Search Results

This chapter covers carbohydrates, the most abundant class of biopolymers on Earth and significant components of water column particulate organic matter and dissolved organic matter in aquatic environments. Carbohydrates are important structural and storage molecules and are critical in the metabolism of terrestrial and aquatic organisms. Carbohydrates can be further divided into monosaccharides (simple sugars), disaccharides (two covalently linked monosaccharides), oligosaccharides (a few covalently linked monosaccharides), and polysaccharides (polymers made up of several mono- and disaccharide units). In phytoplankton, carbohydrates serve as important reservoirs of energy, structural support, and cellular signaling components. Carbohydrates make up approximately 20 to 40% of the cellular biomass in phytoplankton and 75% of the weight of vascular plants. Minor sugars, such as acidic sugars, amino sugars, and O-methyl sugars, tend to be more source-specific than major sugars and can potentially provide further information on the biogeochemical cycling of carbohydrates.

We evolved under high levels of physical activity and energy expenditure, seasonal fluctuations in food availability, and frequent periods of marginal or negative energy balance. Today, we continue to eat about the same amount but exercise less, and the ‘imbalance’ between energy intake and expenditure causes obesity. Consumption of meat from feedlot animals now causes atherosclerosis; eating wild or grass-fed animals does not. For most of human history, simple carbohydrates were a minor element of our diet; today Americans derive almost 40% of calories from simple sugars and refined grain products. Simple carbohydrates contribute to the rise of type 2 diabetes in the industrialized world. The problems of ‘overnutrition’ and energy surplus are causing rates of obesity, diabetes, and hypertension to increase more rapidly in the developing than in the industrialized world. Nutritional interventions should promote increased exercise and activity levels as well as dietary modifications.

The structure and function of biological molecules is to a large degree determined by hydrogen bonding. This is the case for proteins, nucleic acids, carbohydrates, membranes and also the aqueous medium in which these components are held. The three-dimensional architecture of proteins and nucleic acids is stabilised by hydrogen bonds, biological recognition operates mainly by this mechanism, and the molecular mobility required for biological processes is directly connected with rapid formation and breaking of hydrogen bonds. This chapter discusses the weak hydrogen bond in biological structures, the crystal structures of biological molecules, problems associated with determining the crystallographic resolution problem, and weak hydrogen bonding in peptides and proteins, nucleic acids, carbohydrates, and water molecules.

Eating is essentially an act of trust because we trust that the food that we eat, most of which we are not responsible for farming or processing, is safe. However, instances of food contamination and confusing dietary recommendations occur. This chapter examines to what extent we can trust the information we receive from the government and other organizations regarding food safety and health. It discusses the confusion about trans fats and carbohydrates in nutrition as an example of how dietary advice is frequently misleading, misinterpreted, and not based on strong scientific evidence.

This chapter discusses the contributions of the Nurses' Health Study (NHS) and Health Professionals' Follow-up Study (HPFS) to the nutritional epidemiology of coronary heart disease (CHD). Compelling evidence from these studies indicates that CHD is heavily influenced by dietary and lifestyle factors. Replacing saturated and trans fats with unsaturated fats, including sources of n-3 fatty acids, substituting whole grain forms of carbohydrate for refined grains and potatoes, consuming an abundance of fruits and vegetables, and controlling body weight will dramatically reduce the risk of CHD. The magnitude of benefit achievable through diet and lifestyle is large and substantially greater than that due to drug treatment of blood cholesterol or hypertension.

As noted earlier in the general description of the plant cell, there is a site at which photosynthesis, the process which allows plants to capture sunlight and convert it into energy, occurs. It is this process which has produced oxygen on the planet, food for herbivores, and the cool green hills of Earth we enjoy today. The capture of sunlight allows the grape vine to grow and produce fruit. Of course, while the discussion of the “light reactions” (capture of sunlight) and the subsequent so-called “dark reactions” (producing carbohydrates) is necessarily brief here, it is, nonetheless, an exciting story. We are only now beginning to understand a little of it. The earlier picture (Figure 7.1) of the plant cell is repeated here (Figure 9.1) so that the position of the chloroplast is seen. Refer to page 24 for a discussion of the numbered items. As the leaves begin to develop alongside the apical meristem, proplastids, which are present in the meristematic regions of the plant, are formed. Proplastids grow into plastids (such as amyloplasts and chloroplasts) as they mature in different ways dictated by the plant’s DNA. Some plastids (e.g., chloroplasts) carry pigments, discussed more fully below, that allow them to carry out photosynthesis. Others are used for storage of fat, starch (amyloplasts) or specialized proteins. Still other plastids are used to synthesize specialized compounds needed to form different tissues or to produce compounds for protection (e.g., tannins). Each plastid builds multiple copies of its DNA as it grows. If it is growing rapidly, it makes more genome copies than if it is growing slowly. The genes, ignoring epigenetic (literally “above the gene”) and postgenetic (literally “after the gene”) modifications, about which we still have much to learn, encode plastid proteins, the regulation of whose expression controls differentiation and thus which plastid is eventually formed. However, despite the differentiation of plastids, it appears that many plastids remain connected to each other by tubes called stromules through which proteins can be exchanged.

This chapter introduces some basic concepts from chemistry and biology that are often at the heart of various approaches to artificial chemistries. It starts with the problem of how to define life, and the importance of inorganic ingredients such as water, energy, and some small chemical compounds. It then looks at the biomolecules that form the basic building blocks of life, such as proteins, nucleic acids, lipids and carbohydrates. After that it shows how these building blocks are combined into increasingly elaborate structures, until cells and multicellular organisms are formed. The chapter concludes with an overview of some important cellular processes that have inspired many artificial chemistries, such as metabolism, genetic regulation, cell signalling, morphogenesis, and immunity.

We have already seen that some of the basic building blocks used in the biosynthesis of natural products are amino acids such as phenylalanine, tyrosine, and others. These and other crucial construction materials such as the acyl group in acetyl-CoA are all ultimately derived from carbohydrates. In this chapter, we will present an abbreviated overview of the components of carbohydrate structure and metabolism sufficient for our purposes going forward, with a schematic flowchart showing how carbohydrates and amino acids are modified, combined, and branched off in various ways to yield the distinct set of biosynthetic pathways that will form the core of the remainder of the text. We will finish the chapter with a brief, general review of amino acid nomenclature and structure with emphasis on the key amino acids that will be used throughout the remainder of the text. We know that plants make glucose (C6H12O6) by photosynthesis using light, water (H2O), and carbon dioxide (CO2). Another way of looking at the formula for glucose is C6(H2O)6, that is, six carbon atoms and six water molecules. Thus, glucose was originally referred to as a hydrated form of carbon—a carbohydrate. But this is a very general term since there are many different types of carbohydrate compounds. One way to broadly classify carbohydrates is to identify them as either mono- (one), di- (two), oligo- (a few) or poly- (many) saccharides. For example, glucose (C6H12O6) cannot be broken down into simpler carbohydrates by simple hydrolysis, so it is classified as a monosaccharide, that is, a single, discrete carbohydrate compound. On the other hand, the carbohydrate sucrose (C12H22O11) is classified as a disaccharide since when it is subjected to aqueous hydrolysis, it yields two different monosaccharide carbohydrates, namely glucose (C6H12O6) and fructose (C6H12O6). Noting that glucose and fructose are different compounds but with the same molecular formula, they must be related to one another either as stereoisomers or as constitutional isomers, so further refinement of classification is needed. Structurally speaking, most monosaccharide carbohydrates are simply polyhydroxyaldehydes (aldoses) or polyhydroxyketones (ketoses) which can be further classified using a combination of aldo- or keto- prefixes along with suffixes such as triose, tetrose, pentose, or hexose to designate the number of carbon atoms.

This chapter describes how the decline of the low-fat campaign since the late 1990s resulted in alternative weight-loss dietary approaches. By the late 1990s, some nutrition experts believed that the consumption of low-fat foods may have contributed to the twin epidemic of obesity and diabetes. Most nutrition experts discredited the low-fat diet and advocated the reduction in caloric intake as default approach to prevent and treat obesity and diabetes. In the 19th and 20th century, nutritional experts promoted the idea that carbohydrates, not fat were the principal elements in food that caused obesity, making low-carb diets widely popular for weight loss. This approach further developed into Low-GI (glycemic index) diets, a method that emphasized the distinction between good and bad carbs.

This chapter describes the design of a set of mobile phone and desktop computer videogames intended to improve glycemic control in patients with diabetes. It explains that these videogames are a component of a purpose-built Web community called Foodle and they are designed to provide better estimation of carbohydrate intake and selection of less energy foods as a weight-control strategy. It also evaluates existing videogames for diabetes and nutrition and discusses the importance of carbohydrate estimation for glycemic control.

This chapter reflects on the revolution in peptide synthesis that began in 1949, when Robert Bruce Merrifield developed a method called solid-phase peptide synthesis. Working in the laboratory of Dilworth Wayne Woolley, Merrifield isolated a small peptide and determined that it was composed of five amino acids linked together, forming a pentapeptide. These five amino acids are serine, histidine, leucine, valine, and glutamate. Merrifield’s revolution was built upon early pioneering work exploring the utility of solid-phase resins in organic synthesis. A major leap forward in the use of resins came with the invention of synthetic resin materials. This chapter also looks at research that used Merrifield’s solid-phase methods to synthesize other kinds of molecules, including oligonucleotides and carbohydrates. Finally, it discusses various experiments that paved way for the birth of combinational chemistry.

The nature of organic carbon in aquatic sediments and soils with low carbon contents and significant contents of paramagnetic elements such as iron and manganese is difficult to assess by solid-state, cross-polarization magic angle spinning (CPMAS) 13C nuclear magnetic resonance (NMR) spectrometry because of the inherent low sensitivity of 13C NMR analyses, and band broadening and sensitivity losses caused by paramagnetic elements. Other investigators have addressed this problem in the analysis of soils by enriching the organic carbon content by flotation, by magnetic separation of paramagnetic minerals, and by chemical reduction of iron by stannous chloride and sodium dithionite. In this study, they found that satisfactory 13C NMR spectra could be obtained if the C/Fe ratio was greater than 1 wt%. Each of the physical and chemical treatments used to increase the C/Fe ratio resulted in losses of organic matter and changes in the nature of organic matter through physical fractionation and chemical alteration. Suspended stream sediments frequently have equivalent contents of organic carbon and sesquioxide coatings with which the organic matter is associated. These sesquioxide coatings consist predominantly of iron and manganese oxyhydroxides that cause problems with NMR analyses. In this chapter we describe a method to enrich organic matter and remove iron and manganese from low-carbon sediments sampled from the Mississippi, Illinois, and Ohio Rivers with minimal loss and alteration of the organic matter. The second objective is to characterize the sedimentary organic matter by 13C NMR using recent advances that increase instrument sensitivity. Suspended and bed sediments were collected during a sampling cruise on the Mississippi River during May–June 1990. Fine bed sediments were collected in depositional regions of the river or tributaries with a pipe dredge. Suspended silts were collected using a continuous-flow centrifuge operated on board the Research Vessel Acadiana. Both bed sediments and suspended silts were freeze-dried prior to additional treatment procedures and NMR analyses. A flow chart of selective mineral dissolution procedures is presented in Figure 17.1. The acid pyrophosphate treatment6 was placed first in the sequence to remove calcium and magnesium minerals that would form insoluble oxalates in the following extraction.

In this book we are concerned primarily with disequilibrium chemistry, of which the sun is the principal driving force. The sun is not, however, the only source of disequilibrium chemistry in the solar system. We briefly discuss other minor energy sources such as the solar wind, starlight, precipitation of energetic particles, and lightning. Note that these sources are not independent. For example, the ultimate energy source of the magnetospheric particles is the solar wind and planetary rotation; the energy source for lightning is atmospheric winds powered by solar irradiance. Only starlight and galactic cosmic rays are completely independent of the sun. While the sun is the energy source, the atoms and molecules in the planetary atmospheres are the receivers of this energy. For atoms the interaction with radiation results in three possibilities: (a) resonance scattering, (b) absorption followed by fluorescence, and (c) ionization. lonization usually requires photons in the extreme ultraviolet. The interaction between molecules and the radiation field is more complicated. In addition to the above (including Rayleigh and Raman scattering) we can have (d) dissociation, (e) intramolecular conversion, and (f) vibrational and rotational excitation. Note that processes (a)-(e) involve electronic excitation; process (f) usually involves infrared radiation that is not energetic enough to cause electronic excitation. The last process is important for the thermal budget of the atmosphere, a subject that is not pursued in this book. Scattering and fluorescence are a source of airglow and aurorae and provide valuable tools for monitoring detailed atomic and molecular processes in the atmosphere. Processes (c) and (d) are most important for determining the chemical composition of planetary atmospheres. Interesting chemical reactions are initiated when the absorption of solar energy leads to ionization or the breaking of chemical bonds. In this chapter we provide a survey of the absorption cross sections of selected atoms and molecules. The selection is based on the likely importance of these species in planetary atmospheres.

It seems inescapable that at some point primitive cells incorporated chemical reactions related to what we now call metabolism. In all life today, metabolic reactions are driven by sources of chemical or photochemical energy, and each step is catalyzed by enzymes and regulated by feedback systems. There have been multiple proposals for the kinds of reactions that could have been incorporated into early life, but so far there is little consensus about a plausible way for metabolism to begin. This chapter will briefly review the main ideas that are familiar to chemists as solution chemistry but then ask a new question from the epigraph: how can reactions in bulk aqueous solutions be captured in membranous compartments? This question is still virtually unexplored, but I can offer some ideas in the hope of guiding potentially fruitful approaches. Because metabolism is such a complex process, it is helpful to use bullet points to help clarify the discussion. The first is a list of questions that guide the discussion, the second is list of facts to keep in mind, and the third is a list of assumptions that introduce the argument. Questions to be addressed: What are the primary metabolic reactions used by life today? What reactions can occur in prebiotic conditions that are related to metabolism? How can potential nutrient solutes cross membranes in order to support metabolism? How could metabolic systems become incorporated into primitive cellular life? Metabolism can be defined as the activity of catalyzed networks of intracellular chemical reactions that alter nutrient compounds available in the environment into a variety of compounds that are used by living systems. Most of the reactions are energetically downhill, so there is an intimate association between the energy sources available to life and the kinds of reactions that can occur. Here is a summary of energy sources used by life today: Light is by far the most abundant energy source, totaling 1360 watts per square meter as infrared and visible wavelengths. Chemical energy in the form of reduced carbon compounds is made available by photosynthesis.

Chapter 2 describes conversion of cellulose to useful products in the 19th century (rayon, celluloid, guncotton) and the role of glucose in its chemical structure. The preparation of candy floss (cotton candy) is described and how the method is relevant to spinning synthetic fibres. The composition of sugar and the composition of foods is explained. In particular, the distinction among starch, sugar, carbohydrates, monosaccharides, and polysaccharides is made. Conversion of crops to bioethanol is described.

The analysis of large-scale genomic data (such as sequences or expression patterns) frequently involves grouping genes based on common experimental features. The goal of manual or automated analysis of genomics data is to define groups of genes that have shared features within the data, and also have a common biological basis that can account for those commonalities. In utilizing algorithms that define groups of genes based on patterns in data it is critical to be able to assess whether the groups also share a common biological function. In practice, this goal is met by relying on biologists with an extensive understanding of diverse genes that decipher the biology accounting for genes with correlated patterns. They identify the relevant functions that account for experimental results. For example, experts routinely scan large numbers of gene expression clusters to see if any of the clusters are explained by a known biological function. Efficient definition and interpretation of these groups of genes is challenging because the number and diversity of genes exceed the ability of any single investigator to master. Here, we argue that computational methods can utilize the scientific literature to effectively assess groups of genes. Such methods can then be used to analyze groups of genes created by other bioinformatics algorithms, or actually assist in the definition of gene groups. In this chapter we explore statistical scoring methods that score the ‘‘coherence’’ of a gene group using only the scientific literature about the genes—that is whether or not a common function is shared between the genes in the group. We propose and evaluate such a method, and compare it to some other possible methods. In the subsequent chapter, we apply these concepts to gene expression analysis. The major concepts of this chapter are described in the frame box. We begin by introducing the concept of functional coherence. We describe four different strategies to assess the functional coherence of a group of genes. The final part of the chapter emphasizes the most effective of these methods, the neighbor divergence per gene. We present a discussion of its performance properties in general and on its robustness given imperfect groups. Finally we present an example of an application to gene expression array data.

This chapter relates how the elements hydrogen, oxygen, carbon, and nitrogen—dominating in all life on the Earth—make up more than 96% of our body weight. Carbon is the key component of organic molecules, in which it is combined with about 20 other elements to form the basic building blocks of our bodies. The four main categories of organic molecules—carbohydrates, lipids, proteins, and nucleic acids—carry and store energy, form building blocks of the cells, regulate the body’s chemistry, and help store the information from which cell structure and function are derived. A network of metabolic pathways releases energy to the body when needed and stores surplus energy for later use. This chemical machinery, powered by the plants and animals that we consume, constantly works to keep us going

An increased awareness of global atmospheric carbon levels and heightened efforts to recover industrial emissions prior to their release into the environment has led to the availability of an unprecedented amount of carbon dioxide for industrial utilization. Unfortunately, chemical utilization of carbon dioxide as an industrial feedstock is limited by thermodynamic and kinetic constraints. Toxic carbon monoxide, the main competitor in many processes, is used in industry instead because CO2 is perceived to be less reactive and its efficient catalytic conversion has remained elusive. The major commercial uses of CO2 today are in beverages, fire extinguishers, and refrigerants, where inert physical properties such as oxidative and thermodynamic stability are advantageous. It is this stability that has limited the use of CO2 to only a very few synthetic chemical processes (urea, aspirin, carbonates) despite the enormous availability of this resource. The conversion of CO2 into useful organic compounds will likely rely on the use of metal catalysts to lower energy inputs. Increasingly, the use of supercritical carbon dioxide appears to offer significant advantages in the catalytic activation of CO2 to yield useful products. Liquid or supercritical CO2 (sc CO2) can be used as a reaction medium and can potentially replace conventional organic solvents to serve as an environmentally benign reaction medium (Ikariya and Noyori, 1999; Jessop and Leitner, 1999; Jessop et al., 1995b; Noyori, 1999). A supercritical fluid (SCF) is any substance that has a temperature and pressure higher than their critical values and which has a density close to or higher than its critical density (Jessop and Leitner, 1999; Jessop et al., 1995b). Carbon dioxide has a critical temperature of 31.0 °C and a critical pressure of 71.8 bar. The supercritical region of the phase diagram is the one at temperatures higher than the Tc and pressures higher than the Pc at which the liquid and gas phases become indistinguishable. Below Tc, liquid CO2 can be maintained under relatively modest pressures. Subcritical liquid CO2 behaves like any other nonpolar liquid solvent. Properties such as density are continuous above the Tc and discontinuous below it.

To read the press of recent years, one might imagine that the fate of the world rests in the hands of those who would develop the Amazon basin. Waves of incoming colonists are blamed for the bulk of the deforestation and development (Schomberg 1998), but Asian logging firms, multinational oil companies, and gold miners are also portrayed as destructive agents hacking down the forest, systematically undermining its biodiversity, and severely contaminating its myriad ecosystems (Althaus 1996, Ferreira 1996, James 1998). The effects of these varied threats are regularly broadcast in alarming tones. Rueters News Service warned in January 1998 that “Brazil’s Amazon rain forest, the world’s richest trove of biological diversity and source of much of the Earth’s oxygen, continues to be ravaged” (Craig 1998). And, in April 1999, a writer for the Associated Press communicated the “fear” of unspecified scientists that “damage to the rain forest... could throw the Earth’s climate out of balance” (Donn 1999). Clearly, the fate of the Amazon and the implications of its fate to the overall Earth system are topics of enormous scientific and popular interest. While there is little disagreement that the complete destruction of Amazon forests would be catastrophic, what about partial deforestation of the region? How much, and which parts, of the Amazon can be converted to sustainable human land uses without compromising the ecological integrity of the conserved areas? How might this development impact regional climate, adjoining coastal systems, and overall global processes? Answers to these volatile questions remain elusive and seemingly endless strands of controversy swirl about them. At the heart of the matter, yet largely beyond the public discussion, are biogeochemical cycles that support and regulate the functioning of the Amazonia’s biological systems. Moreover, it is the incomplete understanding of these cycles that promotes uncertainty and feeds the controversy. The purpose of this book is to present a coherent assessment of our current understanding of the biogeochemical functioning of the Amazon basin. Although it is surely presumptuous to assume that this presentation will shed sufficient light on the uncertainties to eliminate the current controversies, we hope that it will provide a basis for lifting the discussion to a higher level.