Tutorial Questions (chapter 10)_IVLE MCQ 1. What is a mechanism of condensation shared by both prokaryotes and eukaryotes? A. Nucleosomes B.

Loop domains C. 30 nm fiber D. All of the above E. None of the answers are correct 2. When DNA is compacted by histones into tight 10 nm and 30 nm fibers, the DNA is unable to interact with proteins required for gene expression. Therefore, to allow for these proteins to act, the chromatin must constantly alter its structure. Which process may contribute to this dynamic activity? A. Modifications of histone tails B. DNA supercoiling at or around H1 C. Hydrolysis of DNA molecules where they are wrapped around the nucleosome core D. Accessibility of heterochromatin to helicase E. Accessibility of the supercoils to DNA topoisomerase I and II 3. Which of the following structures of a eukaryotic chromosome is not primarily composed of DNA? A. Telomeres. B. Origin of replication. C. Kinetochore. D. Centromere. E. Transposable elements 4. Which of the following statements regarding a nucleosome is correct in mammals? A. It contains a large protein which is connected to DNA by smaller linker proteins. B. It contains approximately 146 base pairs of DNA. C. It includes histone and nonhistone proteins. D. All of these. E. None of these. 5. Nucleosomal chromatin, with a diameter of 100, supercoils into a 300 superhelix. The histone that appears to be responsible for this compaction is A. H4. B. H3. C. H2.

D. H1. E. None of the above. 6. When a chromosomal rearrangement such as an inversion occurs placing a known gene into or next to a heterochromatic region, the gene's expression A. will turn on. B. may be amplified. C. may cease. D. may not be affected. E. None of the choices are correct. 7. Cohesins are a multisubunit protein complex that functions to A. hold sister chromatids together. B. ensure that proper chromosome arm length is maintained. C. allow easy karyotyping. D. develop meiotic chromosome replication. E. All of the choices are correct. 8. Which of the following promotes the formation of heterochromatin during metaphase? A. Radial loop domains B. Condensin and cohesion C. 30 nm fibers D. Nucleosomes E. Nuclear matrix 9. Chromosome banding patterns can be used for which of the following? A. analyzing chromosomal differences between species B. locating genes C. revealing the cause of certain genetic diseases D. revealing genes activities (are being transcribed or not) E. All of the choices are correct. 10. Which of the following are properties of telomeres? (You may be able to answer this after second part of this module). A. Consist of special repetitive DNA sequences. B. Prevent the loss of DNA through incomplete replication. C. Cap the ends of each chromosome. D. Number of repeats varies with cell type. E. All of the choices are correct.

Open-ended/ structured questions/Essay 1. Practice textbook S3, E4, E9 and E10, textbook P267-269 2. Describe the relationship between chromatin structure and gene function in eukaryotic
chromosomes. 3. Outline the entire process from DNA replication to chromatin formation during a mitotic cell cycle (ignoring the detailed description).

4. The following questions pertain to a previously undiscovered single-celled organism found living at a great depth on the ocean floor. Its nucleus contains only a single, linear chromosome consisting of 7 106 nucleotide pairs of DNA coalesced with three types of histonelike proteins. (application questions) i). A short micrococcal nuclease digestion yielded DNA fractions consisting of 700, 1400, and 2100 base pairs. Predict what these fractions represent. What conclusions can be drawn? ii). The analysis of individual nucleosomes revealed that each unit contained one copy of each protein and that the short linker DNA had no protein bound to it. If the entire chromosome consists of nucleosomes (discounting any linker DNA), how many are there, and how many total proteins are needed to form them? iii). Analysis then revealed the organisms DNA to be a double helix similar to the WatsonCrick model, but containing 20 base pairs per complete turn of the right-handed helix. The physical size of the nucleosome was exactly double the volume occupied by the nucleosome found in any other known eukaryote, and the nucleosomes axis length was greater by a factor of two. Compare the degree of compaction (the number of turns per nucleosome) of this organisms nucleosome with that found in other eukaryotes.

Lecture 3 (chapter 10) MCQ: 1. B, 2. A, 3. C, 4. B, 5. D, 6. C, 7. A, 8. B, 9. E. 10. E. Hints MCQ8: Why is the answer B? Because I was thinking A seems correct too. In euchromatin, the 30 nm fiber forms radial loop domains. In heterochromatin, these radial loop domains become compacted even further. Please look at the Fig 10.24 in our textbook (P265) or my lecture slide to find how condensin molecules compact the radial loop domains. However, our book does not explain how cohesion works for heterochromatin compaction. At molecular level, these two proteins often interact with each other to maintain the heterochromatin structure. Open-ended/ structured questions/Essay: E4: Supercoiled DNA would look all curled up into a relatively compact structure. You could add different purified topoisomerases and see how they affect the structure via microscopy. For example, gyrase relaxes positive supercoils while topoisomerase I relaxes negative supercoils. If we added topoisomerase I to a DNA preparation and it became less compacted, then the DNA was negatively supercoiled. E9: Several answers are possible and include digesting the DNA with DNase and determining if regular multiples of about 200 bp result (from protection by eukaryotic nucleosome formation). DNA associated proteins could be isolated and differences could indicate if the new organism was prokaryotic or eukaryotic. E10: Histones are positively charged and DNA is negatively charged. They bind to each other by these ionic interactions. Salt is composed of positively charged ions and negatively charged ions. For example, when dissolved in water, NaCl becomes individual ions of Na+ and Cl. When chromatin is exposed to a salt such as NaCl, the positively charged Na+ ions could bind to the DNA and the negatively charged Cl ions could bind to the histones. This would prevent the histones and DNA from binding to each other. Q2: The compaction of chromosomes makes DNA inaccessible to the proteins that initiate gene expression. This compaction is greatest at metaphase and anaphase, which curtails most gene transcription at these times. On the other hand decompaction precedes gene expression. The opening up and closing off of chromosomal areas depends on a dynamic network of DNAprotein interactions, which modifies the density of chromatin packaging to appropriate levels for genetic function and passage through the cell cycle. Once established, the chromatin structure that determines a gene's expression is stably transmitted to daughter cells. You may mention and describe position effect variegation and Barr body formation as specialized cases of the relationship between chromatin structure and gene function.

Q3: Before DNA synthesis can occur, the chromatin fiber must unwind. Next, as DNA replication proceeds (with the help of DNA polymerase), newly formed DNA must associate with histones, either preexisting histones or recently synthesized ones that have just made their way to the nucleus. The synthesis and transport of histones must be coordinated with DNA synthesis since the nascent DNA becomes incorporated into nucleosomes within minutes of its formation. Finally, the nucleosomal DNA must interact in specific ways with a variety of proteins (nuclear matrix) to compact in the same pattern as before. (You may also write about the different pattern seen in differentiating cells that allows expression of different genes.) With the progress of cell cycle getting into G2, chromatin fibers are further compact by interaction with scaffold, condensin and cohesin into metaphase chromosome structures during M phase. The chromosome will decompact into radio loop structure in G1 phase. Q4: i). The chromatin fiber may consist of a nucleosome variant containing 700 base pairs of DNA. The 1400- and 2100-bp fractions represent two and three of these nucleosomes, respectively, linked together. Enzymatic digestion may have been incomplete, leading to the latter two fractions. ii). Since the chromosome contains 7 106 base pairs of DNA, the number of nucleosomes, each containing 7 102 base pairs, is equal to 7 106/7 102 = 104 nucleosomes The chromosome thus contains copies of each of the three proteins, for a total of 3 104 proteins. iii). The unique organism compacts a length of DNA consisting of 35 complete turns of the helix (700 base pairs per nucleosome/20 base pairs per turn) into each nucleosome. The normal eukaryote compacts a length of DNA consisting of 20 complete turns of the helix (200 base pairs per nucleosome/10 base pairs per turn) into a nucleosome half the volume of that in the unique organism. The degree of compaction is therefore less in the unique organism.