1
Q
How much energy reaches Earth per year, and what is done with it?
A
• Energy reaching the Earth’s surface is 13x1023 calories per year
o 1/3 reflected back to space
o 2/3 absorbed by the Earth’s surface (most converted to heat)
o 1% of energy converted to chemical potential energy by plants
2
Q
What is the process of photosynthesis?
A
• In the process of photosynthesis, plants convert radiant energy from the sun into chemical energy in the form of glucose:
o 6H2O+ 6CO2 + sunlight –> C6H12O6 + 6O2
3
Q
What was the great oxidation event and what was its effect?
A
• Occurred 2.5 billion years ago
• The earliest ancestors of modern plants caused the great oxidation event
• Bacteria produced free oxygen in the atmosphere, via photosynthesis
o This event is important as it resulted in protection against damage of UV from the sun, which resulted in more complex structures
• Cyanobacteria have chlorophyll and Rubisco
• As the Earth developed an oxygen-rich atmosphere, the evolution of pathways for oxidative respiration allowed the extraction of up to 34 molecules of ATP, giving a maximum of 36 molecules for every molecule of glucose, better than glycolysis which doesn’t require oxygen
4
Q
What is the endosymbiosis theory and what is the evidence for it?
A
Endosymbiosis theory:
The eukaryotic cell was originally a prokarotic cell that engulfed aerobic heterotrophic prokaryote (mitochondria) and/or the free living ancestral photosynthetic eukaryote (plastid)
Proof:
- Double membrane of organelles
- Mitochondria and plastid could live on their own
5
Q
What happened about 450 million years ago?
A
o Plants could start colonizing the land due to oxygen reacting in the upper atmosphere to produce ozone, which provided UV protection
6
Q
What happened 400 million years ago?
A
o Plants are wide-spread on land, but still have very simple morphology
o Carbon dioxide concentration in the atmosphere is low for the first time which is a major problem for plants, as they are taking so much in from the atmosphere that it will eventually cause them to starve later
7
Q
How did first plants overcome the problem of low carbon dioxide concentrations while still maintaining a good water balance?
A
o The plants’ biochemistry is aqueous, but they need to increase their carbon dioxide diffusion
Therefore, they need a way to let carbon dioxide in but to keep their water so as not to dehydrate
The solution to this problem is leaves, which have:
• Large flat surfaces to capture light
• Waterproof cuticles stops water from diffusing from surface
• Complex breathing structures
• Plumbing to transport water and sugars
8
Q
What is ATP and ADP and where does their energy originate?
A
- ATP- Adenosine triphosphate
- ADP- Adenosine diphosphate
- Phosphate bonds are high energy bonds
9
Q
What is the cell’s energy carrier?
A
ATP
10
Q
Describe photosynthetic electron transport chain
A
- Light hits chlorophyll (inside PSII), which gets the electrons excited and induces charge separation
- Photolysis of water releases electrons to replace those lost at PSII, which generates oxygen and releases protons into the thykaloid lumen
a. Manganese complex oxidises water - Electrons on the acceptor molecule of PSII on the stromal side pass to quinone (inside PSII), and then to the mobile plastaquinone
- Plastaquinone is a hydrogen carrier, so takes protons from the stroma to the lumen
- Plastaquinone passes the electrons to the b6f complex. The b6f complex also moves protons into the lumen
- The electrons pass to the luminal protein plastacyanin and then to PSI
- Light hits chlorophyll in PSI, and electrons pass to FeS clusters (in PSI), then to Ferredoxin
- FNR catalyses reduction of NADP+ making NADPH, using the electrons from PSI
- The protons that accumulate in the lumen of the thylakoids create an electrochemical gradient of protons across the membrane.
- Protons pass back to the stroma via the F-type ATPase, and ATP is generated
a. Chemiosmotic coupling, which links the movement of protons down an electrochemical potential gradient to ATP synthesis via an ATP synthase, occurs.
b. In chloroplasts, protons accumulate in thykaloid lumen and pass outwards through the ATP synthase into the stroma
c. For every three protons translocated via ATP synthase, one ATP is synthesized
11
Q
What is the product of photosynthetic electron transport chain?
A
- Oxygen
- NADPH
- ATP
12
Q
Where do the protons accumulate during the photosynthetic process? Why?
A
Lumen
• Protons are lost from the stromal side via protonation of reduced NADP and they are also generated in the lumen during photolysis
13
Q
How are protons for the proton gradient of the photosynthetic electron transport chain derived?
A
• Protons for the proton gradient are derived from the oxidation of water molecules occurring towards the inner surface of PSII and from the transport of four electrons through the Cyt b/f complex, combined with cotranslocation of eight protons from the stroma into the thylakoid space for each pair of water molecules oxidized
14
Q
How is electrical neutrality maintained throughout the electron chain photosynthetic process?
A
• Electrical neutrality is maintained by the passage of magnesium and chlorine across the membrane, and as a consequence there is only a very small electrical gradient across the thykaloid membrane
15
Q
Are PSII, PSI, Cut b/f and ATP synthase evenly distributed in the plant thylakoid?
A
PSII, PSI, Cyt b/f and ATP synthase are not evenly distributed in the plant thylakoid membranes but show a lateral heterogeneity
16
Q
How does cyclic photophosphorylation work?
A
- Light absorbed by PSI (P700)
- Excited electron passed down the electron transport chain-
- light hits psI, goes to fd which goes to ps4 which goes to b6f and pc cycles backs to b6f, and eventually electron goes back to psI - ATP is produced by ATPase
- Electron returns to PSI
17
Q
What are the differences between electron chain synthesis and cyclic photophosphorylation?
A
• Differences: o PSII not involved o FNR not involved o No water splitting o No oxygen produced o No NADPH produced
18
Q
When does cyclic photophosphorylation occur?
A
• Most common in bacteria and isolated chloroplasts
• More common at low carbon dioxide concentrations
• Reduces risk of damage to PSII when there are sudden transitions from light to dark or other factors
o Reduces risk that PSII is damaged by too much energy
• Cyclic electron transport is slightly more efficient at producing ATP, but linear electron transport also generated NADPH
19
Q
How is the balance between cyclic and linear photosynthetic electron transfer controlled?
A
Dynamic changes in thykaloid stacking
20
Q
What are chloroplasts and where can they be found?
A
- Chloroplasts distinctive green organelles suspended in the cytoplasm and usually appressed against cell walls
- Chloroplasts are abundant in mesophyll tissue
21
Q
How is the chloroplast structured and why?
A
• Surrounded by double membrane or envelope that encapsulates a soluble stroma which contains all the enzymes necessary for carbon fixation
• Inner membrane of a chloroplast envelope is an effective barrier between stroma and cytoplasm,
o Houses transporters for phosphate and metabolites as well as some of the enzymes for lipid synthesis
• Suspended within the stroma is an elaborately folded system of photosynthetic membranes of thykaloids
o In these membranes are the two types of photosystem, cytochrome b/f complexes, and ATP synthase complexes
22
Q
What is rubisco and what does it do?
A
• Rubisco is the most abundant protein on earth, constituting up to 50% of the soluble protein in chloroplasts
o Rubisco- Rubilose bis-phosphate carboxylase/ oxygenase
o Multi-protein complex that catalyses carboxylation in the Calvin cycle
• Allows the primary catalytic step in photosynthetic carbon reduction in all green plants and algae
23
Q
Where did Rubisco evolve and where is it now?
A
- Evolved in oxygen depleted atmosphere
* Located in the stroma of chloroplasts (between the stacks of membranes)
24
Q
What are limitations to Rubisco?
A
o Inefficient with a slow catalytic turnover
Hence, plants need to invest large amounts of nitrogen in Rubisco
o Poor specificity for CO2 as opposed to O2
o Inclination for catalytic misfiring resulting in the production of catalytic inhibitors
• These limitations severely restrict photosynthetic performance in C3 plants
• Rubsico also has a requirement for its own activating enzyme, Rubisco activase, which removes inhibitors from the catalytic sites to allow further catalysis
25
What is the difference between Rubisco structure in higher plants vs in microbes?
• Rubisco in higher plants is a large protein comprised of eight large and eight small subunits (16 subunits in total)
o The large subunit gene is encoded in the chloroplast genome
o The small subunit genes are encoded as a multi-gene family in the nucleus
• Microbial rubisco only has large subunits
26
How was the biochemical pathway of carbon dioxide fixation discovered?
• The biochemical pathway of CO2 fixation was discovered by feeding radioactively labelled CO2 in the light to algae and then extracting the cells and examining which compounds accumulated radioactivity
27
What is carbon dioxide fixation?
• Carbon fixation is the capture of atmospheric CO2 and its incorporation into carbohydrates
28
Where does carbon fixation occur in eukaryotes and why?
• In eukaryotes, carbon fixation occurs in the stroma of chloroplasts
o The stroma contains multiple copies of the chloroplast genome, which encodes for many ribosomes and the enzymes needed for photosynthesis
29
What are C3 plants?
Plants which use Rubisco as their primary enzyme of CO2fixation from the air
30
What does the Calvin cycle do and what are its energy requirements?
* Light independent reactions of photosynthesis
* Following the harvesting of light energy and its conversion to chemical energy in the form of ATP and NADH, CO2 is able to be converted to carbohydrate in the Calvin-Benson cycle
* Energy requirements of this cycle are three ATP and two NADPH per CO2 fixed
31
Describe the carboxylation steps of the Calvin cycle
1. CO2 is attached to the 5-carbon sugar, ribulose-1,5- biphosphate (RuBP)
a. 2nd carbon has a double bonded oxygen
b. Double bonded oxygen bonds get rearranged and the double bond is shared between the second and third carbon – enediolate intermediate
2. A short-lived, 6 carbon intermediate is formed in a reaction catalyzed by the enzyme rubisco
a. 6CO2 +12NADP + 12H+ + 18ATP --> Rubisco --> Glucose + 12NADP+ + 18ADP + 18Pi + 6H2O
b. β-Keto intermediate
3. The 6-carbon intermediate splits rapidly into two molecules of phosphoglyceric acid (PGA), a 3 carbon molecule (3-phosphoglyecerate)
32
Describe the reduction steps of the Calvin cycle (after carboxylation steps)
4. PGA is phosphorylated using ATP produced from thykaloid electron transport
5. The intermediate compound is reduced by NADPH and dephosphorylated to form glyceraldehyde-3-phosphate (PGAL)
33
After reduction in the Calvin cycle, what 3 paths can PGAL follow?
a. In the first:
i. Up to two in every 12 PGAL molecules are exported from the chloroplast into the cytoplasm
ii. These PGAL molecules are combined and rearranged into fructose and glucose phosphates
iii. These 2 intermediate compounds condense to form sucrose, the major transport form of carbohydrate in plants
iv. Inorganic phosphate is imported into the chloroplast to replace that exported as part of PGAL
b. In the second path:
i. Up to two PGAL molecules are combined, rearranged and used in the synthesis of starch, which is stored in the chloroplast
c. In the third path:
i. The remaining 10 PGAL molecules are used to form six RuBP molecules to complete the cycle.
1. Need to go from a 3-C phosphate to a 5-C biphosphate
a. Consists of a sequence of 11 steps where 3-phosphoglycerate is phosphorylated, reduced to glyceraldehyde 3-phosphate and isomerized to dihydroxyacetone phosphate
b. Condensation of this three carbon compound with glyceraldehyde 3-phosphate yields a six-carbon compound (fructose bisphosphate)
c. Following a series of carbon shunts involving four-,five- and seven-carbon compounds, RuBP is regenerated
ii. The regeneration of six RuBP molecules uses a further six ATP molecules
34
What is photorespiration?
Photorespiration- The process, occurring only in the light, in which the enzyme that catalyses carbon fixation, Rubisco, can also use oxygen as a substrate and oxygenate RuBP, subsequently producing CO2 from a product of oxygenation
o Instead of adding carbon dioxide, will add oxygen at the second carbon of RuBP
35
Why does photorespiration occur?
• Since, under normal atmospheric conditions, O2 is much more abundant than CO2 and hence oxygen competes effectively for the binding site on Rubisco despite the enzyme having a higher affinity for CO2 than for O2.
o Approximately one molecule of oxygen is fixed for every three molecules of carbon dioxide
o End up with one 2 carbon product and one 3 carbon product
36
Why is photorespiration bad for carbon fixation?
• Photorespiration results in carbon dioxide being released:
o This undoes the binding of carbon that would otherwise result in carbohydrate synthesis means that the higher energy carbon to carbon bond is not made
o Also consumes ATP in the process
o Means that photorespiration has the capacity to reduce significantly the efficiency of carbon fixation
• Plants lose 25% to 50% of the carbon that could be fixed during photosynthesis:
o This didn’t matter billions of years ago when the atmosphere lacked oxygen, but it does matter now
37
Why is oxygen fixation an energy consuming process?
o The competition between oxygen and carbon dioxide for RuBP
o The energy cost of converting the phosphoglycolate product to a form which can be recycled in the Calvin cycle
This energy cost is increased at higher temperatures because oxygen competes more effectively with carbon dioxide at the active site of Rubisco
38
What are the three organelles required for photorespiration and what occurs in each of them?
o Chloroplasts
Oxygenase activity by Rubisco results in formation of phosphoglycolate
This then enters a PCO cycle
This is then responsible for loss of some of the carbon dioxide just fixed in photosynthesis
o Peroxisomes
Oxygen is consumed in converting glycolate to glyoxylate, and aminated to formed glycine
o Mitochondria
Carbon dioxide is released during conversion of glycine to serine
Subsequently, serine is recovered by peroxisomes where it is further metabolized into hydroxypyruvate which is converted to glycerate, which, when moved into the chloroplast, is converted into 3-phosphoglycerate
39
Are the chloroplasts, peroxisomes and mitochondria close together? Why/why not?
• The organelles close proximity in leaf cells plus specific membrane transporters facilitate the exchange of metabolites
40
Why is the chloroplast next to the cell wall?
o Chloroplast right next to cell wall so that it can efficiently get to the carbon dioxide that diffuses into the cell and stays in the air space
41
What does transport of glycerate and glycolate across the inner membrane of chloroplasts involve?
• Transport of glycerate and glycolate across the inner membrane of chloroplasts may involve separate translocators, or it may involve a single translocator that exchanges two glycolate molecules for one molecule of glycerate.
42
How would transport of metabolites through the peroxisomal membrane occur?
• Transport of glycerate and glycolate across the inner membrane of chloroplasts may involve separate translocators, or it may involve a single translocator that exchanges two glycolate molecules for one molecule of glycerate.
43
What is a potential danger of the photosynthetic oxidation pathway?
• Danger of photosynthetic oxidation pathway: ammonia is also produced by mitochondria during synthesis of one molecule of serine from two molecules of glycine, which would be toxic if not metabolized by glutamine synthetase
44
What were the levels of CO2 historically compared to now? Why has it changed and what did this result in?
• Carbon dioxide concentrations was really high for a lot of the Earth’s history
o 3000-5000 ppm
• Right now, 400 ppm
• Plants removed high carbon dioxide concentration and reduced carbon dioxide concentration in the atmosphere
• Resulted in the evolution of angiosperms and grasses (which are very effective at controlling exchange of gases)
45
When do carbon dioxide concentrations change?
• More recently, carbon dioxide concentration for the last 800000 years is rather stable compared to that of the deep time
• Fluctuates over time due to glacial and interglacial periods
o When carbon dioxide concentrations are low, it’s a glacial period
o When carbon dioxide concentrations higher, interglacial period
• We are at an interglacial period
o However, fossil fuels have caused a rather sharp increase in carbon dioxide concentration
46
What has low carbon dioxide concentrations caused the evolution of?
• Low carbon dioxide concentrations caused the evolution of a new photosynthesis type called C4 photosynthesis
o Evolved in grasses but no woody plants
47
What is the first stable product of carbon fixation?
4-carbon compound
48
Describe the anatomy of C4 leaves and why they are this way
• Plants with C4 photosynthesis (such as wheat) have a distinctive leaf anatomy in which the vascular bundles are surrounded by a cylinder of bundle sheath cells and an outer layer of mesophyll cells
o In mesophyll cells, carbon dioxide concentration are quite low (100uM)
• The bundle sheath and mesophyll cells contain chloroplasts that are different in structure and function
o Bundle sheath cells are equipped with a carbon dioxide concentrating mechanism (an internal pool of inorganic carbon) that favours carboxylation over oxygenation reactions due to increased partial pressure of carbon dioxide
o Photorespiratory release of carbon dioxide is further prevented through the activity of PEP carboxylase which refixes any respired carbon dioxide formed from the oxygenase function of rubisco
• In C4 plants, an additional carboxylation enzyme called PEPC (phosphoenolpyruvate) carboxylase
o Operates in the cytoplasm of the leaf mesophyll cells
49
Describe the C4 photosynthetic pathway
• PEPC catalyses the carboxylation of the 3-carbon compound (PEP)
o Requires extra ATP- not as effective when temp is low
• Product of the carboxylation reaction is a 4-carbon organic acid, oxaloacetate, which is immediately converted into another 4-carbon compound
o Once in the chloroplasts of the bundle sheath cells, malatate (4-carbon) is decarboxylated to CO2 and pyruvate (3-carbon).
o Carbon dioxide is then fixed into carbohydrates by Rubisco and other Calvin cycle enzymes
o The pyruvate is transported back into the mesophyll cells and there converted back into PEP to complete the cycle
o The C4 decarboxylation reaction generates NADPH, which is consumed in bundle sheath chloroplasts during PGA reduction
Bundle sheath chloroplasts often have only a few granal stacks and little PSII activity, and hence little capacity for light-dependent NADPH formation
50
Why is C4 photosynthesis useful?
* C4 photosynthesis is a mechanism for concentrating CO2 in bundle sheath cells, which are relatively impermeable to CO2 and tend to hold it within them
* The relatively high CO2 concentration within these cells has the added advantage of inhibiting photorespiration
• Although the C4 pathway uses more ATP than the C3 pathway, the reduction in photorespiration offsets this cost, especially when light is abundant
• In addition, because C4 plants can concentrate CO2, their pores (stomata) are generally not as wide open as those C3 plants and less water is consequently lost
o This is particularly important under conditions of low humidity and high temperature, and when lack of water limits growth
51
Under what circumstances are C3 and C4 photosynthesis useful?
* When temperatures are low, C3 photosynthesis does better
| * When temperatures are high, C4 photosynthesis does better
52
What enzyme is in Mesophyll cells?
PEPC
53
What enzyme is in bundle sheath cells?
Rubisco
54
How have plants evolved to counteract the rubisco issue with oxygen?
o Specificity towards carbon dioxide as opposed to oxygen has improved significantly
Recently evolved angiosperms show a relative specificity almost twice that of older organisms such as photosynthetic bacteria
o Vascular plants have evolved with photosynthetic mechanisms that alleviate an inefficient Rubisco
One key feature of such devise is a mechanism to increase carbon dioxide concentration at active sites within photosynthetic tissues
55
How does light respond to photosynthesis?
o Saturating response- eventually won’t matter how much light you give the plant, you won’t get anymore photosynthesis out of it
o Haven’t got 0 photosynthesis at 0 light because respiration is happening all the time in plant cells
56
What is compensation point?
o Compensation point -> passed as goes from high light to low light
At light compensation point, net flux is 0 (photosynthesis balances out respiration)
Below light compensation point, negative photosynthesis (respiration)
57
What is photosynthesis response to CO2?
Saturating response
58
What is the difference between C4 and C3 photosynthesis response to CO2
o C4 photosynthesis (have carbon dioxide concentrating mechanism) increase photosynthetic rates at low CO2 concentration more quickly than C4 photosynthesis and have lower compensation point
59
What is the photosynthetic response in temperature, taking into account C3 and C4?
o At low temperatures, enzyme reaction rates increase
o If too high, enzyme reaction rates decrease
o In C3, thermal optimum is between 18 and 30 degrees
o In C4 less efficient at colder temperatures because they need that ATP, so have that higher thermal optimum
60
What is the first law of thermodynamics?
1. Energy can be changed from one form to another, but not created or destroyed
61
Where is carbon in the wold?
• Huge flux of carbon (energy) into the terrestrial biosphere via photosynthesis
• Almost balanced by huge flux out as respiration
• Moving carbon stored below ground to atmosphere
o Fossil fuel burners are
• Most carbon in oceans come back out but some stored
• Small carbon sink in terrestrial and ocean
o Don’t keep up with emission of fossil fuels --> this is why there’s an increase in CO2 concentrations
62
What is the consequence of the current trend of increasing CO2 concenrations?
• In northern hemisphere, photosynthesis is causing enormous CO2 concentration swing between seasons
o Due to the fact that there’s more trees and other plants than in southern hemisphere
63
What is oxidation?
Loss of an electron
64
What is reduction?
Gain of an electron
65
What is anabolism and what does it cause/need?
```
• Anabolism synthesis of molecules
o Increase in atomic order
o Decrease in entropy
o Usually energy-requiring
o Involves NADPH (extra phosphate)
o Build up glucose
```
66
What is catabolism and what does it cause/need?
```
• Catabolism breakdown of larger molecules
o Decrease in atomic order
o Increase in entropy
o Usually energy-liberating
o Involves NADH
o What respiration is about
o Break down glucose
```
67
Where does glycolosis occur?
Cytosol and plastid
68
What does glycolysis do?
* Breaks up glucoses’ 6 carbon rings into two 3-carbon pyruvic acids
* Anaerobic process
69
What is a level of regulation for glycolysis depending on high or low respiratory activity?
• A level of regulation of components of glycolysis is their physical location within the plant cell
o Under conditions of high respiratory activity, a greater proportion of the cytosolic enzymes of glycolysis are present on the surface of mitochondria
o Under inhibited respiration, a decrease in the association of glycolitc enzymes with the mitochondria is observed
70
What is involved in the beginning preparation stage of glycolysis?
• Two molecules of ATP are used to phosphorylate and change glucose in preparation for splitting it into 2 3-carbon molecules (glyeraldehyde-3-phosphate)
1. Phosphorylation of glucose by hexokinase to form glucose-6-phosphate in an ATP consuming reaction
2. Glucose-6-phosphate is converted to fructose-6-phosphate by glucose phosphate isomerase
3. Fructose-6-phosphate is phosphorylated to fructose-1,6- biphosphate by one of two enzymes capable of catalyzing this step:
a. PFK (phosphofructokinase)
i. Catalyses an irreversible reaction and occurs in cytosol and plastids
b. PPi-PFK(pyrophosphate-dependent phosphofructokinase)
i. Occurs only in cytosol and utilizes pyrophosphate as the phosphate donor in a reversible reaction
c. Regulation of PFK and PPi-PFK is achieved by pH, concentration of substrates and effector metabolites and changes in subunit association
4. Fructose-1,6- biphosphate is cleaved by fructose biphosphate aldolase to form glyceraldehyde-3-phosphate and dihydroxyacetone phosphate, and these triose phosphates can be interconverted in a reaction catalyzed by triose phosphate isomerase
71
What is involved in the payback stage of glycolysis?
• In the second stage, oxidation of glyceraldehyde-3-phosphate to pyruvate is coupled to ATP synthesis: four ATP molecules are produced, giving a net energy profit of 2 ATP molecules
1. Glyceraldehyde-3-phosphate is oxidized to 1,3 biphosphoglycerate by a nicotinamide adenine nucleotide (NAD+)-dependent glyceraldehyde 3-P dehydrogenase
a. Glyceraldehyde 3-P dehydrogenase is sensitive to inhibition by the reduce pyridine nucleotide cofactor, which must be reoxidised to maintain the flux through the glycolytic pathway
2. A phosphate group is then transferred from 1,3-biphosphoglycerate to ADP forming ATP and 3-phosphoglycerate by phosphoglycerate kinase
3. In the cytosol a bypass is present and can convert glyceraldehyde-3-phosphate directly to 3-phosphoglycerate without phosphorylation by a non-phosphorylating NADP dependent glyceraldehyde 3-phosphate dehydrogenase
4. The resulting 3-phosphoglycerate is then converted to phosphenolpyruvate (PEP) by the action of phosphoglycerate mutase and enolase
5. End product determined by the relative activities of the two enzymes that can use PEP as a substrate:
a. Pyruvate kinase
i. Forms pyruvate + ATP
b. PEP carboxylase
i. Forms oxaloacetate
72
What is the result of glycolysis?
Results in 4 ATPs (2 in profit), 2 NADH and 2 pyruvates
73
What is the overall reaction of glycolysis?
• Glucose + 2NAD+ + 2ADP +2 phosphate groups --> glycolosis--> 2 Pyruvates + 2NADH + 2ATP + 2H+ + 2H2O
74
What is the substrate of the Krebs cycle-Tricarboxylic acid cycle and how is that substrate produced?
• Acetyl CoA is the substrate
o Produced from β-oxidation of lipids and from oxidation of imported pyruvate (the product of glycolysis)
o Produced one molecule of CO2 when we’ve done it and molecule of NADH is formed
75
What is the Krebs cycle?
1. Condensed Acetyl CoA from both these sources enters the Krebs cycle and combines with a 4 carbon molecule, oxaloacetate
2. This releases coenzyme A and forms a 6-carbon molecule, citrate in a reaction catalyzed by citrate synthase
3. Citrate is rearranged into the 6-carbon molecule isocitrate, which is the substrates for a series of oxidation reactions, which is catalyzed by aconitase and involves cis-aconitate as an intermediate
a. Two step reaction (dehydration/hydration)
4. NAD-linked isocitrate dehydrogenase then oxidatively decarboxylates isocitrate to form carbon dioxide and 2-oxoglutarate, and reduce NAD+ to NADH
a. Release CO2
5. The 2-oxoglutarate formed is also oxidatively decarboxylated to succinyl-CoA in a reaction catalyzed by the enzyme 2-oxoglutarate dehydrogenase
6. Succinyl-CoA synthase then catalyses the conversion of succinyl-CoA to succinate, with the concomitant phosphorylation of ADP to ATP
7. Fumurase catalyses the hydration of fumurate to malatate followed by malatate dehydrogenase, oxidizing malatate to OAA and producing NADH
a. Equilibrium constant favours reduction of OAA, so need rapid turnover of OAA and NADH to maintain this reaction in a forward direction
76
What is a summary of what is used/produced in the Krebs cycle?
* In these reactions, electrons and H+ are transferred to form FADH2 and NADH, and one molecule of ATP is produced
* During one turn of the cycle, 3 carbons of pyruvate are released as carbon dioxide, one molecule of ATP is formed directly, an four NADH and one FADH2 are produced
* NAD+ and FAD cycle back after having been oxidized during the next stage, the electron transport system: recycling
77
How is carbon flux regulated through the Krebs cycle?
* Regulation of carbon flux through the TCA cycle probably occurs via phosphorylation/dephosphorylation of pyruvate dehydrogenase , which in turn depends on mitochondrial energy status and feedback inhibition of various enzymes by NADH and acetyl-CoA
* TCA cycle turnover also depends on the rate of substrate provision by reactions in chloroplasts and cytosol
78
What is the mitochondria's structure and why is this so?
• Outer membrane is porous but inner membrane is impermeable
o This allows intermembrane space (IMS) and cytosol to have similar environment but for IMS and matrix to be different (that is have gradients)
o Function- pumps ions from one side to another generates membrane potential across mitochondria
• Inner membrane:
o Has cristae to increase surface area
o Where oxidative phosphorylation occurs
79
Where does the Krebs cycle occur in the mitochondria?
In the matrix of the mitochondria
80
Where does the NADH and FADH2 used in the electron transport chain come from?
Glycolysis/Krebb's cycle
81
List the steps of the electron transport chain
1. Electrons are passed from NADH to NADH Dehydrogenase. Coupled with this transfer is the pumping of 1 hydrogen ion for each electron
2. Electrons are transferred to ubiquinone (mobile transfer molecule) which moves the electrons to cytochrome b-c
a. Cytochrome b-c uses FADH2
3. Each electron from b-c complex moves to cytochrome c which is a mobile carrier that transfers each electron one at a time, pumping on H+ as each electron is transferred
4. Cytochrome c takes the electrons to cytochrome oxidase, where the electrons, hydrogen and oxygen molecules interact to form water- hydrogen ions are pumped across the membrane
5. Hydrogen pumping creates a gradient, gradient used by ATP synthase to make ATP from ADP and inorganic phosphate
a. ATP synthase is turned by the flow of H+ ions moving down their electrochemical gradient
b. ATP synthase consists of two parts:
i. The first part forms a channel across the membrane through which protons can move back down the electrochemical gradient
ii. This movement is the source of energy for ATP synthesis, which is catalyzed by the second part of the complex
c. As ATP synthase turns, it catalyzes the addition of a phosphate to ADP, capturing energy from the proton gradient as ATP
82
How is respiration delibitating to climate change?
* Respiration goes up as temperature goes up
* Photosynthesis goes up as CO2 increases
* Some ecosystems that stored carbon might flip over to release carbon
* Flipping over from net sink to net source as respiration rate increases over photosynthesis rate
* As we increase the Earth’s temperatures
BIOL1997
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