S13 Biol 321 TAKE-HOME Quiz 25 pts total This is Option 1. Answers are due to CT by 5 pm on Friday May 24 No late submissions will be accepted

Transcription

1 S13 Biol 321 TAKE-HOME Quiz 25 pts total This is Option 1 Answers are due to CT by 5 pm on Friday May 24 No late submissions will be accepted Please read carefully through this quiz. I will answer questions about it in class on Mon 5/20 and Wed 5/22. I can t take questions during office hours since I want the entire class to have access to the same information (from me). You can me questions but I will only address them during class. Rules for working this quiz: This is an open-note, open-book, open-internet quiz. You may discuss these questions with your fellow classmates BUT, you MUST write up your answers independently. In other words, if any answers look suspiciously similar I will divide the total possible points between the similar answers. Also please do not consult other faculty members about the quiz. If I can t easily read your answers, I will not grade them. Please word process the text of your answers. Diagrams should be neatly laid out, clearly labeled, and hand drawn. 1

2 PART A 16 pts This problem is divided into a series of questions. You do not have to get the correct answer to a given question in order to answer the next question Antiviral Drug Ribavirin Works by Causing a Genetic Meltdown Ribavirin is an antiviral drug that is currently in widespread clinical use to treat various RNA virus infections including (hepatitis C). It has a broad spectrum of action against members of almost all RNA viruses families that possess an RNA-dependent RNA polymerase. This excludes the retrovirus family that converts an RNA genome to DNA with an RNA-dependent DNA polymerase. The RNA in RNA viruses has the same chemical properties as respectable cellular RNA. Ribavirin is a mutagen whose antiviral activity is exerted through lethal mutagenesis of the viral genetic material: Model of error catastrophe. Viral burst sizes are variable and range from particles released per infected cell. The majority of viruses in a normal RNA virus population are viable. But a small increase in mutation frequency is predicted to push the virus population into error catastrophe (right), where the number of error is sufficiently high to lethally mutate a majority of the virus population. White indicates live virus. Gray indicates dead virus. Most animal RNA virus genomes are ~10 kb long. 2

3 RNA viruses such as hepatitis C and polioviruses contain a single stranded genomic RNA called the plus (+) strand (meaning it is translated to produce virus proteins). The genomic RNA is used as a template to make complementary copies, which are called minus (-) strands. These are in turn used to make more plus strand copies of the genome. 1. The normal (in the absence of ribavirin) error rate in replicating an RNA virus genome (such as poliovirus) has been measured as ~2 X 10-4 mutations per nucleotide replicated -- similar to the error rate made by host RNA polymerase during transcription. Based on this information and on relevant lecture material, is it likely that the viral RNA polymerases have a proofreading function? Very briefly explain two sentences max. Include a statement indicating that you know what a proofreading function is --from the biochemical perspective. Use proper biochemical terminology. 2. The graphs indicate that even in the absence of a mutagen, RNA viruses operate near the outer limit of mutation tolerance. How/why does a virus tolerate a normal error rate of 2 X 10-4 mutations per nucleotide replicated? Compare this error rate to the error rate of DNA replication in a prokaryotic or eukaryotic cell. What factor(s) are important when considering what rate of mutation is tolerable for a virus or an organism? 3-4 sentences. Hints: think about lifestyle issues and be sure to read the legends to the graphs. 3. What general class of mutagens does ribavirin belong to? No explanation here -- just the proper category. Consult your textbook. 4. What chemical modification needs to occur before ribavirin can be used as a substrate by the viral polymerase? Include a drawing of the modified form of ribavirin. 5. Ribavirin pairs only with pyrimidines and interconverts between the two rotational isomers shown on the next page, which are about equally stable. Explain in detail why this compound causes genetic meltdown : Your answer must include a diagram showing H-bonding of the different rotational forms with pyrimidines that would be found in RNA. Orient the base pairs to maximize H-bond formation. Ribavirin can result in 4 different transition mutations. Track a Cà U ribavirin induced mutation starting with this short sequence from the wild-type poliovirus (+) genome: AGAACGG. Be sure to track 5 and 3 ends and indicate each step in the production of a 3

4 mutant (+) strand from a wild-type (+) strand. Assume that ribavirin is present through the genome duplication process along with the natural bases. Neat and clearly-labeled hand drawings are fine here. In lecture we discussed the base-pairing ambiguities of the natural purine and pyrimidines. What is different about the base-pairing ambiguity of ribavirin that would result in a genetic meltdown? 6. Hepatitis virus replication and assembly takes place in the cytosol of the cell. Any good antiviral agent must specifically target the pathogen without traumatizing the host cell too much. Why would ribavirin cause mutations in RNA viruses but not in host DNA? Speculate as to why ribavirin does not appear to interfere with host cell transcription a couple of possibilities here equally stable rotational isomers 4

5 PART B 9 pts At this link read the short sections entitled: The Chemical Breakdown of Alcohol The Genetics Behind Metabolism Here is an abstract of a paper exploring the effects of ADH and ALDH polymorphisms on the risk of alcoholism: Major genetic components underlying alcoholism in Korean population Alcohol metabolism is one of the biological determinants that could significantly be influenced by genetic polymorphisms in alcohol-metabolism genes. Alcohol dehydrogenase (ADH) converts alcohol to acetaldehyde, and aldehyde dehydrogenase (ALDH) converts acetaldehyde to acetate. The well-known genetic polymorphisms in ADH1B(Arg47His) and ALDH2(Glu487Lys) have dramatic effects on the rate of metabolizing alcohol and acetaldehyde, respectively. The protective allele of ADH1B (ADH1B_47His) encodes for a rapid ethanol-metabolizing enzyme, and the protective allele of the ALDH2 (ALDH2_487Lys) results in a decreased rate of acetaldehyde conversion to acetate. However, the combined genetic effects of both functional polymorphisms have not been clarified. 1. The ADH1B*2 polymorphism is also known as the hyperactive ADH1B 47His allele that results in increased catalytic activity compared to the ADH1B 47Arg allele, considered the reference allele with respect to baseline enzymatic activity. Consult the mutation jargon chart found in your lecture material and describe the ADH1B*2 polymorphism using proper jargon. Indicate all applicable terms from the chart. Also indicate whether this is a chemically conservative change or not. 2. The ADH1B*2 polymorphism results from a single nucleotide polymorphism (SNP). Consult a codon table and indicate the single base-pair substitution underlying the polymorphism. Use appropriate mutation jargon to describe the SNP. 3. In 5-6 cogent sentences (max) summarize the data shown in the table below & synthesize it with info from the web site. Indicate dominance for the susceptible/tolerance allele of each gene and briefly provide a physiological rationale (based on the effect of the variant alleles on gene function) for the distribution of genotypes in the two groups of subjects. Combined analysis of association of ADH1B Arg47His and ALDH2 Glu487Lys with the risk of alcoholism in Korean male subjects (n= 1032): distribution of genotypes among alcoholics and normal controls (NC) 5