APPENDICES A. Biological fundamentals EUKARYOTIC VS. PROKARYOTIC CELLS Though phytoplankton is small, the cells of the smallest diatoms and flagellates can be easily seen under an ordinary microscope. However, in order to observe planktonic free-living bacteria, which barely attain a diameter of one thousandth of a millimeter, special optical methods are needed. In all cases, to appreciate the fine details of the cells, one needs an electron microscope, which has a much higher resolving power than an optical microscope. The cells can be divided into two groups: the prokaryotic and the eukaryotic cells. Bacteria and cyanobacteria are prokaryotes, whereas alI other organisms, with the exception of the archaebacteria to which we have alluded in chapter 4, are eukaryotes. In all cases biochemical studies have shown that cells are 90% water and that different functions are performed in the different organelles of the cell. In the following an idealized eukaryotic cell will serve to illustrate the main cellular features. The eukaryotic cell 174 mOLOOliCAlL lF1lJNDAMlENT AJL,§ cytoplasm is enclosed in a double-Iayered membrane, which is so thin that it appears as a single line in our drawing. In the central portion of the cell there is the nucleus surrounded by a membrane. The nucleoplasm contains a nucleolus and more than one linear chromosome, which is an association of DNA with a protein. The cytoplasm also contains various organelles, which are membrane-enclosed spaces, such as the lysosomes, where hydrolysis of polysaccharides occurs yielding monomeric sugars. These are taken up by the mitochondria, as centers of energy metabolism, and are oxidized to carbon dioxide. Another organelle is the endoplasmic reticulum, which contains the ribosomes where the proteins are synthesized. The proteins are then packed and distributed by the Golgi apparatus. The cytoplasm of photosynthetic cells also contains plastids or chloroplasts where photosynthesis occurs. Plant cells also have cavities, called vacuoles, for food storage. Finally, many unicellular organisms possess centrioles, small cavities near the nucleus which act as contractile or locomotory elements in the muscle function of higher animals. As with primary metabolites, though probably with less specificity, the synthesis of secondary metabolites of different classes occurs in different compartments of the cello For instance, certain hormonal regulators of plant growth, the gibbereJlins and abscisic acid, which are terpenes, are mainly produced in the plastids. Why has evolution led to this choice? The reason is probably that the plastids are particularly rieh in the reactants required for the biosynthesis of these hormones. Specialized ceUs are capable of accumulating secondary metabolites, such as brominated acetogenins in the red seaweed Bonnemaisonia nootkana and, as already noted in chapter 6, amino acid metabolites in the sponge Aplysina fistularis. All the ceJlular charaeteristics of eukaryotes are absent in prokaryotes, and the genetic organization is different. In prokaryotic ceJls the major part of the DNA forms a single circular chromosome, not restricted within a nuclear membrane, and genetic information is also eontained in extrachromosomal DNA. Some metabolie functions are also performed in a different way. 175 AlPlP']ENlJ)liClES While there is general consensus that plastids and mitochondria of eukaryotic cells originate from prokaryotic cells along an endosymbiont line, the opinions differ in regard to the cell nucleus: some scientists advocate an endosymbiontic origin of the nucleus as the first step in the evolution of eukaryotes, whereas other scientists have proposed that the nucleus derives from cell compartmentation. CELL TYPE AND EVOLUTIONARY MARKS An important point is that while the eukaryotic cell seeks to maintain its characteristics, the prokaryotic cell lacks such a strict restraint; the prokaryotic cell is able to exchange genetic material, though this occurs less frequently than is generally thought. Genetic engineers have emphasized this property of eukaryotic cells to justify their efforts in mixing the characteristics of all organisms, including eukaryotes, which were devised not to do so; or at least not at the speed of genetic manipulation. In any event, an overall improvement on Nature through genetic manipulation is yet to be seen. This preamble serves to emphasize the fact that patterns of sequences of amino acids in proteins are related to the evolutionary his tory of species. As this is similar for evolutionarily-related species, such patterns can be used as evolutionary marks. An example in chapter 14 concerns the green turtles of Ascension Island. If, however, exchange of genetic material has occurred recently in prokaryotic cells, where it is allowed to happen, such patterns are altered and may not be used as evolutionary marks. Therefore, the prokaryotic cell, though more amenable to investigation than the eukaryotic cell, may be unsuited to unravel the evolutionary history of species. 176 mOlLOOrrCAlL lFUNDAMlEN1l'AlL§ PHOTOSYNTHESIS IN THE SEA Photosynthesis occurs in the sea with or without the evolution of oxygen. When oxygen evolves, photosynthesis occurs the same way as in terrestrial plants, except for the attenuation and change in color of light with increasing depth, which influences both the distribution of marine organisms and the need for accessory pigments. Although all animals depend on photosynthesis for survival, as they feed on products of photosynthetic organisms, the way this occurs in certain marine animals is peculiar. A case in point is that of reef-building corals and other organisms which live in a symbiosis with microscopic photosynthetic algae called zooxanthellae. The corals da not feed on zooxanthellae products in the usual sense; transfer of photosynthetic nutrients from zooxanthellae to corals occurs directly. As a consequence, reef corals need much light to support their zooxanthellae, so that shadowing seaweeds are not allowed to grow excessively. The photosynthetic process of green seaweeds and higher plants involves decomposition of water to give intermediate compounds which have reducing properties. These intermediates react with carbon dioxide to afford sugars in a dark process. Amino acids, fatty acids, and nucleotides, which are essential compounds for the growth of all organisms, are produced in subsequent steps which are difficult to distinguish from photochemical acts. This is the primary production; solar energy and a few simple inorganic compounds, in a process mediated by a complex system, yield the organic compounds which are needed in the construction of the complex molecules of life. It is impressive that nearly half of the total world primary production occurs in the sea although the biomass of photosynthetic organisms is far smaller in the sea than on the land. Even more striking is that net production of oxygen is higher in the sea than on the land; this is due to the fact that many marine organisms (such as reef-building corals and algae, foraminifera, mollusks, calcareous sponges, and 177 ascidians belonging to the family Didemnidae) have the ability to fix carbon dioxide yielding calcium carbonate. This process counteracts the overproduction of carbon dioxide which results from massive fossil fuel burning on the land. One should therefore pay more attention to the conservation of the sea resources and not be only concerned with the problems of the Amazonian forest which is no net porphin oxygen producer. All organisms capable of photosynthesis with oxygen evolution use chlorophyll-a to induce splitting of the water molecule, so that chlorophyll-a has been taken as an index of phytoplankton biomass. This has found practical application with the advent of satellites, which have replaced the slow-cruising research ships. Satellites furnish real-time maps of the distribution of chlorophyll-a which serve in the remote sensing of oceanic o primary production through appropriate COOH algorithms. Green algae and higher COOCH 3 plants also have chlorophyll-b, chlorophyll-c whereas brown seaweeds, diatoms, and (mixture of compounds with R = CH=CIIz or ClIzCH3) dinoflagellates have in its place chlorophyll-c, and red seaweeds have chlorophyll-d. All chlorophylls, in particular chlorophyll-c, are structurally related to heme, the prosthetic group of hemoglobin which is the most common biological carrier of 178 oxygen9l • While heme contains iron, all chlorophylls contain magnesium and chlorophyll-c (actually a mixture of two compounds) has the tetrapyrrole structure of O~COOCH314' l' " H"" 2 (7S,8S,lOR,TR,11 'R)-chlorophyll-a (Rl = CH=~, R2 = CH3) (7S,8S,lOR,TR,11 'R)chlorophyll-b chlorophyll-d (Rl = CH=~, R2 = CHO) heme, with different substituents, and the closure of ring e, at the hypothetical "porphin" nucleus. The magnesium ion is at the center of the tetrapyrrole unit, bound to the four nitrogen atoms; the same occurs in the other chlorophylls, where, however, reduction of the porphin nucleus has occurred. Derivatives of chlorophyll-c, where magnesium has been exchanged for nickel or vanadium, are widely distributed ')Non-heme oxygen-transporting conjugated proteins in which metal atoms are coordinatively bound to amino acids are also known. In hemerythrin, the oxygen carrier of echiurid and sipunculid worms, as weIl as of brachiopods, there are two Fe(II) per place of coordination of O2, On binding oxygen by hemerythrin as peroxidianion (O/'), Fe(II) changes to Fe(III) with a corresponding