Test 2 Part 2.2 Flashcards
1
Q
Rubisco and photosynthesis.
A
- Rubisco is an enzyme that will reduce carbon dioxide to form glucose in the Calvin cycle reactions.
- Rubisco is an enzyme that catalyses Calvin cycle reactions. Carbon fixation.
- In the initial reactions of photosynthesis is the light dependant reactions - water being oxidised to oxygen - remove electrons from water and passed on to carbon dioxide and reduce the carbon dioxide to get glucose - redox reaction.
2
Q
How carbon dioxide is fixed by photosynthesis anually?
A
10^11 tons of CO2 fixed annually.
3
Q
Photosynthesis in bacteria
A
In bacteria the equation is different - in sulfur bacteria instead of water you have hydrogen sulfide and add electrons to carbon dioxide
4
Q
What happens to photosynthesis with climate change?
A
- Climate change - most photosynthesis occurs in the ocean.a s the oceans warm up - the organisms can’t fix co2 nearly as well.
- As temepratures increase there is a decrease in the net primary productivity → carbon fixation by the marine protists.
- Less co2 fixed so more co2 in the atmosphere - temps increase and less co2 fixed - viscous cycle.
5
Q
Photosynthesis process overview
A
- 2 distinct phases - light reactions and calvin cycle reactions.
- Occur in the chloroplasts → the chloroplast has 2 membranes - outer and inner - stacked membranes called the thylakoids - membranous sacs.
- Electron transport chain, atp synthase producing ATP.
- Light reactions are where we oxidise water (drag electrons away from water), because of the input of light energy - pigment molecules the thylakoids absorb the light energy and energise them and enable them to extract electrons from water producing oxygen.
- The electrons (because they are energised) move along the electron transport chain proteins and they will produce a reduced form of electron chain carriers - reduced form: NADPH - NAD but also has a phosphate - acts as an electron carrier.
- The ATP and NADPH fuel carbon fixation in the calvin cycle. Co2 + electrons to reduce it and that’s how plants produce sugar = glucose = sucrose. Calvin cycle reactions take place in the stroma in the chloroplast
6
Q
Chloroplasts role in photosynthesis
A
- Chloroplasts convert light energy to chemical energy - need to capture the light energy - they do this by containing pigment molecules which absorb light.
- Chlorophyll A - Chlorophyll B - absorb light energy in the blue, red and orange spectra.
- Carotenoids absorb light in the blue/green agrea.
- Plants appear green because of this combination of light spectrums being absorbed, the green light is transmitted or reflected.
7
Q
Chlorophyll has a lot of
A
nitrogen
8
Q
What happens to leaves in autumn?
A
- Autumn: the leaves on deciduous trees turn red prior to shedding for winter.
- They look red and orange because the plants are conserving nitrogen.
- Chlorophyll contains nitrogen. The plants breakdown the chlorophyll and transfer the nitrogen to other parts of the plant.
- Don’t want to lose the nitrogen in a shed leaf.
- Carotenoid will be contained.
- In red orange leaves - the red and orange spectra are being reflected.
9
Q
Plants need to retain…
A
- Plants need to retain nitrogen.
- We have a lot of double bonds between the carbon atoms.
- In these electrons the capture of light energy occurs.
10
Q
Chlorophyll absorbs…
A
- Light energy.
- When light energy hits the leaf, the electron gets excited - jumps to a higher orbital giving called the excited state.
- The energy difference between these different orbital levels for this chlorophyll approximates to the energy present in a photon of light. Which is one of the reasons why chlorophyll is a really good pigment molecule for capturing light energy.
- There are four possible things that happen next:
- The electron moves back down to its original orbital and loses energy absorbed as light - released as heat.
- Tt can move back down and instead of heat energy being released you can get light energy released - called fluorescence. The light energy will be of a different wavelength to the light energy originally absorbed.
- Resonance energy transfer: occurs if two chlorophyll molecules are positioned closely together. In the chloroplast light harvesting complexes act as antennas. We get the funelling of light energy from one chlorophyll molecule to another.
- The fourth alternative is energy transduction: The reaction center chlorophyll, located close to an electron acceptor, will pass its excited electron onto the electron acceptor which becomes reduced = a form of chemical energy.
- The electrons are passed through an electron transport chain.
- Because it lost an electron the reaction center chlorophyll is oxidised. The electron needs to be replaced and the electron comes from water.
- That’s why in photosynthesis water is oxidised - removal of electrons from water and those electrons are passed on to these reaction center chlorophylls so that they become excited and can pass their electrons to the electron acceptors again.
11
Q
Key players in the light reactions
A
- Photosystem I and photosystem II.
- Reaction centre chlorophyll - p700 in PSI and P680 in PSII.
- antennae chlorophyll, light harvesting complexes.
- PSII has a water splitting complex.
- Cytochrome complex - acts as a proton pump.
- Electron carriers - plastoquinone, plastocyanin and ferredoxin.
- Enzyme: NADP reductase - will transfer electrons to NADP in the final part of the light reactions.
- Chloroplast ATP synthase - chloroplast contain ATP synthase - rotatory protein that couples the movement of protons to the production of atp.
12
Q
Flow of electrons in the light reactions
A
- Energetics - electrons are energised they move to things they lose energy then they become energised again.
- Z scheme of photosynthesis - showing the flow of electrons relative to the energy of the electrons.
13
Q
Photosystem II process
A
- Energy is funnelled down into photosystem II.
- Light energy passed to reaction centre chlorophyll P680 by antennae chlorophyll.
- Electron in P680 excited and passed onto an electron acceptor. P680 becomes oxidised and the primary electron acceptor becomes reduced.
- Water replaces the electron lost from the P680, now it is ready for more energy to come in.
- Excited electrons moves from the electron acceptor onto an electron transport chain in the thylakoid membrane.
- Electrons are passed onto the cytochrome complex and lose energy which is passed onto the cytochrome complex, which becomes energised and acts as a proton pump.
- Plastoquinone, cyctochrome complex, plastocyanin.
- Protons are moved from the stroma into the thylakoid space.
- Cytochrome complex uses this energy to pump protons from the stroma to the thylakoid space.
- Creates a proton gradient which can be used to rotate ATP synthase which can be used to produce ATP.
- The ATP will be used to fuel the calvin cycle reactions.
14
Q
Photosystem I
A
- From photosystem II - need to pass the electron from the cytochrome complex onto the plastocyanin which will pass the electron onto the reaction center chlorophyll in photosystem I.
- Light energy passed to reaction centre chlorophyll P700 by antennae chlorophylls.
- P700 becomes oxidised and the electrons reduce plastocyanin so it can function again.
- Electron P700 excited and passed onto primary electron acceptor.
- The primary electron acceptor will pass its electron onto ferredoxin which will then pass its electrons onto enzyme NADP reductase which will reduce NADP
- a form of chemical energy - this will be used to fuel the reactions of the calvin cycle.
- Electron replaced by electron from plastocyanin.
15
Q
NADP+ in photosystem I
A
- Excited electron moves from primary electron acceptor onto other electron transporters and then NADP+.
- NADP+ reduced to NADPH = chemical energy.
16
Q
Non cyclic photophosphorylation
A
- Non cyclic photophosphorylation - describes the production of ATP when the electrons move through photosystem II through the electron transport chain and then through photosystem I.
- The flow of electrons is referred to as non-cyclic - a linear flow of electrons.
- The process is energised by light - photo. Then phosphorylation to describe the production of ATP.
17
Q
Cyclic photophosphorylation
A
- Another way of producing ATP - cyclic phosphorylation - occurs because the ferredoxin rather than reducing NADP to NADPH, the ferredoxin transfers it electrons back to the cyctochrome complex and the electrons move back through the cytochrome complex to plastocyanin and passed back to P700 (in photosystem I).
- Cyclic describing the route of the electrons. This additional process evolved is because in the original calvin cycle reactions you need a lot more ATP than you need reduced NADP. photo - energised by light. Phosphorylation - production of ATP
18
Q
Calvin cycle.
A
- Calvin cycle - occurs in the stroma. 3 phases - fixation, reduction, regeneration.
- Produces sugar = sucrose.
- Initial input of CO2 - CO2 is fixed by the enzyme rubisco.
- The metabolite involved in the rubisco reaction is ribulose bisphosphate. Rubisco will add carbon dioxide to ribulose biphosphate.
- ATP is needed, reduced NADPH and some more ATP
- 9 ATPs, and 6 reduced NADP.
19
Q
Rubisco
A
- Adds co2 to ribulose phosphate - referred to as a carboxylase reaction.
- Rubisco - pretty bad enzyme. Will only catalyse 2-3 reactions per second.
- Because its so slow plants need a lot of it.
- Tightly regulated - allosterically controlled → by magnesium ions, pH and presence of reductants.
- Plants need rubisco to be active when the light reactions are occurring.
- Rubisco is closely regulated - occurring at the same time as the light reactions, the ATP is used to fuel the calvin cycle reactions rather than the ATP produced in the breakdown of sugar in the mitochondria.
- Not from respiration so avoids futile cycling.
20
Q
Why is rubisco a “bad” enzyme?
A
- Bad because its not very specific - will also catalyse an oxygenase reaction.
- Oxygen - can add the oxygen to ribulose biphosphate - this is a problem
- when oxygen is added the products that arise from that reaction
- it takes a lot of energy from the plant to make those products into sugar - photorespiration.
21
Q
What determines the activity of rubisco/ What determines whether the the carboxylase or the oxygenase reaction is occuring?
A
- What determines whether the carboxylase or the oxygenase reaction occurring is the ratio of CO2 to O2 present in the leaf.
- If you have a high carbon dioxide to oxygen ratio (a lot of CO2 relative to O2) - the carboxylase reaction will predominate.
- If you have a low CO2 to O2 ratio then the oxygenase reaction will predominate.
- Plants try to keep high levels of CO2 compared to O2 in the leaves - they do this by gas exchange pores - stomata.
- If plants keep the stomata open then the oxygen diffuses out of the leaf and carbon dioxide diffuses into the leaf.
- This keeps the CO2 levels high relative to oxygen levels and the carboxylase reaction predominates.
- This can lead to a problem - if the gas exchange pores open then that can lead to water loss through the process of transpiration. An issue for plants in a dryer environment - those plants like to keep stomata closed to make sure no water is lost.
22
Q
C4 plants: How do these plants then ensure that the carboxylase reaction predominates?
A
- How do these plants then ensure that the carboxylase reaction predominates?
- A special morphology to ensure that they can keep their stomata closed and at the same time maintain their high CO2/O2 ratio where the calvin cycle occurs. C4 plants have a special morphology to make sure that the calvin cycle and the initial step in carbon fixation occur in different cells.
- Mesophyll cells - where carbon dioxide is first fixed into a four carbon compound called oxaloacetate. This seperates the carbon fixation and the calvin cycle - so this ensures that the carbon dioxide levels are high where rubisco is.
- CO2 levels kept high as the initial step in carbon fixation leads to a reaction with a release and the delivery of carbon dioxide
- carbon dioxide comes off the malate - decarboxylation reaction -
- delivery of carbon dioxide to the bundle sheath cells to maintain a high CO2 concentration.
- rubisco is present in these cells so the CO2 can be fixed and we get the calvin cycle occurring.
- Specialised morphology in C4 plants.
- Example: Sugarcane - C4
23
Q
CAM plants
A
- CAM plants separate these processes by time.
- The stomata are open at night - less water loss because it’s not as warm
- CO2 enters the leaf which is fixed into organic acid
- At night there is initial fixation of CO2 and then during the day the stomata close.
- At the same time they release co2 from the organic acids that form in the initial fixation process during the night, co2 is released - even though the stomata are closed they are ensuring there is a high co2 concentration here and the carboxylase reaction of rubisco will predominate.
- Example: Pineapple - CAM.
24
Q
The sturcture of membranes and membrane proteins.
A
- The membrane proteins need to be able to reside in hydrophobic areas and at the same time they need to have parts of the protein that are hydrophilic.
- Alpha helices - may have some hydrophobic residues facing the fatty acid tails whereas the parts of the helices that are facing the interior may be hydrophilic.
25
6 functions of membrane proteins.
* Movement of molecules across a membrane.
* Catalyse reactions.
* Signalling molecule that binds to a membrane protein that acts as a receptor - change in shape enables the signal to be transduced into the cell. Example - growth factor signalling for the cell to divide. In cancer the cells may be diving in an abnormal manner - abnormal signalling.
* The ability of cells to recognise other cells occurs because of membrane proteins - important in the immune system.
* Multicellular organisms - cells need to adhere to other cells - proteins that can join to proteins in the membrane of other cells.
* A protein that can attach cells to the extracellular matrix - the extracellular matrix: located outside the cell that cells can attach to. Collagen is an ECM that a membrane protein will attach to
26
Naked mole rat
* Naked mole rat lifespan - can live about 30 years - 10x as long as a rat or mouse.
* These mammals cannot obtain cancer - part of the ECM - they have a specialised hyaluronan it affects the way the cells divide - the cells are stopped dividing if anything abnormal happens because of this bigger more specialised hyaluronan.
27
Membrane transport: permeability through the lipid bilayer.
How easily to Hydrophobic, hydrophillic and big polar molecules move through the lipid bilayer?
* Membrane transport: Lipid bilayer (the two grey lines).
* Because of the hydrophobic interior that will affect the ability of things to move across the lipid bilayer.
* Hydrophobic molecules - things with an equal distribution of electrons: they can easily move across the hydrophobic interior.
* Things with an uneven distribution of charge in molecules - polar molecules - have less ability to move through the hydrophobic area - things can move through just not as easily.
* Polar molecules that are bigger - less ability to move through again.
* Ions - charged things - protons. Because they have charge they are not permeable across the bilayer.
* Proteins have evolved that allow cells to move these molecules/ions in a controlled manner across the lipid bilayer.
28
Basic principles of membrane transport
* 3 mechanisms at which things can move across membranes.
* Passive transport can occur by proteins and also passive movement through the lipid bilayer
* Active transport
* Secondary active transport can only occur with proteins.
29
Passive transport
* Passive transport. When molecules move down their concentration gradient - something moving downhill.
* Passive transport has a negative delta G - so is spontaneous and no energy input.
* Diagram - dye molecules concentrated on one side of the membrane which will diffuse across until equilibrium is reached.
30
Active transport
* Active transport - ions are moved against their concentration and or charge gradients
* Non spontaneous, needs an energy input - to get something to occur that got a positive delta G value: energy coupling - couple it to hydrolysis of ATP and phosphorylate the protein involved making the protein more reactive and you are able to move things against the concentration charge gradient.
31
Secondary active transport
* Secondary active transport: an ion gradient which is sodium (human) or protons (plant) set up by an active transport protein is used to energise the transport of another ion/solute.
* Plant example:
* Active transport protein (proton pump) which is moving protons against their concentration and electrical gradient - making more protons on the outside of the cell relative to the inside.
* The secondary active transport protein (sucrose proton cotransporter) and its able to couple the re-entry of the proteins back into the cell
* driving force negative delta G value
* It can couple that movement to the movement of another ion or solute. In this case sucrose proton movement - typically high concentration inside compared to the outside - needs to be moved against the concentration gradient - positive delta G value.
32
Two types of passive transport.
* Simple diffusion - molecules moving through the bilayer.
* Facilitated diffusion - molecules moving through transport proteins - channels and carriers.
33
Water movement
* Water movement - the solvent that things are dissolved can also move across membranes by passive transport.
* Water can move across membranes.
34
Passive movement of water - U shaped tube example
* Demonstrated by an experiment where you have U shaped tubes and there is a selectively permeable membrane separating the two sides of the tubes.
* Two different sugar solutions on each side of the membrane. High conc. And low conc.
* The water is able to move across the membrane but not the sugar.
* Where there is a low concentration of the sugar that is actually a high conc. of water.
* And where there is a high concentration of sugar there is a low concentration of water.
* Water concentration gradient across the membrane.
* The water will move across the membrane until there is an equal concentration of water on either side of the membrane.
* Water is moving down the concentration gradient.
35
How does water move in our cells?
* In our cells water can move through simple diffusion.
* Through the bilayer and through facilitated diffusion through transport proteins called aquaporins because we want the water to move quicker that how it would through simple diffusion.
36
Water movements: osmoregulation.
* Cells adjust their internal solute content so they remain isotonic - have the same solute concentration - with the external media.
* Cells have to adjust their internal solute concentrations to counter water movements so that they remain isotonic.
* So no water concentration gradient across the cell. No net movement of water - osmoregulation.
37
Hypotonic solution
* Hypotonic solution - solute concentration higher on the inside compared to the outside.
* Water moves into the cell and the cells explodes.
* In the absence of osmoregulation, lower solute concentration outside the cell compared to inside (outside solution is hypotonic) - water flows into the cell and the cell bursts.
38
Hypertonic solution.
* Hypertonic solution - more solutes outside the cell compared to inside the cell.
* The water will move out of the cell and shrivel.
* In the absence of osmoregulation, higher solute concentration outside the cell compared to inside (outside the cell is hypertonic) water flows out of the cell.
* The cell shrivels.
39
Water movements in plants
* Plants have a cell wall. - they maintain their internal solute concentration so that they are hypertonic to the external media.
* Causes water to move into the cell, the cell expands but does not burst because of the cell wall
* The cell becomes very rigid - referred to as turgidity - calls have an internal water pressure (hydrostatic pressure) called turgor and this is important for plants to stay upright.
* Wall prevents cell from bursting.
* Plants/fungal cells are turgid, non-turgid cells - plant wilts.
40
Facilitated diffusion - ion channels
* Ions move through things called ion channels.
* Provide a pathway for ion to move into the cell.
* They are very specific and selective.
* Intricate interactions with the ion and the amino acid residues that make up the protein.
* Channels are referred to as gated - membrane voltage if there's a channel in that can cause a channel to open.
* Plasma membrane - sodium channels and potassium channels - the sodium atpase sets a resting membrane potential - moves 2 potassiums out 3 sodium.
* You get is a transient change in the membrane potential - depolarisation - membrane potential becomes less negative depolarising phase of the action potential.
* Potassium channels open when the sodium channels are closed, this re polarises the membrane potential
41
Nerve cells - chemical signalling neurotransmission
* Signalling between nerve cells.
* Release of chemicals and stimulation of other ion channels in the postsynaptic cell.
* The signalling process breaking down can lead to drug addiction, depression, schizophrenia etc.
42
Cystic fribrosis
* Defective ion channels. Leads to infection and the breakdown of the lungs.
* Caused by a mutation to a chloride ion channel called CFTR.
* Defective Cl transport affects the airways - increased infections and gradual breakdown of lungs.
43
Facilitated diffusion carriers + diabetes
* Facilitated diffusion carriers bind the solute that moves across the membrane.
* Change shape so that the binding site faces the other side of the membrane.
* Solutes moving down the concentration gradient.
* Typically specific. Lower turn over.
* When you eat - high sugar - produce insulin and insulin will bind to receptors which will set off a signal and will lead to incorporation of GLUT4 in the membrane of the cells.
* Don't have the GLUT4 carrier protein in your blood. GLUT4 moves glucose into cells. Its presence in the membrane is controlled by insulin.
* Diabetes when no insulin produced (Type 1) or insulin receptor not active (Type 2). Thus diabetes are unable to move glucose into their cells.
44
Active transport: general outline
* Ions move against their concentration/charge gradients.
* Pumps - Na/K ATPase, H+ ATPase, Ca ATPase.
* Non spontaneous, energy input, ATP.
* Proton atpase in plant membranes. Calcium atpase - in our muscle cells.
45
Active transport generates...
* Ion gradients across membranes.
* In an animal cell Sodium potassium atpase (blue box) - 3 sodium out and 2 potassium in per ATP - will generate a concentration gradient.
* 2 components to the ion gradient (electrochemical gradient) concentration gradient - high Na+ outside, high K+ inside.
* Charge gradient more + outside, -60 mV (membrane potential).
46
Ion gradients drive...
* secondary active transport.
* Na+ coupled transport proteins, secondary active transport, for example Na+ glucose symporter.
* Kidney - protein Sodium glucose symporter - it can couple the movement of sodium ions to the movement of glucose.
* Low concentration of glucose outside, large concentration inside.
* The glucose can be moved against the concentration gradient by coupling the movement of two sodium ions.
* Very strong protein! 30,000 to one.
* Symporter - the glucose and sodium are moving in the same direction. Some secondary active transport act as antiporters. Antiport - different directions.
47
Active transport in plants and fungi.
* Proton ATPase - move protons outside the cell - one proton per ATP that is hydrolysed.
* Generates a concentration gradient - more protons on one side of the gradient compared to the other and there is a charge component because the protons are charged.
* These electrochemical gradients can drive secondary active transport.
* Active transporter H+ ATPase. Moves 1 H+ per ATP.
48
Active transport: Sodium Potassium ATPase example
* Sodium potassium ATPase - in your brain, is able to move 3 sodium out of the cell.
* High concentration of sodium outside the cell compared to the inside so you need an input to move the 3 sodium into an area of high concentration.
* It's also able to move 2 potassium inside the cell - against the concentration gradient.
* 3 sodium out and 2 potassium in.
* Powered by the active transport protein that is phosphorylated - more reactive due to hydrolysis of ATP which is forming the phosphorylated intermediate.
