MCB3020 Exam 1 Study Guide and Key PDF

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Exam 1 Study Guide + Key Module 1: Introduction to Microbiology (Chapters 1-2) 1. Define Microbiology. The branch of biology that studies microbes. 2. How does microbiology differ from other fields of biology? It can be distinguished from other fields based on: 1. The size of the organisms studied 2. The techniques used to study them 3. What are the two types of microbes and examples of each? Cellular Organisms – made up of cells a. include fungi, protists, bacteria, and archaea Acellular Organisms – Not made of cells a. Include Viruses, Viroids, Satellites, and Prions 4. What are the following composed of? a. Virus – Protein and Nucleic Acids b. Viroid – RNA only c. Satellite – Nucleic Acids d. Prion - Proteins 5. What are prokaryotes and eukaryotes? How do they differ? Eukaryotes are organisms with cells that have DNA in a membrane-bound organelle, called a nucleus, and have other true membrane-bound organelles. Prokaryotes are organisms made up of a single cell lacking membranebound organelles and a nucleus. 6. Name and Describe the three domains of life. Note differences. Domain Eukarya – Eukaryotic; Have cells and organized structures called Organelles; have Multiple Linear chromosomes; more complex morphology Domain Archaea – Prokaryotic; Single-celled organisms with no nucleus or organelles; Have a single and circular chromosome; Found in extreme conditions; Identified by Carl Woese Domain Bacteria – Prokaryotic; Single-celled organisms with no nucleus or organelles; Have a single and circular chromosome

7. What scientist identified that the phylogenetic tree is composed of these three domains of life? How did this scientist discover this? Carl Woese identified the domain Archaea from Bacteria by using ribosomal RNA sequencing data. 8. Which domain is found in extreme environments? Archaea 9. What does LUCA stand for and what branch is it found on? Last Universal Common Ancestor – common ancestor of all three domains of life. States that the domains Achaea and Eukarya diverged from common ancestry, and Bacteria evolved independently. 10. How far back do the earliest fossils of microbial life date back to? 3.5 billion years ago 11. What is the central dogma? States that deoxyribonucleic acid (DNA) contains genetic information that is transcribed into messenger ribonucleic acid (mRNA) then translated to make proteins. DNA ฀(Transcription)฀ mRNA ฀(Translation)฀ Protein 12. What is the RNA world hypothesis? States the earliest self-replicating entity used RNA both to store genetic information and to conduct cellular processes. 13. Know the historical timeline presented in lecture, especially individuals focused on by Dr. Bacusmo: a. Francesco Stelluti – First to observe organisms (bees and weevils) under a microscope b. Robert Hooke – First to publish drawings of microorganisms in book Micrographic in 1665 c. Antony van Leeuwenhoek – First person to observe microorganisms accurately d. Aristotle – Proposed idea of Spontaneous generation e. Louis Pasteur – Disproved Spontaneous generation with his “swanneck flask experiment” and came up with Germ Theory of disease; also came up with idea of pasteurization

f. Joseph Lister – Known as “father of modern surgery” because he developed antiseptic techniques and surgery systems to prevent microorganisms from entering wounds. g. Robert Koch – Known for work with etiology of anthrax and established a list of criteria called Koch’s Postulates. 14. Know these three concepts well: a. Spontaneous Generation – The discredited theory that living organisms arise from nonliving material. b. Swan-Neck flask experiment – Pasteur used a swan neck flask, which has an entry tube that is bent to slow down spread of microbes from outside air. Meat broth was placed in the flasks and in one flask heat was applied to sterilize it, removing all the microbes. The other flask was left open to outside air and was found contaminated with microbes, while the one with the swan neck was not contaminated. c. Germ Theory of Disease – Concept that human and animal diseases are caused by microorganisms. d. Pasteurization – a method to eliminate unwanted organisms in food products. e. Koch’s Postulates – Set of criteria used to link a microorganism to a disease 4 steps: 1) Observe an unhealthy organism containing a microorganism. 2) Isolate the microorganism and grow it in pure culture. 3) Re-infect a healthy organism with the isolated microorganism 4) Observe the healthy organism exhibits the same illness and symptoms, and then re-isolate the harmful microorganism from the organism’s body. Some issues with Koch’s postulates are that some microorganisms are difficult if not impossible to culture. f. Second Golden Age of Microbiology – Rapid advancements in technology, such as DNA analysis, have led some to believe we are in a “second golden age of microbiology”. 15. What are the smallest and largest microorganisms? Smallest – Viruses Largest – Eukaryotic Protists 16. Define a Light and Electron microscope.

Light Microscope: Involves passing light through one or more lenses to create a magnified view of the sample Electron Microscope: Uses electrons rather than light 17. Know the types of light microscopes: a. Bright-field microscope - dark image of the specimen against a bright background b. Dark-field microscope - bright image against a dark background c. Phase-contrast microscope - Uses different densities and refractive indices of cellular components to produce a detailed image d. Fluorescence microscope - Uses fluorescent dyes to visualize cells under UV light. 18. Know the types of Electron microscopes: a. Transmission Electron Microscopes (TEM) – Produce an image of the details of the inside of the cell. b. Scanning Electron Microscopes (SEM) – Produce an image of the details of the cell surface. 19. Why do scientists stain specimens? Allows scientists to increase the specimen’s visibility, accentuate specific morphological features, and preserve the specimen. 20. Why do we fix specimens to the slide? What are the two ways to do this? To ensure the specimen is in position and to preserve the specimen’s internal and external structures. The two ways are: heat fixation and chemical fixation. 21. Define a stain. A solution containing a solute called chromophore, which gives the solution its color. 22. What are the two kinds of stains? Define each. Simple Stain – involves the application of a single dye and provides information about the morphology, size, and arrangement of bacterial cells. Differential Stain – Involves the application of two or more dyes and allows scientists to divide microorganisms into groups based on their staining properties (gram-positive vs gram-negative), or to detect certain structures (endospores, capsules, and flagella). a. Example = Gram staining

23. What are the steps of gram staining? 1. Apply primary stain Crystal Violet – will turn all cells purple 2. Apply a mordant Iodine – Fixes stain in the cells, still purple 3. Apply decolorizer Alcohol or Acetone – removes dye from gramnegative cells but not the gram-positive 4. Apply counterstain Safranin – turns gram-negative cells a red/pink color and leaves gram-positive as is 24. What are the color identifications for gram-positive and gram-negative bacteria? Gram- positive = blue/purple Gram-negative = red/pink 25. What is an acid-fast stain? Type of differential stain that uses a harsh acid to identify members of the genus Mycobacterium, which has a thick waxy-coated cell wall. 26. Define Structural stains and name the three types. Structural stains: Used to identify and highlight the structures of a bacterial cell. Three types include: Endospore stains, Capsule stain, and Flagellar stain.

Module 2A: Bacteria and Archaea Cell Structures (Chapters 3-4) 1. Know these bacterial shapes: a. Cocci - Spherical b. Bacilli – Rods c. Vibrio - Comma d. Spirilla – Spiral with rigid helices e. Spirochete – Corkscrew helices 2. What are the three layers of the cell envelope? (internal ฀ external) Cell envelope: Consists of the plasma membrane, cell wall, and layers outside of the cell wall (Glycocalyx). 3. Describe the three layers above and their roles. Plasma membrane: Selective permeable barrier that controls what substances enter and leave the cell; fluid mosaic model

Cell Wall: Maintains cell shape, protects against osmotic stress, and sometimes plays a role in pathogenicity Glycocalyx: Additional layer outside of the cell wall that consists of carbohydrates, proteins, and lipids; has a capsule and slime layer. 4. What is the fluid mosaic model? Made up of a bilayer that consists of a sea of phospholipids with proteins floating in it. 5. What are the two kinds of protein within the cell membrane? Peripheral proteins: Loosely associated with the outside of the cell membrane; easily removed Integral proteins: Cross into the hydrophobic portion of the bilayer, so they are not easily removed; can be called a transmembrane protein when it crosses the entire membrane. 6. What are hopanoids? Steroid-like molecules that strengthen prokaryotic cell membranes 7. What compound in the cell wall is only found in bacteria? Peptidoglycan 8. What are the major differences between gram+ and gram- bacteria that causes them to stain differently? Gram-positive: Primarily made of a thick peptidoglycan; Some have teichoic acid – add rigidity to cell wall; Have a layer of proteins on the outer surface of peptidoglycan; periplasmic space between plasma membrane and cell wall Gram-negative: Thin peptidoglycan layer; Have an additional membrane called outer membrane that plays a role in defense and immunity; periplasm between the inner and outer membrane. 9. What is the periplasmic space of bacteria? Space between the plasma membrane and cell wall in Gram-positive bacteria 10. What is the S-layer? The extracellular portion of the cell wall commonly found in bacteria and archaea. Has a number of functions including protection from host defenses, adhesion to surfaces, and protection against osmotic stress, predations, and ion and pH fluctuations.

11. What is the glycocalyx? Additional extracellular polymers. Typically made up of polysaccharides and facilitate the formation of the biofilm. 12. Know the two examples of glycocalyx structures and their roles: a. Capsule – well-organized extracellular layer of polysaccharides that can sometimes be visible using a light microscope; Makes the cell resistant to phagocytosis, it excludes viruses and detergents, and protects against desiccation. b. Slime Layer – Similar to capsule except it is diffuse, less organized, and more easily removed; Aids in cell motility. 13. What is a biofilm? Sticky substance that acts as a defensive structure for the immune system. Allows bacterial communities to adhere to surfaces and exchange easier. 14. What is the cytoplasm? Consists of everything inside the cell envelope, including the cytoskeleton, intracytoplasmic membranes, inclusions, ribosomes, the nucleoid, and plasmids. 15. What are the three examples of bacterial cytoskeleton? FtsZ in cell division MreB determines cell shape in rod-shape bacteria CreS creates curve shape in Caulobacter crescentus bacteria 16. What is an inclusion? An aggregate of organic or inorganic substances stored in the cell for later use. 17. Name and define the three types of inclusions. Storage Inclusion: Store carbon, glycogen, amino acids, and other nutrients. Microcompartments: Serve as other functions beside storage Gas Vacuoles: Regulate buoyancy in bacterial cells 18. What is a ribosome? Complexes of RNA and protein that serve as the site of protein synthesis within the cell.

19. What are the ribosome sizes for the three domains? Bacteria and Archaeal ribosomes = 70S with a 50S large subunit and 30S small subunit Eukaryotic ribosomes = 80S with a 60S large subunit and 40S small subunit 20. What is a nucleoid? It is where the single, circular, double-stranded chromosome and associated proteins aggregate within the cell. 21. What is a plasmid? Small, double-stranded, extrachromosomal DNA molecules found in bacteria, archaea, and some fungi. 22. Define the role of the following plasmids: a. R Plasmid – Carry antibiotic resistance genes b. Conjugative Plasmid – Form a sex pilus and transfer DNA c. Col Plasmids – destroy closely related species d. Virulence Plasmids – Virulence genes e. Metabolic Plasmids – Carry genes for enzymes involved in metabolism 23. What are the three types of external structures? Fimbria and Pili: Interchangeable terms; fine, thin, hair like appendages that assist in attachment to surfaces, aid in motility and electron transport. Flagella: thin, rigid, threadlike appendages that are involved in motility, swarming behavior, attachment to surfaces, and virulence. 24. Define chemotaxis. A process in which bacteria move toward an attractant and away from a repellent. 25. What is the most common type of cell wall in archaea? S- layer 26. What are the two external structures unique to archaea? Describe each. Cannulae: hollow, tubelike structures Hami: Look like tiny grappling hooks and may be used for adhesion.

Module 2B: Eukaryotic Cell Structures and Viruses (Chapters 5-6)

1. What is the key distinction between eukaryotes and prokaryotes? Eukaryotes have membrane-bound nuclei and organelles that perform specific functions. 2. True or False. Eukaryotic cell walls contain peptidoglycan. False 3. What is the cytosol? The liquid component of the cytoplasm 4. What are the three components of the Eukaryotic cytoskeleton? (smallest ฀ largest) Microfilaments, intermediate filaments, and microtubules 5. What is difference between secretory and endocytic pathways? Secretory Pathway moves materials from location to location within the cell Endocytic Pathways moves materials into the cell from the outside 6. What is the Endoplasmic Reticulum (ER) and its role? A network of membranous tubules and flattened sacs. It transports proteins, lipids, and other materials within the cell and is the major site of cell membrane synthesis. 7. Name and describe the two types of ER. Rough ER: Studded with ribosomes, which synthesize proteins Smooth ER: No ribosomes attached to it but has enzymes that synthesize lipids. Known for detoxifying as well. 8. What is the Golgi Apparatus and its role? Membranous organelle that consists of stacked cisternae. It is involved in the modification, packaging, and secretion of materials. 9. What are Lysosomes and their role? Provide an example of a Lysosome. Membrane-bound vesicles that contain hydrolytic enzymes that break down large molecules and act as the site of intracellular digestion. Example = White blood cells contain a lot of lysosomes. 10. What is the nucleus? Membrane-bound structure that contains the genetic material of the cell.

11. Define chromatin and nucleosome. Chromatin: complex of DNA, histones, and other proteins Nucleosome: Segment of DNA wrapped around a core of histones. 12. What leaves the nucleus via nuclear pores? Immature ribosomal subunits, mRNA, and tRNA 13. Where is Ribosomal RNA (rRNA) produced? Nucleolus 14. What are Ribosomes made up of? rRNA and protein complex 15.True or False. Ribosomes are the structures where proteins are synthesized. True 16. What is endosymbiosis? Process in which an early eukaryotic cell ingested bacterial cells and formed a symbiotic relationship. These ingested cells became chloroplasts and mitochondria. 17. Describe how the following three organelles are thought to be integrated by endosymbiosis: a. Mitochondria – Similar to bacteria cells in many ways (i.e. binary fission reproduction) b. Hydrogenosomes – Resemble mitochondria c. Chloroplasts – very similar to extant cyanobacteria ** NOTE: Know that mitochondria are the sites of the tricarboxylic acid cycle, electron transport, and ATP synthesis in eukaryotic cells 18. Know the structures of the chloroplast and their roles:

X – Stroma: Fluid that exists outside thylakoid membrane; Where biochemical reactions occur Y – Thylakoid: saclike membranes that are interconnected to form stacks of grana; where light energy is converted to chemical energy Z – Granum: stacks of thylakoids 19. What external structure is unique to eukaryotes? Cilia and Flagella 20. What is virology? Study of viruses, infectious acellular agents. 21. Define a virion. Complete virus particle 22. What are the simplest viruses made up of? Nucleic acid (RNA and DNA) in a protein coat. 23. True or False. Viruses are continuously evolving causing humans to develop new vaccines to combat them. True 24. Prions often lead to _______ diseases that affect both humans and domesticated ______. Neurodegenerative; animals 25. What are the major examples of prion diseases? Scrapie, BSE, kuru, and Creutzfeldt-Jakob disease...