02 Chemistry, Water and Buffers - Oregon State...
Transcript of 02 Chemistry, Water and Buffers - Oregon State...
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