2 From food webs to the life of a cell energyenergyenergy
3 Flow of energy through life Life is built on chemical reactionstransforming energy from one form to anotherorganic molecules ATP & organic moleculessunorganic molecules ATP & organic moleculessolar energy ATP & organic molecules
4 The First Law of Thermodynamics Energy cannot be created or destroyed, only transformed.Living systems need to continually acquire and transform energy in order to remain alive. “Free energy”: The energy available in a system to do work.
5 The Second Law of Thermodynamics Every time energy is transformed, the entropy (“disorder”) of the universe increases.In order to increase/maintain their internal order, living systems must process more ordered forms of matter in to less ordered ones
6 Living Systems are “Open” Systems Matter and energy move in to living systems from the environment. Living systems transform matter and energy and return it to the environment
7 Multi-Step Metabolism To increase control, living systems produce free energy in multiple-step pathways, mediated by enzyme catalysts
8 That’s why they’re called anabolic steroids! MetabolismChemical reactions of lifeforming bonds between moleculesdehydration synthesissynthesisanabolic reactionsbreaking bonds between moleculeshydrolysisdigestioncatabolic reactionsThat’s why they’re called anabolic steroids!
11 Chemical reactions & energy Some chemical reactions release energyexergonicdigesting polymershydrolysis = catabolismSome chemical reactions require input of energyendergonicbuilding polymersdehydration synthesis = anabolismdigesting molecules= LESS organization= lower energy statebuilding molecules= MORE organization= higher energy state
12 Endergonic vs. exergonic reactions - energy released- digestionenergy investedsynthesis+G-GG = change in free energy = ability to do work
13 Energy & life Organisms require energy to live where does that energy come from?coupling exergonic reactions (releasing energy) with endergonic reactions (needing energy)energy++digestionsynthesisenergy++
14 Why don’t stable polymers spontaneously digest into their monomers? What drives reactions?If reactions are “downhill”, why don’t they just happen spontaneously?because covalent bonds are stable bondsWhy don’t stable polymers spontaneously digest into their monomers?starch
15 Activation energyBreaking down large molecules requires an initial input of energyactivation energylarge biomolecules are stablemust absorb energy to break bondsNeed a spark to start a fireenergycelluloseCO2 + H2O + heat
16 Too much activation energy for life amount of energy needed to destabilize the bonds of a moleculemoves the reaction over an “energy hill”Not a match! That’s too much energy to expose living cells to!glucose2nd Law of thermodynamicsUniverse tends to disorderso why don’t proteins, carbohydrates & other biomolecules breakdown?at temperatures typical of the cell, molecules don’t make it over the hump of activation energybut, a cell must be metabolically activeheat would speed reactions, but… would denature proteins & kill cells
17 Reducing Activation energy Catalystsreducing the amount of energy to start a reactionPheeew… that takes a lot less energy!uncatalyzed reactioncatalyzed reactionNEW activation energyreactantproduct
18 Catalysts So what’s a cell got to do to reduce activation energy? get help! … chemical help…ENZYMESCall in the ENZYMES!G
19 Enzymes Biological catalysts proteins (& RNA) facilitate chemical reactionsincrease rate of reaction without being consumedreduce activation energydon’t change free energy (G) released or requiredrequired for most biological reactionshighly specificthousands of different enzymes in cellscontrol reactions of life
20 Enzymes vocabulary substrate product active site active site products reactant which binds to enzymeenzyme-substrate complex: temporary associationproductend result of reactionactive siteenzyme’s catalytic site; substrate fits into active siteactive siteproductssubstrateenzyme
21 Properties of enzymes Reaction specific Not consumed in reaction each enzyme works with a specific substratechemical fit between active site & substrateH bonds & ionic bondsNot consumed in reactionsingle enzyme molecule can catalyze thousands or more reactions per secondenzymes unaffected by the reactionAffected by cellular conditionsany condition that affects protein structuretemperature, pH, salinity
22 Naming conventions Enzymes named for reaction they catalyze sucrase breaks down sucroseproteases break down proteinslipases break down lipidsDNA polymerase builds DNAadds nucleotides to DNA strandpepsin breaks down proteins (polypeptides)
23 In biology… Size doesn’t matter… Shape matters! Lock and Key modelSimplistic model of enzyme actionsubstrate fits into 3-D structure of enzyme’ active siteH bonds between substrate & enzymelike “key fits into lock”In biology… Size doesn’t matter… Shape matters!
24 Induced fit model More accurate model of enzyme action 3-D structure of enzyme fits substratesubstrate binding cause enzyme to change shape leading to a tighter fit“conformational change”bring chemical groups in position to catalyze reaction
25 How does it work?Variety of mechanisms to lower activation energy & speed up reactionsynthesisactive site orients substrates in correct position for reactionenzyme brings substrate closer togetherdigestionactive site binds substrate & puts stress on bonds that must be broken, making it easier to separate molecules
26 Math Skills: Gibbs Free Energy 3.1: All living systems require constant input of free energyBe able to use and interpret the Gibbs Free Energy Equation to determine if a particular process will occur spontaneously or non-spontaneously.ΔG= change in free energy(- = exergonic, + = endergonic) ΔH= change in enthalpy for the reaction(- = exothermic, + = endothermic)T = kelvin temperatureΔS = change in entropy(+ = entropy increase, - = entropy decrease)
27 SpontaneitySpontaneous reactions continue once they are initiated. Non-spontaneous reactions require continual input of energy to continue.
28 Using the EquationTo use the equation, you’ll need to be given values.Exothermic reactions that increase entropy are always spontaneous/exergonicEndothermic reactions that decrease entropy are always non-spontaneous/endergonic.Other reactions will be spontaneous or not depending on the temperature at which they occur.
29 Sample ProblemDetermine which of the following reactions will occur spontaneously at a temperature of 298K, justify your answer mathematically:Reaction 1:A + B → ABΔ H: KJ/molΔ S: KJ / KReaction 2:BC→ B + CΔ H: KJ/molΔ S: KJ/K
32 Factors Affecting Enzyme Function Enzyme concentrationSubstrate concentrationTemperaturepHSalinityActivatorsInhibitorsLiving with oxygen is dangerous. We rely on oxygen to power our cells, but oxygen is a reactive molecule that can cause serious problems if not carefully controlled. One of the dangers of oxygen is that it is easily converted into other reactive compounds. Inside our cells, electrons are continually shuttled from site to site by carrier molecules, such as carriers derived from riboflavin and niacin. If oxygen runs into one of these carrier molecules, the electron may be accidentally transferred to it. This converts oxygen into dangerous compounds such as superoxide radicals and hydrogen peroxide, which can attack the delicate sulfur atoms and metal ions in proteins. To make things even worse, free iron ions in the cell occasionally convert hydrogen peroxide into hydroxyl radicals. These deadly molecules attack and mutate DNA. Fortunately, cells make a variety of antioxidant enzymes to fight the dangerous side-effects of life with oxygen. Two important players are superoxide dismutase, which converts superoxide radicals into hydrogen peroxide, and catalase, which converts hydrogen peroxide into water and oxygen gas. The importance of these enzymes is demonstrated by their prevalence, ranging from about 0.1% of the protein in an E. coli cell to upwards of a quarter of the protein in susceptible cell types. These many catalase molecules patrol the cell, counteracting the steady production of hydrogen peroxide and keeping it at a safe level. Catalases are some of the most efficient enzymes found in cells. Each catalase molecule can decompose millions of hydrogen peroxide molecules every second. The cow catalase shown here and our own catalases use an iron ion to assist in this speedy reaction. The enzyme is composed of four identical subunits, each with its own active site buried deep inside. The iron ion, shown in green, is gripped at the center of a disk-shaped heme group. Catalases, since they must fight against reactive molecules, are also unusually stable enzymes. Notice how the four chains interweave, locking the entire complex into the proper shape.catalase
34 Factors affecting enzyme function Enzyme concentrationas enzyme = reaction ratemore enzymes = more frequently collide with substratereaction rate levels offsubstrate becomes limiting factornot all enzyme molecules can find substrateWhy is it a good adaptation to organize the cell in organelles?Sequester enzymes with their substrates!enzyme concentrationreaction rate
36 Factors affecting enzyme function Substrate concentrationas substrate = reaction ratemore substrate = more frequently collide with enzymereaction rate levels offall enzymes have active site engagedenzyme is saturatedmaximum rate of reactionWhy is it a good adaptation to organize the cell in organelles?Sequester enzymes with their substrates!substrate concentrationreaction rate
38 Factors affecting enzyme function TemperatureOptimum T°greatest number of molecular collisionshuman enzymes = 35°- 40°Cbody temp = 37°CHeat: increase beyond optimum T°increased energy level of molecules disrupts bonds in enzyme & between enzyme & substrateH, ionic = weak bondsdenaturation = lose 3D shape (3° structure)Cold: decrease T°molecules move slowerdecrease collisions between enzyme & substrate
39 Enzymes and temperature Different enzymes function in different organisms in different environmentshot spring bacteria enzymehuman enzyme37°C70°Creaction ratetemperature(158°F)
40 How do ectotherms do it?Enzymes work within narrow temperature ranges. Ectotherms, like snakes, do not use their metabolism extensively to regulate body temperature. Their body temperature is significantly influenced by environmental temperature. Desert reptiles can experience body temperature fluctuations of ~40°C (that’s a ~100°F span!).What mechanism has evolved to allow their metabolic pathways to continue to function across that wide temperature span?
41 Metabolic StrategiesEctothermy: Conform internal temperature to environmental temperature.Endothermy: Regulate internal temperature within a narrow range.Both strategieshave advantages andtradeoffs.
42 Body Size Considerations Smaller animals need to produce more energy per unit of mass due to increased radiation of heat into the environment.
43 Free Energy Considerations & Reproduction Reproductive strategies are optimized for free energy considerations.Ex. Seasonal Reproduction.
44 Insufficient Free Energy Production: Individuals Insufficient free energy production by individuals will lead to disease and death.
45 Insufficient Free Energy Production: Populations If the individuals in the population are unable to survive, the growth rate of the population will decline
46 Insufficient Free Energy Production: Ecosystems If the populations in an ecosystem decline, the ecosystems will decrease in complexity
47 Math Skills: Coefficient Q10 3.1: All living systems require constant inputBe able to use and interpret the Coefficient Q10 equation:t2 = higher temperaturet1 = lower temperaturek2= metabolic rate at higher temperaturek1= metabolic rate at lower temperatureQ10 = the factor by which the reaction rate increases when the temperature is raised by ten degrees of free energy
48 Q10 tells us how a particular process will be affected by a 10 degree change in temperature. Most biological processes have a Q10 value between 2 and 3
49 Sample ProblemData taken to determine the effect of temperature on the rate of respiration in a goldfish is given in the table below. Calculate the Q10 value for this data. (°CTemperature (°C)Heartbeats per minute20182542
53 Factors affecting enzyme function Salt concentrationchanges in salinityadds or removes cations (+) & anions (–)disrupts bonds, disrupts 3D shapedisrupts attractions between charged amino acidsaffect 2° & 3° structuredenatures proteinenzymes intolerant of extreme salinityDead Sea is called dead for a reason!
54 Compounds which help enzymes Fe in hemoglobinActivatorscofactorsnon-protein, small inorganic compounds & ionsMg, K, Ca, Zn, Fe, Cubound within enzyme moleculecoenzymesnon-protein, organic moleculesbind temporarily or permanently to enzyme near active sitemany vitaminsNAD (niacin; B3)FAD (riboflavin; B2)Coenzyme AHemoglobin is aided by FeChlorophyll is aided by MgMg in chlorophyll
55 Compounds which regulate enzymes Inhibitorsmolecules that reduce enzyme activitycompetitive inhibitionnoncompetitive inhibitionirreversible inhibitionfeedback inhibition
56 Competitive Inhibitor Inhibitor & substrate “compete” for active sitepenicillin blocks enzyme bacteria use to build cell wallsdisulfiram (Antabuse) treats chronic alcoholismblocks enzyme that breaks down alcoholsevere hangover & vomiting 5-10 minutes after drinkingOvercome by increasing substrate concentrationsaturate solution with substrate so it out-competes inhibitor for active site on enzymeEthanol is metabolized in the body by oxidation to acetaldehyde, which is in turn further oxidized to acetic acid by aldehyde oxidase enzymes. Normally, the second reaction is rapid so that acetaldehyde does not accumulate in the body.A drug, disulfiram (Antabuse) inhibits the aldehyde oxidase which causes the accumulation of acetaldehyde with subsequent unpleasant side-effects of nausea and vomiting. This drug is sometimes used to help people overcome the drinking habit.Methanol (wood alcohol) poisoning occurs because methanol is oxidized to formaldehyde and formic acid which attack the optic nerve causing blindness. Ethanol is given as an antidote for methanol poisoning because ethanol competitively inhibits the oxidation of methanol. Ethanol is oxidized in preference to methanol and consequently, the oxidation of methanol is slowed down so that the toxic by-products do not have a chance to accumulate.
57 Non-Competitive Inhibitor Inhibitor binds to site other than active siteallosteric inhibitor binds to allosteric sitecauses enzyme to change shapeconformational changeactive site is no longer functional binding sitekeeps enzyme inactivesome anti-cancer drugs inhibit enzymes involved in DNA synthesisstop DNA productionstop division of more cancer cellscyanide poisoning irreversible inhibitor of Cytochrome C, an enzyme in cellular respirationstops production of ATPBasis of most chemotherapytreatments is enzyme inhibition. Many health disorders can be controlled, in principle, by inhibiting selected enzymes. Two examples include methotrexate and FdUMP, common anticancer drugs which inhibit enzymes involved in the synthesis of thymidine and hence DNA.Since many enzymes contain sulfhydral (-SH), alcohol, or acid groups as part of their active sites, any chemical which can react with them acts as a noncompetitive inhibitor. Heavy metals such as silver (Ag+), mercury (Hg2+), lead ( Pb2+) have strong affinities for -SH groups.Cyanide combines with the copper prosthetic groups of the enzyme cytochrome C oxidase, thus inhibiting respiration which causes an organism to run out of ATP (energy)Oxalic and citric acid inhibit blood clotting by forming complexes with calcium ions necessary for the enzyme metal ion activator.
58 Irreversible inhibition Inhibitor permanently binds to enzymecompetitorpermanently binds to active siteallostericpermanently binds to allosteric sitepermanently changes shape of enzymenerve gas, sarin, many insecticides (malathion, parathion…)cholinesterase inhibitorsdoesn’t breakdown the neurotransmitter, acetylcholineAnother example of irreversible inhibition is provided by the nerve gas diisopropylfluorophosphate (DFP) designed for use in warfare. It combines with the amino acid serine (contains the –SH group) at the active site of the enzyme acetylcholinesterase. The enzyme deactivates the neurotransmitter acetylcholine.Neurotransmitters are needed to continue the passage of nerve impulses from one neurone to another across the synapse. Once the impulse has been transmitted, acetylcholinesterase functions to deactivate the acetycholine almost immediately by breaking it down. If the enzyme is inhibited, acetylcholine accumulates and nerve impulses cannot be stopped, causing prolonged muscle contration. Paralysis occurs and death may result since the respiratory muscles are affected.Some insecticides currently in use, including those known as organophosphates (e.g. parathion), have a similar effect on insects, and can also cause harm to nervous and muscular system of humans who are overexposed to them.
59 Allosteric regulation Conformational changes by regulatory moleculesinhibitorskeeps enzyme in inactive formactivatorskeeps enzyme in active formConformational changesAllosteric regulation
60 Cooperativity Substrate acts as an activator substrate causes conformational change in enzymeinduced fitfavors binding of substrate at 2nd sitemakes enzyme more active & effectivehemoglobinHemoglobin4 polypeptide chainscan bind 4 O2;1st O2 bindsnow easier for other 3 O2 to bind
61 Metabolic pathways A B C D E F G A B C D E F G enzyme1enzyme3enzyme2enzymeenzyme4enzyme5enzyme6Chemical reactions of life are organized in pathwaysdivide chemical reaction into many small stepsartifact of evolution efficiencyintermediate branching points control = regulation
62 Whoa! All that going on in those little mitochondria! EfficiencyOrganized groups of enzymesenzymes are embedded in membrane and arranged sequentiallyLink endergonic & exergonic reactionsWhoa! All that going on in those little mitochondria!
63 allosteric inhibitor of enzyme 1 Feedback InhibitionRegulation & coordination of productionproduct is used by next step in pathwayfinal product is inhibitor of earlier stepallosteric inhibitor of earlier enzymefeedback inhibitionno unnecessary accumulation of productA B C D E F Genzyme1enzyme2enzyme3enzyme4enzyme5enzyme6Xallosteric inhibitor of enzyme 1
64 Feedback inhibition Example threonineFeedback inhibitionExamplesynthesis of amino acid, isoleucine from amino acid, threonineisoleucine becomes the allosteric inhibitor of the first step in the pathwayas product accumulates it collides with enzyme more often than substrate doesisoleucine