Some Basic Biochemistry

Len Deighton, Funeral in Berlin, 1964 From the elephant to the butyric acid bacterium—it is all the same  

This may seem obvious, as water is also by far the most familiar fluid in our lives, but it is important to realize that chemistry of reactions in water under mild conditions of acidity and temperature is not what most chemists 

It follows that the reactions necessary for life mnst proceed under conditions vastly milder than those considered in chemistry to be mild. As virtually all the reactions we are concerned with are extremely slow under such mild conditions—for practical purposes most of them do not proceed at all—they reqnire catalysts, which in living systems are, as noted a little earlier, enzymes. Until a few exceptions were discovered in recent years they were all believed to be made mainly or entirely of protein. For most biochemical purposes, and specifically for those of this book, we will not go far wrong if we continne to think of enzymes as proteins. 

However, when we talk about the sizes of things that we cannot handle and are far outside the range of everyday objects, like proteins or planets, we are usually referring to mass rather than length. So, noting that an enzyme like liver hexokinase is some seventy times larger (in mass, and also in volnme, as 

The volume of an enzyme molecule is typically around 50-100 times the combined volume of the molecules it acts on 

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It is now possible for most students to purchase a basic computer system ai low cost. If a personal computer is not in the budget, most colleges and universities provide students access to campus-wide computer systems as part of tuition and fees. By this point in your studies, you are familiar with the use of a computer, but a few introductory comments are made just to help you get started with computing in the biochemistry laboratory. In terms of equipment, you will need a computer, monitor, printer, and some basic software. Some recommendations for specific hardware and software will be given here, but one must be aware that new products and important upgrades are continually being developed. 

Nikitin, V.N. (1966). On some basic factors of ontogenesis (In Russian). In Major Problems of Age, Physiology and Biochemistry (V.N. Nikitin, ed.), pp. 3-31. Meditsina, Moscow. 

Ultimately, most environmental pollutants and hazardous substances are of concern because of their effects on living organisms. The study of the adverse effects of substances on life processes requires some basic knowledge of biochemistry. Biochemistry is discussed in this chapter, with an emphasis on the aspects that are especially pertinent to environmentally hazardous and toxic substances, including cell membranes, deoxyribonucleic acid (DNA), and enzymes. 

In this chapter, the early work on methane fermentation, the basic biochemistry and microbiology of the organisms involved, how the process is performed, some of the advancements that have improved the process, and the status of efforts to expand commercial use are discussed. The microbial generation of hydrogen and the factors that have limited its use are also discussed. 

It is useful at this time to review briefly some basic aspects of enzyme inhibition and enzyme inhibitors. For a broader review of enzymatic mechanisms and kinetics consult any of several excellent biochemistry textbooks. Enzyme inhibitors are chemical agents capable of modifying an enzyme s capacity to catalyze the reactions of its normal substrates. Effecting such changes of enzyme function by altering the pH, changing the temperature, or subjecting the system to radiation such as UV should properly be considered a denatu-ration process. 

A number of modeling tools are available and may cover a large range from basic biochemistry texts to Mathematica or other simulation sofrware. Having modeling expertise available is critical to the success of this portion of the project. Some good introductory articles are given in the References section (7-9). 

The study of the formation of 2,3-butanediol by bacteria has spanned quite a number of years. Early work included the elucidation of the pathway and some of the basic biochemistry of the enzymes. More recently, much of the research has focused on the fermentation process and understanding the parameters that would lead to a fermentation of high yield and productivity. 

The chemical system of even the smallest plant or animal is one of extreme complexity. It has a multitude of compounds, many of polymeric nature, existing in hundreds of interlocking equilibrium reactions whose rates are influenced by a number of specific catalysts. We will not try to study such a system. Instead we will show some parts of it, some examples that have been well studied and which illustrate the applicability of chemical principles. All of our knowledge of biochemistry has come through use of the same basic ideas and the same experimental method you have learned in this course. 

The relationship between medicine and biochemistry has important imphcations for the former. As long as medical treatment is firmly grounded in a knowledge of biochemistry and other basic sciences, the practice of medicine will have a rational basis that can be adapted to accommodate new knowledge. This contrasts with unorthodox health cults and at least some alternative medicine practices, which are often founded on httle more than myth and wishftil thinking and generally lack any intellectual basis. 

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