1. ADHERE AND DEFEND: Our bacterium has entered the host. Now it needs to adhere and get past the normal microbiota.

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1 North Seattle College Stage 02 Colonization and Infection This explanatory model will tell the story of how one bacterium adheres to a host and, through binary fission, ends up making two daughter cells. You should know how to explain this story: For prokaryotic cells to grow by binary fission in order to colonize or infect a host they need to 1. adhere to the host, get past the normal microbiota, 2. have the right environment, 3. transport in necessary nutrients, 4. harvest energy and make precursor metabolites from those nutrients that will allow them to build amino acid, nucleotide, lipid, and carbohydrate subunits 5. use those subunits to build macromolecules (proteins, nucleic acids, lipids, and polysaccharides) through the processes of DNA Replication Transcription Translation, and Enzyme-mediated chemical reactions 6. and, finally, make cellular structures with those macromolecules in order to produce a whole new cell by binary fission. 1. ADHERE AND DEFEND: Our bacterium has entered the host. Now it needs to adhere and get past the normal microbiota. Adhesins on the bacterial cell o Pili (fimbriae) o Cell wall proteins o Capsule surface structures Receptor on the host cell o Highly-specific adhesin-receptor binding Normal microbiota o Binding sites o Nutrients o Toxic products 2. ENVIRONMENT: Our bacterium also needs the right environment to grow. Temperature o a graph showing the temperature ranges for (Figure 4.8) psychrophiles psychrotrophs mesophiles thermophiles hyperthermophiles o protein structure draw a protein with tertiary structure amino acids alpha-helix beta-pleated sheet hydrogen bonds explain what would happen to that structure if the temperature were too high denaturation

2 Oxygen (O 2 ) Availability (Table 4.3) o Energy-harvesting mechanisms (short description of each) Obligate aerobe Facultative anaerobe Obligate anaerobe Microaerophile Aerotolerant anaerobe (obligate fermenter) o Reactive oxygen species Damage cell components Superoxide (O - 2 ) Hydrogen peroxide (H 2 O 2 ) Inactivation by Superoxide dismutase Catalase ph o Neutrophiles o Acidophiles o Alkaliphiles Water availability o Important cell structures: Cell wall Cytoplasmic membrane o Draw/explain what would happen to a bacterial cell in A hypotonic environment A hypertonic environment Plasmolysis 3. TRANSPORT NUTRIENTS: Now that our bacterium has successfully attached, fought off the normal microbiota, and finds itself in the right environment, let s find out what nutrients it needs to grow and how the cell transports them inside. Nutrients o Certain elements are required for cell growth: Redraw Table 4.4 o Growth factors GO TO TRANSPORT WORKSHEET

3 Biology 260 Stage 02 Colonization and Infection Building a model to explain transport of nutrients into a bacterial cell Natural Phenomenon: A few bacteria have entered your body and a short time later they have multiplied to colonize (or infect) you! How do they do this?? What is a model? In science models are a set of ideas that, together, are used to try to explain how natural phenomena might work. A model may be a graph, a diagram, a set of ideas set down in words, or anything that can be used to represent the phenomenon. For example, a drawing of a cell is not a real cell, but helps us to explain what a real cell might look like. Another example is a flow diagram of a metabolic pathway like glycolysis. Although it is not the real molecules going through real chemical reactions, it helps us to explain how the metabolic pathway works. Both of these are models that, although they are not the real biological phenomena, they represent the phenomena and help us to explain how they work. Your textbook is FULL of models!! How were these models created? A scientist or a team of scientists would write down their initial model (a set of ideas of how they think something might work), test that model through library research and experimentation, revise their model as new knowledge is learned, and then go through the process of testing and revising again and again. Hopefully, through this iterative process of creating, testing, and revising, their model comes closer and closer to explaining how that phenomenon actually works in nature. Models can then be used to predict how your system might respond if you perturbed it in some specific way. So far in our story A prokaryotic cell grows by binary fission in order to colonize or infect a host. To do this it needs to 1. adhere to the host, get past the normal microbiota, (and subvert the immune system (that s Stage 04)), 2. have the right environment, and 3. transport in the nutrients that they need To write the third part of this story, we must first follow nutrients, molecules, and ions as they are transported across the cell membrane so that they can be used for metabolism (the next part of our story). Transport across the cell membrane: With your group, draw a skeleton model of a typical bacterial cell and indicate how the membrane functions to regulate nutrient transport, oxygen and carbon dioxide transport, and a hydrogen ion electrochemical gradient across the cell membrane. Be sure to include ALL of the following: A drawing of the cytoplasmic membrane and cell wall of a Gram negative bacterial cell: o Cell wall: Peptidoglycan layer plus outer membrane for Gram negative cells (don t forget about the porins in the outer membrane!) o Cytoplasmic membrane: Phospholipid bilayer plus transport channel proteins Drawing and accompanying explanation about how the process works indicates how the membrane regulates o Nutrient transport into the cell through Facilitated diffusion Active transport Driven by proton motive force Driven by ATP (ABC Transporters) Group Translocation o Oxygen and carbon dioxide transport into and out of the cell through Simple diffusion o Hydrogen ion electrochemical gradient (proton motive force) across the cell membrane through Electron transport chain

4 North Seattle College Colleen Sheridan In-class activity on metabolism, Part I Amount of energy. Which of the following processes harvests more energy? Less energy? Rank them. o Aerobic respiration o Anaerobic respiration o Fermentation Back up your answer by including the following key terms: (see Figure 6.7 for help) Chemical energy source (use glucose as an example) Terminal electron acceptor (use the appropriate acceptor for each process) Electrons Electron affinities What gets oxidized What gets reduced Oxidation-reduction reaction (redox reaction) Energy released Why don t we (and our bacteria) burst into flames when we (they) break down glucose for energy? o What are the different metabolic pathways that cells use to harvest energy? How do enzymes work? o In your answer use the following key terms: Substrate(s) Active site Activation energy Catalyze (what does it mean to catalyze a chemical reaction?) Product(s) o In the picture below, explain why the graph of an enzyme rate of reaction goes down to the left of its optimal temperature goes down to the right of its optimal temperature

5 In-class activity Metabolism, Part II HARVEST ENERGY, MAKE PRECURSORS: Now that the nutrients are inside the cell, the cell must harvest energy and make precursor metabolites from those nutrients to be able to grow. Part A: Harvest energy - Draw a flow chart or diagram that shows how energy is harvested inside each of the following different chemoorganoheterotrophic bacteria using the different catabolic pathways in the table below. o Obligate aerobe o Facultative anaerobe o Obligate anaerobe Table of catabolic processes o The central metabolic pathways Glycolysis Pentose phosphate pathway Tricarboxylic acid cycle (TCA cycle) and transition step o Aerobic respiration o Anaerobic respiration o Fermentation Part B: Now label on each diagram how the harvested energy is stored during each catabolic process. ATP Substrate-level phosphorylation and/or Oxidative phosphorylation Proton motive force Electron transport chain o Oxidation-reduction (redox) reactions o Active transport o Proton (H+) concentration gradient Reducing power Electron carriers o NADH, FADH 2, NADPH Part C: Make precursor metabolites and their subunits. Now for the last part of catabolism, we need to understand that precursor metabolites are made by the central metabolic pathways and are used to make subunits. Label on your diagram where you would expect precursor metabolites to be made.

6 North Seattle College DNA Replication, Transcription, and Translation to make a new cell! PRECURSOR METABOLITES ARE USED TO MAKE SUBUNITS! Understand that all of those precursor metabolites made by the central metabolic pathways can be used to make: Amino acids, nucleotides, monosaccharides, fatty acids, and glycerol! BUILD MACROMOLECULES: In order to make a whole new cell, the bacterium needs to put together the subunits it just made into macromolecules so that it can use those macromolecules to build new cellular structures! Part A: Fill out the following table: Precursor Metabolites Subunits Macromolecules Cellular Structure made out of each macromolecule amino acids nucleotides monosaccharides fatty acids and glycerol Part B: Building Macromolecules o Replicate the DNA chromosome for the new cell DNA Replication Enzymes: DNA gyrase, DNA ligase, DNA polymerases, Helicases, Primase Process: Origin of replication, Primer, Lagging strand, Okazaki Fragments, Leading strand Subunits: DNA nucleotides (G, A, T, C) o Make mrna Transcription Enzyme: RNA polymerase, Sigma Factor Process: (-) strand, (+) strand, Promoter, Terminator Subunits: RNA nucleotides (G, A, U, C) o Make proteins Translation Site of protein synthesis: Ribosome (made of rrna and protein) Process: trna, mrna, start codon (AUG), stop codons, reading frame, anticodon, ribosome binding site Subunits: Amino acids o Make lipids and polysaccharides: just know that many enzymes are involved! BUILD A CELL! Finish off our story by explaining that those macromolecules will be used to make new cellular structures which will eventually allow the cell to go through BINARY FISSION making a whole new cell!! Now that new cell has to find some place to adhere and start all over again..

7 North Seattle College Viruses: life cycles, genome replication, transcription and translation 1. Compare (find the similarities) and contrast (find the differences) between lytic bacteriophage and animal virus life cycles. Attachment Lytic Bacteriophage Animal Virus Genome Entry Penetration and Uncoating Synthesis (You ll look more closely at different animal virus genome replication strategies in question 4 below.) Assembly Release

8 2. How do lytic and lysogenic bacteriophage life cycles compare and contrast? 3. How do lysogenic bacteriophage and animal retrovirus life cycles compare and contrast? 4. Viruses are just a bunch of nucleic acids protected by a protein coat. SO they have to replicate their genomes and make proteins just as their host cells do. Fill out the following table to understand how viral replication enzymes compare and contrast to their eukaryotic hosts. Type of Animal Virus DNA viruses RNA viruses Reversetranscribing viruses Replicating genomes viral or host polymerase? Transcription host or viral RNA polymerase? Making proteins Translation host or viral ribosomes?