Energy, Catalysis, and Biosynthesis

1. Energy, Catalysis, and Biosynthesis The Chemistry & Physics of Life

2. Laws of Thermodynamics • 1st Law • The total amount of energy in any process stays constant OR energy in the universe stays constant • 2nd Law • Although the total energy in the universe doesn’t change, less and less is available for work

3. What is Work? • Moving an object against a force • 4 types • Mechanical – moving against a force • Chemical – creating chemical bonds • Concentration – changing concentration from one area to another • Electrical – changing the separation of charges

4. 1st Law of Thermodynamics • Energy can be converted from one form to another but cannot be created or destroyed

5. Universal Tendency – More Disorder • 2nd Law of Thermodynamics – degree of disorder increases • Movement towards disorder is a spontaneous process • Measure of disorder is entropy, greater disorder = greater entropy

6. Energy can be transformed from one form to another FREE ENERGY (available for work) vs. HEAT (not available for work)

7. Thermodynamics of Cells • Part of the energy that cells use is converted to heat and is released into the area around the cell • While inside the cell becomes more ordered, the heat put into the area around the cell causes more disorder – disorder is greater outside the cell than the order inside the cell

8. CHEMICAL REACTIONS AND ENERGY TRANSFERS ARE CONTROLLED IN LIVING SYSTEMS Enzymes - mediate chemical reactions Energy transfers are done in steps • Example: There are two ways to get from the top of a very tall building to the bottom floor. Keep in mind that a person on the top floor of a building has a lot of potential energy relative to the ground level. • Jump out the window! • Take the stairs and expend the potential energy a little at a time until you get to the bottom floor. • Both methods get you to the bottom floor but one method is destructive, while the other is not. These two situations are analogous to uncontrolled vs. controlled energy transfers. Potential energy transferred gradually so more work is done than heat. • Hydrogen gas + oxygen + activation energy  water and explosion of heat, light and sound! (see http://www.youtube.com/watch?v=iwBYhJ2jHWw) • Hydrogen is broken; electrons and protons released; electron transport system extracts some free energy from electrons in a stepwise manner (redox reactions) + heat; low energy electron combines with oxygen and hydrogen to produce water  process is non-destructive to life & some energy used to do work!

9. Regulation of energy-releasing (cellular respiration) and energy-acquiring chemical reactions in biological systems • Chemically-mediated by enzymes and co-factors • Occur in a step-wise manner 2H2 + O2 2H2O + energy  + +  2H-H + O=O  2H2O + energy

10. Modes of Energy Transformation: Rapid & Uncontrolled • 2H2 + O2 2H2O + energy • Release of energy can be uncontrolled and liberated mostly as heat! On May 6th, 1937 in Lakehurst, New Jersey. The German passenger Zeppelin Airship called the Hindenburg, was attempting a mooring when it exploded.

11. Modes of Energy Transformation: Released in controlled steps or stages • 2H2 + O2 2H2O + energy • Released in steps to salvage free energy and minimize heat production The electrons from the hydrogen bond go through a series of oxidation & reduction reactions. During each step some energy is harvested, while the remainder is released as heat.

12. Chemical Reactions • Occur in the cell under the control of specialized proteins called enzymes • Each one accelerates or catalyzes just one of the many reactions of the cells

13. Enzymes • Metabolic pathways • series of enzyme-controlled reactions leading to formation of a product • each new substrate is the product of the previous reaction • Enzyme names commonly • reflect the substrate • have the suffix – ase • sucrase, lactase, protease, lipase

14. Tyrosinase and Melanin tyrosinase - A copper-containing enzyme of plant and animal tissues that catalyzes the production of melanin and other pigments from tyrosine by oxidation, as in the blackening of a peeled or sliced potato exposed to air. Grey Squirrels: Melanic and Albino Forms

15. Factors that influence enzymatic activity • Coenzymes • organic molecules that act as cofactors • vitamins • Cofactors • make some enzymes active • ions or coenzymes • Factors that alter enzymes • temperature and heat • radiation • electricity • chemicals • changes in pH

16. Factors that influence enzymatic activity • Competitive inhibitor - a substance that binds to the active site of the enzyme and compete with the substrate for this place. • Non-competitive or allosteric inhibitor - a substance that binds to another part of the enzyme and cause an allosteric change in the overall shape of the enzyme; this changes the form of the active site so the substrate can't bind to it. • Allosteric Activators - essentially this is the reverse of an allosteric inhibitor.

17. Temperature Sensitive Tyrosinase – Siamese Cats & Himalayan Rabbits

18. Cells Chemical Pathways All Interconnect

19. PHOTOSYNTHESIS & CHEMOSYNTHESIS • Almost all plants are photosynthetic autotrophs, as are some bacteria and protists • Autotrophs generate their own organic matter through photosynthesis or chemosynthesis • Sunlight energy is transformed into the energy stored in the form of chemical bonds • Chemical energy is transformed into the energy stored in the form of chemical bonds (c) Euglena (d) Cyanobacteria (b) Kelp (a) Mosses, ferns, and flowering plants

20. Bacteria in Thermal Vents on the Sea Floor Tubeworms and other animals living around thermal vents in the ocean depend on chemosynthetic bacteria for food.

21. THE SUN: MAIN SOURCE OF ENERGY FOR LIFE ON EARTH

22. Light Energy Harvested by Plants & Other Photosynthetic Autotrophs 6 CO2 + 6 H2O + light energy → C6H12O6 + 6 O2

23. Sunlight – Ultimate Energy Source • All organisms live on the organic molecules that are made by photosynthetic organisms • Photosynthesis traps the energy of the sun in the chemical bonds of sugars which can be turned into nucleotides, amino acids and fatty acids • 2 steps • Energy stored in ATP and NADPH, release O2 • ATP and NADPH drive carbon fixation  H2O and CO2 from air and make sugars

24. Food Chain

25. THE FOOD WEB

26. Metabolism • 2 opposing pathways make up metabolism • Catabolism – process of obtaining energy and building blocks from ‘food’ molecules • Anabolism – process of using energy and building blocks to create the macromolecules that make up the cell

27. Energy Releasing Metabolic Reactions • Energy • ability to do work or change something • heat, light, sound, electricity, mechanical energy, chemical energy • changed from one form to another • involved in all metabolic reactions • Release of chemical energy • most metabolic processes depend on chemical energy • oxidation of glucose generates chemical energy • cellular respiration releases chemical energy from molecules and makes it available for cellular use

28. Oxidation of Organic Molecules • Oxidation can be the process of adding O atoms • Cells can obtain energy from sugars by allowing the C and H to combine with O2 to produce H2O and CO2 in a process called respiration • Photosynthesis and respiration work together

29. Oxidation and Reduction • Oxidation can also be the process of electron transfer from one atom to another • Oxidation is the removal of electrons • Reduction is the addition of the electrons • Oxidation and reduction always occur simultaneously • These reactions also occur in molecules with a partial shift of electrons as in polar bonds • Also with the addition of a H+ (hydrogenation reaction) or the removal of a H+ (dehydrogenation reaction)

30. Reducing agent (electron donor) Oxidizing agent (electron acceptor) e- A B e- A is oxidized –loses electron B is reduced –gains electron e- e- B A Oxidized Reduced Reducing and Oxidizing Agents

31. LEO the lion goes GER ose lectrons xidized ain lectrons educed Tip to Help Remember

32. Free Energy

33. Free Energy (G) • Energy that can be harvested to do work or drive a chemical reaction (remember the 4 types of work) • Exergonic reactions – go from higher to lower energy level and are spontaneous • Endergonic reactions – go from lower to higher energy levels and require an input of energy

34. Reactions

35. Barriers to Chemical Reactions • Chemical reactions only proceed in the direction of the loss of free energy • Molecules in stable states need to have an input of energy to cause them to go to a lower energy state – activation energy, always positive

36. Activation Energy

37. Activation Energy • In chemistry, molecules that decrease activation energy are catalyst such as platinum and zinc • In cells the activation energy is reduced by a special protein - enzyme • Enzymes link 1 or 2 molecules called substrates and hold them in a way that greatly decreases the activation energy – transition state

38. Transition States

39. Energy Graph

40. Enzymes as Catalysts • Speed up reaction rates (x ~1014) • Selective – usually 1 enzyme for 1 reaction • Have a unique shape that contains the active site and only a particular substrate can fit • site where reaction takes place • Remain unchanged and can be used over and over

41. Reactions • For reactions to occur, the enzyme and the substrate(s) need to be in contact with one another • Heat from other reactions keep the substrate moving through the cell by diffusion, can cover great distances • Enzyme is large and relatively motionless • This arrangement allows for the substrate to finally collide with the active site, held there by multiple weak interactions until they dissociate • If too strong, then would not dissociate • If wrong substrate gets into the active site, no interactions will hold it there and it will leave quickly

42. Enzymatic Reactions are Coupled • Even though enzymes are good catalysts, they are unable to perform reactions that are thermodynamically unfavorable • Enzyme reactions are coupled to harvest the energy and heat from a favorable reaction to drive an unfavorable reaction

43. Coupled Reactions

44. G – Change in Free Energy • Value of G is only important when the system undergoes a change • G is the measure of the amount of disorder when a reaction takes place • -G occur spontaneously • +G are unfavorable • Need to link a -G reaction with a +G so that the overall G is negative

45. Coupled Reactions

46. Concentration of Reactants • The amount of reactants in the reaction mix is important for the G • In a reversible reaction, i.e., can go from A to B and from B to A, when there is more A present, the tendency will be to go from A to B rather than B to A • G° or standard free-energy change – depends on intrinsic characters of the reacting molecules • Equilibrium – forward and reverse reactions proceed at exactly equals rates so that no net chemical change occurs

47. Equilibrium • Equilibrium constant (K) – number that characterizes the equilibrium state for a reversible chemical reaction; given by the ratio of the forward and reverse rate constants of the reaction

48. Enzymes and K • Enzymes will lower the activation energy in the A to B direction to the same degree as in the B to A direction • The equilibrium constant and G° remain unchanged

49. Sequential Reactions • Most of the G° values are known for the reactions of the cells and so we can determine overall G for a pathway – add up the G for each step

50. Activated Carriers • Energy released by catabolism is stored in the chemical bonds of carrier molecules • The energy can be moved around the cell to where it is needed • Carrier molecules in the cell are ATP, NADH and NADPH