Midterm Questions of Differential Chapters - Molecular Biology of Eukaryotes | BIOS 467, Exams of Biology

Download Midterm Questions of Differential Chapters - Molecular Biology of Eukaryotes | BIOS 467 and more Exams Biology in PDF only on Docsity! All of the following questions are taken from the website for your text at www.aw- bc.com/watson. I have chosen questions that could be used for one or more of the longer quesions on the midterm exam. Some of these may be more directly related to the precise material we discussed in class than others are, but all of them force you to think clearly about the concepts we have discussed. Use them as an additional study aid, in addition to the other material I have provided, the text, and your own notes. Critical Thinking Questions, Chapter 3 1. Describe how strong and weak bonds are involved in the process of DNA replication, addressing the role of at least two examples of each type of bond. 2. Describe and compare the three main types of weak chemical bonds that exist in biological systems. 3. Describe the importance of distance to van der Waals interactions. How does this constrain the shape of molecules that rely on such interactions for specific binding to other molecules? 4. Describe the energetic forces underlying hydrophobic bonds. Describe the contribution of each of these forces when two proteins specifically bind to each other in an aqueous solution. 5. Why is it advantageous for the cell to use macromolecules whose shapes are determined by a collection of weak chemical bonds rather than solely by strong chemical bonds? Critical Thinking Questions, Chapter 5 1. Describe the four categories of amino acid side chains. What types of interactions are the members of each of these categories likely to make? 2. Outline the four levels of protein structure, giving a specific example of each. 3. Describe the geometric features of the " helix. Why is this structure especially common? What are the weak bonds that stabilize the $ sheet? 4. How does single-stranded DNA-binding protein ensure specificity for single-stranded DNA as opposed to double-stranded DNA? What do you think the purpose of this protein might be, for example, during DNA replication? 5. What features of the major groove make it especially useful for sequence-specific recognition by proteins? Give at least two examples of DNA binding motifs that binds primarily to the major groove. Provide an example of a protein that does not use the major groove to recognize its target. How does it accomplish its specific binding? Critical Thinking Questions, Chapter 6 1. Draw an A:T base pair. (a) Indicate how each base is joined to deoxyribose. (b) Indicate which edge of each base pair faces into the major groove and which into the minor groove (c) Use two different colors to indicate whether an atom is a hydrogen bond donor or a hydrogen bond acceptor. Do the same for a G:C base-pair 2. Other than hydrogen bonding, what else contributes to the stability of the double helix? 3. Certain chemical agents such as nitrous acid can deaminate cytosine, converting it into uracil. How might this explain why DNA contains thymine in place of uracil? 4. Describe several reasons why the major groove is more often used by proteins to recognize specific DNA sequences than the minor groove. Consider the sequence AATCGG; what information, in terms of hydrogen bond donors, hydrogen bond acceptors, nonpolar hydrogen, and methyl groups, are provided by the major groove and minor groove, in each direction? 5. Describe the ways in which DNA can vary from its ideal B structure, and contrast the B form of DNA with the A and Z forms. What factors or conditions favor these deviations from the B form and the choice between the three possible forms? 6. Draw a graph showing the OD260 as a function of temperature for DNA isolated from a bacterial species having a high GC content, and one from a bacterial species having a low GC content. 7. Draw the reaction that causes RNA to hydrolyze at high pH. (a) Why is RNA more sensitive to high pH than DNA? (b) What is the function of Mg2+ in RNA molecules? Critical Thinking Questions, Chapter 7 1. How is the 2 meters' worth of DNA in every human cell compacted to fit into a nucleus of less than 15 microns? Describe the various ways in which DNA is compacted, describing the proteins or structures involved at each level, and the degree of compaction provided. 2. List the five major types of histone proteins, and describe what role each of them plays in the nucleosome. Based on what you know about them, which histone protein(s) do you think might be the most evolutionarily conserved? Which are likely to be the least conserved? 3. What are the "tails" of the histone proteins, and how are they distinguished from the rest of the protein? 4. Compare the molecular interactions that occur between the histone proteins and DNA and