Topic outline
- General
- Course Introduction
Course Introduction
Even in ancient times, scholars believed that diseases could be spread by organisms too small to be seen by the naked eye. Before we discovered that bacteria cells were the real culprits, many attributed disease to other sources. Now that scientists have definitively identified the microscopic causes of various infectious diseases, microbiology, or the study of microscopic-sized organisms, has become an increasingly important field in biology and in the larger biomedical community. Most microbes are harmless. Some of them are essential for life on Earth, e.g. through their ability to fix nitrogen. Biotechnology, which is truly the industry of our times, takes advantage of microbes for the production of a variety of complex substances, and it also mass-produces natural and engineered microbes for human use. This course will cover a range of diverse areas of microbiology, including virology, bacteriology, and applied microbiology. This course will focus on the medical aspects of microbiology, as medical research has been the primary motivator in microbiology research.
- Unit 1: Microbes
Unit 1: Microbes
Microbes are microscopic; thus, we cannot see them by the naked eye. Antoni van Leeuwenhoek crafted the first microscope lenses that magnified over 200 times, and he turned his lenses towards everything. He saw blood cells, sperm, hatching ants, and every cellular microbe groups that we know of today. About 150 years later, Louis Pasteur's meticulously designed swan-necked flask experiments were instrumental in putting off the spontaneous generation hypothesis for microbes. Pasteur showed that microbes arise from microbes, and they are not generated spontaneously from non-living matter. Before any microbe has ever been linked to a disease, the independent death rate analyses of Semmelweis and Nightingale led to the introduction of procedures that we call antiseptic today. Koch was the first to photograph a pathogen in infected tissue; he also laid down guidelines on how to link a microorganism to a disease. These guidelines are Koch's postulates. Only a few microbes cause disease; most microbes are harmless. Microbes are present in all three domains of life: Bacteria, Archaea, and Eukaryota.
Completing this unit should take you approximately 15 hours.
- 1.1: Microscopic Life
- 1.1.1: Magnification Is the Key: Leeuwenhoek Discovers Animalcules
1.1.1: Magnification Is the Key: Leeuwenhoek Discovers Animalcules
Read this article. Leeuwenhoek crafted superior lenses, which allowed him to observe live microbes, and he also well-documented his observations.
Read this article.
Read this page. Leeuwenhoek described representatives of all cellular microbes, including prokaryotes, protists, and fungi. The magnification and resolution of Leeuwenhoek's lenses were not sufficient to describe infectious non-living particles, such viruses, viroids, and prions.
- 1.1.2: The Modern Microscopes
1.1.2: The Modern Microscopes
Read this page, and click on the links "From Thrilling Toy to Important Tool," "Microscopy Time Line," and "Resolving Power Line" to read these pages as well. You can always return to the starter page by hitting the "Back" button on the top right corner of the window. From the main page, click on the links "Phase Contrast Microscopes," "Fluorescence Microscopes," "Transmission Electron Microscopes," and "Scanning Tunneling Microscopes," and study these pages to learn about modern microscope techniques.
Complete this quiz. There are 20 multiple choice questions, and you will receive immediate feedback after you select a response. You should strive to pass with at least 90% accuracy before moving on.
- 1.2: Spontaneous Generation vs. Biogenesis
1.2: Spontaneous Generation vs. Biogenesis
Read this page. The origin of life has always been fascinating, and the discovery of microbes was also followed by a debate on their origins. Prominent scientists of the time performed experiments to prove or disprove the spontaneous generation of microbes from non-living matter. The debate was going on for about 200 years, when finally Pasteur put off the spontaneous generation theory with a set of smartly designed and carefully performed experiments.
Read this page. Louis Pasteur was a meticulous experimenter, who believed that hard work should bring results. As Pasteur stated, "Chance favors only the prepared mind."
Read this review of Pasteur's experimental design for testing spontaneous generation. Then, click on the "Animation" tab, choose "Step-through" or "Narrated," and follow the instructions. You will be prompted to answer questions during the animation. Read the conclusion after completing the animation. Finally, complete the quiz.
- 1.3: The Germ Theory
1.3: The Germ Theory
Read this page. Note the significance and limits of Koch's postulates in the identification of the causative agent. Koch took the first photomicrograph of bacteria and the first photomicrograph of bacteria in diseased tissue.
- 1.4: Antiseptic Procedures
1.4: Antiseptic Procedures
Read this page. Today, native Hungarians regard Semmelweis as "the savior of mothers"; however, during his life, many rejected his chlorine hand-wash antiseptic procedure. The childbed fever death rates dropped from 18% to 2% when he was in charge in the clinics and increased 10-fold when he was removed. The web media below connects you to a graph that was generated based on Semmelweis' data on childbed fever mortality. The Semmelweis' reflex term is used to describe the irrational rejection of the very obvious.
Study this graph, which was generated from the data published by Semmelweis in 1861. In the Wien maternity clinic, pathological anatomy was permitted; thus, physicians and medical students could carry pathogens from cadavers to patients. The Dublin maternity hospital had no medical pathology. Note the death rate drop after the introduction of the chlorine handwash. Wikimedia Commons user Power.corrupts constructed this graph using Semmelweis' data.
Read this page. Nightingale generated the polar-area diagram; she was very successful in communicating her findings with these graphs.
- 1.5: General Antimicrobial Methods
1.5: General Antimicrobial Methods
Read this chapter to review the methods and techniques used to control the growth of microorganisms. Make sure to click on the "Chapter Continued" link at the bottom of each page to read all 6 pages of the chapter.
- 1.6: Classification System
- 1.6.1: Three Domains of Life
1.6.1: Three Domains of Life
Read this page to review the three domains of life. Microscopic forms of life can be found in all three domains.
Read this page. Genetic data indicate DNA transfer between species to some extent.
- 1.6.2: Prokaryotes and Eukaryotes
1.6.2: Prokaryotes and Eukaryotes
- Read this page to review the prokaryotic and eukaryotic cell structure.
Complete this one question assessment. If your answer is correct, then it is acknowledged with a short explanation. Be sure to read each explanation carefully. If you click on a wrong answer, then you will go to a tutorial page. Read this page carefully and then return to the assessment and attempt to complete it again.
Remember that there are microbes among prokaryotes and eukaryotes as well.
- 1.6.3: Archaea
1.6.3: Archaea
Read this page. Archaea adapt to diverse environments. Many archaea are extremophile, meaning they live in an environment that seems very hostile to the human eye.
Read this page. Note the molecular differences between the bacterial and archaea cell membrane and cell wall.
Read this page. Some archaea traits are similar to eukaryotes, while other traits are similar to prokaryotes.
- 1.6.4: Bacteria
1.6.4: Bacteria
Read this chapter to learn about the structure and function of bacterial cells. Make sure to click on the "Chapter Continued" link at the bottom of each page to move on to subsequent pages.
- 1.6.5: Eukaryotic Cells
1.6.5: Eukaryotic Cells
Navigate your way through these slides on organelles by pressing "Next," located at the bottom of the slide frame. There are a total of 13 slides. There are eukaryotic microorganisms among fungi and protists.
- 1.7 Viruses
1.7 Viruses
Read this page. The cell is the smallest unit of life, because it can support its own life including reproduction. Viruses cannot support their own life, but they can hijack the metabolism of specific host cells. Without a specific host cell, a virus cannot grow, change, develop, or multiply.
- Unit 2: Microbial Metabolism
Unit 2: Microbial Metabolism
Cellular metabolism is the collection of all chemical reaction that takes place in the cell. You have already studied cellular metabolism in BIO101: Introduction to Molecular and Cellular Biology. Take some time to review the cellular metabolism units in these courses before you dive into this unit. In this unit, you will study specifics of microbial metabolism; the most detailed subunit belongs to bacteria. The metabolism in all domains is very divergent; Archaea and Protista are the most divergent. We know most about pathogenic bacteria, because they have medical significance.
Completing this unit should take you approximately 8 hours.
- 2.1: Cellular Metabolism
2.1: Cellular Metabolism
Read this page for a general overview of enzymes and enzyme activity.
Read this page for a brief review of cell metabolism.
Complete the following problem sets: "Features of Enzyme Catalyzed Reactions," "An Energy Barrier Separating Reactions and Products in a Chemical Reaction," "Enzyme Features," and "Understanding Activation Energy." These are multiple-choice assessments. Choosing an option will bring you to a page with an explanation. Read the explanation, if any, and then return to the multiple-choice assessment.
- 2.2: Bacterial Metabolism
2.2: Bacterial Metabolism
Read this page. Compare and contrast the general cellular metabolism to bacterial metabolism.
Complete this one question assessment. If your answer is correct, then it is acknowledged with a short explanation. Be sure to read each explanation carefully. If you click on a wrong answer, then you will go to a tutorial page. Read this page carefully and then return to the assessment and attempt to complete it again.
Aerobic and anaerobic respiration has been observed within the Kingdom of Bacteria as well.
- 2.3: Archaea Metabolism
2.3: Archaea Metabolism
Read this page for an example of characteristic archaeal metabolic adaptations. Thermophile species are present in all four Archaea taxa (Korarcheotes, Euryarcheotes, Crenarcheotes, and Nanoarcheotes). In general, Archaea shares characteristics both with Eukarya (e.g. the initiator tRNA and introns) and with Bacteria (e.g. 70S ribosomes), but Archaea have unique molecular features as well (e.g. cell wall structure and branched membrane lipid hydrocarbones).
- 2.4: The Metabolism of Protists
2.4: The Metabolism of Protists
Read this page. Most eukaryotes are protists. Protista is a diverse domain, reflected by organellar diversity.
- 2.5: Fungal Metabolism
2.5: Fungal Metabolism
Read this chapter. Fungi are decomposers. Compare and contrast the general cellular metabolism to fungal metabolism.
- Unit 3: Bacterial Growth, Reproduction, and Genetics
Unit 3: Bacterial Growth, Reproduction, and Genetics
This course focuses on bacteria, the most studied type of microorganism. We will begin this unit by learning how bacteria cells obtain their energy and how they grow. Metabolism varies greatly among bacteria; not all share the same kinds of mechanisms. While most require oxygen to survive, for example, some will actually die in the presence of oxygen. As the microbiology field increasingly involves the artificial cultivation of bacteria, it is important to know the methods and concepts behind their growth and cultures as well.
Bacteria divide and multiply at amazing rates. Under the right conditions, the fastest bacteria can divide every 20 minutes! That means that if you cultured just one single bacteria cell before you went to bed, you could wake up 8 hours later with a plate of more than 16 million bacteria! Much of bacterial reproduction is asexual, occurring through binary fission. In binary fission, one cell literally divides in two. We will conclude this unit by learning about horizontal gene transfer, a process by which one bacteria cell incorporates genetic changes from another cell without being its offspring. This unique feature has allowed bacteria to adapt and grow in conditions it would not otherwise be able survive. It has also led to the increase of drug-resistant bacterial infections.
Completing this unit should take you approximately 15 hours.
- 3.1: Bacterial Growth
- 3.1.1: Growth and Nutrition Requirements
3.1.1: Growth and Nutrition Requirements
Read this this chapter to learn about the requirements necessary for bacterial growth. Be sure to read each of the subsequent pages in the chapter.
- 3.1.2: Generation Time
3.1.2: Generation Time
Community College of Baltimore County: Gary Kaiser's "Bacterial Growth and Microbial Metabolism" URL
Read this lecture about the concept of generation time. Test your knowledge with the short quiz at the bottom of the page.
- 3.1.3: Bacterial Growth
3.1.3: Bacterial Growth
This chapter provides an overview of bacterial growth. Be sure to read the rest of the chapter by clicking "Chapter Continued" at the bottom of each page.
- 3.1.4: Estimation Methods for Population
3.1.4: Estimation Methods for Population
Read this article to review the different ways bacteria can be counted.
- 3.1.5: Growth Control
3.1.5: Growth Control
Read this page and the following two pages. These pages discuss general microbial growth techniques: sterilization and employing physical and chemical agents. In Unit 1, you learned about the history of antimicrobial techniques, including the independent observations of Semmelweis and Nightingale.
- 3.1.6: Microbial Resistance
- 3.2: Bacterial Reproduction
- 3.2.1: Asexual vs. Sexual Reproduction
3.2.1: Asexual vs. Sexual Reproduction
Read this article to compare and contrast the differences between these two reproductive strategies. Only eukaryotes can reproduce with meiosis.
- 3.2.2: Binary Fission and Budding
3.2.2: Binary Fission and Budding
Read these three pages. Only prokaryotes go through binary fission.
Watch this short video for a discussion of budding in yeasts.
- 3.2.3: Endospore Formation
3.2.3: Endospore Formation
Read these three pages to learn about the special circumstances under which endospores form in certain types of bacteria.
- 3.3: Bacterial Genetics
- 3.3.1: Bacterial Chromosome
3.3.1: Bacterial Chromosome
Read this article to learn how bacterial chromosomes differ from eukaryotes.
- 3.3.2: Processing Genetic Information
3.3.2: Processing Genetic Information
Watch this animation, which shows how transcription and translation occur in bacteria. You should consider reviewing gene transcription and gene expression in prokaryotes and eukaryotes.
- 3.3.3: Genetic Regulatory Mechanisms
3.3.3: Genetic Regulatory Mechanisms
Read this page and review the diagrams in the left panel. Click on Figures 1 to 10 for a graphical explanation of operon mediated bacterial gene expression.
- 3.3.4: Genetic Information Exchange
3.3.4: Genetic Information Exchange
Read this page. Click on Figures 1 to 4 for a graphical explanation of DNA exchange mechanisms in bacteria.
- 3.3.5: Mutations
3.3.5: Mutations
Read this chapter, which summarizes mutations that occur in the cell.
Complete this one question assessment. If your answer is correct, then it is acknowledged with a short explanation. Be sure to read each explanation carefully. If you click on a wrong answer, then you will go to a tutorial page. Read this page carefully and then return to the assessment and attempt to complete it again.
Antibiotic drugs attack both pathogenic and normal flora bacteria.
- 3.4:Reproduction and Genetics in other Microorganisms
3.4:Reproduction and Genetics in other Microorganisms
Read the introduction and then move on to "Question 1" to move to the next page (Reproduction: Bacteria), and answer the question (you can check the correct answer if you click on the "Answer" button). Return to the introduction page, and click on "Next." Explore all animations and answer "Question 2." Return to "Reproduction: Bacteria" and click on "Next" to move to "Reproduction: Fungi." Explore all animations, and answer "Question 3."
- Unit 4: Microbial Characteristics and Identification
Unit 4: Microbial Characteristics and Identification
In this unit, we will examine the different shapes and arrangements of bacteria and compare and contrast bacteria with other microorganisms. We will also survey some of the methods (such as plating and staining) used to distinguish between organisms in order to diagnose the causes of infection. When a sample reaches the clinical lab, differential staining enables technicians to identify the shape, arrangement, and gram stain of the organism that the sample contains. This preliminary information, along with cultures, can be used to identify pathogenic microorganisms and isolate them from normal flora.
Completing this unit should take you approximately 3 hours.
- 4.1: Characteristics of Microorganisms
- 4.1.1: Prokaryote Shapes
4.1.1: Prokaryote Shapes
Read this page. Click on every embedded hyperlink, and explore the linked contents. Finally, click on "Quiz Yourself on This Section" to test your knowledge.
- 4.1.2: Size of Microorganisms
4.1.2: Size of Microorganisms
Read this article, which provides some generalized information on the sizes of various microbes.
- 4.1.3: Morphological Characteristics
4.1.3: Morphological Characteristics
Read this article on distinguishing between the different patterns of bacterial growth for cultures grown on plates.
- 4.2: Identifying Microorganisms
- 4.2.1: Plating and Culturing
4.2.1: Plating and Culturing
Read this article, which describes how media can be used to grow microorganisms, such as bacteria and fungi. Media is prepared using various agents that will either enhance or inhibit the growth of certain organisms.
- 4.2.2: Differential Staining
- 4.2.2.1: Gram Staining
4.2.2.1: Gram Staining
Read these lecture slides for a demonstration of the gram staining procedure.
- 4.2.2.2: Acid Fast Staining
4.2.2.2: Acid Fast Staining
Study this short demonstration of the acid-fast staining procedure. Acid-fast staining is used to differentiate between organisms like the acid-fast positive "Mycobacterium tuberculosis" and other acid-fast negative organisms. Complete the two short review activities to evaluate how much you have learned. You will only be able to access the second activity after completing the first matching activity on the last slide of the presentation.
Complete this quiz. After clicking on the link above, scroll down to "Self-Quiz" at the bottom of the page. After completing the quiz return to the first page and click on "Answers" to see the correct answers. There is a detailed introduction to this assessment above the "Self-Quiz." Be sure to visit the "Results" section, also note that clicking on the links under the empty frames brings you to annotated micrographs.
Complete this quiz. After clicking on the link above, scroll down to "Self-Quiz" at the bottom of the page. After completing the quiz return to the first page and click on "Answers" to see the correct answers. There is a detailed introduction to this assessment above the "Self-Quiz." Be sure to visit the "Results" section, also note that clicking on the links under the empty frames brings you to annotated micrographs.
- Unit 5: Bacteria and Human Disease
Unit 5: Bacteria and Human Disease
Ever since Louis Pasteur first theorized that microorganisms were the source of infectious diseases, scientists have labored to learn more about the causes of disease and, more generally, the field of microbiology as a whole. As a result, the majority of microbiology research has focused on human disease and immunology (the study of the immune system). The following unit will discuss microorganisms and the diseases that they cause.
We will begin with bacteria, learning that they are mainly classified as cocci, bacilli, or spiral shaped. They are also differentiated via gram staining procedures, which indicate the amount of peptidoglycan present in a cell wall. If a bacterium contains a lot of peptidoglycan in its cell wall, it will take up the primary gram stain (crystal violet) and will appear purple (gram positive). However, if the bacterium contains a small amount of peptidoglycan and an outer membrane, it will not take up the primary stain. It will instead take up the secondary stain (safranin) and will appear red (gram negative). Each of the classes listed below has been selected for its importance to modern microbiology; take the time to learn all of their names!
Completing this unit should take you approximately 22 hours.
- 5.1: Pathogenesis
5.1: Pathogenesis
Read this chapter. Take advantage of the PowerPoint lecture slides as you study.
- 5.2: Gram Positive and Negative Cocci
- 5.2.1: Staphylococcus
5.2.1: Staphylococcus
Read the section titled "Staphylococci." Watch the "Catalase Test Movie" under Fig.7. Take advantage of the PowerPoint lecture slides as you study. Study Figures 3 to 5 and 8 for micrographs.
Complete this quiz. After clicking on the link above, scroll down to "Self-Quiz" at the bottom of the page. After completing the quiz return to the first page and click on "Answers" to see the correct answers. There is a detailed introduction to this assessment above the "Self-Quiz." Be sure to visit the "Results" section, also note that clicking on the links under the empty frames brings you to annotated micrographs.
- 5.2.2: Streptococcus
5.2.2: Streptococcus
Read this chapter on Streptococci. Take advantage of the PowerPoint lecture slides as you study. Make sure to view the last image in the left panel to identify Streptococcus.
- 5.2.3: Enterococcus
5.2.3: Enterococcus
Read this article to learn about this microorganism, which is commonly found in fecal matter. Click on every link that is embedded in the text to explore the content.
Complete this quiz. After clicking on the link above, scroll down to "Self-Quiz" at the bottom of the page. After completing the quiz return to the first page and click on "Answers" to see the correct answers. There is a detailed introduction to this assessment above the "Self-Quiz." Be sure to visit the "Results" section, also note that clicking on the links under the empty frames brings you to annotated micrographs.
- 5.2.4: Neisseria
5.2.4: Neisseria
Read the section titled "Neisseria," located near the bottom of the page. The Neisseria genus includes two major classes, N. gonorrhoeae and N. meningitidis. The former causes gonorrhea, while the latter is one major cause of bacterial meningitis. The term "diplococcic" means "two cocci" or "a pair of cocci." Take advantage of the PowerPoint lecture slides as you study.
- 5.3: Gram-Positive Bacilli
- 5.3.1: Bacillus
5.3.1: Bacillus
Read this six-page article on Bacillus. Make sure you understand the relationship between Bacillus and other spore forming bacteria. Note that Bacillus anthracis causes anthrax, a disease commonly associated with bioterrorism.
- 5.3.2: Clostridium
5.3.2: Clostridium
Read the section titled "Anaerobic Spore-Formers (Clostridia)." The clostridium genus produces the botulinum toxin that causes botulism. The toxin is a major cause of human food poisoning throughout the world. Take advantage of the PowerPoint lecture slides as you study.
- 5.3.3: Listeria
5.3.3: Listeria
Read this three-page chapter on listeria.
- 5.3.4: Mycobacterium and Corynebacterium
5.3.4: Mycobacterium and Corynebacterium
Read this chapter about Mycobacterium and Corynebacteria. The Mycobacterium genus of bacteria causes many serious diseases, including tuberculosis and leprosy. By the end of this reading, you should be able to identify which species causes which disease. Take advantage of the PowerPoint lecture slides as you study.
- 5.3.5: Actinomyces and Nocardia
5.3.5: Actinomyces and Nocardia
Read this article. Focus on learning the differences between Actinomyces, Nocardia, and Streptomyces. Take advantage of the PowerPoint lecture slides as you study.
- 5.4: Gram-Negative Bacilli
- 5.4.1: Pseudomonas
5.4.1: Pseudomonas
Read the section titled "Pseudomonas aeruginosa".
- 5.4.2: Brucella
5.4.2: Brucella
Read this article from the CDC to learn about Brucella, which typically infects only animals but can also infect humans with as little as 10 to 100 Brucella cells.
- 5.4.3: Bordetella and Legionella
5.4.3: Bordetella and Legionella
Read this chapter covering Bordetella, Haemophilus, and Legionella. Take advantage of the PowerPoint lecture slides as you study. There is a very helpful diagram on the binding of pertussis toxin to the cell membrane. To access the diagram, click on the link to the diagram about half way down the left side panel.
- 5.4.4: Escherichia, Salmonella, Shigella, and Yersinia
5.4.4: Escherichia, Salmonella, Shigella, and Yersinia
Read the sections "Escherichia coli," "Shigella," "Salmonella," and "Yersinia." Some of these names might be familiar to you. For example, you might have heard of Escherichia before; it is the "E" in E. coli, one of the most commonly studied organisms in microbiology. Meanwhile, Salmonella is most commonly found on uncooked meats and raw vegetables and is one of the most common agents of food poisoning. Salmonella has nothing to do with the fish, salmon; it was named after Daniel Salmon, the first individual to hold a doctorate in veterinary medicine in America. Lastly, Yersinia is the cause of the bubonic plague, one of the deadliest diseases in human history. Also known as the "Black Death," it wiped out entire cities and killed hundreds of millions of people. It was so devastating that the total population of Europe was not able to recoup its numbers until more than a century later, permanently altering the course of European history.
- 5.5: Other Bacteria
- 5.5.1: Treponema and Leptospira
5.5.1: Treponema and Leptospira
Read the sections titled "Treponema pallidum" and "Leptospirosis." The Treponema genus causes syphilis, a common sexually transmitted disease. Take advantage of the PowerPoint lecture slides as you study.
- 5.5.2: Vibrio and Campylobacter
5.5.2: Vibrio and Campylobacter
Read the sections titled "Vibrio Species" and "Campylobacter and Helicobacter." Vibrio cholerae causes cholera. Take advantage of the PowerPoint lecture slides as you study.
- 5.5.3: Chlamydia
5.5.3: Chlamydia
Read this article on Chlamydia. Chlamydia, a common sexually transmitted disease, is caused by Chlamydia trachomatis. Take advantage of the PowerPoint lecture slides as you study.
- 5.5.4: Mycoplasma
5.5.4: Mycoplasma
Read this chapter, which covers Mycoplasma and Ureaplasma. All Mycoplasma species lack a cell wall. Because they lack a cell wall, they are unaffected by many antibiotics (such as penicillin) that destroy bacteria by targeting cell walls. Take advantage of the PowerPoint lecture slides as you study.
Complete this quiz. After clicking on the link above, scroll down to "Self-Quiz" at the bottom of the page. After completing the quiz return to the first page and click on "Answers" to see the correct answers. There is a detailed introduction to this assessment above the "Self-Quiz." Be sure to visit the "Results" section, also note that clicking on the links under the empty frames brings you to annotated micrographs.
- 5.6: Antibiotics
5.6: Antibiotics
Read this chapter on the antibiotic medication used to kill microorganisms in humans and animals.
Complete this assessment. After clicking on the link above, select the "Self-Quiz" link to download the assessment PDF file, afterwards click on "Answers" and compare your responses. There is a detailed introduction to this assessment above the "Self-Quiz." Be sure to visit the "Results" section, and click on the links to study annotated figures.
Complete this one question assessment. If your answer is correct, then it is acknowledged with a short explanation. Be sure to read each explanation carefully. If you click on a wrong answer, then you will go to a tutorial page. Read this page carefully and then return to the assessment and attempt to complete it again.
- Unit 6: Fungi
Unit 6: Fungi
Mycology, or the study of fungi, focuses on a diverse set of eukaryotic organisms that range from microscopic single-cells to large mushrooms. Fungi include yeasts, molds, and mushrooms. They are decomposers that have chitin in their cell walls. Fungi range from harmless, tasty mushrooms to fatally poisonous toxins. Humans have cultivated fungi not only for food but also for pest control and bioremediation. Penicillin, the first common antibiotic, was derived from the Penicillium mold. Even today, many newly discovered antibiotics have ties to fungi. In this unit, we will look at both those fungi commonly associated with disease as well those that have been cultivated for specialized purposes.
Completing this unit should take you approximately 12 hours.
- 6.1: Fungi and Human Disease
6.1: Fungi and Human Disease
Read this article to learn about pathogenic and non-pathogenic fungi.
Read this article for an introduction to fungi, their growth requirements, and their reproductive properties.
- 6.2: True Pathogenic Fungi
6.2: True Pathogenic Fungi
Read this article. It does a great job discussing pathogenic (disease-causing) fungi. Take advantage of the PowerPoint lecture slides as you study.
- 6.3: Mycotoxins
6.3: Mycotoxins
Watch this video, which discusses how mycotoxins can contaminate a home and spread to humans.
- 6.4: Opportunistic Fungi
- 6.4.1: Yeasts
6.4.1: Yeasts
Read this article. Candida is one of the most common causes of yeast infections in humans. Other yeasts, such as Cryptococcus, also cause opportunistic infections. Candida includes many species that cause infections, such as thrush and common yeast infections in women.
- 6.4.2: Pneumocystis
6.4.2: Pneumocystis
Read this article about pneumocystis.
- 6.4.3: Aspergillus
6.4.3: Aspergillus
Read the section titled "Aspergillus." Aspergillus is commonly found in the environment and can act as on opportunistic pathogen.
- 6.5: Specialized Fungi
- 6.5.1: Penicillium
6.5.1: Penicillium
Read this article on the fungus from which the antibiotic penicillin is derived.
- 6.5.2: Saccharomyces
6.5.2: Saccharomyces
Read this article about Saccharomyces Cerevisiae, which makes baker's and brewer's yeast, which is then used to bake bread, brew beer, and ferment wine.
Complete this quiz. After completing the quiz return to the first page and click on "Answers" to see the correct answers. There is a detailed introduction to this assessment above the "Self-Quiz." Be sure to visit the "Results" section, also note that clicking on the links under the empty frames brings you to annotated micrographs.
Complete this quiz. After completing the quiz return to the first page and click on "Answers" to see the correct answers. There is a detailed introduction to this assessment above the "Self-Quiz." Be sure to visit the "Results" section, also note that clicking on the links under the empty frames brings you to annotated micrographs.
- 6.6: Antifungals
6.6: Antifungals
Read this article on the antifungal drugs used to treat a variety of fungal infections.
- Unit 7: Protozoa and Helminths
Unit 7: Protozoa and Helminths
Pro/Eukaryotes include Fungi, Algae, Protozoa, and Helminths. This unit discusses protozoa and helminths, which are parasites. Parasites are, by definition, organisms that benefit only at the expense of their living hosts. Protozoa are usually single-celled organisms that have highly complex life cycles. Helminths (also known as parasitic worms) live inside their hosts, often in intestinal tracts, where they hijack their host's nutrient absorption pathway. An astounding number of people are believed to be infected with helminths; most estimates claim that at least 1 billion individuals have been affected!
Completing this unit should take you approximately 14 hours.
- 7.1: Protozoa
- 7.1.1: Protozoa Characteristics
7.1.1: Protozoa Characteristics
Read this chapter, which focuses on protozoa and their unique features.
- 7.1.2: Types of Protozoa
- 7.1.2.1: Intestinal and Luminal Protozoa
7.1.2.1: Intestinal and Luminal Protozoa
Read this chapter about intestinal and luminal protozoa. Take advantage of the PowerPoint lecture slides as you study. Be sure to examine all of the life cycle diagrams that are embedded in the text when you study.
- 7.1.2.2: Blood-Borne Protozoa
7.1.2.2: Blood-Borne Protozoa
Read this chapter on blood-borne protozoa. Take advantage of the PowerPoint lecture slides as you study. Be sure to examine the life cycle diagrams that are embedded in the text when you study.
- 7.1.2.3: Trichomonas
- 7.2: Helminths
- 7.2.1: Helminths Characteristics
7.2.1: Helminths Characteristics
Read this chapter to understand the characteristics of Helminths. Unlike Protozoa and Algae, which fall under the kingdom "Protists," Helminths fall under the kingdom "Animalia."
- 7.2.2: Types of Helminths
- 7.2.2.1: Nematodes
7.2.2.1: Nematodes
Read this article on the round worms known as nematodes. Take advantage of the PowerPoint lecture slides as you study. Be sure to examine all of the life cycle diagrams that are embedded in the text when you study.
- 7.2.2.2: Trematodes
7.2.2.2: Trematodes
Read this article on the flukes known as trematodes. Take advantage of the PowerPoint lecture slides as you study. Be sure to examine all of the life cycle diagrams that are embedded in the text when you study.
- 7.2.2.3: Cestodes
7.2.2.3: Cestodes
Read this article on tapeworms, also known as cestodes. Take advantage of the PowerPoint lecture slides as you study. Be sure to examine all of the life cycle diagrams that are embedded in the text when you study.
Complete this quiz. After completing the quiz return to the first page and click on "Answers" to see the correct answers. There is a detailed introduction to this assessment above the "Self-Quiz." Be sure to visit the "Results" section, also note that clicking on the links under the empty frames brings you to annotated micrographs.
- 7.3: Antiparasitics
7.3: Antiparasitics
Study these slides. Use the arrows to work your way through the presentation, which thoroughly covers the drugs used to treat parasites.
- Unit 8: Viruses
Unit 8: Viruses
This unit will introduce you to viruses. Viruses are in the grey zone between life and inorganic matter. You have learned that the cell is the smallest unit of life, because it can sustain all life functions including reproduction on its own. Most viruses are smaller than cells. They do not feed or reproduce on their own; instead, they hijack their host's metabolism when they multiply. All viruses are comprised of a nucleic acid core surrounded by a protein coat. Viruses are all categorized into seven groups based on the type of nucleic acid they carry. Viruses, while tiny, have powerful effects on their hosts; they can even cause cancer, birth defects, and death.
Completing this unit should take you approximately 21 hours.
- 8.1: Virus Characteristics
8.1: Virus Characteristics
Watch this lecture, which identifies the major characteristics of viruses.
Read this overview of DNA and RNA viruses, which are either single or double stranded and can vary in size and morphology.
- 8.2: Viral Replication Cycles
8.2: Viral Replication Cycles
Read this chapter to learn about viral replication cycles.
- 8.3: dsDNA Viruses
- 8.3.1: Poxviruses
8.3.1: Poxviruses
Study these slides. Note that poxviruses cause most diseases with the word "pox" in their names. The major exception is chickenpox, which is caused by herpesvirus, our next topic.
- 8.3.2: Herpesviruses, Adenoviruses, Papillomaviruses, and other Oncogenic Viruses
8.3.2: Herpesviruses, Adenoviruses, Papillomaviruses, and other Oncogenic Viruses
Read this chapter to learn about viruses that can cause cancer. Herpes viruses cause a variety of diseases, from genital herpes to mononucleosis to chickenpox. The human papillomavirus (HPV) has been associated with cervical cancer. A vaccination is now available for both females and males to prevent HPV infection. Take advantage of the PowerPoint lecture slides as you study.
- 8.4: ssDNA Viruses
- 8.4.1: Parvoviruses
8.4.1: Parvoviruses
Read this article to understand parvoviruses and their threat to our pets.
- 8.4.2: Geminiviruses
8.4.2: Geminiviruses
Read this article about the ssDNA viral family.
- 8.5: dsRNA Viruses
- 8.5.1: Arboviruses
8.5.1: Arboviruses
Read this article on Arboviruses, which include the mosquito-spread West Nile Virus and Reoviridae. Reoviridae causes the gastroenteritis illness known as "Rotavirus."
- 8.5.2: Birnaviruses
8.5.2: Birnaviruses
Read the first three paragraphs of the introduction to gain an understanding of birnaviruses.
- 8.6: +ssRNA Viruses
- 8.6.1: Coronaviruses
8.6.1: Coronaviruses
Read this article to learn about Coronavirus and SARS. SARS, also known as severe acute respiratory syndrome, is caused by a type of coronavirus.
- 8.6.2: Picornaviruses
8.6.2: Picornaviruses
Read this article to learn about Picornaviruses, which cause intestinal problems as well as the common cold.
Read the article to learn about Rhinoviruses.
- 8.6.3: Caliciviruses
- 8.7: -ssRNA Viruses
- 8.7.1: Orthomyxoviruses
8.7.1: Orthomyxoviruses
Read this chapter to learn about different types of flu viruses. Orthomyxoviruses are more commonly known as the flu virus. There are many kinds of flu viruses, including H1N1.
- 8.7.2: Paramyxoviruses
8.7.2: Paramyxoviruses
Read this chapter, which discusses Paramyxoviruses.
- 8.7.3: Rhabdoviruses
8.7.3: Rhabdoviruses
Read this chapter to further understand the dangers of rabies to animals and humans. One type of virus in the rhabdovirus family is called lyssavirus, which causes rabies. Rabies is infallibly lethal; if left untreated, it has a death rate of 100%.
- 8.7.4: Filoviruses
8.7.4: Filoviruses
Read this article to learn about Filoviruses and hemorrhagic fever. Filoviruses cause viral hemorrhagic fevers, a particularly destructive set of conditions that often leads to death. One such virus is the Ebolavirus, which causes Ebola.
- 8.8: DNA and RNA Retroviruses
- 8.8.1: Hepadnaviruses
8.8.1: Hepadnaviruses
Read this chapter to learn about hepatitis. Retroviruses use intermediates to make copies of themselves. DNA retroviruses use RNA intermediates, while RNA viruses use DNA intermediates.
- 8.8.2: Lentiviruses
8.8.2: Lentiviruses
Read this article to learn about the HIV virus and AIDS. The most famous lentivirus is the human immunodeficiency virus, also known as HIV.
Read this page, and then click on the "Next" button on the bottom of the page. On the next page choose "What is alive?" This is a multiple-choice assessment. Choosing an option will bring you to a page that indicates whether you answered correctly or incorrectly and provides a short explanation. If you answer incorrectly, click on "try again" to repeat the question. If you answer correctly, click on the link to the next problem.
Complete this one question assessment. If your answer is correct, then it is acknowledged with a short explanation. If you click on a wrong answer, then you will go to a tutorial page. Read this page carefully and then return to the assessment and attempt to complete it again.
- 8.9: Antivirals
8.9: Antivirals
Read this chapter on anti-viral medications. Although the word "chemotherapy" is almost exclusively used in common language to refer to cancer treatment, it actually refers to the chemicals used in drug therapy for a variety of illnesses. Refer to Figure 1 on the attack mechanism of an enveloped virus as you study.
- Unit 9: Defense Against Microbes
Unit 9: Defense Against Microbes
This unit will discuss the major defenses we have against disease-causing microbes. With all of the microorganisms that threaten to infect and harm an individual, our bodies have evolved sophisticated defenses against these foreign invaders. However, our immune systems can still be overwhelmed; we often need the help of medication to win the battle. In this unit, we will learn about the primary human defenses against disease before discussing the generalized agents that we use outside of the human body to combat different types of microbes.
Completing this unit should take you approximately 7 hours.
- 9.1: Non-Specific Immunity (Skin and Mucous Membrane and Innate Immunity)
9.1: Non-Specific Immunity (Skin and Mucous Membrane and Innate Immunity)
Read this chapter, which describes how the body combats the invasion of microorganisms in a non-specific manner. Non-specific mechanisms include skin and mucous membranes, as well as the innate immune response. Take advantage of the PowerPoint lecture slides as you study. Click on the icons of Figures 1 to 3 and 9 to 14 for summaries and mechanisms.
- 9.2: Adaptive Immunity
9.2: Adaptive Immunity
Read this article on how the adaptive immune system protects the body. Once you have completed the reading assignment, test your knowledge by clicking on the link, titled "Quiz Yourself on this Section," at the bottom of the page.
Study this page, and then select the "Test Yourself" link at the bottom of the page. Complete the "Antigen-specific immune response" and "White blood cell regulating production of antibodies and destruction of infected cells" problems. These are multiple-choice assessments. Choosing an option will bring you to a page with explanation. If this explanation is a "Tutorial," then read it carefully and return to the multiple-choice assessment. Be sure to complete both problems.
Complete this assessment. Select the "Self-Quiz" link to download the assessment in a PDF file and take the quiz. Click on "Answers" to see the correct answers. There is a detailed introduction to this assessment above the "Self-Quiz." Be sure to visit the "Results" section, and click on the links to study annotated figures.
- 9.3: Vaccination
9.3: Vaccination
Read this chapter to learn about the different types of vaccines and how they work.
- Unit 10: Applied Microbiology
Unit 10: Applied Microbiology
In this last unit, we will learn about other major sub-fields of microbiology, including environmental microbiology, biotechnology, and microbial food preparation. We briefly touched upon these topics in our introduction, but we will now go through them in more detail. We will also consider some of the many applications of microbiology. Note that bacteria and fungi (yeast) are used to make vitamins, antibiotics, and beer and to clean up petroleum.
Completing this unit should take you approximately 7 hours.
- 10.1: Environmental Microbiology
- 10.1.1: Bioremediation
10.1.1: Bioremediation
Read this article on how oil spills are cleaned up by the process of bioremediation. Follow the links in the "Why Bioremediation Works” section; these links will take you to U.S. Geological Survey (USGS) reports. Study the introductory paragraph on each of the following USGS pages and "Project Headlines” pages: for "Crude Oil Contamination in the Shallow Subsurface: Bemidji, Minnesota,” study the project headline "Predicting Plume Growth rates;” for "Sewage-Contaminated Ground Water - Cape Cod, Massachusetts,” study the project headlines "Hydrogen Measured in a New Test for Determining Subsurface Microbiological Activity at Contamination Sites” and "Decades Required for Natural Processes to Clean Wastewater-Contaminated Ground Water;” and for "San Francisco Bay Estuary Priority Ecosystem Study,” study the project headline "Phytoplankton in Coastal Waters and Global Climate Change?”
- 10.1.2: Sewage Treatment
10.1.2: Sewage Treatment
Read this article to learn how wastes are treated and disposed of. Follow the "Chlorination" and "Eutrophication" links, and study these sections as well.
- 10.2: Food Microbiology
- 10.2.1: Aseptic Packaging
10.2.1: Aseptic Packaging
Read this introduction to learn about how we ensure that the food that we eat is packaged in a manner that will prevent microbial contamination. This document was prepared by the FDA to act as a guide for industries involved in packaging food.
- 10.2.2: Fermentation
10.2.2: Fermentation
Study this laboratory guide, which explains how microbiology is used in the preparation of foods such as yogurt, beer, and sauerkraut. Directions are even given as recipes so you can make your own. Let's get cooking!
Complete the following assessments: "Lactic Acid Production," "Pyruvate/ Lactate Ratio," and "Fermentation" problems. These are multiple-choice assessments. Choosing an option will bring you to a page with explanation. Read the explanation, if any, and return to the multiple-choice assessment. Be sure to complete all problems.
- 10.3: Industrial Microbiology
10.3: Industrial Microbiology
Study this resource by clicking on the links on the left sidebar and reading each section from "Fermentation & Human History," "Beer," "Chocolate" and "Discover a New Antibiotic."
- 10.3.1: Industrial Products of Microbes
10.3.1: Industrial Products of Microbes
Watch Parts I-IV of the lecture and take notes.
- 10.3.2: Bioconversion
10.3.2: Bioconversion
Read this article about the various types of microbes that are used during composting.
Watch the slides in this video, which discuss bioconversion.
- 10.3.3: Biofuels
10.3.3: Biofuels
Read the article and watch the video to learn about biofuels and the research that is being done to create this new source of energy.