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Chapter 17 : Physical Analysis and Purification Methods

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Abstract:

This chapter deals with the basic physical analytical methods and separation procedures of spectrophotometry, electrodes, chromatography, radioactivity, and electrophoresis. It talks about the simple procedures which are appropriate for laboratory classes or are routinely used in a research laboratory. Gas chromatography (GC) is used to monitor production of methane gas, an end product of the consortium growing on the phenol. Additional options for filters are offered by scintillation cocktails that dissolve cellulose acetate, nitrocellulose, and other types of filter membranes, aiding reproducibility and counting efficiency. Even though these formulations are classified as biodegradable, nonradioactive aliquots still need to be disposed of as organic hazardous waste by the proper chemical or radiation safety authorities. Gels used for separations of proteins and short oligonucleotides are usually made of polymerized and cross-linked acrylamide. A particularly effective example of the original method is described by O'Farrell, who separated 1,000 proteins from an extract. Chromatographic methods have been successfully used in enzyme purification. The chapter attempts to describe analytical and purification methods most commonly used by the microbiologist. There are many other methods that rely on instrumentation that is too expensive to be found in all but a few individual labs.

Citation: Mulrooney S, Wood W, Paterek J. 2007. Physical Analysis and Purification Methods, p 424-461. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch17

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Figures

Image of FIGURE 1
FIGURE 1

(A) Natural bandwidth diagram of NADH; the bandwidth is 58 nm. (B) Spectral bandwidth diagram (schematic) of spectrophotometer exit beam; the spectral bandwidth is 8 nm.

Citation: Mulrooney S, Wood W, Paterek J. 2007. Physical Analysis and Purification Methods, p 424-461. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch17
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Image of FIGURE 2
FIGURE 2

Comparison of absorbance and corrected fluorescence spectra. (A) Absorbance spectrum of the flavin-containing enzyme thioredoxin reductase. (B) Corrected fluorescence spectra: the excitation spectrum (excitation with a scanned spectrum and recorded at 530 nm emission) is on the left (solid line) and the emission spectrum (recorded by exciting at 455 nm and recording the spectrum of emitted light) is on the right (dashed line). Note the similar shapes and peak locations of the absorbance and fluorescence excitation spectra.

Citation: Mulrooney S, Wood W, Paterek J. 2007. Physical Analysis and Purification Methods, p 424-461. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch17
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Image of FIGURE 3
FIGURE 3

Pulse height spectrum showing counts per minute as a function of β-particle energy. Discriminators are set so that channel 1 counts exclusively the higher-energy C and channel 2 counts all of the lower-energy H with a small amount of C overlap. After determining the counting efficiency of each isotope in each channel, the equations in section 17.4.7.4 are used to calculate the disintegrations per minute.

Citation: Mulrooney S, Wood W, Paterek J. 2007. Physical Analysis and Purification Methods, p 424-461. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch17
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Tables

Generic image for table
TABLE 1

Standard buffers for calibration of pH meters at 25°C

Data from reference .

Citation: Mulrooney S, Wood W, Paterek J. 2007. Physical Analysis and Purification Methods, p 424-461. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch17
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TABLE 2

Ion-selective electrodes

Data compiled from manufacturers' specifications.

Citation: Mulrooney S, Wood W, Paterek J. 2007. Physical Analysis and Purification Methods, p 424-461. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch17
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TABLE 3

Chemical groups used in ion-exchange chromatography

Data from various manufacturers' specifications.

Citation: Mulrooney S, Wood W, Paterek J. 2007. Physical Analysis and Purification Methods, p 424-461. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch17
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TABLE 4

Affinity tags used for purification of recombinant proteins

Data from reference .

Citation: Mulrooney S, Wood W, Paterek J. 2007. Physical Analysis and Purification Methods, p 424-461. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch17
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TABLE 5

Physical properties of selected radionuclides

Data from reference .

Citation: Mulrooney S, Wood W, Paterek J. 2007. Physical Analysis and Purification Methods, p 424-461. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch17

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