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Introtoacidbase
Introtoacidbase
Introtoacidbase
Introtoacidbase
Introtoacidbase
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Introtoacidbase

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  • 1. Biochemistry Study of chemistry in biological organisms Understand how the chemical structure of a molecule is determining its function www.freelivedoctor.com
  • 2. Focus on important biochemical macromolecules
      • amino acids ----->proteins
      • fatty acids----->lipids
      • nucleotides---> nucleic acids
      • monosaccharides---> carbohydrates
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  • 3. Focus on important processes
      • Protein Function
      • Compartmentalization/regulation
      • Metabolism-
      • DNA synthesis/replication
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  • 4. Protein Function
      • What is a protein’s structure and what role does it play in the body?
      • What are some important proteins in the body?
      • What are some key principles behind protein’s functions?
    www.freelivedoctor.com
  • 5. Enzymes
    • What are enzymes?
    • What is the role of enzymes in an organism?
    • How do they work?
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  • 6. Lipids
    • What are lipids and their structures
    • What are roles of lipids
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  • 7. Membranes and Transport
    • What is the structure of a membrane?
    • What is compartmentalization and why is it important?
    • How can molecules and information get across a membrane?
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  • 8. Carbohydrates
    • What the structures of carbohydrates and what is their role?
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  • 9. Metabolism
    • Glycolysis, Krebs cycle, Oxidative Phosphorylation, beta oxidation
        • How does a cell convert glucose to energy?
        • How does a cell convert fat to energy?
    • Roles of ATP, NAD and FAD
    • vitamins
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  • 10. Nucleic Acids
    • What are their structures?
    • What their functions?
    • How do they replicate?
    • What is the relationship between nucleic acids and proteins?
    www.freelivedoctor.com
  • 11. Connecting structure and function requires chemistry
    • Chemistry knowledge needed:
      • Intermolecular forces
      • Properties of water
      • Equilibrium
      • Acid/Base Theory
        • Definitions
        • Buffers
        • Relation of structure to pH
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  • 12. Connecting structure and function requires chemistry
      • Oxidation-Reductions
      • Thermodynamics: study of energy flow
      • Organic functional groups
      • Important organic reactions
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  • 13. Intermolecular forces
    • Hydrogen bonds
    • Dipole/dipole interactions
    • Nonpolar forces
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  • 14. Dipole/Dipole interactions
    • Polarity in molecules
      • Polar bonds
      • Asymmetry
    • Positive side of one polar molecule sticks to negative side of another
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  • 15. Dipole-Dipole interactions www.freelivedoctor.com
  • 16. Hydrogen Bonding
    • Special case of dipole dipole interaction
      • Hydrogen covalently attached to O, N, F, or Cl sticks to an unshared pair of electrons on another molecule
        • H-bond donors
          • Have the hydrogen
        • H-bond acceptors
          • Have the unshared pair
        • Strongest of intermolecular forces
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  • 17. Hydrogen bonding www.freelivedoctor.com
  • 18. Hydrogen bonding
    • Affect the properties of water
    • Water has a higher boiling point than expected
    • Water will dissolve only substances that can interact with its partially negative and partially positive ends
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  • 19. Nonpolar forces
    • Nonpolar molecules stick together weakly
    • Use London dispersion forces
    • Examples are carbon based molecules like hydrocarbons
    • Velcro effect
      • Many weak interactions can work together to be strong
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  • 20. Dissolving process
    • Solute—solute + solvent—solvent -  2 solute---solvent
    • Have to break solute—solute interactions as well as solvent—solvent interactions
    • Replace with solute-solvent interactions
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  • 21. Like dissolves like
    • Hydrophobic = nonpolar
    • Hydrophilic = polar
    • Overall, like dissolves like means that polar molecules dissolve in polar solvents and nonpolar solutes dissolve in nonpolar solvents
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  • 22. Like dissolves like
    • Salt dissolving in water
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  • 23. Amphipathicity
    • Some molecules have both a hydrophilic and hydrophobic part
    • soap is an example
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  • 24. Amphipathicity www.freelivedoctor.com
  • 25. Equilibrium
    • Two opposing processes occurring at the same rate:
    • walking up the down escalator
    • treadmill
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  • 26. Equilibrium
    • For chemical equilibrium, It is when two opposing reactions occur at the same rate.
    • mA + nB <=  pC + q D
      • Two reactions:
        • Forward: mA + nB -  pC + qD
        • Reverse: pC + qD -  mA + nB
      • Equilibrium when rates are equal
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  • 27. Reaction Rates
      • Rate of reaction depends on concentration of reactants
      • For the reaction: mA + nB  => pC + qD
      • Forward rate (R f ) = k f [A] m [B] n
      • Reverse rate (R r ) = k r [C] p [D] q
      • (rate constants k f and k r as well as superscripts have to be determined experimentally)
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  • 28. Equilibrium
    • When rates are equal:
      • R f = R r so (from previous slide)
        • k f [A] m [B] n = k r [C] p [D] q
      • Putting constants together: (Law of Mass Action)
        • k f = [C] p [D] q = K eq
        • k r [A] m [B] n
        • K eq is the equilibrium constant
        • Solids and liquids don’t appear…they have constant concentration
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  • 29. Equilibrium in quantitative terms
    • The equilibrium state is quantified in terms of a constant called the Equilibrium Constant K eq. It is the ratio of products/reactants
    • It is determined by Law of Mass Action
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  • 30. Possible Situations at Equilibrium
    • 1. There are equal amounts of products and reactants. K=1 or close to it
    • 2. There are more products than reactants due to strong forward reaction
      • equilibrium lies right)
      • K >>1
    • 3. There are more reactants than products due to strong reverse reaction
      • equlibrium lies left
      • K <<1
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  • 31. K eq Constant Expression
    • Given the following reactions, write out the equilibrium expression for the reaction
    • CaCO 3 (s) + 2HCl(aq) ---> CaCl 2 (aq) + H 2 O(l) + CO 2 (g)
    • 2SO 2 (g) + O 2 (g) --->2SO 3 (g)
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  • 32. Answers
    • [CaCl 2 ][CO 2 ]
    • [HCl] 2
    • [SO 3 ] 2
    • SO 2 ] 2 [O 2 ]
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  • 33. Le Chatelier’s Principle
    • When a system at equilibrium is stressed out of equilibrium, it shifts away from the stress to reestablish equilibrium.
      • Shifts away from what is added
      • Shifts towards what is removed
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  • 34. Le Chatelier’s Examples
    • N 2 + 3 H 2  => 2 NH 3
      • If we add nitrogen or hydrogen, it shifts to the right, making more ammonia
      • Removal of ammonia accomplishes the same thing
      • Shifts to the left if add ammonia
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  • 35. Le Chatelier’ and Regulation of Metabolism
    • What the diet industry doesn’t want you to know!
      • Food -  A  B  C  D  energy
        • A  fat
      • What happens if energy is used up?
      • What happens if eat a big meal and don’t use energy
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  • 36. Acid/Base Theory
    • Definitions
      • Acid is a proton (H + ) donor
        • Produces H 3 O + in water
        • HCl + H 2 O -  H 3 O + + Cl -
      • Base is a proton (H + ) acceptor
        • Produces OH - in water
        • NH 3 + H 2 O  > NH 4 + + OH -
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  • 37. Strong acids v weak acids
      • Strong 100 percent ionized
        • No Equilibrium or equilibrium lies to the right
        • K eq >>> 1 and is too large to measure
      • Weak acids not completely ionized
        • Equilibrium reactions
        • Have K eq
          • For acids, K eq called a K a
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  • 38. Acetic Acid as Example of a Weak Acid
    • HC 2 H 3 O 2 (aq) <---> H + (aq) + C 2 H 3 O 2 - (aq)
    • K = [H + ] [C 2 H 3 O 2 - ]
    • [HC 2 H 3 O 2 ]
    • value is 1.8 x 10 -5
    • 1.8 x 10 -5 <<< 1
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  • 39. Weak acids, K a and pK a
      • pK a = - log K a
      • For weak acids, weaker will be less dissociated
        • Make less H 3 O +
        • Eq lies further to left
        • Lower K a
      • Since pKa and Ka inversely related: the lower the K a , the higher the pK a, the weaker the acid
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  • 40. pH
    • pH= -log [H + ]
    • increasing the amount of H + (in an acidic solution), decreases the pH
    • increasing the amount of OH - decreases the amount of H + (in a basic solution), therefore, the pH increases
    • pH< 7 acidic
    • pH>7 basic
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  • 41. Conjugate Base Pairs
    • Whatever is produced when the acid (HA) donates a proton (H + ) is called its conjugate base (A - ).
    • Whatever is produced when the base (B) accepts a proton is called a conjugate acid (HB + ).
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  • 42. Conjugate Base Pairs
    • HA( aq )+ H 2 O( l )  H 3 O + ( aq )+ A – ( aq )
    • Acid Base conjugate acid conjugate base
    • differ by one H + for acids/bases
    • Example: HC 2 H 3 O 2 and C 2 H 3 O 2 -
    • acid conj. base
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  • 43. Buffers
    • A buffer is a solution that resists a change in pH upon addition of small amounts of acid or base.
    • It is a mixture of a weak acid/weak base conjugate pair
      • Ex: HA/ A -
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  • 44. Buffer with added acid
    • Weak base component of the buffer neutralizes added acid
    • A - + H + --  HA
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  • 45. Buffers with added base
    • Weak acid component of the buffer neutralizes added base
    • Equation: OH - + HA --> H 2 O + A -
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  • 46. Relationship of pH to structure
    • We can think of a weak acid, HA, as existing in two forms.
      • Protonated = HA
      • Deprotonated = A -
    • Protonated is the acid
    • Deprotonated is the conjugate base
      • Titrated form
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  • 47. Henderson-Hasselbach Equation
    • pH = pK a + log ([A - ] / [HA])
    • Can be used quantitatively to make buffers
    • K a is the equilibrium constant for the acid
      • HA (aq) + H 2 O (l) <  H 3 O + (aq) + A - (aq)
      • K a = [H 3 O + ][A - ]
          • [HA]
      • Higher K a = more acidic acid
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  • 48. Henderson Hasselbach continued
    • pH = pK a + log ([A - ] / [HA])
    • pK a = -logK a
    • Since negative, lower pK a = more acidic
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  • 49. Henderson Hasselbach and structure
    • In a titration if we add base to the acid:
    • HA + OH - -  H 2 O + A -
    • For every mole of HA titrated, we form a mole of A -
    • So, if we add enough OH - to use up half the HA (it is half-titrated) we end up with equimolar HA and A -
    • Looking at the equation:
    • pH = pK a + log ([A - ] / [HA])
    • If [A - ] = [HA] then [A - ] / [HA] = 1 and log ([A - ] / [HA]) = log (1) – 0
    • So pH = pK a
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  • 50. So what?
    • We can now relate the pH of the solution to the structure of weak acid using Henderson-Hasselbach
    • pH = pK a + log ([A - ] / [HA])
    • If pH = pK a, we have equal amounts of protonated and deprotonated forms
    • If, pH < pK a , means log term is negative so [HA]>[A - ] and protonated form dominates
    • If pH > pK a , means log term is postive so [HA] < [A - and deprotonated form dominates.
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