practice tests
ANSWERS ON MBI HW DOC
Practice Test 1
How does Luria-Delbrück and Lederberg experiments support Darwinian evolution in bacteria?
Explain Griffith's transformation experiment and its impact on bacterial evolution.
Distinguish bacterial core vs. accessory genomes in terms of adaptation and virulence.
Compare short-read and long-read sequencing benefits for bacterial genome assembly.
Detail Lambda phage lytic/lysogenic decision-making via key proteins.
How do bacterial operons coordinate gene expression for environmental adaptation?
Discuss the significance of coupled bacterial transcription-translation.
Describe bacterial ribosome composition, rate, and antibiotic targeting.
Outline traditional biochemical tests (e.g., TSI) for Gram-negative ID principles.
Which modern DNA method best identifies diverse unculturable environmental bacteria?
Explain proton motive force generation via prokaryotic ETC electron transfer.
How does proton motive force power ATP synthesis through ATP synthase?
Why are bacteria ideal for carbon capture and value-added product biotechnologies?
Summarize the Calvin cycle's three phases and its role in bacterial carbon fixation
Provide two crucial non-structural functions of the bacterial cell membrane.
Contrast cell membrane structural differences across bacteria, archaea, and eukaryotes.
How do diverse sigma factors regulate bacterial gene expression for adaptation?
Propose a transcriptomics experiment to study bacterial antibiotic response and its insights.
What evolutionary insights emerged from the E. coli Long-Term Evolution Experiment?
Describe phage therapy's mechanism and successful application against resistant bacteria.
Practice Test 2
While enzymes are typically proteins, the lecture mentions exceptions. Discuss these exceptions and provide two specific examples, explaining their catalytic function
Differentiate between cell membranes and walls of archea, bacteria, and eukarya. Be sure to highlight important aspects and components.
Describe the Z-scheme of electron flow in oxygenic photosynthesis, emphasizing why it is non-cyclic and the contributions of Photosystems I and II
Discuss the evolutionary and physiological factors contributing to why some organisms are strictly anaerobic
Compare the energy requirements (in ATP per six-carbon molecule fixed) for the Calvin cycle, the reversed TCA cycle, and the reductive acetyl-CoA pathway.
Under what cellular conditions would ATP synthase operate in reverse, and what are three critical cellular functions this reversal supports?
a 3x sugar agar slant shows yellow butt, red slant, and blackening cracks throughout media. what does this indicate?
describe the positive result of a DNase test
A lysogenic bacteriophage lambda, integrated into a bacterial genome, is exposed to UV radiation. Explain the molecular events that lead to the phage switching from the lysogenic to the lytic cycle, and how this decision benefits the phage
explain roles that recA protein has in bact cells
Outline the key steps and limitations of Sanger sequencing, including read length and throughput.
Describe the replica‑plating technique developed by Joshua and Esther Lederberg and how it demonstrates that streptomycin‑resistant colonies existed before antibiotic exposure
Contrast generalized and specialized transduction, specifying the packaging error that generates each type.
Summarize the adaptive immune mechanism of CRISPR, including spacer acquisition and interference with invading phage DNA.
Practice Test 3
Why do large conjugative plasmids often carry antibiotic‑resistance genes, and what evolutionary trade‑off does this create for the host bacterium?
Using the Klebsiella pneumoniae outbreak at the NIH Clinical Center as a case study, explain how whole‑genome SNP analysis identified the source of transmission despite ambiguous patient location data.
answer: during the outbreak, it wasn’t obvious how the infection was spreading and there were no clear patterns from the patient location data. whole genome SNP analysis was used to identify the single nucleotide differences between the strains isolated from the infected patients. this allowed them to make a phylogenetic tree of the different strains so they could figure out how it was spreading and what the path of infection was
corrections: none
Explain the principle of Oxford Nanopore long‑read sequencing, its typical read lengths, and the trade‑off between read length and accuracy.
the oxford nanopore seqing method involves using a polymerase to feed dna thru a chip with an electrical fiend and a computer to measure the disruptions caused by the different nucleotides. it can read long seqs and record them fairly accurately, but it’s more prone to errors than sanger and illumina seqing. however, you can repeat it multiple times and take the “average” seq to make a consensus seq
corrections: none
Explain how transcription and translation are physically coupled in bacteria and why ribosome binding prevents premature termination by Rho
in bact, transl drives transc. one method of termination in bact uses the rho protein binding to the rut seq and if ribos are there, it won’t bc it only recognizes naked dna. when it binds, it travels up the mrna strand and destabilizes the rna polymerase so it falls off the strand. if transl doesn’t happen at the same time as transc, then transc stops.
corrections: ribos occupancy of SD seq and mrna block rut sites
Describe the dual role of the lambda repressor protein in maintaining the lysogenic state of bacteriophage lambda. Elaborate on explain its auto-regulatory mechanism for maintaining consistent protein levels
the c1 lambda repressor promotes the lysogenic state and represses the lytic lifecycle by binding to or1 with the highest affinity and or3 with with the lowest - ensuring that whenever c1 is present above a specific threshold, it will stop rnap from binding to or1 and transc the cro operon. when the [c1] gets high enough and it crosses a threshold, c1 proteins bind to the or2 site and slightly obscure the rnap binding site (or3). when it crosses another threshold and there’s a lot of c1 protein, then all 3 or seq are bound and the rnap is prevented from binding until the protein levels drop back down below the threshold and the or3 seq becomes available again for limited transc.
corrections: autoreg stabilizes c1 around set point - allows stable lysogeny but responsive to induction when reca cleaves c1
list significant limitations of using 16s rRNA gene seqing for bact ID?
expensive, not always useful bc its pretty uncommon for there to be more than 1 disease causing org, the ID it gives of the species / genus isn’t always accurate
corrections: don’t get any functional information
Outline the core mechanistic overlaps between bacterial respiration's ETC and photosynthetic electron transport, particularly regarding PMF generation
both etc involve moving e- around from protein to protein (from low reductive potential (e- donors) to high reductive potential (e- recievers) and using the energy from moving the e- around to pump h+ across the membrane, generating the pmf. both also use the pmf to power atp synthase, which uses the h+ gradient to convert mechanical energy into chemical and overcome the endergonic rxn of “charging” atp from adp + pi
corrections: uses mobile carriers - Q and cytochrome c to transport btwn complexes, involve h+ translocation
Differentiate the electron-shuttling mechanisms and capacities of ubiquinones and cytochrome c within the ETC
Q is a small nonpolar molecule the moves throughout the membrane used for the etc and shuttles e- from complex i and complex ii to complex iii. they have a higher reduction potential than ci and cii but less than ciii to make sure that e- release enough energy to pump h+ across the mem. undergoes Q cycling to become QH2 while transporting e-
cytochrome c is a small polar molecule that can exit the membrane while travelling btwn c-iii and c-iv to shuttle e-. it has a higher reduction potential than c-iii but less than c-iv to ensure e- travel the correct way through the etc. it falls under the categorization of a heme protein and the Fe atom is what grabs the e- during transportation
corrections: Q accepts 2 e- → QH2, cytochr c only carries 1 e- and no h+
Analyze the structural and functional resemblances between bacterial flagella and ATP synthase, and what these suggest about their evolutionary origins
bacterial flagella and atp synthase both have a “basal body” or analogous struct that is rooted in the mem of the bact and rotate similarly to perform their necessary function. they utilize the pmf to move and perform work and the direction of their rotation is vital to their function - clockwise is the “normal” direction of movement (atp synthase → charge atp, flagella → run) while counterclockwise is generally considered less common (atp synthase → hydrolysis, flagella → tumble). these similarities support the theory that the two may have a common ancestor in a protein that also used an ion gradient to spin and perform mechanical work.
corrections: none
Explain how the redox potential gradient dictates the direction and efficiency of electron flow within the ETC
the redox potential gradient goes from low to high redox potential with the lowest being the e- donors as they don’t hold onto them well and the highest being e- acceptors as they want more e-. following their gradient is the most energetically favorable thing that e- can do as it releases energy, which is what drives the pumping of h+ across the membrane. in instances where the e- carrier has a slightly higher redox potential (such as in the case of FADH2 and complex ii), there isn’t enough energy generated to pump any h+ across, so if e- don’t follow the flow of their gradient, the etc loses its integrity
corrections: greater diff btwn donor and acceptor → more energy released
A pathogenic bacterium residing in a host experiences a sudden scarcity of glucose. Describe how its central metabolism might adapt to synthesize essential components like fatty acids and amino acids, specifically mentioning relevant cycles and their "amphibolic" nature
many metabolic cycles feed into glycolysis, both anabolically and catabollicaly. when glycolysis flux changes, then most other metabolic ones are as well as the cell rushes to reestablish the equilibrium. some systems like fatty acid / beta oxidation would ramp up to turn fats into glucose that would then be broken down the supply energy or into other compounds. others, like fatty acid synthesis and purine synthesis that requires intermediates from the tca cycle might slow down to reduce stress on the tca cycle. gluconeogenesis and any carbon fixation pathways might also ramp up to try to generate more sugars and glucose to compensate and prevent necessary pathways (like amino acid synthesis) from falling out of balance. alternate pathways, like the reverse tca cycle or glyoxylate pathway would also increase in activity since glucose wasn’t present.
corrections: tca is amphibolic pathway - can catabolize acetylcoa for energy but supplies biosynthesis; use alt C sources (fa, other sugars, aa)
Explain the crucial role of NAD+/NADH cycling in fermentation for the continuation of glycolysis under anaerobic conditions
NAD+ is required in glycolysis after g3p has been converted into 1,3 phosphoglycerate to accept e- (forming NADH) in order for the pathway to continue. without it, the pathway would not be able to proceed. in addition, nadh from glycolysis goes on to power other pathways like the etc. nadh/nad+ is also a regulator and its levels affect how other pathways increase or decrease. nadh needs to be recycled into nad+ in order for glycolysis to continue, especially in anaerobic conditions since the etc requires O as the final e- acceptor and so without it, neither the tca nor the etc can run. to prevent everything from getting backed up, nadh needs to be converted into nad+ which is where fermentation comes in to fix this
corrections: without nad+ recycling, glycolysis would stall and ATP synth would stop
Identify the three irreversible enzymatic steps in glycolysis and discuss their significance for metabolic regulation
the three irreversible steps are steps 1, 3, and 10 where atp is used (1, 3) and made (10). these steps are the most energetically costly / beneficial so when reversing the process for gng, there needs to be alternate enzymes and pathways available to circumvent the high energy associated with it. these alternate steps require different locations than the glycolysis enzymes to prevent a futile cycle
corrections: create control points for flux; enzymes: hexokinase, pfk-1, pyruvate kinase
How do bacterial cells link catabolic and anabolic reactions, and what is the central role of ATP and free energy in this coupling?
catabolic and anabolic rxns are linked via intermediates in pathways like glycolysis, the tca cycle, and other metabolic pathways. for example, acetyl-coa is a big intermediate and used in a lot of different pathways. catabolically, pyruvate and beta oxidation feed into it while fatty acid synthesis and the tca cycle pull out from it, using the intermediate as a bridge to make sure all the levels stay fairly consistent. atp and e- carriers are like coenzymes in these rxns and needed to drive the unfavorable endergonic rxns, which are usually coupled with favorable exergonic rxns
corrections: exergonic rxns drive endergonic ones, atp hydrolysis provides -dG that drives enderonic ones fwd
Which characteristic primarily contributes to the fluidity of a cell membrane?
hphobic tails of the plipid structure. the hphilic heads face outward and the hphobic tails are sequestered away from the aq cytoplasm and environ
corrections: unsaturation of fa chains in plipids → prevent tight packing and inc fluidity. shorter chains also inc fluidity and cholesterol content also affects