Chapter 5 Ground Rules of Metabolism Sections 1-5

1. Chapter 5Ground Rules of MetabolismSections 1-5

2. Energy • We define energy as the capacity to do work • One form of energy can be converted to another • Familiar forms of energy include light, heat, electricity, and motion (kinetic energy) • The energy in chemical bonds is a type of potential energy, because it can be stored

3. 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)

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

5. Energy’s One Way Flow • The total amount of energy available in the universe to do work is always decreasing • Each time energy is transferred, some energy escapes as heat (not useful for doing work) • On Earth, energy flows from the sun, through producers, then consumers • Living things need a constant input of energy

6. Chemical Bond Energy • 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

7. Equations Represent Chemical Reactions

8. 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

9. Why the Earth 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

10. Activation Energy Reactants: 2H2 O2 Activation energy Free energy Products: 2H2O Difference between free energy of reactants and products Time

11. Take-Home Message:How do cells use energy? • Activation energy is the minimum amount of energy required to start a chemical reaction • Endergonic reactions cannot run without a net input of energy • Exergonic reactions end with a net release of energy • Cells store energy in chemical bonds by running endergonic reactions that build organic compounds; they harvest energy by breaking the bonds

12. 5.4 How Enzymes Work • Enzyme • In a process called catalysis, an enzyme 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

13. The Transition State • 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

14. Active Site of an Enzyme

15. Mechanisms of Enzyme-Mediated Reactions • Binding at enzyme active sites may bring on the transition state by four mechanisms • Helping substrates get together • Orienting substrates in positions that favor reaction • Inducing a fit between enzyme and substrate (induced-fit model) • Shutting out water molecules

16. 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

17. Take-Home Message:How do enzymes work? • Enzymes greatly enhance the rate of specific reactions. • Binding at an enzyme’s active site causes a substrate to reach its transition state. In this state, the substrate’s bonds are at the breaking point • Each enzyme works best at certain temperatures, pH, and salt concentration

18. Types of Metabolic Pathways • Ametabolic pathway is any series of enzyme-mediated reactions by which a cell builds, rearranges, or breaks down an organic substance • Anabolic pathways build molecules • Catabolic pathways break apart molecules • Cyclic pathways regenerate a molecule from the first step

19. 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 siteto activate or inhibit enzymes • Feedback inhibition

20. reactant X enzyme 1 intermediate enzyme 2 intermediate enzyme 3 product Stepped Art Figure 5-14 p84

21. 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)

22. glucose + oxygen carbon dioxide + water Figure 5-16 p85

23. 1 glucose + oxygen e– H+ 2 carbon dioxide + water 3 e– Figure 5-16 p85

24. Take-Home Message:What are metabolic pathways? • Metabolic pathways are sequences of enzyme-mediated reactions; some are biosynthetic; others are degradative • Control mechanisms enhance or inhibit the activity of many enzymes; the adjustments help cells produce only what they require in any given interval • Many metabolic pathways involve electron transfers, or redox reactions. • Redox reactions occur in electron transfer chains; the chains are important sites of energy exchange in photosynthesis and aerobic respiration

25. Chapter 5Ground Rules of MetabolismSections 6-10

26. Table 5-1 p86

27. Cofactors and Coenzymes • Cofactors • Atoms or molecules (other than proteins) that are necessary for enzyme function • Example: Iron atoms in catalase • Coenzymes • Organic cofactors such as vitamins • May become modified during a reaction

28. Catalase and Cofactors • Catalase is an antioxidant that neutralizes free radicals (atoms or molecules with unpaired electrons that attack biological molecules) • Catalase has four hemes (small organic compound with an iron atom at its center) • 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

29. ATP—A Special Coenzyme • 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)

30. adenine three phosphate groups ribose A ATP ADP AMP adenine ribose B energy in energy out C ADP + phosphate Figure 5-18 p87

31. Take-Home Message:How do cofactors work? • Cofactors associate with enzymes and assist their function. • Metal ions stabilize the structure of many enzymes. They also participate in some enzymatic reactions by donating or accepting electrons • Many coenzymes carry chemical groups, atoms, or electrons from one reaction to another • The formation of ATP from ADP is an endergonic reaction; ADP forms again when a phosphate group is transferred from ATP to another molecule – energy from such transfers drives cellular work

32. The Fluid Mosaic Model • Fluid mosaic model • Describes the organization of cell membranes • Phospholipids drift and move like a fluid • The bilayer is a mosaic mixture of phospholipids, steroids, proteins, and other molecules

33. Cell Membrane Organization one layer of lipids one layer of lipids

34. Types of Membrane Proteins • Each type of protein in a membrane has a special function • Adhesion proteins • Recognition proteins • Receptor proteins • Enzymes • Transport proteins (active and passive)

35. Types of Membrane Proteins B Recognition proteins such as this MHC molecule tag a cell as belonging to one’s own body. c Receptor proteins such as this B cell receptor bind substances outside the cell. B cell receptors help the body eliminate toxins and infectious agents. D Transport proteins bind to molecules on one side of the membrane, and release them on the other side. This one transports glucose. E This transport protein, an ATP synthase, makes ATP when hydrogen ions flow through its interior. Extracellular Fluid Lipid bilayer Cytoplasm

36. Table 5-2 p88

37. Take-Home Message:What is a cell membrane? • The structural foundation of all cell membranes is the lipid bilayer • Adhesion proteins, recognition proteins, transport proteins, receptors, and enzymes embedded in or associated with the lipid bilayer impart functionality to a cell membrane

38. 5.8 Diffusion and Membranes • Ions and molecules tend to move spontaneously from regions of higher to lower concentration • Water diffuses across cell membranes by osmosis

39. Diffusion • Diffusion • The net movement of molecules down a concentration gradient • Moves substances into, through, and out of cells • A substance diffuses in a direction set by its own concentration gradient, not by the gradients of other solutes around it

40. The Rate of Diffusion • Rate of diffusion depends on five factors • Size • Temperature • Steepness of the concentration gradient • Charge • Pressure

41. Concentration Gradients • Concentration • The number of molecules (or ions) of substance per unit volume of fluid • Concentration gradient • The difference in concentration between two adjacent regions • Molecules move from a region of higher concentration to one of lower concentration

42. Tonicity • Tonicity • The relative concentrations of solutes in two fluids separated by a selectively permeable membrane • For two fluids separated by a semipermeable membrane, the one with lower solute concentration is hypotonic, and the one with higher solute concentration is hypertonic • Isotonic fluids have the same solute concentration

43. Osmosis • Osmosis • The movement of water down its concentration gradient – through a selectively permeable membrane from a region of lower solute concentration to a region of higher solute concentration

44. Osmosis selectively permeable membrane

45. Membrane Permeability • Selective permeability • The ability of a cell membrane to control which substances and how much of them enter or leave the cell • Allows the cell to maintain a difference between its internal environment and extracellular fluid • Supplies the cell with nutrients, removes wastes, and maintains volume and pH

46. Selective Permeability of Lipid Bilayers glucose and other polar molecules; ions gases lipid bilayer water

47. Effects of Fluid Pressure • Hydrostatic pressure (turgor) • The pressure exerted by a volume of fluid against a surrounding structure (membrane, tube, or cell wall) which resists volume change • Osmotic pressure • The amount of hydrostatic pressure that can stop water from diffusing into cytoplasmic fluid or other hypertonic solutions

48. Effects of Fluid Pressure

49. Take-Home Message: What influences the movement of ions and molecules? • Molecules or ions tend to diffuse into an adjoining region of fluid in which they are not as concentrated • he steepness of a concentration gradient as well as temperature, molecular size, charge, and pressure affect the rate of diffusion • Osmosis is a net diffusion of water between two fluids that differ in water concentration and are separated by a selectively permeable membrane • Fluid pressure that a solution exerts against a membrane or wall influences the osmotic movement of water

50. How Substances Cross Membranes • Gases and nonpolar molecules diffuse freely across a lipid bilayer • Ions and large polar molecules require other mechanisms to cross the cell membrane • Passive transport • Active transport • Endocytosis and exocytosis