ProbSet1_solutions(2) - MCB-C100A/ChemC130 Answers to...

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MCB-C100A/ChemC130 Fall 20 10 Answers to Problem Set 1 1. DNA damage prior to replication may alter the pattern or hydrogen bond donors and acceptors on the Watson-Crick face of a nucleotide. When this nucleotide is then part of the template strand during replication, the altered pattern of hydrogen bond donors and acceptors may base pair more stably with the incorrect base for that position, leading to the incorporation of a different base by the polymerase and a point mutation in the DNA strand. 2. Replication proceeds only in the 5’ 3’ direction, and not 3’ 5’, because there only exists in the cell nucleotide triphosphates with the triphosphate group attached to the 5’ carbon of the sugar. This is the high-energy reactive end of the molecule. A replication fork moving in one direction on a double helix is able to replicate both strands simultaneously because, while one strand is replicated continuously in the 5’ 3’ direction (leading strand), the other is replicated in fragments, also in the 5’ 3’ direction (lagging-strand) 3. A new species of nucleotide triphosphates in which the triphosphate group was linked to the 3’ sugar carbon rather than the 5’ sugar carbon could be postulated. The high energy 3’ triphosphate would be susceptible to attack by the 5’ –OH group in the growing strand, allowing the chain to grow in the 3’ 5’ direction. 4. Polymers found in living systems include proteins, nucleic acids (DNA and RNA) and carbohydrates (complex sugars). Proteins and nucleic acids are directly related to each other by the genetic code. Carbohydrate polymers are of variable length and structure, and are produced by enzymes. Although the enzymes are proteins that are directly related to the genetic code in their sequences, carbohydrate polymers bear no direct relationship to the code. Hence, proteins and nucleic acids, but not carbohydrates, contain genetic information that is specific to an individual organism. * 5. Upper left: C:G base pair, found in duplex DNA Upper right: G:G base pair. This is not a proper base pair and is not found in Watson-Crick DNA Lower left: A:G base pair. Not found in Watson-Crick DNA. Lower right: U:A base pair. The use of uracil instead of thymidine is seen in RNA, not DNA. No te that this is a NOT a Watson-Crick pair, also not a standard Hoogsteen base pair (the U is flipped in a Hoogsteen b.p.) but could occur in a folded RNA.
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6. Adenine A-minor interaction. In this interaction, there are hydrogen bonding contacts between the minor groove face of adenine Guanine and the minor groove face of the guanine Guanine Not an A-minor interaction because it utilizes the major groove face of the adenine Adenine * 7. (Note: You are expected to know the chemical structures of the amino acids) 8. Three species of RNA in cells are messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). These different types of RNA have various structures, which are related to their base structures, which are related to their base sequence and, in part, determine their function.
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