)

Copyright © Kevin Ahern