Ground Rules of Metabolism

1. Ground Rules of Metabolism Chapter 6 Hsueh-Fen Juan Oct. 2, 2012

2. Impacts, Issues:A Toast to Alcohol Dehydrogenase • In the liver, alcohol dehydrogenase helps break down toxic alcohols, but at the expense of liver function and energy metabolism

3. Video: Alcohol, enzymes, and your liver

4. 6.1 Energy and the World of Life • Assembly of the molecules of life starts with energy input into living cells

5. Energy Disperses • First law of thermodynamics • Energy is neither created nor destroyed, but can be transferred from one form to another • Second law of thermodynamics • Entropy (a measure of dispersal of energy in a system) increases spontaneously • The entropy of two atoms decreases when a bond forms between them (endergonic reaction) • 熵要仔細看課本

6. Motion: A Form Of Energy

7. Entropy

8. One Way Flow of Energy • The total amount of energy available in the universe to do work, called free energy, is always decreasing • Each time energy is transferred, some energy escapes as heat (not useful for doing work) • Free energy 和總能量以熵及相關 • On Earth, energy flows from the sun, through producers, then consumers • Living things need a constant input of energy

9. Energy Conversion • Only about 10% of the energy in food goes toward building body mass, most is lost in energy conversions

10. Energy Flow ENERGY IN energy input, mainly from sunlight Sunlight energy reaches environments on Earth. Producers of nearly all ecosystems secure some and convert it to stored forms of energy. They and all other organisms convert stored energy to forms that can drive cellular work. PRODUCERS plants and other self-feeding organisms nutrient cycling ENERGY OUT CONSUMERS animals, most fungi, many protists, bacteria With each conversion, there is a one-way flow of a bit of energy back to the environment. Nutrients cycle between producers and consumers. energy output, mainly heat Fig. 6-5, p. 95

11. 6.2 Energy in the Molecules of Life • All cells store and retrieve energy in chemical bonds of the molecules of life • Free energy • The amount of energy in a molecule that is available to do work

12. Energy In, Energy Out • Reaction • A chemical change that occurs when atoms, ions, or molecules interact • Reactant • Atoms, ions, or molecules that enter a reaction • Product • Atoms, ions, or molecules remaining at the end of a reaction

13. Chemical Reactions

14. Reactions Require or Release Energy • We can predict whether a reaction requires or releases energy by comparing the bond energies of reactants with those of products • Endergonic (“energy in”) • Reactions that require a net input of energy • Exergonic (“energy out”) • Reactions that end with a net release of energy

15. Endergonic and Exergonic Reactions

16. Why the World Doesn’t Go Up in Flames • Activation energy • The minimum amount of energy needed to get a reaction started • Some reactions require a lot of activation energy, others do not

17. Activation Energy

18. ATP – The Cell’s Energy Currency • ATP (adenosine triphosphate) • A nucleotide with three phosphate groups • Transfers a phosphate group and energy to other molecules • Phosphorylation • A phosphate-group transfer • ADP binds phosphate in an endergonic reaction to replenish ATP (ATP/ADP cycle)

19. Fig. 6-9a, p. 97

20. Fig. 6-9b, p. 97

21. Fig. 6-9c, p. 97

22. Animation: Mitochondrial chemiosmosis

23. 6.1-6.2 Key Concepts:Energy Flow in the World of Life • Energy tends to disperse spontaneously; each time energy is transferred, some of it disperses • Organisms maintain their organization only by continuously harvesting energy • ATP couples reactions that release usable energy with reactions that require energy

24. 6.3 How Enzymes Make Substances React • Enzyme • A catalyst that makes a specific reaction occur much faster than it would on its own • Enzymes are not consumed or changed by participating in a reaction • Most are proteins, some are RNA • Substrate • The specific reactant acted upon by an enzyme

25. How Enzymes Work • Enzymes lower the activation energy required to bring on the transition state, when substrate bonds break and reactions run spontaneously • Active sites • Locations on the enzyme molecule where substrates bind and reactions proceed • Complementary in shape, size, polarity and charge to the substrate

26. Active Site of an Enzyme

27. Fig. 6-10b, p. 98

28. Fig. 6-10c, p. 98

29. Activation Energy

30. Animation: Activation energy

31. Animation: Enzymes and activation energy

32. Mechanisms of Enzyme-Mediated Reactions • Binding at enzyme active sites may bring on the transition state by four mechanisms • Helping substrates get together (拉近距離) • Orienting substrates in positions that favor reaction (有效碰撞) • Inducing a fit between enzyme and substrate (induced-fit model) • Shutting out water molecules (隔絕水分子)

33. Effects of Temperature, pH, and Salinity • Raising the temperature boosts reaction rates by increasing a substrate’s energy • But very high temperatures denature enzymes • Each enzyme has an optimum pH range • In humans, most enzymes work at ph 6 to 8 • Salt levels affect the hydrogen bonds that hold enzymes in their three-dimensional shape

34. Enzymes and Temperature

35. Enzymes and pH

36. Help from Cofactors • Cofactors • Atoms or molecules (other than proteins) that are necessary for enzyme function • Example:Iron atoms in catalase • 常固定在酶的內部(或為結構中心)、反應後不變 • Coenzymes • Organic cofactors such as vitamins • May become modified during a reaction • 細胞質內自由飄移，反應後結構常被改變

37. Catalase and Cofactors • Catalase is an antioxidant that neutralizes freeradicals (atoms or molecules with unpaired electrons that attack biological molecules) • 自由基很不好，因為容易搶別人電子讓人氧化，隨著年紀增加，體內自由基含量也會增加。抗氧化劑(通常是酶)藉由中心金屬吸引自由基的未成對電子以「解毒」(注意！僅吸引，未進行氧化還原) • Catalase works by holding a substrate molecule close to one of its iron atoms (cofactors) • Iron pulls on the substrate’s electrons, bringing on the transition state

38. 6.3 Key Concepts:How Enzymes Work • On their own, reactions proceed too slowly to sustain life • Enzymes tremendously increase the rate of metabolic reactions • Environmental factors such as temperature, salt, and pH influence enzyme function

39. 6.4 Metabolism – Organized, Enzyme-Mediated Reactions • ATP, enzymes, and other molecules interact in organized pathways of metabolism (activities by which cells acquire and use energy)

40. Types of Metabolic Pathways • A metabolic pathway is any series of enzyme-mediated reactions by which a cell builds, rearranges, or breaks down an organic substance • Anabolic pathways build molecules • Catabolicpathways break apart molecules • Cyclicpathways regenerate a molecule from the first step (例子：光合作用暗反應的卡爾文循環)

41. Controls Over Metabolism • Concentrations of reactants or products can make reactions proceed forward or backward • Feedback mechanisms can adjust enzyme production, or activate or inhibit enzymes • Regulatory molecules can bind to an allosteric site to activate or inhibit enzymes (結構變異區) • Feedback inhibition

42. Allosteric Control

43. Animation: Allosteric activation

44. Animation: Allosteric inhibition

45. Feedback Inhibition

46. Animation: Feedback inhibition

47. Redox Reactions • Oxidation-reduction reactions (paired reactions) • A molecule that gives up electrons is oxidized • A molecule that accepts electrons is reduced • Coenzymes can accept molecules in redox reactions (also called electron transfers) (電子轉移者、電子攜帶者…etc.) (NADH, FADH2之類)

48. ATP Synthesis • 細胞不能承受一次放能太多，要讓放能過程拆解成一個個小步驟，而這些小步驟幾乎都是氧化還原反應 • Coenzymes deliver electrons to electron transfer chains for ATP synthesis • Electron transfer chain • A series of redox reactions in membrane-bound enzymes or molecules (特別注意強調固定在膜上的) that release energy in small, controlled steps

49. Uncontrolled and Controlled Reactions

50. Overview: Energy Pathways