MICR 2101 Midterm

It's all in the title

What does the field of microbiology study?

It examines microorganisms and other infectious agents, how they function, and how they interact with humans, animals and the environment.

What is bacteriology the study of?

Bacteria

What is mycology the study of?

Fungi

What is parasitology the study of?

Parasites

What is immunology the study of?

A person’s response to infectious agents

What is virology the study of?

Viruses

What does recombinant DNA technology do?

Uses microbes as tools to study and manipulate DNA

Why did microbiology develop alongside microscope technology?

Because most microbes are too small for the human eye to see unaided.

Why is the presence of a microbe not enough to prove it is causing infection or disease?

Because we are continuously exposed to microbes we cannot immediately say that the mere presence of any one microbe is the definitive cause without other evidence

True or false: “Microbe” is another word for “pathogen”

False, most microbes do not cause disease

Fill in the blank: ___% of the world’s photosynthesis is performed by marine phytoplankton

50%

What microorganism is believed to be the world’s first oxygen-producing phototroph?

Cyanobacteria

True or false: microbes are the basis of marine and freshwater food chains.

True

Define microbiota

The diverse microbiological community within the human body

How do the normal microbial flora of the human body help prevent pathogenic microbes from colonizing? (2)

They compete for attachment sites and nutrients with the pathogens

True or false: exposure to a microorganism by a susceptible host means they will become infected.

False, exposure alone does not mean infection

What is the difference between being infected by a microorganism and a microorganism causing disease?

Infections can occur without obvious symptoms or harm, whereas you are only considered diseased when the microbial activity and host response produce meaningful dysfunction or tissue damage.

What do the outcomes of a microbial exposure depend on? (5)

1. The kind of microorganism

2. The infectious dose

3. The route of entry

4. The host defenses/immunity

5. Environmental conditions

True or false: two people exposed to the same microorganism can experience vastly different outcomes.

True

What are the five major cellular microbes groups that are studied in microbiology?

Bacteria, Archaea, Fungi, Protozoa and Algae

Define a virus

A virus is an acellular infectious agent that can only replicate within host cells

True or false: Fungal ancestors are believed to have been the first living cells on Earth

False, it was bacterial ancestors

How long can endospores survive in the environment?

The exact length is unknown, but we have found endospores that are millions of years old

True or false: Mycobacterium tuberculosis DNA has been found in 3000 year old Egyptian mummies.

True

What microbes are considered to have produced Earth’s oxygen atmosphere?

Photosynthetic cyanobacteria

What did Zacharias Janssen contribute to the field of microbiology?

Though to have invented the microscope

What did Robert Hooke contribute to the field of microbiology?

Hooke published a book called Micrographia which included detailed microscopic observations of biological material like mold. He demonstrated that microscopy could be helpful as a scientific method for examining structures of microorganisms, and also used the term “cell”

What did Antonie van Leeuwenhoek contribute to the field of microbiology?

He discovered living microscopic organisms living in water, showing that there was a living world that humans could not see. He also made microscopes, and made drawings and slides that are still useable 300 years later.

Explain spontaneous generation theory.

Worms, flies and other organisms arise from decaying matter without the need of a parent organism (promoted as early as 4 BCE by Aristotle!)

Who used controlled comparison (3 sealed jars of meat and three unsealed jars of meat left to sit) to challenge spontaneous generation (SG) theory in 1668? And what did pro-SG theory advocates claim was wrong with this approach?

Francesco Redi | the fresh air was needed for spontaneous generation. Redi later performed a second experiment in which he covered the open jars in a fine mesh lace and maggots did not occur, disproving the need for fresh air

Describe the “broth debate” between John Needham and Lazzaro Spallanzani.

John Needham briefly heated nutrient broth and poorly sealed them in containers in 1745. When microbial growth occurred, he claimed this was evidence of spontaneous generation (SG) theory. In 1765, Lazzaro Spallanzani repeated the experiment with more extensive heating and proper sealing, and the broth remained microbe free. This showed the importance of experimental design. Critics still argued that prolonged heating had killed a ‘vital force’ necessary to cause SG

How did Louis Pasteur disprove spontaneous generation (SG) theory for microbes?

Using a long curved-necked flask he heated nutrient broth and left it to sit. Air was not excluded but the airborne microbes were trapped in the curved neck of the flask and the broth remained nutrient free. Later he cracked the neck off and showed that it then grew microbes.

What was the Golden Age of Microbiology? (4)

A 60 year period from 1857-1914, marked by advancements in:

1. microscope and culture technique

2. study of microorganism chemical activity

3. development of vaccines

4. surgical techniques

What industry asked Louis Pasteur to investigate the spoilage of their product leading to his determination that microbes were responsible for fermentation and spoilage?

The French beer and wine industry

What is pasteurization, what does it do, and who invented it?

Pasteurization is the process of heating liquid food products like milk or beer to protect against microbial colonization and spoilage. It was invented by Louis Pasteur

_____ role in __________ was the first link between the activity of microbes and physical and chemical changes in organic materials.

Yeasts’ | fermentation

What is germ theory and who proposed it?

Germ theory is that microbes/germs cause disease in plants, animals and humans. It was proposed first by Louis Pasteur

Explain miasma theory.

A theory in which disease is caused by foul-smelling air arising from decaying sewage and visibly unhealthy environments.

Why did some controls designed around miasma theory sometimes reduce disease despite miasma theory being biologically incorrect?

Because things that are foul-smelling like sewage and garbage can cause disease, just not because of the odour like miasma theory suggests. Thus heightened waste removal and drainage reduced exposure.

Explain contagion theory.

Contagion theory proposes that some diseases spread through contact with affected people, contaminates materials or other transmissible influences.

What was Ignaz Semmelweis’s contribution to microbiology?

After noticing that childbed fever (CBF) was more common in maternity wards that were attended by doctors/med students than in wards attended by midwives, he investigated whether this was due to the doctors/med students handling autopsies before delivering babies. He instituted a protocol of chlorine-based handwashing before delivery, which reduced mortality rate drastically. Despite not knowing the underlying biology, he was able to make an effective procedure to prevent nosocomial disease

What was John Snow’s contribution to microbiology?

During a London cholera outbreak in 1854, John Snow plotted cases on large maps and surmised that the Broad Street water pump was the likely transmission route of the outbreak. He prevented further deaths by shutting down the affected pump.

What was Joseph Lister’s contribution to the field of microbiology?

Surgeon Joseph Lister applied emerging ideas about microorganisms to his surgical practice to prevent post-operative infections which were common at the time. He used carbolic acid as an antiseptic by soaking bandage dressing, cleaning surgical tools and misting the surgical environment. This was the foundation of modern aseptic technique, antispesis, disinfection and sterilization practices.

What was Robert Koch’s contribution to the field of microbiology?

He created Koch’s postulates which transformed germ theory from a broad idea into an experimental framework linking particular microorganisms to particular diseases. He is particularly remembered for his work with Bacillus anthracis (which causes anthrax).

What are Koch’s postulates? (4)

1. The suspected pathogenic organism should be present in all cases of the disease and absent from healthy animals

2. The suspected organism should be grown in pure culture.

3. Cells from a pure culture of the suspected organism should cause disease in a healthy animal

4. The organism should be re-isolated and shown to be the same as the original

What were Fanny Hesse’s and Julius Petri’s contributions to the field of microbiology?

Fanny Hesse suggested to Robert Koch’s lab that they use agar as a solid culture media. Julius Petri (an assistant in Koch’s lab) designed the Petri dish to hold agar.

What do disease outcomes depend on? (7)

1. Infectious dose

2. Route of entry

3. Host immunity

4. Microbial virulence

5. Normal microbiota

6. Co-infections

7. Environmental conditions

Because disease outcomes are not simple, modern healthcare and public health keep the causal power of germ theory while adding ____, _____ and _____-level complexity.

host | ecological | population

True or false: vaccination predates germ theory

True

What was Edward Jenner’s contribution to the field of microbiology?

He observed that milkmaids seemed immune to smallpox while often developing a case of far milder cowpox. Because of this, he tried innoculating a boy named James Phipps with cowpox. After James’s mild case of cowpox passed, Jenner exposed him to active smallpox which James was not immune to. Essentially, he created a smallpox vaccine, and would go on to inoculate thousands in his back garden.

Explain smallpox variolation.

An early vaccination predecessor originating in 10th century China involving drying smallpox lesion pus and blowing it up the nose of a patient in an attempt to inoculate them with a mild case of the disease to produce immunity. This method was inconsistent and dangerous as it used actual smallpox.

What is the origin of the term vaccination?

Coming from the Latin term Vacca meaning cow, it was coined in honour of Edward Jenner’s work on smallpox vaccines and the contribution of the cow in that work.

What is bacterial attenuation/avirulence? Who discovered it?

Bacterial attenuation describes the fact that if hundreds of generations of pathogenic bacteria are grown in lab culture, the bacteria lose their disease-causing capabilities. It was discovered by Louis Pasteur

How did bacterial attenuation affect vaccine development?

It allowed people to be inoculated with a microbe without chance of disease. Pasteur used in it 1881 to immunize sheep against anthrax, and again in 1885 to immunize people against rabies.

Define chemotherapy in microbiological terms.

The use of chemical agents to prevent and treat infections caused by microorganisms. These include antibiotics and sulfonamides.

What was Alexander Fleming’s contribution to microbiology?

He (accidentally) discovered penicillin and by extension biotics. While working with a plate of Staphylococcus aureus, it became contaminated with the mould Penicillium. He noticed that around the fungal growth the S. aureus growth was inhibited, which lead to the use of penicillin as an antibiotic treatment against infection.

What can a microorganisms’s broad group often tell you? (4)

1. Whether it is cellular or acellular

2. Whether or not it has a nucleus

3. How it reproduces

4. Which structures it may possess

What is the central goal of the logical classification of microorgaisms? (5)

To organize the broad diversity of microbial life into useful groups that can help predict cell organization, reproduction, likely lab features, treatment targets and control vulnerabilities.

What is the difference between classification and taxonomy?

Classification asks how organisms should be arranged into groups, whereas taxonomy provides the formal framework used to recognize and organize those groups.

_______ asks what organisms and taxa should be called according to agreed naming rules.

Nomenclature

_______ asks which known organism or group best matches an unknown specimen or isolate.

Identification

________ asks how organisms are related through evolutionary history

Phylogeny

Define systematics.

Systematics is the scientific study of biological diversity, evolutionary relationships through time, and the classification of organisms.

What does the nested hierarchy of taxa allow species names to communicate.

It allows a single name to communicate several levels of biological relationship without having to list every trait of an organism.

True or false: Taxonomic ranks like family or genus always confer the same amount of “relatedness” between species in their group. i.e. two bacteria in the Escherichia genus are as closely related/similar to each other as two bacteria in the Bacillus genus are to each other.

False, ranks cannot be treated as equivalent units

What is the first major distinction between types of microorganisms?

Cellular organisms vs. acellular infectious agents

Bacteria, archaea, fungi, protozoa and microscopic algae are all examples of what kind of microbe?

Cellular organisms

Viruses, viroids, and prions are all examples of what kind of microbe?

Acellular infectious agents

Define a viroid.

Infectious RNA molecules without a protein capsid

Define a prion.

Infectious proteins without a nucleic-acid genome (basically a misfolded protein)

What is a prokaryotic cell and give two examples of prokaryotic microbes.

A prokaryotic cell is an organic cellular unit that lacks a membrane-bound nucleus and membrane-bound organelles. Two examples are bacteria and archaea

What is a eukaryotic cell and give three examples of eukaryotic microbes.

A eukaryotic cell is an organic cellular unit that contains a membrane-bound nucleus and membrane-bound organelles. Three examples are: fungi, protozoa and algae

Name the three domains listed in the three-domain framework.

1. Domain Bacteria

2. Domain Archaea

3. Domain Eukarya

The separation of domains _______ and ________ reflects major molecular and biochemical differences that are not apparent from cell shape alone.

Bacteria | Archaea

In what major ways do archaea differ from bacteria? (3)

1. Membrane chemistry

2. Cell-envelope features

3. Information-processing systems

To what domain do “extremophiles” (microbes that thrive in unusual conditions, such as high heat, high salt, etc.) usually belong?

Archaea

Why can the antimicrobial treatment for eukaryotic microbes sometimes be more difficult than for prokaryotic microbes?

Because eukaryotic microbes share the same cell type as us it’s more difficult to target specific parts of the cell without damaging native human cells as well.

What are the two most common forms of fungal microorganisms?

Unicellular yeasts and filamentous molds

The term _______ is still widely used in introductory microbiology for many unicellular, heterotrophic eukaryotic microorganisms despite modern phylogeny showing that organisms traditionally called ________ do not form an evolutionary clade.

protozoa | protozoa

True or false: the term algae includes several evolutionary lineages of organisms rather than one natural group.

True

Why do viruses fall outside of the three cellular domains?

Because virions are not cells, they are acellular infectious particles.

A _____ contains a nucleic-acid genome inside a protein capsid, and may also possess a lipid envelope.

virus

How do viruses reproduce?

Viruses rely on host-cell machinery together with viral gene products to produce new virions; they cannot reproduce on their own and must infect a host cell to do so.

Detailed viral structure, taxonomy, and genome strategies are developed in the dedicated ________.

virology blocks

How to prions propagate?

By promoting abnormal folding in host proteins

True or false: While viruses fall outside the three-domain framework, viroids and prions belong to domain Bacteria

False, viroids and prions also fall outside of the three-domain framework

A species name is written as a two-part combination: the ______ name, which is capitalized, followed by a specific _______, which is not.

genus | epithet

What typography (bolded, underlined, etc.) is usually used for scientific names?

Italics

What code governs the names of bacteria and archaea internationally?

The International Code of Nomenclature of Prokaryotes (ICNP)

Before routine molecular sequencing, bacteria were grouped mainly by ________ characteristics.

Phenotypic

Name three phenotypic criteria can be used to help categorize bacteria

1. Cell shape

2. Staining reaction

3. Growth characteristics

4. Metabolic tests

5. Biochemical behaviour

True or false: despite not being used to classify bacteria alone anymore, phenotypic evidence is still valuable for practical identification today because it measures traits that organisms actually express under defined conditions.

True

Why are DNA and RNA sequencing valuable to phylogeny?

It makes it possible to test how closely microbes are actually related genetically outside of phenotypic evidence

Why is comparing ribosomal RNA sequences important when inferring relationships between microorganisms? (3)

1. It is present in all lifeforms

2. Its translation function constrains where in the cell certain protein sequences end up, making specific cellular regions that can be aligned and compared across distantly related organisms

3. Other cell regions vary enough between cells to preserve information about evolutionary divergence

True or false: comparison between single molecular markers is just as accurate in predicting microbial relationships as whole-genome comparison

False, whole genome comparison is more accurate

What can whole-genome data tell us besides evolutionary relationships between microbes? (3)

1. Gene gain

2. Gene loss

3. Horizontal gene transfer

True or false: A scientific name change for an organism represents and change in the organism itself

False, it represents a change in how it is classified taxonomically

What is the difference between classification and identification?

Classification organizes known organisms into groups, whereas identification places an unknown specimen into that classification framework

What does a MALDI-TOF mass spectrometer do?

Identifies cultured microorganisms by comparing characteristic protein profiles against validated reference libraries

What do targeted nucleic-acid tests do?

Detect organism-specific genes or sequences to aid in identification