Blatant Biology: Questions

Microbiology 2

These are questions related to the module microbiology 2

• Explain the role of nucleoid-associated proteins (NAPs) in organizing bacterial DNA. How do different NAPs contribute to gene regulation in bacteria?
• Discuss the importance of efficiency and flexibility in prokaryotes for their survival in competitive environments. Provide examples to support your explanation.
• Describe the process of supercoiling in bacterial DNA and its impact on gene expression. How do topoisomerases regulate supercoiling in bacteria?
• Examine the significance of operons in bacterial gene regulation. How do operons contribute to the efficiency of transcription in prokaryotes?
• Discuss the role of sigma factors in bacterial gene regulation and how they allow for the transcription of different sets of genes. Provide examples of different sigma factors and their specific functions.
• Explain the regulatory mechanisms involved in the transition from σ70 to σ38 in bacterial gene regulation. How do anti-sigma factors like Rsd and HscC play a role in this transition?
• Describe the function of σ32 in controlling heat-shock response genes in bacteria. How does the secondary protein structure change at higher temperatures, and what are the consequences for the cell?
• Explore the significance of the sigma factor cascade involving σ28 in ensuring the correct assembly of flagella in bacteria. How does this cascade maintain the temporal control of gene expression?
• Discuss the significance of two-component systems in bacterial gene regulation, emphasizing their role in responding to changing environments. Provide examples to support your explanation.
• Explain the structural components and activation process of histidine kinases in two-component systems. How does this activation lead to changes in bacterial cell physiology? Provide a detailed description with examples.
• Explore the evolutionary aspects of two-component systems in bacteria, detailing how gene duplication events and mutations have led to the formation of diverse TCS. Provide examples to illustrate the evolutionary process of TCS in bacteria.
• Discuss the significance of riboswitches in gene expression regulation and tRNA function. How do riboswitches interact with small molecules to induce changes in protein expression?
• Explain the concept of attenuation in RNA riboswitches. How does the antitermination conformation allow for transcription to occur?
• Describe the mechanism of action of t-box riboswitches in sensing uncharged tRNAs. How do t-box riboswitches control the expression of enzymes for amino acid synthesis?
• Explain the concept of RNA thermometers and their role in modulating protein expression levels. Provide examples of conditions that trigger changes in RNA secondary structures.
• Discuss how phase variation allows bacteria to evade immune responses by changing the antigens they present. Provide examples of mechanisms used by bacteria for phase variation.
• Explain the role of slip-strand mispairing in phase variation. How does slip-strand mispairing differ from epigenetic control of gene expression?
• Discuss the significance of glycolysis in cellular respiration, highlighting its occurrence in almost all cells and its net synthesis of NADH and ATP. Why is glycolysis considered an ancient process?
• Explain the role of the link reaction in aerobic respiration, detailing the conversion of pyruvate to acetyl coenzyme A and the production of NADH. How does the link reaction connect glycolysis to the Krebs cycle?
• Compare and contrast the ATP synthesis processes in glycolysis, the Krebs cycle, and oxidative phosphorylation. How do these processes collectively contribute to the overall ATP yield in aerobic respiration?
• Evaluate the role of Ndh and Cyd in the bacterial electron transport chain during aerobic respiration. Why are these complexes essential for pathogenesis, and how could they be targeted for antimicrobial drug development?
• Explain the metabolic flexibility of E. coli in aerobic conditions, emphasizing the role of Ndh and Cyd in respiration. How does the presence of these complexes enhance the survival and infection chances of pathogenic bacteria?
• Discuss the significance of using alternative electron acceptors and donors in anaerobic respiration compared to aerobic respiration, focusing on the metabolic versatility of E. coli.
• Explain the significance of fermentation in the absence of aerobic and anaerobic respiration. How does the use of endogenous organic molecules impact ATP synthesis?
• Discuss the role of Zymomonas mobilis in alcohol fermentation. How does its ethanol tolerance compare to yeast? Explain the potential applications of engineering Z. mobilis for bioethanol synthesis.
• Discuss the acetone-butanol-ethanol (ABE) fermentation process in Clostridium species. How does this pathway contribute to biofuel synthesis, and how can genetic engineering optimize product yields?
• Discuss the differences between batch, continuous, and fed-batch fermentation methods in industrial microbiology. How do these methods impact bacterial growth and product synthesis?
• Explain the concept of metabolic engineering in bacterial product synthesis. How can metabolic engineering techniques be utilized to enhance product yield and quality?
• Describe the properties that industrial microbes should possess for efficient product synthesis. How do these properties contribute to successful industrial fermentation processes?
• Explore the process of enhancing yields in industrial bacterial product synthesis. Discuss the various approaches, such as mutation and selection, metabolic engineering, and optimization of fermentation conditions.
• Discuss the significance of cyanobacteria in the evolution of photosynthesis and the impact of the great oxygenic event on Earth. How do cyanobacteria contribute to global carbon fixation?
• Explain the role of carboxysomes in cyanobacteria and how they enhance CO2 fixation efficiency. How could introducing carboxysomes to plant chloroplasts potentially improve crop yields?
• Describe the process of FaRLiP in cyanobacteria and its adaptation to far-red light. How does the synthesis of chlorophyll d and f in response to far-red light enhance the organism's competitiveness?
• Explore the concept of heterocysts in cyanobacteria, detailing their differentiation process and role in nitrogen fixation. How do heterocysts create a microoxic environment and facilitate the exchange of nutrients within the filamentous cyanobacteria?
• Analyse the potential of cyanobacteria in biotechnology, highlighting their advantages as a chassis organism and their ability to synthesize various products. What are the current limitations in commercializing cyanobacterial products compared to traditional organisms like E. coli and yeasts?
• Discuss the application of bio-photovoltaics using cyanobacteria to convert light into electricity. How does the process of transferring electrons from the photosynthesis electron transport chain to an electrode work, and what are the challenges in scaling up this technology for practical use?
• Discuss the importance of bacterial differentiation in stress survival and its implications on the formation of spores and other dormant states.
• Explain the role of Myxococcus xanthus as a model organism in studying bacterial differentiation, highlighting its unique genetic features and social behaviour.
• Explore the concept of kin recognition in Myxococcus and how the expression of TraA alleles influences outer membrane protein exchange and the formation of fruiting bodies.
• Discuss the roles of ppGpp production and A-signalling in Myxococcus during stress responses and starvation, highlighting their effects on protein expression and metabolism.
• Discuss the significance of cyanobacteria in global nitrogen fixation and their impact on ocean ecosystems. How can the control of mass blooms potentially benefit agriculture?
• Explain the motility mechanisms of cyanobacteria, including the role of pili and nozzles in different species. How do filamentous cyanobacteria move without flagella?
• Explore the genetic regulation of heterocyst formation in cyanobacteria. How do NtcA and HetR play key roles in the development of heterocysts?
• Analyse the production of cyanotoxins and cyanobactins by certain cyanobacteria species. How can these compounds be potentially utilized in pharmaceutical applications?
• Discuss the advantages of forming resting bacterial spores and how they increase resistance to physical and chemical stressors.
• Explain the process of endospore formation in Bacillus subtilis, detailing the key steps involved in spore development and release.
• Compare and contrast the spore formation mechanisms in Bacillus and Myxococcus, highlighting the differences in cell types and genetic screening challenges.
• Describe the role of dipicolonic acid (DPA) in stabilizing bacterial spores, including its interactions with DNA and water molecules.
• Explore the significance of sigma factors in spore formation, focusing on their roles in regulating gene expression during different stages of spore development.
• Analyse the unique characteristics of glycerol spores in Myxococcus, comparing their resistance levels to traditional fruiting body spores and explaining the structural differences.
• Discuss the role of virulence factors in bacterial pathogenesis, providing examples of different types of virulence factors and their effects on the host. How do these factors contribute to the distinction between symptomatic and asymptomatic carriage?
• Explain Koch's postulates and their significance in identifying the causative agent of a disease. Discuss situations where these postulates may not be applicable in determining the pathogen responsible for a disease.
• Describe the differences between strict (professional) pathogens and opportunistic pathogens, highlighting their unique characteristics and modes of transmission. Provide examples to illustrate these distinctions.
• Explore the concept of facultative pathogens and their adaptability to different lifestyles. How does the flexibility of facultative pathogens impact their pathogenicity compared to other types of pathogens?
• Discuss the challenges associated with culturing certain pathogens in the lab and how this limitation affects the study of infectious diseases. Provide examples of pathogens that are difficult to culture and explain the implications of this difficulty on research and treatment strategies.
• Discuss the limitations of using LD50 and ID50 as measures of pathogenicity, especially in comparing different strains of pathogens. How do these measures reflect the severity of infection inaccurately?
• Explain the concept of virulence factors in bacteria and how they contribute to pathogenicity. Provide examples of virulence factors and their roles in causing disease.
• Why is it important for bacteria to be invasive in order to cause disease? Discuss the factors that contribute to a bacteria's invasiveness and ability to damage the host.
• Describe the significance of studying pathogenesis in the development of antibiotics and therapeutics. How can anti-virulence factor therapeutics be utilized in treating bacterial infections?
• Compare and contrast the use of animal models, cell lines, and organoids in studying pathogenesis. Discuss the ethical, practical, and cost considerations associated with each method.
• Compare and contrast targeted mutagenesis methods with random mutagenesis methods in studying virulence factors. How do these methods help in understanding the function of specific genes in pathogens?
• Describe the process of nutrient acquisition by bacteria as a virulence factor. How do siderophores and iron-binding proteins contribute to bacterial survival and pathogenicity?
• Discuss the significance of adhesins, fimbriae, and pili in bacterial virulence. How do these structures facilitate bacterial adherence to host tissues and surfaces?
• Discuss the significance of having 2 copies of the chromosome in myxospore formation and how it aids in faster germination.
• Explain the different methods of bacterial cell division, focusing on synchronous septation and vivipary.
• Describe the role of OPG (osmoregulated periplasmic glucans) in protecting spores during sporulation and how it differs from endospores.
• Compare and contrast the sizer mechanism and adder mechanism in controlling cell division, providing examples of organisms where each mechanism is observed.
• Analyse the DNA replication initiation process in bacterial cell division, detailing the role of DnaA, hemi-methylated DNA, and the eclipse period.
• Investigate the mechanisms that control the rate of DNA replication in bacterial cells, including the influence of RNR, primase, and nutritional status.
• Explain the differences between antiseptics, disinfectants, and antibiotics in terms of their applications and toxicity levels. Discuss the requirements for an effective antibiotic, including selective toxicity and pharmacokinetics.
• Explain the mechanisms of antibiotic resistance, focusing on innate and acquired resistance types. Provide examples of each type and discuss their implications in healthcare settings.
• Discuss the economic impact of antibiotic resistance on the global economy by 2050, considering the projected 10 million deaths annually. How can this issue be addressed?
• Explore the role of prophylactic antibiotic use in agriculture in contributing to antibiotic resistance. How does this practice impact human health and what measures can be taken to mitigate its effects?
• Analyse the various causes of antibiotic resistance, including over-prescription, misuse by patients, and agricultural practices. How can healthcare professionals and policymakers collaborate to combat this global issue?
• Describe the different ways bacteria develop resistance to antibiotics, such as efflux mechanisms and inactivation of drugs. Provide examples of specific enzymes involved in resistance and discuss their significance in the context of antibiotic efficacy.
• Discuss the current challenges posed by multi-drug resistant bacteria like MRSA and VRSA. How do these strains develop resistance, and what strategies can be implemented to prevent their spread in healthcare settings?
• Discuss the differences between innate and adaptive immunity, highlighting their specificities and response times. How do these two systems work together in defending the body against pathogens?
• Explain the role of phagocytes in the innate immune response. How do neutrophils and macrophages contribute to combating infections? Provide examples of infections where phagocytes play a crucial role.
• Explore the activation pathways of the complement system in response to pathogens. How do the classical, alternative, and lectin pathways contribute to pathogen killing and inflammatory responses?
• Analyse the significance of barriers in the innate immune system, focusing on the role of epithelial cells, skin, and mucosal surfaces. How do these barriers prevent pathogen entry and infection? Provide examples of infections that breach these barriers.
• Describe the mechanisms of action of defensins in the innate immune system. How do these peptides disrupt bacterial membranes and aid in controlling infections? Provide examples of infections where defensins are particularly effective.
• Discuss the role of fever in the innate immune response. How does fever help in combating infections and activating the immune system? What are the underlying mechanisms of fever induction?
• Discuss the role of pattern recognition receptors (PRRs) in innate immunity and how they contribute to the immune response. Provide examples of microbe-associated molecular patterns (MAMPs) and their significance in pathogen recognition.
• Explain the process of phagocytosis in killing pathogens. Describe the formation of phagolysosomes and the role of bactericidal agents in destroying pathogens.
• Describe the function of natural killer (NK) cells in recognizing and killing infected cells. Discuss the role of MHC I in inhibiting NK cell killing and how cancerous cells evade this mechanism.
• Compare and contrast humoral immunity by B cells and cell-mediated immunity by T cells in adaptive immunity. Explain the process of antigen recognition and the differentiation of B and T lymphocytes.
• Discuss the significance of cytokines in regulating immune cell behaviour. Provide examples of different groups of cytokines and their effects on the immune response.
• Explain the concept of clonal selection in adaptive immunity. Describe the role of memory cells in mounting a faster and stronger immune response upon subsequent exposure to the same pathogen.
• Explain the role of Pattern Recognition Receptors (PRRs) in the innate immune system and how they contribute to the recognition of pathogens. Provide examples of microbe-associated molecular patterns (MAMPs) recognized by PRRs.
• Discuss the importance of antibodies in extracellular bacterial infections and intracellular pathogens, highlighting their role in antigen recognition and elimination. Provide examples to support your explanation.
• Explain the process of class switching in antibody synthesis and its significance in the immune response. How does class switching enhance the flexibility of the immune system? Provide a detailed explanation with relevant examples.
• Discuss the process of affinity maturation in antibody production, explaining how B cells increase the affinity of antibodies for antigens. How does affinity maturation contribute to the effectiveness of the immune response? Provide examples to support your explanation.
• Discuss the role of T Helper cells in the immune response, including their interactions with B cells, macrophages, and NK cells. How do they contribute to the development of T Cytotoxic cells?
• Discuss the significance of regulatory T cells in immune regulation, including their synthesis of IL-10 and TGF-beta. How do these cells contribute to preventing autoimmune responses and downregulating inflammation?
• Explain the process of cytotoxic T cell activation and their role in inducing apoptosis in infected target cells. How do viruses evade cytotoxic T cell responses, and what implications does this have for the immune system?
• Discuss the historical significance of variolation and its impact on the development of vaccines. How did Lady Montagu contribute to popularizing this method in Europe?
• Explain the concept of herd immunity and its importance in preventing the spread of diseases. Provide examples of diseases where herd immunity plays a crucial role.
• Compare and contrast the mechanisms of action of attenuated, killed pathogen, and subunit vaccines. Analyse the advantages and disadvantages of each type of vaccine.
• Describe the process of attenuating live vaccines and the potential risks associated with them. How do attenuated live vaccines differ from killed vaccines in terms of immune response stimulation?
• Discuss the factors contributing to the increase in sexually transmitted infections (STIs) cases, including the impact of 'the pill' and online dating apps. How can these trends be addressed?
• Explain the mechanisms of transmission and symptoms of gonorrhoea in males and females. How can asymptomatic cases lead to severe complications?
• Compare and contrast the virulence factors of Neisseria gonorrhoeae and the strategies it employs to evade the immune response. How does this contribute to antibiotic resistance?
• Describe the challenges in treating multi-drug resistant gonorrhoea and the potential implications of untreatable infections. What strategies can be implemented to combat this issue?
• Analyse the symptoms and long-term effects of syphilis infection, including the neurological manifestations and the concept of 'sleeper cells'. How does the unique biology of Treponema pallidum contribute to its pathogenicity?
• Discuss the significance of screening programs for Chlamydia trachomatis, considering the asymptomatic nature of the infection in many individuals. What are the challenges in treating Chlamydia due to its unique characteristics?
• Discuss the factors contributing to the re-emergence of pathogens in the context of globalisation and urbanisation.
• Explain how natural disasters and decreased public health measures can lead to the spread of infectious diseases, using specific examples.
• Describe the mechanisms of antibiotic resistance in pathogens and how it impacts their spread, with relevant examples.
• Explore the role of zoonotic transfer in the emergence of new pathogens, providing instances where this has occurred.
• Analyse the pathogenesis of Helicobacter pylori infections, detailing its unique properties and the mechanisms it employs to cause disease.
• Discuss the significance of Legionnaire's disease as an emerging infection, including its origins, transmission, and control measures.
• Discuss the importance of rapid changes in gene expression for bacteria living in highly competitive environments. Provide examples of environmental changes that would require rapid gene regulation.
• Explain the role of nucleoid-associated proteins (NAPs) in organizing and condensing bacterial DNA. How does this organization contribute to bacterial gene regulation?
• Describe the process of supercoiling in bacterial DNA and its impact on transcription. Discuss the role of topoisomerases in regulating supercoiling and the potential consequences of antibiotic resistance.
• Compare and contrast Rho-dependent and Rho-independent transcription termination mechanisms in bacteria. Discuss the significance of these mechanisms in regulating gene expression.
• Discuss the structure and function of RNA polymerase in bacterial transcription. Explain the role of sigma factors in initiating transcription and the formation of closed and open complexes.
• Explain the concept of operons in bacterial gene regulation and their significance in coordinating the expression of multiple genes. Provide examples of operons and their role in bacterial adaptation.
• Briefly discuss the organisation of the E. coli chromosome.
• Briefly discuss the functions of sigma factors in E. coli.
• Briefly discuss the roles of accessory proteins in the operation of two-component systems.
• Write brief notes on how a T-box riboswitch works.
• Discuss the diversity of gene regulatory mechanisms involving changes in the secondary structure of the 5’ untranslated regions of mRNA.
• Briefly discuss how RNA thermometers work.
• What is the purpose of phase variation?
• How does continuous culture differ to batch culture? Explain what is meant by a fed-batch culture and why this is often the preferred growth setup in industrial fermentations.
• Give some examples of products produced by microorganisms and the microbes that produce them.
• What properties make a microorganism well suited to use in commercial applications. 
• What is metabolic engineering? List some general ways that product yield can be enhanced using metabolic engineering approaches.
• Explain how allosteric feedback inhibition can be overcome with anti-metabolites using LysC as an example.
• Explain how lysine production in Corynebacterium glutamicum was improved by: (a) branchpoint engineering; (b) optimising cofactor supply; and (c) increasing product efflux.
• Describe the cyanobacterial carbon concentrating mechanism.
• What is the FaRLiP response? How does this benefit some species of cyanobacteria?
• Describe the role of heterocysts in filamentous cyanobacteria.
• What are the characteristics of a good antibiotic?
• Why are antiseptics and disinfectants not be used as antibiotics?
• How do beta-lactam antibiotics work?
• What is the origin of antibiotic resistance?
• What are the main sources of antibiotic resistance in the Western World?
• What methods can be employed to reduce the misuse of antibiotics?