Medical brain Notes 9

  Production of Cellular Energy Cellular energy is present mainly in the form of ATP and to a lesser extent, GTP (Figure 2.4) which are high energy molecules, so called because a large amount of chemical energy is released on hydrolysis of the phosphate groups. The energy to make these molecules is derived from the catabolism of a food, or from photosynthesis. A food source is commonly carbohydrate, lipid or to a lesser extent, protein but if a compound considered to be a contaminant can enter a catabolic pathway, then it can become a ‘food’ for the organism. This is the basis of bioremediation. The way in which energy is transferred from the ‘food’ molecule to ATP may take two substantially different routes. One is cytoplasmic synthesis of ATP which is the direct transfer of a phosphate group to ADP, storing the energy of that reaction in chemical bonds. The other involves a fairly complicated system involving transfer of electrons and protons, or hydrogen ions, which originated f...

  Fermentation and respiration The electrons derived from the catabolism of the carbon source are eventually either donated to an organic molecule in which case the process is described as fermentation, or donated to an inorganic acceptor by transfer along an electron chain. This latter process is respiration and may be aerobic where the terminal electron acceptor is oxygen, or anaerobic where the terminal electron acceptor is other than oxygen such as nitrate, sulphate, carbon dioxide, sulphur or ferric ion. Unfortunately, respiration is a term which has more than one definition. It may also be used to describe a subset of the respiration processes mentioned above to include only oxidation of organic material and where the ultimate elec-tron acceptor is molecular oxygen. This latter definition is the basis of biological oxygen demand (BOD), which is often used to characterise potential environmen-tal pollutants, especially effluents, being a measure of the biodegradable material a...

  Photosynthesis and the Basis of Phytotechnology The sun is the biosphere’s ultimate source of energy and photosynthesis is the only means there is on this planet to trap incident sunlight and convert it into chemical energy available to biological processes. Thus, with very rare excep-tions, organisms which do not photosynthesise, which is the majority, are totally dependent on those which do. With this introduction it is hardly surprising to find a description of this process in a book which specifically addresses the capabili-ties of biological organisms and their interplay. Leafy plants obviously feature in this section but so too do photosynthetic eukaryotic micro-organisms and bacte-ria. A knowledge of this vital process is essential to appreciating the role which photosynthesising organisms play in the environment, their limitations and the strengths upon which biotechnology can capitalise.  The energy from this process is used to drive all the biochemical synthesis an...

  The light reactions Visible light is the outcome of the nuclear fusion of hydrogen atoms, resulting in the production of helium atoms, gamma radiation and two electrons. This fusion occurs in the sun at a temperature of approximately 20 000 000 K. The gamma radiation and electrons combine to produce quanta of visible light. The entrap-ment of light is performed in photosynthetic cells by pigments; the most important of which are the chlorophylls. These are flat ring structures, with regions of con-jugated double and single bonds, and a long hydrophobic tail well designed for anchoring the pigments into membrane. Only red and blue light is absorbed by the chlorophylls in most organisms. Consequently, when white light from the sun shines upon them, they reflect green light, thus making these organisms appear green. Variation in the types of chlorophylls and the presence of additional acces-sory pigments all contribute to the observed colour of the organism and are the result of evo...

The dark reactions The result of illumination of a photosynthetic organism is to stimulate electron transport which leads to the production of NADPH or NADH, and synthesis of ATP. Both are required for the next stage which in eukaryotes and cyanobacteria (blue-green algae) is the synthesis of sugar from carbon dioxide involving the Calvin cycle. Many biochemistry textbooks give excellent descriptions of this process and so only a summary is given in Figure 2.10.  In brief, ribulose diphosphate is carboxylated with carbon dioxide catalysed by the enzyme rubisco to form an unstable six-carbon sugar which is then cleaved to form two molecules of 3-phosphoglycerate, an intermediate of glycolysis. This is not the only route of entry of carbon dioxide into carbohydrate synthesis, the other being the Hatch – Slack pathway. This subject is discussed in more detail later.  Returning to the Calvin cycle, rearrangements of 3-phosphoglycerate produced by rubisco then take place by similar...

  The Nitrogen Cycle Nitrogen is constantly taken, or fixed, from the atmosphere, oxidised to a form able to be utilised by plants and some bacteria, to be subsumed into metabolic pathways, and through the various routes described above is then excreted into the environment as reduced nitrogen where it may be reoxidised by bacteria or released back into the atmosphere as nitrogen gas. These combined processes are known collectively as the nitrogen cycle. The previous discussions have referred to the release of nitrogen during degradation of proteins and nucleic acid bases, either in the form of ammonia, the ammonium ion, urea or uric acid. The fate of all these nitrogen species is to be oxidised to nitrite ion by  Nitrosomas , a family of nitrifying bacteria. The nitrite ion may be reduced and released as atmospheric nitrogen, or further oxidised to nitrate by a different group of nitrifying bacteria,  Nitrobacter.  The process of conversion from ammonia to nitrate i...

  Using Biological Systems Consequently, a number of themes and similarities of approach exist, which run as common and repeated threads throughout the whole of the science. Thus, optimisation of the activities of particular organisms, or even whole biological communities, to bring about any desired given end, typically requires manipula-tion of local conditions. Control of temperature, the accessibility of nutrients and the availability of oxygen are commonly the tools employed, especially when the target effectors are microbes or isolated biological derivatives. For the kind of whole organism approaches typified by phytotechnological interventions discussed, this may prove a more difficult proposition, but nevertheless, one which still remains relevant at least in principle. The typical factors affecting the use of biological systems in environmental engineering relate to the nature of the substances needing to be removed or treated and to the localised envi-ronmental conditions ...