BIOL 311 - General Microbiology Study Guide PDF

BIOL 311 – General Microbiology Study Guide for Exam 1 Chapter 1 -Microbial Life -What is a microbe and where can you find them? -What are some examples of fields of study/work for which microbiology is an important aspect? -In general, what groups of orga...

BIOL 311 – General Microbiology Study Guide for Exam 1 Chapter 1 -Microbial Life -What is a microbe and where can you find them? -What are some examples of fields of study/work for which microbiology is an important aspect? -In general, what groups of organisms are considered microorganisms in the prokaryotes and eukaryotes? -Are viruses microbes? What kind of organisms are these (prokaryotes/eukaryotes, or none of those? -Be familiar with the metric measuring system -What are some of the characteristics used to differentiate microorganisms? -What is the definition of a genome? Why would it be useful/important to know the genome of an organism? -What is a metagenome? -Can you give a few examples of how or why microbes are important for humans, animals, and the planet? -Why is Florence Nightingale considered an important figure in the field of medicine? -Be familiar with the main role or discovery from the following historical figures: Antonie van Leewenhoek, Robert Hooke, Louis Pasteur, -What is the idea behind spontaneous generation and the scientist that helped debunk this idea? -What is the “Germ Theory” and who came up with it? -What is Robert Koch known for? -No need to memorize, but be able to understand Koch’spostulates -Why is immunization considered one of the greatest medical developments? -Why was Jenner vaccination important in our understanding or disease and immunity? -What is the difference between antiseptics and antibiotics? -What is the first antibiotic to be discovered and by whom? -Recognize the names of scientists involved in the discovery of viruses -Which was the first virus to be identified and what is the disease it causes? -What is Sergi Winogradsky known for? -What are some of the roles that microbes have in ecosystems? -What are endosymbionts? Know some examples -What is astrobiology? -How studying microbes on Earth can help us understand our universe better? -What is the idea behind the theory of endosymbiosis? -What are the domains of life based on Carl Woese studies? What is this classification based on? Chapter 2 – Observing Microbes -What is considered to be microscopic? -What is resolution? And what is the average resolution for the human eye? -What is the fovea? -Know the difference between detection and resolution? -What is magnification and how is this normally achieved? -What are the general shapes in which bacteria are classified? -What is light? And what is the wavelength of the visible light (for humans)? -What are the 3 conditions needed to resolve an object using microscopy? -Be able to distinguish the different ways in which light interacts with objects (absorption, reflection, refraction, scattering) -What is a refractive index and why is this important when observing an object in a microscope? -How do lenses help in forming a focal point? -What can you do to increase resolution when using a microscope? -What is a compound microscope? -What does it mean when a microscope is parfocal? -Be able to calculate total magnification when using a microscope -What is a wet mount and some of the advantages and disadvantages of this method -What are some of the steps needed to be performed before observing a specimen under a light microscope? -What is the difference between simple and differential stains? Know an example for each -Be familiar with the steps used in Gram staining and why this method can help us differenctiate between different bacteria? -Which bacteria are usually considered Gram (+)? And Gram (-)? -Be able to differentiate between acid-fast, spore- and negative staining? -What is fluorescence? -Understand the relationship between wavelength and excitation and emission of a fluorophore -What is the main advantage of confocal laser microscopy? -What are you “looking at” when using chemical imaging microscopy? -Be familiar with the way specimens are observed in dark-field and phase-contrast microscopy -What are the two main types of electron microscopes? What is the type of images you can obtain with each? -Why do we use magnets instead of lenses to focus electrons in a TEM or SEM? -What is the type of information obtained using X-ray crystallography? Chapter 3 -Cells Structure and Function -What are some of the characteristics shared among bacterial cells? -Are Archae cells similar to bacteria? -Bacteria and Archae belong to the _________________ domain -What is one of the most important differences between Prokaryotes and Eukaryotes in terms of cellular structure? -Be able to identify and differentiate the various components of the bacterial cell envelope (cell membrane, cell wall, capsule-if any) -What is the cell cytoplasm and what does it contain? -What is the nucleoid? -Why is the ultracentrifuge thought to be so important in the study of cells and their components? -What is the composition and function of the cell (plasma membrane)? -What is the difference between the inner and outer membranes in a bacterial cell? Know where these are located -What are mycoplasmas and why are they thought to be interesting? -Be familiar with the various components of the cell membrane -Know the different terminology associated with the interaction of molecules with water (hydrophilic, hydrophobic, amphipathic) -What are the components of phospholipids? Be able to draw one (simply) and label these -Know the different saturation states of fatty acids and the relevance of this for membrane fluidity -What are hopanoids and their function? -What is one know difference between bacteria and archae in terms of membrane structure? -What are some of the roles that proteins can have in the structure of cell membranes? -What does it mean when we say that the membrane is a semi-permeable barrier? -What molecules can pass “for free” (passively) across a cell membrane? Which ones can’t and why? -Review the concepts of membrane transport (active, passive) -What is osmosis and passive diffusion? -What is the role of the cell wall and what is it made of? -Recognize the 2 sugars that make the peptidoglycan chains and how they are connected by peptides -In general, how do penicillin and vancomycin kill bacteria? -Why is the enzyme transpeptidase so important in cell wall integrity? -Be able to distinguish the difference in the structure of Gram (=) and Gram (-) bacterial cell envelopes -Why are mycobacteria so unique? -What are bacterial capsules made of and where are they located? -What is an S-layer? -What is the outer membrane and what organisms have this structure? -What is the outer membrane made of? Be able to distinguish the components in a diagram -What is LPS and why is it important? -What is unique about mycobacteria cell envelopes? -Do bacteria have cytoskeletons? What are these components useful for? -What is cell fission and how is it different to mitosis? -What is septation and what is the main protein involved in this process? -What is the nucleoid and why is it important? -Why is it important to divide symmetrically? Is that always the case for bacteria? -What are endospores and why are these important? -Be familiar with other cellular structures such as vesicles, nanotubes, thylakoids, carboxysomes, and storage granules -What is the difference between pili and flagellum? -How does the flagellum help a bacterium move directionally? Chapter 6 -Viruses -Where do you find viruses and why are they important? -What is a virus (or virion) and its main components? -What are bacteriophages and viriophages? -What was the first virus to be identified? How did they find it? -What are some of the characteristics of viruses that make them different than most cells? -What are prophages and proviruses? -What is the difference between a provirus and an endogenous virus? -What are the various forms in which you can find viruses in nature? -What is a virome? Know some examples of these -What does it mean when people say that viruses are important for nutrient cycling? -What is/are the differences between acute and chronic virus infections? -What do we mean when we talk about viruses host range and host trophism? -Why do you think antibiotics do not work to control virus infections in a host? -What are the different options for a virus genome? -What are viral capsids made of and their main function? -What is a viral envelope made of and its main function? -What are the tree main types of shape-groups for viruses? What are the common symmetrical structures fund in viruses? -What are viroids and prions? Why are we interested in studying them? -What are the possible options for the type of genome in a virus? -How small can a virus genome be? And how big? -What are the criteria used by the ICTV to classify viruses? -What is the basis for the Baltimore classification of viruses? And how many groups of viruses have been identified using this system? -What are the various replication types for bacteriophages? Know the differences among these. -What are the main steps in a lytic replication cycle? Understand in general what happens in each -How does a lysogenic virus replicate? -What is the third way in which some bacteriophages replicate? How is this different from the Lytic cycle? -What are some mechanisms by which bacteria protect against virus infections? -What are the steps used by animal and plant viruses for infections and replication? -Why is uncoating important for some viruses? -What is a reverse transcriptase? What types of viruses need it? -What are the two ways in which animal viruses are released from the host cell? -What ae oncogenic viruses? Know some examples -What is one of the main differences in the infection methos used by plant viruses compared to bacteriophages and animal viruses? -What are some of the defense mechanisms in animals and plants against viruses infection? -What is the cause of Covid-19? What type of genome does this virus have? -What is a zoonotic disease? -Be familiar with the terms of pandemic and spillover in relation to viral infections -What are the cell targets for the SARS-Cov-2 virus? And how does the virus enter a host cell? -What do you need to grow viruses in a lab? -What is the difference between batch culture and plate culture? -How do you know your virus is growing in each of these two culture methods? Chapter 11 -Viral Molecular Biology -What is lambda phage? Why is it an important virus? -Know the various structures in a lambda phage -How does the lambda phage replicate? -What virus causes the flu? -What kind of virus is influenza? -Know the important components of the flu virus and the role of the NA and HA proteins -What is gene reassortment? And why can this process occur in viruses like influenza? -What are the implications of its segmented genome in terms of virus diversity and evolution? -Why do we have to worry about viruses that infect animals, such as the bird flu? -What is the virus that causes AIDS? -What is AIDS and how is it transmitted? -What is unique about the genome of this type of viruses? -Why is a single antiviral drug usually not enough to combat HIV infections? -What is a quasispecies? -How does HIV enter host cells? -Know the main steps of HIV replication cycle -What is a gene-transfer vector? -Why can these viral vectors be used to treat diseases with genetic basis?