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This document covers a wide range of topics in microbial genetics and molecular biology, including mutations, genetic engineering techniques, DNA sequencing, evolutionary mechanisms, and the classification and characteristics of various bacterial groups. It provides a comprehensive overview of key concepts and principles, making it a valuable resource for students and researchers interested in understanding the genetic and molecular underpinnings of microbial life. The document delves into topics such as mutations, genetic engineering, PCR and reverse transcription, gene function annotation, microbial genome evolution, and bacterial taxonomy. This could serve as an excellent study guide, lecture notes, or reference material for courses in microbiology, genetics, or molecular biology.
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what can restore a frameshift mutation? - ✔✔another frameshift, microdeletion, and microinsertion A mutation in a particular gene that results in the premature halting of transcription (and, consequently, protein translation) is a___________ mutation. - ✔✔nonsense Consider a mutation in which the change is from UAC to UAU. Both codons specify the amino acid tyrosine. Which type of point mutation is this? - ✔✔Silent mutation A ʺpoint mutationʺ refers to mutations involving - ✔✔a substitution, deletion, or addition of one base- pair. Nutritionally defective mutants can be detected by the technique of - ✔✔replica plating Which method would be the MOST powerful approach to isolating a single mutant from a population of billions? - ✔✔selection for a gain of function (like finding a needle in a haystack) A mutant that has a nutritional requirement for growth is an example of a(n) - ✔✔auxotroph A plasmid may - ✔✔replicate independently of the chromosome, integrate into the chromosome, or be transferred cell-to-cell during conjugation. The uptake of free DNA from the environment is referred to as ________, while the transfer of DNA with cell-to-cell contact is known as ________. - ✔✔transformation/conjugation The CRISPR system - ✔✔recognizes foreign DNA sequences that have previously entered the cell and directs the Cas proteins to destroy them.
Lysogeny probably carries a strong selective advantage for the host cell because it - ✔✔confers resistance to infection by viruses of the same type. F+ strains of Escherichia coli - ✔✔have the F factor as a plasmid When DNA is transferred into a prokaryotic cell, it may. - ✔✔be degraded by enzymes, replicate independent of the host chromosome, or recombine with the host chromosome. Consider the following experiment. First, large populations of two mutant strains of Escherichia coli are mixed, each requiring a different, single amino acid. After plating them onto a minimal medium, 45 colonies grew. Which of the following may explain this result? A) The colonies may be due to back mutation (reversion). B) The colonies may be due to recombination. - ✔✔Either A or B is possible The F (fertility) plasmid contains a set of genes that encode for the ________ proteins that are essential in conjugative transfer of DNA. - ✔✔pili During electrophoresis, DNA - ✔✔is separated by charge Which is NOT true about PCR? A. It uses DNA polymerases from psychrophilic microbes B. It is used for making DNA for cloning and DNA sequencing C. It amplifies DNA sequences D. It uses oligonucleotide primers that are complementary to the flanking regions of target DNA - ✔✔A. It uses DNA polymerases from psychrophilic microbes RT-PCR makes _______ from a(n) _______ template. - ✔✔cDNA; mRNA If you wanted to compare the relative abundance of mRNA transcribed for a specific gene by two different strains of bacteria, you would perform - ✔✔a Northern blot
Genetic engineering involves - ✔✔in vitro methods to alter genes in the laboratory A termocylcer is - ✔✔a machine used for PCR reaction Nucleic acid probes comprise - ✔✔ss DNA fragments complementary to the sequence of interest A southern blot is a hybridization procedure in which - ✔✔DNA is in the gel Cutting DNA with EcoR1 will produce - ✔✔5' overhangs Genetic engineering requires - ✔✔various genetic building blocks, a cloning vector and a host for expression During gene cloning, the vector and the foreign D N A are cleaved ________ restriction enzyme(s) and then are joined ________. - ✔✔the same / DNA ligase A common screening mechanism used in cloning involves assaying for β-galactosidase (lacZ) activity, in which __________-colored colonies suggest that a gene has been successfully inserted/cloned. - ✔✔white What is NOT true regarding the use of yeast artificial chromosomes (YAC s) for cloning? A. They have features to allow them to replicate and segregate like normal eukaryotic chromosomes B. Large fragments of DNA can be inserted into them C. They contain a gene for selection D. They are circular vectors - ✔✔D. They are circular vectors
B. large size C. easily screenable insertion D. ampicillin resistance for selection - ✔✔B. large size The splicing of any two genes together is considered gene - ✔✔fusion Which technique uses synthetic D N A plus D N A cloning techniques to introduce nucleotide changes at specific sites? - ✔✔site-directed mutagenesis When using a reporter gene to investigate expression of a target protein, the promoter of _________ is ligated to the coding sequence of the ____________. - ✔✔target gene / reporter gene Gene disruption, in which large fragments of D N A are inserted in the middle of a gene's coding sequence, is a type of - ✔✔cassette mutagenesis The synthetic molecule used in CRISPR gene editing is - ✔✔synthetic guide RNA (s g RNA). T/F? Escherichia coli is naturally transformable - ✔✔false What is the difference between PCR and RT-PCR? - ✔✔RT-PCR uses an RNA template whereas PCR uses a DNA template. Agarose gels are generally used to - ✔✔ascertain the purity and size of DNA fragments Reverse transcriptase - ✔✔converts RNA into complementary DNA (cDNA) FISH is a method in which - ✔✔fluorescent probes are used to target specific target DNA or RNA in cells What is the important advantage of Pfu polymerase over Taq polymerase? - ✔✔Unlike Taq polymerase, Pfu polymerase has proofreading activity
What molecular mechanism/feature does site-directed mutagenesis exploit to introduce a mutation at a specific site? - ✔✔Flanking complementary bound nucleotides permit noncomplementary base pairing The genes encoding green fluorescent protein (GFP) and β-galactosidase are typically used in cloning as - ✔✔reporter genes Which process results in the production of a hybrid polypeptide? - ✔✔protein fusion T/F? Although various codons often code for the same amino acid, it is important to choose the codon preferred by the expression host itself - ✔✔true What makes eukaryotic transcripts easier to isolate than bacterial transcripts? - ✔✔mRNA is polyadenylated in eukaryotes Gene function is annotated based on homology between the ORFs of a genome and proteins whose function has been proven experimentally. What ʺ-omicʺ approach could help us determine the function and structure of proteins encoded by uncharacterized ORFs? - ✔✔proteomics Genes encoding compounds such as pyruvate, acetyl-CoA, fructose- 6 - phosphate, oxaloacetate, and other small organic compounds could be part of a(n) - ✔✔Metabolome The most abundant genes in prokaryotic genomes are - ✔✔those involved in metabolism. A surprising finding of environmental metagenomic studies is that a majority of genes in the environment are - ✔✔viral in origin The very first DNA sequencing technology called the Sanger method relies on - ✔✔the incorporation of dideoxynucleotides that terminate chain extension during DNA synthesis. Why can bacteria undergo rapid evolutionary change? - ✔✔Bacterial populations are large and can reproduce quickly
Which bacterial trait is NOT useful for experiments in evolution? A. Bacterial populations are large and reproduce quickly B. Some bacteria are naturally transformable C. The ancestral organism can be frozen and compared to the evolved descendant D. Selective pressure on bacteria is easily manipulated - ✔✔B. Some bacteria are naturally transformable _____________ occur(s) at greater frequency than ______________ in microbial genomes. - ✔✔Deletions / insertions T/F? EACH member of a bacterial species contains the pan genome - ✔✔false The E. coli long-term evolution (L T E E) experiment tracked E. coli for more than _______________ generations. - ✔✔50, Two tubes are inoculated from the same tube containing a bacterial culture. The cultures are then transferred every day for two months. All of the media and growth conditions are the same in every tube. After two months of cultivation, the fitness and genotype frequencies of the populations in the two tubes are compared. The fitness of the two cultures is the same, but the genotype frequencies are very different in the two cultures. How is this possible? - ✔✔Genetic drift within the small populations in the test tubes resulted in different genotype frequencies Both deletions and insertions occur during the evolution of microbial genomes. Insertions bring in new genes that may be useful for the cell. Deletions - ✔✔may increase fitness of a microorganism by eliminating unneeded genes Chromosomal islands contain clusters of genes for - ✔✔virulence, biodegradation of pollutants, and symbiotic relationships T/F? Horizontal gene transfer is one plausible explanation as to why organisms in Archaea, Bacteria, and Eukarya still share so many genes among such distinct domains. - ✔✔true
T/F? It is generally accepted that independent mutation, rather than gene duplication, is the mechanism for evolution of most new genes - ✔✔False Which of the following is/are NOT produced using lactic acid bacteria? - ✔✔antibiotics How can endospore-forming Firmicutes be selected? - ✔✔by heating the sample for 10 min at 80°Celsius Which genus contains members that are human pathogens? - ✔✔Neisseria Which class is the largest and most diverse of the Proteobacteria? - ✔✔Gammaproteobacteria Mycobacterium cells are acid-fast because of - ✔✔the presence of mycolic acids in the cell walls. T/F? Proteobacteria are ALL Gram positive - ✔✔false Select the proper order (species ect) - ✔✔Domain/Phylum/Class/Order/Family/Genus/Species Rickettsia are - ✔✔Alphproteobacteria Genera which are characterized by 2,3-butanediol fermentation include - ✔✔Enterobacter, Klebsiella, Serratia T/F? Actinobacteria generally have a high G+C content - ✔✔true You want to know whether the virulence genes present in Bordetella pertussis are evolutionarily related to genes in the less pathogenic species Bordetella bronchiseptica or if the virulence genes were acquired via horizontal gene transfer. What characteristic(s) would you compare to answer this question? - ✔✔Percentage of GC content and codon usage T/F? Paralogs always have the same function - ✔✔false
A gene for a specific trait may have more than one form, allowing the trait to vary. These sequence variants of a gene are called - ✔✔alleles Microbial species have a core genome and a pan genome. What is the difference between the two? - ✔✔The core genome is a set of genes shared by all members of a species, while the pan genome includes the core genes as well as genes that are not shared by all members. T/F? Chromosomal rearrangements due to insertion sequences have apparently contributed to the evolution of several human pathogens - ✔✔true T/F? Gene families are composed of homologous genes that have different evolutionary origins but the same function - ✔✔false Most mobile DNA consists of - ✔✔transposable elements Isolating a bacterium of the___________ class would be of high impact because it has only ONE cultures representative - ✔✔Zetaproteobacteria Staphylococcus aureus is known to cause all of the following diseases EXCEPT - ✔✔acne Which species produces spores? - ✔✔Clostridium botulinum The order Lactobacillales within Firmicutes are also called the lactic acid bacteria because these bacteria
Which phylum harbors the most functional diversity observed and also has the most cultured representatives? - ✔✔Proteobacteria Which feature(s) differentiate(s) Actinobacteria from Firmicutes? - ✔✔Relative G+C content in their genomes The sum of all biosynthetic reactions in a cell is known as - ✔✔anabolism Selective medium differs from differential medium because - ✔✔selective medium permits growth of a particular microbial type while differential medium is used to distinguish between types of organisms. A halotolerant facultative anaerobe would grow BEST in which of the following environments? - ✔✔Oxygenated non-saline Obligate anaerobes which are sensitive to O2 would be found growing - ✔✔only at the bottom of a tube of thioglycolate broth. Organisms able to live in environments with high sugar concentrations are - ✔✔osmophiles. Most mesophilic organisms can grow in a temperature range of - ✔✔ 20 - 45 °C. A ________ agent is a chemical that inhibits bacteria from reproducing, but does NOT necessarily kill them. - ✔✔bacteriostatic Which of the following statements is FALSE? a. Bacteria typically divide by binary fission, producing two daughter cells. b. The generation time of bacteria may vary from species to species. c. In the death phase, bacterial growth may cease as a result of oxygen and nutrient depletion. d. In the lag phase, cell death exceeds cell division. - ✔✔d. In the lag phase, cell death exceeds cell division.
Which method would be LEAST effective at sterilizing a glass hockey stick to use in the spread-plate method? a. Gamma radiation b. Hight temperature short time pasteurization c. Ethanol soaking d. Autoclaving - ✔✔b. Hight temperature short time pasteurization The time between inoculation and the beginning of growth is usually called the - ✔✔lag phase The use of chemical agents directly on exposed body surfaces to destroy or inhibit vegetative pathogens is - ✔✔antisepsis The time interval required for the formation of two cells from one is called the - ✔✔generation time A microbe growing in a refrigerator is likely - ✔✔psychrotolerant or psychrophilic. Bacteria that are able to grow in humans and cause disease would be classified as - ✔✔mesophiles.