Metabolism & Enzymes

1. Metabolism & Enzymes

2. 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 organic moleculesATP & organic molecules solar energyATP& organic molecules

3. ∆G < 0 ∆G = 0 (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. Figure 8.7 A Reactions in a closed system • Eventually reach equilibrium

4. ∆G < 0 ∆G < 0 ∆G < 0 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. Reactions in an open system • Cells in our body • Experience a constant flow of materials in and out, preventing metabolic pathways from reaching equilibrium

5. 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

6. Chemical energy (a) 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). Figure 8.3  1st Law of Thermodynamics

7. Heat co2 + H2O 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) Figure 8.3  2nd Law of Thermodynamics

8. Living systems • Increase the entropy of the universe • Use energy to maintain order

9. Metabolism • Chemical reactions of life • forming bonds between molecules • dehydration synthesis • synthesis • anabolic reactions • breaking bonds between molecules • hydrolysis • digestion • catabolic reactions

11. enzyme enzyme Examples • dehydration synthesis (synthesis)-anabolic • hydrolysis (digestion) - catabolic

12. ∆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.

13. More free energy (higher G) • Less stable • Greater 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 . • Less free energy (lower G) • More stable • Less work capacity Gravitational motion. Objects move spontaneously from a higher altitude to a lower one. Chemical reaction. In a cell, a sugar molecule is broken down into simpler molecules. (a) (c) (b) Diffusion. Molecules in a drop of dye diffuse until they are randomly dispersed. Figure 8.5  At maximum stability-The system is at equilibrium

14. Endergonic vs. exergonic reactions exergonic endergonic - energy released - digestion • energy invested • synthesis +G -G G = change in free energy = ability to do work

15. Energy & life • Organisms require energy to live • where does that energy come from? • couplingexergonic reactions (releasing energy) with endergonic reactions (needing energy) energy + + digestion synthesis energy + +

16. 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

17. Adenine NH2 C N C N HC O O O CH C N - N O O O O CH2 O - - - O O O H H Phosphate groups H H Ribose Figure 8.8 OH OH The Structure and Hydrolysis of ATP • Provides energy for cellular functions

18. P P P Adenosine triphosphate (ATP) H2O Energy + P i P P Adenosine diphosphate (ADP) Inorganic phosphate Figure 8.9 Energy is released from ATPWhen the terminal phosphate bond is brokenand the negative charge on the PO4 groups repel

19. Endergonic reaction: ∆G is positive, reaction is not spontaneous NH2 NH3 + ∆G = +3.4 kcal/mol Glu Glu Glutamine Glutamic acid Ammonia Exergonic reaction: ∆ G is negative, reaction is spontaneous ∆G = - 7.3 kcal/mol + P ADP H2O ATP + Coupled reactions: Overall ∆G is negative; together, reactions are spontaneous ∆G = –3.9 kcal/mol Figure 8.10 ATP hydrolysiscan be coupled to other reactions ATP hydrolysis

20. P i P Motor protein Protein moved (a) Mechanical work: ATP phosphorylates motor proteins Membrane protein ADP ATP + P i P P i Solute Solute transported (b) Transport work: ATP phosphorylates transport proteins P NH2 + + NH3 P i Glu Glu Reactants: Glutamic acid and ammonia Product (glutamine) made Figure 8.11 (c) Chemical work: ATP phosphorylates key reactants ATP drives endergonic reactionsBy phosphorylation, transferring a phosphate to other molecules Three types of cellular work are powered by the hydrolysis of ATP

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

22. ∆ G = +7.3 kcal/mol ∆ G = -7.3 kcal/mol

23. Day 2 Enzymes and Activation Energy

24. What drives reactions? • If reactions are “downhill”, why don’t polymers spontaneously digest into their monomers • because covalent bonds are stable bonds starch

25. energy Activation energy • Breaking down large molecules requires an initial input of energy • activation energy • large biomolecules are stable • must absorb energy to break bonds cellulose CO2 + H2O + heat

26. 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 exposeliving cells to! glucose

27. Catalysts • So what’s a cell got to do to reduce activation energy? • get help! … chemical help… ENZYMES G

28. Reducing Activation energy • Enzymes are Biological Catalysts • reduce the amount of energy to start a reaction uncatalyzed reaction catalyzed reaction NEW activation energy reactant product

29. 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 reactionsof life

30. 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)

31. 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 active site products substrate enzyme

32. The active site can lower an EA 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

33. 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

34. 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!

35. 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

36. Factors that Affect Enzymes

37. Factors Affecting Enzyme Function • Enzyme concentration • Substrate concentration • Temperature • pH • Salinity • Activators • Inhibitors catalase

38. reaction rate enzyme concentration 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

39. reaction rate substrate concentration Factors affecting enzyme function • 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

40. 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

41. 0 1 2 3 4 5 6 7 8 9 10 11 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

42. 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!

43. Compounds which help enzymes Fe inhemoglobin • 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 toenzyme near active site • many vitamins • NAD (niacin; B3) • FAD (riboflavin; B2) • Coenzyme A Mg inchlorophyll

44. Compounds which regulate enzymes • Inhibitors • molecules that reduce enzyme activity • competitive inhibition • noncompetitive inhibition • irreversible inhibition • feedback inhibition

45. Competitive Inhibitor • Inhibitor & substrate “compete” for active site • penicillinblocks enzyme bacteria use to build cell walls • disulfiram (Antabuse)treats chronic alcoholism • blocks enzyme that breaks down alcohol • severe hangover & vomiting5-10 minutes after drinking • Overcome by increasing substrate concentration • saturate solution with substrate so it out-competes inhibitor for active site on enzyme

46. Non-Competitive Inhibitor • Inhibitor binds to site other than active site • allosteric inhibitorbinds toallosteric site • causes enzyme to change shape • conformational change • active site is no longer functional binding site • keeps enzyme inactive • some anti-cancer drugsinhibit enzymes involved in DNA synthesis • stop DNA production • stop division of more cancer cells • cyanide poisoningirreversible inhibitor of Cytochrome C, an enzyme in cellular respiration • stops production of ATP

47. 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

48. Allosteric regulation • Conformational changes by regulatory molecules • inhibitors • keeps enzyme in inactive form • activators • keeps enzyme in active form Conformational changes Allosteric regulation

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

50. Efficiency • Organized groups of enzymes • enzymes are embedded in membrane and arranged sequentially • Link endergonic & exergonic reactions