Themes in Biochemistry

Oxygen activation is a central theme in biochemistry and is performed by a wide range of different iron and copper enzymes. In addition to our studies of the dinuclear non-heme iron enzymes MMO and RNR, we also studied oxygen activation in the mononuclear non-heme iron enzyme isopenicillin N synthase (IPNS). This enzyme uses O2 to transform its substrate ACV to the penicillin precursor isopenicillin N [53], a key step in the synthesis of the important P-lactam antibiotics penicillins and cephalosporins [54, 55],... 

Metabolic regulation, a central theme in biochemistry, is one of the most remarkable features of a living cell. Of the thousands of enzyme-catalyzed reactions that can take place in a cell, there is probably not one that escapes some form of regulation. Although it... 

Proteins are linear polymers built of monomer units called amino acids. The construction of a vast array of macromolecules from a limited number of monomer building blocks is a recurring theme in biochemistry. Does protein function depend on the linear sequence of amino acids The function of a protein is directly dependent on its threedimensional structure (Figure 31). Remarkably, proteins spontaneously fold up into three-dimensional structures that are determined by the sequence of amino acids in the protein polymer. Thus, proteins are the embodiment of the transition from the one-dimensional world of sequences to the three-dimensional world of molecules capable of diverse activities. 

The synthesis of UDP-glucose exemplifies another recurring theme in biochemistry many biosynthetic reactions are driven by the hydrolysis of pyrophosphate. 

This reaction is quite favorable because the equivalent of two molecules of ATP is hydrolyzed, whereas only one high-transfer-potential compound is formed. We see here another example of a recurring theme in biochemistry many biosynthetic reactions are made irreversible by the hydrolysis of inorganic pyrophosphate. 

A dominant theme in biochemistry is understanding regulatory checkpoints, for example, how a cell senses changes in the environment at the molecular level and what events are set in motion to respond to those signals. 

Real-space numerical solutions to problems in electrostatics have been a predominant theme in biochemistry and biophysics for some In condensed-matter physics, on the other hand, EFT methods for periodic systems have dominated electrostatic calculations. One reason for this difference is that computations in chemical and biophysical electrostatics typically focus on large, but finite, molecules bathed in a solution. Thus, periodic boundary conditions are often not appropriate. Also, increased resolution near molecular surfaces is much easier to enact with a real-space approach. The early biophysics computational work focused on solving the PB equation for solvation free energies of molecules and ions. Recent efforts have been directed at more efficient solvers and... 

Innovations in separation science continued on this theme and provided one of the most powerful separation techniques used in biochemistry, where proteins are separated with isoelectric focusing (IEF) applied in one direction, and gel electrophoresis (GE) applied at aright angle to the first separation direction (O Farrell, 1975 Celis and Bravo, 1984). In this case, proteins are first separated according to their isoelectric point, measured in p/units, and then according to their molecular weight by gel electrophoresis. The size separation step is usually aided by addition of a surfactant, most typically sodium dodecyl sulfate (SDS), and the gel material is a polyacrylamide formulation. 

The six chapters in this volume each focus on a significant topic in organic chemistry, and branch out to include themes from biochemistry, theoretical chemistry, and materials chemistry. 

Our study of heterocyclic compounds is directed primarily to an understanding of their reactivity and importance in biochemistry and medicine. The synthesis of aromatic heterocycles is not, therefore, a main theme, but it is useful to consider just a few examples to underline the application of reactions we have considered in earlier chapters. From the beginning, we should appreciate that the synthesis of substituted heterocycles is probably not best achieved by carrying out substitution reactions on the simple heterocycle. It is often much easier and more convenient to design the synthesis so that the heterocycle already carries the required substituents, or has easily modified functions. We can consider two main approaches for heterocycle synthesis, here using pyridine and pyrrole as targets. 

Enzymes represent a special case of protein function. Enzymes bind and chemically transform other molecules—they catalyze reactions. The molecules acted upon by enzymes are called reaction substrates rather than ligands, and the ligand-binding site is called the catalytic site or active site. In this chapter we emphasize the noncatalytic functions of proteins. In Chapter 6 we consider catalysis by enzymes, a central topic in biochemistry. You will see that the themes of this chapter—binding, specificity, and conformational change—are continued in the next chapter, with the added element of proteins acting as reactants in chemical transformations. 

The relation of structure and function has always been a dominant theme of Biochemistry. This relation becomes even clearer to students using the fifth edition through the extensive use of molecular models. These models are superior to those in the fourth edition in several ways. 

Cell assays in microfluidics can be classified into four themes intracellular biochemistry, extracellular biochemistry, mechaiucal properties, and electrical properties. 

Metabolic engineering is inherently multidisciplinary, combining knowledge and techniques from cellular and molecular biology, biochemistry, chemical engineering, mathematics, computer science, and physiology. The purpose of this chapter is to provide an overview of the main themes in metaboKc... 

Hydrolytic degradation of polyphosphates is the main theme of this book. Not only is it of ultimate importance (Focal Points 8, 9, 12, and 13) in phosphate chemistry, but also in biochemistry and most other biological sciences. It is the hydrolytic degradation of ATP that has been discussed over and over as an example of the types of reactions expected from phosphate fibers. 

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