1b. What is a metabolic pool, and how does it relate to a lag phase?
Within a cell (or organelle such as a chloroplast) there exists a resevoir of molecules upon which an enzymes can operate. This size of this resevoir, is referred to as its "metabolic pool." The metabolic pool concept is important to cellular biology. Let's consider an analogy:
In certain ways, a metabolic pathway is similar to a factory assembly line. Products are assembled from parts by workers who each perform a specific step in the manufacturing process. Enzymes of a cell are like workers on an assembly line; each is only responsible for a particular step in the assembly process. A lag period also occurs when a new factory is constructed, a time period before finished products begin to roll off the assembly line at a steady rate. This lag period partially results from the time needed to fill supply bins with the necessary parts. As you might imagine, when parts are not readily available, production is slow, or stops. Molecular pools are somewhat analogous to the parts bins of a factory. The Calvin-Benson cycle will only operate at full speed when the cellular 'bins' are full of the molecule building blocks that lie between PGA and RUBP.
What would a factory be like if it operated like a cell?
To better illustrate how the size of a metabolic pool affects the rate of an enzymatic process, let's build a factory that operates in the same way as an enzymatic pathway, such as the Calvin-Benson cycle.
First, we would need to build our factory in space where there's no gravity. We won't actually use 'bins' to store the parts, rather, we will dump them all into one big assembly room where they can mix together, floating in space. (Just as the intermediates of the Calvin-Benson cycle are all mixed together, dissolved in the liquid of the stroma.) Next, we'll let the factory workers also float around in the factory space. Factory workers are still responsible for only a single step in the assembly process, but they can only perform that step when the necessary parts happen to float their way. After each worker performs his or her task, the 'intermediate product' is released so that it can float around. The next step of the assembly process can't occur until an intermediate product encounters a worker responsible for that step. As you can imagine, the factory space would eventually become filled with 'intermediate products' in all stages of assembly (or disassembly, depending upon your point of view).
We would say that the factory contains 'pools' of parts, analogous to the 'pools' of molecules that exist within the stroma. The parts include raw materials and intermediate products. Intermediate products are analogous to "intermediate metabolics" of an enzymatic pathway --the molecular forms that exist between reactants and endproducts. Factories would indeed be very interesting places to visit if they assembled products in the fashion of metabolic pathways.
The rate at which finished products are produced in our outer-space (or spaced-out) factory will depend upon how quickly each worker receives the parts needs. (The rate will also depend upon how fast workers perform their task, but we will ignore this factor). Remember, the parts are just floating around, bouncing off the walls, and encountering only by chance a worker with the right tools to do something with them. The rate at which a worker encounters the right parts will depend upon how many of those parts are floating around. The more of each kind of part, the more frequently will one float by a worker who can perform the next step in the assembly operation.
A biologist would call the amount of each type of part in the factory space as the 'size' of its particular pool (size here refers to concentration, not physical dimension). Likewise, the concentration of each metabolite in the stroma represents the size of its metabolic pool. As in our factory, the larger the metabolite pools in the stroma, the faster carbon can be fixed into carbohydrates and cycled back into RUBP.
When assembly begins in our factory (or a leaf is exposed to light), the pools of parts or metabolites (in the stroma) will increase progressively as the reactions proceed. Each process will reach steady rate of output when the pools have reached full, operational levels. This is when the lag phase ends.
For Biology majors:
1c. It is possible to experimentally uncouple the light-dependent and light-independent reactions of photosynthesis using purified thylakoid membranes. In these thylakoids, water splitting and electron transport occur, but ATP and NADPH synthesis and the Calvin-Benson cycle do not. If you were to measure O2 evolution using purified thylakoids, what pattern of O2 evolution would you expect to see? (Click on letter of choice.)
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