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Biology Notes Exam 2

by: Leslie Lenchak

Biology Notes Exam 2 Bio121

Marketplace > Biology > Bio121 > Biology Notes Exam 2
Leslie Lenchak

GPA 3.8
Principals of modern biology1
william tezaghi

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Principals of modern biology1
william tezaghi
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Date Created: 10/14/15
September 28 15 Characteristics of life i CellularOrganization 2 Metabolism METABOLISM all reactions performed by an organism anabolism use energy to make bondspotentia energy change in free energy deltaG catabolism break bonds by the food you eat to get energy you needkinetic energy change in free energydeltaG BIOENGINEERS energy ability to do work in 2 states in cells 1 Potential stored energy generate electricity 2 Kinetic mOVeable energy The First Law of Thermodynamics used to do work Energy Life transforms potential into kinetic transformhtion potential to kinetic whats left is heat Laws of thermodynamics itquot The Second Law of Thermodynamics lincrgv tranmvrmatnm a V iFrrst Law Energy cant be created nor destroyed but can be i M39s 5quot I am El ll transformed l a r A J 39on earth energyflows from sun to heat 39some is diverted via life 2 Second Law When energy is transformed some become unavailable to do work lost as heat 3Third Law Definition The third law of thermodynamics states the Energy is transformed i entropy of a perfect crystal approaches zero as the temperature UNNW approaches absolute zero energy L tunable energy mvr luwd xtrm 1st Law Asystem is a region of space that includes the atoms or molecules that we are studying quoteverything elsequot is called surroundings States the amount of energy of the system plus the amount of energy of O 13939l ir our A3911quot ir a the surroundings is constant the total energy of the universe is constant energy cannot be created nor destroyed energy can only be transformed from one form to another 2nd Law is defined in term of entropy entropy measures disorders is a quantity that measures the randomness of the universe States the entropy of the universe always increases the entropy of a system can decrease as long as the entropy of the surround is increased by a greater amount DELTA H Enthalpy change is the name given to the amount of heat evolved or absorbed in a reaction carried out at constant pressure Gibbs Free Energy DeltaGdeltaHTdeltaS Free energy G energy available to do work 2 parts 1 Order Enthalpy H bond energy 2 Disorder T temperature EntropyS G Order Disorder G HTS deltaG lt O spontaneous exergonic deltaG gt O spontaneous backward endergonic deltaGO equilibrium AGO AHo TASo Iffree energy is NOT available the AHo A30 A60 Reaction reaction does not occur Gibbs Free Energy changes for reactions exo increase Productfavored endo decrease Reactanttavored EEEEpaIreactronchangefree O H decrease Tdependem 39 deltaGdeltaHTdeltaS endo in ame 7 TdePGNdem deltaG predicts waya reaction will spontaneous in last 2 cases only if 90 Temperature is such that AG lt 0 reactions go way that lowers free energy l 3quotquot quot En w Fov Browquot 39ti n39t 39 39x BIOENERGETICS delta predicts the way reactions will go reactions with triangle go as written exergonic reactions that release energy why does potassium chloride spontaneously disable in water even though its reaction is endothermic exergonic reactions that release energy Glucose in the presence of oxygen exergonic release energy while move from glucose to oxygen number becomes endergonic reactions that consume energy Photosynthesis makes glucose becomes requires energy exothermic release heat endothermic absorb heat deltaG says how reactions will go Rates depend on the activation energy E3 Energy needed to start reactions forms barrier Catalysts chemicals that up reactions rate by downing activation energy Stress bonds easierto break reactions both ways deltaG sets direction released unchanged Most metabolic reactions do not go at useful rates Ea is to high Solution catalysts substrate must be correct shape amino acids in active site bind structure and stress bonds ATP transferring energy cells All living cells use ATP for capture transfer and storage energy 4 Whats the role of ATP mpm pw39 WWW ATP captures and transfers free l ATP releases a large amount of l T 39 L J energy when hydrolyzed i Phosphate ATP can phosphorylate or donate phosphate groups to other molecules exogenic and endogenetic can be coupled ATPenergy created in Mitochondria ATP travels to where it is needed like the plasma membrane sodium potassium pump Currquot glut 3quot Vicsue quotOdua m rmo with m ninth11 rm 1 Arr4o quotdo Enzymes most biocatalysts are enzymes proteins that up rates gt l39OOO OOOX 10003 Of enzymes Substrate e iemg Enrymefsctst39ate Erzymerorcducts P39ccuts lea39mg Catalysts diff reactions acme ate 0t enr e cc rm39tx comicx actm Me of enzyme Control metabolism by controlling enzymes Diff cells have diff enzymes Named after substrate plus quotase DNase protein that destroys DNA Ribosomes catalyze reactions 12gt Cigt II II asequot enzyme Enzymes are the majority ofthe reactions and processes that occur in the human body are generated by biomolecules called enzymesVirtually all enzymes are proteins that act as catalysts in biological reactions such as glycolysis The rate of chemical reactions depends on its activation energy and enzymes increase the rates of reactions by decreasing the activation energyThe activation energy is the amount of energy that must be added to transform the reactants of the products 1All enzymes Increase the rate ofthe forward reaction as well as the reverse reaction by lowering the activation energy 2Although enzymes increase the rate ofthe reaction they do not increase or decrease how much product is formed That means that for catalyzed reactions the same concentration of products is reached at equilibrium as forthe un catalyzed reaction 3 Enzymes do not change the energy of the products and reactantsThis means that enthalpy change deltaHbond energy and the Gibbs free energy deltaG does not change 4 Enzymes themselves are not actually consumed during reactions Although they might alter in some ways momentarily they are always regenerated at the end of the reactionThis is a really important property of enzymes bc it means that a small quantity of enzymes can be used over and over again Enzymes lower Ea overcoming energy barrierEa activation energy Bind specific reactant molecules called substrates at the active site Enzymes are highly specific Specificity results from exact3 D shape of the active site eg ES gt ES gt EP Enzymes catalyze reactions using one or more of the following mechanisms 1 Orienting substrates to bond atoms together 2 Inducing strain in substances making them unstable 3 Temporarily add chemical groups to Iiu na39omtr substrates 5 U I u FERva 39 0 v 0 hoov 39 leasnuo N v quot In u quot 0 9quot sltolunu g Q0 39 kctinoAl 39 Al I mow quot o are quot 39 J 39 m talk u a 639 5quot 0quot C C an Enzymesubstrate models I lock and key active H quotquot0 a quot can add cyao site matches l substrates does not explain how they stress bonds does not explain whythey release products 2 Induced fit changes shape to fit upon binding substrate Explains how bonds are stressed Explains why products are released Regulation of Enzymes Irreversible inhibition permanently inactive enzyme Reversible inhibition Competitive inhibition noncompetitive inhibition Allosteric regulation n quot 11391390 0 9 v 0 N unii7 Sn 0 N quot 0 W n o 39rr39nlCA J wow u l 3961 0 Metabolism and the regulation of enzymes End product inhibition orfeedback inhibition one way to control a metabolic pathway end product non completely inhibits first step in pathway commitment step which shuts down the pathway Metabolic Pathways Metabolism is the set of chemical reactions that occur in a cell which enable it to keep living growing and dividing Metabolic processes are usually classified as catabolism obtaining energy and reducing powerfrom nutrients anabolism production of new cell components usually through processes that require energy and reducing power obtained from nutrient catabolism There is a very large number of metabolic pathways In humans the most important metabolic pathways are glycolysis glucose oxidation in order to obtain ATP citric acid cycle Krebs39 cycle acetyICoA oxidation in order to obtain GTP and valuable intermediates oxidative phosphorylation disposal of the electrons released by glycolysis and citric acid cycle Much of the energy released in this process can be stored as ATP pentose phosphate pathway synthesis of pentoses and release of the reducing power needed for anabolic reactions urea cycle disposal of NH4 in less toxic forms fatty acid Boxidation fatty acids breakdown into acetylCoA to be used by the Krebs39 cycle gluconeogenesis glucose synthesis from smaller percursors to be used bythe brain Catabolic Pathways and Production of ATP the breakdown of organic molecules is exergonic Fermentation is a partial degradation of sugars that occurs without 02 Aerobic respiration consumes organic molecules and 02 yields ATP Cellular Respiration Anaerobic Respiration is similar to aerobic respiration but consumes compounds other than 02 LABS 1 measuring enzymes 2 effect of enzyme 3 effect of T 4 effect of pH 5 other factors affecting enzymes Enzyme catalytic cycle 1 free substrate and enzyme enzyme binds substrate active site changes shape Reaction occurs Products released restart 2 and 4 are separate events boom l l LJ39I How good is an enzyme since catalysts increase rates measure reaction rates delta substrate or delta product Factors affecting enzymes a factors affecting any reaction 1 substrates and products 2 T increase substrate energy 3 catalysts must bind substrates b factors affecting protein shape c Activators amp Inhibitors d Cofactors factors that aid enzymes B Factors affecting Protein Shape Must be right shape to do theirjob T If temp gets to high it will denature proteins It will always go fastestjust before it starts to fall apart pH At low pH protein will have charge at high pH protein will be negative charged 39 alters ionizable amino acid more polar if charged must be charged to form ionic bonds Salt Competes for Hydrogen bonds also competing with ionic bond and active site Organic Solvents Break hydrophobic bonds Reducing agents Break disulfide bonds Covalent mods example P04 C Activators and Inhibitors Competitive inhibitor block active site Beat with more substrate Noncompetitive inhibitors bind allosteric sitesecond bonding site Different part of protein Activators bind allosteric site changes active site to active shape D Cofactors Many micronutrients are cofactors All nucleases need Mg as cofactor Deficiencies may cause disease example goitersiodine deficiency Coenzymes organic cofactors often carry chemicals removed in reactions they are made from vitamins B1 thiamine cofactor in respirationLACKof beriberi Rickets LACK of vitamin D Scurvy LACK of vitamin C Pellagra LACK of vitamin B3niacin NADnicotinamide adenine dinucleotide Pellagra lack ofvitamin B3niacin B3 niacin is active part of NAD2 nucleotides AMP is handle bound by many enzymes NMP is active oxidized NAD and reduced NADH carrier in respiration NAD takes two electrons from food the enzyme its bound to is taking e from food feeding it in and changing itPart of cells quotenergy currencyquot Carriers in many reactionsTrade energy NADH donates them Q Life s main energy currency Also makes RNA 3 subunits i ribose 2Adenine on i C 3 3 P04 on 5 C quotHigh energy covalent bonds linkthe P04quot High energy covalent bonds linkthe P04 Unstable due to 3 negative charges electrostatic repulsion entropy 39 ATP ADP P04 has low Ea ADP P04 gt stores energy ATP H20 ADP P04 gt breaks energy CELLS USE ATP TO DRIVE ENDERGONIC REACTIONS COUPLED REACTIONS join exergonic reaction releases energy amp endergonic reaction require energy 39 Total free energy of products lt substrates If less reaction will go 39 Couple many anabolic reactions to ATP hydrolysis Frees more energythan other reaction absorbs CELLS MAKE ATP AS NEEDED ATP is unstable so is not stored 39 Cell have ATPADP and P04 pool ATP is recycled ATPADP cycle BIOCHEMICAL PATHWAYS bio reactions occur in series A s product is B s substrates euk put all enzymes in same organelle Placing in membranes keep them closer Often join enzymes in complexes FEEDBACK INHIBITION Best to stop at start when have enough product PROBLEM product is differentfrom ist substrate SOLUTION product is noncompetitive inhibition of 1st enzyme RESPIRATION How cells harvest energy stores in food To stay alive cells need 1 Energy 2 Reducing power REDUCING POWER oxidation is normal since air is 21 OZ Reducing power is rare valuable Energy and Reducing power are often coupled Extract it by redox reactions Energy is extracted in stages 1 Digestion breakingfood macromolecules into subunits 2 Extracting e taking electrons away from subunits to oxidize them 3 Recovering energy by electron transport Use energy to make ATP Cellular respiration steps 23 Oxidative respiration 02 is final electron acceptor Fermentation organic is final electron acceptor HARVESTING ENERGY BY EXTRACTION E Energy transfer between atoms changes energy delta Energy depends on delta electronegativity electronegativity depends on 1 Distance to nucleus 2Atomic H e are lest electronegative transferfrees energy reason you can store energy in bonds between carbon and hydrogens Oxygen is most electronegative Most chemicals get oxidized Free energy by transferring energy to oxygen Electrons transfer from hydrogen to oxygen direct transfer from Hydrogen to Oxygen is an explosion Energy transport does it in steps Passes electrons to electronegative molecules Energy Freed by e transport makes ATP HETEROTROPHS MAKE ATP 2 WAYS i Substrate level phosphorylation direct transfer of P04 from substrate to ADP 2 Oxidative respiration 2 stages 1 Oxidizing food extracting electrons 2 Making ATP Occur in different places only link each makes substrates the others need GLUCOSE OXIDATION 3 parts i glycolysis in cytoplasm 2 Pyruvate oxidation in mito matrix 3 Krebs Cycle in mito matrix ATP generation 2 stages 1 electrontransport 2 ChemiosmoticATP synthesis Glycolysis 10 reactions in cytoplasm change 1 glucose to 2 pyruvate 2 phases 1 stage 1 energy input traps glucose in the cell and destabilizes its structure 2 stage 2 Payoff breaks down the glucose 6C molecules into smaller components 3 stage 3 harvests the energy to form ATP molecules and pyruvate STAGE 1aims to transform glucose into fructose 16 diphosphate in thee different steps phosphoration of glucose glucose moves into the cell with the help of a membrane transporter once inside the cytoplasm it undergoes a phosphoration process that catalyzes by a protein kinase called hexokinse this step is significant for 2 reasons 39 H makes glucose more polar which traps the glucose inside the cellThe negatively charged phospjate group prevents the glucose from moving across the cell membrane 39 The addition of a charged moiety onto the glucose destabilizes the structure and increases its energy this makes it more reactive and more likely to undergo glycolisis 39 The functionality of hexokinase like all protein depends on the presence of a divalent metal atom such as Mg2 or Mn2 The movement of glucose into the active site of hexokinase cause the two domains to rotate towards another creating an induced fit this steals off the glucose positions the 6th carbon next to the ATP and prevents the ATP from being hydrolyze by water isomerization In the second step the enzyme phosphoglucose isometric transformation an aldose 6phosphate into ketosefrutose 6 phosphate second phosphorylation phosphafructokinase PFK adds a second phosphoryl group onto the sugar this commits the sugar to glycolysis STAGE 2 the aim of stage 2 is to cleave the fructose 16 diphosphate into two three carbon molecules called glyceralehyde 3phosphate GAP Breakdown of fructose 16 diphosphate 39 An enzyme called aldalase catalyzes the breakdown of fructose 16 diphosphate into 2 different 3 carbon molecules glyceraldehyde 3phosphate and dihydroxyacetone phosphate DHAP INPUT 1 glucose 2 ATP 4 ADP 2 NAD Products OUTPUT 2 Pyruvate 2 ADP 4 ATP 2 NADH 4 steps glucose priming uses 2 ATP 1Glucose gt Fl 6bP 2 Cleavage and isomerization 3 Oxidation 4ATP generation Yields 2 ATPglucose used for2 priming 35 ofenergy available most is left in pyruvate and NADH all cells do glycolysis cells don39t need 02 evolved before 02 REGENERATING NAD Cells can reduce all NAD to NADH Glycolysis stops NO NAD M 1 oxidative respiration 2 Fermentation Organics final electron acceptor we product pyruvate to lactate Plants yeast pyruvate ethanol make 02 THE KREBS CYCLE 4 oxidations 1 makes NADH amp C02 2 Makes NADH and C02 same cofactors s PDH Oxidative respiration 1 oxidizingfood 2 MakingATP electron transport 3 parts i Glycolysis gt takes place outside mitochondria inside the cytoplasm of the cell its taking glucose break it down into 2Pyruvate with BC generate 2 ATP also chemical called NAD 2 Kreb cycle break down 2C acetyl CoA private dehydrogenase complex which gives off C02 also producing 2 ATP and adding energy to NAD and FADH2 they have high energy electrons 3 electron transport chain all energythat is in glucose is in NAD and FADH2 generate Hprotons as every p comes via makes ATP synthase lactic anaerobic respiration if to much tap build lactate acid need more 02 to break it down M Measuring glycolysis by fermentation measuring PDH and Krebs by delta pH due to delta HCO3 Measuring ETS by delta 02 Effects of ATP 02 food other factors affecting respiration PYRUVATE SYM PORTER H are also used to move many ets across IMM PHOTOSYNTHESIS Photosynthesis occurs in two stages both of which occur inside the chloroplasts of plant cells and algae Transforms light to chemical energy which are stored into chemical bonds Used to reduce organics Transform lightto potential energy Photosynthesis reverses oxidative respiration similar org 2 sep pathways 1 Light reactions in which light energy from the sun is converted into chemical energy which is temporarily stored in ATP and NADPH which is the energy carrier molecule use lightto pump protons by ets use pH to make ATP by chemisomosis 39 The first stage of photosynthesis includes the light reactions which require light to happenThis begins with light being absorbed in the chloroplasts of plant and algae cells 2 Light independent CALVIN CYCLE in the Calvin cycle In the Stroma Carbon dioxide and the chemical energy stored in ATP and NADPH is used to form organic compounds dark reactions use ATP and NADPH from light reactions to make organic compounds Only link each make others substrates The light reactions are sometimes referred to as lightdependent reactions because energy from light is required for the reactions The Calvin cycle is then referred to as lightindependent reactions orthe dark reactions because the Calvin cycle does not require light directly Energy Cycle Products of one are substrates for other Several parts are very similar Change lightto heat Respiration evolved from photosynthesis Early Workers Van Helmont plants do not change soil into plant Priestly i 771 Plants quotrestorequot air Ingenhousz 1806 C02 H20 light CH20 02 Van Niel 1930 C02 H28 light CH20 28 02 comes from H20 provided with H2l 8 O Blackman l 905 2 sets of reactions 1 light reactions quotT independent 2 quotdarkquot reactions quotT dependentquot enzymatic Light reactions 3 stages 1 catching a photon 1 photoevent 2 electron transport 3 ATP synthesis by chemiosmosis Photoevent pigment absorbs a photon 3 fats for excited electron 1 Returns to ground state emitting heat and longer wavelength light fluorescence 2 Transfer to another molecule by inductive resonance Excited e vibrates and induces adjacent electron to vibrate at same frequency transfers only energy Energy returns to ground state 1Catching a Photon photons energy particles that travel as waves Energy inversely related to wavelength visible light 400 700 nm caught by pigments molecules that absorbs light can only absorb specific photons Photons with exact energy need to push electrons to an outer orbital from ground to excited state Each pigment has an absorption spectrum wavelength it can absorb Pigments Chlorophyll a is most abundant pigment looks green Absorbs all wavelength but green green is reflected it absorbs many wavelengths due to complex structure Located in the membrane of the thylakoids are several pigments of which chlorophylls are the most important While there are several different types of chlorophyll the most important types are chlorophyll a and chlorophyll b Chlorophyll a absorbs less blue light but more red lightthan chlorophyll b does Neither ofthem absorbs much green light and they allow it to be reflected or transmitted This is why leaves and other parts of plants that have a lot of chlorophyll look green Only chlorophyll a is directly involved in the light reactions of photosynthesis Chlorophyll b assists chlorophyll a in doing so therefore it is an accessory pigment Other compounds in the thylakoid membrane include carotenoids which also function as accessory pigments Accessory pigments absorb the colors that chlorophyll a cannot absorb and so they enable plants to capture more of the energy in light In the leaves of plants the chlorophylls are generally present in larger numbers and so mask the colors of other pigments But in parts of a plant not involved in photosynthesis such as fruit and flowers the colors of other pigments are visible Additionally when plants lose their chlorophylls in the fall their leaves take on the colors of the carotenoids Absoxption Spectra of Photosynthetic Pigments Relative absorption 400 500 600 700 Wavelength nm CONVERTING LIGHT ENERGYTO CHEMICAL ENERGY Once the pigments in the chloroplast have captured light energy the next step is to convertthe light energy into chemical energy This chemical energy is temporarily stored in ATP and NADPH Oxygen is given off during these reactions Chlorophylls and carotenoids are clustered in groups of a few hundred pigment molecules in the thylakoid membrane Each group of pigment molecules and the proteins they are embedded in are called a photosystemTwo types of photosystems are photosystem I and photosystem They have similar kinds of pigments but have different roles in the light reactions Accessory pigments gcarotenoidsxanthophyll Absorbs wavelength which Chlorophyll misses 39 Chlorophyll B is an accessory pigment Others xanthophyll RED and carotenoids ORANGE Red Pigments are in the Vacuole they absorb sunlight 39 Action spectrum shows use of accessory pigments wavelength used for photosynthesis Plants use entire visible spectrum Wavelength Chlorophyll absorbs work best PHOTOSYSTEM Arrays that channel energy absorbed by any pigment to reaction center channel 2 photosystems PSI and PSII PSI reaction center absorbs 700 nm P700 PSII absorbs 680 nm P680 reaction center passes energy to primary electron acceptor a Photosystem n P680 Producing Chemical Energy Stroma Light energy is converted into chemical energy in a multiprotein complex Reacmn pm gm called a photosystem Two types of photosystems photosystem I PSI and WOWquot center electron photosystem II PSII are found in thethylakoid membrane inside the mama mm chloroplast Each photosystem consists of multiple antenna proteins that contain a mixture of 300 400 chlorophyll a and b molecules as well as other pigments like carotenoids Cytochrome b f Thylakom complex and ATP synthase are also major protein complexes quot39emb39ane in the thylakoid membrane that work with the photosystems to create ATP and NADPH b Photosystem I P700 Light A photosystem consists of a lightharvesting complex and a reaction center Pigments in the lightharvesting complex pass light energy to two special chlorophyll a molecules in the reaction center The light excites an electron from the chlorophyll a pair which passes to the primary electron acceptor The excited electron must then be replaced In a photosystem II the electron comes from the splitting of water which releases oxygen as a waste product In b photosystem I the electron comes from the chloroplast electron transport chain The two photosystems absorb light energy through proteins containing pigments such as chlorophyll The lightdependent reactions begin in photosystem II In E energy from sunlight is used to split water which releases two electrons two hydrogen atoms and one oxygen atom When a chlorophyll a molecule within the reaction center of PSII absorbs a photon the electron in this molecule attains a higher energy level Because this state of an electron is very unstable the electron is transferred to another molecule creating a chain of redox reactions called an electron transport chain ETC The electron flow goes from PSII to cytochrome b6f to PSI as electrons move between these two photosystems they lose energy Because the electrons have lost energy prior to their arrival at PSI they must be reenergized by PSI Therefore another photon is absorbed by the PSI antenna That energy is transmitted to the PSI reaction center This reaction center known as P700 is oxidized and sends a highenergy electron to reduce NADP to NADPH This process illustrates oxygenic photosynthesis wherein the first electron donor is water and is created as a waste product 9m transom mm Photosystem II In the photosystem II PSII reaction center energy from sunlight is used to extract electrons from water The electrons travel through the chloroplast electron transport chain to photosystem I PSI which reduces NADP to NADPH The electron transport chain moves protons across the thylakoid membrane into the lumen At the same time splitting of water adds protons to the lumen while reduction of NADPH removes protons from the stroma The net result is a low pH in the thylakoid lumen and a high pH in the stroma ATP synthase uses this electrochemical gradient to make ATP Cytochrome b6f and ATP synthase work together to create ATP This process called photophosphorylation occurs in two different ways 1 In noncyclic photophosphorylation cytochrome b6f uses the energy of electrons from PSII to pump hydrogen ions from the lumen an area of high concentration to the stroma an area of low concentration The energy released by the hydrogen ion stream allows ATP synthase to attach a third phosphate group to ADP which forms ATP This flow of hydrogen ions through ATP synthase is called chemiosmosis because the ions move from an area of high to an area of low concentration through a semipermeable structure 2 ln cyclic photophosphorylation cytochrome b6f uses the energy of electrons from both PSII and PSI to create more ATP and to stop the production of NADPH Cyclic phosphorylation is important to maintain the right proportions of NADPH and ATP which will carry out lightindependent reactions later on The netreaction of all lightdependent reactions in oxygenic photosynthesis is 2H20 2NADP 3ADP 3Pi gt 02 2NADPH 3ATP Replacing Electrons in Light Reactions The electrons from chlorophyll molecules in photosystem II replace the electrons that leave chlorophyll molecules in photosystem The replacement electrons are provided by water molecules An enzyme inside the thylakoid splits water molecules into protons electrons and oxygen 2H20 gt 4H 4e 02 For every two molecules of water split four electrons become available to replace those lost by the chlorophyll molecules in photosystem The protons produced are left inside the thylakoid and the oxygen diffuses out ofthe chloroplast to leave the plant Making ATP in Light Reactions An important part of the light reactions is chemiosmosis a process in which ATP in synthesized Chemiosmosis relies on a concentrated gradient of protons across the thylakoid membrane Some protons are produced by the splitting of water molecules and other protons are pumped from the stroma to the interior ofthe thylakoidThe energy required to pump these protons is supplied by the excited electrons passing through the electron transport chain of photosystem The concentration of protons is higher inside the thylakoid than in the stroma The concentration gradient represents potential energy which is harvested by an enzyme called ATP synthase located in the thylakoid membrane It makes ATP by adding a phosphate group to adenosine diphosphate ADP ATP synthase converts the potential energy of the proton concentration gradient into chemical energy stored in ATP Some ofthe protons in the stroma area also used to make NADPHTogether ATP and NADPH provide energy forthe second set of reactions in photosynthesis Cyclic Photophosphorylation Photophosphorylation refers to the use of light energy to ultimately provide the energy to convert ADP to ATP thus replenishing the universal energy currency in living things In the simplest systems in prokaryotes photosynthesis is used just forthe production of energy and not forthe building of any biological molecules In these systems there is a process called cyclic photophosphorylation which just accomplishes the ADP to ATP process for immediate energy for these cells This process uses only Photosystem and the chlorophyll P700 Photosynthetic phosphorylation or photophosphorylation is the process of phosphate group transfer into ADP to synthesize energy rich ATP molecule making use of light as external energy source According to chemi osmotic hypothesis Mitchell 1961 the ATP is synthesized on ATPase complexes located on the non appressed portions ofthylakoid membranes particularly towards margins A khcmok Otoqvom Show the hymn d Pom N quotam Combun one quot3904 Cotw n mmohouhxwm quot 939 039 A b quot391Cquot 39 An Was 39q quotgt a 0 2 I lt A y 39 ICy hf quot v 0 39 quot3 c l a t 39vx CW3 a r Iquot 4 0 395 com MO V y 2 O z 3 4w V 0 H u ramp cquot 39C quot lquotquot H I 03960 quot quot3 quotquot9 quot CQC Olygon honHg Cow During photosynthetic electron transport hydrogen protons H accumulate in the thylakoid space due to splitting of water and transport between PQH2 to Cytf Increase in the number of hydrogen protons in the thylakoid space results in increase of proton gradient Down flow of protons from high to low concentration along H conc gradientthrough ATPase complex provides the energy that allows an ATP synthase enzyme to produce ATP from ADP Pi Redox potential ev 13 1 40 q 03 O6 l 04 O2 lt Electron transpon chain CTS 1 Primary name electrons Energy for ATP e39ecquoton 2 e production acceptor as USN from E l 5 a 9 0 0amp0 energy d NADP gt Cb 2 LIV 3 S moon gt o H g Photophos inf39 H 5 phorylolloi 2 2e xx lilo a wwwma ordl etcnccscom Reaction canquot quotmi 4 2H V202 llghl Phololysls H20 PHOTOSYSTEM II Light Electron Transport flow and Noncyclic Photophosphorylation The electrons lost by P680 PSll are taken up by P700 PSl and do not get back to P680 ie unidirectional and hence it is called non cyclic phosphorylation The electrons pass through the primary acceptor plastoquinone PQ cytochrome complex plastocyanin PC and finally to P700 The electrons given out by P700 are taken up by primary acceptor and are ultimately passed on to NADP The electrons combine with H and reduce NADP to NADPHz The hydrogen ions also called protons are made available by splitting up of water Noncyclic photophosphorylation needs a constant supply of water molecules The net result of noncyclic phosphorylation is the formation of oxygen NADPH and ATP molecules Oxygen is produced as a waste product of photosynthesis Problem It only makes ATP No reducing power No electrons to make organics Redox potential ev Cyclic Photophosphorylation The electrons released by P700 of PSl in the presence of light are taken up by the primary acceptor and are then passed on to ferredoxin Fd plastoquinone PQ cytochrome complex plastocyanin PC and finally back to P700 ie electrons come back to the same molecule after cyclic movement A Hechon acceptor O8 E o C U m c 0 29 o N cyl be 39 39 quot ADP P 2 U 7 Reacllon centre 0392 39 ATP c l P700 0 Antenna molecules 02 PHOTOSYSTEM l Cyclic Photophosphomlation The cyclic photophosphorylation also results in the formation of ATP molecules just like in non cyclic Light photo phosphorylation As the electrons move downhill in the electron transport chain they lose potential energy and ATP molecules are formed in the same way as in mitochondria during respiration During cyclic photophosphorylation electrons from photosystem I are not passed to NADP from the electron acceptor Instead the electrons are transferred back to P700 This downhill movement of electrons from an electron acceptor to P700 results in the formation of ATP and this is termed as cyclic photophosphorylation It is very important to note that oxygen and NADPH2 are not formed during cycle photophosphorylation Comparison of Noncyclic PhotoPhosphorylation and Cyclic PhotoPhosphorylation N0 ncyclic photophosp ho rylati on Cyclic photophos phorylat ion Electrons do not come back to the Electrons come back to the same same molecule molecule First electron donor is water First electron donor is P700 PSI Involves both PSI amp PSII Involves PSI onlv Last electron acceptor is NADP Last electron acceptor is P700 PSI The net products are ATP NADPH and The product is ATP only 02 Photosystem 11 Evolved to get reducing power grafted onto PST t alters reaction centerto absorb P680nm cf P700nm oxidized P680 to make water Chemiosmotic ATP synthesis Same idea as Mito Create DELTApH Make ATP by rotational catalysis as H reenter Stroma Diff 1 Pump H into lumen Lumen pH is lowerthan Stroma Reverse orientation of ATP synthase 2 DELTApH is much larger pH less than 5 in lumen pH 8 in Stroma 3 DELTApH is made by ETS cyclic pho water splitting and NADPH synthesis Light Independent reaction take place in plant chloroplasts In this process sugars are made from carbon dioxideThe process known as the Calvin cycle uses products of the lightdependent reactions ATP and NADPH and various enzymes Light Dependent Reaction light energy from the sun is used to split water photolysis which has been sucked in by plants by transpirationWater when broken makes oxygen hydrogen and electronsThese electrons move through structures in chloroplasts and by chemiosmosis make ATP Calvin Cycle 3 parts i fixing C02 makes the plants one needs 2 reversing glycolysis 3 regenerating RuBP Plants use energy from the sun in tiny energy factories called chloroplasts Using chlorophyll in the process of photosynthesis they convert the sun39s energy into storable form in ordered sugar molecules such as glucose In this way from the air and water from the soil in a more disordered state are combined to form the more ordered sugar molecules Carbon dioxide is captured in a cycle of reactions known as the Calvin cycle or the CalvinBenson cycle after its discoverers It is also known as just the C3 cycle Those plants that utilize just the Calvin cycle for carbon fixation are known as C3 plants Carbon dioxide diffuses into the stroma of chloroplasts and combines 6H20 6C02 IZPCA Requires C lOG3Plo RuBP wnlhmix C 3cycle 12 ADP F i 2 MOPquot 392 12 G3 Provides 2 635 for synthesis of via UCtOSQ organk molecules diphosphate GGGGGG glwose sucrose others with a fivecarbon sugar ribulose15biphosphate RuBP The enzyme that catalyzes this reaction is referred to as RuBisCo a large molecule that may be the most abundant organic molecule on the Earth This catalyzed reaction produces a 6carbon intermediate which decays almost immediately to form two molecules of the 3carbon compound 3phosphoglyceric acid 3PGA The fact that this 3carbon molecule is the first stable product of photosynthesis leads to the practice of calling this cycle the C3 cycle In C3 plants the photosynthesis carbon fixation and Calvin cycle all occur in a single chloroplast C3 LOSE 500 H20C02 FIXED cell 030 0 quot rear ln C4 plants the photosynthesis takes place in a chloroplast of a thinwalled mesophyll ceFIXC02 C and a 4carbon acid is handed off to a thickwalled 6M 39 bundle sheathMAKE CH20 cell where the Calvin cycle occurs in a chloroplast of that second cell This a M M protects the Calvin cycle from the effects of photorespiration a a a FIX Increase the concentrationC02 at Rubisco 3W4 a n a a a C4ampCAM decrease Photorespiration amp WATRER MCquot PEP carboxylase fixes Later releases and rubiscoUse energy to increase C02 at Rubisco LOOSE 200 LOSS LOSS fix by WATER 1m ln CAM plants HAVE KRATZ ANATOMY The photosynthesis and initial carbon fixation occur at night and a 4carbon acid is stored in the cell39s vacuole During the day the Calvin cycle operates in the same chloroplasts Energy from E and from the reduced coenyzme NADPH is used to remove a phosphate group from 3PGA and reduce the resulting diphosphoglycerate DPGA to produce the 3 carbon sugar glyceraladehyde3phosphate G3P Some of this G3P is used to regenerate the RuBP to continue the cycle but some is available for molecular synthesis and is used to make fructose diphosphate The fructose diphosphate is then used to make glucose sucrose starch and other carbohydrates LOSE 50 WATER LOSS C4 isolates rubisco in space CAM isolates rubisco in Fixing C02 C02 RuBP two 3Phosphoglycerate PGA In orderto find this calvin student needed to feed cells 14 C02 C3 Photosynthesisis Enzyme Rubisco ribulose 15 biphosphate carboxylaseoxygenase most abundant amp important protein on earth Reversing Glycolysis PGA gt Glyceraldehyde 3PO4GBP uses 1 ATP and 1 NADPH REGENERATING RUBP In the Calvin Cycle is attached to ribulose biphosphateRuBP using the enzyme rubisco causing instability making the molecule split in half becoming 2 molecules of 3phosphoglycerate which are then reduced by NADPH becoming 3biphosphoglycerate and in the cycle 6 3biphosphoglycerates are made but only one ofthem is used to make sugarThe other 5 remaining molecules of 3biphosphoglycerate are then recycled to regenerate 3 molecules of ribulose bisphosphateRuBP using 3 ATP molecules PROBLEM changing 3C to C compound IN five 3C sugars OUT three 5C sugars uses 1 ATPRuBP C4SEPERATION IN SPACE BENEFITS 1 NO PHOTORESPIRATION 2 2 DECREASE H20 LOSS PROBLEM C4 USE 30 ATP GLUCOSE C3 USE 18 ONLY USEFUL IN HIGH LIGHT CRASSULACEAN ACID METABOLISIM CAM uses C3 and C4 pathways C4 at night use stroma let in FIX with PEP Case makes C4 acids stored in the vacuole Close stroma in day Decarboxylate C4 Fix CO3 by rubisco in cytoplasm Benefits 1 NO PR 2 decrease H20 loss 3 photosynthesize when have lots of energy Problems i cant store much C4 2 uses lots of energy 3 USE cam in dry environments PHOTORESPIRATION Rubisco can fix 02 cf C02 Phosphoglycplate becomes glycolatepoison Glucolate detox releases C02 undoes photosynthesis C3 plants can lose 50 of their fixed C both reactions occur at the same time It has long intrigued biologists that 02 has an inhibitory effect upon photosynthesis In the presence of elevated 02 levels photosynthesis rates are lower It is now known that this response to oxygen is due to competition between 02 and C02 on the Rubisco enzyme of the CalvinBenson cycleYou will recall that in the quotnormalquot reaction C02 isjoined with RUBP to form 2 molecules of 3PGA In the process called photorespiration 02 replaces C02 in a nonproductive wasteful reaction It is believed that photorespiration in plants has increased over geologictime and is the result of increasing levels of 02 in the atmospherethe byproduct of photosynthetic organisms themselvesThe appearance of C4type plants appears to be an evolutionary mechanism by which photorespiration is suppressed It has long been the dream of biologists to increase the production of certain crop plants such as wheat that carry on C3type photosynthesis by genetically reengineerthem to perform C4 type photosynthesis It seems unlikely that this goal will be accomplished in the nearfuture due to the complex anatomical and metabolic differences that exist between C3 and C4type plants Glycolate Detox Uses chloroplast peroxisomes and mitochondria Releases lCOZ Zglycolate Uses C02 and 1 ATP Why peroxisomes are near CP and Mito Catalyses break down LECTURE OU ESTIONS WHY DO SOME RNA MOLECULES ACT AS CATALYSTS THEY FOLD INTO JUSTTHE RIGHT SHAPE TO BIND SUBSTRATES AND STRESS CRITICAL BONDS SO AS TO LOWER THE ENERGY OF ACTIVATION OF CERTAIN REACTIONS HOW CAN CELLS CONTROL METABOLISM BY CONTROLLING THEIR ENZYMES How good is an enzyme How much does it increase the rate of the reaction it catalyses Succinylcholine is almost identical to acetylcholine but if mixed with enzyme that hydrolyzes acetylcholine the enzyme stops working this suggests that Succinycholine is a competitive inhibitor Why can one enzyme generate thousands of products Enzymes are released unchanged after each reaction and are therefore free to catalyze another reaction WHAT is a COENZYME a non protein organic molecule that binds enzymes and helps it catalyze a reaction Why are the bonds between ATPs P04 unstable The negatively charged phosphate groups repel each other WHATWILL HAPPEN TO THIS PATHWAY IF A MUTATION STOPS THE CELL FROM MAKING ENZYME 3 The pathway will stop atthe missing enzyme and an intermediate will accumulate WHICH OFTHE FOLLOWING WOULD YOU EXPECT IFYOU POISON YOUR LAB PARTNER WITH AZIDE WATER PRODUCTION WILL DECREASE YOU GO ON A DIET and LOSE 20 POUNDS WHAT HAPPENED to the FAT It was released as C02 and H20 YOU FIND THAT CELLS TREATED WITH AZIDE PROTON IONOPHORES OR CARBON MONOXIDE CANT IMPORT PYRUVATE INTO THER MITOCHONDRIA HOW DO THEY IMPORT PYRUVATE Active Transport WHY DOES CHLOROPHYLL LOOK GREEN Chlorophyll emits green Iightwhen its excited WHY IS NADPH THE E CARRIER PRODUCEED BY PHOTOSYNTHESISWHEREAS NADH lSTHE E CARRIER PRODUCTED BY ENZYMES NADPH HAS A DIFFERENT CHARGE AND SHAPE THEN NADH SO lT CCANT BE USED BYTHE SAME ENZYME HOW MANY PHOTONS FPR 02 8 i photon for every electron for every electron to get to water requires 2 photons have to take 4 different electrons from two different waters so 4 electrons elaborate an oxygen so 8 all together


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