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Questions and Answers of Biology

In Noll's experiment of Figure 10.12, explain where the DNase I cuts the DNA. Why were the bands on the gel in multiples of 200 bp at lower DNase I concentrations?
When chromatin is treated with a moderate salt concentration, the linker histone HI is removed (see Figure 10.13a). Higher salt concentration removes the rest of the histone proteins (see Figure
If you were given a sample of chromosomal DNA and asked to determine if it is bacterial or eukaryotic, what experiment would you perform, and what would be your expected results?
Consider how histone proteins bind to DNA and then explain why a high salt concentration can remove histones from DNA (as shown in Figure 10.19b).
In Chapter 22, the technique of fluorescence in situ hybridization (FISH) is described. This is another method for examining sequence complexity within a genome. In this method, a DNA sequence, such
Bacterial and eukaryotic chromosomes are very compact. Discuss the advantages and disadvantages of having a compact structure.
The prevalence of highly repetitive sequences seems rather strange to many geneticists. Do they seem strange to you? Why or why not? Discuss whether or not you think they have an important function.
Discuss and make a list of the similarities and differences between bacterial and eukaryotic chromosomes.
As shown in Figure 11.5, five DnaA boxes are found within the origin of replication in E. coli. Take a look at these five sequences carefully. A. Are the sequences of the five DnaA boxes very similar
Obtain two strings of different colors (e.g., black and white) that are the same length. A length of 20 inches is sufficient. Tie a knot at one end of the black string, and tie a knot at one end of
Sometimes DNA polymerase makes a mistake, and the wrong nucleotide is added to the growing DNA strand. With regard to pyrimidines and purines, two general types of mistakes are possible. The addition
A short genetic sequence, which may be recognized by primase, is repeated many times throughout the E. coli chromosome. Researchers have hypothesized that primase may recognize this sequence as a
The ability of DNA polymerase to digest a DNA strand from one end is called its exonuclease activity. Exonuclease activity is used to digest RNA primers and also to proofread a newly made DNA strand.
In the following drawing, the top strand is the template DNA, and the bottom strand shows the lagging strand prior to the action of DNA polymerase I. The lagging strand contains three Okazaki
Describe the three important functions of DnaA protein.
What is an Okazaki fragment? In which strand of DNA are Okazaki fragments found? Based on the properties of DNA polymerase, why is it necessary to make these fragments?
Discuss the similarities and differences in the synthesis of DNA in the lagging and leading strands. What is the advantage of a primosome and a replisome as opposed to having all replication enzymes
Explain the proofreading function of DNA polymerase.
What is a processive enzyme? Explain why this is an important feature of DNA polymerase.
What enzymatic features of DNA polymerase prevent it from replicating one of the DNA strands at the ends of linear chromosomes? Compared with DNA polymerase, how is telomerase different in its
A diagram of a linear chromosome is shown here. The end of each strand is labeled with an A, B, C, or D. Which ends could not be replicated by DNA polymerase? Why not?
As discussed in Chapter 17, some viruses contain RNA as their genetic material. Certain RNA viruses can exist as a provirus in which the viral genetic material has been inserted into the chromosomal
Telomeres contain a 3' overhang region, as shown in Figure 11.21. Does telomerase require a 3' overhang to replicate the telomere region? Explain.
The compound known as nitrous acid is a reactive chemical that replaces amino groups (-NH2) with keto groups (=O). When nitrous acid reacts with the bases in DNA, it can change cytosine to uracil and
One way that bacterial cells regulate DNA replication is by GATC methylation sites within the origin of replication. Would this mechanism work if the DNA was conservatively (rather than
The chromosome of E. coli contains 4.6 million bp. How long will it take to replicate its DNA? Assuming DNA polymerase III is the primary enzyme involved and this enzyme can actively proofread during
Here are two strands of DNA. ---------------------DNA polymerase → ------------------------------------------- The one on the bottom is a template strand, and the one on the top is being
A DNA strand has the following sequence: 5'-GATCCCGATCCGCATACATTTACCAGATCACCACC-3' In which direction would DNA polymerase slide along this strand (from left to right or from right to left)? If this
List and briefly describe the three types of sequences within bacterial origins of replication that are functionally important.
Answer the following questions that pertain to the experiment of Figure 11.3. A. What would be the expected results if the Meselson and Stahl experiment were carried out for four or five
An absentminded researcher follows the steps of Figure 11.3, and when the gradient is viewed under UV light, the researcher does not see any bands at all. Which of the following mistakes could
Figure 11.4b shows an autoradiograph of a replicating bacterial chromosome. If you analyzed many replicating chromosomes, what types of information could you learn about the mechanism of DNA
As described in Table 11.3, what is the difference between a rapid-stop and a slow-stop mutant? What are different roles of the proteins that are defective in rapid-stop and slow-stop mutants?
The technique of dideoxy sequencing of DNA is described in Chapter 20. The technique relies on the use of dideoxyribonucleotides (shown in Figures 20.11 and 20.12). A dideoxyribonucleotide has a
Another technique described in Chapter 20 is polymerase chain reaction (PCR) (see Figures 20.5 and 20.6). This method is based on our understanding of DNA replication. In this method, a small amount
Compare and contrast DNA replication in bacteria and eukaryotes.
DNA replication is fast, virtually error-free, and coordinated with cell division. Discuss which of these three features you think is the most important.
Genes may be protein-encoding genes that encode polypeptides, or they may not. A. Describe three examples of genes that are not protein-encoding genes. B. For protein-encoding genes, one DNA strand
At the molecular level, describe how σ factor recognizes a bacterial promoter. Be specific about the structure of σ factor and the type of chemical bonding.
Let's suppose a DNA mutation changes the consensus sequence at the -35 location in a way that inhibits σ factor binding. Explain how a mutation could inhibit the binding of σ factor to the DNA.
What is the complementarity rule that governs the synthesis of an RNA molecule during transcription? An RNA transcript has the following sequence: 5'-GGCAUGCAUUACGGCAUCACACUAGGGAUC-3' What is the
Describe the movement of the open complex along the DNA.
Discuss the differences between ρ-dependent and ρ-independent termination.
In Chapter 11, we discussed the function of DNA helicase, which is involved in DNA replication. Discuss how the functions of ρ-protein and DNA helicase are similar and how they are different.
Discuss the similarities and differences between RNA polymerase (described in this chapter) and DNA polymerase (described in Chapter 11).
Mutations that occur at the end of a gene may alter the sequence of the gene and prevent transcriptional termination. A. What types of mutations would prevent p-independent termination? B. What types
If the following RNA polymerases were missing from a eukaryotic cell, what types of genes would not be transcribed? A. RNA polymerase I B. RNA polymerase II C. RNA polymerase III
What sequence elements are found within the core promoter of protein-encoding genes in eukaryotes? Describe their locations and specific functions.
For each of the following transcription factors, how would eukaryotic transcriptional initiation be affected if it were missing? A. TFIIB B. TFIID C. TFIIH
Describe the allosteric and torpedo models for transcriptional termination of RNA polymerase II. Which model is more similar to ρ-dependent termination in bacteria and which model is more similar to
Which eukaryotic transcription factor(s) shown in Figure 12.14 play(s) an equivalent role to σ factor found in bacterial cells?
The initiation phase of eukaryotic transcription via RNA polymerase II is considered an assembly and disassembly process. Which types of biochemical interactions-hydrogen bonding, ionic bonding,
Describe the processing events that occur during the production of tRNA in E. coli.
Describe the structure and function of a spliceosome. Speculate why the spliceosome subunits contain snRNA. In other words, what do you think is/are the functional role(s) of snRNA during splicing?
What is the unique feature of ribozyme function? Give two examples described in this chapter.
What does it mean to say that gene expression is colinear?
What is the meaning of the term consensus sequence? Give an example. Describe the locations of consensus sequences within bacterial promoters. What are their functions?
What is meant by the term self-splicing? What types of introns are self-splicing?
What is alternative splicing? What is its biological significance?
The processing of ribosomal RNA in eukaryotes is shown in Figure 12.16. Why is this called cleavage or processing but not splicing?
In the splicing of group I introns shown in Figure 12.20, does the 5' end of the intron have a phosphate group? Explain.
Mutations in bacterial promoters may increase or decrease the rate of gene transcription. Promoter mutations that increase transcription are termed up-promoter mutations, and those that decrease
According to the examples shown in Figure 12.5, which positions of the -35 sequence (i.e., first, second, third, fourth, fifth, or sixth) are more tolerant of changes? Do you think these positions
In Chapter 9, we considered the dimensions of the double helix (see Figure 9.15). In an α helix of a protein, there are 3.6 amino acids per complete turn. Each amino acid advances the α helix by
What is the subunit composition of bacterial RNA polymerase holoenzyme? What are the functional roles of the different subunits?
A research group has sequenced the cDNA and genomic DNA from a particular gene. The cDNA is derived from mRNA, so it does not contain introns. Here are the DNA
What is an R loop? In an R loop experiment, to which strand of DNA does the mRNA bind, the coding strand or the template strand?
If a gene contains three introns, draw what it would look like in an R loop experiment.
Chapter 20 describes a technique known as Northern blotting that can be used to detect RNA transcribed from a particular gene. In this method, a specific RNA is detected using a short segment of
A gel retardation assay can be used to study the binding of proteins to a segment of DNA. This method is described in Chapter 20. When a protein binds to a segment of DNA, it retards the movement of
As described in Chapter 20 and in experimental question E5, a gel retardation assay can be used to determine if a protein binds to DNA. This method can also determine if a protein binds to RNA. In
The technique of DNA footprinting is described in Chapter 20. If a protein binds over a region of DNA, it will protect the DNA in that region from digestion by DNase I. To carry out a DNA
As described in Table 12.1, several different types of RNA are made, especially in eukaryotic cells. Researchers are sometimes interested in focusing their attention on the transcription of
Based on your knowledge of introns and pre-mRNA splicing, discuss whether or not you think alternative splicing fully explains the existence of introns. Can you think of other possible reasons to
Discuss the types of RNA transcripts and the functional roles they play. Why do you think some RNAs form complexes with protein subunits?
What is a recombinant microorganism? Discuss examples.
As described in Chapter 5, not all inherited traits are determined by nuclear genes (i.e., genes located in the cell nucleus) that are expressed during the life of an individual. In particular,
Discuss the concerns that some people have with regard to the uses of genetically engineered organisms.
A conjugation-deficient strain of A. radiobacter is used to combat crown gall disease. Explain how this bacterium prevents the disease and the advantage of a conjugation deficient strain.
What is bioremediation? What is the difference between biotransformation and biodegradation?
What is a biological control agent? Briefly describe two examples.
As described in Table 21.2, several medical agents are now commercially produced by genetically engineered microorganisms. Discuss the advantages and disadvantages of making these agents this way.
What is a mouse model for human disease?
What is a transgenic organism? Describe three examples.
Explain the difference between gene addition and gene replacement. Are the following descriptions examples of gene addition or gene replacement? A. A mouse model to study cystic fibrosis B.
Recombinant bacteria can produce hormones that are normally produced in humans. Briefly describe how this is accomplished.
What is a chimera? How are chimeras made?
Evidence suggests that Dolly may have been "genetically older" than her actual age would have suggested. As mammals age, the chromosomes in somatic cells tend to shorten from the
When transgenic organisms are made, the transgene may integrate into multiple sites within the genome. Furthermore, the integration site may influence the expression of the gene. For example, if a
What is molecular pharming? Compared with the production of proteins by bacteria, why might it be advantageous?
What is reproductive cloning? Are identical twins in humans considered to be clones? With regard to agricultural species, what are some potential advantages to reproductive cloning?
Researchers have identified a gene in humans that (when mutant) causes severe dwarfism and mental impairment. This disorder is inherited in an autosomal recessive manner, and the mutant allele is
Treatment of adenosine deaminase (ADA) deficiency is an example of ex vivo gene therapy. Why is this therapy called ex vivo? Can ex vivo gene therapy be used to treat all inherited diseases? Explain.
Several research studies are under way that involve the use of gene therapies to inhibit the growth of cancer cells. As discussed in Chapter 24, oncogenes are mutant genes that are overexpressed and
Bacillus thuringiensis makes toxins that kill insects. This toxin must be applied several times during the growth season to prevent insect damage. As an alternative to repeated applications, one
In the experiment of Figure 21.1, why was it necessary to link the coding sequence for the A or B chains to the sequence for β-galactosidase? How were the A or B chains separated from
Explain how it is possible to select for homologous recombination in mice. What phenotypic marker is used to readily identify chimeric mice?
To produce transgenic plants, plant tissue is exposed to Agrobacterium tumefaciens and then grown in media containing kanamycin, carbenicillin, and plant growth hormones. Explain the purpose behind
List and briefly describe five methods for the introduction of cloned genes into plants.
What is a gene knockout? Is an animal or plant with a gene knockout a heterozygote or homozygote? What might you conclude if a gene knockout does not have a phenotypic effect?

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