2. AP Biology Metabolism & Enzymes

3. AP Biology Day 1 - Flow of energy through life  Life is built on chemical reactions  transforming energy from one form to another organic molecules  ATP & organic molecules sun solar energy  ATP & organic molecules

4. AP Biology Reactions in a closed system  Eventually reach equilibrium Figure 8.7 A (a) A closed hydroelectric system. Water flowing downhill turns a turbine that drives a generator providing electricity to a light bulb, but only until the system reaches equilibrium. ∆G < 0 ∆G = 0

5. AP Biology Reactions in an open system  Cells in our body  Experience a constant flow of materials in and out, preventing metabolic pathways from reaching equilibrium Figure 8.7 (c) A multi-step open hydroelectric system. Cellular respiration is analogous to this system: Glucose is broken down in a series of exergonic reactions that power the work of the cell. The product of each reaction becomes the reactant for the next, so no reaction reaches equilibrium. ∆G < 0

6. AP Biology Metabolism A cell is a miniature factory where thousands of reactions occur  Metabolism is the totality of an organism’s chemical reactions  Arises from interactions between molecules  Transforms matter and energy, subject to the laws of thermodynamics

7. AP Biology 1 st Law of Thermodynamics Figure 8.3 First law of thermodynamics: Energy can be transferred or transformed but Neither created nor destroyed. For example, the chemical (potential) energy in food will be converted to the kinetic energy of the cheetah’s movement in (b). (a) Chemical energy

8. AP Biology 2 nd Law of Thermodynamics Figure 8.3 Second law of thermodynamics: Every energy transfer or transformation increases the disorder (entropy) of the universe. For example, disorder is added to the cheetah’s surroundings in the form of heat and the small molecules that are the by-products of metabolism. (b) Heat co 2 H2OH2O +

9. AP Biology Living systems  Increase the entropy of the universe  Use energy to maintain order

10. AP Biology Metabolism  Chemical reactions of life  forming bonds between molecules  dehydration synthesis  synthesis  anabolic reactions  breaking bonds between molecules  hydrolysis  digestion  catabolic reactions

11. AP Biology

12. Examples  dehydration synthesis (synthesis)-anabolic  hydrolysis (digestion) - catabolic enzyme

13. AP Biology ∆G is Gibbs Free Energy Calculation to tell us if a reaction will proceed to the left or to the right…..  The sign of ∆ G tells us in what direction the reaction has to shift to reach equilibrium.  Reactions go towards a NEGATIVE ∆ G  The magnitude of ∆ G tells us how far the reaction is from equilibrium at that moment.

14. AP Biology Chemical reaction. In a cell, a sugar molecule is broken down into simpler molecules.. Diffusion. Molecules in a drop of dye diffuse until they are randomly dispersed. Gravitational motion. Objects move spontaneously from a higher altitude to a lower one. More free energy (higher G) Less stable Greater work capacity Less free energy (lower G) More stable Less work capacity In a spontaneously change The free energy of the system decreases (∆G <0) The system becomes more stable The released free energy can be harnessed to do work (a) (b) (c) Figure 8.5 At maximum stability-The system is at equilibrium

15. AP Biology Endergonic vs. exergonic reactions exergonicendergonic - energy released - digestion - energy invested - synthesis -G-G  G = change in free energy = ability to do work +G+G

16. AP Biology Energy & life  Organisms require energy to live  where does that energy come from?  coupling exergonic reactions (releasing energy) with endergonic reactions (needing energy) ++ energy + + digestion synthesis

17. AP Biology ATP – Adenosine Tri-phosphate  ATP powers cellular work by coupling exergonic reactions to endergonic reactions  A cell does three main kinds of work  Mechanical  Transport  Chemical

18. AP Biology The Structure and Hydrolysis of ATP  Provides energy for cellular functions Figure 8.8 O O O O CH 2 H OH H N HH O N C HC N C C N NH 2 Adenine Ribose Phosphate groups O O O O O O - --- CH

19. AP Biology Energy is released from ATP When the terminal phosphate bond is broken and the negative charge on the PO 4 groups repel Figure 8.9 P Adenosine triphosphate (ATP) H2OH2O + Energy Inorganic phosphate Adenosine diphosphate (ADP) PP PPP i

20. AP Biology ATP hydrolysis can be coupled to other reactions Endergonic reaction: ∆G is positive, reaction is not spontaneous ∆G = +3.4 kcal/mol Glu ∆G = - 7.3 kcal/mol ATP H2OH2O + + NH 3 ADP + NH 2 Glutamic acid Ammonia Glutamine Exergonic reaction: ∆ G is negative, reaction is spontaneous P Coupled reactions: Overall ∆G is negative; together, reactions are spontaneous ∆G = –3.9 kcal/mol Figure 8.10 ATP hydrolysis

21. AP Biology ATP drives endergonic reactions By phosphorylation, transferring a phosphate to other molecules (c) Chemical work: ATP phosphorylates key reactants P Membrane protein Motor protein P i Protein moved (a) Mechanical work: ATP phosphorylates motor proteins ATP (b) Transport work: ATP phosphorylates transport proteins Solute PP i transportedSolute Glu NH 3 NH 2 P i + + Reactants: Glutamic acid and ammonia Product (glutamine) made ADP + P Figure 8.11 Three types of cellular work are powered by the hydrolysis of ATP

22. AP Biology The Regeneration of ATP  Catabolic pathways  Drive the regeneration of ATP from ADP and phosphate ATP synthesis from ADP + P i requires energy ATP ADP + P i Energy for cellular work (endergonic, energy- consuming processes) Energy from catabolism (exergonic, energy yielding processes) ATP hydrolysis to ADP + P i yields energy Figure 8.12

23. AP Biology ∆ G = -7.3 kcal/mol ∆ G = +7.3 kcal/mol

24. AP Biology Day 2 Enzymes and Activation Energy

25. AP Biology What drives reactions?  If reactions are “downhill”, why don’t polymers spontaneously digest into their monomers  because covalent bonds are stable bonds starch

26. AP Biology Activation energy  Breaking down large molecules requires an initial input of energy  activation energy  large biomolecules are stable  must absorb energy to break bonds energy cellulose CO 2 + H 2 O + heat

27. AP Biology Too much activation energy for life  Activation energy  amount of energy needed to destabilize the bonds of a molecule  moves the reaction over an “energy hill” Not a match! That’s too much energy to expose living cells to! glucose

28. AP Biology Catalysts  So what’s a cell got to do to reduce activation energy?  get help! … chemical help… ENZYMES GG

29. AP Biology Reducing Activation energy  Enzymes are Biological Catalysts  reduce the amount of energy to start a reaction reactant product uncatalyzed reaction catalyzed reaction NEW activation energy

30. AP Biology Enzymes  are proteins (& RNA)  facilitate chemical reactions  increase rate of reaction without being consumed  reduce activation energy  don’t change free energy (  G) released or required  required for most biological reactions  highly specific  thousands of different enzymes in cells  control reactions of life

31. AP Biology Naming conventions  Enzymes named for reaction they catalyze  sucrase breaks down sucrose  proteases break down proteins  lipases break down lipids  DNA polymerase builds DNA  adds nucleotides to DNA strand  pepsin breaks down proteins (polypeptides)

32. AP Biology Enzymes vocabulary substrate  reactant which binds to enzyme  enzyme-substrate complex: temporary association product  end result of reaction active site  enzyme’s catalytic site; substrate fits into active site substrate enzyme products active site

33. AP Biology The active site can lower an E A barrier by:  Orienting substrates correctly  Synthesis: brings substrate closer together so they can bond to one another  Straining substrate bonds  Digestion: active site binds substrate and puts stress on bonds that must be broken, making it easier to separate molecules  Providing a favorable microenvironment  Covalently bonding to the substrate

34. AP Biology Properties of enzymes  Reaction specific  each enzyme works with a specific substrate  chemical fit between active site & substrate  H bonds & ionic bonds  Not consumed in reaction  single enzyme molecule can catalyze thousands or more reactions per second  enzymes unaffected by the reaction  Affected by cellular conditions  any condition that affects protein structure  temperature, pH, salinity

35. AP Biology Lock and Key model  Simplistic model of enzyme action  substrate fits into 3-D structure of enzyme’ active site  H bonds between substrate & enzyme  like “key fits into lock” In biology… Size doesn’t matter… Shape matters!

36. AP Biology Induced fit model  More accurate model of enzyme action  3-D structure of enzyme fits substrate  substrate binding cause enzyme to change shape leading to a tighter fit  “conformational change”  bring chemical groups in position to catalyze reaction

37. AP Biology 2007-2008 Factors that Affect Enzymes

38. AP Biology Factors Affecting Enzyme Function  Enzyme concentration  Substrate concentration  Temperature  pH  Salinity  Activators  Inhibitors catalase

39. AP Biology Factors affecting enzyme function  Enzyme concentration  as  enzyme =  reaction rate  more enzymes = more frequently collide with substrate  reaction rate levels off  substrate becomes limiting factor  not all enzyme molecules can find substrate enzyme concentration reaction rate

40. AP Biology Factors affecting enzyme function substrate concentration reaction rate  Substrate concentration  as  substrate =  reaction rate  more substrate = more frequently collide with enzyme  reaction rate levels off  all enzymes have active site engaged  enzyme is saturated  maximum rate of reaction

41. AP Biology Factors affecting enzyme function  Temperature  Optimum T°  greatest number of molecular collisions  human enzymes = 35°- 40°C  body temp = 37°C  Heat: increase beyond optimum T°  increased energy level of molecules disrupts bonds in enzyme & between enzyme & substrate  H, ionic = weak bonds  denaturation = lose 3D shape (3° structure)  Cold: decrease T°  molecules move slower  decrease collisions between enzyme & substrate

42. AP Biology Factors affecting enzyme function  pH  changes in pH  adds or remove H +  disrupts bonds, disrupts 3D shape  disrupts attractions between charged amino acids  affect 2° & 3° structure  denatures protein  optimal pH?  most human enzymes = pH 6-8  depends on localized conditions  pepsin (stomach) = pH 2-3  trypsin (small intestines) = pH 8 72013456891011

43. AP Biology Factors affecting enzyme function  Salt concentration  changes in salinity  adds or removes cations (+) & anions (–)  disrupts bonds, disrupts 3D shape  disrupts attractions between charged amino acids  affect 2° & 3° structure  denatures protein  enzymes intolerant of extreme salinity  Dead Sea is called dead for a reason!

44. AP Biology Compounds which help enzymes  Activators  cofactors  non-protein, small inorganic compounds & ions  Mg, K, Ca, Zn, Fe, Cu  bound within enzyme molecule  coenzymes  non-protein, organic molecules  bind temporarily or permanently to enzyme near active site  many vitamins  NAD (niacin; B3)  FAD (riboflavin; B2)  Coenzyme A Mg in chlorophyll Fe in hemoglobin

45. AP Biology Compounds which regulate enzymes  Inhibitors  molecules that reduce enzyme activity  competitive inhibition  noncompetitive inhibition  irreversible inhibition  feedback inhibition

46. AP Biology Competitive Inhibitor  Inhibitor & substrate “compete” for active site  penicillin blocks enzyme bacteria use to build cell walls  disulfiram (Antabuse) treats chronic alcoholism  blocks enzyme that breaks down alcohol  severe hangover & vomiting 5-10 minutes after drinking  Overcome by increasing substrate concentration  saturate solution with substrate so it out-competes inhibitor for active site on enzyme

47. AP Biology Non-Competitive Inhibitor  Inhibitor binds to site other than active site  allosteric inhibitor binds to allosteric site  causes enzyme to change shape  conformational change  active site is no longer functional binding site  keeps enzyme inactive  some anti-cancer drugs inhibit enzymes involved in DNA synthesis  stop DNA production  stop division of more cancer cells  cyanide poisoning irreversible inhibitor of Cytochrome C, an enzyme in cellular respiration  stops production of ATP

48. AP Biology Irreversible inhibition  Inhibitor permanently binds to enzyme  competitor  permanently binds to active site  allosteric  permanently binds to allosteric site  permanently changes shape of enzyme  nerve gas, sarin, many insecticides (malathion, parathion…)  cholinesterase inhibitors doesn’t breakdown the neurotransmitter, acetylcholine

49. AP Biology Allosteric regulation  Conformational changes by regulatory molecules  inhibitors  keeps enzyme in inactive form  activators  keeps enzyme in active form Conformational changesAllosteric regulation

50. AP Biology Metabolic pathways A  B  C  D  E  F  GA  B  C  D  E  F  G enzyme 1  enzyme 2  enzyme 3  enzyme 4  enzyme 5  enzyme 6   Chemical reactions of life are organized in pathways  divide chemical reaction into many small steps  artifact of evolution   efficiency  intermediate branching points   control = regulation A  B  C  D  E  F  GA  B  C  D  E  F  G

51. AP Biology Efficiency  Organized groups of enzymes  enzymes are embedded in membrane and arranged sequentially  Link endergonic & exergonic reactions

52. AP Biology allosteric inhibitor of enzyme 1 Feedback Inhibition  Regulation & coordination of production  product is used by next step in pathway  final product is inhibitor of earlier step  allosteric inhibitor of earlier enzyme  feedback inhibition  no unnecessary accumulation of product A  B  C  D  E  F  GA  B  C  D  E  F  G enzyme 1  enzyme 2  enzyme 3  enzyme 4  enzyme 5  enzyme 6  X

53. AP Biology Feedback inhibition  Example  synthesis of amino acid, isoleucine from amino acid, threonine  isoleucine becomes the allosteric inhibitor of the first step in the pathway  as product accumulates it collides with enzyme more often than substrate does threonine isoleucin e

54. AP Biology Review Feedback Loops  Learned about feedback loops at the start of school (August)  Negative Feedback Loops  Positive Feedback Loops  The END!

55. AP Biology 7 pH reaction rate 20134568910 pepsintrypsin What’s happening here?! 11121314 pepsin trypsin

56. AP Biology Enzymes and temperature  Different enzymes function in different organisms in different environments 37°C temperature reaction rate 70°C human enzyme hot spring bacteria enzyme (158°F)