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BBMB 405 : EXAM 1
Overall, what is produced by the light reactions of photosynthesis? |
oxygen, chemical energy (ATP, NADPH) |
Overall, what is produced by the dark reactions of photosynthesis? |
hexose, ADP, NADP+ |
In the Calvin Cycle/dark reactions, what are NADPH and ATP used for? |
to drive CO2 reduction to form hexose |
How is reducing power generated in the light reactions? |
electron transfer through photosystems I and II |
Where do the primary events of photosynthesis take place? |
thylakoid membranes |
What is the stroma? |
-space between the inner membrane and the thylakoid membranes
-location of the dark reactioins |
What are stroma lamellae? |
regions of the thylakoid membrane linking different grana (stacks of thylakoids) |
What are the major components of thylakoid membranes? |
galactolipids and sulfolipids |
Describe the major structural features of chlorophyll. |
-magnesium center
-pyrrole ring structure, with one reduced pyrrole ring
-an additional 5 carbon ring fused to a pyrrole ring
-a phytol group |
Why are chlorophylls such effective photoreceptors? |
the conjugated double bonds in their structure |
What happens when an electron is excited, and how does being near the photosystems change this? |
-normally when an electron is excited, it releases heat and returns to ground state
-in photosystems, there is an acceptor molecule nearby |
What is photoinduced charge separation? |
-the excited electron moves from excited (donor) molecule to the acceptor, thus resulting in a positive charge on the donor and a negative charge on the acceptor |
What is the name given to the site of charge separation? |
reaction center |
What initiates charge separation? |
-a special pair of chlorphylls
-absorb a very specific wavelength of light, which often gives the special pair its name |
What is the makeup of the reaction center in bacteria? |
-4 bacteriochlorophyll
-2 bacteriophytin
-2 quinones
-1 ferrous non-heme iron |
What is the major difference between bacteriochlorophyll and chlorophyll? |
-magnesium center
-pyrrole ring structure, with one reduced pyrrole ring
-an additional 5 carbon ring fused to a pyrrole ring
-a phytol group |
Describe the structure of bacteriophytin. |
1. P960 absorbs light and transfers an electron to bacteriophytin (BPh) via bacteriochlorophyll (BCh), giving P960+ and BPh-
2. Quinone A quickly grabs the electron from BPh-, forming BPh and Qa-. One of the hemes on the reduced cytochromes gives an electron to P960+, thus restoring P960.
3. The electron moves to Qb. A 2nd photon is absorbed and transferred throught he pathway to Qb, reducing Qb to QbH2. Qb is near the cytoplasmic side, so it pulls two protons in, contributing to the proton gradient.
4. QbH2 then enters the quinone pool, where it is reoxidized to Qb by bc1. bc1 transfers the electrons back to the cytochrome, thus completing the cycle. The process of bc1-->cytochrome pumps protons into the periplasmic space, thus generating the proton gradient. |
What are the steps of the electron chain in the photosynthetic bacterial reaction center? |
-normally when an electron is excited, it releases heat and returns to ground state
-in photosystems, there is an acceptor molecule nearby |
What are the steps of the electron chain in the photosynthetic bacterial reaction center? |
1. P960 absorbs light and transfers an electron to bacteriophytin (BPh) via bacteriochlorophyll (BCh), giving P960+ and BPh-
2. Quinone A quickly grabs the electron from BPh-, forming BPh and Qa-. One of the hemes on the reduced cytochromes gives an electron to P960+, thus restoring P960.
3. The electron moves to Qb. A 2nd photon is absorbed and transferred throught he pathway to Qb, reducing Qb to QbH2. Qb is near the cytoplasmic side, so it pulls two protons in, contributing to the proton gradient.
4. QbH2 then enters the quinone pool, where it is reoxidized to Qb by bc1. bc1 transfers the electrons back to the cytochrome, thus completing the cycle. The process of bc1-->cytochrome pumps protons into the periplasmic space, thus generating the proton gradient. |
What is a major difference between the electron transport chain in bacteria and in plants? |
-in plants, the electron flow is not cyclic |
Summarize the electron transport chain in plants. |
-PSI forms NADPH using electrons PSII took from 2 H2O
-electrons move from PSII to PSI through cytochrome bf |
What does Photosystem II do? |
-transfers electrons from water to plastoquinone
-generates a proton gradient
|
Why does PSII need to used light energy? |
-the reaction driven by PSII is thermodynamically uphill, the light energy allows it to go forward |
How many chlorophyll molecules does PSII contain? |
>30 |
Describe the structure of PSII. |
-the special pair and the water-oxidizing complex (WOC/manganese center) are pointing towards the thylakoid space |
What is the structure of the water-oxidizing complex? |
-a calcium ion
-4 manganese ions
-4 water molecules |
Describe the steps of electron flow through PSII. |
1. P680 absorbs light and transfers an excited electron to a nearby pheophytin.
2. The electron is transferred to plastoquinone Qa and then to a mobile plastoquinone Qb.
3. Another photon triggers another electron moving through the system to Qb, where, with the uptake of 2H+, it forms reduced QbH2.
4. P680+ extracts electrons form H2O bound at the WOC. |
How is P680+ restored to P680? |
-P680+ extracts an electron from tyrosine (in WOC), forming a radical
-tyrosine radical removes electron from manganese ion |
How many electrons from H2O are needed to reduced 2 molecules of Q to QH2? |
4 |
What is the purpose of cytochrome bf? |
-transfers electrons from QH2 to plastocyanin (Pc)
-releases the protons from QH2 into the thylakoid lumen |
What does Photosystem I do? |
-uses light energy to generate reduced ferredoxin |
What is ferredoxin? |
-a soluble protein containing a 2Fe-2S cluster
-a powerful reductant |
How is PSI linked to cytochrome bf? |
-the reduced plastocyanin gives its electrons to P700+ to restore P700 |
After being reduced, what does ferredoxin do? |
-carries the electrons to Ferredoxin-NADP+ reductase, a flavoprotein |
What does Ferredoxin-NADP+ reductase do |
-converts NADP+ into NADPH
-has an FAD prosthetic group
-two molecules of reduced ferredoxin form FADH2, which then converts NADP+ into NADPH |
Why is NADPH used over FADH2 in Ferredoxin-NADP+ reductase? |
-it carries two electrons and is more widely used |
What is the major difference between the ATP synthase of the chloroplast and that of the mitochondria? |
-the membrane orientation is flipped in photosynthesis so as to release ATP into the stroma for the dark reactions |
What happens when NADP+ is in short supply or when the concentration of NADPH is high? |
-cyclic electron flow
-leads to the production of ATP instead of NADPH
-ferredoxin, instead of moving to the reductase, moves back to cytochrome bf and reduces plastocyanin, bringing in a proton and contributing to the gradient |
What results from the absorption of eight protons? |
-one O2
-two NADPH
-three ATP (2.7 photons per ATP) |
What is the purpose of accessory pigments? How do they work? |
-funnel energy into the reaction centers
-resonance energy transfer allows energy to move from the site of initial absorbance to the reaction center |
How do inhibitors of PSII work? |
-block electron flow |
What are the herbicides diruon and atrazine? |
-inhibitors of PSII |
How do inhibitors of PSI work? |
-accept electrons from PSI, thus inhibiting NADP+ reduction
|
What is the herbicide paraquat? |
-inhibitor of PSI
-becomes a radical and damages the membrane |
What are 4 light-driven changes in the stroma of chloroplasts? |
1. increased pH (from protons pumped into the thylakoid lumen) --> promotes carbamate formation on lysine of Rubisco
2. increased Mg2+ (transfer from lumen to stroma) --> promotes formation of magnesium carbamate
3. increased NADPH (product of light reactions) --> activates phosphoribulose kinase and GAP dehydrogenase
4. increased reduced ferredoxin (product of light reactions) --> reduces thioredoxin that then activates Rubisco |
What is the net effect of the light reactions? |
-activation of the rate-controlling reaction of the Calvin cycle |
Overall, what happens in the Calvin cycle? |
-carbon dioxide and water is used to synthesize hexoses |
What are the three stages of the Calvin cycle? |
1. Fixation
2. Reduction
3. Regeneration |
What is the first step of the Calvin cycle? |
-carbon dioxide reacts with ribulose 1,5-bisphosphate to form two molecules of 3-phosphoglycerate
-catalyzed by rubisco
-occurs on the stromal surface of the thylakoid membrane |
What is rubisco? |
-Ribulose 1,5-bisphosphate carboxylase/oxygenase
-a slow enzyme that catalyzes the rate-limiting step of hexose synthesis
-made of 8 large subunits and 8 small subunits
-most abundant protein |
Why does rubisco depend on magnesium and carbamate? |
-helps with positioning of rubisco
-activates rubisco so that it reacts with CO2 |
What happens to rubisco when CO2 isn't present? |
-rubisco binds ribulose 1,5-bisphosphate too tightly for enzyme activity |
How is rubisco forced to have the correct structure for enzyme activity? |
-rubisco activase uses ATP to force correct structure
-ATP dependence of rubisco links light and dark reactions |
What makes rubisco "catalytically imperfect"? |
-it catalyzes a wasteful oxygenase reaction
-instead of two 3-phosphoglycerate we get phosphoglycolate and one 3-phosphoglycerate |
How is the phosphoglycolate salvaged? |
-it's dephosphorylated and transported to a peroxisome
-oxygen reacts with glycolate to form glyoxylate and hydrogen peroxide, which regenerates oxygen
-glyoxylate is transaminated to glycine
-2 clycines lose CO2 (wasteful) and NH4+ to generate serine
-serine loses another NH4+ to make 3-PGA, which can then be used to form 3-phosphoglycerate |
3-phosphoglycerate --> 1,3-bisphosphoglycerate |
phosphoglycerate kinase (requires ATP) |
1,3-bisphosphoglycerate --> glyceraldehyde 3-phosphate |
NADPH-specific glyceraldehyde 3-phosphate dehydrogenase (requires NADPH) |
glyceraldehyde 3-phosphate --> dihydroxyacetone phosphate |
triose phosphate isomerase |
glyceraldehyde 3-phosphate --> fructose 1,6-bisphosphate |
aldolase |
fructose 1,6-bisphosphate --> fructose 6-phosphate |
fructose 1,6-bisphosphatase |
fructose 6-phosphate --> glucose 6-phosphate |
phosphoglucose isomerase |
glucose 6-phosphate --> glucose 1-phosphate |
phosphoglucomutase |
fructose 6-phosphate + glyceraldehyde 3-phosphate --> erythrose 4-phosphate + xylulose 5-phosphate |
transketolase |
erythrose 4-phosphate + dihydroxyacetone phosphate --> sedoheptulose 1,7-bisophosphate |
aldolase |
sedoheptulose 1,7-bisphosphate + H2O --> sedohetpulose 7-phosphate |
sedoheptulose 1,7-bisphosphatase |
sedoheptulose 7-phosphate + glyceraldehyde 3-phosphate --> ribose 5-phosphate + xyulose 5-phosphate |
transketolase |
ribose 5-phosphate --> ribulose 5-phosphate |
phosphopentose isomerase |
xylulose 5-phosphate --> ribulose 5-phosphate |
phosphopentose epimerase |
ribulose 5-phosphate --> ribulose 1,5-bisphosphate |
phosphoribulose kinase (requires ATP) |
Summarize the regeneration part of the Calvin cycle. |
F6P+2GAP+DHAP+3ATP --> 3Ru15BP+3ADP |
How many/what molecules are needed to bring carbon dioxide to the level of a hexose? How many rounds of the Calvin cycle? |
-three ATP, 2 NADPH
-6 rounds of the Calvin cycle are needed |
Give the net reaction of the Calvin Cycle. |
6CO2 + 18 ATP + 12 NADPH +12 H2O --> C6H12O6 + 18 ADP + 18Pi + 12 NADP+ + 6H+ |
What role does thioredoxin play in the Calvin cycle? How is it made? |
-presence of reduced form of thioredoxin regulates rubisco
-produced by reduced ferredoxin |
What is the purpose of the C4 pathway? |
-accelerates photosynthesis by concentrating carbon dioxide |
How does the C4 pathway work? Why is it needed? |
-found mostly in tropical plants
-high temps lead to higher oxygenase activity of rubisco
-uses the Hatch-Slack pathway (using conversions between OAA, malate, and pyruvate as transporters) to facilitate a 20 fold increase in CO2 in the bundle sheath cells to favor carboxylase activity |
How does the CAM pathway work? Why is it needed? |
-found mostly in desert plants
-close stomata during day to conserve water and open at night to absorb H2O
-store CO2 as malate during the night
-during the day, malate is converted back to pyruvate and a CO2, which then goes to the Calvin Cycle
-results in photosynthesis without water loss |
What does the pentose phosphate (HMP) pathway do? |
-generates NADPH and synthesizes five carbon sugars |
What is the physiological significance of the HMP pathway? |
-produces NADPH for reductive reactions
-generates pentoses for RNA, DNA, coenzyme, and nucleotide synthesis
-uses diet-derived pentoses
-reduces peroxides
-keeps cysteine of proteins as -SH
-keeps hemoglobin in the Fe2+ state
-helps with the respiratory burst in neutrophils
-helps with creation of bile pigments
-hydroxylation reactions
-photosynthesis in plants (Ru 1,5-BP + CO2 --> 2 GAP) |
Where does the HMP pathway occur? |
-cytoplasm |
What are the two phases of the HMP pathway? |
-oxidative generation of NADPH
-nonoxidative inter-conversion of sugars |
When glucose 6-phosphate is converted into ribulose 5-phosphate, what is generated? |
-2 molecules of NADPH |
How are the HMP pathway and glycolysis linked? |
-transketolase
-transaldolase |
What happens to excess ribulose 5-phosphate created by the HMP pathway? |
-can be converted completely into glycolytic intermediates |
glucose 6-phosphate + NADP+ --> 6-phosphoglucono-d-lactone + NADPH |
glucose 6-phosphate dehydrogenase |
6-phosphoglucono-d-lactone + H2O --> 6-phosphogluconate |
lactonase |
6-phosphogluconate + NADP+ --> ribulose 5-phosphate + CO2 + NADPH |
6-phosphogluconate dehydrogenase |
ribulose 5-phosphate --> ribose 5-phosphate |
phosphopentose isomerase |
ribulose 5-phosphate --> xylulose 5-phosphate |
phosphopentose epimerase |
xylulose 5-phosphate + ribose 5-phosphate --> sedoheptulose 7-phosphate + GAP |
transketolase |
sedoheptulose 7-phosphate + GAP --> fructose 6-phosphate + erythrose 4-phosphate |
transaldolase |
xylulose 5-phosphate + erythrose 4-phosphate --> fructose 6-phosphate + GAP |
transketolase |
The metabolism of _________________ by the pentose phosphate pathway is coordinated with glycolysis. |
glucose 6-phosphate |
How is the rate of the pentose pathway controlled? Why is this control exerted? |
-controlled by the level of NADP+
-greater concentrations of NADP+ leads to more HMP pathway activity (controls dehydrogenation of glucose 6-phosphate)
-ensures that NADPH is not generated unless the supply needed for reductive biosynthesis or protection against oxidative stress is depleted |
When does Mode 1 of the HMP pathway occur? What makes it unique? What is the situation that might be occurring in the cell? |
-occurs when much more ribose 5-phosphate than NADPH is needed
-most of G6P is converted to F6P and GAP by glycolytic pathway; doesn't go through oxidation reactions
-cell needs to make nucleic acids (ex. a rapidly dividing cell) |
When does Mode 2 of the HMP pathway occur? What makes it unique? What is the situation that might be occurring in the cell? |
-occurs when the needs for NADPH and ribose 5-phosphate are balanced
-oxidation reactions only (G6P-->Ru5P-->R5P); gives off CO2 and 2 NADPH
-cell is very metabolically active (ex. a liver cell) |
When does Mode 3 of the HMP pathway occur? What makes it unique? What is the situation that might be occurring in the cell? |
-occurs when much more NADPH than ribose 5-phosphate is required
-the pathway becomes cyclic; G6P is completely oxidized to CO2; three sets of reactions
-red blood cell (no nucleic acids); cells with active fatty acid synthesis (adipose tissue) |
When does Mode 4 of the HMP pathway occur? What makes it unique? What is the situation that might be occurring in the cell? |
-occurs when both NADPH and ATP are required
-very similar to cyclic pathway, but instead of regenerating G6P, the molecules enter the glycolytic pathway to form pyruvate, generating ATP
-ex. brain cells |