Microbiology Notes PDF (MCB 3020 Fall 2024)

Microbiology Notes  Microbiology Notes (MCB 3020) ~ Fall 2024 The Discovery of Microbes Antoine Van Leeuwenhoek was the first ever microscopist. His instrument, a “facsimile microscope”, used a tiny polished sphere to magnify small...

Microbiology Notes  Microbiology Notes (MCB 3020) ~ Fall 2024 The Discovery of Microbes Antoine Van Leeuwenhoek was the first ever microscopist. His instrument, a “facsimile microscope”, used a tiny polished sphere to magnify small objects In 1674 Van Leeuwenhoek looked at pond What is a “Microbe”? water and saw “animacules” *“Microbe” is a synonym for the *“Microbes” are only unicellular word “bacteria” A. True B. False A. True B. False *All “Microbes” are prokaryotes *“Microbes” are all cells/ (bacteria and archaea) organisms that are “small” A. True B. False A. True B. False Microorganisms vary greatly in size and shape. Trivia: Approximately how many Escherichia coli cells t would fit the width of a human hair? A. Less then 5 B. ~7-100 C. ~110-500 D. ~510-1000 Most bacteria are between 1-2 microns (um) Which of these tree tips contain organisms that are NOT “microbes ↳ Eukarya: Animals & Plants are not microbes. The “single-cell” rule of microbes has some nuance Multi-cellular assemblies of microbes are also possible. Such cases have specific terms attributed to them.  Major types of microorganisms Q Algae ⑪Fungi G ⑤ Archaea Protists ③ Bacteria ⑳Viruses We now know that microbes are ubiquitous Most of the total abundance of bacteria and Estimates of global biomass show that microbes have the second largest total archaea are found in deep continental and oceanic subsurface! - biomass on earth (also, “plants” in the picture includes some microorganisms!) - One of the largest living groups of cells is Armillaria solidipes (Honey fungus) at a size of 4 square miles (visible fruiting body shown) Cells shape and size has important function Microbes have different cellular structure & activity * But all cells have the same properties* · Microbes are medically important *For much of human history, infectious disease has been a major cause of death. * Since “germ theory” was proven in the late 1800s, this has greatly improved. *What have microbes ever done for us? (besides make us sick) 4 1. They help us breathe. 4.) Microbes carry out Microbes first made oxygen (approx. 2.7BYA) - natural recycling processes - (and still make ≤70% of it.) 3 - I. 5 3) Microbes support the food webs we need. 5.) Microbial fermentation creates desirable products · 2) Microbes give us energy and nutrients. 6.) Microbes support our health 2 I.e. Producing vitamins that we need from bacteria are present in our gut  Quiz 1 (Chapter 1-2) ?’s & Answers 1. The cytoplasmic membrane is termed "semi-permeable" because.... some substances, like water and alcohols, can pass freely through 7. Which of the following attaches the gram-negative outer membrane to while others, like sugars, amino acids, and ions, cannot. What the peptidoglycan layer? molecular characteristics largely determine whether or not a substance * porins can pass through the membrane? * Sec translocase * usefulness to the cell * fmbriae * osmolarity * lipoprotein * size and hydrophobicity * organic versus inorganic molecules 8. In what/which domain(s) of life is/are microorganisms represented? * archaea 2. In archaeal membranes, what serves the same function as the fatty * bacteria acids of bacterial membranes? * eukarya * phosphate groups * All of the Above * hopanoid molecules * isoprene chains 9. Differential selection and decent with modification occurs during a * glycerol process called * transformation. 3. Which of the following is NOT a function of the cytoplasmic * cellular differentiation. membrane? * evolution. * barrier to hydrophilic molecules * growth. * protection from hypotonic stress caused by osmosis * transport of nutrients 10. Cells move polar molecules across the cell membrane against a * provide the framework for the generation of proton motive force concentration gradient using * modifications to membrane lipids. 4. What molecule cleaves the ß-1,4 bond between N- * simple diffusion. acetylglucosamine and N-acetylmuramic acid? * random molecular movement. * diaminopimelic acid * energy and transport proteins. * lysozyme * d-alanine 11. which of the following terms are mismatched? * penicillin * gram-negative outer membrane; teichoic acids *peptidoglycan; D-alanine 5. Which of the following structures enable a Bacterial or Archaeal cell *endospore; dipicolinic acid MATCHED to adjust its position in a water column? *LPS; outer membrane * gas vesicles * S-layer proteins 12. A pure culture * type IV pili * is sterile. * polyphosphate granules * is a population of identical cells. * is made of a clearly defined chemical medium. 6. Which of the following terms refers to a bacterium with a spherical * contains one microbial cell shape? * bacillus * spirochete * coccus * spirillum  Session 2 Class Notes #Why can’t we include viruses, on the tree of life? A) Some viruses contain multiple strands of RNA. B) Their genetic elements cannot be sequenced. C) They lack ribosomal RNA (rRNA). D) They can infect other organisms, which complicates the genetic comparisons. Ribosomes are made of proteins, and viruses Prokaryotes are the most abundant, and the most diverse organisms on the planet. & attack other hosts to get their proteins. Since Some of the (few) well-studied prokaryotes: viruses lack RNA they must find host that Eukaryas have a nucleus, but Escherichia coli Bacillus subtilis can provide it for them. Bacteria & Archea do not Caulobacter crescentus Streptococcus pneumoniae have a nucleus like a Salmonella enterica Listeria monocytogenes * Which domain of life is NOT a prokaryote? prokaryote Vibrio cholera. Staphylococcus aureus A) Bacteria B) Archaea Surface-to-volume ratio (S:V) is a cell property that is overall affected by cell size & shape C) Eukarya D) All 3 above are in-fact prokaryotes ⑨ S:V is one of several important factors that determines how many molecules enter and leave the cell at a time Classical shapes of prokaryotic cells Surface-to-volume ratio differs between shapes Elongated (and/or flattened) cells generally have higher surface/vol ratio (note here that volume is same in all 3) How is prokaryotic cell shape specified? First requirement: Structural support from a “cell wall” Consider: Prokaryotic cells are FULL of solute. Second requirement: Strategic construction of the cell wall This draws water inward, creates intense turgor pressure inside the cell. A “cell wall” is firstly required to keep prokaryotic cells from exploding Recall: principle of Osmosis. Water is drawn toward solute Second requirement: Strategic construction of the cell wall What a bacterial “cell wall” looks like The cell wall, aka “peptidoglycan sacculus” is actually one huge net-like macromolecule peptidoglycan Zoomed view: Peptidoglycan backbone is a repeating polysaccharide How peptidoglycan sticks together: (i.e. sugar) subunit, cross-linked by covalent bonds A cell wall in bacteria is analogous to a scaffold (but less rigid) For a portion of the scaffold to change shape (example, add more curvature), cross-linking rods need to be taken apart and put elsewhere How does a prokaryotic cell grow? Peptidoglycan “shell” would have to expand. Two examples growth models in rod-shaped bacteria: What drives a prokaryotic cell to add peptidoglycan molecules to any particular location? Current theory: MreB (actin homolog, a type of protein) helix helps direct peptidoglycan growth. Cell shape & cell growth are intrinsically linked Rod-shaped cells can grow by length & width. Cells can (impart) control their shape Bacteria cell growth and shape varies by species based on where they direct (We have so far focused on rod shaped cells in previous peptidoglycan addition slides) Some Archaea do not have peptidoglycan. These have an outer “S-layer”, made of protein. S-layers have analogous roles to cell walls by giving cell shape and cell structure support Archaea S-layers lack peptidoglycan, and so gram stains are not useful (they look like gram + bacteria) *Eukarya cell shape is also determined by peptidoglycan A) True B) False C) Depends on Eukarya species  Cell wall forms part of Cell Envelope (structure varies across species) -Series of layered structures (and spaces) surrounding cytoplasm and governing interactions with environment -(species vary in composition of these envelope layer structures) Cytoplasmic membrane Cellwall : Periplasmspace Outermembrane S-layers Gram staining is commonly used to classify bacteria The stain indicates how much peptidoglycan on the outside of the cell. (Thick cell walls hold stain better) Gram-negative Bacteria Cell Envelope Note that gram(–) bacteria have distinct LPS (chain of sugars) on outer membrane LPS are important for surface recognition which is an important virulence factor in pathogens Gram (+) has only 1 Membrane Gram (-) has 2 Membranes Gram- bacteria have a periplasm, while Gram+ bacteria do not A. True B. False General structure of membranes These often contain amphipathic molecules: one end polar, one end nonpolar. These spontaneously form a “lipid bilayer” & Major property of a lipid membrane 1.) Lipid membranes self-seal After membrane lipids form a sheet: This shields many fatty acid tails. Lipid tails at edge still exposed though! If the sheet is large enough, It encloses into a sphere! (this = most “energetically favorable” state)  “Hydrophobic clustering forces” drive (and keep) nonpolar molecules together. Repulsion of nonpolar groups by water leads to clustering outcomes. Other major properties of a lipid membrane 2.) Lipid membranes are Differentially/selectively permeable to different substrates (note that these are passive diffusion properties of lipid membranes) 3.) Lipid membranes carry membrane-associated proteins. (some of these proteins are also very important in determining what enters/leaves the cell) Some transmembrane proteins allow passage of solute (i.e. porins) Active transport (uses ATP): Allows cells to accumulate solutes against concentration gradient Cell Surface Structures #In archaeal membranes, what serves the same function as the fatty acids of bacterial membranes? A.Hopanoid molecules B. Glycerol C. Phosphate groups D.Isoprene chains Some bacteria contain “capsules” or a “slime layer” Below are other cell structures that provide some species with unique ecological/ physiological functions Phospholipids of described Archaea (so far) have different biochemical composition compared to Bacteria and Eukarya -  Chapter 2 ~ Textbook Notes Archaeal Cytoplasmic Membranes *The cytoplasmic membrane of Archaea is structurally similar to Microbial Cell Structure and Function those of Bacteria and Eukarya, but the chemistry is somewhat I The Cell Envelope different. II Cell Surface Structures and Inclusions * In the lipids of Bacteria and Eukarya the hydrophobic fatty acid III Cell Locomotion tails are bound to glycerol by ester linkages IV Eukaryotic Microbial Cells * In contrast, the lipids of Archaea have hydrophobic isoprenoid The Cytoplasmic Membrane (rather than fatty acid) tails, which are bound to glycerol by ether bonds The cytoplasmic membrane surrounds the cytoplasm—the mixture of macromolecules and small molecules inside the cell —and separates it from the environment. Bacterial Cytoplasmic Membranes The cytoplasmic membrane of all bacterial and eukaryal cells is a phospholipid bilayer containing embedded proteins. The cytoplasmic membrane of Archaea is constructed from either phosphoglycerol diethers, which can have C20 side - chains (called a phytanyl group), or diphosphoglycerol - tetraethers (C40 side chains, called a biphytanyl group) - Although physically weak, the cytoplasmic membrane controls at least three critically important cellular functions: maintaining selective permeability, anchoring proteins, and conserving energy -  Quiz 2 (Chapter 1-2) ?’s & Answers 1. Although the inner leaflet of the gram-negative outer membrane is composed 7. While examining cellular material, you find that organelle DNA is mainly of phospholipids, the outer leaflet of the outer membrane contains present. What organelle(s) must be within the sample? * poly-B-hydroxybutyric acids (PHB). * Golgi complex * lipoteichoic acids. * rough or smooth endoplasmic reticulum * lipopolysaccharides (LPS). * lysosomes *pseudopeptidoglycans. * chloroplasts or mitochondria 2. Which is/are a function(s) of the cytoplasmic membrane in prokaryotes? 8. Modern endosymbiotic theory proposes that eukaryotic cells arose * It is an anchor for many proteins involved in bioenergetic reactions and from _____ transport * a bacterial cell taking up residence within an archaeal cell * It is a major site of energy conservation. * an archaeal cell taking up residence within another archaeal cell * It functions as a permeability barrier. * a bacterial cell taking up residence within another bacterial cell * It serves as a permeability barrier, a docking station for proteins involved in * an unknown cell taking up residence within an archaeal cell bioenergetics reactions and transport, and a site for energy conservation. 9. All of the following contain chloroplasts in their cells EXCEPT 3. All eukaryotes contain _______ * mitochondria. * plants * a membrane-enclosed nucleus. * red algae * hydrogenosomes. * cyanobacteria * a nucleus, mitochondria, and hydrogenosomes. * green algae 4. Where within a eukaryotic cell is ribosomal RNA (rRNA) synthesized? 10. The energy source derived from the charge separation across the * nucleolus cytoplasmic membrane is referred to as * cytoplasm * the proton motive force. * lysosome * adenosine triphosphate. * mitochondrion * carbohydrate charging. * the voltage source. 5. Membrane-enclosed organelles, such as nuclei, lysosomes, endoplasmic reticulum, mitochondria, and chloroplasts 11. What would happen to a eukaryotic cell if the membranes of its * increase structural complexity, help eukaryotes overcome diffusion limitation due lysosomes are disrupted? to their size, and form specialized environments for specific functions to * the cell would loose its DNA into the cytoplasm occur. * the cell metabolism would slow down but other processes would * form specialized compartments within eukaryotic cells for specific functions to kick in to keep the cell alive occur. * the cell would be digested from the inside out. * increase the structural complexity of eukaryotic cells. * the cell would not be able to breakdown certain molecules but * help large eukaryotic cells overcome the limitations of diffusion imposed by would be otherwise fine their large cell size. 12. Cells move polar molecules across the cell membrane against a 6. Transport proteins located in the cytoplasmic membrane are necessary when concentration gradient using * the level of nutrients in nature is very low. * modifications to membrane lipids. * diffusion will not allow adequate amounts of a substance to enter the cell. * random molecular movement. * movement into the cell is against a concentration gradient. * simple diffusion. * nutrient concentration is very low in the environment, transport is needed * energy and transport proteins. against the concentration gradient, or diffusion is not possible.  Parts of Chapter 2: Prokaryotes & Eukaryotes How peptidoglycan unit and how it sticks together: *The cytoplasm forms part of the cell envelope A. True B. False cytoplasm is not part of the cell envelope it’s inside the cell *Gram-positive bacteria have an outer membrane while, gram- negative bacteria do not A. True B. False ONLY Gram — Has an outer membrane *BOTH gram-negative and gram-positive bacteria have a periplasm. A. True B. False Yes! Both have a perpierplam Recall : You saw the cell wall is NOT in the *Gram-negative bacteria have thinner cell wall then gram-positive cytosol. But peptidoglycan is needed for cell walls bacteria Gram — Have thinner cell walls Then Gram + How does MreB in the cytoplasm specify A. True B. False peptidoglycan growth outside the cytoplasmic membrane? Peptidoglycan makes up the cell walls of most prokaryotes * A. True B. False No, Archea isn’t made up of peptidoglycan, Archea is made of an S layer. S layer is made out of proteins Unlike Bacteria, Archaea cell membranes are not hydrophobic · A. True B. False Cell walls are not hydrophobic in Archea · · *How easily do these diffuse across a plasma membrane? A.) Can easily diffuse across Data suggest: MreB directs peptidoglycan-synthesizing B.) Cannot diffuse across enzymes to specific areas via transmembrane proteins Some molecules that can diffuse are small non polar elements like oxygen or nitrogen, co2. This molecule It’s a large polar molecule so it’s Note: You do NOT need to know what all the proteins are to large and has a charge to diffuse through in the PG synthesis complex for the exam! naturally. -cell metabolism, if a cell can’t go across the membrane then they need transport proteins in active transport to help.  Data suggest: MreB directs peptidoglycan-synthesizing enzymes to specific areas via transmembrane proteins Peptidoglycan biosynthesis starts in the cytoplasm Via transmembrane protein complexes, PG synthesis completes in the periplasm Recall the cell envelope for gram- and gram + bacteria. *Evaluate the statement: Active transport is required to get Glucose molecules (from outside the cell) into the periplasm for both cell- types below? A. True B. False False, glucose can’t naturally pass. They need to be actively transported by transmembrane proteins to cross the periplasim. Gram + cell has similar molecules to glucose. Each layer has physical properties that Last class you also learned enable molecules to get threw. glucose can just go threw Gram +. But Gram - has few peptidoglycon units that the outer membrane of so the mesh like structure is still pourisis, but requires active transport. Gram + bacteria do not have Gram- bacteria is rich in a polysaccharides molecule called Organic chemistry review only: What is a saccharide? “Lipopolysaccharide” 1.) They consist of carbon, hydrogen and oxygen, with a hydrogen–oxygen ratio of 2:1 same as water 2.) Many of the saccharides we discuss are hexose (6 carbons). A lipopolysaccharide is a 3.) They can exist in open or closed-ring conformations. glycosylated, crosslinked set of lipids *Which statement is most likely? A. Lipopolysaccharides are synthesized outside the cell and attached to the outer membrane using various peripheral proteins B. Lipopolysaccharides are synthesized inside the cytosol and transported to the outer membrane through various transmembrane proteins O-antigen (purple) in some bacteria has virulent properties: C. Lipopolysaccharides are synthesized inside the cytosol region is very inflammatory. and diffuse across both membranes to attach to the outer membrane Lipopolysaccharides are synthesized inside the cytosol and transported to the outer membrane through various transmembrane proteins. (Cells will never make something outside the cell wall, and transport it in.)  Cell Differentiation: Endospore Example The Life Cycle of an Endospore-Forming Bacterium Endospores Specialized spores Highly differentiated, dormant cells resistant to heat, radiation, chemical exposure, drying, lack of nutrients Survival structures to endure unfavorable growth conditions Ideal for dispersal via wind, water, or animal gut Present only in some gram-positive bacteria, (e.g., Bacillales and Clostridiales) Endospore Germination in Bacillus Endospores can remain dormant for years but converts rapidly back to vegetative state Structure of the Bacterial Endospore Many more layers compared to vegetative cells Note that Bacillus is a gram+ bacteria (you don’t need to know all the individual layer names for the exam) · ·  Eukaryotic vs Prokaryotic cell structure Overview: prokaryotes vs. eukaryotes Eukaryotic Cells are generally larger than prokaryotic cells (on average 10x bigger) Increased cellular compartmentalization in Eukaryotes allows size increase Prokaryotes still thought to rely on diffusion in cytosol #How do prokaryotes and eukaryotes differ? A. All Eukaryotes have a membrane enclosed nucleus, all prokaryotes do not. B. Prokaryotes are microbes, and eukaryotes are not. All Eukaryotes have a membrane enclosed nucleus, all prokaryotes do C. Prokaryotes have cell walls, and eukaryotic cells do not. not. Prokaryotes do not have a nucleus D. Answers A, B and C are all correct. A thought exercise: think about a Gram- cell. What would that look like with Dogma in microbiology: a larger periplasm? Eukaryotes have membrane-bound organelles (including nucleus), whereas Prokaryotes don’t. New finding: Planctomycete gram- bacteria show evidence of membrane-bound organelles (i.e. Anammoxosome), including nucleus-like Planctomycete membranes as according to structures (not membrane-bound) transmission Electron microscope data Areas of the periplasm visibly curl into the cytoplasm Computerized reconstructions of EM images Planctomycetes are not the only prokaryotes with a very large periplasm: (EM tomography) enables modeling of Planctomycete cell organization Ignicoccus islandicus (this Archaea is found in hydrothermal vents deep in the ocean)  Ribosomes are found in all living cells, but there is variation Ribosome distribution differs for prokaryotes and eukaryotes Ribosomes occur throughout cytosol in prokaryotes Many of the subunits are conserved (homologous) Eukaryotic Golgi Apparatus: Golgi Apparatus packages Packages proteins in membrane- & sends proteins Can make RNA & Ribosomes at the same time bound vesicles and sends them to 3D rendering of TEM images (EM tomography) indicates vesicle trafficking in various places in cell Ignicoccus (Archaea) EM tomography further indicates extended Has similar properties as the Golgi apparatus projections of the inner membrane in Parallel between prokaryotes & eukaryotes: Ignicoccus (Archaea) Eukaryotes use mitochondria to generate ATP A notable parallel is that eukaryotic nuclei are enclosed by ER membranes. This compartment enables NADH oxidation (aerobic). Generates ATP for the cell. This is one piece of evidence (among others) that Mitochondria – evolved from highly eukaryotes may be more closely related to Archaea specialized bacterial symbiont than to Bacteria. ATP-generating compartments have also been found in bacteria. One type: Anammoxosome This compartment carries out ammonium oxidation (through anaerobic respiration). Generates ATP for the cell. Anammoxosome does the same as mitochondria (makes. Flagella are also considered as microbial “organelles” ATP) power house of cell *What is the main function of MreB? Though this image shows a Gram- cell, Gram+ Select the correct option bacteria and Eukaryotes also have flagella A. Gene that encodes a protein that binds helps balances nutrient passage #What do Anammoxosomes and Mitochondria have in B. Increases the strengthens of common? peptidoglycan covalent bonds in cell wall A. They have analagous roles in energy conversion. C. Directs proper placement of B. They all support aerobic respiration. peptidoglycan cell wall construction C. They are all derived from bacterial endosymbionts. D. A, B and C are all correct D. They are membrane-bound E. Answers A, B, C and D are all correct Anammaxosome has anaerobic propertied, & are membrane bound