Science Practice Challenge Questions
14.1 Historical Basis of Modern Understanding
The proof that DNA, not protein, is the carrier of genetic information involved a number of historical experiments, including transformation or horizontal gene transfer (HGT), which is the uptake and expression of extracellular DNA.
A. As described in Figure 14.3, transformation or HGT was first reported by Griffith in 1928 in an experiment in which the following occurred:
- heat-treated, pathogenic bacteria recovered their pathogenicity when incubated with nonpathogenic bacteria
- plasmids were transferred to nonpathogenic bacteria from pathogenic bacteria through conjugation
- nonpathogenic bacteria acquired pathogenicity when incubated in a broth containing heat-treated, pathogenic bacteria
- polysaccharide cell capsules from pathogenic bacteria were transferred to nonpathogenic bacteria
B. Griffith’s experiment, however, left undetermined the identity of the cellular component that encoded genetic information. The identity of DNA as the carrier of genetic information was resolved through the experiments by Martha Chase and Alfred Hershey because they observed the following:
- injections with a serum containing chemically isolated polysaccharides and nonpathogenic bacteria were not lethal
- pathogenic bacterial DNA that was radioactively labeled using a phosphorus isotope was not present in mice that died
- bacteriophages from a bacterial culture grown in a nutrient-containing medium and radioactively labeled using a sulfur isotope transferred the label to bacteria incubated in an unlabeled nutrient-containing medium
- bacteriophages from a bacterial culture grown in a nutrient-containing medium and radioactively labeled using a sulfur isotope did not transfer the label to bacteria incubated in an unlabeled nutrient-containing medium
C. Transformation and transduction increase variation within populations of bacteria and archaebacteria by the following:
- transferring DNA among different species
- transferring free DNA across the cell membrane without energy expenditure
- transferring DNA between different strains of the same species of bacteria
- phagocytosis of bacteriophages
The evolution of antibiotic resistance via HGT poses a challenge to medical technology. On the other hand, transformation is often assayed by incorporating an antibiotic-resistance gene in the plasmid to be transferred into the host organism. In natural environments, bacterial and archaebacterial cells become competent (able to transport DNA through the cytoplasmic membrane) in response to stress such as UV radiation, high population density, or heat shock. Such conditions are often difficult to model in the laboratory, where competence can be induced by high concentrations of divalent cations, Ca+2 or Mg+2, or electrical shock. In either setting, extracellular DNA can be transported into the cell, and (to a good approximation) uptake is proportional to the concentration of extracellular DNA.
D. Identify a factor that might affect transformation or HGT. Then, design a plan to evaluate the dependence of transformational efficiency (defined as the number of transformations per gram of extracellular DNA) of plasmids that transfer antibiotic resistance to a particular strain of Escherichia coli that is not resistant on that factor.
Prior to the work of Hershey and Chase, scientists thought that inheritance involved “nucleoproteins.” The amount of information to be transmitted between generations did not seem consistent with the chemical simplicity of the few nucleotides found in polymers of deoxyribonucleic acids in comparison to the diversity of protein polymers. Briefly explain:
- the relationship between the structure of polymeric DNA and the information stored
- the relationship between the interactions between base pairs on complementary strands of the double helix and Chargaff’s observation on the relative abundance of nucleotides in DNA
- the meaning of the statement from the Nature publication on the structure of DNA by Watson and Crick: “It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.”
14.2 DNA Structure and Sequencing
In 1977, Fred Sanger developed a method to determine the order of nucleotides in a strand of DNA. Sanger won a Nobel Prize for his work, and his method of sequencing based on dideoxy chain termination (Figure 14.8) has been foundational to the rapid development of more modern, rapid, and cheap methods of sequencing. The challenge of the $1,000 in one-day sequencing of the human genome was achieved in 2016 by next-generation sequencing (NGS), a “catch-all” term describing several sequencing methods.
A. Using the diagrams shown above for reference, explain the effect of the addition of dideoxynucleotides on chain growth of the DNA strand that is copied during sequencing in terms of the structures of dideoxyribose and deoxyribose.
B. Suppose that a single strand to be sequenced is 5’CGAGTACG3’. In the presence of each of the four deoxynucleotides and the dideoxynucleotide ddCTP, describe the strands that would be formed from this template. Include in your description an annotation indicating the 3’ and 5’ ends of the fragments resulting from the procedure.
C. Next-generation sequencing makes termination technology very rapid and relatively inexpensive. All babies born in the U.S. are currently screened by state-mandated tests for several genetic conditions. The number of conditions tested ranges from 29 (GA and KS) to 59 (IL and MS). It is proposed that whole-genome sequencing should be mandatory for all newborns. The Genetic Information Nondiscrimination Act (2008) prevents health insurers from denying coverage or increasing costs of premiums based on genetic information. It also prohibits employers from making use of these data for hiring, firing, or promotion. The act passed in the House with a vote of 420 to 3, although it was lobbied against by organizations representing business (human resources, health insurance, and manufacturers), including the U.S. Chamber of Commerce. The act does not cover life, long-term care, or disability insurance. Pose three questions that are relevant to the use of whole-genome data.
14.3 Basics of DNA Replication
Our understanding of the mechanisms of DNA replication is important to research on cancer and aging. Additionally, the molecular basis of Mendelian genetics was established.
A. The mechanism of DNA replication was investigated by Meselson and Stahl. The diagram below from their 1958 paper summarizes their findings. Describe how this representation illustrates the manner in which DNA is copied for transmission between generations.
B. During the synthesis of new strands of DNA from the parent strands, DNA polymerase can only add nucleotides at the terminal 3’ of a growing strand. Using the diagram below, describe the similarities and differences between the DNA replication of both strands.
C. Shown at the left end of the upper parent strand is the six-base repeat sequence TTAGGG. In humans, this is the repeated, telomeric sequence that is attached to the telomere. The RNA primer in humans spans 10 base pairs, unlike in the drawing where it spans only three. In somatic cells, an enzyme called telomerase no longer functions. Explain the function of telomerase in the development of stem cells and cancer cells, and the inhibition of telomerase in programmed cell death or apoptosis.
14.4 DNA Replication in Prokaryotes
The mitochondria of eukaryote cells contain their own circular DNA (mtDNA), consistent with their origin according to the theory of endosymbiosis. The mitochondrial genome is highly conserved in Eukarya. In humans, the 50 to 100 mitochondria in each of the cells in most tissues have 5 to 10 copies of the genome. Each has 37 genes that primarily encode proteins of the electron transport chain. Point mutations in which a single nucleotide is incorrectly placed is not repaired because the error-checking provided by DNA polymerase is not present in the mitochondria. The mutation rate for mtDNA is approximately 100 times higher than the mutation rate for nuclear DNA. The simultaneous existence of multiple alleles in each cell is likely, a condition called heteroplasmy. In mammals, sperm mitochondria are destroyed prior to fertilization.
A. Explain how point mutations in mtDNA can result in a loss of function in critical cellular components such as cytochrome c yet not be lethal to the cell.
B. Oocyte mitochondria are randomly segregated during meiosis, resulting in variation in the frequency of mtDNA mutations in offspring relative to the parent. Explain how a loss of function does not accumulate, lowering the metabolic performance from generation to generation.
As described in the Evolution Connection in this chapter of the text, a fossil fingertip found in a Siberian cave revealed an evolutionary link between Neanderthals and Denisovans. Fossils from 28 individuals were located in the “pit of bones,” Sima de los Huesos, in Spain, thousands of miles from the Siberian cave. In 2013, mtDNA from a femur of one of these individuals was compared with mtDNA of Denisovans, Neanderthals, and modern humans. It was found that the Sima fossil shared many more alleles with Denisovans than with either Neanderthals or modern humans. In 2016, the same group of scientists who sequenced the mtDNA from the femur of one of the Sima fossils partially sequenced the DNA from that fossil, showing a clear connection to Neanderthals.
C. Analyze these data to draw alternative conclusions regarding the relatedness of the three fossils and support each with evidence.
D. Design a plan to differentiate or resolve these alternative conclusions.