1. 2- Enzymes, Coenzymes, and Energy Chapter 5

2. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Enzymes Enzymes: molecules that catalyze - speed up - biochemical reactions in living cells Three rules to be considered an enzyme 1. Most are proteins (some RNA enzymes) 2. Lower the energy of activation required for a reaction to occur 3. Are not changed or consumed by the reaction Cofactors, Coenzymes

3. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Enzyme Functions Enzymes catalyze cellular chemical reactions Metabolism - the chemical reactions in a cell: Two categories of cellular chemical reactions: 1. Anabolic Reactions Build larger molecules for growth, repair, reproduction Dehydration Synthesis Reactions require energy and nutrients 2. Catabolic Reactions Breakdown larger molecules Hydrolysis Reactions mobilize nutrients for energy making it available to the cell

4. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Metabolism Metabolism is the sum total of all anabolic and catabolic reactions that occur in the cell The metabolism of cells is carried out and controlled by the ezymes – There are catabolic enzymes – those that cleave larger molecules into smaller ones Ex. Hydrolysis Reactions – There are also anabolic enzymes – those that assemble smaller molecules into larger ones Ex. Dehydration Reactions

5. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Enzymes Enzymes interact with substrates Substrates: molecules that will undergo a reaction when bound to the enzyme – lactose, hydrogen peroxide (H 2 O 2 ) On the Enzymes: – Active site: region of the enzyme that binds to the substrate – Allosteric site: region of the enzyme that binds substances other that the substrate

6. Figure 5_02

7. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Enzymes Enzymes are very specific: – Enzymes will only interact with a specific substrates – The substrate fits into the active site like a key fits into a lock (Lock and Key Hypothesis) – Substrate binding causes the enzyme to change shape, producing a better induced fit between the molecules (Induced Fit Hypothesis) Changing the shape of an enzyme affects its ability to function

8. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Enzymes Enzyme/Substrate Complex: E + S ES EP E + P 1. The Enzyme and the Substrate come together (E+S) 2. The Enzyme/Substrate Complex is formed (ES) 3. The Enzyme’s Substrate is changed to the Enzyme’s - Product in the active site of the enzyme (EP) 4. The Enzyme and Product Separate (E+P) 5. The Enzyme is free to bind to another Substrate

9. Figure 5_03b

10. 10

11. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Enzyme Naming Convention Because enzymes catalyze specific reactions each enzyme has a unique name: – The first part of an enzyme’s name usually describes the substrate – The second part of an enzyme’s usually indicates the type of reaction it will catalyze All enzyme names end in the suffix -ase Examples of enzymes: – DNA polymerase – Glycogen synthetase – Lactase – Catalase

12. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. How Enzymes Work Enzymes lower the activation energy of biochemical reactions. Enzymes make it easier for chemical reactions to occur: by destabilizing the bonds in the substrate by bringing substrates together so they react by decreasing entropy - disorder - in the system Enzymes make the chemical reactions possible in the cell’s environment Enzymes make cells very efficient

13. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Lowering Activation Energy

14. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. How Enzymes Work Enzymes make cells very efficient Through enzymes, cells can carry out anabolic and catabolic reactions and end up with a net profit of energy Cellular respiration is the process of breaking down glucose and storing the excess energy from the molecule into a form of energy that is available and useful to the cell

15. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Cells Use Enzymes to Process Energy and Matter Reactions that break chemical bonds release their internal potential energy. Example: burning wood Oxidation reactions Organisms obtain energy through enzyme- catalyzed biochemical reactions. Ethane

16. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Coenzymes and Cofactors Many enzymes require special molecules to help them function correctly: – Cofactors inorganic molecules ions, such as zinc or iron – Coenzymes organic molecules Vitamins are the precursors for many coenzymes. Vitamins must be acquired from the diet, cells cannot make them.

17. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. The Role of Coenzymes ADase oxidizes alcohol - Alcohol cannot be oxidized unless something else is reduced - NAD + is reduced to NADH

18. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. The Environment Affects Enzyme Function The rate at which an enzyme can bind to a substrate is called the turnover number. The turnover number is maximized under the ideal conditions for that enzyme. Each enzyme has ideal conditions that include: 1. Temperature 2. pH 3. Substrate concentration

19. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 1. Temperature Temperature has two effects on enzymes: 1. Changes the rate of molecular motion Increasing temperature increases molecular motion and increases turnover number Decreasing temperature decreases molecular movement and decreases turnover number 2. Causes changes in the shape of an enzyme Temperature changes above optimum will denature the enzyme. This changes its shape, and it can no longer bind substrate and catalyze the reaction.

20. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. The Effect of Temperature on Turnover Number

21. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 2. pH Enzymes are composed of amino acids – In a basic environment The acidic side chains (R groups) could donate protons which affects the charge of the side chain A neutral side chain that donates protons would become negatively charged – In an acidic environment The basic side chains (R groups) could accept protons which affects the charge of the side chain A neutral side chain that accepts protons would become positively charged Both of these events can change the enzyme’s shape

22. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. The Effect of pH on the Turnover Number

23. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 3. Enzyme-Substrate Concentration The rate of turnover increases as the amount of – Enzyme increases – Substrate increases As substrate increases enzymes will reach a saturation point – once all of the enzymes are occupied, the rate of catalysis will not increase even if more substrate is added because all the enzyme active sites are filled – recall facilitated diffusion and the SM bldg. elevators

24. 87 Enzyme-Substrate Concentration Substrate Concentration Turnover Rate

25. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Biochemical Pathways Enzymes work together in chains of reactions known as biochemical or metabolic pathways Biochemical pathways are a series of reactions in which the product of one reaction becomes the substrate for the next reaction. Examples: photosynthesis, cellular respiration, protein synthesis, etc.

26. 26

27. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Enzyme Regulation Metabolism is tightly regulated There is a delicate balance between all of the reactions that take place in the cell Metabolism is commonly regulated 3 ways: 1. Enzymatic competition for substrate 2. Gene regulation 3. Enzyme inhibition

28. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Enzyme Regulation 1. Enzymatic competition for substrate Enzymatic competition occurs when more than one enzyme interacts with the same substrate Each enzyme converts the substrate to a different product. The enzyme that “wins” is the one that is the most abundant at the time.

29. Figure 5_07

30. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Enzyme Regulation 2. Gene regulation Enzymes are proteins. Protein production is controlled by genes. Certain chemicals in the cell turn particular enzyme- producing genes on or off depending on the situation. – Called gene-regulator proteins Those that decrease the amount of an enzyme made are called gene-repressor proteins. Those that increase the amount of an enzyme made are called gene-activator proteins.

31. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Enzyme Regulation 3. Enzyme inhibition Inhibitors are molecules that attach to enzymes and make them unable to bind to substrate. Many drugs, pesticides and herbicides target enzymes. Three types of inhibition: A. Negative Feedback Inhibition B. Competitive Inhibition C. Noncompetitive Inhibition

32. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. A. Negative-Feedback Inhibition The end-product of the metabolic pathways accumulate – Those molecules feedback and bind to an enzyme early in the sequence. – They inhibit that enzyme, and stop the sequence. – This decreases the amount of end-product made. This functions to keep levels of the end-product within a certain range.

33. 33 Feedback Inhibition

34. Text art 5_05

35. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. B. Competitive Inhibition Competitive inhibitors closely resemble the substrate. – they bind to the active site of the enzyme and block the substrate from binding.

36. Figure 5_09

37. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. C. Noncompetitive Inhibition Noncompetitive inhibitors bind to sites other than the enzyme’s active site - allosteric sites “allo” = other; “steric” = shape – binding to an allosteric site changes the shape of the enzyme and affects its function Noncompetitive because the noncompetitive inhibitor does not compete with the substrate to bind to the active site

38. 38

39. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Cellular Respiration Cellular Respiration is a metabolic pathway that breaks down glucose and extracts the energy to produce energy C 6 H 12 O 6 + 6O 2 6H 2 O + 6CO 2 + Energy Glucose Oxygen Water Carbon Dioxide The Energy is in the form of ATP

40. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Cellular Respiration Before C 6 H 12 O 6 + 6 O 2 6 H 2 O + 6 CO 2 + Energy Now C 6 H 12 O 6 + 6O 2 + 38 ADP + 38 P 6 H 2 O + 6CO 2 + 38 ATP

41. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. ATP - The Energy Currency of Cells ATP is the molecule that cells use to store, transfer, and provide energy The energy from ATP is used to fuel anabolic reactions - recall: for growth, repair, and reproduction ATP = Adenosine TriphosPhate - Adenosine (same molecule from DNA and RNA) –+–+ - Three inorganic phosphates (functional group PO 4 )

42. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. ATP - The Energy Currency of Cells ATP - 1 PO 4 = ADP (Adenosine Diphosphate) ADP - 1 PO 4 = AMP (Adenosine Monophosphate) ADP + 1 PO 4 = ATP

43. Figure 5_12

44. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. ATP - The Energy Currency of Cells The covalent bonds between the phosphates contain a lot of potential energy. It requires energy to make phosphate bonds – i.e. ADP + 1 PO 4 = ATP Breaking those bonds releases energy. – i.e. ATP - 1 PO 4 = ADP Because of enzymes, cells can build ATPs for less energy than ATPs can provide – i.e. a net profit of energy

45. Text art 5_06 ATP/ADP Cycling

46. Text art 5_07 ATP/ADP Cycling

47. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. ATP/ADP Cycling The energy from ATP is used to fuel anabolic reactions

48. ATP/ADP Cycling AT P ADP

49. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Other Functions of ATP ATP regulates enzyme activity Phosphorylation and dephosphorylation - process of adding or removing phosphate groups - can activate or deactivate enzymes ATP serves as a source of phosphate groups

50. ATP/ADP Cycling

51. Figure 5_08a

52. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Other Sources of Cellular Energy Oxidation-Reduction (Redox) Reactions produce elections and protons These Electrons and Protons can be used by cells for energy Recall the structure of the Hydrogen atom:  When Hydrogen (or a molecule containing Hydrogen) is oxidized an electron and proton are released

53. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Electrons for Energy During redox reactions valence electrons in the outer energy level of atoms are lost to the other atoms Special molecules can receive these high energy electrons and harness that energy. These molecules are known as electron carriers. – To important electron carriers: NAD and FAD

54. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Protons for Energy Energy from electrons is used to power Proton Pumps Proton Pumps are used to pump protons (H + ’s) to one side of a cell membrane establishing a concentration gradient of protons on one side of the membrane The protons diffuse through a special protein called ATP synthase. The ATP synthase uses the energy from the flowing protons to make ATP.

55. 5- Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Electron Transport and Proton Gradient