Chapter 8 An Introduction to Metabolism

Transcription

1 Chapter 8 An Introduction to Metabolism Sep 7 9:07 PM 1

2 Metabolism=all of the chemical reactions within an organism metabolic pathways are chemical reactions that change molecules in a series of steps enzymes are important in these reactions by speeding them up Sep 7 9:09 PM 2

3 Two types of metabolic pathways: 1.Catabolic pathways release energy by breaking down complex molecules into simpler ones 2. Anabolic pathways consume energy to build molecules from simpler compounds energy released by catabolic pathways is used to run the anabolic pathways= energy coupling relates to bioenergetics = the study of how organisms manage their energy resources Sep 7 9:14 PM 3

4 What is the difference between potential and kinetic energy? Oct 28 9:13 AM 4

5 Definitions: 1. Energy= capacity to do work, can rearrange matter by moving it against opposing forces 2. Kinetic energy= energy of motion ex. motion, photons(light), heat 3. Potential energy=energy that matter possesses because of its location or structure ex. water behind a dam(energy stored due to altitude) 4. Chemical energy= is a form of potential energy in molecules because of the arrangement of the atoms Sep 7 9:19 PM 5

6 Can energy be changed from one form to another? How? Oct 28 9:14 AM 6

7 Energy can be converted from one form to another Ex. light energy to chemical energy of plants to potential energy of food taken in body and kinetic energy of movement cellular respiration is a catabolic pathway that releases energy stored in sugar and other complex molecules living organisms must be able to transform energy Sep 7 9:24 PM 7

8 Energy transformations subject to 2 laws Thermodynamics= study of energy transformation closed system = matter is isolated from its surroundings ex. liquid in a thermos open system = matter can be transferred between system and surroundings ex. organisms absorb energy (light or chemical energy), release heat and metabolic wastes Sep 7 9:31 PM 8

9 1st law of thermodynamics energy can be transferred and transformed, but not created or destroyed a.k.a. = Principle of Conservation of energy ex. plants transform light energy to chemical energy Sep 7 9:41 PM 9

10 2nd law of thermodynamics every energy transformation must make the universe more disordered Entropy= quantity used as a measure of disorder, or randomness more random matter is, greater the entropy is a trend towards randomness of the universe entropy of universe is in form of heat (random molecular motion) lots of heat is lost by organisms during these energy transformations Sep 7 9:43 PM 10

11 putting the 2 laws together: "quantity of energy in the universe is constant, but the quality is not" in an animal: food starch, proteins catabolic pathways animals release carbon dioxide and water and heat Sep 7 9:50 PM 11

12 Organisms live at the expense of free energy spontaneous processes occur without outside help used to perform work ex. downhill flow of water increase stability of a system nonspontaneous processes only occur if energy is added to a system ex. water against gravity with a pump cell expending energy to move substances out of cell decrease stability of a system Sep 7 9:53 PM 12

13 The relationship of free energy to stability, work capacity and spontaneous change Sep 10 9:57 PM 13

14 Free energy measures the spontaneity of a system free energy = the portion's of the system's energy that is able to perform work when temperature is uniform throughout the system free energy (G) is related to the total energy (H) and its entropy (S) in G=H TS T= temperature in Kelvin (K) units K = degrees celsius increase in temperature amplifies the entropy term Sep 7 10:00 PM 14

15 therefore; free energy is a measure of the stability of a system ex. high free energy systems (compressed springs, separated charges) are unstable and want to go to a more stable state (less free energy) *in a spontaneous process, the free energy of a system decreases Sep 7 10:05 PM 15

16 free energy equation G = G (final state) G (starting state) or G = H T S to be spontaneous: system gives up energy (decrease H) give up order (decrease in S) or both G must be negative Sep 7 10:09 PM 16

17 A system at equilibrium is at maximum stability rate of forward rxn = rate of backward rxn no change in concentration of products or reactants if G = 0, then the system can not do work going away from equilibrium, movements are nonspontaneous and need energy from an outside energy source chemical reactions are classified as exergonic or endergonic based on free energy Sep 7 10:16 PM 17

18 Exergonic reaction = reaction that proceeds with a net release of free energy and G is negative for cellular respiration reaction G = 686 kcal/mol 686 kcal are available to do work in the cell the products have 686 kcal less energy than the reactants Sep 7 10:21 PM 18

19 Endergonic Reaction a reaction that absorbs free energy from its surroundings these reactions store energy, G is positive photosynthesis requires energy G = +686 kcal/mol powered by absorption of light energy reactions in closed systems reach equilibrium and can do no work, if G = 0, then the cell is dead Sep 10 5:07 PM 19

20 cells maintain disequilibrium because they have constant flow of substances into and out of cell in an open system a catabolic process in a cell releases free energy in a series of reactions, not a single step some reactions get pulled one way because the products become reactants for another reaction sunlight is a source of free energy for photosynthetic organisms in the environment nonphotosynthetic organisms depend on transfer of free energy from photosynthetic organisms in the form of organic molecules Sep 10 5:12 PM 20

21 Disequilibrium and work in closed and open systems Sep 10 10:00 PM 21

22 a cell does three kinds of work: 1. mechanical work ex. beating of cilia, contraction of muscle cells, movement of chromosomes 2. transport work pumping substances across membranes against the direction of spontaneous movement 3. chemical work driving endergonic reactions, ex. synthesizing polymers from monomers *It is ATP's job to be the source of energy to power cellular work Sep 10 5:18 PM 22

23 Adenosine Triphosphate made of nucleotide of adenine (nitrogenous base), ribose (sugar) and a chain of three phosphate groups Sep 10 7:38 PM 23

24 bonds between phosphate groups can be broken by hydrolysis to release energy (breaks weak covalent bonds) under standard conditions releases 7.3 kcal/mole of ATP in cell G = 13 kcal/mol in a cell, the energy from hydrolysis of ATP is coupled directly to endergonic processes by transferring the phosphate group to another molecule the new molecule is phosphorylated makes new molecule more reactive ATP is continually regenerated by adding a phosphate group to ADP Sep 10 7:40 PM 24

25 Energy coupling by phosphate transfer Sep 10 10:02 PM 25

26 Ex. in a muscle cell, the entire amount of ATP is recycled once each minute, over 10 million ATP consumed and regenerated per second per cell regeneration consumes energy in the amount of G = 7.3 kcal/mol Sep 10 7:46 PM 26

27 How do enzymes speed up metabolic reactions? catalyst a chemical agent that changes the rate of a reaction without being consumed by the reaction enzyme is a catalytic protein, it helps break bonds and form bonds Sep 10 7:48 PM 27

28 ex. to hydrolyze sucrose, the bond between glucose and fructose must be broken and then new bonds formed with hydrogen ion and hydroxyl group from water Sep 10 10:05 PM 28

29 free energy of activation or activation energy In an exergonic reaction the reactants must absorb energy from their surroundings in order to break bonds, when new bonds are formed energy is released activation energy (E ) is the amount of energy needed to push the reactants over an energy barrier at the summit the molecules are unstable (transition state) Sep 10 7:52 PM 29

30 Energy profile of an exergonic reaction Sep 10 10:06 PM 30

31 free energy of products free energy of reactants = G some reactions have a low barrier so room temperature has enough thermal energy to reach transition state most of time E is higher so more energy is needed in cell there is not usually enough temperature to make it over the activation energy if the cell used direct heat, enzymes would denature and kill cells Sep 10 8:00 PM 31

32 So how do enzyme function in metabolic systems? Enzymes speed reactions by lowering the activation energy they do not change the G of the reaction they just speed up normal reactions they are selective so they can control which chemical processes happen at which time Sep 10 8:05 PM 32

33 Enzymes lower the barrier of activation Sep 10 10:07 PM 33

34 Properties of enzymes enzymes are substrate specific substrates are reactants that bind to enzymes when substrate(s) bind to the enzyme, the enzyme catalyzes the conversion of the substrate to the product Active site of an enzyme is a groove on the surface of a protein into which the substrate fits when the substrate binds to the active site, the enzyme changes shape leading to a tighter induced fit, that brings chemical groups closer so a reaction can happen Sep 10 8:09 PM 34

35 Induced fit of a substrate into an enzyme Sep 10 10:09 PM 35

36 Sep 10 10:10 PM 36

37 more about active sites substrates are held in place by weak bonds (hydrogen and ionic) one molecule of enzyme can catalyze thousands of reactions/second enzymes are unaffected by the reaction and can be reused enzymes can catalyze a reaction in both directions based on the relative concentrations of products and reactants catalyze reactions in the direction of equilibrium Sep 10 8:14 PM 37

38 How do enzymes lower activation energy and speed the reaction? 1. active site orients substrates in the correct orientation for the reaction 2. when active site binds to substrate, it can stress the bonds that must be broken, so transition state can be reached easier 3. R groups at the active site may create a conducive microenvironment for a specific reaction 4. enyzmes may even bind covalently to substrates in an intermediate step before going back to normal Sep 10 8:18 PM 38

39 What might be some limiting factors that affect enzyme reactions? Oct 29 7:09 AM 39

40 *rate that a specific number of enzymes converts substances to products depends on substrate concentration low substrate concentration, an increase in substrate speeds binding to available active sites is a limit to how fast a reaction can occur *at some [ ], active sites are all full = enzyme saturation *only way to increase productivity at enzyme saturation is to add more enzyme molecules Sep 10 8:35 PM 40

41 Enzyme activity depends on cell environment 1. Temperature: as temperature increases, collisions between substrates and active sites increases as molecules move faster too high temperature denatures protein each enzyme has an optimal temperature Sep 10 8:45 PM 41

42 2. ph ph influences shape and reaction rate of enzymes each enzyme has an optimal ph, usually between ph 6 8 digestive enzymes in stomach work at ph 2 digestive enzymes in intestine work at ph 8 Sep 10 8:51 PM 42

43 Sep 10 10:11 PM 43

44 3. Cofactors nonprotein helpers that some enzymes require for catalytic activity cofactors bind permanently or reversibly to the enzyme some cofactors are iron, zinc, and copper inorganic cofactors(coenzymes) = vitamins or molecules from vitamins Sep 10 8:53 PM 44

45 some cofactors can be inhibitors that prevent enzymes from catalyzing reactions if covalently bonded, then inhibition is irreversible if binding is weak, inhibition may be reversible Sep 10 8:57 PM 45

46 competitive inhibition when an inhibitor binds to the same site as the substrate, it blocks the substrate from binding noncompetitive inhibition when an inhibitor binds somewhere other than the active site, it blocks substrate binding Oct 29 7:11 AM 46

47 Sep 10 10:12 PM 47

48 binding by inhibitors alters the shape of the enzyme so active site is ineffective or unreceptive reversible inhibition is natural in regulation of metabolism Sep 10 9:02 PM 48

49 Metabolic control can depend on allosteric regulation in some cases, molecules that naturally regulate enzyme activity behave like reversible noncompetitive inhibitors Sep 10 9:04 PM 49

50 these molecules bind to an allosteric site = a specific receptor on the enzyme that is not the active site can inhibit or stimulate the enzyme most allosteric regulated enzymes are made of two or more polypeptide chains if inhibiting stabilizes the conformation of the enzyme that lacks an active site if stimulating, it helps stabilize the conformation that has the functional active site Oct 29 7:13 AM 50

51 Allosteric regulation of enzyme activity Sep 10 10:13 PM 51

52 depending on the cell's chemical conditions, inhibitors and activators can compete for the same allosteric site ex. some catabolic pathways have allosteric sites that are inhibited when ATP binds and activated when AMP binds when ATP levels are low, AMP levels are high and pathway is turned on until ATP level rises, then AMP levels fall and inhibition by ATP dominates Sep 10 9:11 PM 52

53 Feedback inhibition= process in which a metabolic pathway is turned off by the end product of the reaction end product acts as an inhibitor of an enzyme in the pathway if product high = pathway turned off if product low = pathway is active cooperativity= In enzymes have multiple catalytic subunits, binding of a substrate to one active site stabilizes conformational changes at all other subunits Sep 10 9:16 PM 53

54 Feedback Inhibition Sep 10 10:14 PM 54

55 Cooperativity Sep 10 10:15 PM 55

56 can have multienzyme complexes = a team of enzymes for several steps in a pathway products pass from one enzyme to the next some complexes and enzymes are found in specific cell structures such as membranes, or inside organelles Sep 10 9:21 PM 56

57 Sep 14 10:11 AM 57