Bke2 Biochemistry Exercises

Suggested answers to group exercise: Plant biochemistry

Explain the role of plants in the carbon cycle.

Answer: Carbon is circulated between heterotrophic and autotrophic organisms. Heterotrophs (mainly mammals) evolve carbon dioxide as one of the end products of their metabolism. Carbon dioxide is fixed or assimilated by autotrophs (mainly plants and photosynthetic bacteria) into organic molecules that serve as foodstuffs for heterotrophs.
Where are the light- and dark-reactions of photosynthesis taking place?

Answer: In green plants the photo-chemical reactions (light reactions, photophosphorylation) of photosynthesis take place in the tylakoid membrane of the chloroplast. The dark reactions (carbon dioxide fixation and carbohydrate synthesis) take place in the stroma of the chloroplasts.
In photosynthetic bacteria the light reactions take place in the cell membrane, and the dark reactions in the cytoplasm inside the bacterial cell. The chloroplast is the descendant of a photosynthetic bacterium that started to live inside a eucaryotic host cell.
The redox potential is a key concept for the understanding of what drives electron transport in biological membranes. Describe this.

Answer: The redox potential is a measure of a substance's affinity for electrons relative to that of the H⁺/H₂ reference halfcell. A negative redox potential means that the substance is a strong reducing agent (such as NADH) and is prone to donate electrons. Conversely, a positive redox potential signifies a strong oxidising agent (such as O₂) that likes to accept electrons. See Horton 319-321 (2nd Ed) or 331-333 (3rd Ed).
a) What are the main components of light-driven photosynthesis? b) The Z scheme is often used to describe how the main components of the light driven photosynthetic electron transfer work together to create redox energy. Draw this scheme as simple as possible, i.e. organise the main components relative to each other and with respect to the redox potential.

Answer: a) First of all you need a compartment, such as an organelle, surrounded by a membrane. You need pigments (such as chlorophylls) that can absorb sunlight in a productive way, i.e. that contain excitable electrons. You also need proteins to fix the pigments in the membrane. Pigments and proteins together constitute a photosystem, plants have two photosystems, PSII (photosystem II) and PSI. You may need additional protein complexes containing redox centres that can transport electrons. Small soluble carrier proteins (plastoquinol, plastocyanin) may be needed to carry electrons between the protein complexes. Finally you need a source of electrons and a final electron acceptor. In plants the source of electrons is water, and the final acceptor is NADP⁺.

b) The main components are in order: (1) an oxygen-evolving (watersplitting) complex with a relatively positive redox potential, (2) a reaction centre, photosystem (PS) II, (3) a chain of electron carriers, (4) another reaction centre (PS I), (5) another chain of electron carriers, (6) a final acceptor with a relatively negative redox potential. See Horton pp 440-441 (2nd Ed) or 467-471 (3rd Ed).
What is the major difference between antenna pigments (chlorophylls) and the reaction centre?

Answer: When a light photon hits (exites) an antenna molecule (chlorophyll a or b), an electron is excited to a higher energy level. Light energy is passed from one antenna molecule to the neighbouring antenna molecules, without concomittant electron transfer, by a process called resonance energy transfer. Energy rapidly migrates from pigment to pigment until it reaches the reaction centre. Because this chlorophyll is in a very special environment, the exited electron can be transferred to an electron acceptor in the vicinity (against an electrochemical gradient).
How is light energy used to produce ATP? What is the role of the membrane? Differentiate between cyclic and noncyclic photophosporylation in green plants and describe how photosystems I and II are involved in each process.

Answer: Light excitation of the reaction centre leads to charge separation over the membrane which creates a pH gradient which in turn drives an ATPase (or ATP synthase).

The membrane is essential for anchoring protein molecules to which the pigments are bound. The membrane also acts as an impermeable barrier to charged metabolites. Thus a spatial separation of charge is achieved, the forward (desired) reaction is promoted and the risk of energy loss due to back- or side-reactions is minimised.

Photophosphorylation is the process of ATP generation driven by the proton gradient generated during the light-driven electron transfer. Noncyclic photophosphorylation requires the net electron tranfer from a donor (H₂O) to an acceptor (NADP⁺) with vectorial H⁺ translocation (over the membrane). Cyclic photophosphorylation is driven by a proton gradient generated by electron transfer from photosystem I through the quinone pool and the electron-transfer system, back to photosystem I. In this way ATP is formed without concomittant water splitting and without reduction of NADP⁺.
What is the main purpose of the dark reaction?

Answer: CO₂ (inorganic) is converted into carbohydrates (organic).
Triose-phosphate is an important intermediate in the photosynthetic dark reaction. a) What are the steps leading to triose-phosphate? b) What is the fate of triose-phosphate (inside the Calvin cycle, as well as outside)?

Answer: In the dark reaction, atmospheric CO₂ is fixed to ribulose-1,5-bisphosphate to form 2 molecules of 3-phosphoglycerate which is the first stable intermediate of the dark reaction (carboxylation stage). In the next stage (reduction stage), 3-phosphoglycerate is converted into 1,3-bisphosphoglycerate in an ATP-dependent reaction and then reduced to glyceradehyde-3-phosphate by NADPH. Glyceradehyde-3-phosphate is in equilibrium with its isomer, dihydroxyacetone phosphate, and these go under the collective name triose-phosphate. The further fate of triose-phosphate is manyfold: A major part (5/6) is used to regenerate ribulose-1,5-bisphosphate in a complex manner (regeneration stage). The remaining 1/6 is removed from the cycle for the synthesis of hexoses. Hexoses are either used as a carbohydrate reserve in the chloroplast stroma (starch), circulated to other parts of the plant (sucrose synthesised in the cytosol), or used as building material for cell walls (cellulose).
What is the name of the CO₂-fixing enzyme? What other reaction(s) are catalysed by this enzyme? What consequences does this have for net carbon fixation?

Answer: Ribulose-1,5-bisphosphate carboxylase/oxygenase, Rubisco, is the main catalyst for CO2 fixation. In addition to its main reaction, carboxylation of ribulose-1,5-bisphosphate (RuBP) to yield 2 molecules of 3-phosphoglycerate, Rubisco also catalyses the oxygenation of RuBP to yield one molecule of 3-phosphoglycerate and one molecule of phosphoglycolate. The oxygenation reaction diminishes the amount of fixed carbon and reduces photosynthetic yields by up to 50%. This reduces harvest yields.
Compare and contrast CO₂ fixation in C3 and C4 plants.

Answer: In C3 plants, CO₂ is fixed to ribulose-1,5-bisphosphate and the 6-carbon intermediate is cleaved to yield 3-phosphoglycerate, a 3-carbon molecule. In C4 plants, CO₂ is instead fixed to phosphoenolpyruvate, a 4-carbon acid. This initial process takes place in the mesophyll cells. In the next phase, CO₂ is released by oxidative decarboxylation of malate in the bundle sheath cells of C4 plants, causing the CO₂/HCO₃^- concentration to exceed the CO₂/HCO₃^- concentration in the mesophyll cells. The higher concentration increases the fraction of ribulose bisphosphate that is carboxylated rather than oxygenated. Net photorespiration is lower in C4 plants as compared with C3 plants.

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