Micrb265 Objectives PDF

Learning objectives for Topic 1: Introduction to Microbial life Lecture 1-1: History of Microbiology o Understand that for most of human history we were unaware of microbes and the many important ways they influence our lives. o Explain the importance of microscopy for the development...

Learning objectives for Topic 1: Introduction to Microbial life Lecture 1-1: History of Microbiology o Understand that for most of human history we were unaware of microbes and the many important ways they influence our lives. o Explain the importance of microscopy for the development of the field of microbiology and identify some pioneers in this field and their early contributions. robertnoonantonivannewnone.eupasteur o Discuss the historical concept of spontaneous generation and key experiments that disproved this erroneous idea. rainlewispasteur o Demonstrate an understanding of the key contributions of the prominent microbiology figures Louis Pasteur and Robert Koch. culturedisease pure indust microbe o State Koch’s Postulates and demonstrate a working knowledge of how to apply these postulates to determine the cause of infectious disease. Describe the importance and strengths of Koch’s postulates, as well as their limitations. pathogens correlationvscausation dormant Pure is.fi 9ikkeaaiaisitfromneaitnyaniman o Describe the general methodology used in isolating pure microbial cultures and how these methods were important for the advancement of the field of microbiology. platesmedia stainagar gram steaking Lecture 1-2: A Diverse World of Microbes archaeabacteriaeuranga bacteriaarcheae o List the three domains of life and whether organisms in those domains are prokaryotic or eukaryotic. Understand that a remarkably diverse spectrum of microbes is present in all three domains. RNAwasfirstgenetic materialbecausesimple can produceaminoacid proteins o Explain the RNA world hypothesis and describe evidence that supports it. presentin anorganism o Explain the significance of “LUCA” and describe some of its presumed features and are imgur.inth.p o iii ancestor common p Describe how atmospheric oxygen emerged on earth and explain the transformative effects this had for life on earth 02ozone o Discuss the endosymbiotic theory and the evidence that supports it. mitomondria amoroplasts Dna haveown o Recognize the remarkable diversity of microbes the exist on earth and their abundance in virtually every environment on the planet. of 8 o Describe some of the major ways in which microbes influence our day-to-day lives and the tremendous impacts that the field of microbiology has had on society. wastewishment cheese Lecture 1-3: Naming and Classifying Microbes andevolution ancestors o Understand the terms “taxonomy” and “phylogeny” and the difference between them name Yardsity o Be familiar with the different taxonomic ranks (Domain, Kingdom, Phylum…) and how they apply to microbial life. D RP C O F G S o Describe different naming systems that exist to separate out lineages of the same species for bacteria (e.g. subspecies, serovar) biochemicald ifferences sugg.fi figer geste o Describe the role of Carl Linnaeus in the field of taxonomy reducechaosand know howtonameherorganisms o Demonstrate the ability to correctly write the names of microbes, using the appropriate conventions of capitalization and the use of italics. o List some ways in which microbes have historically been named weeanimaculesmorphology o Discuss the importance of taxonomy for the field of microbiology o Interpret a phylogenetic tree and its basic structure/elements. o Describe how DNA sequences are used to infer phylogenetic relationships and what features of a DNA element makes it more or less suitable for this. outt.itis titration o Explain 16S rDNA sequencing, including who first developed this technology, why rDNA from the small subunit of the ribosome is particularly well suited for this purpose and the importance of its variable and conserved regions. andvariablepriver snaredinall bacteriaconserved o Describe some limitations of phylogenetic trees predictionhorizontal genehomologousmixing seleptue  Learning objectives for Topic 2: Structure & Function of Microbial Cells Lecture 2-1: Prokaryotic Cells & Their Morphology o Describe the differences in the ways that prokaryotic and eukaryotic cells are structured. nucleus o Demonstrate a familiarity with the relative sizes and typical sizes of prokaryotic and eukaryotic cells and an awareness of the variability that exists in these cell sizes. o Explain the connection between cell size, surface to volume ratio and cell growth. o Explain the importance of prokaryotic cell morphology, particularly in the early days of microbiology o Be able to list and recognize the major prokaryotic cell morphologies o Provide an example of a bacterial species that adopts each of the major prokaryotic morphologies discussed and describe its relevance to our society (e.g. as a pathogen, or as a model system to understand some aspect of microbiology) nmanstomaaspiropnete line IEp E in o Summarize some factors that dictate the morphology of a prokaryote as well as some of the potential benefits of adopting different shapes. swimmingnutrients o Explain the difference between monomorphic and pleomorphic prokaryotes. List some factors that could cause a change in cell morphology. lifecyclenutrientavailability Lecture 2-2: Bacterial Cytoplasmic Membranes o Explain the term “cell envelope” and list different structures that can be included under this umbrella term membrane wall elayer o Demonstrate an awareness of the ubiquity of the cell membrane in all life o Describe the primary function of a cell membrane, as well as other important functions of cell membranes in bacterial cells barrier protection o Demonstrate a detailed understanding of the composition of bacterial cytoplasmic membranes including the structure of their phospholipids o Explain the basic forces at work that result in phospholipid bilayers adopting the structure that they adopt (hydrophobicity) o Outline some different functions of bacterial membrane proteins peripheraltransmembraneintegral  o Summarize the different categories (e.g. peripheral) of membrane proteins and the different ways they interact with membranes, and understand the importance of topology for their functions amino Eation Lecture 2-3: Bacterial Cell Walls o Understand the importance of cell walls for bacteria osmoticpressure o Describe what bacterial cell walls are made of and whether or not other domains of life use this same structure Nae nae L Yikes o Demonstrate a detailed understanding of the chemical structure of peptidoglycan and how the different subunits are connected o Describe the differences between the cell walls of Gram-negative and Gram-positive bacteria o Explain the extent to which peptidoglycan is permeable and what can/cannot penetrate this layer o Summarize the properties and functions of teichoic acids. Describe how they are incorporated into the cell walls of Gram-positive bacteria. o Explain the basis of Gram staining o Describe conditions that can permit bacteria to survive without a cell wall Lecture 2-4: Bacterial Outer Membranes & More o Describe the difference between the cytoplasmic and outer membranes of Gram- negative bacteria o List the 3 major “parts” of LPS. Describe the important properties and basic chemical makeup of each of these parts and their location with respect to the outer membrane (i.e., Lipid A inserted in membrane, core polysaccharide, O-specific polysaccharide outermost) o Understand the basic differences between the structure of lipid A and that of the phospholipids that make up the inner leaflet of the outer membrane o Explain why LPS is sometimes called “endotoxin” and which part of the molecule is primarily responsible for this toxicity  o Explain which part of LPS is the most variable and how we use this to classify different members of the same species o Describe the asymmetry of the outer membrane o Summarize the function of Braun’s lipoprotein o Describe porins and their function o Explain the functions of the outer membrane o List some important functions of the periplasmic space of Gram-negative bacteria and understand the difference between the periplasm of Gram-negative and Gram-positive bacteria o Describe S layers including their composition, their distribution in bacteria (do all bacteria have them?), and their functions o Describe the functions and compositions of capsules and slime layers and the major difference between them o Describe pili, including their composition and some different functions they can have. o Compare and contrast the different parts and structures of the bacterial cell envelope including their functions and their distributions (e.g. always present, present in most bacteria, present in some bacteria) Lecture 2-5: Transport in Bacterial Cells o Understand the permeability of the cytoplasmic membrane to different types of molecules (sizes, chemical composition) o Explain the difference between active and passive transport o Describe facilitated diffusion and its purpose and outline the different types (specific vs. nonspecific) o Define symport and antiport and the energy source typically used to power these systems o Explain the functions of the simple transporter examples given in the lecture - the sodium proton antiporter and the lac permease symporter  o Summarize group translocation and the phosphotransferase system, including the energy source and the modification of the molecule being transported o Explain ABC transporters and how they work. List the components (different types of proteins) of ABC transporters used for nutrient uptake in bacteria and describe the functions of each. o Demonstrate a detailed understanding of the uptake mechanism for vitamin B12 in E. coli including how it crosses both membranes Lecture 2-6: Movement of Bacterial Cells o Understand that while many bacteria are motile, some are not and that motility can be regulated o Define the different terms used to describe the arrangements of flagella on bacterial cells (e.g. peritrichous) o Explain how a flagellum enables a bacterium to move and change direction and how this can vary depending on the arrangement of flagella on the cell o Demonstrate a detailed understanding of the structure and function of the flagellum including its different segments, the functions of the different parts of the basal body, how the filament is constructed, and where the energy comes from that powers the flagellum o List some ways in which flagellar motility can vary between different bacteria o Define chemotaxis, aerotaxis and phototaxis. Describe how “taxis” works in the context of flagellar motility o Describe how a type IV pilus can be used for a different type of motility. Lecture 2-7: Bacterial Cell Inclusions & Endospores o Explain the most common type of carbon storage granules used by prokaryotes including its function and the specific storage molecules used o Summarize other types (other than carbon) of storage granules that have been identified in prokaryotes. What is the function of these granules and what drives the need to evolve the ability to produce these granules o Describe gas vesicles including what they made of and what function they serve  o Explain microcompartments, including what they are made of and how their function differs from storage granules. o Describe the function of endospores, what triggers their production, and which bacteria produce them o Explain adaptations made by endospores that confer their extremely stable and resistant nature o Summarize the basic anatomy of an endospore and the major events in endospore formation Lecture 2-8: Unique Aspects of Archaea Cell Biology o Understand the evolutionary relationships between Archaea, Eukarya and Bacteria. o Demonstrate a detailed understanding of the unique aspects of the cell membranes of Archaea and of their chemical makeup o Describe the diversity that exists in archaea cell walls and contrast this with bacteria o Explain the similarities and differences between peptidoglycan and pseudomurein o Describe the unique hamus produced by certain archaea o Explain the similarities and differences between the flagella used by bacteria and the archaella used by archaea, including their evolutionary relationships to other cell appendages o Explain the importance of the discovery of Asgard archaea and how this relates to the evolution of eukaryotes o Describe where Asgard archaea have been found and understand the recent nature of their discovery/characterization. Lecture 2-9: Eukaryotic Microbial Cells o Demonstrate a basic understanding of the functions of the major organelles found within eukaryotic cells including the nucleus, the mitochondria, the Golgi complex and the Endoplasmic Reticulum and an awareness of the other compartments (e.g. vacuoles) discussed in this lecture. o Compare and contrast the cells of Saccharomyces cerevisiae (a model eukaryotic microbe) and Escherichia coli (a model prokaryotic microbe) o Explain what is meant by LECA and some presumed features of this organism o Describe (broadly speaking) the distribution of some key eukaryotic microbes (e.g. green algae, or yeast) in the different branches of the Eukarya domain and how closely they are related to major branches of “non-microbes” such as animals or plants. o Explain what is meant by a “secondary endosymbiosis” in the context of photosynthetic eukaryotic microbes o Explain what the term “algae” means, the different types of algae & some real world applications of microbial algae. o Summarize some major features of microbial fungi and how these organisms are relevant to our society o Describe the major distinctive features of an amoeba. o Understand the terms “protist”, “protozoa”, “plankton” and “parasite” and how they can relate to eukaryotic microbes  Learning objectives for topic 3 - Genomes, Genetics & Genomics Lecture 3-1: Microbial Genomes o Demonstrate a firm command of the basics of nucleic acid structures and terms (e.g. nucleotides, thymine, purine, etc). o Summarize the basic structure and organization of a prokaryotic chromosome and how this compares to eukaryotes o Summarize the composition of a typical prokaryotic genome with respect genes & non- coding regions o Describe the typical genome size range for prokaryotes and explain which types of prokaryotes have atypically large or small genomes and the types of genes that are present in higher or lower proportions those species. o Define the “core genome” and the “pan genome” of a given lineage and understand how to apply those terms. o Describe genomic islands/islets and prophages and how they can influence genome content and an organism’s phenotypic traits. o Describe plasmids and their basic properties Lecture 3-2: Prokaryotic Genetics - in nature o Demonstrate a firm command of key genetics terms, such as: mutant, mutation, genotype, wild-type, etc. o Describe how the genome of a bacterium can change intrinsically (ie, without horizontal gene transfer) and demonstrate a working understanding of the natural mutation rate of a prokaryote o Summarize the different ways foreign DNA can get into a prokaryotic cell, and the different fates for that DNA (degraded, replicating separately, enter genome) once it is taken up o Define the genetics terms “transformation” and “competence”. Describe how naturally competent bacteria can take up DNA from their environment o Demonstrate an understanding of the basics of phage infections of bacterial cells, including the lytic and lysogenic pathways  o Explain generalized and specialized transduction and how these processes can result in DNA from one cell being transferred to another cell. o Explain the basics of how conjugation works using the F plasmid example discussed in class, including some key elements involved in this process (conjugative pilus, Type IV secretion system) o Describe the basic concept of homologous recombination and understand its potential to lead to the incorporation of foreign DNA into a genome if that DNA carries similar or identical sequences o Explain the basics of what transposable elements are and how they work o Describe the possible outcomes of acquiring foreign DNA via horizontal gene transfer. Lecture 3-3: Prokaryotic Genetics - in the lab o Demonstrate a firm command of the conventions for naming prokaryotic genes and proteins and be able to apply this knowledge. o Demonstrate a firm command of the basic premise of “genetics” as an approach to study biology, as well as the process of using genetics to study a particular aspect of biology o Summarize the different ways that genetic diversity (mutants) can be generated for use genetic studies. o Explain genetics approaches that tie viability to a phenotype (i.e. selection), and why this can be such a powerful approach. o Explain why replica plating would be used in genetics, and how this works. o Explain how Tn-seq (INseq) works, and describe the advantages of this technology as a means to study which gene(s) contribute to a particular phenotype Lecture 3-4: Genomics o Summarize the changes in accessibility and scale of DNA sequencing over the past ~25 years and the impact this has had on the availability of genomic DNA sequences o Explain how Sanger DNA sequencing works o Summarize how modern Illumina massively-parallel (next generation) DNA sequencing works o Summarize some of the types of information that can be gleaned from analyzing the genomic DNA sequences of microbes o Describe metagenomics and some of the ways it can be applied o Explain what is meant by “RNA-seq”, how it works, and how it can be applied o Summarize some of the ways that proteomics can be used to study microbial biology  Learning objectives for topic 4 - Gene expression & Regulation Lecture 4-1: Transcription o Understand what transcription is and its essential role in how genes are expressed o Explain the role the sigma factor subunit of RNA polymerase and how it achieves this function o Understand how the housekeeping sigma factor recognizes promoters, including the terms for the DNA sequences it binds (e.g. -35 region) o Demonstrate an understanding of the fact that bacteria produce multiple specialized sigma factors in addition to the “housekeeping” version, and that they recognize different promoter sequences and control the expression of different types of genes o Understand and apply the terms “upstream” and “downstream”, as well as the numbering convention at bacterial promoters (+1 site, how to number other residues based on this) o Describe the makeup of RNA polymerase (subunits) and how it carries out the process of transcription in bacteria o Explain the process of transcriptional elongation in bacteria o Summarize the major ways in which transcription is terminated in bacteria, including the basics of the underlying mechanisms o Describe the different “types” of RNAs (e.g. rRNA), and the general structure of a bacterial mRNA, including the 5’ and 3’ untranslated regions and what sequence elements can reside in those parts of a transcript. o Summarize the major differences between bacterial transcription and eukaryotic transcription o Summarize how transcription in Archaea relates to transcription in the other two domains of life Lecture 4-2: Translation o Describe the composition and structures of proteins o Summarize the different groupings of amino acids (different types of chemical properties)  o Explain the differences between primary, secondary, tertiary and quaternary structure of proteins o Demonstrate a clear understanding of the basic structure and function of tRNAs and how they translate nucleic acid sequences using the genetic code o List the major start and stop codons o Describe the structure and composition of the prokaryotic ribosome and the role of rRNA in ribosome function o Explain how translation is initiated in bacteria including the role of the ribosome binding site as well as where the RBS is found within the mRNA o Summarize the different steps in the process of translation, including the different tRNA binding sites. Explain how tRNAs, mRNAs and growing polypeptides are processed through the ribosome. o Explain what is meant by “polysome” and “transcriptional/translational coupling” o Summarize the major differences between how translation works in prokaryotes and eukaryotes o Describe the function(s) of chaperones and their importance to all cells o Demonstrate an understanding of the importance of the translocation of proteins to difference compartments o Summarize how the two different branches of the Sec secretion system work. Lecture 4-3: Transcriptional regulation o Understand the basic premise behind why regulation of gene expression/activity is essential. o Describe some general features of DNA-binding regulatory proteins o With respect to gene regulation, explain what is meant by activator, repressor, inducer and co-repressor o Explain how the ArgR and Lac operon regulatory systems work o Explain what signalling molecules (second messengers) are and how they are used. Provide examples of specific signalling molecules used in bacteria  o Describe what is meant by quorum sensing, how it works, and what types of behaviours it typically regulates o Explain how two-component regulatory systems work o In a big-picture sense, summarize how Archaeal gene regulation relates to that of bacteria and eukaryotes. Lecture 4-4: Post-transcriptional regulation o Summarize the different “levels” at which regulation occurs, from DNA through protein levels/activity o List the major ways in which gene expression is regulated at the level of RNA and describe the major RNA structures involved in (some of) these processes o Explain what is meant by RNA lifetime and what factors control RNA lifetime o Describe small regulatory RNAs (sRNAs) and the different mechanisms by which they generally control gene expression o Summarize the function of Hfq in sRNA-mediated regulation of gene expression o Define what is meant by the term “riboswitch” and describe how riboswitches differ from sRNAs o Explain the mechanisms by which riboswitches regulate gene expression including what is common to all riboswitch-mediated regulation and what differs depending upon the individual riboswitch o Summarize why riboswitches are of evolutionary interest and what role they might have played in the early stages of (pre-)life o Summarize different ways that regulation can occur at the protein level o Understand the importance of proteases, both their housekeeping functions and their regulatory functions  Learning objectives for topic 5 - Energetics & Metabolism Lecture 5-1: Enzymes o Explain the important role that enzymes play in dictating what chemical reactions take place in the cell & why many energetically favourable reactions do not occur at an appreciable rate in the absence of enzymes o Demonstrate a clear understanding of what enzymes do - their effects on activation energies & reaction rate and the features of a reaction that they do not change (e.g. DG) o Describe the mechanisms by which enzymes lower the activation energy of a reaction o Understand that cofactors/prosthetic groups can add functionality to enzymes o Explain competitive inhibition, allosteric inhibition and allosteric activation - how they work and how they differ from one another o Describe how feedback inhibition works and how it can be used to help ensure efficient use of the cell’s resources Lecture 5-2: Energetics & Redox Reactions o Explain (at the big picture level) the importance of microbial metabolism for life on our planet. o List and describe the requirements for all life from a metabolism perspective. o Explain the need for nutrients, describe some nutrients (building blocks) needed for all life, and understand that different microbes will require different nutrients depending on their metabolic capabilities. o Describe ATP’s central role in the metabolism of all life o Be aware of other high energy bonds in microbial cells (such as in PEP) and that this energy can be used in a similar manner as ATP hydrolysis for some processes. o Explain the terms: metabolism, anabolism, catabolism, phototroph, chemotroph, chemoorganotroph, chemolithotroph, autotroph and heterotroph o Describe how Gibbs free energy applies to a chemical reaction and explain the difference between the standard Gibbs free energy (DGo’) and the actual free energy (DG) for a reaction o Understand the connection between the concentration of substrates and products and the actual free energy (DG) for a chemical reaction. o Demonstrate a basic understanding of the relative electronegativity of some key atoms commonly found in organic molecules (H, C, N, O) o Describe the concept of a “redox reaction” and what a “half reaction” is. o Understand the difference between an electron donor and an electron acceptor and what it means to be oxidized or reduced in a redox reaction. o Demonstrate an understanding of the redox reaction that was used as an example through the lecture (glucose oxidized using O2 as an electron acceptor) o Explain why oxygen (O2) is such a good electron acceptor and why O2 provides a significant metabolic advantage for aerobic microbes when O2 is available. o Describe the redox tower, how it can be used, and what reduction potential (Eo’) values signify. Understand which combinations of redox couples on a redox tower will release more or less free energy. o Explain how electron carrier molecules such as NAD+/NADH work, and their roles in facilitating redox reactions in cells and serving as an intermediate for capturing energy using redox reactions.  Learning objectives for topic 5 - Energetics & Metabolism Lecture 5-1: Enzymes o Explain the important role that enzymes play in dictating what chemical reactions take place in the cell & why many energetically favourable reactions do not occur at an appreciable rate in the absence of enzymes o Demonstrate a clear understanding of what enzymes do - their effects on activation energies & reaction rate and the features of a reaction that they do not change (e.g. DG) o Describe the mechanisms by which enzymes lower the activation energy of a reaction o Understand that cofactors/prosthetic groups can add functionality to enzymes o Explain competitive inhibition, allosteric inhibition and allosteric activation - how they work and how they differ from one another o Describe how feedback inhibition works and how it can be used to help ensure efficient use of the cell’s resources Lecture 5-2: Energetics & Redox Reactions o Explain (at the big picture level) the importance of microbial metabolism for life on our planet. o List and describe the requirements for all life from a metabolism perspective. o Explain the need for nutrients, describe some nutrients (building blocks) needed for all life, and understand that different microbes will require different nutrients depending on their metabolic capabilities. o Describe ATP’s central role in the metabolism of all life o Be aware of other high energy bonds in microbial cells (such as in PEP) and that this energy can be used in a similar manner as ATP hydrolysis for some processes. o Explain the terms: metabolism, anabolism, catabolism, phototroph, chemotroph, chemoorganotroph, chemolithotroph, autotroph and heterotroph o Describe how Gibbs free energy applies to a chemical reaction and explain the difference between the standard Gibbs free energy (DGo’) and the actual free energy (DG) for a reaction  o Understand the connection between the concentration of substrates and products and the actual free energy (DG) for a chemical reaction. o Demonstrate a basic understanding of the relative electronegativity of some key atoms commonly found in organic molecules (H, C, N, O) o Describe the concept of a “redox reaction” and what a “half reaction” is. o Understand the difference between an electron donor and an electron acceptor and what it means to be oxidized or reduced in a redox reaction. o Demonstrate an understanding of the redox reaction that was used as an example through the lecture (glucose oxidized using O2 as an electron acceptor) o Explain why oxygen (O2) is such a good electron acceptor and why O2 provides a significant metabolic advantage for aerobic microbes when O2 is available. o Describe the redox tower, how it can be used, and what reduction potential (Eo’) values signify. Understand which combinations of redox couples on a redox tower will release more or less free energy. o Explain how electron carrier molecules such as NAD+/NADH work, and their roles in facilitating redox reactions in cells and serving as an intermediate for capturing energy using redox reactions. Lecture 5-3: Catabolism in chemoorganotrophs o Explain each of the three terms used to describe how cells can generate ATP and understand the differences (and similarities) between them o Demonstrate an awareness of the multi-step/gradual approach used by biology to release energy from organic molecules o Describe the basic function of glycolysis, the results of glycolysis, and the overall reaction (what goes in/comes out) o Explain how ATP is generated using glycolysis o Explain why glycolysis must be coupled with further metabolism (fermentation, respiration) in order to be sustained as the cell’s source of energy production o Describe the basic function of the citric acid cycle and some key steps emphasized in class (pyruvate to acetyl-CoA, acetyl-CoA + oxaloacetate to citrate). o Describe the results of the citric acid cycle and the overall reaction (what goes in/comes out). o Demonstrate an awareness of the heavily integrated nature of the citric acid cycle to other metabolic pathways - anabolic and catabolic. o Describe the basic function of electron transport chains. Understand the basic mechanisms and principles common to different electron transport chains and how the electron transport chain generates a proton motive force o Describe the major classes of electron carriers summarized in the lecture and some features of these molecules and demonstrate an awareness of their relative reduction potentials o Explain the crucial role that the terminal (external) electron acceptor plays in respiration and why a continuous source of this molecule is required for respiration to continue. Understand that diversity exists in terms of electron acceptors (and donors) used in respiration o Summarize the activity/function of ATP synthase and understand some of its attributes/properties, such as: its wide distribution, where it is localized in the cell, its reversible nature, the approximate numbers of protons required to generate a molecule of ATP o Regarding the process of glycolysis followed by aerobic respiration: describe where the 6 carbons from glucose “go”, the different ways that ATP is generated, the relative contributions of substrate level vs. oxidative phosphorylation o In addition to glucose, describe (in general terms) how some other organic energy sources can be incorporated into aerobic respiration o Describe how E. coli is able to use different electron acceptors for respiration and the consequences of using nitrate instead of oxygen as a terminal electron acceptor o Explain fermentation - its function, and the common principles that apply to different forms of fermentation o For both lactic acid fermentation and ethanol fermentation: describe the reaction that starts at glucose and ends with excreted fermentation products. Demonstrate an awareness of the use of these processes in making food/beverages  o Demonstrate an awareness of the tremendous diversity of fermentation that is conducted by microbes o Compare the energy recovered by cells from the breakdown of organic molecules when using respiration compared to when using fermentation Lecture 5-4: Chemolithotrophs & Phototrophs o Describe the differences and similarities between how chemolithotrophs and chemoorganotrophs get their energy o Explain how H2 can be used to power a cell’s metabolism (ATP and reducing power) using the Ralstonia eutropha example used in this lecture o Demonstrate an awareness of other electron donors commonly used by chemoorganotrophs. Summarize the basic principle of how these molecules are used to provide microbes with ATP and reducing power o Explain photophosphorylation and how it is similar and different from oxidative phosphorylation o Describe chlorophyll and bacteriochlorophylls, their function, their diversity and their basic chemistry (i.e., what class of molecules do they resemble?) o Explain what photosynthetic reaction centers and antenna pigments are o Describe the cyclic anoxygenic phototrophy used by purple bacteria and compare the reduction potentials of different components of this process. o Explain reverse electron transport and why it can be required o Describe the oxygenic phototrophy conducted by cyanobacteria and algae and compare the reduction potentials of different components of this process. Explain what the electron donor and the ultimate electron acceptors are for this process. Lecture 5-5: Biosynthesis o Summarize the Calvin cycle including its function and the first reaction of this cycle and the enzyme that catalyzes it. Describe what goes into/what is generated by this cycle o Explain what is meant by “nitrogen fixation” and summarize the mechanism by which this occurs o Demonstrate an awareness of the important role that glutamate/glutamine as nitrogen donors for the cell’s nitrogen-containing molecules, as well as the role of a- ketoglutarate (from the citric acid cycle) in this process. o Summarize how microbial cells produce their major sugar-containing compounds such as sugar storage molecules (glycogen, starch) and the cell envelope molecules that contain sugar moieties o Explain where the precursors to the cell’s amino acids are derived from o Summarize how fatty acids/lipids are produced by microbial cells and where the precursors to this come from o Summarize how nucleotides are produced by microbial cells and summarize some of the key functions of the pentose phosphate pathway  Learning objectives for topic 6 - Microbial Growth & Growth Control Lecture 6-1: Bacterial Cell Division o Define binary fission and outline the major steps that occur in bacterial cell division o Describe some of the major functions and steps that need to be coordinated to ensure cell division occurs successfully o Explain how it is possible for a bacterium to have a shorter generation time than its chromosomal replication time o Describe the divisome and the function of FtsZ in cell division o Summarize two major mechanisms that ensure the divisome is localized at the midcell o Explain how new cell wall is incorporated during bacterial growth o Explain how rod-shaped bacteria like E. coli maintain their morphology, and the role of the cytoskeletal protein MreB in this process o Identify alternatives to simple binary fission for microbial cell division Lecture 6-2: Culturing Microbes o Demonstrate an understanding of the composition of microbial cells and the fractions of the total cell mass contributed by (i) the different elements and (ii) the major macromolecules o Describe how micronutrients and trace elements can be important for microbial biology o Differentiate between defined and complex growth media o List some growth factors for microbial cells and explain why certain cells might require these factors for growth, while other microbes might not o Define auxotrophy o Explain some factors that go into the decision of which growth medium should be used to culture a microbe of interest o Describe selective media, differential media and enrichment cultures  o Describe the importance of isolating single colonies on agar plates for culturing microbes o Explain syntrophy and why it could result in a microbe that cannot be cultured in the lab o Describe different ways in which microbes are quantified when being studied or cultured including the advantages, drawbacks and limitations of each of these methods. o Explain the difference between a batch culture and a continuous culture o Outline the growth phases often observed during batch culture growth and describe what is occurring at each of these growth phases o Describe generation time and understand the enormous impact it has on how quickly a microbial population expands during exponential growth o Understand the equations “g = t/n” and “Nt = N0 x 2n” and understand they can be used to model microbial growth under exponential growth conditions o Define planktonic growth, sessile growth and biofilm. o Describe how biofilms develop, from the planktonic state through dispersion. Demonstrate an understanding of the developmental complexities of biofilms Lecture 6-3: Environment Effects on Microbial Growth o Demonstrate a clear understanding of the remarkable adaptability of microbes to just about any niche on the planet and the consequences of evolving to excel in an “extreme” environment o Describe the general trend of microbial growth as a function of temperature and what occurs at temperatures significantly above or below an organism’s optimal growth temperature o Define psychrophile, mesophile, thermophile and hyperthermophile and describe some environments where each can be found o Explain some adaptations made by psychophiles and thermophiles/hyperthermophiles to enable them to grow at “extreme” temperatures o Define acidophile and alkaliphile and describe the major challenge these organisms must overcome to live in “extreme” pH environments.  o Demonstrate an awareness of the important role that the pH of stomach acid plays in preventing infections by food-borne pathogens o Describe how the osmolarity of the environment can influence microbial growth/survival, and what is meant by the term halophile. Explain compatible solutes and how they are used by organisms to adapt to higher solute environments o Explain the differences between obligate aerobes, obligate anaerobes, facultative anaerobes, microaerophilic organisms, and aerotolerant organisms. o Explain why oxygen can be toxic to microbes and how aerobic/aerotolerant organisms can overcome this toxicity o Explain the concept of tolerance as it relates to the environmental conditions described in this lecture, and why an organism might evolve such tolerances. Lecture 6-4: Microbial Growth Control o Understand the difference between sterilization and disinfection/decontamination o Define “decimal reduction time” and describe this principle as it relates to reducing microbial contamination using heat. o Using the concept of decimal reduction time, explain why small differences in the temperatures of cooked food can result in very different amounts of bacterial contamination. o Describe the purpose an autoclave and how it achieves this purpose. o Describe pasteurization, how it works and what it does (and doesn’t) do to control microbial growth o Demonstrate an awareness of the use of radiation and filtration to remove microbial contamination and the utility and limitations of these methods o Summarize chemicals that act as sterilants, disinfectants, sanitizers and antiseptics and the types of microbial killing/growth control mechanisms they employ o Explain the difference between agents that are “cidal” (bactericidal), “static” (bacteriostatic), and “lytic” (bacteriolytic). o Explain what an MIC is, how it is usually determined, and describe the plate-based approach that has a similar function. o Summarize some of the early history of antibiotic discovery and the different approaches that led to the identification of penicillin and sulfa drugs. o Summarize the different cellular (bacterial) targets that are exploited by antibiotics currently in use o Describe the mechanism by which penicillin kills bacterial cells o Explain where most clinically-used antibiotics come from o Describe the problem of antibiotic resistance and summarize the different types of mechanisms that can lead to antibiotic resistance o List some factors that contribute to the difficulty of overcoming the major global issue of antibiotic resistance o Explain what is meant by “persister” cells that remain following antibiotic treatments, and the difference between antibiotic resistance and persistence  Learning objectives for topic 7 - Microbial Communities & Interactions Lecture 7-1: Microbial Communities o Explain the difference between an organism’s fundamental niche and its realized niche - what is a (the) major factor the differences between them? o Summarize our current level of understanding of the intricacies of microbial communities o Describe what is meant by “symbiosis” and the list/summarize the different types of symbiotic relationships o Define the term obligate symbiont o Explain what a “lichen” is, and some basic features of their composition and growth o Describe the symbiotic relationship underlying lichen formation including how each organism benefits from the interaction and the type(s) of symbiosis that can be used to describe this relationship o Describe the symbiotic relationship underlying photosynthetic consortia including how each organism benefits from the interaction and the type of symbiosis that can be used to describe this relationship o Demonstrate an awareness of the rich and complex microbial communities that exist in soils as well as the diverse and complex interactions that occur within these environments. Lecture 7-2: Microbial warfare o Be able to list and summarize several different (but related) mechanisms microbes use to inhibit the growth and/or kill neighbouring microbes. o Demonstrate an awareness of the antibiotic production by Streptomyces species and explain when/why they are thought to employ these molecules. Link this information back to the antibiotics lecture (6-4) and how this has benefited humans. o Explain what type VI secretion systems (T6SS) are, how they work, what type of cells they typically target, and how they are used o Describe bacteriocins and explain how they are similar and different from antibiotics and T6SSs. o Demonstrate an awareness of the connections between microbial killing mechanisms and competence in certain bacteria, and the proposed reasons for this o Explain what a “killer yeast” is and the types of organisms they target with their killing mechanisms. o Describe the basic process by which amoebae consume bacteria. o Explain why the virulence of Legionella pneumophila is thought to be a result of its long- term evolutionary relationship with predatory amoebae. o Describe the most important virulence factor of Legionella pneumophila, and how it enables this organism to establish an infection in a human macrophage  Learning objectives for topic 8 - Microbes in Health & Disease Lecture 8-1: The Human Microbiome o Demonstrate an appreciation for the massive numbers of microbes living on/in us, including the approximate human:microbe ratios of cells and genes. o Describe the major ways we are able to study the microbiome and summarize some areas of microbiome science that we currently know quite a bit about, or very little about. o Understand the difference between links (correlations) between the microbiome composition and disease and microbiota constituents that have been demonstrated to cause disease. o Describe when a person’s microbiota develops, how an individual’s microbiota generally compares to the microbiota of other people, and what is meant by the “resilience” of microbiota o List locations on/in the body where there is a vibrant microbiome and other areas that are generally free of microbes o Summarize how the environment and the number of microbes varies in some different components of the GI tract o Explain how mucous membranes help mediate our interactions with the gut microbiota o Demonstrate an awareness of the extent of gut microbiota variability that exists at the phylum level and at the genus level. o List the three phyla in the GI tract that we discussed in class; for each, classify as either aerobic, anaerobic or facultative anaerobic o Explain the role that “primary fermenter” organisms play in the metabolism that takes place with the gut microbiome; cite the phylum described in class that is notoriously good at this type of metabolism. o Justify whether our interactions with our gut microbiome (as a whole) should be viewed as commensal or mutualistic. o Describe what dental plaque is. o Demonstrate an understanding of the changing landscape of the skin microbiome  o Explain why certain individuals might be more prone to get a S. aureus infection if they have an open wound than other individuals. o Explain the important role that Lactobacilli play in the vaginal microbiome o Differentiate between a probiotic and a prebiotic and explain a more drastic alternative to such interventions that can be taken in the event of a C. difficile infection. Lecture 8-2: Microbial Pathogenesis o Explain what a “pathogen” is and what is meant by its “virulence” o Summarize frequency of microbial pathogens compared to non-pathogens - what is this ratio for Archaea? o Define phytopathogen, and demonstrate an awareness of microbial pathogens that target plants. Cite examples of microbial pathogens that have devastated the populations of certain plants. o Explain the difference between an infection and an infectious disease o Define “opportunistic pathogen” o Explain whether inflammation is beneficial, detrimental…or both. o Explain what a mucous membrane is, where they are found, and what role they play in many bacterial infections o Define an invasive infection. Describe a key mechanism used by S. pyogenes to mediate invasion. o Summarize some common types/actions of virulence factors o Summarize some features of adherence of bacterial pathogens and list some structures they use for this purpose and the nature of common host cell targets for adherence. o Describe some different ways that microbial pathogens evade detection by the immune system o Describe, using examples, how extracellular enzymes can be used as virulence factors o Summarize what Type III Secretion Systems (T3SS) are and how they work. o Describe what a bacterial exotoxin (or “toxin”) is and how toxins are involved in some bacterial diseases. o Summarize how S. aureus a-toxin and C. botulinum botulinum toxin work. o Explain what AB-type toxins are; what major features differentiate such toxins from a toxin like a-toxin. o Summarize some major features of the plague including: (i) the organism that caused it and how it was thought to be transmitted, (ii) when the most severe pandemic occurred and its effects on the population, (iii) the different types of disease caused by “plague” and their mortality rates, (iv) where Y. pestis came from (evolutionarily) and some major changes that facilitation its more virulent nature compared to its ancestors, (v) the basic “strategy” underlying Y. pestis pathogenesis, and (vi) be able to list/describe some of Y. pestis’ major virulence factors.