Energy, Enzymes, and Biological Reactions

1. Energy, Enzymes, and Biological Reactions Chapter 4

2. Energy Definition: The Capacity to do work Types of Energy: • Potential: Stored energy, measured as a capacity to do work. example: stretched spring • Kinetic: Energy of motion, released potential energy. example: releasing of a stretched spring • Thermal: Energy released as heat • Chemical: Potential energy stored in molecules. Measured as Kilocalories (Kcal) aka Calories (C) (1 calorie (c) = heat req’d to raise 1g of H2O 1C)

4. Why do cells need energy? • Chemical work, build, rearrange, tear apart compounds • Mechanical work, move cilia, flex a muscle • Electrochemical work, nerve impulses

5. Where does energy come from? • The universe contains a huge, but finite amount of energy • The original source of energy for most life on earth is from the sun • Energy is governed by the Laws of Thermodynamics

6. First Law of Thermodynamics • The total amount of energy in the universe remains constant • Energy can be converted from one form to another, but it is never destroyed

7. Second Law of Thermodynamics • Entropy tends to increase in a closed system • (No energy conversion is 100% efficient) • Overall energy flows in one direction from useable (lots of potential energy) to nonuseable (little potential energy) forms

8. So how can life exist? • Energy flows from the sun to plants, which lose energy directly or indirectly to other organisms • Overall energy flows in one direction and entropy increases as at each step energy is lost • Producers builds complex molecules from simpler building blocks using the energy of the sun • i.e. – the sun is constantly supplying us with new energy

9. Energy and chemical reactions Reactant(s) → Product(s) • Energy is stored in chemical bonds – all molecules contain energy • Endergonic reactions: reactions in which the products contain more energy than reactants • Exergonic reactions: reactions in which the products contain less energy than the reactants

10. Endergonic Reactions • Requires energy input

11. glucose - a product with more energy + 6O2 Energy in energy-poor reactants Endergonic Reaction: Photosynthesis • Original source of energy for most life on earth • Overall reaction: 6CO2 + 6H2O  C6H12O6 + 6O2 • Very endergonic – where does the plant get the energy? →SUN

12. Exergonic Reactions • Releases energy

13. Exergonic Reaction – Cellular Respiration • Breakdown of glucose; very exergonic • The source of ATP energy in cells • Overall reaction: C6H12O6 + 6O2  6CO2 + 6H2O -686Kcal glucose - energy-rich starting substance + 6O2 Energy out 6 6 products with less energy

14. Adenosine Triphosphate (ATP) • ATP is the cell’s energy currency nearly all energy in a cell is stored within the ATP molecule • Energy releasing rxns→ ATP→ Energy requiring rxns • Cells cleave ATP into ADP & Pi releasing energy • This energy can be used to do work such as synthesize other molecules or move muscles

15. How is ATP synthesized? • ATP are renewable and are recycled by cells:

16. How is the energy from ATP utilized? Reaction coupling: thermodynamically unfavorable reactions (endergonic) are coupled to the favorable reactions of ATP cleavage (exergonic) • ATP → ADP + Pi = –7.3Kcal • X → → → → Y = +5Kcal • Net energy = -2.3Kcal • Total reaction still increases entropy and conforms to the 2nd Law of Thermodynamics

17. Chemical Reactions (Rxn) • The conversion, accumulation, & disposal of substances by a cell is done through energy-driven reactions Parts of a Reaction (Rxn) • Reactants: substances that enter into a reaction • Intermediates: substances formed in the middle of a reaction • Products: end results of a reaction

18. How are cellular reactions defined? • Catabolism: breaking down of complex molecules • Anabolism: the building up of complex molecules • Metabolism: the sum of all these reactions

19. Anabolic and Catabolic Reactions large energy-rich molecules ADP + Pi BIOSYNTHETIC PATHWAYS (ANABOLIC) DEGRADATIVE PATHWAYS (CATABOLIC) ATP simple organic compounds energy-poor products ENERGY INPUT

20. Types of Reaction Sequences A B C D E F LINEAR PATHWAY CYCLIC PATHWAY G K J I BRANCHING PATHWAY N M L H

21. Activation Energy • Exergonic reactions are spontaneous - Why don’t exergonic reactions happen all the time? • Because of Activation Energy (EA) – the energy required to get a reaction started • The EA of a reaction can prevent it from occurring or cause it to occur slowly

22. Activation Energy Initial input of energy to start a reaction, even if it is spontaneous

23. Catalysts • Agents that speed up chemical reactions without getting used up

24. Biological Catalysts: Enzymes • Enzymes are protein catalysts (ribozymes are RNA catalysts) • They are required in small amounts • They are not altered permanently by the reaction • They do not change the thermodynamics of a reaction • They can only accelerate the rate at which a favorable reaction proceeds

25. Role of Enzymes in Biological Reactions Enzymes accelerate reactions by reducing activation energy Enzymes combine with reactants and are released unchanged Enzymes reduce activation energy by inducing the transition state

26. Enzymes and Activation Energy Enzymes decrease activation energy required for a chemical reaction to proceed

27. Biological Catalysts Example: A phosphatase enzyme can catalyze a rxn in 10 milliseconds Without the enzyme the rxn would take… 1 trillion yrs. (1,000,000,000,000) THE REACTION IS CONSIDERED SPONTANEOUS

28. Enzyme Specificity Enzymes are usually very specific Substrates interact with enzyme’s active site

29. Enzyme Activity:Induced Fit Model

30. Transition State • During catalysis, the substrate and active site form an intermediate transition state Fig. 4-12, p. 81

31. How do enzymes lower EA? • Catalytic mechanisms induce transition state • Bringing substrates into close proximity • Orienting substrates • Altering environment around substrates

32. Factors That Affect Enzymes Temperature: • increasing temperature speeds up rxns (both enzymatic and non-enzymatic) up to a point (WHY?) • High temperatures will destroy the enzyme • Enzymes are proteins • Proteins get denatured (unfolded) at high temps

33. Factors That Affect Enzymes Concentration of substrate and products: • increasing substrate will increase reaction up to a point • increased product will slow reaction (known as negative feedback) Concentration of enzyme • Increasing concentration increases enzyme activity up to a point

34. Factors That Affect Enzymes pH: • [H+] affects enzyme shape, so enzymes work best at narrow ranges of pH • Optimal pH – pH at which enzyme can catalyze best • For most enzymes, optimal pH is around neutral, depending on the environment in which the enzymes work • E.g. Pepsin – digestive enzyme in stomach, optimal pH ~2

35. Controlling Enzyme Activity • Enzymes are very efficient at what they do • Because of this they need to be carefully controlled • The cells needs to be able to regulate when a reaction occurs • The cell also has to be able to regulate how much product is produced from a reaction

36. Enzyme inhibitors • Competitive inhibitors • Bind to active site of enzyme • Prevent substrate from binding • Non-competitive inhibitors • Also called Allosteric inhibitors • Bind to enzyme in a region other than the active site called allosteric site • Change the shape of the active site to prevent substrates from binding

37. Enzyme Regulation • Enzyme activity is often regulated to meet the needs for reaction products • Allosteric regulation occurs with reversible combinations of regulatory molecules with an allosteric site on the enzyme • High-affinity state (active form); enzyme binds substrate strongly • Low-affinity state (inactive form);enzyme binds substrate weakly or not at all

38. Allosteric Regulation • Allosteric activators and allosteric inhibitors Fig. 4-17, p. 84

39. Feedback inhibition • If too much product is created the first enzyme may be shut off by the product becoming an allosteric or competitive inhibitor:

40. Cofactors and Coenzymes • Some enzymes need assistance in the form of cofactors • Minerals – inorganic cofactors • Examples: Potassium, Sodium, Calcium • Vitamins – organic cofactors or coenzymes • Examples: The specialized nucleotides NAD+ and FAD act as cofactors for enzymatic reactions; NAD+ contains the vitamin niacin and FAD contains the vitamin riboflavin

41. Ribozymes • RNA-based catalysts • Help remove surplus segments of RNA molecules with cutting and splicing reactions • In ribosomes, help join amino acids together when building proteins

42. Some coenzymes accept and hold onto electrons (e-) and protons (H+) during the breakdown glucose Why are these coenzymes required? Enzymes are not used up or modified during a reaction If the enzyme accepted the e- or H+ it would be modified

43. Oxidation/Reduction (Redox) Reactions One compound gains e- or H+ lost by another compound The oxidized compound loses electrons or H+ The reduced compound gains electrons or H+ Reduction acts as a mechanism for storing energy

44. Redox Reactions