Fundamentals of Biochemical Engineering Part 1 - Bailey J., Ollis D. 1989

Introduction to Microbiology
Prospects for Further Study

The Brief Overview of Cell Structure and Classification presented in this chapter confirms the validity and usefulness of the Cell Theory as the foundation of biological science. Throughout this chapter, we have also repeatedly emphasized The Importance of fundamental biochemical principles for understanding biochemical engineering processes. In the subsequent chapters, we will continually focus on the core concepts of cell biology.

Chapter 2 will cover the MAIN TYPES OF chemical compounds that a cell must synthesize to ensure normal vital activity and reproduction; Chapters 3 and 4 are dedicated to biological catalysts utilized by The Cell to carry out Chemical Reactions. Next, in Chapter 5, we will examine the reaction sequences required for normal cellular function, while Chapter 6 will focus primarily on Methods for controlling and regulating these reactions, as well as on genetics. In Chapter 7, we will discuss the growth kinetics of microbial systems, followed by chapters addressing the analysis, design, control, and optimization of biochemical engineering processes.

Exercises

1.1. Eminent Microbiologists. Familiarize yourself with the biography of a well-known microbiologist from the past, such as Robert Hooke, Antonie van Leeuwenhoek, Lazzaro Spallanzani, Louis Pasteur, Walter Reed, D. I. Ivanovsky, P. Rous, Theodor Schwann, or M. J. Schleiden. Prepare a brief review outlining the technical and social challenges these scientists had to overcome, the methodological breakthroughs (or lack thereof) achieved during their work, and the role that induction and deduction played in their research.

1.2. Experimental Microbiology. Microbiology employs numerous simple and well-established techniques that may, however, be unfamiliar to specialists in general, organic, and physical chemistry. Since any experimental study relies on observation and measurement, it is essential to become familiar with practical Research Methods, including their inherent accuracy. If you have not previously taken a laboratory course in microbiology, it is advisable to do so concurrently with or immediately following this theoretical course. If this is not possible, carefully study the sections of a concise laboratory manual (e.g., [7]) corresponding to the chapters of this book. In doing so, keep in mind Claude Bernard's remark: "To experiment without a preconceived idea is to wander aimlessly." When studying experimental methods in the laboratory or from a manual, try to formulate the objective(s) of each experiment. Consider what additional information can be obtained from each experiment.

1.3. Methods of Investigation. Review the brief descriptions of Microscopy Techniques, including dark-field, phase-contrast, fluorescence, and Electron microscopy. Outline the relative Advantages and disadvantages of each method.

1.4. Terminology Definitions. Define the terms listed below; where multiple terms appear on a single line, provide a comparative assessment of them:

a) Cell wall, Plasma Membrane, Endoplasmic reticulum;

c) Cytoplasm;

d) Nucleus, nucleoid;

e) ribosome, mitochondrion, chloroplast;

f) Morphology;

g) spiral, spherical, and rod-shaped bacterial forms;

h) budding, sexual fusion, fission, sporulation;

i) Protozoa, Algae, mycelium, amoebae.

1.5. Identification and Classification. a) Sketch a diagram of The Kingdom Protista from memory. b) The taxonomic division of microorganisms into species is largely based on visual observations using an optical Microscope. Locate images of the microorganisms Escherichia coli, Staphylococcus aureus, Bacillus cereus, and Spirillum serpens in reference manuals [e.g., Bergey's Manual of Determinative Bacteriology or A Guide to the Identification of the Genera of Bacteria by Skerman]. List the distinguishing features of any two of these bacterial species that would allow for their reliable identification. Begin with the broadest characteristics and progressively move from the family down to more detailed subdivisions (subfamily, genus) and, finally, to the species.

1.6. Case Study. Choose an interesting microbiological topic (e.g., brewing Fermentation, antibiotic production, Yeast growth, wastewater Treatment, soil microbiology, Vaccines, pickling, cheese making, lake ecology, marine microbiology, etc.). First, review the topic as presented in general reference works, such as Kirk-Othmer's Encyclopedia of Chemical Technology. Draw a process flow diagram or a diagram of the phenomena occurring in a natural system, indicating the key microorganisms involved, their nutrient sources, and influent or effluent streams. As you progress through the course, add one or two pages of text to this diagram each week, highlighting, in particular, the relevance (or lack thereof) of the material covered in the completed chapter to the process in question. At the end of the course, prepare a short report on your topic and present it to your study group.

1.7. Industrial Microbiology. A brief overview of The history of industrial microbiology and several suggestions for its future development can be found in the article "Industrial Microbiology" [Demain A. L., Solomon N. A., Scientific American, 245, 67–75 (1981)]. Read this article and prepare a short review (approximately one page) on the historical development of industrial microbiology, the dates of key milestones, the products and/or processes of this industry, and the types of microorganisms utilized.

1.8. Protozoan Motility. Suppose that using a microscope you observe the movement of spherical protozoa and are able to determine their dimensions and swimming speed expressed in body lengths per unit of time.

a) Calculate the Reynolds numbers for the fluid flow around the Organism for the sizes and speeds listed below, assuming that the fluid is Water at 20 °C and that the flow

is substantially undisturbed by flagella, mucous coatings, or the Rotation of the organisms.

Sizes: 10 µm, 50 µm, 100 µm.

Speeds: 10 body lengths per second;

1 body length per second;

0.1 body length per second.

What flow regimes are characteristic of these cell movements?

b) To slow down the movement of microorganisms and thereby facilitate microscopic observation, a methylcellulose solution is often used. How would a 10⁴-fold increase in the viscosity of the surrounding fluid affect the cell swimming speed, assuming that the Energy Expenditure for locomotion remains constant?

1.9. Streak plating of E. coli. When culturing E. coli for further experiments, it is desirable to have a genetically homogeneous population. Typically, the original broth is diluted for this purpose to a concentration that yields individual colonies derived from a single cell on Agar plates. The population is then propagated from one such colony.

а) Suppose we are given a circular agar plate with a radius of 4 cm, 1 ml of broth with a concentration of 10¹⁰ Cells per liter, and 1 l of sterile broth for dilution. How much should the bacterial broth be diluted to yield about 100 individual colonies on the agar plate? (Assume that a plate with a radius of 4 cm can be covered with 5 ml of solution.)

б) How could you obtain colonies from individual cells if the cell concentration in the broth is unknown?

1.10. Separation by centrifugation. Consider a dilute suspension of particles of type A and type B. An initially homogeneous suspension is centrifuged at an angular velocity ω for a time t. Derive an equation to determine how many particles of type A remain in the supernatant suspension after centrifugation (relative to the initial relative concentration f₀ of particles A). The time t should be assumed small enough so that both type A and type B particles remain in the suspension.

1.11. Centrifugation with an angle rotor. Consider the centrifuge schematically shown in Fig. 1U11.1, in which the tubes are positioned at an angle to the axis of rotation. Find the time required for a spherical particle of radius R and density ρ_p to travel from r = r₁ to r = r₂ at an angular rotor velocity ω, fluid density ρ_f, and fluid viscosity μ_f, if the angle of orientation is θ from the vertical. Note that the Glass wall of the tube exerts a vertically directed force on the particle.

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FIG. 1U11.1.

References

1. Sistrom W. R., Microbial Life, 2d ed., Holt, Rinehart and Winston, Inc., N.Y., 1969. The first three chapters of this Introduction to Microbiology cover most of the topics in Chapter 1 of this textbook. This book also includes information on microbial METABOLISM, growth, and genetics, which will be discussed in subsequent chapters here.

2. Frobisher M., Fundamentals of Microbiology, 8th ed., W. B. Saunders Company, Phila., 1968. This book describes Various Forms of microbial life, cell classification, Viruses, and issues of sterilization, immunology, and Applications of microorganisms. Special attention is paid to the numerous connections between microorganisms and humans.

3. Pelczar M. J., Jr., Reid R. D., Chan E. C. S., Microbiology, 4th ed., McGraw-Hill, New York, 1977. A comprehensive manual for advanced study of microbiology. Fungi, algae, protozoa, and viruses are discussed in detail, along with industrial and environmental microbiology, and Physical and Chemical methods for controlling Microbial growth.

4. Stanier R. Y., Doudoroff M., Adelberg E. A., The Microbial World, 4th ed., Prentice-Hall, Inc., Englewood Cliffs, N.J., 1975. A profound and exceptionally well-written book. It covers the history of microbiology, classes of microorganisms, Symbiosis, The Nature of disease, and microbial metabolism. Molecular-level genetics is covered in detail, including mutation and regulation.

5. The Living Cell, readings from Scientific American, W. H. Freeman and Company, San Francisco, 1965. A collection of articles from Scientific American focusing on Cell Structure, Bioenergetics, synthesis, division, and differentiation, as well as several Specialized Topics such as Intercellular Communication, cell stimulation, and Muscle contraction. Although some articles are somewhat dated, this diverse and well-illustrated collection is still well worth reading.

6. Paul J., Cell and Tissue Culture, 5th ed., Churchill Livingstone, Edinburgh, 1975. An excellent, comprehensive introductory monograph dedicated to animal cell lines, cell culture methods and principles, and the Practical Applications OF biological research.

References for the "Exercises" Section

7. Crabtree K. T., Hinsdill R. D., Fundamental Experiments in Microbiology, W. B. Saunders Co., Phila., 1974.