Microbiology Final Exam

Robert Koch used a set of postulates to demonstrate that a specific disease was caused by a specific causative agent (i.e, microbe). Which of the following describe Koch's postulates (Select all that apply, incorrect answers will be penalized)?

- All diseased individuals must have the microbe and all healthy individuals must not., The microbe must be isolated and grown outside of the host., The microbe must be introduced into healthy individuals, which should then develop the disease., When healthy individuals become diseased due to experimental introduction of the microbe, the microbe isolated from these experimentally diseased individuals should be the same as the microbe originally isolated from diseased, but not healthy, individuals.

Which of the following are advantages of inflammation (select all that apply, incorrect answers will be penalized)?

- Allows access of cells and antimicrobial peptides to infected tissue, - Activates phagocytes, - Activates the adaptive immune system and phagocytes

Shown above is the result of a Diffusion Susceptibility Test/ Kirby Bauer Test using Mueller-Hinton agar to test the potential effect of a number of different antibiotics on the bacteria Pseudoaltermonas haloplanktis. Three antibiotic disk results are labeled, A, B, and C above. Based on the above results, you can infer that Pseudoaltermonas haloplanktis is resistant to the antibiotic in the disk(s) labelled:

A

Gram-positive bacteria have a cell wall containing ________ layer of peptidoglycan, whereas gram-negative bacteria have a cell wall containing ________ layer of peptidoglycan.

a thick, a thin to no

According to most biologists, viruses are not considered to be alive because viruses (select all that apply, incorrect answers will be penalized)

- lack the ability to grow and reproduce independently, - cannot respond to the environment or metabolize on their own, - do not have a functional cytoplasmic membrane

When electrons are transferred from an electron donor to an electron acceptor this is referred to as

A redox reaction

Glycocalyces (capsules) and/or slime layers can be useful to microbes for

All of the Above - protection against drying out - additional protection from the environment - evasion of the immune system

Animal viruses can enter host cells via a number of mechanisms. Match each mechanisms of animal viral entry with its appropriate description.

An animal viral capsid containing a viral genome enters a host cell through fusion of the animal viral envelope and a host cell cytoplasmic membrane → Membrane fusion, An animal viral genome, but not its capsid enters through host endomembrane proteins or receptors in the cytoplasmic membrane → Direct penetration, A host cell membrane folds and engulfs and animal virion → Endocytosis

Anaerobic and aerobic respiration utilize [NADH and FADH2] from [the Kreb's/Citric Acid Cycle] to transfer electrons to membrane bound carriers in [the Electron Transport Chain (ETC)], which generates [a H+/proton gradient] harnessed by ATP synthase to make energy in the form of ATP in many microorganisms.

Anaerobic and aerobic respiration utilize [NADH and FADH2] from [the Kreb's/Citric Acid Cycle] to transfer electrons to membrane bound carriers in [the Electron Transport Chain (ETC)], which generates [a H+/proton gradient] harnessed by ATP synthase to make energy in the form of ATP in many microorganisms.

Match each of the following types of chemical reactions to its appropriate description.

Catabolic/Decomposition Reactions → break bonds in large complex molecules into smaller products generally releasing energy, Exchange/Transfer Reactions → involve breaking and reforming chemical bonds often involving anabolic and catabolic steps, Anabolic/Synthesis Reactions → form larger complex molecules usually requiring energy

Several studies have recently shown that coating hospital surfaces with copper can reduce hospital acquired infections. Copper-responsive genes in Mycobacterium tuberculosis are under negative control wherein a repressor protein, (CsoR) binds to the DNA when copper is low/absent. When copper is present, CsoR changes shape and no longer binds DNA. Using this information and the diagram above, answer the following questions: a) In a low copper environment, describe the likely positions for RNA polymerase (RNAP), copper, and the copper-specific repressor (CsoR). Be specific. (3 pts.) b) Is transcription more likely to occur in a low or high copper environment? (1 pt.) c) Why is gene regulation in operons beneficial to bacteria? (1 pt.)

Comment: a) RNAP will bind to the promoter, but will not be able to proceed because CsoR will bind to the operator, which will block the progress of RNAP (no transcription). Copper is low/absent and does not bind to DNA. Copper and CsoR are not co-repressors, so they will not bind together to the operator. b) Correct, transcription is more likely to occur in a high copper environment when copper binds to the CsoR so that it can not bind to the operator to repress transcription. This makes sense because transcription of copper-response genes should only occur when copper is present. c) Why is gene regulation in operons beneficial to bacteria? (1 pt.) Proteins are able to be synthesized more easily and they are also able to respond to different changes within their environment

Klebsiella pneumonia are gram-negative bacteria. a) What is one feature of gram-negative bacteria absent from gram-positive bacteria? (1 pt.) b) What component of the cell wall is common to gram-positive and gram-negative bacteria, and what are the two monomers (building blocks shown above) of this component? (2 pts.) c) A patient infected with the gram-negative bacteria Klebsiella pneumonia is treated with the correct antibiotic. After treatment, the bacteria are no longer present in the blood stream, but the patient's symptoms of fever and inflammation have worsened. Explain why the condition worsened by the treatment. (2 pts.)

Comment: a) Outer membrane and lipopolysaccharides. b) Correct, peptidoglycan. NAG and NAM are the monomers that are shown above that make up peptidoglycan. c) Gram-negative bacteria contain lipopolysaccharides in the outer membrane. When gram-negative bacteria are killed in the bloodstream, these lipopolysaccharides, some of which contain lipid A, can be released in the bloodstream. Lipid A causes fever and inflammation and can ultimately lead to sepsis and death.

You have isolated a few promising antibiotic drug candidates in a screen for antibiotic killing and have started testing dosages in mice. Shown above are the therapeutic index results for two different candidate drugs (A and B). Which drug is more likely to cause severe side effects in patients during treatment?

Compound/drug A

In bacteria, the enzyme that facilitates DNA replication by removing supercoiling by cutting the DNA, rotating the cut ends in the direction opposite of supercoiling, and then rejoining the cut ends is

DNA gyrase

The correct order of steps of binary fission from start to finish is:

DNA replication, cell elongation, septum forms, daughter cells form

Ebola virus is a negative-sense, single-stranded RNA virus with an envelope. It does not encode or carry reverse transcriptase. Based on this information,

Ebolavirus must carry a viral RNA-dependent RNA polymerase within its capsid to replicate

Match each of the bacterial cell structures with its appropriate description.

Endospore → environmentally resistant structure produced in a vegetative cell, Nucleoid → region of a bacterial cell where the bacterial chromosome(s) is/are located, Cytoplasm → jelly-like aqueous substance inside a cell, Inclusions → reserve deposits that can contain fats, lipids, starches, or gases

A research group thinks they have discovered a pathogenic microbe, but they have been unsuccessful in growing it. One method the group could successfully use to identify this microbe is phage typing.

False

High oxygen levels are detrimental to obligate aerobes because these organisms lack enzymes, such as catalase, that are needed to remove highly reactive oxygen forms that are toxic.

False

Low temperatures make microbial membranes flexible and more fluid.

False

One major difference between prokaryotic and eukaryotic microbial gene expression is that transcription and translation can occur concurrently in the nucleus of eukaryotes.

False

Physical mutagens, such as UV light, as well as chemical mutagens, such as base analogs, decrease the rate of mutation occurring in the protein of the microbial cell.

False

Specific to prokaryotes, endocytosis and exocytosis are passive transport processes used for metabolism.

False

The DNA of bacterial chromosomes is wound around histone proteins and packed into chromatin in the nucleus, whereas the DNA of eukaryotes is packed by DNA binding proteins into a region called the nucleoid.

False

The bacterial cytoplasmic membrane is made of peptidoglycan surrounded by an outer membrane.

False

When hydrogen ions move through a channel in the bacterial cytoplasmic membrane without the use of energy, this is an example of group translocation.

False

Antibodies are immunoglobulin proteins that recognize epitopes of antigens. The class of antibodies that makes up 80% of all of our body's antibodies and is responsible for resistance against bacteria, toxins, and viruses is

IgG

The final electron acceptor in anaerobic respiration of microorganisms is

an inorganic molecule

One name for an enzyme that joins molecules together, often with the use of ATP, is

Polymerase

Bacterial growth refers to an increase in population size rather than the size of an individual bacterial cell.

True

A method that quantifies microbial growth by plating a series of dilutions on agar plates and counting the number of colonies post-incubation is

Serial dilution and viable plate counts

Severe combined immunodeficiency (SCID) is a general term for inherited defects in the immune system that prevent the cell from responding effectively to viruses, bacteria and fungi. Patients with SCID are highly susceptible to disease. One mutation associated with SCID is a loss of the RAG1 recombinase gene. RAG1 is responsible for the recombination of V, D and J genomic segments in the genomes of B and T cells. Briefly explain why loss of RAG1 recombination would cause severe immunodeficiency. (3 pts.)

Severe combined immunodeficiency (SCID) is a general term for inherited defects in the immune system that prevent the cell from responding effectively to viruses, bacteria and fungi. Patients with SCID are highly susceptible to disease. One mutation associated with SCID is a loss of the RAG1 recombinase gene. RAG1 is responsible for the recombination of V, D and J genomic segments in the genomes of B and T cells. Briefly explain why loss of RAG1 recombination would cause severe immunodeficiency. (3 pts.) The loss of RAG1 recombination would not allow the correct B and T cells to be created and associated with fighting infection and viruses. They would be unable to create an immune response to these antigens and would cause severe immunodeficiency There is some good thinking here, I am unsure what you mean by "correct B and T cells" here, as this is a random process. A connection that needs to be made here is that this recombination is what generates the antigen-binding sites of BCRs and TCRs of B and T cells, respectively, that is essential for the function of these cells. RAG recombinase is essential for generating diverse and functional BCRs of B cells and TCRs of T cells. The antigen-binding region of the BCR of each B cell and TCR of each T is unique because of this random recombination process. Without this enzyme, there would be no adaptive immune response without these diverse antigen-binding sites and adaptive immune cells. Individuals with a loss of this enzyme would only have innate immune responses for defense against pathogens.

During transcriptional initiation bacteria, the protein that must bind to the promoter region of DNA to facilitate binding and activity of RNA polymerase is

Sigma factor

Many microbes require specific environmental conditions for growth. Match each description with its appropriate term.

The correct answer is: Require environments with a pH near that of the human body → Neutrophiles, Reside in high salt environments and withstand high osmotic pressure → Halophiles, Are found in solutions/conditions with low H+ concentrations → Alkalinophiles, Live deep below the earth's surface and withstand extreme atmospheric pressure → Barophiles, Are found in solutions/conditions with high H+ concentrations → Acidophiles

When a competent cell takes up foreign DNA from the environment, this process is called

Transformation

Translation is the process by which ribosomespolymerases use the genetic information of RNA to synthesize DNARNAproteins . In this process, triplets of mRNA nucleotides called anticodonscodonsamino acids bind to triplets of nucleotides called anticodonscodonsamino acids in transfer RNAs (tRNAs), which carry anticodonscodonsamino acids that are then linked in peptide bonds.

Translation is the process by which [ribosomes] use the genetic information of RNA to synthesize [proteins]. In this process, triplets of mRNA nucleotides called [codons] bind to triplets of nucleotides called [anticodons] in transfer RNAs (tRNAs), which carry [amino acids] that are then linked in peptide bonds.

After Louis Pasteur boiled a nutrient infusion in a swan-necked flask, no growth (cloudiness) was observed for up to 18 months. However, if the neck of the flask was broken or tilted, then growth was observed.

True

An antiseptic uses chemicals, heat, or radiation to inhibit or destroy pathogens on human skin or tissues, whereas a disinfectant uses these on inanimate surfaces.

True

DNA sequencing of ribosomal RNA sequences was undertaken by Carl Woese and others to determine evolutionary relationships between microorganisms because morphological and biochemical analyses were insufficient.

True

Glycolysis is part of aerobic respiration, fermentation, and anaerobic respiration.

True

Hami are specialized structures with a barbed end that are unique to archaea.

True

Jane Hinton made a major contribution to the field of microbiology by developing Mueller-Hinton agar, which can be used to determine susceptibility of bacteria to antibacterial agents.

True

Lipids are hydrophobic and contain nonpolar bonds.

True

Many antibiotic drugs have been phased out due to antibiotic resistance, which is an important public health concern.

True

Peptidoglycan is a strong mesh like complex of polysaccharides and peptides that is held together by strong covalent bonds.

True

Plant cells have mitochondria and chloroplasts, which each contain DNA separate from nuclear DNA.

True

Research on viral diseases such as Ebola is limited because of the difficulty of working with viruses in the lab and the potential biosafety issues of working with dangerous viruses that cause a high death rate.

True

Stimulated by pyrogens, fever is an increase in body temperature that may inhibit pathogens directly or help stimulate immune responses.

True

Viruses are not considered alive by most biologists because viruses are acellular and lack the ability to grow, reproduce, and metabolize on their own (i.e., without a host).

True

The step immediately following the third step of endospore formation where the spore septum surrounds the isolated portion to form the forespore, which has two membranes is:

a layer of peptidoglycan forms between membranes

The endosymbiotic theory suggests that an early eukaryote obtained chloroplasts by phagocytosis of

a photosynthetic bacterium

Human noroviruses are highly contagious viruses that cause vomiting and diarrhea and can be spread by human contact or by humans into food, which has happened at popular food chains like Arby's and Chipotle. a) Briefly describe the process of how an endogenous norovirus antigen, such as part of a noroviral protein, would be presented as an antigen on the surface of a human intestinal cell infected with norovirus. Be sure to specify whether this would be MHC I or MHC II presentation. (2 pts.) b) Cytotoxic CD8 T cells (TC) play a major role in clearance of norovirus infections. How would a cytotoxic T cell recognize an intestinal cell infected with norovirus? Briefly describe the recognition mechanism and one mechanism by which the cytotoxic T cell induces apoptosis in the infected cell. (3 pts.) c) For Cytotoxic CD8 T cells (TC) to be activated and for memory T cells to be produced, Helper CD4 T cells (Th) are involved. What do the activated Helper CD4 T cells (Th) secrete to activate Cytotoxic CD8 T cells (TC) and the production of memory T cells? (1 pt.) d) Noroviruses have a high rate of mutation. Because of these higher mutation rates over time, norovirus undergoes significant changes in its surface proteins (antigens). How would changing surface antigens allow a norovirus to infect individuals even if they have established immunity to a prior version of the norovirus? (2 pts.) e) Imagine researchers are able to develop a successful vaccine against norovirus, and you vaccinate a patient against norovirus. If your patient's body encounters norovirus in the future, briefly describe one way that the patient's antibodies could function to provide protection against norovirus infection. (2 pts.)

a) Briefly describe the process of how an endogenous norovirus antigen, such as part of a noroviral protein, would be presented as an antigen on the surface of a human intestinal cell infected with norovirus. Be sure to specify whether this would be MHC I or MHC II presentation. (2 pts.) It would be presented as an antigen through the TCRs. They are able to recognize certain antigens, and then are brought to the MHC 1 class cells surface. MHC 1 are presented to the cytotoxic T cells. MHC 2 presentation is presented to the helper T cells b) Cytotoxic CD8 T cells (TC) play a major role in clearance of norovirus infections. How would a cytotoxic T cell recognize an intestinal cell infected with norovirus? Briefly describe the recognition mechanism and one mechanism by which the cytotoxic T cell induces apoptosis in the infected cell. (3 pts.) It recognizes these by their TCRs that are able to recognize a specified antigen. Their antigens are young to MHC 1 molecules and then go to that cells surface, then they are recognized c) For Cytotoxic CD8 T cells (TC) to be activated and for memory T cells to be produced, Helper CD4 T cells (Th) are involved. What do the activated Helper CD4 T cells (Th) secrete to activate Cytotoxic CD8 T cells (TC) and the production of memory T cells? (1 pt.) The activated helper CD4 T cells secrete cytokines to be able to activate CD8 T cells and the production of memory T cells d) Noroviruses have a high rate of mutation. Because of these higher mutation rates over time, norovirus undergoes significant changes in its surface proteins (antigens). How would changing surface antigens allow a norovirus to infect individuals even if they have established immunity to a prior version of the norovirus? (2 pts.) The changing surface antigens would not be able to detect the previous version of the norovirus because they would be unable to recognize the prior norovirus. The changing surface antigen was not in the previous detection of the prior norovirus, so it would be unable to have the ability to fight that norovirus the same way the prior surface antigen e) Imagine researchers are able to develop a successful vaccine against norovirus, and you vaccinate a patient against norovirus. If your patient's body encounters norovirus in the future, briefly describe one way that the patient's antibodies could function to provide protection against norovirus infection. (2 pts.) The patient's antibodies could function to provide protection against norovirus infection by being able to recognize that same type of norovirus and eliminate it with the antibodies that are already created to defeat that certain norovirus. a) You are correct that this is MHC I presentation. How are MHC I antigens presented? A human intestinal cell that is infected with norovirus would be presenting antigens from norovirus on MHC class I molecules on its surface. This process of MHC class I presentation starts with degradation of a Noroviral protein, for example, by the protease activity of the proteasome. The resulting Noroviral antigens (Noroviral peptides) are imported into the ER by the TAP complex. MHC class I molecules in the ER membrane recognize and bind a specific Noroviral antigen. ER vesicles containing these MHC I-viral antigen complexes bud off from the ER and then fuse with the Golgi, and then bud off from the Golgi and fuse with the cytoplasmic membrane where the MHC class I present the viral antigen at the cell surface. b) You are correct that TCRs of a cytotoxic CD8+ T cell recognize a noroviral antigen presented by a MHC I molecule on the surface of a virally infected cell. How is this immunological synapse stabilized? What does the cytotoxic CD8+ T cell do after this recognition? The T cell receptors (TCRs) of a cytotoxic CD8+ T cell recognize their specific Noroviral antigen presented by an MHC class I molecule on the surface of a Norovirus-infected intestinal cell. The cytotoxic CD8+ T cells recognizes this MHC class I molecule using the CD8 protein, which stabilizes this immunological synapse. After this recognition of the Norovirus-infected intestinal cell, the cytotoxic CD8+ T cell can induce apoptosis by signaling through the CD95/death receptor that activates apoptotic enzymes within the virally infected cell or by secreting perforin to make a pore in the virally infected cell and granzyme, which enters the cell to trigger apoptosis of the virally infected cell. c) Correct, cytokines, such as interleukins, are signals secreted by Helper CD4 T cells that activate cytotoxic CD8 T cells and the production of memory T cells. d) You are thinking in the right direction here. Key adaptive immune system components that would no longer recognize this virus and be activated are the memory B and memory T cells, so a faster, more effective adaptive immune response by memory cells will not be triggered, so the individual will not be protected against Noroviral infection. Interestingly, because noroviruses can change surface antigens readily, this is one reason that researchers have not been able to design a vaccine to this virus. e) Vaccination that triggers a strong immune response will trigger the production of memory T and memory B cells. Memory B cells will secrete antibodies that will then act against this virus. Antibodies can act in a number of possible ways to provide protection, which is what the question is asking here. Antibodies binding to the surface of a virus can prevent the virus from attaching to host cells, this is called neutralization. Antibodies binding to the virus can be recognized by receptors of phagocytic cells and phagocytosed, this process is known as opsonization. Antibodies binding to the virus could also lead to destruction of the virus by free oxygen radicals (oxidation) or lead to clumping of virions (agglutination), which can allow easier detection and destruction of virions. Antibodies binding to MHC I presented viral antigens on infected cells could also be killed by natural killer cells as part of ADCC.

Escherichia coli bacteria are found in biofilms. a) Besides flagella, what is one structure that E. coli bacteria might possess that would aid in attachment to surfaces or in associations with other bacteria? (1 pt.) b) After attachment, what are the other steps of biofilm formation? (2 pts.) c) Interestingly, E. coli cannot form endospores. How might associating in a biofilm be useful for E. coli? (1 pt.) d) Suppose you are a clinical microbiologist studying human gastrointestinal biofilms that contain E. coli. You isolate a population of bacteria from a healthy patient that has a unique colony morphology and an orange color. You perform biochemical tests to identify the bacteria, but the results don't match any known species. Describe another method that you could use to characterize and classify the bacteria. Briefly explain your rationale for this choice. (2 pts.)

a) Correct, fimbriae, pili, glycocalyx, and potentially flagella too. b) After attachment, an extracellular matrix is produced. The microbes then secrete quorum signaling molecules, which allow microbes to communicate with one another and sense the number of microbes nearby. Next, water channels form between microbes allowing the exchange of nutrients. c) Biofilms can protect microbes from environmental stresses such as antimicrobial drugs and unfavorable environmental conditions regarding pH, temperature, etc. d) DNA sequencing of ribosomal RNA sequences is the best method here because the combination of physical characteristics and biochemical tests with a dichotomous will likely be unsuccessful for an unknown microbe. Phage typing and serological tests would not work here because it is a unique species that is likely unknown.

Varicella-zoster virus, also known as Human Herpes Virus 3, causes chicken pox and can later cause shingles. a) Varicella-zoster virus is a double-stranded DNA virus that can cause latent infections. Why can't Ebola or SARS-CoV2 establish latent infections? (2 pts.) b) Varicella-zoster virus is an enveloped, double-stranded DNA virus. During lytic infection this virus enters by membrane fusion and the capsid is removed. Briefly describe the next steps in the lytic cycle and the location of these processes. Do not describe the final step of release. (3 pts.) c) An issue with treating chicken box infections with acyclovir is that this treatment inhibits active viral replication, but cannot eliminate latent viruses. Briefly describe one other type of human viral infection that is difficult to eliminate because of latency in nerve cells. (2 pts.)

a) Ebola and SARS-CoV2 are unable to establish latent infections because latent infections are caused by DNA viruses. Ebola and SARS-CoV2 are RNA viruses, meaning that they are only able to establish acute infections, not latent infections. - Correct, note that they are also not retroviruses, which can make a DNA intermediate, such as HIV. b) Varicella-zoster virus enters that nucleus and inserts into the host genome. It is replicated and transcribed by host DNA and RNA polymerases, respectively. The mRNA of the virus is transported into the cytoplasm where host ribosomes translate the viral proteins from this viral mRNA. These viral proteins re-enter the nucleus for viral assembly and budding of newly assembled viruses from the nuclear membrane. c) Varicella-zoster virus is a herpes virus. HIV is the other latent virus we talked about.

The fungal species Candida albicans grows in environments with temperatures between 20 and 40 degrees Celsius. a) Is this fungal species prokaryotic or eukaryotic? (1 pt.) b) What is one feature of bacteria that this fungal species would lack? (1 pt.) c) What is one feature of archaea that is in common with this fungal species? (1 pt.) d) Is this fungal species a psychrophile, mesophile, or thermophile? Based on your answer, explain whether or not this species might be pathogenic to humans. (2 pts.)

a) Fungi are eukaryotes. b) What is one feature of bacteria that this fungal species would lack? (1 pt.) Peptidoglycan layers in the cell wall c) What is one feature of archaea that is in common with this fungal species? (1 pt.) They both have a cell wall d) Is this fungal species a psychrophile, mesophile, or thermophile? Based on your answer, explain whether or not this species might be pathogenic to humans. (2 pts.) The fungal species would be a mesophile because of the temperature that it is able to survive in (20-40 degrees Celcius). I would assume that this species would be pathogenic to humans, as human pathogens are mesophiles and are able to live at a human body temperature.

If human skin is torn or cut deeply, normal skin microbes can be released into the bloodstream to cause a serious bacterial infection known as sepsis. a) What are two features of the skin surface that normally prevent microbial infection as part of this first line of defense? (1 pt.) 1. 2. b) When gram-positive bacteria are released into the bloodstream, peptidoglycan monomers, lipoteichoic acids, and flagellin can act as a PAMPs that can trigger the innate immune system. Explain what recognize PAMPs and the subsequent consequences of this recognition. (2 pts.) c) Some pathogenic bacteria can avoid phagocytosis, though most bacteria released into the bloodstream are eliminated by phagocytic white blood cells of our innate immune system. Briefly describe the steps of phagocytosis of a bacterium by a phagocytic cell. (3 pts.) d) The complement cascade is also activated in the blood during the development of sepsis. What are two outcomes of complement activation? (2 pts.)

a) Mucous membranes are interior in the lungs and digestive track. Human skin has many layers. There is constant shedding of these layers. There are also tightly packed cells. The skin is also salty and produces sebum, an oily substance that act in this first line of defense. b) PAMPS are recognized by pattern-recognition receptors, also called PPR's PPR's are able to recognized these PAMPS, they are then able to be used to bind RNA and induce following steps b) You are right that Pathogen Associate Microbial Patterns (PAMPs) are recognized by Toll-like Receptors (TLRs), also known as Pattern Recognition Receptors. For the second part here, the question asks about these "following steps". The recognition of PAMPs by TLRSs triggers TLR signaling that leads to the expression of genes involved in innate immune responses, such as bradykinins, leukotrienes, histamines, and prostaglandins that lead to inflammation as well as phagocytosis and interferons. c) Overall, great work outlining and describing these steps. One important part that needs some description here is how the pathogen is killed in this process. Killing is achieved by degradation of the microbe by oxygen radicals, DNases, proteases, low pH, etc., which occurs when the phagosome fuses with the lysosome containing these enzymes and chemicals. - 1. Chemotaxis of phagocyte to microbes: phagocytes go toward the infected site 2. Adherence: Phagocytes connect to opsonins 3. Ingestion of microbes by phagocytes: the microbe becomes engulfer 4. Fusion of a series of vesicles: the phagocytes mature 5. Killing of microbes: microbes are killed 6. Elimination by exocytosis: This is when the waste is eliminated from the cell by exocytosis d) The complement cascade is also activated in the blood during the development of sepsis. What are two outcomes of complement activation? (2 pts.) The two outcomes that I studied were... Cell lysis and membrane attack complex Opsonization

a) What is the specific name of the bond formed between the monomers (building blocks) shown above? (1 pt.) b) The above monomers (building blocks) are joined together to form what macromolecule found in microbes? (1 pt.) c) Briefly describe one function of the macromolecules comprised of such monomers (building blocks) in microbes. (1 pt)

a) Phosphodiester bond b) Nucleic acids c) Storing and transmitting genetic information.

A typical lysogenic replication cycle for bacteriophage lambda infecting Escherichia coli bacteria is shown above. Each stage is numbered. a) For stage 3 (top right of image), please state the name of the stage and describe the major processes during this stage. (2 pts.) b) You decide to test a number of bacteriophage strains for their ability to form plaques. Many of them form cloudy plaques, but others have visible plaques with complete clearing. What type of phage likely caused the completely clear plaques? Briefly explain. (2 pts.) c) Phage cannot cause infections in human cells, but do affect human health via their interactions with bacteria. What is one way in which phage may negatively impact human health? (1 pt.)

a) Prophage in chromosome. The viral DNA genome attaches to the bacterial chromosome to form a prophage. b) Correct, lytic here, but the explanation is incorrect. Lytic phages, such as T4 bacteriophages, cause lysis of all infected bacterial cells, resulting in a plaque that has complete clearing. I think that the types of phages that cause the completely clear plaques are lytic phages. They are able to change the cell without destroying is, and wouldn't change much is appearance c) The question here asks how phage are detrimental to human health. Lysogenic conversion can lead to the production of toxins, which are detrimental to human health. If phages kill beneficial bacteria in our gut microbiome, such as those that help with nutrient absorption, this is also detrimental.

Together with his team, Robert Koch studied disease and modified the scientific method to propose four postulates, known as Koch's postulates. a) What did Koch's postulates aim to associate with a specific disease? (1 pt.) b) What is Koch's third postulate? (1 pt.) c) Describe one issue with implementing this third postulate. (1 pt.) d) Koch's discoveries about disease were Nobel Prize winning, but these discoveries were made based on the contributions of unrecognized others including, Fanny Hesse. What major unrecognized contribution did Fanny Hesse make? (1 pt.)

a) What did Koch's postulates aim to associate with a specific disease? (1 pt.) It was aimed for the postulates to associate a microorganism with a specific disease. b) What is Koch's first postulate? (1 pt.) The microorganism must be found in a diseased individual but not in a healthy individual c) Describe one issue with implementing this first postulate. (1 pt.) Some microorganisms are in healthy bodies as well but don't cause the disease in those individuals. d) Koch's discoveries about disease were Nobel Prize-winning, but these discoveries were made based on the contributions of unrecognized others including, Fanny Hesse. What major unrecognized contribution did Fanny Hesse make? (1 pt.) She was the first to use agar to create a bacterial culture to be able to grow bacteria. This also allows the bacteria to be isolated from the rest of the environment and grow on their own.

Based on experiment, Louis Pasteur concluded that life, such as that of bacteria, did not arise by spontaneous generation. His experiment supports the Cell Theory, which states that cells are the smallest units of life, and that cells arise from pre-existing cells. a) What was one key element of Pasteur's experiment on spontaneous generation mentioned in lecture? (1 pt.) b) By what process do bacterial cells arise from pre-existing cells? Briefly outline the steps of this fundamental process of bacterial Life (3 pts.)

a) What was one key element of Pasteur's experiment on spontaneous generation mentioned in the lecture? (1 pt.) One key element is using the Swan Neck Flask. This cut off oxygen from the outside for the flask, not letting other microbes in. When the flash was broken, growth occurred due to microbes coming into the flask. b) By what process do bacterial cells arise from pre-existing cells? Briefly outline the steps of this fundamental process of bacterial Life (3 pts.) - The process is called binary fission. The process is an asexual reproduction where one cell separates into two separate daughter cells. The cell makes a copy of its DNA, and divides that DNA into two separate cells that are identical to each other. These cells are going through cytokinesis. They are then their own cells. - Correct, binary fission. You are correct that the first step is replication of the bacterial chromosome, and the last step is the generation of two identical daughter cells. The steps that are missing are the elongation of the cell and separation of the chromosomes and the formation of a new cell membrane and cell wall (septum).

Globally 11-20 million people get typhoid each year and as many as 140,000 die as a result of this infection caused by the bacteria Salmonella enterica Typhi. One important drug used to treat typhoid is ciprofloxacin, which inhibits the enzyme DNA gyrase. a) Why is ciprofloxacin selectively toxic? (2 pts.) b) Treatment of typhoid using ciprofloxacin is accomplished via oral administration. What are one advantage and one disadvantage of oral administration? (2 pts.) c) Some strains of Salmonella enterica Typhi are resistant to ciprofloxacin. Briefly explain how Salmonella enterica Typhi might become resistant to ciprofloxacin and still cause typhoid. (2 pts.) d) Imagine you are a clinical microbiologist. A patient with typhoid has been unresponsive to ciprofloxacin treatment. You are given a sample of the Salmonella enterica Typhi strain from this patient and confirm it is ciprofloxacin-resistant. Fortunately, you also determine that the patient's strain is susceptible/sensitive to the drug azithromycin. Describe how you would determine the MIC of azithromycin using this patient's strain of Salmonella enterica Typhi. (2 pts.) e) The patient was given a second prescription of ciprofloxacin while you were testing the patient's strain. After you determine that this prescription will be ineffective, the patient is notified and told to not take this second prescription of ciprofloxacin. Suppose the patient is considering giving this second ciprofloxacin prescription to a friend that has similar symptoms (stomach pain, cough, fever) but has been diagnosed with viral influenza. What are the potential negative consequences resulting if this second ciprofloxacin prescription is taken by this friend? (2 pts.)

a) Why is ciprofloxacin selectively toxic? (2 pts.) Ciprofloxacin is selectively toxic because it only targets the infected microbe and isn't likely to attack the healthy human cells. It is able to recognize the infected microbe and act on those rather than other cells - You have a nice definition of selective toxicity here, but how does it apply here? Ciprofloxacin is selectively toxic because it inhibits DNA gyrase, which relieves supercoiling of DNA and is found in bacteria but not in humans. Humans have DNA topoisomerase to relieve supercoiling of DNA, but this enzyme is different in structure and is not targeted by the drug. b) Treatment of typhoid using ciprofloxacin is accomplished via oral administration. What are one advantage and one disadvantage of oral administration? (2 pts.) A advantage of oral administration is that it is very easy for a person to self-administer the dose. They are able to take it orally and do it on their own A disadvantage of oral administration is that a person may not take the correct amount of the dosage or take the full dosage. c) Some strains of Salmonella enterica Typhi are resistant to ciprofloxacin. Briefly explain how Salmonella enterica Typhi might become resistant to ciprofloxacin and still cause typhoid. (2 pts.) Salmonella enterica Typhi might become resistant to ciprofloxacin because they are able to adapt and change overtime with the changes in its structure/genome, so they are able to be unrecognizable by cyprofloxacin when it is trying to target Salmonella enterica Typhi - You are on the right that a mutation could lead to resistance, but how? There are many possibilities discussed in lecture like alteration of the drug target, over expression of the drug target, inactivation of the drug, etc. d) Imagine you are a clinical microbiologist. A patient with typhoid has been unresponsive to ciprofloxacin treatment. You are given a sample of the Salmonella enterica Typhi strain from this patient and confirm it is ciprofloxacin-resistant. Fortunately, you also determine that the patient's strain is susceptible/sensitive to the drug azithromycin. Describe how you would determine the MIC of azithromycin using this patient's strain of Salmonella enterica Typhi. (2 pts.) I would determine the MIC by measuring how infectious this patients strand of Salmonella enterica Typhi is - A description of how you would perform and analyze an E test or broth dilution test is what you were looking for here. e) The negative consequences would be not having the second dose taken, completing the production of antibodies and would thus result in insuffienct antibodies to be able to fight the infection. The shot would have little to no effective on their condition or production of antibodies. - Oops, there was a misinterpretation of the question here. If someone were to take another person's antibiotics to treat a viral infection could lead to side effects, disruption of normal microbiota, and/or antibiotic resistance.

Fungi, protozoa, algae, and small multicellular organisms

are eukaryotic

If a patient is given antibodies from someone whom has survived SARS-COV2 infection, it might be possible for this patient to obtain temporary immunity as an example of

artificial passive immunity

Assisting a microbiologist at the Food and Drug Administration (FDA) during the summer, you identify a potential toxin being secreted from the fungus Aspergillus carbonarius found growing on some grapes that led to human illness. You decide to conduct an Ames test to determine whether the toxin is a mutagen in bacteria. You combine his- Salmonella mutants, rat liver extract and the toxin. You then plate this mixture on an agar plate lacking histidine. a) What results on the medium lacking histidine would you expect to see if the toxin is indeed a mutagen? (2 pts.) b) What is one difference you would expect between the genome and/or chromosomal structure of bacteria and Aspergillus carbonarius? (1 pt.) c) Further research shows that the toxin primarily causes mutations that lead to misfolded proteins. What type of substitution point mutation leads to misfolded proteins, and why are the proteins misfolded as a result? (2 pts.)

a) You are right that there would be growth, but higher number of growth than what? What would the growth look like? You would expect to see colonies on the medium lacking histidine if the mutagen reverses the his- mutation of the Salmonella bacteria, producing revertant his+ Salmonella cells that have the ability to synthesize histidine. b) Yes, but how might these genomes differ? One difference between the genome and/or chromosomal structure of prokaryotes and eukaryotes is that eukaryotes generally have multiple, linear chromosomes packed into the nucleus with the help of histone proteins. Prokaryotes generally have a single, circular chromosome. c) A frameshift mutation is due to an insertion or a deletion of a base pair. A substitution point mutation is substitution for one base pair for another and doesn't cause a frameshift. How does a change in an amino acid lead to misfolding? A substitution point mutation in a DNA sequence could cause a missense mutation, which is a change in a codon specifying one amino acid to a codon specifying a different amino acid. This often effects the folding because a different amino acid may have different side chains that would change the bonding (hydrogen, ionic, etc.) that it undergoes within the tertiary structure of the polypeptide.

Influenza A viruses are the causative agents of seasonal influenza. Last year, the primary subtypes of influenza A were H1/N1 and H2/N3. a) Influenza viruses possess a segmented RNA genome that can evolve via antigenic drift and antigenic shift. Briefly explain the mechanisms of antigenic shift. (2 pts.) b) Influenza virus has a negative-sense ssRNA genome. Can the viral genome be replicated with proteins normally found in the human cell? Explain why or why not? (2 pts.) c) Influenza is an enveloped virus. Based on this, what can you conclude about how the virus exits the cell? (2 pts.) d) In 1918, there was an influenza pandemic that infected approximately 1/3 of the population worldwide and killed an estimated 50 million people. There are several features that contributed to the high pathogenicity of this particular influenza virus. In particular, the virus caused a severe immune reaction called a cytokine storm. How is this similar to another type of viral infection discussed in the online lectures? (2 pts.)

a) You have the big picture here, what is missing here is that antigenic shift occurs when two different viral strains infect the same host cell. This allows the exchanges of genetic segments, genes, and/or antigens, that are then packaged into a new viral strain that exits the cell containing information from both viral strains. - Antigenic shift is a process that happens when 2+ different strains of a virus combine and form a new type of antigens. This can cause different strains of a disease that are not yet found to have a treatment for. b) No, a negative-sense ssRNA viral genome can not be replicated using host enzymes because viral RNA-dependent RNA polymerase is needed to generate a positive-sense ssRNA template to make more negative-sense ssRNA viral genomes and to be used by host ribosomes to synthesize viral proteins. c) Influenza is an enveloped virus. Based on this, what can you conclude about how the virus exits the cell? (2 pts.) I would conclude that Influenza uses budding to exit the cell from the cellular membrane of the host cell. This allows the virus and the cell to exit and seperate. d) In 1918, there was an influenza pandemic that infected approximately 1/3 of the population worldwide and killed an estimated 50 million people. There are several features that contributed to the high pathogenicity of this particular influenza virus. In particular, the virus caused a severe immune reaction called a cytokine storm. How is this similar to another type of viral infection discussed in the online lectures? (2 pts.) COVID-19 and the influenza virus pandemic are similar because they both have a cytokine storm effect in some patients. The virus is able to damage organs and kill tissues, causing sudden effects in patients, such as death. This is in both COVID-19 and the influenza virus.

Escherichia coli is a gram-negative, motile bacteria normally found in the human gastrointestinal track. a) Briefly describe the following: i) the motion of the E. coli flagella, and the source of energy for motility (1 pt.) ii) why motility might be beneficial for E. coli (1 pt.). b) E. coli is a facultative anaerobe. You inoculate two liquid broth cultures of E. coli and grow one in the presence of oxygen and the other in an anaerobic environment. Which culture will have more growth post-incubation? Briefly explain your answer (2 pts.) c) You want a fast an easy method for quantifying the growth in these two cultures. Which method of quantifying microbial growth is most appropriate? Why? (2 pts.) d) In low oxygen conditions, E. coli runs the membrane ATP synthase backwards. How can you explain this observation? (2 pts.)

a) i) Bacterial flagella rotate 360 degrees in a propellor-like motion that can occur clockwise or counter-clockwise. This motion is powered by the H+ gradient. ii) why motility might be beneficial for E. coli (1 pt.) The E. coli flagella are able to move around and cause the cell to either evade dangers or be able to find nutrients that the cell needs to survive and thrive. b) E. coli is a facultative anaerobe. You inoculate two liquid broth cultures of E. coli and grow one in the presence of oxygen and the other in an anaerobic environment. Which culture will have more growth post-incubation? Briefly explain your answer (2 pts.) The culture that will have the more growth post-incubation would be the one in the presence of oxygen because the E. col is able to use aerobic respiration, which is able to produce more ATP than that in the anaerobic conditions performing anaerobic respiration and fermentation. c) Serial dilutions and plate counts would be time consuming, turbidity is the best choice here as it is a fast and easy method to quantify growth in laboratory liquid cultures. d) In low oxygen conditions, there is little/no oxygen for aerobic cellular respiration, which produces the H+ gradient needed to power flagella. Thus, in these conditions, ATP synthase can run backward to produce an H+ gradient that can be used for motility. Using ATP to generate this H+ gradient allows the bacteria to move and thus seek conditions with higher oxygen levels.

Why are there so many different receptors that signal for activation of immune responsive chemicals?

all of the above a. Allows for different levels of response b. Allows for detection of many different types of microbes c. Provides "back-up" in case a pathogen inhibits response

Endospores often form

all of the above a. asymmetrically from a mother cell b. as a defense strategy c. in nutrient starved conditions

Which of the following eukaryotic cells have a cell wall?

all of the above a. fungi b. algae c. plants

Bacterial Motility is important because

all of the above a. it allows bacteria to move toward nutrients b. it allows bacteria to move away from toxins c. it allows bacteria to invade cells and tissues

Microbial Classification is useful for

all of the above a. providing order for various microbial species b. predicting the structure and function of microbial species based on features of a given group c. uncovering evolutionary relationships

Which of the following organelles would typically be found in an algal cell?

all of the above a. rough endoplasmic reticulum b. mitochondrion c. chloroplast

How do so many different viruses cause similar symptoms in patients?

all of the above a. the viruses infect similar cell types b. the viruses cause similar levels of tissue damage c. the viruses cause similar immune responses

What factors determine bacterial susceptibility?

all of the above a.Presence or absence of specific antibiotic-resistance genes b. Expression of import and export transporters c. Type of bacteria (ex., Gram-positive versus Gram-negative)

Bacterial cells have different arrangements. The image above shows bacteria arranged in

cuboidal packets (sarcinae)

Eukaryotic cells can bring material into the cell through manipulation of the cytoplasmic membrane in a process called

endocytosis

Louis Pasteur employed the scientific method to study fermentation."Boiling a swan-necked flask of grape juice to kill all microbes and leaving it open to the air" was his __________. When he did not observe fermentation, he rejected his ________ that air ferments grape juice.

experiment, hypothesis

When a sodium ion moves through a channel in the bacterial cytoplasmic membrane into the bacterial cell without the use of energy,

facilitated diffusion

Bacterial fimbriae are

finger- or bristle-like projections that can be used for adherence to substrates or other bacteria

The aerobic spore-forming bacteria of the Bacillus genus grow in the cocoa pile when the pH, temperature, and oxygen levels increase in the pile. However, they do not grow at the start of the process when these environmental conditions are low. Bacillus survive in these unfavorable conditions by

forming spores that remain inert

Polysaccharides and proteins made in the bacterial cell are secreted outside the bacterial cell to form a gelatinous, sticky sheath called

glycocalyx

Sulfonamides are antibiotics that act by competing as PABA (Para-aminobenzoic acid) analogs with PABA for PABA enzymatic active sites to

inhibit metabolic pathways

Cations and anions are attracted to one another to form a/an

ionic bond

Atoms of a given element that differ only in the number of neutrons are called

isotopes

A typical microbial growth curve is pictured above.When microbes are adjusting to their environment, signaling, and preparing for active division,this phase is called ________ phase and is labelled with the letter ________ in the growth curve shown above.

lag, C

A microorganism that acquires electrons from an inorganic source is a/an

lithotroph

The Moderna and Pfizer/BioNTech SARS-CoV2 vaccines are RNA-based vaccines of the SARS-CoV2 spike protein. These vaccines are examples of

nucleic acid-based vaccines

Fusobacterium necrophorum is an _________ because it performs anaerobic respiration and oxygen is toxic to these microorganisms.

obligate anaerobe

Eukaryotic cells can move using which of the following structures?

only a) and b) a. Flagella b. Cilia

Above is a graph of the percent of deaths attributed to influenza viral infections by weeks of the year for the years of 2008 through 2012. From this graph, you can conclude that

only a) and b) a. influenza viral infections fluctuate seasonally b.influenza viral infections fluctuate in number from year to year

Which biochemical pathways are likely to be inducible?

only a) and b) a. pathways allowing the cell to use nutrients b. pathways allowing the cell to produce toxins for pathogenesis

The bacterial cytoplasmic membrane is made of

only a) and b) a. phospholipids b. proteins

Which of the following are important components of the lymphatic system?

only a) and b) a. thymus b. spleen

When an electron donor, such as NADH, gives an electron, the electron donor is said to be

oxidized

Some microorganisms use alternative pathways to breakdown glucose. Match each alternative pathway to its appropriate description:

produces NADPH that can be used in photosynthesis, one ATP, and five-carbon, phosphorylated sugars → Pentose phosphate pathway, produces pyruvic acid but with different enzymes than those used in glycolysis → Entner-Doudoroff pathway, produces NAD+ by partially oxidizing sugar to release energy using an endogenous organic molecule → Fermentation

In obligate aerobes, the glycolytic products ________ are used in ________ .

pyruvate and NADH, cellular respiration with oxygen as the final electron acceptor

Most bacteria cannot grow and thrive in human blood because erythrocytes (red blood cells) bind up iron, which is needed for bacterial growth. However, a few bacterial pathogens can grow and thrive in blood by stealing iron from the human host using

siderophores

The movement of two different substances in the same direction against their concentration gradients across the bacterial cytoplasmic membrane using energy is known as

symport

The leading strand of DNA replication is synthesized by DNA polymerase

toward the replication fork in the 5' to 3' direction continuously

FtsZ is a protein homologue of the eukaryotic ________ protein that is part of the ________.

tubulin, cytoskeleton