Published on

  • Be the first to comment

  • Be the first to like this

No Downloads
Total Views
On Slideshare
From Embeds
Number of Embeds
Embeds 0
No embeds

No notes for slide


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

    Clipping is a handy way to collect important slides you want to go back to later.