CHAPTER 24 – Evolution of Protein Molecules

The chemical composition of natural water is derived from many different sources of solutes, including gases and aerosols from the atmosphere, weathering and erosion of rocks and soil, solution or precipitation reactions occurring below the land surface, and cultural effects resulting from human activities. Broad interrelationships among these processes and their effects can be discerned by application of principles of chemical thermodynamics. Some of the processes of solution or precipitation of minerals can be closely evaluated by means of principles of chemical equilibrium, including the law of mass action and the Nernst equation. Other processes are irreversible and require consideration of reaction mechanisms and rates. The chemical composition of the crustal rocks of the Earth and the composition of the ocean and the atmosphere are significant in evaluating sources of solutes in natural freshwater. The ways in which solutes are taken up or precipitated and the amounts present in solution are influenced by many environmental factors, especially climate, structure and position of rock strata, and biochemical effects associated with life cycles of plants and animals, both microscopic and macroscopic. Taken together and in application with the further influence of the general circulation of all water in the hydrologic cycle, the chemical principles and environmental factors form a basis for the developing science of natural-water chemistry. Fundamental data used in the determination of water quality are obtained by the chemical analysis of water samples in the laboratory or onsite sensing of chemical properties in the field. Sampling is complicated by changes in the composition of moving water and by the effects of particulate suspended material. Some constituents are unstable and require onsite determination or sample preservation. Most of the constituents determined are reported in gravimetric units, usually milligrams per liter or milliequivalents

Study and Interpretation of the Chemical Characteristics of Natural Water

Influence of diet on the distribution of nitrogen isotopes in animals

The influence of diet on the distribution of nitrogen isotopes in animals was investigated by analyzing animals grown in the laboratory on diets of constant nitrogen isotopic composition. 
The isotopic composition of the nitrogen in an animal reflects the nitrogen isotopic composition of its diet. The δ^(15)N values of the whole bodies of animals are usually more positive than those of their diets. Different individuals of a species raised on the same diet can have significantly different δ^(15)N values. The variability of the relationship between the δ^(15)N values of animals and their diets is greater for different species raised on the same diet than for the same species raised on different diets. Different tissues of mice are also enriched in ^(15)N relative to the diet, with the difference between the δ^(15)N values of a tissue and the diet depending on both the kind of tissue and the diet involved. The δ^(15)N values of collagen and chitin, biochemical components that are often preserved in fossil animal remains, are also related to the δ^(15)N value of the diet. 
The dependence of the δ^(15)N values of whole animals and their tissues and biochemical components on the δ^(15)N value of diet indicates that the isotopic composition of animal nitrogen can be used to obtain information about an animal's diet if its potential food sources had different δ^(15)N values. The nitrogen isotopic method of dietary analysis probably can be used to estimate the relative use of legumes vs non-legumes or of aquatic vs terrestrial organisms as food sources for extant and fossil animals. However, the method probably will not be applicable in those modern ecosystems in which the use of chemical fertilizers has influenced the distribution of nitrogen isotopes in food sources. 
The isotopic method of dietary analysis was used to reconstruct changes in the diet of the human population that occupied the Tehuacan Valley of Mexico over a 7000 yr span. Variations in the δ^(15)C and δ^(15)N values of bone collagen suggest that C_4 and/or CAM plants (presumably mostly corn) and legumes (presumably mostly beans) were introduced into the diet much earlier than suggested by conventional archaeological analysis.

Influence of Diet On the Distribtion of Nitrogen Isotopes in Animals

The use of stable isotopes to solve biogeochemical problems in ecosystem analysis is increasing rapidly because stable isotope data can contribute both source-sink (tracer) and process information: The elements C, N, S, H, and all have more than one isotope, and isotopic compositions of natural materials can be measured with great precision with a mass spectrometer. Isotopic compositions change in predictable ways as elements cycle through the biosphere. These changes have been exploited by geochemists to understand the global elemental cycles. Ecologists have not until quite recently employed these techniques. The reasons for this are, first, that most ecologists do not have the background in chemistry and geochemistry to be fully aware of the possibilities for exploiting the natural variations in stable isotopic compositions, and second, that stable isotope ratio measurements require equipment not normally available to ecologists. This is unfortunate because some of the more intractable problems in ecology can be profitably addressed using stable isotope measurements. Stable isotopes are ideally suited to increase our understanding of element cycles in ecosystems. This review is written for ecologists who would like to learn more about how stable isotope analyses have been and can be used in ecosystem studies. We begin with an explanation of isotope terminology and fractionation, then summarize isotopic distributions in the C, N, and S biogeochemical cycles, and conclude with five case studies that show how stable isotope measurements can provide crucial information for ecosystem analysis. We restrict this review to studies of natural variations in C, N, and S isotopic abundances, cxcluding from consideration ~5N enrichment studies and hydrogen and oxygen isotope studies. Our focus on C, N, and S derives in part from our

Stable isotopes in ecosystem studies

In 1947, in his classical paper on the thermodynamic properties of isotopic substances, H. C. Urey [1] laid the foundation of modern isotope geochemistry. At the same time, A. O. Nier [2] designed a new mass spectrometer which allowed the measurement of small differences in isotope abundance ratios. A modification in the Nier-type mass spectrometer and a refinement in instrumentation techniques by McKinney et al. [3] finally initiated stable isotope studies of the type that will be discussed in this review.

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Biogeochemistry of Stable Carbon Isotopes

The cell walls of diatoms consist of a silica frustule encased in an organic coating. Biochemical characterization of this coating should allow insight into: (1) the mechanism of silicification; (2) taxonomy and evolution of diatoms; (3) preservation of fossil frustules. The amino acid and sugar composition of cell walls from 6 diatom species have been elucidated. When compared to cellular protein, cell-wall protein is enriched in serine plus threonine and glycine, and depleted in acidic, sulfur-containing and aromatic amino acids. The sugars of the cell-wall carbohydrates are quite variable and fucose tends to replace glucose in estuarine species. Condensation of silicic acid, in epitaxial order, on a protein template enriched in serine and threonine, is suggested as the Si-depositing mechanism in diatoms. The nature of this template and the polysaccharides in the cell wall may determine the solubility of diatom frustules in various environments. There is sufficient variability in cell-wall amino acids to warrant further investigation of their taxonomic utility. The sugars appear to be related to environmental factors, but they may also serve in biosystematic studies.

The amino acid and sugar composition of diatom cell-walls

Oxygen and carbon isotope studies of carbonatites from the Laacher See district, West Germany and the Alno district, Sweden.

Hot Brines and Recent Heavy Metal Deposits in the Red Sea

MONSOONS cause seasonal reversals in the surface circulation of the northern Indian Ocean1. In the Arabian Sea this results in the upwelling of nutrient-rich water along the coasts2–4, making it one of the highly productive regions of the world's oceans. To assess the impact of monsoon-driven processes on the downward particle flux variations in the open ocean we deployed three moored arrays consisting of six time-series sediment traps at selected locations in the western, central and eastern parts of the deep northern Arabian Sea. Strong seasonality was recorded in particle flux at all three sites with peaks during the south-west and northeast monsoons. High primary productivity during the monsoons resulting from wind-induced mixed-layer deepening and the associated nutrient injection to the euphotic zone appeared to be the main factor controlling the observed particle flux pattern. These findings may shed light on CO2 uptake during glaciation when wind speeds were higher.

Egon T. Degens

Papers

Biogeochemistry of Stable Carbon Isotopes

The amino acid and sugar composition of diatom cell-walls

Oxygen and carbon isotope studies of carbonatites from the Laacher See district, West Germany and the Alno district, Sweden.

Hot Brines and Recent Heavy Metal Deposits in the Red Sea

Increased particle flux to the deep ocean related to monsoons