Chapter 20

Photosynthesis:

* What is photosynthesis?
* What is light-dependent reactions?
* What is CO2 assimilation reaction? (light independent reactions)

* Photosyn: Encompassed by two reactions…
* Light-dependent reactions: Sunlight provides the energy for the synthesis of ATP and NADPH
* CO2 assimilation: ATP and NADPH are used to reduce CO2 to form triose phosphate through the Calvin cycle

What is the general pathway of the calvin cycle?

The flow of electrons:

* Where do electrons flow from?
* What are the three carriers?
* What are they coupled to?
* What is the driving force?

* Electron flow from the electron donors through a series of membrane-bound carriers
* Carriers: Cytochrome, quinones, and iron-sulfur proteins
* Electrons flow to coupled to the pumping of protons across a membrane to create an electrochemical gradient potential
* Serves as the driving force for ATP synthesis from ADP + Pi

* What is photophosphorylation?
* What do electron flow thorugh?
* What is the final electron donor?
* What is formed in the process?

* Photo: ATP synethsis driven by light
* Electrons flow through a series of membrane carriers to coupled to proton pumping
* H2O is the electron donor
* NADPH is formed

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What are the difference is the chemiosmotic mechanism for ATP synthesis in Chloroplast vs Mitochondria

Light energy creates good electron donors and electron acceptors

* Is water a good or bad electron donor? What about NADH?
* Why does photosynthesis need light energy?
* What is light energy coupled to?
* What agent is produce from this process? What does it produce?

* Water is a poor electron donor while NADH is a good one
* Photosynthesis requires light energy, needs light energy to create a good electron donor and electron acceptor
* The light-driven flow of electrons through specialized protein carriers is coupled to ATP synthesis
* A strong reducing agent (NADPH) is also produced and simultaneously, water is oxidized to O2, which is release into the atmoshpere

Chloroplasts are the site of light-driven electron flow and photosynthesis in plants:

* What are choloplasts?
* How permeable is there outer and inner membranes?

* Chloroplast: Organelles when both the light-dependent and CO2 assimilation reactions take place
* Contain a permeable outer membrane and an impermeable inner membrane with specific transporters

* What is the stroma?
* What is it analogous to?
* What does it contain?
* What are thylakoids?
* What does this contain?
* What are granal thylakoids?

* Stroma: Aqueous phase enclosed by the inner membrane
* Analogous to mitochondria matrix
* Contains most of the soluble enzymes required for assimilation reactions
* Thylakoids: Flattened sacks formed from an internal membranes system in the stroma
* Membranes contain the photosynthetic machinery
* Granal thylakoids: Disk-like pouches arranged in stacks connected by stromal thylakoids

The hill reaction:

* What is the hill reaction?
* What is the hill reagent?
* Where is the hill reaction perform?

* Reaction: Look at picture
* A is an artificial electron acceptor, or hill reagent
* Leaf extracts containing chloroplasts perform the hill reaction

* What are chlorophylls?
* What is occupying the central position?
* What is contained within cholorplasts?

* Phylls: Green, light-absorbing pigments in the thylakoid membrane
* Have polycyclic, planar structures with Mg2+ occupying the central position
* Chloroplasts contain both chlorophyll a and chlorophyll b

Electronmagnetic Radiation:

* What is a photon?
* On the visible color spectrum which color has the most photon energy? What about the least?

* Photon: A quantum of light
* Greater at the violent end of the spectrum than the red end

The Planck Equation:

* What wavelength have the highest energy? What about the lowest energy?
* What is the planck equation?

* A shorter wavelength or higher frequency corresponds to higher energy
* Taller or larger wavelengths or lower frequency corresponds to lower energy
* Equation: Picture

Excited and Ground States:

* What is the defintiion of quantum?
* What is its fate?
* What is an excited state?
* Stable or unstable?
* What is a ground state?

* Quantum: A quantity of energy in the photon equal to the energy of the electronic transition to a higher energy level
* To be absorbed, a photon much contain a quantum
* Excited state: A molecules state of energy following the absorption of a photon
* Generally unstable
* Ground: Stable state of energy

Fluorescence vs Excition:

* What if fluorescence?
* What light is fluoresced?
* What is exciton?

* Fluorescence: Light emission accompanying decay of excited moleculars
* Always at a longer wavelength (lower energy) than that of the absorbed light
* Exciton: Quantum of energy passed from an excited molecules to another molecule

* What are photosystems?
* What is a photochemical reaction center?
* What is it associated with?

* Systems: Functional arrays of light-absorbing pigments located in the thylakoid or bacterial membrane
* Center: Location where a photochemical reaction converts the energy of a photon into a separation of charge
* Associated with one pair of chlorophyll molecules that transduces light into chemical energy

What is the action spectrum?

Describes the relative rate of photosynthesis for illumination with a constant number of photons of different wavelengths

Accessory Pigments in Plants:

* What are these pigments?
* What do these pigments allow for?
* What are carotenoids?
* What is beta-carotenes?
* What are lutein?

* Pigments: Secondary light-absorbing pigments called carotenoids
* Accessory pigments allow for more visible light to be used
* Cartenoids: Yellow, red, or purple
* beta: A red-orange isoprenoid
* Lutein: A yellow carotenoid.

Organization for photosystems in the Thylakoid membrane?

* What are antenna molecules?
* Where is the energy absorbed move to?

* Antenna: Absorb light energy and transmit it rapidly and efficiently to the reaction center
* The energy from an absorbed photon moves from one antenna chlorophyll to another and another, until it arrives at the reaction center, where it promotes the photochemical reaction that sends electrons through a series of electron carriers.

What are light harvesting complexes (LHCs)?

Complexes of chlorophyll, other pigments, and binding proteins are located around the periphery of the core complex, usually in antennae.

What are the steps to the harvested light energy exciting electrons in the reaction center?

Charge separation initiates electron flow:

* What is used to create a charge separation?
* What does this separation induce?

* In the reaction center, energy (exciton) is used to create a charge separation
* The electric charge separation initiates electron flow through an oxidation-reduction chain

* What is type II photosystems?
* What microorangism is this mainly present in? (only this system)
* Where do electrons pass through?
* What is the cyclic electron transfer?

* Type II: Contains a single P870 reaction center, a cytochrome bc1 electron-transfer complex, and an ATP synthase
* In purple bacteria
* Electrons pass through pheophytin (chlorophyll alpha lacking its central Mg2+), quinone, and the cytochrome bc1 complex.
* Transfer: Light-driven cycle that provides the energy for proton pumping by the cytochrome bc1 complex

Type 1 Photosystems:

* What is type I?
* What microorganism is this present in?
* What is linear electron transfer?

* System: can send electrons through a cyclic electron transfer path or through a linear path that reduces NAD+ to NADH
* In green sulfur bacteria
* Linear: Pathway from the reaction center to the soluble iron-sulfur protein ferredoxin to ferredoxin: NAD+ reductase to NAD+

What the difference between cyclic. and linear?

Cyclic: Proton pumping so production of ATP

Linear: Production of NADH

What do reactions centers look like in vascular plants?

The first photosystem:

* What was the first one found?
* What type of system is it?
* What is the ratio of chlorophylls a and b?
* Where do electron pass through? Where does it end up?
* Why are electrons lost?

* The first one discovered was Photosystem II
* System: Pheophytin-quinone type of system like the purple bacteria photosystem
* Contains roughly equal amounts of chlorophyll a and b
* Electrons pass from the excited P680 special pair to the cytochrome b6f complex
* Electrons lost from P680 are replaced by electrons from H2O

The first photosystem: : Photosystem II

* What is the structure?
* What are the proteins that make it up?
* What forms the core?
* What composes the center?

* PSII is a dimer
* Proteins:
* 16 transmembrane and 3 peripheral
* 35 chlorophyll
* 2 phenophytins
* 11 beta carotenes
* 2 plastoquinones
* CP43 and CP47 form the core anteanea
* PSII reaction center is composed of D2 and D1

The first photosystem: PSII

* What is water oxidized to? Where is this done?
* Where does the exciton move between?

* What is oxidized to O2 at the MnCaO5
* Exciton moves between antenna molecules to P680 (the special pair of chlorophyll a molecules (Chla)2) in the reaction center.

Excitation of P680 in PSII

* Where is the electron passed?
* Where are the electrons removed from?
* What are plastoquinones?

* An electron passes from P680\* to pheophytin to a protein-bound plastoquinone PQA to PQB
* The electrons removed from P680 is replaced with an electron from the oxidation of water.
* Plastoquinones: Structurally and functionally similar to ubiquinones

* What is the overall reaction initated by light in PSII?
* What is PSII considered in terms of an enzyme?
* What does this do?

* Look at picture
* PSII is an oxidoreductase
* It oxidizes water molecules to produce protons and oxygen molecules and it reduces plastoquinone (PQ) to produce plastoquinol (PQH2)

Water is Split at the Oxygen-Evolving Center:

* What is the oxygen-evolving center?
* What is the cofactor?

* Center: Passes four electrons one at a time to P680+ (can only accept one electron at a time)
* Contains a Mn4CaO5 cofactor

Photosystem I:

* What is photosystem I (PSI)?
* What is the ratio of chlorophyll a and b?
* What is the structure?
* How many monomeric proteins are there?
* What is LHC? (just the aconym not the def)

* PSI: Structurally and functionally related to the photosystem of the green sulfur bacteria
* Contains a high ratio of chlorophyll a to b
* Structures: Trimer
* There are 16 proteins
* LHC: Light Harvesting Complex

Excitation of P700 in PSI:

* Where do electrons pass from?
* Where are electrons acquired from?
* What is Ferredoxin: NADP+ reductase?

* An electron passes from P700\* to an acceptor A0 (a chlorophyll molecule) to phylloquinone (Qk) through three Fe-S centers to ferredoxin
* P700+ acquires an electron from plastocyanin, a soluble Cu-containing electron-transfer protein
* Ferredoxin: NADP+ reductase: The fourth electron carrier in the chain which transfers electrons from reduced ferredoxin (Fd) to NADP+.

The Second Photosystem: Photosystem I

* What are the two paths of electron transfer?

* Linear: Electrons pass from the excited P700 special pair through a linear chain to NADP+
* Cyclic: Electrons pass from Fd to PQ through cytochrom b6f

What is the overall reaction of PS1?

PS1:

* How to light flows through the PS1?
* What is produced from it?
* What is oxidized?
* where are electrons flowing? What is the reaction?

* The light driven flow of electrons through specialized protein carriers is coupled to ATP synthesis
* A strong reducing agent (NADPH) is also produced and simultaneously water is oxidized to O2, which is released into the atmosphere.
* Electron flow from H2O to NADP+ according to the reaction→

The Cytochrome b6f Complex Links Photosystem II and I Conserving the Energy of Electron Transfer

* What is the cytochrome b6f complex?
* What is it analogous to?
* Where are electrons flowing from? What is produced?

* Cytochrome b6f complex: Contains a b-type cytochrome with two heme groups, a Rieske iron-sulfur protein, and cytochrome f
* Analogous to Complex III in mitochondria
* Electron flow through the complex produces a proton gradient across the thylakoid membrane

Cyclic Electron Transfer Allows Variation in the Ratio of ATP/NADPH Synthesized:

* What do linear electron create?
* What do cyclic electron produce?
* What does this allow for?

* Linear electrons produce NADPH and ATP
* Cyclic electrons transfer produces only ATP
* Allows plants to adjust the ratio of ATP to NADPH to match its needs

State Transitions Change the Distribution of LHCII between the Two Photosystems:

* What is the energy differences between PSl and PSll?
* How would PSII be underexcited?
* How is this prevented?

* The energy needed to excite PSl is less than the energy needed to excite PSll
* PSll would be chronically under excited if the two photosystems were physically contiguous
* Prevented by physically separating the two photosystems

Localization of PSl and PSll in Thylakoid Membranes:

* What is the definition of appressed?
* Where is PSII appressed?
* What does LHCII (light harvesting II) do?
* Is PSl appressed?

* Appressed: Pressed close to or lying flat against something
* PSII is appressed by the stroma
* LHCII mediates tight associations of adjacent membranes
* PSI is nonappressed

State Transition:

* What is it?
* What are the three steps?

* State transitions: Mechanism that adjust the distribution of LHCII between PSI and PSII


1. Accumulation of PQH2 (generated reduced by PSII faster than PSI can oxidize it)
2. Activates a protein kinase
3. Phosphorylated LHCII captures excitons for PSI to reverse the imbalance between electron flow in PSI and PSII

A Proton Gradient Couples Electron Flow and Phosphorylation:

* What does photoinduced electron flow result in?

* Photoinduced electron flow results in the net movement of protons across the membrane, from the stromal side to the thylakoid lumen

The Approximate Stoichiometry of Photophosphorylation has Been Established:

* How many protons are moved across the stroma into the lumen?
* What is the energy stored in the proton gradient per mole of protons?
* What is the overall reaction?

* around 12 protons move from the stroma into the thylakoid lumen per 4 electrons passed (1 O2)
* delta G = 2.3RT(pH)+ZF(delta lamba)= -17kj/mol
* Reaction: →

The ATP Synthase Structure and Mechanism Are Nearly Universal:

* What is the CF0CF1 complex?
* What is CF0?
* What is it similar to?
* What is CF1?
* What is it similar to?

* Complex: Enzyme responsible for ATP synthesis in chloroplast
* CF0: Transmembrane proton pore that is homologous to mitochondria F0
* CF1: Peripheral membrane protein complex similar to mitochondrial F1

The Mechanism of Chloroplast ATP Synthase:

* What is it identical to?
* What is condensed on the mitochondrial enzyme surface?
* What is released? What does it require to be released?
* What does the rotational catalysis engage?

* Identical to its mitochondrial analog
* ADP and Pi condensed to form ATP on the enzyme surface
* Release of enzyme-bound ATP required a proton-motive force
* Rotational catalysis sequentially engages each of the three beta subunits of the ATP synthase in ATP synthesis, ATP release, and ADP + Pi binding

The Appearance of Oxygenic Photosynthesis:

* When did cyanobacteria appear on earth?
* What did it acquire?
* What type of activity did it have?

* Appeared on Earth around 2.5 billion years ago
* Acquired two photosystems that operated in tandem: one of type II and one of type I
* Had water-splitting activity that released oxygen into the atmosphere

Photosynthetic Microorganisms Can Acquire Electrons From Other Donors:

* Where do photosynthetic microorganisms obtain electrons from?
* What does it form?
* What is the equation?

* Many photosynthetic microorganisms obtain electrons for photosynthesis from donors such as H2S or lactate
* Forms an oxidized product, such as elemental sulfur or pyruvate
* Equation →

What is the general form of phososynthesis?

Modern Cyanobacteria:

* How is ATP synthesized?
* Do they have mitochondria or chloroplasts?

* Can synthesize ATP by oxidative phosphorylation or by photophosphorylation
* Do not have mitochondria or chloroplasts

Dual Roles of Cytochrome b6f and Cytochrome c6:

* What is the functional homology of this?
* What does this give evidence to?

* Homology between:
* Cyanobacterial cytochrome b6f complex and the mitochondrial cytochrome bc1 complex
* Cyanobacterial cytochrome c6 and plant plastocyanin
* Gives evidence that the processes have a common evolutionary origin

Products of Photosynthesis:

* What do photosynthetic organism use?

* Photosynthetic organisms use ATP and NADPH to reduce atmospheric CO2 to trioses

CO2 Assimilation and CO2 Fixation:

* What is CO2 assimilation?
* What is the Calvin cycle? What is this also called?
* What is CO2 fixation?
* What do high concentration of ATP and NADPH allow for?

* CO2 assimilation: The process of converting CO2 to simple (reduced) organic compounds
* Via a cyclic pathway called the Calvin Cycle (reductive PPP)
* Fixation: The process of incorporation (fixing) CO2 into the triose phosphate 3-phosphoglycerate
* High concentrations of ATP and NADPH allow the chloroplast to carry out redox reactions that are thermodynamically unfavorable

Carbohydrate Metabolism is More Complex in Plant Cells:

* What pathways do plants have?

* The following:


1. Glycolysis pathway
2. Gluconeogenesis pathway
3. The PPP
4. And pathway for the reduction of CO2 to triose phosphate and the associated reductive PPP

The Carbon Dioxide Assimilation Occurs in Three Stages:

* How many enzymes are in this pathway?
* Where does it occur?


* What are the three stages?

* 13 enzymes in the pathway
* Occurs in the stroma of chloroplasts
* 3 stages: fixation, reduction, and acceptor regeneration

Stage 1 of CO2 Assimilation:

* What is made first?
* What are condensed together to form what?
* What is the total of this?

* 3-phosphoglycerate was made first with some of the carboxyl carbon radioactively labeled
* CO2 condenses with a five-carbon acceptor, ribulose 1,5-bisphosphate, to form two molecules of 3-phosphoglycerate
* A total of six molecules of 3-phosphoglycerate are formed

Stage 1 of CO2 Assimilation:

* What is C3 plants?
* What are some examples of this?
* What does rubisco do?
* What does it catalyze?

* C3 plants: Plants in which the three-carbon compound 3-phosphoglycerate is the first intermediate in photosynthesis
* trees, wheat, oats, rice, beans, peas, and spinach
* Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase): catalyzes the incorporation of CO2 into an organic form
* Catalyzes:
* The covalent attachment of CO2 to ribulose 1,5-bisphosphate
* The cleavage of the unstable 6C intermediate to form two molecules of 3-phosphoglycerate

Form I and Form II Rubisco:

* What is the first form?
* What concentration is it present in?
* What is the second form?

* Form I: Enzyme of vascular plants, algae, and cyanobacteria
* Present in high concentrations due to its low turnover number
* Form II: Enzyme of photosynthetic bacteria

Central Role of Mg2+ in the Active Site of Rubsico

* What is bound to the Mg2+?
* What does the Mg2+ bring together and orientate?

* A carbamoylated Lys side chain has a bound Mg2+ ion
* The Mg2+ ion brings together and orientates the reactants at the active site

What are the five general stages of CO2 Fixation (first stage of calvin cycle)

* The five steps are…


1. Enolate formation
2. CO2 nucleophilic attack by enolate
3. Hydroxylation at C3 carbonyl
4. Cleavage
5. Carbanion protonation

* In the first step of CO2 fixation (of the first stage) what is happening?
* What does Mg2+ do for this step?

* Step 1: Creation of an Enediolate Intermediate
* Mg2+ facilitates the interaction of carbamoylated Lys to ribulose 1,5-bisphosphate

* In the second step (of the first stage) of CO2 fixation what is happening?
* What does Mg2+ do for this step?

* Step 2: Nucleophilic Attack to Create a Beta-Keto Acid Intermediate
* Mg2+ polarizes CO2 to accept nucleophilic attack by enolate

* What is the third step (of the first stage) of CO2 fixation?
* What is the reaction?

* Step 3: Hydroxylation at C3
* Hydroxylation occurs at C3 of the beta-keto acid intermediate

* What is the fourth step (of the first stage) of CO2 fixation?
* What is the reaction?

* Step 4: Cleavage to Yield the first 3-Phosphoglycerate
* Cleavage of the hydrated intermediate produces one molecule of 3-phosphoglycerate

* What is the fifth step (of the first stage) of CO2 fixation?
* What is the reaction?

* Step 5: Protonation and Release of a Second 3-Phosphoglycerate
* Deprotonation of Lys resets the active site

Role of Rubsico Activase:

* What is the role when it is inactive/
* What is rubisco activase?
* What is exposed?

* Rubsico is inactive until carbamoylated on the e-amino group of Lys
* Rubisco activase: Promotes ATP-dependent release of ribulose 1.5-bisphosphate
* Exposes Lys to nonenzymatic carbamoylation

Stage 2 of CO2 Assimilation:

* What is the overall reaction?
* What is formed?

* 3-phosphoglycerate is reduced to triose phosphates
* A total of six molecules of triose phosphate are formed

Reduction part one (of stage two of CO2 assimilation):

* What are the two steps that occur during this part?
* How does the reaction proceed?

* Steps…


1. Transfer of phosphoryl group from ATP to 3-phosphoglycerate
2. NADPH reduced 1,3-bisphosphoglycerate
* The high concentrations of ATP and NADPH allow this thermodynamically unfavorable reaction to proceed

Reduction part two (of stage two fo CO2 assimilation):

* What are the two steps that occur during this part?
* What is used to regenerate this product? What is the product?

* Steps…


1. Triose phosphate isomerase makes glyceraldehyde 3-phosphate and DHAP
2. Condenses both fructose 1,6-bisphosphate
* Most G3P and F-1,6-BP gets used to regeneration ribulose 1,5-bisphosphate

Stage 3 of CO2 Assimilation Acceptor Regeneration:

* What is most of the triose phosphate used for?
* What about the rest?

* Five of the six molecules of phosphate are used to regenerate three molecules of 1,5-bisphosphate
* The sixth phosphate is the net product of photosynthesis

The third stage of CO2 Assimilation:

* What is the third stage (generally)?

* Stromal enzymes rearrange the carbon skeletons of triose phsphates to generate intermediates
* The Pentose Phosphates are converted to ribulose 5-phosphate, which is phosphorylated to ribulose 1,5-bisphosphate to complete the clavin cycle

The third stage of CO2 assimilation:

* What three reactions makes the process irreversible?

* Reactions…


1. Fructose 1,6-bisphosphate
2. Sedoheptulose 1,7-BP
3. Ribulose 5-phosphate kinase

Synthesis of Each Triose Phosphate from CO2 Requires Six NADPH and Nine ATP:

* What reactants make anabolic processes?
* What is provided for light dependent reactions?
* What is the ratio of consumption and production?

* Fixation of three CO2 yields one glyceraldehyde 3-phosphate (triose phosphate) for anabolic processes
* ATP and NADPH are provided by the light-dependent reactions of photosynthesis
* They are produced at roughly the same ratio as they are consumed (2:3)

A Transport System Exports Triose Phosphates from the Chloroplast and Imports Phosphate:

* Where is sucrose made? Where is starch made?
* What is the inner chloroplast membrane impermeable?

* Unlike starch, sucrose is made in the cytosol
* The inner membrane is impermeable to phosphorylated compounds

Roles of the Antiporter in the Transport of ATP and Reducing Equivalents:

* How is ATP and NADPH generated?
* Where is ATP and NADPH moved it?

* Oxidation of DHAP in the cytosol generates ATP and NADPH
* Moves ATP and reducing equivalents from the chloroplast to the cytosol

These processes are regulated by light:

* What are the two steps for light regulation?
* Are they coordinate?

* Steps


1. Light changes pH and Mg2+ in stroma
2. Light reduces disulfide bonds
* Processes that use light are coordinated

Four Enzymes of the Calvin Cycle Are Indirectly Activated By Light:

* What happens when chloroplasts are illuminated?
* What is promoted?

* Then they are illuminated?
* Concentrations of ATP and NADPH increase
* Stromal pH increases
* Stromal \[Mg2+\] increases
* Higher \[Mg2+\] and higher pH promotes
* Rubsico formation
* Fructose 1,6-BP activity

Some Stromal Enzymes Are More Active in an Alkaline Enviroment and at High \[Mg2+\]:

* What is compounds increased when pH and \[MG2+\] Increase

* F-1,6-BP activity increased more than 100 fold when pH and \[Mg2+\] rise

Light Activation of Several Enzymes of the Calvin Cycle:

* How are enzymes activated?
* What enzymes are activated?
* How are these enzymes deactivated?

* Enzymes are activated by light-driven reduction of disulfide bonds between critical Cys residues
* Ribulose 5-phosphate Kinase
* Fructose 1,6-BP
* Sedopetulose 1,7-BP
* Glyceraldehyde 3-phosphate DH
* Enzymes are inactive in the dark so hexose synthesis doesn’t compete with glycolysis

Light Activation of Several Enzymes of the Calvin Cycle:

* What is ferredoxin:thioredoxin reductase?
* Where are donated electrons going?

* Reductase: Catalyzes the reaction that passes electrons from ferredoxin to thioredoxin
* Reduced thioredoxin donates electrons from the reduction of the disulfide bonds of the light-activated enzymes

Processes that produce CO2:

* What is mitochondrial respiration?
* Where does this occur?
* What is photorespiration?
* What is it driven by?
* What does this result in?

* Mitochondrial Respiration: The oxidation of substrates to CO2 and the conversion of O2 to H2O
* Occurs in the dark
* Photorespiration: A costly side of the reaction of photosynthesis that consumes O2 and produces CO2
* Driven by light
* Results from the lack of specificity of rubisco (also an oxidase)

Photorespiration Results from Rubisco’s Oxygenase Activity:

* Why is Rubisco not specific?
* How many turns does it take to bind O2?
* What is 2-phosphoglycolate?
* What happens to carbons?

* Rubisco is not specific for CO2 as its substrate
* around 1 in every 3 or 4 turns, O2 binds and is incorporated into ribulose 1,5-BP
* 2-phosphoglycolate: A metabolically unneeded product resulting from rubisco using O2 as its substrate
* Carbons much be salvaged

Phosphoglycolate Is Salvaged in a Costly Set of Reactions in C3 Plants:

* What is glycolate pathway?
* What is consumed?
* What does this result in?

* Pathway: Converts two molecules of 2-phosphoglycolate to a molecule of serine and molecules of CO2
* ATP and O2 Consuming process
* Results in loss of carbon as CO2 by mitochondrial decarboxylation of glycine

Glycine Decarboxylase Complex:

* What is glycine decarboxylase complex?
* How much does it make up of all proteins?
* What is the serine hydroxymethyltransferase?
* What is the net reaction?

* glycine decarboxylase complex = catalyzes oxidative decarboxylation of glycine in the mitochondrial matrix
* makes up 50% of all proteins in the mitochondrial matrix in photosynthetic parts of some plants
* serine hydroxymethyltransferase = transfers the one-carbon unit of the glycine decarboxylase complex reaction from tetrahydrofolate to glycine, yielding serine•
* The net reaction is: 2 glycine + NAD+ + H2O ⟶serine + CO 2 + NH3 + NADH + H+

Glycolate Salvage Pathway is Wasteful:

* How much CO2 is produced during this pathway?
* How is this flux generated?
* How much of the proteins makes up the glycine decarb complex?
* How much does this reduce plant yield?

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* The carbon flux through the glycolate salvage pathway can produce 5x more CO2 than that produced by all oxidations of the citric acid cycle!
* To generate that much flux there needs to be tons of glycine decarboxylase
* The glycine decarboxylase complex makes is up to half the protein in some mitochondrial matrices!
* Usage of this pathway reduces plant yield 20 – \n 36%

The Process of Photorespiration:

* What is photorespiration?
* What is consumed?
* What is produced?
* What isn’t conserved?
* What is inhibited?

* photorespiration = the combined activity of the rubisco oxygenase and the glycolate salvage pathway
* consumes O 2
* consumes ATP from the chloroplast stroma
* produces CO 2
* does not conserve energy
* inhibits net biomass formation

In C4 Plants, CO2 Fixation and Rubisco Activity Are Spatially Separated

* What is a C4 pathway?
* What is C4 plants?
* Where do tropical plants and crops grow? Why?
* What prefers the C4 pathway?
* What do C4 have high rates of?

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* C4 pathway = the CO 2-assimilation process
* C4 plants = plants that utilize a CO2 assimilation process to minimize photorespiration
* Tropical plants and crops that grow at high light intensity and high temperatures
* High temperatures prefer this method b/c as temperature increases rubisco affinity for CO2 decreases
* C4 plants have high photosynthetic rates, high growth rates, low photorespiration rates, low rates of water loss and specialized leaf structure

Phosphoenolpyruvate (PEP) Carboxylase Fixes CO2:

* What is PEP carboxylase?

* Catalyzes the fixation of CO2 (as HCO3-) into oxaloacetate in the cytosol of leaf mesophyll cells

Reduction or Transamination of Oxaloacetate:

* What are the two things that oxaloacetate to do?

* Either:
* Reduction to malate by malate DH in a reaction that requires NADPH
* Transamination to aspartate

Oxidation and Decarb of Malate:

* What does malate pass through?
* What is a malic enzyme?
* What is reduced?

\
* malate passes through plasmodesmata into neighboring bundle-sheath cells
* malic enzyme = catalyzes the oxidation and decarboxylation of malate to yield pyruvate \n and CO 2
* reduces NADP + to \n NADPH

Rubisco Fixes CO2 as in C3 Plants:

* How is CO2 incorporate?

* Rubsico incorporates CO2 into C1 of 3-phosphoglycerate

Pyruvate Phosphate Dikinase:

* Where is pyruvate transferred to?
* What is the pyruvate Phosphate Dikinase?

* Pyruvate is transferred backs to the mesophyll cells
* Dikinase: Catalyzes the conversion of pyruvate to PEP and phosphate to pyrophosphate

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High Concentrations of CO2 Are Released From Malate:

* What happens when CO2 is released from malate?
* What does this allow for?
* What is suppressed?
* How is separation increases efficiency?

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* release of CO2 from malate in the bundle-sheath cells yields a sufficiently high local concentration of CO 2
* allows Rubisco to function near its maximal rate
* suppresses rubisco’s oxygenase activity
* So the separation into the bundle sheath increases efficiency!

Energy Cost of CO2 Assimilation:

* How many ATP does C4 plants need?
* How about C3?
* Why are C4 less efficient?

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* C4 plants need five ATP molecules to assimilate one molecule of CO 2
* C3 plants need three ATP molecules
* So less efficient than C3 CO2 assimilation but at high temperatures that becomes so inefficient that this is \n better

In CAM Plants, CO2 Capture and Rubisco Action Are Temporally Separated":

* What is a CAM plant?
* What plants are included with this?
* How does it present water loss?
* What do C4 separate?
* What are stomata?

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* CAM plants = plants that fix CO2 into malate in the dark and store it in vacuoles until daylight, when the stored malate serves as a source of CO2 for Rubisco
* succulents such as cactus and pineapple
* reduces loss of water vapor through stomata
* C4 separates trapping CO2 and CO2 fixation spatially, CAM plants separate trapping and fixation temporally!
* Stomata = pores in the leaves of plants. Only opening stomata at night prevents water vapor loss (during the day). CO2 is fixed and stored as malate at night, then released and fixed by rubisco during the day!

The Fate of Excess Carbohydrate:

* What happens during active photosynthesis?
* What happens to excess carbohydrates?
* What is it used for?
* What is startch?
* How is sugar nucleotide (ADP-glucose) made?
* What is starch synthesis?
* What is the reaction?

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* during active photosynthesis, plant leaves produce more carbohydrates than needed
* excess carbohydrate is converted to sucrose and transported to other parts of the plant
* used as fuel or stored (as starch or sucrose)
* starch = a high molecular weight polymer of D-glucose
* condensation of glucose 1-phosphate with ATP yields an activated sugar nucleotide (ADP-glucose)
* starch synthase = transfers glucose residues from ADP-glucose to preexisting starch molecules
* the overall reaction is: starchn + glucose 1-phosphate + ATP ⟶ starchn+1 + ADP + 2Pi

UDP-Glucose Is The Substrate for Sucrose Syn in the Cytosol of Leaf Cells:

* How is sucrose synthesized?
* What is Sucrose 6-phosphate Synthase?
* Where is sucrose transported?
* Is sucrose a good transporter? Why?

* sucrose is synthesized from UDP-glucose and fructose 6-phosphate, which are synthesized from triose phosphates in the plant cell cytosol
* sucrose 6-phosphate synthase = catalyzes the reaction of fructose 6-phosphate with UDP-glucose to form sucrose 6-phosphate
* Sucrose is transported to non-photosynthetic parts of the cell
* Sucrose is a good transport sugar because the unusual linkage is not hydrolyzed by common carbohydrate cleavage enzymes (amylase, etc.)

When does a plant cell make sucrose and when does it make starch?

The partitioning of triose phosphates between sucrose synthesis and starch synthesis is regulated by the enzyme F26BP, the concentration of which varies inversely with the rate of photosynthesis. F26BP inhibits synthesis of a sucrose precursor..

Fructose 2,6-BP As Regulator of Sucrose Synthesis:

* What is F26BP?
* What does it inhibit?
* What does it stimulate?
* What does it vary inversely to?
* What does inhibit that deal with sucrose formation?

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* Fructose 2,6-bisphosphate (F26BP) = regulates the partitioning of triose phosphates between sucrose synthesis and starch synthesis
* inhibits fructose 1,6-bisphosphatase (FBPase-1)
* stimulates PPi-dependent phosphofructokinase (PP-PFK-1)
* \[F26BP\] varies inversely with the rate of photosynthesis
* F26BP inhibits the synthesis of fructose 6-phosphate (the precursor of sucrose)

How do seeds store energy for germination?

* Seeds need energy because they can’t do photosynthesis
* They contain triglycerols that are converted to acetyl-coa
* Then the glyoxylate cycle can generate succinate

The Glyoxylate Cycle and Gluconeogenesis Produce Glucose in Germinating Seeds:

* What is glyoxysomes?
* What is the glyoxylate cycle?
* What is the reaction?

* glyoxysomes = specialized peroxisomes where acetyl-CoA is formed from triacylglycerols and the glyoxylate cycle occurs
* glyoxylate cycle = converts acetate to succinate or another four-carbon intermediate of the citric acid cycle
* Reaction: 2 acetyl-CoA + NAD+ + 2H2O ⟶ succinate + 2CoA + NADH + H+