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Photosynthesis, Glycolysis, Cell Division, DNA replication and Genes WITH HELPFUL ILLUSTRATIONS & DIAGRAMS

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University of Alberta
Biology (Biological Sciences)
Frank Nargang

The Process of Photosynthesis Occurs in chloroplasts; consider overall reaction Overall Reaction of Photosynthesis: LESS CHEMICAL ENERGY MORE CHEMICAL ENERGY Light Energy + nCO + nH O (CH O) + nO reduced oxidized 2 n 2 Essentially a redox reaction:  e- as part of H atoms in 2 O transferred to C2 , reducing it to a carbohydrate (CHO) o H O is oxidized to give O s 2 2  e- increase their potential energy as a result o ie. e- in CHO have more potential energy than in 2 O Energy to accomplish this is provided by light Overall reaction occurs via many steps A. The Light Reactions i) Light → electromagnetic energy; travels in waves; light from the sun is a mixture of wavelengths, which can be split by a prism. Physics of light complicated -some properties best described as waves -others best described as particles *photons → each carries a discrete amount of energy (shorter wavelength, more energy) When light hits matter 1. Reflected (Bounces 2. Transmitted 3. Absorbed off) through) ("Disappears" visibly) ii) Pigments → substances that absorb light of certain wavelengths if certain other wavelengths are White Light reflected and/or transmitted, then pigment has color of these Pigment wavelengths absorbs certain wavelengths if all wavelengths are absorbed, then pigment is black Green plants contain many pigments  Most abundant is chlorophyll a  Others collectively called 'accessory pigments' o includes chlorophyll b & other molecules (eg. carotenoids)  pigments each absorb distinct wavelengths of light o Therefore, range of wavelengths harvest for photosynthesis is quite broad; green is reflected. What happens when a pigment molecule absorbs a photon? Photon 'disappears' → true only because it no longer exists as visible light. But, photons carry energy & energy cannot disappear (1st TD law) Photon absorbed by pigment An e- in the pigment molecule is raised from its ground state to a higher, excited energy state 1. 2. -Returns to ground state -Returns to ground state -Gives off heat -Gives off a photon of lesser energy (longer wavelength than original → 'fluorescence') -Heat Would not be useful for a plant → energy is not harnessed However, in a chloroplast, chlorophyll a molecules are assembled with other components in the thylakoid membrane → allows the energy of absorbed photons to be harnessed for a useful purpose iii) Structures involved in photosynthetic election transfer  Exist in thylakoid membrane of chloroplast  Various small molecules & large enzyme complexes involved Photosystem II (PS II) PS II & PS I are named in order of discovery, not Water splitting enzyme according to any sequence of events Photosystem I (PS I) Cytochrome b -6 complex NADP reductase PS I & PS II structures  Both contain hundreds of pigment molecules (chlorophyll a. & accessory pigments) arranged with proteins specific for each system called light harvesting complexes or antennae o Absorb a broad range of wavelengths  Both contain reaction centers o Consist of a special pair of chlorophyll a molecules complexed to specific proteins o These reaction center chlorophylls absorb their own characteristic wavelengths due to the way they are controlled in the reaction center  P680: In PS II, reaction center chlorophyll absorbs 680 nm  P700: in PS I, reaction center chlorophyll absorbs 700 nm o Reaction centers are special. Energy from photons absorbed by all other pigment molecules in a photosystem is transferred to 2 chlorophyll a molecules in reaction center iv) Photosynthetic e- Transfer Reactions (Steps 1 & 2) light hits PS II Energy transferred to reaction center -energy absorbed by pigments chlorophyll a molecules e- in these chlorophyll a molecules excited to a higher energy state *Special structure of the reaction center keeps e- from falling back down to ground state s e- transferred to the primary electron acceptor and trapped (can't fall back to chlorophyll a) by molecule 'pheophytin' *Key step since energy from photons is not lost After e- transfer from the reaction center chlorophyll a molecules to the primary electron acceptor, the chlorophyll a molecules have become oxidized (photo-oxidized, because it's caused by light); primary electron acceptor reduced. Energy transfer between pigment molecules and eventually to chlorophyll a reaction centers is by 'resonance' → only transfer of energy, not electrons themselves. However, when chlorophyll a reaction center molecules have excited electrons, these are actually transferred to primary acceptor. M IDTERM CUTOFF (Step 3) s This leaves 'electron holes in the reaction center chlorophyll a molecules. e- are replaced by water water splitting enzyme (associated with PS II) H 2 1/2O +22 H + 2 e- utilized (indirectly) in Reduce reaction center later process of chlorophyll a molecules reducing NADP that have given up e- s Redox Reaction: H O 2xidized, chlorophyll a molecules reduced (Step 4) Now, a series of further electron transfer occurs (each is a redox reaction) Primary electron acceptor (pheophytin) plastoquinone (Pq) *At PS I, the electrons cytochrome b -f6 replace those electrons complex lost from PS I as it Potential Energy of e- plastocyanin harvests light energy* decreases with each transfer (Pc) (TD Law 2) PS I e- have been transferred from PS II to PS I using an electron transport chain in a series of redox reactions Has anything 'useful' happened? Yes. As e- pass from +lastoquinone to cytochrome b -6 complex, some of their energy is harnessed → results in transfer/pumping of H ions across thylakoid membrane from stroma to thylakoid space/lumen e- chain puts in energy to push H + Lumen Stroma + Then, H naturally diffuse back out. ATP is like a turbine, creating energy from ion flow Lumen Stroma Bacterial plasma membrane and the mitochondrial inner membrane also contain ATP synthases that have a similar structure  Also function by a similar mechanism: harnessing energy in an H gradient to form ATP o This type of reaction is called chemiosmotic coupling → first proposed by Peter Mitchell, 1961 Electrons have flowed from PS II to PS I. At PS I, they fill 'electron holes' Excited e- transferred from chlorophyll a reaction Energy transferred to PS I light energy harvested by reaction center chlorophyll center to PS I primary PS I antennae a molecules electron acceptor •NOT pheophytin; unknown molecule This leaves e- holes in reaction center chlorophyll a molecules of PS I. Filled by e- originating from PS II (which arise from splitting of H O) 2 (Step 6) From here, electrons will undergo another series of electron transfers in which they will gradually lose potential energy PS I primary electron acceptor ferridoxin This enzyme uses e- & H (from NADP+ reductase the H 2 splitting) to catalyze: enzyme + + + Potential Energy of e- NADP + 2 H + 2 e- → NADPH + H decreases with each transfer Reduced Oxidized (TD Law 2) + In NADPH + H , electrons still have relatively high potential energy → plant will take advantage of that in the carbon-fixation reactions Entire process is referred to as the 'non-cyclic electron flow pathway' of photosynthesis. Formation of ATP by this process is called 'non-cyclic photophosphorylation' + Summary: A series of e- transfers (redox reactions) has given NADPH + H and ATP Used in carbon fixation (Steps 7 & 8) Note: i) 2 O is the source of electrons for this pathway as they continually replace those lost from chlorophyll a reaction center molecules. ii) the series of reactions is also known as the 'Z' scheme → plot of electron potential energy looks like a sideways letter Z + Non-cyclic electron flow creates virtually equal amounts of ATP and NADPH + H . + However, carbon fixation reactions require ~1.5X more ATP than NADPH + H Solution: Plants can utilize PS I and some of the other components for e- transfer to make only ATP Cyclic electron flow pathway of photosynthesis To achieve correct balance of ATP and NADPH + H , plants sense levels of NADPH + H . Depending on the balance, they can engage the cyclic pathway to make ATP (uses PS I to harvest light energy) Notes: 1. Electrons end up back in PS I → travel a cyclic pathway s 2. Transfer of e- from ferridoxin to plastoquinone (instead of to NADP reductase as in non-cyclic pathway + 3. Proton pumping creates an H gradient which is harnessed by ATP synthase to make ATP + 4. ATP, but not NADPH + H is produced → called cyclic phosphorylation Use of both pathways gives correct amounts for use in carbon fixation reactions B. The Carbon-Fixation Reactions Occurs via the Calvin cycle & Occurs in stroma of chloroplast Melvin Calvin won Nobel Prize The step that actually fixes CO 2atalyzed by an enzyme  ribulose 1,5-biphosphate carboxylase/oxygenase (rubisco)  The enzyme adds CO to a 5-carbon sugar called ribulose 1,5-biphosphate (RuBP); already 2 present in the stroma CO + RuBP Unstable Intermediate 2 3-phosphoglycericacid 2 •5-carbon •6-carbon •3-carbons each So, CO 2as been fixed in this first step of the Calvin Cycle → didn't use ATP or NADPH + H in the reaction Required later in cycle to regenerate a Needed as a substrate for carbon supply of RuBP (CO 2 fixation CO 2ixation is a cyclic process & as the cycle continues, some of the fixed carbon can be 'siphoned off' for further use by cell  the 3-carbon molecule G3P (glyceraldehyde-3-phosphate) is required as a substrate in the cycle, but after 3 'turns' (each turn fixes 1 CO ) of the cycle, 2 one extra G3P exists and gets 'siphoned' off. Therefore, when looking at the cycle, consider it with respect to 3 CO being fixed 2 KNOW: -names of molecules & abbreviations -# of carbons and phosphates in each -where ATP +nd NADPH + H are consumed -where rubisco acts Note:  Grey balls=carbon atoms; yellow=phosphate  note where products of the light reactions are consumed  Cycle occurs in 3 phases  For every 3 CO2fixed, 1 G3P is 'siphoned' off Additional sets of 3 turns give more G3 Used to synthesize 6-carbon glucose & more complex molecules -often converted to starch for storage OR Serve as energy sources when broken down Serve as a carbon source for building other molecules needed by plant Both require further metabolic pathways + Generation of one molecule of G3P consumes 9 ATP & 6 NADPH + H Used in endergonic reactions of Used to reduce the fixed CO 2 the cycle to allow rearrangement of atoms A phenomenon occurs in plants that work against CO fixation: photorespiration 2 Often considered the 'yield' of photosynthesis +  From a certain amount of ATP & NADPH + H we get a certain amount of CO fixed 2  The 'goal' of photosynthesis is to fix CO into carbohydrate 2 Rubisco: We know that the CO fixa2ion step is done by Rubisco.  The letter C in rubisCo refers to carboxylase (which also refers to CO fi2ation reactions)  The letter O in rubiscO refers to oxygenase (oxygenase results in reduction of the net yield of photosynthesis) o How? Sometimes, rubisco combines RuBP with O instead of CO 2 2 RuBP + O2 3-Carbon molecule + 2-Carbon molecule "glycolate" stays in Calvin cyclleaves the Calvin cycle The opposite of what should happen occurs: -further metabolized *requires O consumption 2 -CO2is released Balance between the 2 possible reactions (O or C2 )? 2  That depends on the concentration of reactants competing for the active site on rubisco  When is relatively high (as in normal air), photosynthesis favored  When is relatively low, photorespiration favored Relatively low ratio develops on very bright hot days. Why? 1. Plants photosynthesize at high rates → CO consu2ed, O 2 produced 2. Pores on leaves (stomata) closed to prevent H O los2, but normally CO e2ters & O lea2es through the stomata. Since neither of these can occur with closed stomata, CO 2 concentration goes down, O concentration goes up 2 In some plants, this causes around 50% of CO originally fixed by 2 photosynthesis to be lost → big effect on production in agriculture Some species of plants have developed elaborate mechanisms to reduce photorespiration (ie. 4 photosynthesis or CAM metabolism) Chemoautotrophs Almost all life on earth depends on the sun for energy (directly/indirectly) However, some prokaryotes are capable of using energy stored in inorganic chemicals to fix CO . 2 They use reactions similar to the Calvin cycle to fix CO , but the starting sources for obtaining electrons 2 and energy for the fixation reactions differs completely from photosynthesis. Sources of chemical energy vary in different organisms. Eg. ammonium, nitrite, H , H S, S, Fe 2 2 Example: bacterium Alcaligenes eutrophus an e- transport chain used to transfer electro2s to O and to hydrogenase enzyme pump protons (H+) ProtoATP synthasesed by an (Overall Reaction: 2 H + 2 e- + 1/2 2 → 2 O) H2molecules cytoplasmic h+drogenase Used to redu+e NAD to NADH enzyme (2 → 2 H + 2 e-) + H Term Definition Photoautotroph An organism that harnesses light energy to drive the synthesis of organic compounds from carbon dioxide Photoheterotroph An organism that uses light to generate ATP but must obtain carbon in organic form Chemoautotroph An organism that obtains energy by oxidizing inorganic substances and needs only carbon dioxide as a carbon source Chemoheterotroph An organism that requires organic molecules for both energy and carbon Anabolic pathways (anabolism) A metabolic pathway that consumes energy to synthesize a complex molecule from simpler molecules Catabolic pathways (catabolism) A metabolic pathway that releases energy by breaking down complex molecules to simpler molecules Metabolism The totality of an organism's chemical reactions, consisting of catabolic and anabolic pathways, which manage the material and energy resource of the organism Extraction of Energy How is energy stored in carbohydrate molecules re-extracted for use in other processes? How to make ATP which can be used by the cell to perform energy-requiring reactions: We will consider with respect to 6-carbon molecule glucose as our starting point. Why?  Almost all organisms do metabolize glucose at least sometimes  Many energy-storing molecules are converted to glucose for energy extraction General scheme for metabolizing glucose in eukaryotes (for ATP production) Glycolysis(in cytosol) Glucose→ 2 Pyruvate Furthermetabolismofpyruvateby oneoftwo possibleroxygen)dependson abundanceof AEROBICRESPIRATION ANAEROBICRESPIRATION KrebsCycleand e- transportchain (-Convertspyruvateto waste products (ethanol, mitochondria) lacticacid) -use2O as a final electronacceptor -Differentpathways indifferentorganisms *DOESNOT u2e O or an electrontransportchain Glycolysis A series of enzyme catalyzed reactions and occurs in the cytosol. Net Result: 1 Glucose 2 Pyruvate + 2 ATP + 2 NADH + H + •6 carbons •3 Carbons Each *Note: An energy investment phase (steps 1-5: 2 ATP invested) and an energy yielding phase (steps 6-10: 4 ATP synthesized) → Net gain 2 ATP **Still lots of energy in 2 NADH + H & 2 Pyruvate; further metabolized Direct formation of ATP in an enzyme catalyzed reaction is called substrate level phosphorylation What to know about glycolysis pathway:  Pathway  Names of molecules and number of carbons; NOT structures or enzymes  Energy investment and yielding phases  Reactions where ATP or NADH + H are consumed/made Possible routes for further metabolism •pyruvate and electons of NADH + H enter mitochondria for oxidation by O via an aerobic If O present respiration pathway 2 2 •A fermentation pathway (which one depends on organism) If no O present 2 Fermentation (no O in cel2) Occurs in cytosol. 2 common types of fermentation; which used depends on organism. One 6-carbon If only glycolysis occurred, glucose If only glycolysis occurred, One 6-carbon cell's NAD would all exist + cell's NAD would all exist + Glycolysis 2 NAD + glucose as NADH + H (2 ATP produced) 2 NADH + Has NADH + H Glycolysis 2 NAD 2 pyruvate (3- (2 ATP produced) + carbon) 2 NADH + H 2 pyruvate (3-carbon) 2 acetaldehyde + 2 NADH + HNAD regenerated in 2 CO (2-carbon) NAD regenerated in 2 NADH + H 2 NAD conversion of + conversion of pyruvate → lactate 2 NAD acetaldehyde → ethanol 2 ethanol (2- (fermentation) 2 lactate carbon) This type of fermentation occurs in muscle cells This is the process by which yeast (Saccharomyces during extreme work. O consu2ed faster than it's cerevisae) produce ethanol being delivered → cells become anaerobic.  Brewing industry Therefore, cells have to use fermentation to get  Baking industry ATP from glycolysis Note: not all cells can perform fermentation → lack necessary enzymes Eg. nerve cells (brain), first to die if deprived 2f O Aerobic Respiration via Krebs cycle and electron transport chain; Take the oxidation of glucose to completion. Process begins by taking pyruvate from cytosol into mitochondria. Here, it's converted to an active form of acetic acid (acetate) called acetyl-CoA  NAD is reduced  acetyl group will enter Krebs cycle CoA = Coenzyme A → a B vitamin derivative; acts in a number of metabolic reactions  most common role is to transfer 1 molecule to another Example: first reaction of Krebs cycle acetyl-CoA (2C) + oxaloacetate (4C) citrate (6C) + CoA GTP = guanosine triphosphate related to ATP & ADP GDP = guanosine diphosphate As with ATP, GTP releases energy when broken down to GDP+P i FAD = flavin adenine dinucleotide s Carrier of e- and H atoms (like NAD or NADP) FAD (oxidized form); FADH (r2duced form) stores electrons in a relatively high energy state, but not as high as in NADH + H + Krebs Cycle AKA citric acid cycle/TCA (tricarboxylic acid) cycle; worked out by Hans Krebs (1930s)  Each step catalyzed by a specific enzyme  Acetyl group that enters the cycle and brings 2C atoms → 2 C atoms are later lost during cycle as C2 What to know about Krebs cycle:  Sequence of events in cycle  Names of molecules, # of C's  Don't need to know structure  Know what happens at each step Overall results so far (from 1 molecule of pyruvate entering mitochondria to finishing one turn of the cycle) i) 3 carbons entered mitochondria as pyruvate → 3 carbons oxidized to CO 2 ii) 1 molecule of ATP created by substrate level phosphorylation iii) Many reduced electron carriers formed (high energy electrons) Numbers would *per pyruvate molecule double if  1 NADH + H from acetyl-CoA formation considered per + glucose molecule  3 NADH + H from Krebs Cycle  1 FADH f2om Krebs Cycle Energy in the electrons of the reduced electron carriers used in the mitochondrial electron transport chain, found in mitochondrial inner membrane  Electrons flow down the chain (as pairs of electrons) in a series of redox reactions o O2is the final electron acceptor  Chain contains small electron carriers (Coenzyme Q, cytochrome C) and 4 large enzyme complexes o NADH dehydrogenase complex (Complex I) o Succinate dehydrogenase (Complex II) o cytochrome bc c1mplex (Complex III) o cytochrome c oxidase complex (Complex IV) *Note: Complex II is the Krebs cycle enzyme that does the reaction; electrons from FADH add2d directly to the electron transport chain during the reaction FAD FADH2 Succinate Fumarate Where’s the ATP? ATP is synthesized in mitochondria by mitochondrial ATP synthase that uses a chemiosmotic mechanism (as in the process of making ATP in photosynthesis) The mitochondrial 3 of the large enzyme complexes (I, III, IV but not II) use the potential energy ofATP synthase also electrons as the electrons flow through the compex to pump protons (H ) exists in the inner membrane  Contains a pore through which the H + From matrix to inter-membrane space  ATP synthase harnesses energy released as gradient dissipates Establishes electrochemical gradient of protons across the mitochondrial inner membrane ADP + P i ATP Oxidative Phosphorylation (OXPHOS) The processes of oxidizing substrates and transfer of electrons through the electron transport chain. + + Coupled to H pumping to give H gradient → used by ATP synthase to make ATP How many ATP formed by this process? Consider: 3 complexes (I, III, IV) t
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