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Chapter 8 Metabolism & Enzymes From food webs to the life of a cell energy.

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Presentation on theme: "Chapter 8 Metabolism & Enzymes From food webs to the life of a cell energy."— Presentation transcript:


2 Chapter 8 Metabolism & Enzymes

3 From food webs to the life of a cell energy

4 Flow of energy through life Life is built on chemical reactions –transforming energy from one form to another organic molecules ATP & organic molecules sun solar energy ATP & organic molecules

5 Concept 8.1: An organism s metabolism transforms matter and energy, subject to the laws of thermodynamics Metabolism is the totality of an organisms chemical reactions Metabolism is an emergent property of life that arises from interactions between molecules within the cell

6 Enzyme 1 AB Reaction 1 Enzyme 2 C Reaction 2 Enzyme 3 D Reaction 3 Product Starting molecule

7 Metabolism Chemical reactions of life –forming bonds between molecules dehydration synthesis synthesis anabolic reactions –breaking bonds between molecules hydrolysis digestion catabolic reactions Thats why theyre called anabolic steroids!

8 Examples dehydration synthesis (synthesis) hydrolysis (digestion) + H2OH2O + H2OH2O enzyme

9 Examples dehydration synthesis (synthesis) hydrolysis (digestion) enzyme

10 Forms of Energy Energy is the capacity to cause change Energy exists in various forms, some of which can perform work –Kinetic energy is energy associated with motion Heat (thermal energy) is kinetic energy associated with random movement of atoms or molecules –Potential energy is energy that matter possesses because of its location or structure Chemical energy is potential energy available for release in a chemical reaction Energy can be converted from one form to another

11 On the platform, the diver has more potential energy. Diving converts potential energy to kinetic energy. Climbing up converts kinetic energy of muscle movement to potential energy. In the water, the diver has less potential energy.

12 The Laws of Energy Transformation Thermodynamics is the study of energy transformations A closed system, such as that approximated by liquid in a thermos, is isolated from its surroundings In an open system, energy and matter can be transferred between the system and its surroundings Organisms are open systems

13 The First Law of Thermodynamics According to the first law of thermodynamics, the energy of the universe is constant –Energy can be transferred and transformed –Energy cannot be created or destroyed The first law is also called the principle of conservation of energy

14 The Second Law of Thermodynamics During every energy transfer or transformation, some energy is unusable, often lost as heat According to the second law of thermodynamics, every energy transfer or transformation increases the entropy (disorder) of the universe

15 LE 8-3 Chemical energy Heat CO 2 First law of thermodynamicsSecond law of thermodynamics H2OH2O

16 Living cells unavoidably convert organized forms of energy to heat Spontaneous processes occur without energy input; they can happen quickly or slowly For a process to occur without energy input, it must increase the entropy of the universe

17 Biological Order and Disorder Cells create ordered structures from less ordered materials Organisms also replace ordered forms of matter and energy with less ordered forms The evolution of more complex organisms does not violate the second law of thermodynamics Entropy (disorder) may decrease in an organism, but the universes total entropy increases

18 Concept 8.2: The free-energy change of a reaction tells us whether the reaction occurs spontaneously Biologists want to know which reactions occur spontaneously and which require input of energy To do so, they need to determine energy changes that occur in chemical reactions

19 Free-Energy Change, G A living systems free energy is energy that can do work when temperature and pressure are uniform, as in a living cell

20 The change in free energy (G) during a process is related to the change in enthalpy, or change in total energy (H), and change in entropy (TS): G = H - TS Only processes with a negative G are spontaneous Spontaneous processes can be harnessed to perform work

21 Free Energy, Stability, and Equilibrium Free energy is a measure of a systems instability, its tendency to change to a more stable state During a spontaneous change, free energy decreases and the stability of a system increases Equilibrium is a state of maximum stability A process is spontaneous and can perform work only when it is moving toward equilibrium

22 LE 8-5 Gravitational motionDiffusionChemical reaction

23 Free Energy and Metabolism The concept of free energy can be applied to the chemistry of lifes processes

24 Chemical reactions & energy Some chemical reactions release energy –exergonic –digesting polymers –hydrolysis = catabolism Some chemical reactions require input of energy –endergonic –building polymers –dehydration synthesis = anabolism digesting molecules= less organization= lower energy state building molecules= more organization= higher energy state

25 Endergonic vs. exergonic reactions exergonicendergonic - energy released - digestion - energy invested - synthesis - G G = change in free energy = ability to do work + G

26 Energy & life Organisms require energy to live –where does that energy come from? coupling exergonic reactions (releasing energy) with endergonic reactions (needing energy) ++ energy + +

27 What drives reactions? If reactions are downhill, why dont they just happen spontaneously? –because covalent bonds are stable bonds Stable polymers dont spontaneously digest into their monomers

28 Activation energy Breaking down large molecules requires an initial input of energy –activation energy –large biomolecules are stable –must absorb energy to break bonds energy cellulose CO 2 + H 2 O + heat

29 Too much activation energy for life The amount of energy needed to destabilize the bonds of a molecule –moves the reaction over an energy hill Not a match! Thats too much energy to expose living cells to!

30 Reducing Activation energy Catalysts –reducing the amount of energy to start a reaction Pheeew… that takes a lot less energy!

31 Equilibrium and Metabolism Reactions in a closed system eventually reach equilibrium and then do no work Cells are not in equilibrium; they are open systems experiencing a constant flow of materials A catabolic pathway in a cell releases free energy in a series of reactions Closed and open hydroelectric systems can serve as analogies

32 Concept 8.3: ATP powers cellular work by coupling exergonic reactions to endergonic reactions A cell does three main kinds of work: –Mechanical –Transport –Chemical To do work, cells manage energy resources by energy coupling, the use of an exergonic process to drive an endergonic one

33 The Structure and Hydrolysis of ATP ATP (adenosine triphosphate) is the cells energy shuttle ATP provides energy for cellular functions

34 LE 8-8 Phosphate groups Ribose Adenine

35 The bonds between the phosphate groups of ATPs tail can be broken by hydrolysis Energy is released from ATP when the terminal phosphate bond is broken This release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves

36 LE 8-9 Adenosine triphosphate (ATP) Energy PP P PP P i Adenosine diphosphate (ADP) Inorganic phosphate H2OH2O + +

37 In the cell, the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction Overall, the coupled reactions are exergonic

38 LE 8-10 Endergonic reaction: G is positive, reaction is not spontaneous Exergonic reaction: G is negative, reaction is spontaneous G = +3.4 kcal/mol G = –7.3 kcal/mol G = –3.9 kcal/mol NH 2 NH 3 Glu Glutamic acid Coupled reactions: Overall G is negative; together, reactions are spontaneous AmmoniaGlutamine ATP H2OH2O ADP P i + + +

39 How ATP Performs Work ATP drives endergonic reactions by phosphorylation, transferring a phosphate group to some other molecule, such as a reactant The recipient molecule is now phosphorylated The three types of cellular work (mechanical, transport, and chemical) are powered by the hydrolysis of ATP

40 LE 8-11 NH 2 Glu P i P i P i P i NH 3 P P P ATP ADP Motor protein Mechanical work: ATP phosphorylates motor proteins Protein moved Membrane protein Solute Transport work: ATP phosphorylates transport proteins Solute transported Chemical work: ATP phosphorylates key reactants Reactants: Glutamic acid and ammonia Product (glutamine) made + + +

41 The Regeneration of ATP ATP is a renewable resource that is regenerated by addition of a phosphate group to ADP The energy to phosphorylate ADP comes from catabolic reactions in the cell The chemical potential energy temporarily stored in ATP drives most cellular work

42 LE 8-12 P i ADP Energy for cellular work (endergonic, energy- consuming processes) Energy from catabolism (energonic, energy- yielding processes) ATP +

43 Concept 8.4: Enzymes speed up metabolic reactions by lowering energy barriers A catalyst is a chemical agent that speeds up a reaction without being consumed by the reaction An enzyme is a catalytic protein Hydrolysis of sucrose by the enzyme sucrase is an example of an enzyme-catalyzed reaction

44 LE 8-13 Sucrose C 12 H 22 O 11 Glucose C 6 H 12 O 6 Fructose C 6 H 12 O 6

45 The Activation Energy Barrier Every chemical reaction between molecules involves bond breaking and bond forming The initial energy needed to start a chemical reaction is called the free energy of activation, or activation energy (E A ) Activation energy is often supplied in the form of heat from the surroundings

46 LE 8-14 Transition state CD A B EAEA Products CD A B G < O Progress of the reaction Reactants C D A B Free energy

47 How Enzymes Lower the E A Barrier Enzymes catalyze reactions by lowering the E A barrier Enzymes do not affect the change in free- energy (G); instead, they hasten reactions that would occur eventually Animation: How Enzymes Work Animation: How Enzymes Work

48 LE 8-15 Course of reaction without enzyme E A without enzyme G is unaffected by enzyme Progress of the reaction Free energy E A with enzyme is lower Course of reaction with enzyme Reactants Products

49 Substrate Specificity of Enzymes The reactant that an enzyme acts on is called the enzymes substrate The enzyme binds to its substrate, forming an enzyme-substrate complex The active site is the region on the enzyme where the substrate binds Induced fit of a substrate brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction

50 LE 8-16 Substrate Active site Enzyme Enzyme-substrate complex

51 Catalysis in the Enzymes Active Site In an enzymatic reaction, the substrate binds to the active site The active site can lower an E A barrier by –Orienting substrates correctly –Straining substrate bonds –Providing a favorable microenvironment –Covalently bonding to the substrate

52 LE 8-17 Enzyme-substrate complex Substrates Enzyme Products Substrates enter active site; enzyme changes shape so its active site embraces the substrates (induced fit). Substrates held in active site by weak interactions, such as hydrogen bonds and ionic bonds. Active site (and R groups of its amino acids) can lower E A and speed up a reaction by acting as a template for substrate orientation, stressing the substrates and stabilizing the transition state, providing a favorable microenvironment, participating directly in the catalytic reaction. Substrates are converted into products. Products are released. Active site is available for two new substrate molecules.

53 Effects of Local Conditions on Enzyme Activity An enzymes activity can be affected by: –General environmental factors, such as temperature and pH –Chemicals that specifically influence the enzyme

54 Effects of Temperature and pH Each enzyme has an optimal temperature in which it can function Each enzyme has an optimal pH in which it can function

55 LE 8-18 Optimal temperature for typical human enzyme Optimal temperature for enzyme of thermophilic (heat-tolerant bacteria) Temperature (°C) Optimal temperature for two enzymes Rate of reaction Optimal pH for pepsin (stomach enzyme) Optimal pH for trypsin (intestinal enzyme) pH Optimal pH for two enzymes 0 Rate of reaction

56 Cofactors Cofactors are nonprotein enzyme helpers Coenzymes are organic cofactors

57 Enzyme Inhibitors Competitive inhibitors bind to the active site of an enzyme, competing with the substrate Noncompetitive inhibitors bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective

58 LE 8-19 Substrate Active site Enzyme Competitive inhibitor Normal binding Competitive inhibition Noncompetitive inhibitor Noncompetitive inhibition A substrate can bind normally to the active site of an enzyme. A competitive inhibitor mimics the substrate, competing for the active site. A noncompetitive inhibitor binds to the enzyme away from the active site, altering the conformation of the enzyme so that its active site no longer functions.

59 Concept 8.5: Regulation of enzyme activity helps control metabolism Chemical chaos would result if a cells metabolic pathways were not tightly regulated To regulate metabolic pathways, the cell switches on or off the genes that encode specific enzymes

60 Allosteric Regulation of Enzymes Allosteric regulation is the term used to describe cases where a proteins function at one site is affected by binding of a regulatory molecule at another site Allosteric regulation may either inhibit or stimulate an enzymes activity

61 Allosteric Activation and Inhibition Most allosterically regulated enzymes are made from polypeptide subunits Each enzyme has active and inactive forms The binding of an activator stabilizes the active form of the enzyme The binding of an inhibitor stabilizes the inactive form of the enzyme

62 LE 8-20a Allosteric enzyme with four subunits Regulatory site (one of four) Active form Activator Stabilized active form Active site (one of four) Allosteric activator stabilizes active form. Non- functional active site Inactive form Inhibitor Stabilized inactive form Allosteric inhibitor stabilizes inactive form. Oscillation Allosteric activators and inhibitors

63 Cooperativity is a form of allosteric regulation that can amplify enzyme activity In cooperativity, binding by a substrate to one active site stabilizes favorable conformational changes at all other subunits

64 LE 8-20b Substrate Binding of one substrate molecule to active site of one subunit locks all subunits in active conformation. Cooperativity another type of allosteric activation Stabilized active form Inactive form

65 Feedback Inhibition In feedback inhibition, the end product of a metabolic pathway shuts down the pathway Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed

66 LE 8-21 Active site available Initial substrate (threonine) Threonine in active site Enzyme 1 (threonine deaminase) Enzyme 2 Intermediate A Isoleucine used up by cell Feedback inhibition Active site of enzyme 1 cant bind theonine pathway off Isoleucine binds to allosteric site Enzyme 3 Intermediate B Enzyme 4 Intermediate C Enzyme 5 Intermediate D End product (isoleucine)

67 Specific Localization of Enzymes Within the Cell Structures within the cell help bring order to metabolic pathways Some enzymes act as structural components of membranes Some enzymes reside in specific organelles, such as enzymes for cellular respiration being located in mitochondria

68 LE 8-22 Mitochondria, sites of cellular respiration 1 µm

69 Catalysts So whats a cell got to do to reduce activation energy? –get help! … chemical help… ENZYMES G Call in the ENZYMES!

70 Enzymes Biological catalysts –proteins (& RNA) –facilitate chemical reactions increase rate of reaction without being consumed reduce activation energy dont change free energy ( G) released or required –required for most biological reactions –highly specific thousands of different enzymes in cells –control reactions of life

71 Enzymes vocabulary substrate reactant which binds to enzyme enzyme-substrate complex: temporary association product end result of reaction active site enzymes catalytic site; substrate fits into active site substrate enzyme products active site

72 Properties of enzymes Reaction specific –each enzyme works with a specific substrate chemical fit between active site & substrate –H bonds & ionic bonds Not consumed in reaction –single enzyme molecule can catalyze thousands or more reactions per second enzymes unaffected by the reaction Affected by cellular conditions –any condition that affects protein structure temperature, pH, salinity

73 Naming conventions Enzymes named for reaction they catalyze –sucrase breaks down sucrose –proteases break down proteins –lipases break down lipids –DNA polymerase builds DNA adds nucleotides to DNA strand –pepsin breaks down proteins (polypeptides)

74 Lock and Key model Simplistic model of enzyme action –substrate fits into 3-D structure of enzyme active site H bonds between substrate & enzyme –like key fits into lock Size doesnt matter… Shape matters!

75 Induced fit model More accurate model of enzyme action –3-D structure of enzyme fits substrate –substrate binding cause enzyme to change shape leading to a tighter fit conformational change bring chemical groups in position to catalyze reaction

76 How does it work? Variety of mechanisms to lower activation energy & speed up reaction –synthesis active site orients substrates in correct position for reaction –enzyme brings substrate closer together –diegstion active site binds substrate & puts stress on bonds that must be broken, making it easier to separate molecules

77 Got any Questions?!

78 Factors that Affect Enzymes

79 Factors Affecting Enzyme Function Enzyme concentration Substrate concentration Temperature pH Salinity Activators Inhibitors catalase

80 Enzyme concentration enzyme concentration reaction rate Whats happening here?!

81 Factors affecting enzyme function Enzyme concentration –as enzyme = reaction rate more enzymes = more frequently collide with substrate –reaction rate levels off substrate becomes limiting factor not all enzyme molecules can find substrate enzyme concentration reaction rate

82 Substrate concentration substrate concentration reaction rate Whats happening here?!

83 Factors affecting enzyme function substrate concentration reaction rate Substrate concentration –as substrate = reaction rate more substrate = more frequently collide with enzyme –reaction rate levels off all enzymes have active site engaged enzyme is saturated maximum rate of reaction

84 37° Temperature temperature reaction rate Whats happening here?!

85 Factors affecting enzyme function Temperature –Optimum T° greatest number of molecular collisions human enzymes = 35°- 40°C –body temp = 37°C –Heat: increase beyond optimum T° increased energy level of molecules disrupts bonds in enzyme & between enzyme & substrate –H, ionic = weak bonds denaturation = lose 3D shape (3° structure) –Cold: decrease T° molecules move slower decrease collisions between enzyme & substrate

86 Enzymes and temperature Different enzymes function in different organisms in different environments 37°C temperature reaction rate 70°C human enzyme hot spring bacteria enzyme (158°F)

87 How do ectotherms do it?

88 7 pH reaction rate pepsintrypsin Whats happening here?! pepsin trypsin

89 Factors affecting enzyme function pH –changes in pH adds or remove H + disrupts bonds, disrupts 3D shape –disrupts attractions between charged amino acids –affect 2° & 3° structure –denatures protein –optimal pH? most human enzymes = pH 6-8 –depends on localized conditions –pepsin (stomach) = pH 2-3 –trypsin (small intestines) = pH

90 Salinity salt concentration reaction rate Whats happening here?!

91 Factors affecting enzyme function Salt concentration –changes in salinity adds or removes cations (+) & anions (–) disrupts bonds, disrupts 3D shape –disrupts attractions between charged amino acids –affect 2° & 3° structure –denatures protein –enzymes intolerant of extreme salinity Dead Sea is called dead for a reason!

92 Compounds which help enzymes Activators –cofactors non-protein, small inorganic compounds & ions –Mg, K, Ca, Zn, Fe, Cu –bound within enzyme molecule –coenzymes non-protein, organic molecules –bind temporarily or permanently to enzyme near active site many vitamins –NAD (niacin; B3) –FAD (riboflavin; B2) –Coenzyme A Mg in chlorophyll Fe in hemoglobin

93 Compounds which regulate enzymes Inhibitors –molecules that reduce enzyme activity –competitive inhibition –noncompetitive inhibition –irreversible inhibition –feedback inhibition

94 Competitive Inhibitor Inhibitor & substrate compete for active site –penicillin blocks enzyme bacteria use to build cell walls –disulfiram (Antabuse) treats chronic alcoholism blocks enzyme that breaks down alcohol severe hangover & vomiting 5-10 minutes after drinking Overcome by increasing substrate concentration –saturate solution with substrate so it out-competes inhibitor for active site on enzyme

95 Non-Competitive Inhibitor Inhibitor binds to site other than active site –allosteric inhibitor binds to allosteric site –causes enzyme to change shape conformational change active site is no longer functional binding site –keeps enzyme inactive –some anti-cancer drugs inhibit enzymes involved in DNA synthesis stop DNA production stop division of more cancer cells –cyanide poisoning irreversible inhibitor of Cytochrome C, an enzyme in cellular respiration stops production of ATP

96 Irreversible inhibition Inhibitor permanently binds to enzyme –competitor permanently binds to active site –allosteric permanently binds to allosteric site permanently changes shape of enzyme nerve gas, sarin, many insecticides (malathion, parathion…) –cholinesterase inhibitors »doesnt breakdown the neurotransmitter, acetylcholine

97 Allosteric regulation Conformational changes by regulatory molecules –inhibitors keeps enzyme in inactive form –activators keeps enzyme in active form Conformational changesAllosteric regulation

98 Metabolic pathways A B C D E F G enzyme 1 enzyme 2 enzyme 3 enzyme 4 enzyme 5 enzyme 6 Chemical reactions of life are organized in pathways –divide chemical reaction into many small steps artifact of evolution efficiency –intermediate branching points control = regulation A B C D E F G enzyme

99 Efficiency Organized groups of enzymes –enzymes are embedded in membrane and arranged sequentially Link endergonic & exergonic reactions Whoa! All that going on in those little mitochondria!

100 allosteric inhibitor of enzyme 1 Feedback Inhibition Regulation & coordination of production –product is used by next step in pathway –final product is inhibitor of earlier step allosteric inhibitor of earlier enzyme feedback inhibition –no unnecessary accumulation of product A B C D E F G enzyme 1 enzyme 2 enzyme 3 enzyme 4 enzyme 5 enzyme 6 X

101 Feedback inhibition Example –synthesis of amino acid, isoleucine from amino acid, threonine –isoleucine becomes the allosteric inhibitor of the first step in the pathway as product accumulates it collides with enzyme more often than substrate does threonine isoleucin e

102 Dont be inhibited! Ask Questions!

103 Cooperativity Substrate acts as an activator –substrate causes conformational change in enzyme induced fit –favors binding of substrate at 2 nd site –makes enzyme more active & effective hemoglobin Hemoglobin 4 polypeptide chains can bind 4 O 2 ; 1 st O 2 binds now easier for other 3 O 2 to bind

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