Econstudentlog

Photosynthesis in the Marine Environment (II)

Here’s my first post about the book. I gave the book four stars on goodreads – here’s a link to my short goodreads review of the book.

As pointed out in the review, ‘it’s really mostly a biochemistry text.’ At least there’s a lot of that stuff in there (‘it get’s better towards the end’, would be one way to put it – the last chapters deal mostly with other topics, such as measurement and brief notes on some not-particularly-well-explored ecological dynamics of potential interest), and if you don’t want to read a book which deals in some detail with topics and concepts like alkalinity, crassulacean acid metabolism, photophosphorylation, photosynthetic reaction centres, Calvin cycle (also known straightforwardly as the ‘reductive pentose phosphate cycle’…), enzymes with names like Ribulose-1,5-bisphosphate carboxylase/oxygenase (‘RuBisCO’ among friends…) and phosphoenolpyruvate carboxylase (‘PEP-case’ among friends…), mycosporine-like amino acid, 4,4′-Diisothiocyanatostilbene-2,2′-disulfonic acid (‘DIDS’ among friends), phosphoenolpyruvate, photorespiration, carbonic anhydrase, C4 carbon fixation, cytochrome b6f complex, … – well, you should definitely not read this book. If you do feel like reading about these sorts of things, having a look at the book seems to me a better idea than reading the wiki articles.

I’m not a biochemist but I could follow a great deal of what was going on in this book, which is perhaps a good indication of how well written the book is. This stuff’s interesting and complicated, and the authors cover most of it quite well. The book has way too much stuff for it to make sense to cover all of it here, but I do want to cover some more stuff from the book, so I’ve added some quotes below.

“Water velocities are central to marine photosynthetic organisms because they affect the transport of nutrients such as Ci [inorganic carbon] towards the photosynthesising cells, as well as the removal of by-products such as excess O2 during the day. Such bulk transport is especially important in aquatic media since diffusion rates there are typically some 10 000 times lower than in air […] It has been established that increasing current velocities will increase photosynthetic rates and, thus, productivity of macrophytes as long as they do not disrupt the thalli of macroalgae or the leaves of seagrasses”.

Photosynthesis is the process by which the energy of light is used in order to form energy-rich organic compounds from low-energy inorganic compounds. In doing so, electrons from water (H2O) reduce carbon dioxide (CO2) to carbohydrates. […] The process of photosynthesis can conveniently be separated into two parts: the ‘photo’ part in which light energy is converted into chemical energy bound in the molecule ATP and reducing power is formed as NADPH [another friend with a long name], and the ‘synthesis’ part in which that ATP and NADPH are used in order to reduce CO2 to sugars […]. The ‘photo’ part of photosynthesis is, for obvious reasons, also called its light reactions while the ‘synthesis’ part can be termed CO2-fixation and -reduction, or the Calvin cycle after one of its discoverers; this part also used to be called the ‘dark reactions’ [or light-independent reactions] of photosynthesis because it can proceed in vitro (= outside the living cell, e.g. in a test-tube) in darkness provided that ATP and NADPH are added artificially. […] ATP and NADPH are the energy source and reducing power, respectively, formed by the light reactions, that are subsequently used in order to reduce carbon dioxide (CO2) to sugars (synonymous with carbohydrates) in the Calvin cycle. Molecular oxygen (O2) is formed as a by-product of photosynthesis.”

“In photosynthetic bacteria (such as the cyanobacteria), the light reactions are located at the plasma membrane and internal membranes derived as invaginations of the plasma membrane. […] most of the CO2-fixing enzyme ribulose-bisphosphate carboxylase/oxygenase […] is here located in structures termed carboxysomes. […] In all other plants (including algae), however, the entire process of photosynthesis takes place within intracellular compartments called chloroplasts which, as the name suggests, are chlorophyll-containing plastids (plastids are those compartments in cells that are associated with photosynthesis).”

“Photosynthesis can be seen as a process in which part of the radiant energy from sunlight is ‘harvested’ by plants in order to supply chemical energy for growth. The first step in such light harvesting is the absorption of photons by photosynthetic pigments[1]. The photosynthetic pigments are special in that they not only convert the energy of absorbed photons to heat (as do most other pigments), but largely convert photon energy into a flow of electrons; the latter is ultimately used to provide chemical energy to reduce CO2 to carbohydrates. […] Pigments are substances that can absorb different wavelengths selectively and so appear as the colour of those photons that are less well absorbed (and, therefore, are reflected, or transmitted, back to our eyes). (An object is black if all photons are absorbed, and white if none are absorbed.) In plants and animals, the pigment molecules within the cells and their organelles thus give them certain colours. The green colour of many plant parts is due to the selective absorption of chlorophylls […], while other substances give colour to, e.g. flowers or fruits. […] Chlorophyll is a major photosynthetic pigment, and chlorophyll a is present in all plants, including all algae and the cyanobacteria. […] The molecular sub-structure of the chlorophyll’s ‘head’ makes it absorb mainly blue and red light […], while green photons are hardly absorbed but, rather, reflected back to our eyes […] so that chlorophyll-containing plant parts look green. […] In addition to chlorophyll a, all plants contain carotenoids […] All these accessory pigments act to fill in the ‘green window’ generated by the chlorophylls’ non-absorbance in that band […] and, thus, broaden the spectrum of light that can be utilized […] beyond that absorbed by chlorophyll.”

“Photosynthesis is principally a redox process in which carbon dioxide (CO2) is reduced to carbohydrates (or, in a shorter word, sugars) by electrons derived from water. […] since water has an energy level (or redox potential) that is much lower than that of sugar, or, more precisely, than that of the compound that finally reduces CO2 to sugars (i.e. NADPH), it follows that energy must be expended in the process; this energy stems from the photons of light. […] Redox reactions are those reactions in which one compound, B, becomes reduced by receiving electrons from another compound, A, the latter then becomes oxidised by donating the electrons to B. The reduction of B can only occur if the electron-donating compound A has a higher energy level, or […] has a redox potential that is higher, or more negative in terms of electron volts, than that of compound B. The redox potential, or reduction potential, […] can thus be seen as a measure of the ease by which a compound can become reduced […] the greater the difference in redox potential between compounds B and A, the greater the tendency that B will be reduced by A. In photosynthesis, the redox potential of the compound that finally reduces CO2, i.e. NADPH, is more negative than that from which the electrons for this reduction stems, i.e. H2O, and the entire process can therefore not occur spontaneously. Instead, light energy is used in order to boost electrons from H2O through intermediary compounds to such high redox potentials that they can, eventually, be used for CO2 reduction. In essence, then, the light reactions of photosynthesis describe how photon energy is used to boost electrons from H2O to an energy level (or redox potential) high (or negative) enough to reduce CO2 to sugars.”

“Fluorescence in general is the generation of light (emission of photons) from the energy released during de-excitation of matter previously excited by electromagnetic energy. In photosynthesis, fluorescence occurs as electrons of chlorophyll undergo de-excitation, i.e. return to the original orbital from which they were knocked out by photons. […] there is an inverse (or negative) correlation between fluorescence yield (i.e. the amount of fluorescence generated per photons absorbed by chlorophyll) and photosynthetic yield (i.e. the amount of photosynthesis performed per photons similarly absorbed).”

“In some cases, more photon energy is received by a plant than can be used for photosynthesis, and this can lead to photo-inhibition or photo-damage […]. Therefore, many plants exposed to high irradiances possess ways of dissipating such excess light energy, the most well known of which is the xanthophyll cycle. In principle, energy is shuttled between various carotenoids collectively called xanthophylls and is, in the process, dissipated as heat.”

“In order to ‘fix’ CO2 (= incorporate it into organic matter within the cell) and reduce it to sugars, the NADPH and ATP formed in the light reactions are used in a series of chemical reactions that take place in the stroma of the chloroplasts (or, in prokaryotic autotrophs such as cyanobacteria, the cytoplasm of the cells); each reaction is catalysed by its specific enzyme, and the bottleneck for the production of carbohydrates is often considered to be the enzyme involved in its first step, i.e. the fixation of CO2 [this enzyme is RubisCO] […] These CO2-fixation and -reduction reactions are known as the Calvin cycle […] or the C3 cycle […] The latter name stems from the fact that the first stable product of CO2 fixation in the cycle is a 3-carbon compound called phosphoglyceric acid (PGA): Carbon dioxide in the stroma is fixed onto a 5-carbon sugar called ribulose-bisphosphate (RuBP) in order to form 2 molecules of PGA […] It should be noted that this reaction does not produce a reduced, energy-rich, carbon compound, but is only the first, ‘CO2– fixing’, step of the Calvin cycle. In subsequent steps, PGA is energized by the ATP formed through photophosphorylation and is reduced by NADPH […] to form a 3-carbon phosphorylated sugar […] here denoted simply as triose phosphate (TP); these reactions can be called the CO2-reduction step of the Calvin cycle […] 1/6 of the TPs formed leave the cycle while 5/6 are needed in order to re-form RuBP molecules in what we can call the regeneration part of the cycle […]; it is this recycling of most of the final product of the Calvin cycle (i.e. TP) to re-form RuBP that lends it to be called a biochemical ‘cycle’ rather than a pathway.”

“Rubisco […] not only functions as a carboxylase, but […] also acts as an oxygenase […] When Rubisco reacts with oxygen instead of CO2, only 1 molecule of PGA is formed together with 1 molecule of the 2-carbon compound phosphoglycolate […] Not only is there no gain in organic carbon by this reaction, but CO2 is actually lost in the further metabolism of phosphoglycolate, which comprises a series of reactions termed photorespiration […] While photorespiration is a complex process […] it is also an apparently wasteful one […] and it is not known why this process has evolved in plants altogether. […] Photorespiration can reduce the net photosynthetic production by up to 25%.”

“Because of Rubisco’s low affinity to CO2 as compared with the low atmospheric, and even lower intracellular, CO2 concentration […], systems have evolved in some plants by which CO2 can be concentrated at the vicinity of this enzyme; these systems are accordingly termed CO2 concentrating mechanisms (CCM). For terrestrial plants, this need for concentrating CO2 is exacerbated in those that grow in hot and/or arid areas where water needs to be saved by partly or fully closing stomata during the day, thus restricting also the influx of CO2 from an already CO2-limiting atmosphere. Two such CCMs exist in terrestrial plants: the C4 cycle and the Crassulacean acid metabolism (CAM) pathway. […] The C 4 cycle is called so because the first stable product of CO2-fixation is not the 3-carbon compound PGA (as in the Calvin cycle) but, rather, malic acid (often referred to by its anion malate) or aspartic acid (or its anion aspartate), both of which are 4-carbon compounds. […] C4 [terrestrial] plants are […] more common in areas of high temperature, especially when accompanied with scarce rains, than in areas with higher rainfall […] While atmospheric CO2 is fixed […] via the C4 cycle, it should be noted that this biochemical cycle cannot reduce CO2 to high energy containing sugars […] since the Calvin cycle is the only biochemical system that can reduce CO2 to energy-rich carbohydrates in plants, it follows that the CO2 initially fixed by the C4 cycle […] is finally reduced via the Calvin cycle also in C4 plants. In summary, the C 4 cycle can be viewed as being an additional CO2 sequesterer, or a biochemical CO2 ‘pump’, that concentrates CO2 for the rather inefficient enzyme Rubisco in C4 plants that grow under conditions where the CO2 supply is extremely limited because partly closed stomata restrict its influx into the photosynthesising cells.”

“Crassulacean acid metabolism (CAM) is similar to the C 4 cycle in that atmospheric CO2 […] is initially fixed via PEP-case into the 4-carbon compound malate. However, this fixation is carried out during the night […] The ecological advantage behind CAM metabolism is that a CAM plant can grow, or at least survive, under prolonged (sometimes months) conditions of severe water stress. […] CAM plants are typical of the desert flora, and include most cacti. […] The principal difference between C 4 and CAM metabolism is that in C4 plants the initial fixation of atmospheric CO2 and its final fixation and reduction in the Calvin cycle is separated in space (between mesophyll and bundle-sheath cells) while in CAM plants the two processes are separated in time (between the initial fixation of CO2 during the night and its re-fixation and reduction during the day).”

July 20, 2015 - Posted by | biology, Botany, Chemistry

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