Read each question carefully. Write your response in the space provided for each part of each question. Answers must be written out in paragraph form. Outlines, bulleted lists, or diagrams alone are not acceptable and will not be scored.

Scientists studying transcription in yeast (Saccharomyces cerevisiae) created an experimental strain that produced a modified RNA polymerase containing a single amino acid substitution. The scientists determined the maximum elongation rate during transcription with and without the modified RNA polymerase enzyme (Figure 1).

The compound amanitin, which is commonly found in toxic mushrooms, is a specific RNA polymerase inhibitor. Amanitin binds to the RNA polymerase active site and inhibits transcription. In a second experiment, the scientists treated the wild-type and experimental strains of S. cerevisiae with a 40 μg/mL solution of amanitin and recorded the maximum elongation rate of the mRNA (Figure 2). Error bars represent ±2SEx¯.

The figure presents a bar graph with two bars of data. The horizontal axis contains categories for Wild Strain and Experimental Strain. The vertical axis is labeled Maximum Elongation Rate, in nucleotides per second, and the numbers 0 through 16, in increments of 4, are indicated. The data represented in the graph are as follows. Note that the values are approximate. Wild Strain. 12 nucleotides per second, with an error bar that ranges from 9 to 15 nucleotides per second. Experimental Strain. 2 nucleotides per second, with an error bar that ranges from 1 to 3 nucleotides per second. The figure presents a bar graph with two bars of data. The horizontal axis contains categories for Wild Strain and Experimental Strain. The vertical axis is labeled Maximum Elongation Rate, in nucleotides per second, and the numbers 0 through 16, in increments of 4, are indicated. The data represented in the graph are as follows. Note that the values are approximate. Wild Strain 0.7 nucleotide per second, with an error bar that ranges from 0.6 through 0.8 nucleotides per second. Experimental Strain 1.4 nucleotides per second, with an error bar that ranges from 1 through 1.8 nucleotides per second.
Figure 1. Maximum elongation rate under natural conditions Figure 2. Maximum elongation rate in a 40 μg/mL amanitin solution
(a) Describe the three structural components of an RNA nucleotide monomer. Explain the role of RNA polymerase during transcription.

Question 2
(b) Identify the dependent variable in the experiments. Identify a control group missing from the second experiment. Justify the need for this control group in the second experiment.

Question 3
(c) Describe the effect of amanitin on the maximum elongation rate for the wild-type and modified RNA polymerases. Determine the ratio of the average maximum elongation rate for the modified RNA polymerase compared to the wild strain RNA polymerase in Figure 1.

Question 4
(d) State the null hypothesis for the experiment in Figure 1. Provide reasoning to justify the claim that the change in the amino acid sequence in the modified RNA polymerase affected the shape of the active site on the enzyme.

Submit

Structural components of RNA nucleotide monomer includes the following a nitrogen base(adenine/guanine/cytosine/uracil) , A ribose sugar(with 2’-OH group present) and Three phosphate groups.

The role of the RNA POL is for transcribing DNA to RNA

Explanation:

Solution

(1) Structural components of RNA nucleotide monomer are:

a. A nitrogen base(adenine/guanine/cytosine/uracil)

b. A ribose sugar(with 2’-OH group present)

c. Three phosphate groups

Role of RNA POL- RNA pol is the principle enzyme for transcribing DNA to RNA. Bacteria has a single RNAP , while eukaryotes have 3 RNAP(plants have additional 2 polymerases).RNAP catalyses the joining of two ribonucleotides one with another by using nucleophilic attack mecvhanism using the 2 metal ions present in the active site of the RNA pol. The two nucleotides added over the template strand are complementary to it. The RNA pol does this job in 5 to 3 direction

(2) The dependent variable in the experiments is the- Maximum elongation rate the control group in the second experiment is the WILD STRAIN.

Use of control group- Control group consists of individual (here the wild type RNAP) that will show a known result under a particular experimental condition(amanitin treatment). This known response is used as a reference to access the response in a experimental group both qualitatively and quantitatively.

(3). Effect of amanitin-

For wild type- the maximum elongation rate decreased, since the Amanitin binds to the active site of the enzyme. So naturally the maximum elongation rate decreased.

For Mutant- The maximum elongation rate also decreased , but it appears the rate is little more than the wild type. This may be due to the particular amino acid substitution that countered the effect of Amanitin and gave the following result.

The ratio is= 1:6

( 4). The null hypothesis for experiment 1: The maximum elongation rate of the experimental strain will not change due to the amino acid substitution.

Reasoning- The shape of a protein is greatly determined by its amino acid sequence. Even a single amino acid change can cause a big change. So have done the said single amino acid substitution. Since the substitution was in the active site of the enzyme(which is involved in catalyzing the elongation process), so the mutant have definitely caused a change in the shape, that has caused to a reduction in the maximum elongation rate of the enzyme.