Week 6 HW

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May 16, 2024

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Paige Rewerts Names of other students you worked with to complete this assignment (if applicable): ______________________________________________________________________________ Week 6 BIO200 Homework For your homework assignment, please read each section and then answer the following questions in your own words. If you don’t completely understand the concept being asked, that is okay. But for credit, you need to explain what you do understand and what you don’t understand regarding the concept/topic being asked. Section 5.1 Section Learning Objectives:  Construct a model that explains how mutations can accumulate in DNA.  Explain the role of primers in DNA polymerization. 1. What is being measured in the graphs in Figure 5.1? What do the different lines represent? DNA polymerase activity is being measured (pmoles dGMP incorporated over time). Each line in graph A represents a different amount of DNA primer. Each line in graph B represents a different type of primer. 2. What is being measured in Tables 5.1-5.3? What is being compared in each table? In Table 5.1, the activity of cell extracts is being measured. DNA polymerase activity in young and old cell extracts is being compared. In Table 5.2, bases polymerized and error rate of DNA polymerase and different ions are being measured. Young and old DNA polymerase capacity is being compared, as well as different ions. In Table 5.3, error rate of different ions is being measured. Ions on young human DNA are being compared. 3. We learned 4 mechanisms of evolution in 4.1. Which mechanism is being shown in this section? Mutation 4. Using what you learned about the central dogma in Chapter 2, what happens to RNA and protein when DNA is mutated? The protein sequence is changed, usually resulting in a different amino acid. This means that the structure and function changes. The RNA and protein will also be mutated. Section 5.2 (read up to horizontal gene transfer), BME 5.1, and ELSI 5.1 Section Learning Objectives:  Describe the range of genomic changes that can lead to speciation.

 Analyze DNA and protein sequence information to elucidate evolutionary relationships.  Explore the power of dot plots to reveal sequence similarities and differences.  Compose a policy statement on genetically modified organisms (GMOs) based on data and not misconceptions. 1. Compare and contrast a point mutation, inversion, deletion, and duplication. Point Mutation = single base difference; Inversion = a segment of DNA that is flipped; Deletion = a gap in DNA (segment deleted); Duplication = a segment of DNA is duplicated 2. What is being illustrated in Figure 5.3. What are the two axes? The horizontal axis is the chromosome of E. coli, strain O157:H7. The vertical axis is the chromosome of E. coli, strain K-12. The figure is comparing these two by showing how much of the DNA is in the same orientation, and how much is in reverse orientation. The green dots indicate similar DNA sequences are inverted, while red dots indicate similar DNA sequences that are not inverted. 3. How can you tell that the reference and comparison sequences are identical by looking at the sliding window similarity dot plot in BME 5.1 (CH05_dotplot.xlsx)? Change the comparison sequence to acgtggccatatatcgccacACTGGCTGCG (where upper case denotes changed nucleotides). What is the corresponding change in the pattern of dots? What could you conclude about these two DNA sequences from the dot plot? You can tell that the reference and comparison sequences are identical by looking at the sliding window similarity dot plot because there are no gaps or inversions that indicate a part of the sequence being different. When you change the comparison sequence to the one listed above, the reference and comparison sequence are not the same. However, I am confused on how to figure out the corresponding change in the pattern of dot plots. I tried to enter the new sequence, but nothing happened and I’m not sure what I’m doing wrong. Since I can’t figure out how to do this, the only thing I can conclude is that the two sequences are different. 4. Construct two arguments: 1) GMOs are beneficial and should be encouraged, and 2) GMOs are dangerous and should be prohibited. 1) GMOs have many benefits. They can increase food production, reduce pollution, and improve healthcare. They can even produce glow-in-the-dark fish, seedless plants that increase profits for businesses in agriculture, and alter farm animals to become organ donors for humans. The benefits don’t stop there, either. We are still learning what else we can do with GMOs. 2) GMOs are dangerous and should be prohibited. GMOs can have terrible effects on several different things, like making crops sterile and passing on diseases. Another hazard of GMOs is horizontal gene transfer, where there is movement of DNA between different species. Section 5.3 and ELSI 5.2 Section Learning Objectives:  Review immune primary and secondary responses.

 Organize the steps involved in producing a more robust antibody response over time.  Prepare guidelines for a school to determine whether peanut butter should be banned from the lunchroom. 1. What is being measured in each graph in Figure 5.9? Pay attention to the scale of each axis! How does this compare to Figure 5.10? In both graphs of 5.9, relative antibody concentration(x1000) of guinea pig blood over days is being measured. In graph A, the primary response is being measured, while in graph B, the secondary response is being measured. In figure 5.10, relative antibody concentration of rats over days after injection is being measured. The rats were injected with an antigen once and again 6 weeks later. The second one contained a new protein antigen as well as a second dose of the first. They used different proteins in this graph compared to 5.9. 2. Explain what is happening in Figure 5.11. In this figure, the primary and secondary response of antibodies is being shown. The primary response produces B cells, creating antibodies and memory B cells. During the secondary response, the memory B cells produce many more antibody-secreting B cells. 3. What is being measured/shown in Figure 5.12? Specifically, what are the letters along the top? What do you think it means when there is a --- vs letters in the sections below? The changes of amino acids is being showed, I believe. The letters along the top are the amino acids each codon codes for. The letters represent a change in DNA, while the dashes represent no change. 4. Briefly describe what is happening in Figure 5.13. The responses of long-term B cells are shown. Antigen stimulates B cells to make antibody and memory B cells. Second generation B cells undergo somatic hypermutation. B cells with the highest affinity receive the most survival signals and produce the most B cells and memory B cells. 5. What are the pros and cons of banning peanut butter from a school lunchroom? Pros: Those with allergies do not have to worry about being exposed to peanuts and being harmed or potentially killed. It limits the risk of those with a peanut allergy being endangered. Cons: PB&J’s are the most popular lunch in America. They are very easy and convenient to make and almost everyone can make them. A lot of children are very picky and this is one of the few things they will eat. By banning peanut butter, the majority of students will be at an inconvenience and could potentially not eat as much. Section 6.1 Section Learning Objectives:  Determine how eukaryotes inherited genes from bacteria and archaea.  Review the evolutionary origin of the nucleus.

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