Meanwhile, even as Miescher's name fell into obscurity by the twentieth century, other scientists continued to investigate the chemical nature of the molecule formerly known as nuclein. One of these other scientists was Russian biochemist Phoebus Levene. A physician turned chemist, Levene was a prolific researcher, publishing more than 700 papers on the chemistry of biological molecules over the course of his career. Levene is credited with many firsts. For instance, he was the first to discover the order of the three major components of a single nucleotide (phosphate-sugar-base); the first to discover the carbohydrate component of RNA (ribose); the first to discover the carbohydrate component of DNA (deoxyribose); and the first to correctly identify the way RNA and DNA molecules are put together.
During the early years of Levene's career, neither Levene nor any other scientist of the time knew how the individual nucleotide components of DNA were arranged in space; discovery of the sugar-phosphate backbone of the DNA molecule was still years away. The large number of molecular groups made available for binding by each nucleotide component meant that there were numerous alternate ways that the components could combine. Several scientists put forth suggestions for how this might occur, but it was Levene's "polynucleotide" model that proved to be the correct one. Based upon years of work using hydrolysis to break down and analyze yeast nucleic acids, Levene proposed that nucleic acids were composed of a series of nucleotides, and that each nucleotide was in turn composed of just one of four nitrogen-containing bases, a sugar molecule, and a phosphate group. Levene made his initial proposal in 1919, discrediting other suggestions that had been put forth about the structure of nucleic acids. In Levene's own words, "New facts and new evidence may cause its alteration, but there is no doubt as to the polynucleotide structure of the yeast nucleic acid" (1919).
Indeed, many new facts and much new evidence soon emerged and caused alterations to Levene's proposal. One key discovery during this period involved the way in which nucleotides are ordered. Levene proposed what he called a tetranucleotide structure, in which the nucleotides were always linked in the same order (i.e., G-C-T-A-G-C-T-A and so on). However, scientists eventually realized that Levene's proposed tetranucleotide structure was overly simplistic and that the order of nucleotides along a stretch of DNA (or RNA) is, in fact, highly variable. Despite this realization, Levene's proposed polynucleotide structure was accurate in many regards. For example, we now know that DNA is in fact composed of a series of nucleotides and that each nucleotide has three components: a phosphate group; either a ribose (in the case of RNA) or a deoxyribose (in the case of DNA) sugar; and a single nitrogen-containing base. We also know that there are two basic categories of nitrogenous bases: the purines (adenine [A] and guanine [G]), each with two fused rings, and the pyrimidines (cytosine [C], thymine [T], and uracil [U]), each with a single ring. Furthermore, it is now widely accepted that RNA contains only A, G, C, and U (no T), whereas DNA contains only A, G, C, and T (no U) (Figure 1).
Figure 1: The chemical structure of a nucleotide.
A single nucleotide is made up of three components: a nitrogen-containing base, a five-carbon sugar, and a phosphate group. The nitrogenous base is either a purine or a pyrimidine. The five-carbon sugar is either a ribose (in RNA) or a deoxyribose (in DNA) molecule.
1: SOME PRINCIPLES
1. How is it possible to discover the functions of the 'non-coding' sequences in and around a gene? To what extent have these techniques yielded satisfactory answers?
2. Repetitive DNA sequences are a major component of mammalian genomes. Describe the different classes of such sequences, and outline what - if any - biological function they may serve.
3. Write an essay on the recognition of information in nucleic acids.
4. What forces maintain the structure of a DNA duplex?
5. Illustrate how differences between the structure of DNA and RNA are reflected in the ways that proteins interact with them.
6. Genes have been defined in many different ways over the years. Describe as many of these ways as you can. What definition is appropriate today?
7. What is DNA supercoiling? How is it generated? What are its biological roles?
8. Discuss redundancy in the genome, and the roles that it plays.
9. Estimates for gene numbers suggest that mammals have four times more genes than flies, and ten times more than yeast. Discuss.
10. What is the role of the nuclear membrane?
11. What are the three primary lineages of the living world, and how do they differ?
12. What design principles are used in the construction of large biological structures like virus particles, the cytoskeleton, and chromosomes.
1. How is the structure of the nuclear pore related to its function?
2. Discuss how proteins are imported into the nucleus.
3. Describe what we know about the synthesis and processing of ribosomal RNA.
4. Would you describe the nucleolus as a ribosome factory, when we know so little about the assembly of ribosomal RNA into a ribosome?
5. Describe the hierarchies of organization of DNA from the double helix to the chromosome. What problems does the organization pose for transcription and replication?
6. How is the structure of DNA in the isolated 'nucleoid' related to that found in vivo?
7. What is the evidence that clusters of chromatin loops are organized into 'clouds' around transcription 'factories'?
8. The cytoplasm contains a well-characterized skeleton. Discuss the evidence for and against the existence of an analogous skeleton within the nucleus.
9. Write an essay on compartmentalization in the nucleus.
10. Why has it been so difficult to determine the structure of a eukaryotic chromosome, whether in interphase or mitosis?
11. Most eukaryotic chromosomes have similar shapes, even though they may contain very different amounts of DNA. How adequately do current models for the organization of the DNA fiber within a chromosome account for its general shape?
12. Discuss current models for the structure of chromatin and chromosomes. How far do they account for the various functions of DNA?
13. What are polytene chromosomes, and how are they formed?
14. Why do mitotic chromosomes have the shape they do?
15. Discuss telomeres in terms of their discovery, location, universality, duplication, and relationship with ageing and cancer.
1. Discuss the evidence for and against the idea that active DNA polymerases are organized into factories.
2. What problems does the double-helical structure of DNA pose for the process of replication?
3. Describe the roles of the different proteins involved in replicating a DNA duplex.
4. How does the process of replication on one side of a replication fork differ from that on the other?
5. DNA polymerases make mistakes. Describe the mechanisms that ensure that parental and daughter duplexes have the same DNA sequences.
6. Describe how the origins of replication in pro- and eu-karyotes can be defined.
7. Compare and contrast the origins of replication found in simple organisms with those of mammalian cells.
8. 'There is no such thing as a specific origin of DNA replication in eukaryotes'. Discuss.
9. Discuss the role played by transcription during replication.
10. Discuss the problems associated with replicating the ends of a chromosome. How are these problems solved?
1. Describe the topological problems associated with transcribing a double-helical template. How are these problems solved?
2. Outline the molecular events that lead to the synthesis of a primary transcript by RNA polymerase II, and describe how evidence for the process was obtained.
3. Discuss the evidence for and against the idea that active RNA polymerases are organized into factories.
4. Describe the properties of the three eukaryotic RNA polymerases and their templates.
5. Comparison of the promoter sequences of a family of mammalian genes reveals that all share a sequence of eight nucleotides. Outline how you would test experimentally the possible role of this octamer sequence in regulating the expression of these genes.
6. Outline the modifications that occur to ribosomal RNA as it matures. How were these modifications discovered?
7. The initiation of transcription by eukaryotic RNA polymerases requires the assembly of a large complex. Outline the order of events that result in initiation, and indicate the type of molecular interactions that are involved.
8. RNA polymerases make mistakes. Describe the mechanisms that ensure that messages contain the correct coding information.
9. To what extent can a transcriptional activity found in vivo be reproduced in vitro?
10. Discuss the role played by the C-terminal domain of RNA polymerase II in the production of a transcript.
11. Describe how a transcript made by RNA polymerase II is modified.
12. How are primary transcripts processed and what roles do such modifications play?
13. Describe the role played by RNA:RNA interactions in the removal of introns from the primary transcript of eukaryotic genes transcribed by RNA polymerase II.
1. Describe the lesions that are commonly found in DNA. What are the consequences if they go unrepaired?
2. Discuss the advantages and disadvantages of the different approaches that have been used to detect the ways in which damaged templates are normally repaired.
3. Illustrate how the study of human disease has helped us to understand the different pathways involved in repairing damage in DNA.
4. Compare and contrast the major pathways involved in repairing damage in human DNA.
5. What are the consequences of a failure to repair damaged templates?
6. Genomes seem to contain more genes involved in repairing DNA than in replicating it. Why?
7. Outline the evidence that some repair of damage in DNA is coupled to transcription.
6: REGULATION OF GENE EXPRESSION
1. The expression of bacterial genes is controlled by the action of diffusible repressors and activators. To what extent is the expression of mammalian genes controlled similarly?
2. How true is the statement that all cells in a mammal contain the same genetic information?
3. Outline the various levels at which the expression of genes is controlled? What methods would you use to identify which control mechanisms were operating in a particular case?
4. The differentiated state is generally stable and can be inherited from one somatic cell to another. What mechanisms might account for this stability and how might you distinguish experimentally between them?
5. Describe the experimental approaches that have been used to analyze how gene expression is regulated at the level of the nucleosome (and/or) chromatin loop?
6. How do covalent modifications of histones and DNA affect gene expression?
7. How far has a detailed knowledge of the nucleotide sequence in and around genes helped to explain their tissue-specific expression?
8. Discuss the relative importance of cis- and trans-acting factors in the control of transcription.
9. Discuss the advantages and disadvantages of the various approaches being used to obtain an understanding of tissue-specific gene expression?
10. Are locus control regions any different from transcriptional enhancers?
11. Describe the experimental approaches used to define enhancers and locus control regions, and explain how the functions of the two sequences differ.
12. What are the major factors underlying the inactivity of heterochromatin?
13. 'Methylation of DNA results from, but does not cause, differentiation.' Discuss.
14. Assess the significance of DNA methylation as a mechanism for suppressing gene expression.
15. How close are we to a complete molecular definition of the inactivity of heterochromatin?
16. Outline the various mechanisms that are involved in creating (and/or maintaining) the differentiated state.
17. 'The techniques of structural biology have told us little about the regulation of gene expression that we did not already know'. Discuss.
18. What does the birth of the first parthenogenetic mouse tell us about imprinting and mammalian development?
19. Cellular protein levels can be controlled by regulating the rate of translation. Give some examples of the mechanisms involved, and discuss the experimental approaches used to confirm that control is exerted at the level of translation.20. To what extent does the position of a gene in the genome determine gene expression? Outline the experimental approaches that have been used to answer this question.
21. An enduring idea in biology sees genomes as looped, with the ties that maintain loops as barriers between different functional domains. What is the evidence for looping, and how might those barriers work?
22. A histone 'code' is thought to regulate gene expression. Describe the experimental approaches that have been used to establish how this code might operate.
7: THE CELL CYCLE
1. Discuss the role that microtubules play in chromosome segregation.
2. The spindle contains millions of moving parts. How are these movements controlled?
3. Centromeres exhibit a bewildering structural variation. What are their main functions?
4. The cell cycle is regulated by the reversible phosphorylation of proteins. Discuss.
5. How is the synthesis of DNA controlled in eukaryotes?
6. Review the evidence supporting current models for the initiation of DNA replication in eukaryotic cells.
7. Compare the checkpoints in the cell cycles of yeast and man.
8. Assess the evidence that the mechanisms for controlling passage through the cell cycle are conserved in eukaryotes.
9. Review the mechanisms that ensure orderly progression through the cell cycle.
10 .Discuss the evidence that genetic defects are responsible for malignancy.
11. Describe the advantages and disadvantages of the various approaches being used to identify genes involved in cancer.
12. Discuss the view that malignancy results from an imbalance in the activity of oncogenes and anti-oncogenes.
13. Cancer is a multi-step process. Discuss.
14. How have studies of the nematode, Caenorhabditis elegans, contributed to our understanding of apoptosis? How does the process in the worm differ from that in higher vertebrates?
15. How is the apoptotic machinery controlled?
16. 'Cancer chemotherapy owes nothing to molecular biology.' Discuss.
17. How has the study of developmental biology impinged upon our understanding of cancer?
8: MEIOSIS AND RECOMBINATION
1. Compare and contrast the processes of mitosis and meiosis.
2. Discuss the roles that the synaptonemal complex and the chiasma play during meiosis.
3. Describe the mechanisms involved in the exchange of genetic information from one chromosome to another.
4. Describe the phenomenon of gene conversion in yeast.
5. How effectively do current models account for the properties of meiotic and mitotic recombination?
6. The breaking and joining of DNA are widespread in both prokaryotes and eukaryotes. What do we know of the various mechanisms that are used in these processes?
7. How do chromosomes pair?
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