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Water and other inorganic molecules

Water and other inorganic molecules. Chapter 2 pages 21 - 29. Water. Most important molecule in all living tissues Solvent for many organic and inorganic molecules Polar properties of water confer “self-assembly” to insoluble molecules Important for 3D structure of lipids and proteins

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Water and other inorganic molecules

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  1. Water and other inorganic molecules Chapter 2 pages 21 - 29

  2. Water • Most important molecule in all living tissues • Solvent for many organic and inorganic molecules • Polar properties of water confer “self-assembly” to insoluble molecules • Important for 3D structure of lipids and proteins • Dissociative properties of water leads to acid-base chemistry • Add charges to previously uncharged molecules

  3. Hydrophobic vs. hydrophilic Panel 2-2 from Molecular Biology of the Cell (4th ed.) by Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter

  4. Hydrophobic vs. hydrophilic • Polar/ionic compounds soluble in water are called hydrophilic (“water loving”) • Large non-polar compounds insoluble in water are called hydrophobic (“water fearing”) • Lipids and proteins can have polar and non-polar regions that determine orientation or arrangement of these compounds in water • Large molecules with polar and non-polar regions are called amphipathic

  5. Acid-base chemistry Panel 2-2 from Molecular Biology of the Cell (4th ed.) by Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter

  6. Acid-base chemistry • [H+] is measured as pH = -log10 [H+] or [H+] = 10-pH • pH = 2 means [H+] = 10-2 M • pH = 9.4 means [H+] = 10-9.4 M = 4 x 10-10 M • pH 7.2 – 7.4 is normal range for extracellular fluids • pH 7.0 – 7.2 is normal range for intracellular fluids • Dissociation of other compounds can alter this equilibrium • Add protons to solvated molecules • Remove protons from solvated molecules

  7. Solvation, also sometimes called dissolution, is the process of attraction and association of molecules of a solvent with molecules or ions  of a solute. As ions dissolve in a solvent they spread out and become surrounded by solvent molecules. Solvation

  8. Acid-base chemistry • Acids tend to add or donate protons to water • Decreases pH • pH < 7.0 is called acidic • Bases tend to remove or accept protons from water • Increases pH • pH > 7.0 is called basic • Acids and bases have equilibrium: acid ↔ base + H+ • Addition or removal of H+ ions can alter this equilibrium • Low pH: bases readily accept protons and are converted into acids • Low pH: solvated molecules increase in positive charge • High pH: acids readily donate protons and are converted into bases • High pH: solvated molecules increase in negative charge

  9. Acid-base equilibrium • pH where acid-base pair has 50-50 equilibrium is called pKa • Define association constant Ka for reaction HA ↔ H+ + A- • From chemistry Ka = [H+] [A-] / [HA] • Define pKa same as pH, pKa = -log10 (Ka) • Solve for concentration of reactants when pH = pKa • pKa = -log10 ([H+] [A-] / [HA]) • pKa = -log10 [H+] - log10 [A-] + log10 [HA] • pKa = pH - log10 [A-] + log10 [HA] • When pH = pKa, then log10 [A-] = log10 [HA] or [A-] = [HA] • Therefore concentration of acid HA equals concentration of base A- when pH = pKa

  10. Given HA ↔ H+ + A- where pKa of HA is 10.7, solution pH is 10.7, what is [HA] relative to [A-] at equilibrium? • [HA] < [A-] • [HA] = [A-] • [HA] > [A-]

  11. pH/pKa problems • Definition of pKa means acid concentration [HA] equals base concentration [A-] when pH = pKa • How can we calculate relative amount of acids and bases when pH ≠ pKa? • Ex: consider HA ↔ H+ + A- where pKa of HA is 4.5, solution pH = 8.3 • Is there more HA or A- in this solution? • Ex: consider HA ↔ H+ + A- where pKa of HA is 4.5, solution pH = 2.3 • Is there more HA or A- in this solution?

  12. pH/pKa problems • Start at pH = pKa with a 50-50 equilibrium of acid/base • Consider whether solution pH produces excess or lack of H+ relative to compound pKa • Ex: pKa = 4.5, pH = 8.3, lack of H+ relative to pKa since pH > pKa • Ex: pKa = 4.5, pH = 2.3, excess of H+ relative to pKa since pH < pKa • Determine how direction of equilibrium of HA ↔ H+ + A- shifts due to excess or lack of H+ • Excess protons shift equilibrium toward HA or acid formation • Lack of protons shifts equilibrium toward A- or base formation • Can verify results using charge of dominant species • Excess protons make solvated species more positive • Lack of protons makes solvated species more negative • Can also verify using pKa = pH - log10 [A-] + log10 [HA]

  13. pH/pKa problems • Ex: HA ↔ H+ + A- where pKa of HA is 4.5, solution pH = 8.3 • Start at pH = pKa = 4.5, 50-50 split between acid HA and base A- • Raising solution pH from 4.5 to 8.3 produces lack of protons • Then the base A- is the dominant species at equilibrium • Verify with charge: dominant species A- is more negative than HA • Also 4.5 = 8.3 - log10 [A-] + log10 [HA], therefore log10 [A-] > log10 [HA] • Ex: HA ↔ H+ + A- where pKa of HA is 4.5, solution pH = 2.3 • Start at pH = pKa = 4.5, 50-50 split between acid HA and base A- • Lowering solution pH from 4.5 to 2.3 produces excess of protons • Then the acid HA is the dominant species at equilibrium • Verify with charge: dominant species HA is more positive than A- • Also 4.5 = 2.3 - log10 [A-] + log10 [HA ], therefore log10 [HA] > log10 [A-]

  14. Given HA ↔ H+ + A- where pKa of HA is 10.7, solution pH is 7.3, what is [HA] relative to [A-] at equilibrium? • [HA] < [A-] • [HA] = [A-] • [HA] > [A-]

  15. Physiologic pH and protonation • Extracellular pH is tightly regulated between pH 7.2 – 7.4 • Adding acidic and basic compounds will not change pH significantly • Pulmonary and renal reflexes to maintain pH will be discussed later in the semester • More convenient to look at whether acidic or basic compounds will accept or donate protons at physiologic pH • Tells us whether a compound will carry extra positive charge • Diagram below shows relative % of compound in protonated (+) form based on magnitude of compound pKa relative to physiologic pH • Forms a continuum of compounds that are 0% → 100% protonated (+) as the pKa of the compound increases from below 7.3 to above 7.3

  16. pKa of organic compounds • Various organic molecules have acidic or basic regions • Acidic carboxyl group: R-COOH ↔ R-COO- + H+ • pKa typically < 4, varies with composition of side group R • Produces lack of protons going from pKa = 4 to pH = 7.2 • Vast majority are negative R-COO- at physiologic pH 7.2 – 7.4 • Basic amine group: R-NH3+ ↔ R-NH2 + H+ • pKa typically > 10, varies with composition of side group R • Produces excess of protons going from pKa = 10 to pH = 7.2 • Vast majority are positive R-NH3+ at physiologic pH 7.2 – 7.4 • Charged acidic or basic regions very important for protein structure

  17. pKa of H2O • H2O can serve as both acid and base • Amphoteric compounds can serve as both acids and bases • Water as a base: H2O + H+ ↔ H3O+ • pKa << 7, this is pH where [H2O] = [H3O+] • Remember [H2O] >> [H3O+] at pH 7 • Requires excess of H+ to protonate H2O so that [H2O] = [H3O+] • Water as an acid: H2O ↔ H+ + OH- • pKa >> 7, this is pH where [H2O] = [OH-] • Remember [H2O] >> [OH-] at pH 7 • Requires lack of H+ to remove H+ from H2O so that [H2O] = [OH-]

  18. pKa of H2O • Why isn’t the pKa of H2O equal to 7? • Adding other species to solution brings solution pH toward species pKa • The pH of pure H2O is 7 • Remember H2O can simultaneously accept and donate protons • Simultaneously moves water pH in two directions • Toward H2O + H+ ↔ H3O+ pKa << 7 • Toward H2O ↔ H+ + OH- pKa >> 7

  19. Charged acids and bases • Acids and bases can be neutral or charged • Started using example HA ↔ H+ + A- • Has neutral acid HA, negative base A- • Reaction could also be HA+ ↔ H+ + A • Has positive acid HA+, neutral base A • Acids can be neutral or (+) but not (-) • Difficult to pull H+ from (-) compound • Bases can be neutral or (-) but not (+) • Difficult to add H+ to (+) compound • Important to identify charges on acid/base pairs

  20. Which compound is most likely to act as a base? • HPO42- • NH4+ • H2S

  21. Strength of acids and bases • Strength of acids and bases determined by propensity to donate/accept protons • Strong acids can donate protons in acidic environment • Have pKa << 7 and donate all protons at neutral pH • Water is a weak acid: H2O ↔ H+ + OH- has pKa >> 7 • Strong bases can accept protons in basic environment • Have pKa >> 7 and are protonated at neutral pH • Water is a weak base: H2O + H+ ↔ H3O+ has pKa << 7

  22. Which value is closest to the pKa of HCl? • 1.5 • 6.3 • 9.5 • 13.8

  23. Other inorganic molecules • Mostly soluble metallic ions • Cations and anions, monovalent and divalent • Common ones are H+, Na+, K+, Ca2+, Mg2+ and Cl- • Trace metals such as Fe3+ and Zn2+ also play important roles in physiological function • Molecular ions ammonium NH4+, bicarbonate HCO3-, and phosphate PO43- • Covalent bonds in HCO3- and PO43- have resonance structures that promote stability

  24. Phosphorylation Panel 2-1 from Molecular Biology of the Cell (4th ed.) by Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter

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