Learning Objectives Final 2024 PDF

LEARNING OBJECTIVES FINAL Here are the learning objectives for the final exam. Use these to guide your studying. Mastering these learning objectives will help you answer questions that are more applied, but you still need to synthesize and contextualize this knowledge in the best way you can. GENE...

LEARNING OBJECTIVES FINAL Here are the learning objectives for the final exam. Use these to guide your studying. Mastering these learning objectives will help you answer questions that are more applied, but you still need to synthesize and contextualize this knowledge in the best way you can. GENERAL LEARNING OBJECTIVES Apply knowledge to problem-solving, interpretation of data or real-world context. Demonstrate time-management skills by submitting all you work on time. Demonstrate science literacy skills in both reading and writing scientific work. BACTERIA Describe common cell morphologies and cellular arrangements typical of bacterial cells o Identify the main shapes of bacteria o Describe the structure and function of the glycocalyx (capsule/slime layer) o Compare and contrast the cell walls of gram-positive, gram-negative and acid-fast bacteria o Describe the structure, function and biochemistry of the bacterial plasma (cytoplasmic) membrane o Describe the structure, biochemistry and function of the bacterial cytoskeleton in comparison to the eukaryotic cytoskeleton and explain how cells maintain their morphology o Describe the function of the nucleoid and ribosomes o Describe the structure and function of endospores. o Explain the mechanism of sporulation and describe the advantages given to bacteria that can sporulate. o Differentiate flagella, fimbriae, and pili o Describe the different mechanisms used by bacteria for locomotion. Identify structures unique to bacteria ARCHAEA Explain why archaea are considered a separate domain of life Describe internal and external structures of archaeal cells in terms of their physical/chemical structure and function o General shapes and characteristics of archaea o Cell wall structure BIO3124 General Microbiology  o Plasma (cytoplasmic) membrane structure o Archaeal cytoskeleton Identify and describe structures, metabolic pathways unique to archaeal cells Compare the distinguishing characteristics of bacterial, archaeal, and eukaryotic cells. VIRUSES Describe the structures and composition of viruses Differentiate among bacteriophages, plant viruses, and animal viruses Describe the mechanism of lytic and lysogenic life cycles of bacteriophages Describe the several mechanisms of defense bacteria have against viral infections o Genetic resistance o Restriction endonucleases o CRISPR Describe the 3 mechanisms of entry utilized by animal viruses Describe the replication process of animal viruses (what is particular to animal infections) Describe unique characteristics of retroviruses and latent viruses MICROBIAL METABOLISM Describe how nutrients are transported into cells (cell membrane transport systems) Differentiate between catabolism and anabolism Describe the importance of oxidation-reduction reactions in metabolism Compare and contrast the differences between substrate-level and oxidative phosphorylation Describe the roles of ATP, NAD+, and other electron carriers in metabolism and explain why they are so important in a cell Compare and contrast autotrophs and heterotrophs, chemotroph, phototroph, organotroph, lithotroph and organotroph (and combinations of). Distinguish these terms regarding energy source, carbon source, electron source. Explain what the proton-motive force is Describe the function and location of ATP synthase in a prokaryotic versus eukaryotic cell Compare and contrast aerobic and anaerobic respiration (in principle, not metabolic details) Explain what fermentation is and why it does not require oxygen Compare and contrast fermentation and anaerobic respiration (in principle, not metabolic details) MICROBIAL GROWTH Describe the general mechanism of binary fission. Explain the differences between batch culture and continuous culture 2  Describe the different growth phases in a batch culture Differentiate between sessile growth, planktonic growth, biofilms, and cell mats Describe different categories of microbes with temperature requirements for growth: psychrophile, mesophile, thermophile, hyperthermophile, and what is the difficulty encountered when growing in these environments. Describe the molecular adaptations that allows microorganisms to cope and grow in high or low temperatures Describe the different categories of microbes with pH requirements for growth: acidophiles, neutrophiles, and alkaliphiles. Describe different categories of microbes with requirements for growth with or without oxygen: obligate aerobe, obligate anaerobe, facultative anaerobe, aerotolerant anaerobe, microaerophile, and what is the difficulty encountered when growing in these environments. Explain how oxygen can be toxic and how oxygenic organisms cope with ROS. Describe different categories of microbes with specific growth requirements such as altered salinity (halophiles), osmotic pressure (osmophiles) or dry environments (xerophiles) Biofilms Explain what a biofilm is Describe the formation, biochemistry, and characteristics of biofilms in general. Identify health and environmental risks associated with biofilms, what causes these risks and how they can be addressed. MICROBIAL REGULATORY SYSTEMS Quorum sensing Explain what quorum sensing is. Explain the roles and advantages in cell-to-cell communication and coordination of cellular activities through quorum sensing Explain what is an autoinducer Describe molecular mechanisms of quorum sensing in Gram – and Gram + bacteria (use one example for each). Explain what quorum quenching is and why it could benefit us clinically (3 examples) Discuss how what could be drawbacks if any in using quorum quenching techniques for clinical benefits. Spatial organization Explain the role of each of these structural proteins: MreB, FtsZ, Crescentin and FilP. Explain what cell polarity is Regulatory systems Describe the difference between negative and positive gene regulation in prokaryotes Compare and contrast differences and similarities in the transcriptional control mechanisms between bacteria and eukarya. 3  Describe the structure of an operon and the general mechanisms by which operons are regulated (keep it general) Describe what is a two-component system. Explain how a two-component system functions (mechanism) using an example. Describe how chemotaxis is regulated in E. coli with Che proteins when presented with the name of each protein. (If asked to describe the regulatory process, I would provide at minimum the name of the proteins in play or most likely, a schematic representation of the signal transduction that is NOT the one you have seen in your slides) Apply your understanding of regulatory mechanisms in bacteria. For example, this means I could present you with a completely new regulatory pathway and ask you questions on that pathway that would demonstrate you can transfer knowledge from a general conceptual understanding of regulatory mechanisms to a new situation. Explain what the stringent response is and what is its purpose. Describe one example of a stringent responses due to environmental conditions. Describe what is a general global network response Explain what a regulon is. Explain what a stress-response is and what is its purpose. Explain the concepts of persistence and dormancy in resistant bacteria Describe the mechanism of persistence using the Toxin-Antitoxin module system MICROBIAL GENETICS AND GENOMICS Discuss the benefits and trade-off of sexual vs asexual reproduction Explain what vertical transmission and horizontal (or lateral) transmission of genetic material are Explain in detail each of these processes (mechanism): transformation, transduction, and conjugation (ie, no need for any more details than what we have seen) Distinguish between generalized and specialized transduction. Discuss the consequences for bacterial genetic diversity of each of these processes (mechanism): transformation, transduction, and conjugation. Describe the notions of pan genome and core genome Explain what chromosomal islands are and describe why we think they are of foreign origin Discuss how microorganisms have evolved such a huge diversity of organisms using the processes we have seen in class MICROBIAL SYMBIOSIS WITH HUMANS Discuss, in a general way, what we know of the diversity and dynamics of microbial populations in humans so far. Explain what is dysbiosis. 4  Describe the different microbial microhabitat in the oral cavity and airways, the characteristic of the microbiota present and what mechanisms the oral cavity and airways have to clear or contain the microorganisms present. Names of microorganisms are not necessary. Describe the different microbial microhabitat in the urogenital tract, the characteristic of the microbiota present and what mechanisms it uses to clear or contain the microorganisms present. Names of microorganisms are not necessary. Describe the different microbial microhabitat in the skin, the general characteristics of the microbiota present. Names of microorganisms are not necessary. Describe how the microbiota of any ecological niche on the human body can both protect against pathogenesis and at times participate in diseases. Explain what needs to happen for an infectious or opportunistic agent to cause disease. Explain the role and utility of the commensal bacteria in our gut. Describe the microbial microhabitat in the gastro-intestinal tract and the interactions between the commensal microbiota and the GI tract (GI tract tissues and immune system underlying the GI tract) Describe the many roles of the gut microbiota in healthy individuals Describe the composition of the commensal flora in the GI tract and how it may change through time or under various selective pressures (bottle fed infant vs breast-fed infant, meat diet vs complex fiber diet, age, physiology, etc.…) GUT MICROBIOTA AND DISEASE Name factors that can potentially strengthen a healthy gut microbiota and factors that may participate or influence the development of dysbiosis. Explain how the factors named above may act on the symbiosis or dysbiosis of the gut microbiota. Describe how pathogens can cause dysbiosis and disease. Describes what conditions must be met for inflammation to occur in the gut. Describes what links the gut microbiota to energy metabolism and obesity. Discuss the limitation of mouse models to study the role of the gut microbiota in health and disease. Describe at least one experiment showing the gut microbiota can influence metabolic disorders. Explain how the microbiota might influence obesity, emphasizing the suspected systemic role of SCFA, the presence of Archaea and the role of dietary fibers. Distinguish between probiotics and prebiotics, discuss their limitations. Note: I have deliberately omitted the gut-brain axis and IBD. HOST-PATHOGEN RESPONSES Describe what conditions need to be met for an infection and/or disease to occur (in humans or animals) 5  Describe the cell structures or biochemical armoury that microorganisms can deploy to infect us (virulence factors) and explain the mechanisms with which they can cause disease: o For adhering to cells and tissues (adhesins, capsule, fimbriae, pili, and flagella) o For invading cells and tissues (enzymes, cytolytic exotoxins) o For helping their growth and toxicity (virulence plasmid, exotoxins, endotoxins, anti- phagocytic proteins, immune inhibitors, T3SS and effector proteins, …) Distinguish between the terms: infection, bacteremia, and septicemia. Explain what virulence means. Explain what LD50 and ID50 are. Distinguish between the terms cytotoxin, endotoxin, exotoxin, hemotoxin. Describe the virulence mechanisms of the following toxins and their effect at the cellular, tissue or systemic levels when appropriate: o Diphtheria toxin o Botulinum and Tetanus toxins o Cholera toxin o Cytolytic toxins (hemolysins and Staph alpha-toxin o Endotoxins Note: I have deliberately omitted the secretion systems, but you should recognise they are of importance, especially the T3SS, that’s all. 6