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Questions and Answers of Biology

What are the two points at which the amount of protein synthesis can be regulated?
Most biosynthetic operons need only be under negative control for effective regulation, whereas most catabolic operons need to be under both negative and positive control. Why?
What is the difference between an operon and a regulon?
Describe the mechanism by which cAMP receptor protein (CRP), the regulatory protein for catabolite repression, functions. Use the lactose operon as an example.
What are the two components that give their name to a signal transduction system in prokaryotes? What is the function of each of the components?
Adaptation allows the mechanism controlling flagellar rotation to be reset. How is this achieved?
How can quorum sensing be considered a regulatory mechanism for conserving cell resources?
What would happen to regulation from a promoter under negative control if the region where the regulatory protein binds was deleted? What if the promoter was under positive control?
Promoters from Escherichia coli under positive control are not close matches to the promoter consensus sequence for E. coli. Why?
The attenuation control of the tryptophan biosynthetic pathway genes in Escherichia coli involves coupled transcription and translation. Can you describe why this mechanism of regulation would not be
Most of the regulatory systems described in this chapter employ regulatory proteins. However, regulatory RNA is also important. Describe how one could achieve negative control of the lac operon using
Many amino acid biosynthetic operons under attenuation control are also under negative control. Considering that the environment of a bacterium can be highly dynamic, what advantage could be
How would you design a regulatory system to make Escherichia coli use succinic acid in preference to glucose? How could you modify it so that E. coli prefers to use succinic acid in the light but
Define virus. What are the minimal features needed to fit your definition?
Bacteriophage T4 has “early genes” and “late genes.” What is meant by these classifications, and what types of proteins are encoded by each?
Describe the types of genomes found in bacterial viruses. Give an example of one virus for each type of genome.
Why can it be said that the retrovirus genome is unique in all of biology?
Explain how viruses can affect Bacteria and Archaea in nature in both positive and negative ways.
In what ways do viral genomes differ from those of cells?
What are the major components of a virus particle?
Why does a one-step growth curve differ in shape from that of a bacterial growth curve?
Describe the events that occur on an agar plate containing a bacterial lawn when a single bacteriophage particle causes the formation of a bacteriophage plaque.
How is a viral suspension quantified and what is meant by the word “titer”?
What is different about the penetration process of bacteriophages versus animal viruses?
What causes the viral plaques that appear on a bacterial lawn to stop growing larger?
The promoters on genes encoding early proteins in viruses like T4 have a different sequence than the promoters on genes encoding late proteins in the same virus. Explain how this benefits the virus.
Under some conditions, it is possible to obtain nucleic acid–free protein coats (capsids) of certain viruses. Under the electron microscope, these capsids look very similar to complete virions.
Contrast the enzyme(s) present in the virions of a retrovirus and a positive-strand RNA bacteriophage. Why do they differ if each has plus configuration single-stranded RNA as its genome?
If the MS2 or poliovirus virions did not contain a specific enzyme, explain why these viruses could not replicate.
What is the function of the VPg protein of poliovirus, and how can coronaviruses replicate without a VPg protein?
Rabies virus and poliovirus both have single-stranded RNA genomes, but only in poliovirus can the genome be translated directly. Explain.
Compare the reovirus genome to those of influenza virus and bacteriophage MS2.
Why do both hepadnaviruses and retroviruses require reverse transcriptase when their genomes are double-stranded DNA and single-stranded RNA, respectively?
What are the similarities and differences between viruses and viroids?
What are the similarities and differences between prions and viruses?
Describe the classes of viruses based on their genomic characteristics. For each class, describe how viral mRNA is made and how the viral genome is replicated.
What are the similarities and differences between viroids and prions?
How might viruses help explain the differences observed in the DNA replication machinery of cells of the three domains?
What are overlapping genes? Give examples of viruses that have overlapping genes.
Describe how the genome of bacteriophage ϕX174 is transcribed and translated.
Why can it be said that transcription of the bacteriophage T7 genome requires two enzymes?
Why is bacteriophage Mu mutagenic? What features are necessary for Mu to insert into DNA?
List three unusual features of the archaeal virus that infects Acidianus that distinguish it from bacteriophage T7.
Of all the double-stranded DNA animal viruses, pox viruses stand out concerning one unique aspect of their DNA replication process. What is this unique aspect and how can this be accomplished without
Not all proteins are made from the RNA genome of bacteriophage MS2 in the same amounts. Can you explain why? One of the proteins functions very much like a repressor, but it functions at the
Replication of both strands of DNA in adenoviruses occurs in a continuous (leading) fashion. How can this happen without violating the rule that DNA synthesis always occurs in a 5′ S 3′ direction?
Imagine that you are a researcher at a pharmaceutical company charged with developing new drugs against human RNA viral pathogens. Describe at least two types of drugs you might pursue, what class of
Reoviruses contain genomes that are unique in all of biology. Why? Why can't reovirus replication occur in the host cytoplasm? Contrast reovirus genomic replication events with those of a cell. Why
Write a one-sentence definition of the term "genotype." Do the same for "phenotype." Does the phenotype of an organism automatically change when a change in genotype occurs? Why or why not? Can
What does an F+ cell need to do before it can transfer chromosomal genes?
Explain why performing genetic selection is difficult when studying Archaea. Give examples of some selective agents that work well with Archaea.
What are the major differences between insertion sequences and transposons?
Explain why incoming DNA recognized by a short RNA molecule expressed from the CRISPR region cannot be completely foreign to the cell.
Explain why an Escherichia coli strain that is His− is an auxotroph and one that is Lac− is not.
What are silent mutations? From your knowledge of the genetic code, why do you think most silent mutations affect the third position in a codon?
Give an example of one biological, one chemical, and one physical mutagen and describe the mechanism by which each causes a mutation.
What are heteroduplex regions of DNA and what process leads to their formation?
Explain why recipient cells do not successfully take up plasmids during natural transformation.
Explain how a generalized transducing particle differs from a specialized transducing particle.
What is a sex pilus and which cell type, F− or F+, would produce this structure?
A constitutive mutant is a strain that continuously makes a protein that is inducible in the wild type. Describe two ways in which a change in a DNA molecule could lead to the emergence of a
Although a large number of mutagenic chemicals are known, none is known that induces mutations in only a single gene (gene-specific mutagenesis). From what you know about mutagens, explain why it is
Why is it difficult in a single experiment to transfer a large number of genes to a recipient cell using transformation or transduction?
Transposable elements cause mutations when inserted within a gene. These elements disrupt the continuity of a gene. Introns also disrupt the continuity of a gene, yet the gene is still functional.
What are restriction enzymes? Why does the presence of a restriction enzyme in a cell not cause the degradation of that cell’s DNA?
How does the insertional inactivation of β-galactosidase allow the presence of foreign DNA in a plasmid vector such as pUC19 to be detected?
Describe two prokaryotic cloning hosts and the beneficial and detrimental features of each.
Describe the similarities and differences between expression vectors and shuttle vectors.
How has bacteriophage T7 been used in expressing foreign genes in Escherichia coli, and what desirable features does this regulatory system possess?
What advantages are there to using a lambda-based cloning vector rather than a plasmid vector?
What are the essential characteristics of an artificial chromosome? What is the difference between a BAC and a YAC?
What classes of mammalian proteins are produced by biotechnology? How are the genes for such proteins obtained?
What is the Ti plasmid and how has it been of use in genetic engineering?
What is a subunit vaccine and why are subunit vaccines considered a safer way of conferring immunity to viral pathogens than attenuated virus vaccines?
How has metagenomics been used to find novel useful products?
What is pathway engineering? Why is it more difficult to produce an antibiotic than to produce a single enzyme via genetic engineering?
Describe the basic principles of gene amplification using the polymerase chain reaction (PCR). How have thermophilic and hyperthermophilic prokaryotes simplified the use of PCR?
Genetic engineering depends on vectors. Describe the properties needed in a well-designed plasmid cloning vector.
How could you detect a colony containing a cloned gene if you did not know the gene sequence but had available purified protein encoded by the gene?
What are the major uses for artificially synthesized DNA?
What does site-directed mutagenesis allow you to do that normal mutagenesis does not?
What is a reporter gene? Describe two widely used reporter genes.
How are gene fusions used to investigate gene regulation?
Suppose you are given the task of constructing a plasmid expression vector suitable for molecular cloning in an organism of industrial interest. List the characteristics such a plasmid should have.
Suppose you have just determined the DNA base sequence for an especially strong promoter in Escherichia coli and you are interested in incorporating this sequence into an expression vector. Describe
Many genetic systems use the lacZ gene encoding β-galactosidase as a reporter. What advantages or problems would there be if (a) luciferase or (b) green fluorescent protein were used instead of
You have just discovered a protein in mice that may be an effective cure for cancer, but it is present only in tiny amounts. Describe the steps you would use to produce this protein in therapeutic
What is the age of planet Earth? When did the oceans form? What is the age of the earliest known microfossil?
What is the difference between a gene tree and an organismal tree?
Describe the steps for determining an SSU phylogeny of three bacteria you have isolated from nature.
What is evolution? What processes give rise to genetic variation? What processes can cause allele frequencies to change over time?
What is fitness? To what degree does fitness depend on the environment in which organisms live?
Contrast the impacts of homologous and nonhomologous recombination on the evolution of the core genome and the pan genome.
What is the “species problem” and why is the concept of microbial species difficult to resolve?
How many bacterial species are there? Why do we not know this number more precisely?
What major phenotypic and genotypic properties are used to classify organisms in bacterial taxonomy?
What is measured in FAME analyses?
What is a stromatolite and when can they be found in Earth’s history?
How does 16S rRNA gene sequence analysis differ from multilocus sequence typing as an identification tool?
Why was the evolution of cyanobacteria of such importance to the further evolution of life on Earth? What component of the geological record is used to date the evolution of cyanobacteria?

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