Microbes, Infections and Responses MIIM20002-Practise-questions PDF

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Microbes, Infections and Responses MIIM20002-Practise-questions 2021...

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MIIM Practise questions History 1. What is spontaneous generation and how did Louis Pasteur prove it to be wrong? 2. How did Lazzaro Spallanzani contribute to the spontaneous generation debate? 3. What is the germ theory of disease? 4. What are miasmas? 5. List the 4 humors of the body 6. Explain Koch’s postulates 7. Explain Koch’s molecular postulates. 8. What is the difference between Koch’s postulates and Koch’s molecular postulates? 9. Why are Koch’s postulates not always feasible? Bacterial cells 1. What are the 3 domains of cellular organisms and their rRNA sequence? 2. Define pure culture 3. Define species 4. Define strain 5. What is genotypic and what are some of its methods? 6. What are some features archaea shares with bacteria? 7. What are some differences between archaea and bacteria? 8. Describe the gram stain process 9. The gram stain technique didn’t achieve the outcome that was expected. What could have gone wrong? 10. What is the peptidoglycan cell wall composed of and what is its purpose? 11. What are the differences of the cell envelope between gram + and – strains? 12. What do teichoic acids do and what gram stain contains it? 13. What does LPS do and what gram stain contains it? 14. What are some cell envelope additional layers and how do they differ? 15. How do you determine if bacteria have endospores and when are they released? 16. What is the structure of flagella? 17. What ways can a bacteria have motility? 18. What are the functions of different pili? 19. Explain the process of DNA replication in bacteria 20. How is the peptidoglycan cell wall constructed? 21. What is the function of penicillin binding proteins? 22. Describe the stages in bacteria culture growth Bacterial metabolism 1. What are some requirements that bacteria need to grow? 2. What incubation conditions would need to be considered when growing bacteria? 3. What is the difference between basal media, enriched media and enrichment media? 4. What is an indicator when using horse blood agar? 5. What type of media is MacConkey agar? What does it contain and how can that determine a feature of a bacteria? 6. What is the difference between HBA and chocolate agar? 7. What are reactive oxygen species?

8. What are the differences between microaerophiles and facultative anaerobes/aerobes? 9. How is a biofilm constructed and what are its benefits to bacteria? 10. What happens if antibiotics can’t penetrate the centre of a biofilm? 11. Explain quorum sensing 12. What are siderophores and what are they used for? Parasites 1. What is the difference between definite host and intermediate host? 2. Explain the blood/life cycle of malaria 3. What species causes malaria and what animals can they effect? 4. What ways can you diagnose malaria? 5. Why is anaemia a symptom of malaria? 6. What causes Giardia lamblia and what is the parasites life cycle? 7. How does the parasite for giardia lamblia infect the body? 8. What are the three groups of helminths? 9. How are hookworms transmitted? Fungi 1. What does it mean when a fungi is Saprophytic? 2. How many major groups are there of fungus? 3. What is the difference between moulds and yeasts? 4. What is a aseptate hyphae compared to a septate hyphae? 5. Are spores produced sexually or asexually in yeasts and moulds? 6. How can yeast and moulds reproduce; sexually and asexually? 7. What is mycelium? 8. What does it mean when a fungus shows dimorphic growth? 9. What are 4 reasons fungus can be used for? 10. What fungus can contaminate food? 11. What medicine is mainly used on fungus and what does it target? 12. Name 2 types of fungi species; one which is dimorphic 13. In a dimorphic species, what determines the growth of either a mould or yeast? Gene structure, replication and mutation 1. What molecule differentiates between nucleosides and nucleotides? What do each contain? 2. How are sugar of RNA and DNA linked? 3. What is a replisome? 4. What are the 3 things DNA polymerase requires to function? 5. What is the lagging strand coated with? 6. Explain the process of the replication fork in E.coli 7. What are the 4 sections of a bacterial gene? 8. What do each of the sections involve? 9. What are the 4 evolutionary consideration mutations and what do they do to the protein sequence?

Gene expression and regulation 1. Name at least 3 mechanisms used for global regulation 2. What is the difference between inducible genes and repressible genes? 3. Give an example of an inducible and repressible gene 4. How are riboswitches in translation regulated? Plasmids 1. What are the 3 common replication schemes? 2. Explain the rolling circle scheme 3. What is host range and what is the difference between broad and narrow host range? 4. Define copy number 5. Do small plasmids have high or low copy numbers? 6. What is conjugation? 7. What is the mechanism of a conjugation? 8. Is a recipient cell or donor cell able to be called a transconjugant? 9. What is the difference between a competent and transformant bacterium? 10. Explain the process of PCR 11. Explain the difference between a sticky end and blunt end 12. What does a PCR require? Bacteriophage and transposons 1. What type of infection does virulent phages produce and what is the process? 2. What two types of infections can temperate phages produce? 3. What is the differences between the 2 infection cycles? 4. What is transduction and what are the two types? 5. How is transduction actioned? 6. What is the difference between the 2 types of transduction? 7. What is a transposon? 8. What are the 3 types of transposition and how do they differ? 9. What is horizontal gene transfer? 10. Plasmids, phages and transposons can contribute to HGT. What process do all of these undergo to transfer genes? Microbial genomics and evolution 1. Explain the 3 stages of CAS 2. What are the uses of CAS? 3. What is a read? 4. Explain the Sangar sequencing method 5. What do you need to know about the sequence and what are the downfalls of using it? 6. What are the 3 steps of sequencing a genome? 7. What is read mapping and reference assembly? 8. What is de novo sequencing? 9. What are 4 types of genomics and what do they all specify in?

Hosts 1. What are 3 reasons to transport molecules in cells? 2. What type of transport involves microtubules? 3. Where are proteins synthesised for the PM, endosome/lysosome and secretion? 4. Which side do ER vesicles enter the golgi apparatus? 5. What are motifs/signal sequences and how are they recognised? 6. What are 3 types of motifs? 7. Explain the ER import process 8. What is the difference between COPI and COPII? 9. Explain the motif-KDEL and its role in ER transport 10. What are the differences between KDEL and KKXX motif transport? 11. Explain the membrane fusion transport system 12. What is glycosylation and in what organelle is it used in? 13. In which direction does kinesin and dynein transport by microtubules? 14. How does the poxvirus utilise the cytoskeleton? 15. In what ways is cellular homeostasis regulated? 16. What protein aids in protein maturation? 17. What 3 outcomes undergoes when the ER is stressed? 18. Match the outcome with PERK, IRE1 and ATF6 19. What happens if glycan is presented in the cytosol? 20. What is the general process of cellular quality control? 21. What is the difference between ubiquitin and proteasome? 22. what is polyubiquitylation? 23. What isn’t recycled In autophagy? 24. What is an autophagosome? 25. How is the process autophagy done? 26. How does autophagy play in the immune response? 27. What mechanisms can endocytosis play in? 28. What are the 3 ways external material can enter the cell? 29. Describe the clathrin mediated endocytosis 30. How do viruses enter the cell? 31. Where do lysosomes come from and what are they involved in? Introduction to the immune system 1. Define immunotherapy 2. What can the immune system cause? 3. What molecules can microorganisms express to be seen as non-self by the immune system? 4. What 2 cells are used for both the innate and acquired immunity? 5. What are the 9 cells used for innate immunity? 6. What 5 cells are used for the acquired immunity response and what are they categorised as? 7. What 3 cells are classified as granulocytes? 8. What are the differences between innate and acquired immunity? 9. Explain the physical barriers of the innate immune response 10. What are the 3 proteins used in innate immunity? 11. Explain the difference between a humoral and cellular response?

12. How is the acquired immunity response activated from the innate response? 13. What is an epitope? 14. What does MHC stand for and what are they used for? 15. Match the lymphocyte that is responsible for intracellular protection and the one for extracellular protection 16. What is the function of CD4+ and CD8+ T cells? 17. What lymphoid organs are each of the lymphocytes developed and matured? 18. What is the difference between primary and secondary lymphoid organs for lymphocytes? 19. What are some secondary lymphoid organs? 20. Where are lymphocytes only found 2% in and >50% in? 21. Describe and draw the structure of the lymph node 22. What is the spleen for? 23. How are antigens encountered by lymphocytes? 24. Where does innate and adaptive encounter antigens? Innate immunity 1. List 3 barriers for all mechanical, physical and chemical 2. What are the3 major effecter functions of the innate immune system? 3. What does PAMP and MAMP stand for and what is their purpose? 4. What are the 4 receptors for PAMPs? 5. What is the overall function of TLRs? 6. What are the 3 roles of macrophages? 7. Describe the process of phagocytosis 8. What are opsonins? Name 2. 9. How can opsonisation enhance phagocytosis? 10. What is the difference between antigen presentation and opsonisation? 11. Describe the different functions between cytokines and chemokines 12. Describe the similar functions of cytokines and chemokines 13. What cells can produce cytokines or chemokines? 14. Describe the functions for all 3 granulocytes 15. What chemotaxin triggers the release of neutrophils from the bone marrow? 16. Which granulocytes contribute to allergic responses? 17. What is degranulation and why is it used? 18. Where are mast cells found? 19. What is the role of mast cells? 20. Describe the differences between immature and mature dendritic cells 21. What molecules do activated natural killer cells release to initiate apoptosis? 22. Name the 3 pathways of complement 23. What do the 3 pathways lead to in the complement process? 24. What do each of the outcomes of complement do? 25. What is the difference between opsonisation and complement? Acquired immunity – B cells 1. What does BCR engagement lead to? 2. What functions can antibodies achieve? 3. Describe the 3 phase process of B cells in the bone marrow

4. How and where are receptors generated on B cells? 5. What is the generalised version of colonial selection in lymphocytes? 6. What are the 2 forms of immunoglobin and what are their functions? 7. Describe the immunological structure with a diagram 8. What are the two sub regions for each of the regions? 9. What is the Fc and Fab fragments composed of? 10. What segments make up the light chain and heavy chain? 11. What do each of the segments stand for? 12. Draw a diagram on how the gene rearrangement selection process for both light and heavy chains is completed 13. Why would isotype switching be important and what part of the chain is switched? 14. What are the 5 classes of immunoglobin and their functions? 15. Why is IgM important to be the first antibody produced? 16. What is somatic hypermutation? 17. What are the effector functions of Fab and Fc and the immunoglobin associated with them? Acquired immunity – T cells 1. Describe the process of thymic education 2. Describe the T cell receptors structure with a diagram 3. Which chains have which gene segments? 4. What happens to protein antigens for T cells to be activate? 5. How can T cell recognise short antigenic peptides? 6. What is the difference with binding of an antigen on B cells and T cells? 7. What cells are MHCI and MCHII expressed on and what are their function for the cell? 8. Which T cells recognise which MHC molecule? 9. Where are the peptides derived from on each of the MHC molecules? 10. Describe the process of antigen processing and presentation for both MHC molecules 11. Which cells are antigen presenting cells? 12. Describe the activation process of T cells in secondary lymphoid organs with dendritic cells 13. How are dendritic cells activated? 14. Explain the 3 signals needed for T cell activation from dendritic cells Immunity to infection 1. List 5 functions of CD8 T cells 2. List 4 functions of CD4 T cells 3. Explain the process of how CD8 T cells kill host cells 4. What are the costimulatory molecules used for T cell expression and T cell activation? 5. Name the 5 functions CD4 T cells help for B cells 6. Which 2 cytokines influence isotype switching and what do they switch to? 7. Describe how CD4 helps activate CD8 T cells 8. What is the other method to kill self recognising T cells? 9. What are the 2 types of CD4 T cells and what responses to they undertake? 10. How are the different CD4 T cells initiated?

11. Which CD4 T cell is initiated for bacterial, viral and parasitic infections? 12. How can bacteria and viruses impact the immune cells? 13. Describe the differences between antibody isotype and affinity for primary and secondary responses 14. Fill in the table below Source of B cells PRIMARY RESPONSE

SECONDARY RESPONSE

ISOTYPE AFFINITY MUTATION 15. Fill in the table below Properties of T cells Naïve

Activated

Memory

Previously encountered pathogen Dependent on co-stimulation Access to nonlymphoid tissues Effector function Bacterial pathogenesis 1. Where are invasive microbes found in the body? 2. What makes a microbe a pathogen and give 3 causes? 3. List the 5 obstacles pathogens must overcome 4. List at least 3 physical barriers 5. How does a pathogen colonise with the host? 6. List the 3 ways a pathogen can adhere to host cells and the differences between them 7. What part of the pili mediates adhesion? 8. What type of adhesion does ETEC E.coli use? 9. What are the 2 types of toxins ETEC can produce and what do they do? 10. What are 4 reasons pathogens invade? 11. What are the 2 types of mechanisms pathogens use to invade? 12. Describe the process of each mechanism and provide an example Bacterial invasion 1. How do bacteria evade soluble factors? 2. How do bacteria evade Cytotoxic T cells? 3. What are the three pathways a complement cascade can be facilitated and what are the outcomes?

4. How does C6-9 kill a pathogen? 5. What are the 3 ways opsonisation can occurs? 6. What features do bacteria have to avoid complement fixation? 7. Explain the 5 ways bacteria can avoid detection of antibodies. 8. How is a pathogen killed within a phagocyte and what molecules are involved? 9. Explain the 6 ways a bacteria can evade a phagocyte 10. Name the virulence factors that enhance pathogen spreading 11. What are the 4 in which bacteria can uptake iron from host cells? Bacterial toxins 1. What type of toxin is good to make vaccines and what are toxoids? 2. What does the A and B stand for in AB toxins? 3. What are the 2 types of AB toxins and what is the different between them? 4. What are the 3 types of exotoxins? 5. Explain how the A-B toxins enter a cell 6. Explain how diphtheria toxin enters the cell and how does it affect the cell? 7. Explain how cholera toxin enters the cell and how does it affect the cell? 8. Explain how botulinum toxins prevent acetylcholine from entering the synaptic cleft and what does it cause 9. Explain how tetnus toxin causes spastic paralysis 10. Name the 3 types of membrane disrupting toxins and their mechanism of action 11. How do superantigens cause organ failure and shock? 12. What gram cell envelop is associated with bacterial endotoxin? 13. What are the 3 effects of LPS and what is the toxic component? 14. What does LPS stand for? 15. What can septic shock result in? 16. What indirect damage can be caused? 17. How do bacteria become pathogens and what are they? 18. What is an example of a virulence plasmid and how is it pathogenic? 19. What does the lysogenic bacteria need to be pathogenic? 20. What are pathogenicity islands and what are the 6 definitions? 21. What is EHEC stand for and what does it cause and how? 22. What is the new EHEC recently discovered and what 3 things were learnt from it? Antibiotic control of bacterial infections 1. Describe the history of antimicrobial agents 2. What are the 8 ideal properties of antimicrobials? 3. Explain what the 3 ways for minimum inhibitory concentrations are 4. What do antibiotics target on a bacterium? 5. What does penicillin target and how? 6. what is penicillin not active against? 7. What do all penicillins have? 8. How can bacteria resist penicillin? 9. What antibiotic does streptomyces spp produce? 10. How does the antibiotic inhibit protein synthesis? 11. What are the 4 ways the bacteria can resist the antibiotic? 12. What does chloramphenicol target and how does it do it?

13. What is the resistance mechanism for chloramphenicol? 14. What are the 3 broad mechanisms for inhibiting nucleic acid synthesis? 15. How is folic acid synthesised by bacteria? 16. What do sulfonamides do and what is it? 17. How are sulfonamides resisted? 18. What is the function of quinolones and how is it resisted? 19. What antibiotic targets cytoplasmic membranes and how? 20. Which antibiotics are bactericidal or bacteriostatic? 21. How is R plasmid resistance achieved? Viruses and prions 1. What is the definition of virology? 2. What are the 3 reasons where viruses came from? 3. What are the 7 categories to classify something as living? 4. What are virions? 5. Draw and label a virion structure 6. What criteria is needed to place viruses in their taxonomy? 7. Describe the 4 category components of the virus structure 8. What are the versions of viral nucleic acid? 9. What are the differences between enteric viruses and respiratory viruses? Provide an example for each 10. What are arboviruses and hepatitis viruses? 11. What are the types of hepatis viruses and how do they spread? Viral replication 1. Outline briefly the stages of the virus lifestyle 2. What are some types of receptors for viral attachment? 3. Describe the 3 ways a virus can undergo fusion and endocytosis 4. Explain how HIV fuses with a host membrane 5. How do alphaviruses enter the cell? 6. Where do DNA and RNA viruses replicate? 7. What does DdDp and RdRp stand for? 8. What 3 things RdRps always do/need? 9. What activities can reverse transcriptase do? 10. What is the difference between negative and positive strand viruses in replication? 11. What functions are host dependent and/or virus dependent in translation? 12. What structure does non-enveloped animal viruses have? 13. What are the difference between enveloped and non-enveloped virus assembly and release? 14. Fill in the table below” Stage Entry RNA replication DNA replication Assembly Exit and Maturation

Enzymes/proteins

location

15. List at least 3 effects of animal viruses Viral pathogenesis 1. What are the 3 ways viruses need to be maintained in nature? 2. How does the intestinal tract allow for viruses to attach? 3. What are 2 alimentary tract viruses and how are they acquired? 4. What are 5 other routes viruses can enter? Provide an example for each. 5. What are the 4 mechanism of spread in the body? 6. What does disseminated and systemic infection mean? 7. What are the differences between cell-associated and free in plasma viruses? 8. Describe the movement stages of viraemia 9. Name at least 3 areas/bodily substances in which a virus sheds 10. What is cytocidal virus and what does it cause? 11. What are non-cytocidal virus 12. Explain what happens between SARS-cov-2 and ACE2 13. What’s the difference between immunopathology and immunosuppression? 14. What does cytokine release syndrome increase? 15. What 5 factors determine host resistance and susceptibility? 16. Summarise the 4 outcomes of virus infections 17. Why do diseases reoccur? 18. What are 4 types of viral genetic evolution? 19. Why do some disea...