Test 1 Flashcards
Explain the mechanism by which Rubisco is activated in the light through Rubisco activase. Note: Rubisco activase also undergoes further activation by the Thioredoxin-Ferredoxin system discussed in class.
Rubisco activase uses ATP to remove inhibitors from the active site of Rubisco that ‘stick’ in the dark, including the substrate RuPB.
-This allows Rubisco to be activated in the light.
-RubisCO activase links RubisCO with the light reactions of photosynthesis
What is the Thioredoxin-Ferredoxin system and exactly how does it alter the activity of enzymes in the light?
Many enzymes required for photosynthesis are activated post-translationally through the reduction of disulfide bridges
-The reduction of disulfide bridges in these proteins occurs through the Thioredoxin-Ferredoxin system
-Thioredoxin is a small polypeptide containing a conserved amino acid sequence cys-gly-pro-cys that is reduced by Ferrodoxin. Once reduced, Thioredoxin can reduce the disulfide bonds in photosynthetic proteins, which works to activate them.
How many active sites per Rubisco
8
since it contains 8 large subunits where the active site resides.
What does RuBP binding to the RubisCO active site prevent?
the Carbamylation reaction that activates RubisCO
are the activation site and active site are in the same position on Rubisco
No
Carbamylation occurs on a lysine residue in the protein separate from the active site
What is a specific characteristic of enzymes that are affected by the Thioredoxin-Ferredoxin system (i.e., this characteristic is not necessarily found in isozymic forms present in other cellular compartments)?
disulfide bridges that activate or deactivate the enzymes
What are the two categories of enzymes activated or deactivated by the Thioredoxin-Ferredoxin system, respectively?
activated: photosynthetic proteins
deactivated: oxidative pentose phosphate pathway (OPPP) proteins
Provide 2 examples in each category of enzymes activated or deactivated by the Thioredoxin-Ferredoxin system.
activated: rubisco activase, ATP synthase
deactivated: glucose-6P dehydrogenase, transaldolase
What is the functional significance of deactivation of OPPP enzymes in the light?
it prevents a futile cycle with the CBB Cycle
In general terms, what determines the direction of any biochemical reaction that involves a readily reversible enzyme-catalyzed reaction?
concentration of substrates and products determine the direction
Compare the Calvin cycle to the OPPP in terms of intermediary metabolites shared by both pathways;
Intermediary metabolites that are shared are transketolase, R-5-p Epimerase, and R-5-p l (these are enzymes, what are the substrates?)
Compare the Calvin cycle to the OPPP in terms of the enzymes shared and the direction of the reaction catalyzed by these enzymes.
the enzymes shared work at opposite times (light vs. dark) and work in opposite direction
Explain the division-of-labour between the CBB cycle and the OPPP in terms of function in a photosynthetic cell, including their role in providing intermediary metabolites for other synthetic reactions in the cell.
OPPP cycle generates 2 NADPH/ glucose in the dark + generates the same intermediary metabolites as the CBB Cycle for synthesis of various compounds in the dark
-CBB cycle provides intermediary metabolites sucrose, starch and for other synthetic pathways in the light
What is ‘net C assimilation/net photosynthesis’ and the methodologies used to measure it photosynthetic organisms?
net C assimilation is the overall rate at which a plant takes in CO2, subtracting the amount of CO2 it loses through respiration
-can measure it by using an O2 electrode to measure O2 concentration in solution or by using a leaf cuvette to measure leaf C exchange rates
Why is CO2 uptake measured for terrestrial plants and O2 evolution for aquatic organisms?
CO2 for terrestrial = the atmospheric CO2 concentration is low and there is a much reduced background of CO2, much easier to quantify small differences in CO2 concentration in air compared to O2
O2 for aquatic = in water the background O2 concentration is much reduced compared to air
What parameters can be determined from a CO2 response curve that examines the relationship between atmospheric CO2 level and net C assimilation?
as CO2 levels increase phoresp decreases
What is the Warburg effect and how was it determined?
-elevated O2 concentration inhibited CO2 fixation in plants
-determined by measuring O2 evolution in cuvettes
Provide a definition for photorespiration.
a light-dependent respiratory process that involves uptake of O2 and release of CO2
What environmental factors influence the rate of photorespiration?
-elevated O2
-decreased CO2
-(changes in the CO2/O2 ratio)
-drought due to closed stomates (restricts CO2 movement into a leaf)
-increased air temp
-high light due to increased leaf temp
What is the biochemical basis for photorespiration in plants?
oxygenation reaction catalyzed by Rubisco
Provide the reaction mechanisms for the carboxylation and oxygenation reactions catalyzed by Rubisco. You should know these reaction mechanisms, including where the O and C from O2 and CO2, respectively, are found in the reaction products.
oxygenase- O from O2 is found in 2-P glycolate and one is in OH-
carboxylase- C from CO2 ends up in 3- phosphoglycerate
What is the function of the photorespiratory C/N cycle in plants?
to recycle some of the C that ends up in 2-phosphoglycolate (for every 2 2-phosphoglycolate, 3 out of 4 Cs are recycled, 1 lost as CO2
Describe the C2 oxidative photosynthetic C/N cycle according to the nature of the pathway, including the metabolites consumed in the cycle
phosphoglycolate to glycolate that diffuses to the peroxisome. glycolate to glyoxylate and H2O2. glycine and serine are synthesized. Ammonium is also synthesized, and that must be re-assimilated into amino acids. The remainder of the reactions convert the 3-C amino acid serine to 3-PGA, which can re-enter the Calvin cycle.
Describe the C2 oxidative photosynthetic C/N cycle according to the metabolites synthesized in the cycle that have been shown to exit the cycle
H2O, 1/2O2, CO2, NH4+, ATP, NADPH and NADH
Describe the C2 oxidative photosynthetic C/N cycle according to the toxic intermediary metabolites produced
2-phosphoglycolate, glycolate, glyoxylate, and H2O2
Describe the C2 oxidative photosynthetic C/N cycle according to the enzymes involved in the pathway;
There are 8 enzymes in total (not including Rubisco) compartmentalized in three organelles.
Describe the C2 oxidative photosynthetic C/N cycle according to the three organelles involved and their specific roles in the photorespiratory cycle, including their association in the cell.
Chloroplast - RuBP to phosphoglycolate with Rubisco
Peroxisome - glycolate to glyoxylate to glycine
mitochondrion - glycine to serine with CO2, NH4+ and NADH produced
What are the 3 ways in which photorespiration affects net C fixation?
- competition between O2 and CO2 at Rubisco
- release of CO2 by glycine decarboxylase (1 CO2 evolved per 2 O2 fixed by Rubisco
- consumption of ATP and NADPH
What is the RubisCO specificity factor (SC/O) and what does it indicate about the relative rates of carboxylation to oxygenation by RubisCO?
Specificity Factor is used to calculate the specificity of a RubisCO for CO2 versus O2. As the factor increases, its preference for CO2 over O2 increases.
Explain how the relative rate of photorespiration to net C assimilation can be determined/modeled using the specificity factor.
based on an SC/O of 80 at 400ppm CO2 there are 3 corboxylations for each oxygenation by Rubisco
Explain why temperature impacts photorespiration.
As temp increases, the solubility of any gas decreases
The solubility of CO2 is decreased more than O2 as the temperature increases, and thus the CO2/O2 ratio decreases as temperature increases.
This favors the oxygenation over the carboxylation reaction by Rubisco, and thus higher temps favor phoresp
Not all organisms use Rubisco and the Calvin cycle for C fixation. What are general characteristics of the four alternative pathways for C fixation based on the organisms involved and the environments in which they are found;
-alternate pathways are only in archaea and bacteria
-most are chemolithotrophs or thermophilic
-mostly in low O2 or high temp environments
Not all organisms use Rubisco and the Calvin cycle for C fixation. What are general characteristics of the four alternative pathways for C fixation based on how these alternative pathways are adapted to specific environments
certain enzymes in the pathway are inhibited by O2 and would not work in terrestrial or many aquatic environments
Not all organisms use Rubisco and the Calvin cycle for C fixation. What are general characteristics of the four alternative pathways for C fixation based on nature of the cycles discussed in terms of key metabolites and end products of C fixation.
key metabolites = succinyl-CoA and acetyl-CoA
end products = acetyl-CoA (2C) or pyruvate (3C)
What are carboxysomes and how do they enhance C fixation in certain prokaryotic autotrophs?
They are protein based organelles in prokaryotes that facilitate CO2 fixation by allowing efficient utilization of bicarbonate (by carbonic anhydrase) and by suppressing photorespiration through concentrating CO2
Provide 5 reasons for why all eukaryotic photoautotrophs use the CBB cycle.
- alternate pathways operate in anoxygenic conditions and CBB can under aerobic
- some alternate pathways need reduced heavy metals which are not readily available in aerobic environments
- some alternate pathways have reduced ATP demands (good when light is low intensity) but most have sufficient access to light energy so use CBB
- only CBB produces triose-P, to produce this from other pathways needs gluconeogenesis which is energetically unfavorable
- euk. photoautotrophs needs lots of carbohydrates for storage and to synthesize cell walls, CBB allows the needed rates of synthesis
Define the quantum requirement of net C fixation.
QR = photons required per net C fixed
Why does the atmospheric O2 concentration effect QR
as atmospheric O2 decreases the amount of phoresp decreases so the QR decreases because it needs less photons for C fixation
Why does the quantum requirement level off at ~12.5 in C3 plants?
because this is the theoretical lowest QR to be expected in land plants due to the suppression of the oxygenation reaction by Rubisco at low O2 level. Why is the theoretical lowest limit not 9.5 photons per C fixed as discussed in Module 1? This is because products of the light reactions are needed for processes in addition to C-fixation, such as N- and S-assimilation, and sucrose and starch synthesis.
Provide 5 characteristics of C4/CAM plants as discussed in class.
- have a C3 cycle
- concentrate CO2 in photosynthetic cells up to ~1200ppm = suppressed phoresp
- initial fixation product in C4 plants is a 4C acid
- initial fixation product in C4 plants is a 4C acid fixed at night
- adapted to hot/ dry environments (allow less open stomata in the light
Explain how the model based on Rubisco kinetics can be used to quantify the quantum requirement of net C fixation in plants.
can use it to figure out how many RuBP were used at a specific CO2 level and then how many net CO2 were fixed which lets you calculate the QR
C4 plants can be further subdivided into three specific C4 types. What two factors are the basis for this subdivision?
- the product transported from the mesophyll to the BSC
- the pathway for regeneration of PEP
Provide some examples of C4 plants.
corn, sorghum, and sugar cane
Describe the CO2 concentrating mechanism found in C3-C4 photosynthetic intermediates
concentrated in the BSC because of Kranz anatomy
What are the three phases in C4 metabolism and their specific function?
- carboxylation of PEP in MC by PEP carboxylase to form a 4C organic acid
- transport of the 4C acid to a BSC and decarboxylation of the 4C acid to release CO2 and a C3 acid, CO2 is used by Rubisco in the C3 cycle
- C3 acid is transported back to the MC to regenerate PEP to complete the cycle
Explain the roles of PEP carboxylase and Rubisco in this process.
PEP Carboxylase is found in mesophyll cells and the 1st CO2-fixing enzyme to which CO2 comes into contact. Phosphoenolpyruvate (PEP) is a substrate for PEP Carboxylase in the mesophyll cells, and it combines with CO2 to form oxaloacetate (OAA), which is a 4 C organic acid.
Rubisco is used for the CBB cycle in the process to use the concentrated CO2
what is an advantage of having only PSI in the BSC
there are no stacked thylakoids in the BSC so cant have PSII which is primarily located on stacked thylakoids- This adaptation helps to reduce photorespiration in bundle sheath cells.
Why is a specialized anatomy necessary for C4 photosynthesis?
Because the chloroplasts containing PEP carboxylase need to be beside and surround chloroplasts containing RubisCO.
What is the nature of this specialized anatomy in C4 plants that require multiple cell types for C4 metabolism (i.e. Kranz anatomy), and in C4 plants that can perform C4 metabolism in single cells?
Kranz anatomy- specialized mesophyll and BSC
Some land plants show C4 phosyn in a single cell - requires dimorphic chloroplasts located in different cytoplasmic compartments
How does chloroplast ultrastructure vary between the bundle sheath and mesophyll cells in NADP-ME C4 types?
BSC- contain stroma-exposed thylakoids (no PSII only PSI)
MC- contain highly stacked thylakoids and stroma-exposed thylakoids (both PSII and PSI)
What is the functional significance of this ultrastructure in relation to Calvin cycle function?
The significance of this ultrastructure is that without PSII, there is no water splitting and thus no O2 evolution in bundle sheath cells. Thus, O2 generated by water splitting will not accumulate in the bundle sheath cells, which have thickened cell walls to prevent diffusion of CO2 out of the cell. This adaptation helps to reduce photorespiration in bundle sheath cells.
Why do C4 plants require an extra 2 ATP for C fixation compared to C3 plants?
Protein kinases require ATP as substrate to allow the phosphorylation, and a phosphatase removes the phosphate and deactivates PEP carboxylase
Describe the mechanism by which PEP carboxylase activity is regulated in C4 plants.
PEP carboxylase in C4 plants becomes activated in the light through phosphorylation of the protein mediated by PEP carboxylase kinase.
Protein kinases require ATP as substrate to allow the phosphorylation, and a phosphatase removes the phosphate and deactivates PEP carboxylase.
-regulated by the circadian clock.
Why does the quantum requirement for net C fixation remain relatively constant as temperature changes for C3 plants at saturating CO2 and for C4 plants at ambient CO2, but it changes with temperature for C3 plants at ambient CO2?
Changes with temperature for C3 plants at ambient CO2 because as the temp increases the QY decreases and the plants gets less efficient because phoresp is favoured.
Describe the CO2 concentrating mechanism found in C3-C4 photosynthetic intermediates.
glycine is exported from the mesophyll to BSC and then decarboxylated by glycine decarboxylase to release and concentrate CO2 in the bundle sheath
What characteristics are found in CAM plants, and what are examples of CAM plants?
they have a CO2 conc. mechanism and the first product of C fixation is a 4C organic acid
-ex. cacti, agave and orchids
What are the two major categories of CAM plants?
- obligate, constitutive CAM
- facultative inducible CAM = C3-CAM intermediates
What is the function for glucan and malate in CAM metabolism?
glucan = a type of starch that provides the C skeletons for malate formation
malate = acts as a temporary storage molecule for carbon dioxide
What are the roles for PEP carboxylase and Rubisco in CAM metabolism?
CO2 fixation
What are Phase II and IV metabolism in CAM plants?
Phase II = PEPC and Rubisco
Phase IV = Net CO2 fixation Rubisco/PEPC
under what condition can these Phase II and IV occur?
involve a situation when the stomates are open in the light in CAM plants, such that CO2 becomes available for further CO2 fixation by Rubisco. These phases typically occur near the beginning or end of day when water stress is reduced,
What do the terms C3, C4, and CAM mean in terms of the photosynthetic apparatus?
C3- C3 is first produced
C4- C4 is first produced
CAM - C4 is first produced but at night
Why can the quantum requirement for net C fixation be lower in C4/CAM plants compared to C3 plants?
when the temp increases C4 can become more efficient because phoresp is more enhanced and the C3 plants don’t have a CO2 conc. mechanism
-C4 plants have a higher ATP requirement per C fixed, at lower temps where phoresp is less favored C3 plants have a better quantum yield
Why is the water use efficiency better in C4/CAM plants?
they have evolved mechanisms to conc CO2 around Rubisco, allowing them to keep their stomata partially closed during the day, minimizing water loss through transpiration while still maintaining high photosynthetic rates
Why is Triose-P called the 1st end product of photosynthesis, whereas sucrose and starch are termed the principle or main end products of photosynthesis?
triose-P synthesized in the chloroplast is used to synthesize starch in the chloroplast and sucrose in the cytosol.
Compare sucrose and starch according to the compartmentation of their pathways for synthesis and their function in the plant cell.
sucrose
-synthesized in the cytosol during the light
and dark periods
- mobile
-water soluble
starch
-deposited in the stroma during the light
period
-used to make sucrose and other sugars in
the dark
-immobile, insoluble
Provide 4 reasons why sucrose is the primary transport sugar in plants.
- high energy content
- relative unreactive in living tissue (phloem); non-reducing
- uncharged and highly soluble
- not inhibitory to metabolic reactions
Why is sucrose called a non-reducing sugar, and how does sucrose differ from maltose?
because it does not have a reducing end like maltose which does on one side
What is starch?
Starch is a carbohydrate that stores energy in plants and is found in many foods. It’s a complex carb made of many sugar molecules joined together
Distinguish between amylose and amylopectin.
amylose = a straight chain of 1000 glucose units on average, has a helical structure
amylopectin = a branched chain of amylose
Why is leaf starch synthesized during photosynthesis often called ‘transitory’ starch, whereas starch synthesized in seeds is called a ‘storage’ form of starch?
What are the commonalities and differences between the pathways for sucrose and starch synthesis in photosynthetic tissues?
similarities: has triose-P isomerase, aldolase, fructose 1,6-bisphosphate, phosphoglucoisomerase…
differences: cellular location of enzymes and last synthesis steps
How are the pathways for sucrose and starch synthesis metabolically connected?
through the exchange of Triose-P and inorganic phosphate (Pi) between the chloroplast and cytosol
How does this metabolic connection affect partitioning between sucrose and starch?
connection makes it that sucrose and starch synthesis how reciprocity such that increased partitioning into one decreases partitioning into the other
Photoperiod can affect the proportion of triose-P partitioned into sucrose and starch in the leaf. How does photoperiod affect this partitioning, and what is the functional significance of this observation? (discussed in lecture)
Which enzymes are highly regulated in the sucrose and starch synthetic pathways?
-cytFBPase
-sucrose-P synthase
-ADP-glucose pyrophosphorylase
What reaction is catalyzed by cytosolic fructose-1,6-bisphosphatase?
makes Fructose 1,6-bisphosphate turn into fructose 6-phosphate which releases a Pi that moves back into the chloroplast
What reaction is catalyzed by sucrose phosphate synthase?
the synthesis of sucrose 6-phosphate from UDP-glucose and fructose 6-phosphate
What reaction is catalyzed by ADPglucose pyrophosphorylase?
the synthesis of ADP-glucose and PPi from glucose 1-phosphate and ATP,
How is this enzyme regulated?
Allosterically and post-translationally by phosphorylation (SPS).
What are 3 specific functions for the chloroplastic phosphate translocator in photosynthesis?
- provides triose-P in the cytosol for sucrose synthesis
- recycles inorganic phosphate (Pi) back to the chloroplast to make ATP
- maintains high stromal PGA/Triose-P ratio, which favors reduction of PGA to G3P
Describe the experiment showing that a correlation exists between the activation state of Rubisco and ATP levels in the chloroplast.
a correlation exists between the activity of RubisCO and the amount of ATP extracted from the stroma of chloroplasts; this correlation exists because the activity of RubisCO activase is mediated by ATP levels. Cycling of Pi between the chloroplast and cytosol provides a link between end product synthesis, the light reactions of photosynthesis (since Pi is need to synthesize ATP), and RubisCO (since ATP is needed by RubisCO activase to activate RubisCO).
Provide 3 properties of the chloroplastic phosphate translocator.
1.considered an ‘Antiporter’; an antiporter is a membrane-bound transport protein that simultaneously transports two compounds in the opposite direction across a membrane
2. only transports divalent cations, and thus the transporter is electrically neutral
3. It is the major protein found on the chloroplast inner membrane.
Provide 3 ways in which phosphate (Pi) cycling and the availability of Pi provide a link between components of photosynthesis.
- availability of ATP for Rubisco activation by activase in the chloroplast
- availability of Pi for ATP synthesis in the chloroplast
- the cycling of Pi released during end product synthesis in the cytosol and chloroplast
What regulates the breakdown of transitory leaf starch at night?
-conditions of darkness
-controlled by the circadian clock
How is starch remobilized in the chloroplast in the dark?
starch is degraded in the chloroplast at night and produces maltose and glucose and then transported into the cytosol
- glucose is then phosphorylated by a hexose kinase to allow further metabolism
How do the daytime and nighttime pathways for sucrose synthesis differ?
starch degradation at night is the only light-independent pathway in phosyn C metabolism
Since maltose/glucose are transported out of the chloroplast at night and not triose-P, the first three enzymes involved in sucrose synthesis in the light are not needed for sucrose synthesis in the dark, including cytFBPase
What are the 5 major inorganic forms of N on earth?
- Dinitrogen
- Ammonia
- Ammonium
- Nitrate
- Nitrite
Which form is the most prevalent on earth?
The majority of inorganic N is in gaseous N2
Which two major forms of N are available to plants through the soil and how do their properties differ?
nitrate and ammonium are the two forms of inorganic N directly available to plants through the soil. Note that nitrate and ammonium differ in their oxidation state and charge; ammonium has a + charge and thus can bind to soil colloids, whereas nitrate has a - charge does not and thus it can leach from soil
Why are N and N-containing compounds important for plants?
-N is a component of proteins, a.a., nucleic acids, pigments and plant hormones…
-it regulates growth processes
-C/N ratio is a signal for many processes
What are the 3 major N sinks in photosynthetic tissues?
- Rubisco
- e- transport
3.PSI, PSII and LHC
How much of the fixed N produced by the Haber-Bosch process ends up in waterways each year?
On average, estimates show that ~50% of the N used in agriculture leaches in the water system.
Why does so much N end up in the water system and what are the ecological consequences?
runoff and eutrophication
What are the three major processes by which plant tissues obtain N either as inorganic or organic N?
- from air (N-fixing bacteria)
- uptake from soil via roots as NO3- or NH4+
- assimilation of recycled N in the form of a.a (remobilization of organic N in leaves into seeds)
What is the driving force that allows uptake of nitrate and other compounds from the soil into the cell?
the proton gradient across the plasmalemma generated by a H+ ATPase
carrier protein
A carrier protein is a transmembrane protein that moves molecules and ions across cell membranes.
symport
a process that moves two different substances across a cell membrane in the same direction
antiport
a process that moves two or more molecules in opposite directions across a cell membrane.
What are the characteristics of the nitrate transporters in plants based on category of transporter (i.e., symporter or antiporter)
