MMG301 Learning Objectives Unit 2 v3 - Microbiology Course

### **Course Learning Objectives** Students that successfully complete this course will be able to: - Apply the central dogma of molecular biology to the molecular processes of bacteria and viruses. - Explain why bacteria have been ideal models for determining the fundamental processe...

### **Course Learning Objectives** Students that successfully complete this course will be able to: - Apply the central dogma of molecular biology to the molecular processes of bacteria and viruses. - Explain why bacteria have been ideal models for determining the fundamental processes of life. - Recognize broad similarities and significant differences between active processes in eukaryotic cells and bacterial cells. - Relate the survival and growth of bacteria in a specific environment to metabolic, genetic, and physiological (i.e. cell structure) characteristics unique to specific bacteria. - Predict how cellular structures and processes of bacteria are altered by mutations, horizontal gene transfer, antimicrobials, and host immune response. - Explain the beneficial, neutral, or detrimental interactions that bacteria and viruses have with the environment or their hosts. - Predict how diseases and symptoms arise due to the molecular interactions between pathogenic bacteria or virus and their hosts. - Explain how viral replication is related to the unique structures and genomes of that virus. - Predict how viral replication is altered by mutations, host immune response, or antivirals. - Discuss why viruses are parasitic nucleic acid. - Form a hypothesis and predict the results of experiments using concepts from microbiology and molecular biology. - Analyze and interpret the results from a variety of microbiological techniques to construct an explanation or develop a model for phenomenon in microbiology. - Plan an investigation to solve a scientific question in microbiology. - Use the [Claim-Evidence-Reasoning](#_Claim-Evidence-Reasoning_structure) structure to form and defend conclusions drawn from experimental data or primary literature. - Practice the collaborative nature of the scientific process and practices through participation in direct peer-peer and instructor-peer interactions during recitation. - Develop the [soft skills](https://www.forbes.com/advisor/business/soft-skills-examples/) needed for a career in science and medicine and for the student to effectively contribute to their team\'s success. Unit 2 ====== - **Microbial Growth Control: Radiation, Non-chemotherapeutic antimicrobials** - Using heat to reduce or kill microbe - Describe Pasteurization and explain the two methods it is applied - Explain the decimal reduction time and be able to interpret a survival semi-log graph - Control of growth by UV/ionizing radiat - Provide examples of biological damage caused by ionizing radiation and UV light - Provide examples of the most appropriate use of UV or ionizing radiation - Sterilization of gasses and liquids by filtration - Distinguish the types of filters that are most commonly used to remove microbes from gasses and liquids - Explain the advantages and disadvantages of the two most commonly used personal protective filtration devices - Non-therapeutic chemical antimicrobial agents - Using semi-log graphs of viable cell number, total cell number vs time, plot the effects of the three types of chemical antimicrobial agents (static, cidal, lytic) based on their effect on microbial growth - Briefly state the purpose and uses of sterilizers, disinfectants, antiseptics, and sanitizers - Describe the factors that influence effectiveness of antimicrobial agents, and what types of microbes are most and least resistant - **Microbial Genomics** ---------------------- - Information storage and retrieval - Explain what a genome is - What parts of information flow are performed by storage, retrieval, and execution functions - DNA sequencing of genomes - Explain why you would use a targeted versus a whole genome sequencing approach. - Order the steps of a genome sequencing project from small fragment sequences to annotation - Describe the features of a sequence that are used to detect an ORF​ - Genome evolution - Briefly explain why microbes that live as parasites have smaller genomes than microbes that are free-living - Describe what can a genome sequences reveal about uncultured organisms - Briefly explain why microbes that live as parasites have smaller genomes than microbes that are free-living - Comparative genomics - Describe comparative genomics and how it is useful - Distinguish a pan genome from a core genome - **Regulation of Metabolic Pathways** - Review of the central dogma steps - Explain the "central dogma" of biology - Describe coupled transcription/translation in prokaryotes - Distinguish rho-dependent and rho-independent termination of transcription - Regulation of transcription initiation - Explain regulation of transcription by negative control with a repressor protein using the arg operon, and lac operon as examples, including all required proteins and DNA regulatory regions - Describe why regulation of transcription is beneficial to an organism - Describe the roles of the activator protein and DNA regulatory regions involved in transcriptional regulation of the maltose operon - Catabolite repression - Create a circuit diagram that shows catabolite repression and how cAMP, CRP, lac repressor, and lactose control transcription of the lac operon - Provide details about how diauxic growth is observed when E. coli are grown with lactose and glucose - Distinguish small RNAs and riboswitches: how does each control translation of mRNA? - Describe how allosteric regulation of enzyme activity works and this typically is used in multi-step biochemical pathway - **Bacterial Genetics 1: Mutations and Repair** - Introduction and types of mutations - Differentiate between genotype vs. phenotype, and spontaneous vs. induced mutations. - Correlate each of the 3 types of base pair substitutions with their effect on the resulting protein - Explain the different ways that a frameshift mutation affects the resulting protein. - Explain what reversions are and how a second site insertion/deletion mutation can correct a frame shift mutation. - Mutagens and DNA repair - Explain what mutagens are and describe the three main types of chemical mutagens. - Describe the main ways that UV and ionizing radiation damage DNA (see table on slide 10) - **Bacterial Genetics: Horizontal Gene Transfer and Homologous Recombination** - Horizontal gene transfer and homologous recombination - Use the central dogma of molecular biology to explain how horizontal gene transfer can lead to phenotypic changes in bacteria. - Explain the roles of the following biomolecules and structures in homologous recommendation: nicked DNA, RecA, SSB, donor DNA, recipient DNA, Holliday junction. - Use experimental data to determine the step or biomolecule in homologous recommendation that was altered by mutation. - Explain why homologous recombination is necessary for most horizontal gene transfer event to be heritable to daughter cells. - Phage (virus) replication cycles - Describe the general replication cycle of phage T4. - Distinguish the lytic and lysogenic paths that an *E. coli* cell can take after it is infected with bacteriophage lambda. - Create a diagram the steps after induction of a prophage and ending in cell lysis. - Transformation - Use experimental data to determine the step in transformation that was altered by mutation.  - Transduction - Contrast the steps of horizontal gene transfer in generalized and specialized transduction. - Use experimental data to differentiate between generalized and specialized transduction. - Plasmids - List the important general characteristics of plasmids. - Explain the features of a conjugative plasmid, including the structure and function of a pilus. - Conjugation - Differentiate between F- cells, F+ cells, and Hfr cells. - Explain the role of homologous recombination in the formation of a Hfr cell from a F+ cell. - Use experimental data to determine the biomolecule or step in the formation of a Hfr cell from an F+ cell that was altered by mutation. - Draw a diagram that illustrates the differences in the transfer of an F plasmid to a recipient cell when the F plasmid is integrated in the chromosome of the donor cell with a F plasmid that is free of the donor cell's chromosome. - **Evolution and Phylogeny of Prokaryotes** - Molecular phylogeny - Provide examples of how molecular sequences are used to determine phylogenetic relationships of organisms. - Describe what molecules are most commonly used for phylogenetic studies, and how these can be used as a "molecular clock" to measure evolution. - Phylogenetic trees - Explain the domains of the phylogenetic tree of life and how they were determined. - In general terms, describe how phylogenetic trees are constructed starting with a set of similar sequences from different organisms. - Explain the interpretation of branch length, nodes, clades, and evolutionary time in a phylogenetic tree - **Microbial Ecology: Ecology Concepts and Methods** - Habitats and niches - Differentiate between a niche and a microenvironment. - Be able to briefly describe each of the biotic factors that define a niche. - General concepts of microbial ecology - Distinguish populations, guilds, communities, habitats, and ecosystem - Describe how is a freshwater lake an example of a microbial ecosystem and explain what the energy inputs. - Explain the difference between species richness and species abundance. - Culture-independent methods of community analysis - Explain what culture-independent methods are and the examples shown in the module; what are the two types of culture-independent analysis that can be done without using DNA sequencing. - Explain what viability staining is and how it can be useful for studying microbial communities. - Order the steps for the basic method of Fluorescence *In Situ* Hybridization and explain what the method is used for. - Analysis of Community Diversity Using Sequences - Describe how PCR of single genes can be used for analysis of microbial community diversity. - Distinguish how DNA sequences are analyzed by the community sampling or the environmental genomics approaches and explain what information each approach provides. - Provide examples of the types of information that can be determined by sequencing all of the genomes in a microbial community. - Define the human microbiome. - Discuss the human microbiome project, including its goals and the major method used - **Beneficial host microbe interactions: Plant** - Soil Microbiology - Describe the O, A, B, and C horizons in a mature vertical soil profile. - Describe the types of conditions found in the various microenvironments within soil aggregates. - Explain why microbial fermentation products are found in the interior of soil aggregates. - Trace the carbon involved in rhizodeposition, starting with atmospheric CO~2~ and ending with nutrients in soil around roots. - Legume Plant-Microbe N~2~-Fixing Symbiosis - List some common legume plants. Explain the advantage of these plants having symbiotic nitrogen-fixing bacteria. - Explain how chemical communication is used to establish symbiosis between nitrogen-fixing bacteria and plants. - Describe the steps in formation of a root nodule, starting with bacteria in the soil and ending with nodule formation. - Explain the source of energy for nitrogen fixation, and the role of leghemoglobin in this process - **Beneficial host microbe interactions: Animal** - - - - - - - - - - - - - - - - - - - - - - - - - - -