Modeling the Impact of CRISPR on DNA and Protein Synthesis

Part 1: Summary

Part 1: Summary

Did you read the instructions above?

1.Research your CRISPR topic, and consider what we have learned so far in class. Genes in the DNA code for proteins. Some parts of the DNA sequence regulate gene expression (i.e., protein synthesis). When CRISPR is used in your case study to alter the DNA, what is it altering? Is it changing the DNA that codes for protein (i.e., a gene) or is it altering the DNA used for regulating gene expression? Is it creating a new protein or is it preventing or triggering gene expression? 

a.If you have a more general topic, such as “Create resistance in crops to insect pests”, then narrow down your topic to a specific crop.

b.If your case study involves altering multiple pieces of DNA then just select one part for this assessment. 

c.Describe in a few sentences in the worksheet what your topic is, what part of the DNA is being modified, and how that impacts protein and the resulting phenotype

Part 2: Modeling

2.Using the information that you summarized for Part 1, model the two DNA molecules: one before CRISPR and one after CRISPR. Consider the following as you create your model.

a.At this point, you do not need to model how CRISPR works; we will be doing that on the next assessment. 

b.The actual DNA sequence is going to be 100s of bases long. For this model, just use enough to model the process. Feel free to make up a base sequence. What makes it specific to your topic is that you alter the part of the DNA (e.g., promoter) that is changed for your topic.

c.Include bases for the transcription regulatory features and label them (e.g., switches, promoter, and gene coding sequence). 

d.It is fine to model just one of the strands for each molecule.

e.Indicate how the DNA is different between the two molecules.

f.It might be helpful to work backwards a bit; that is, brainstorm what you want to use for the resulting amino acids in the final protein (step #7)- this assessment will have you model each stage of the process, and points are deducted if the DNA, mRNA, and amino acids do not align.

3.Model how transcription is activated and at least one stage of transcription, using just one of your DNA molecules from the previous question. The model will answer the following questions:

a.How does transcription begin? In other words, how are switches/enhancers, activator proteins and transcription factors used? 

b.Where on the DNA sequence does transcription begin?

c.What does transcription look like while the mRNA sequence is elongating?

d.Where on the DNA sequence does transcription terminate?

4.Provide the complete mRNA sequence for both DNA sequences. Or, if your case study involves preventing expression of a protein, then just include the mRNA of the pre-CRISPR molecule and note that CRISPR prevents expression.

5.Draw all tRNAs for the mRNA sequence(s) produced from question #3 above- include anti-codons (bases/nucleotides) and amino acids.

6.Model at least two stages of translation for one of the sequences. The model does not need to include all tRNAs but needs to illustrate the process of translation. Your model will answer the following questions:

a.How are tRNAs and mRNA used during translation?

b.How does translation begin?

c.What happens to the amino acids during translation?

d.What happens once a stop codon is reached?

7.Create a model that illustrates the structural differences between the resulting proteins of both DNA sequences. Or, if your case study involves preventing expression of a protein, then just include the protein of the pre-CRISPR molecule and note that CRISPR prevent expression. Address the following questions in your model.

a.How different or similar do you think the two protein structures are, given their function? 

b.To what extent would the amino acid sequence for each protein differ, based on your answer to question “b” above?

c.How would the amino acid sequence impact the shape of each protein? Consider how charged amino acids interact (positive or negative) and when disulfide bonds form. Label amino acids and charges either directly on the drawing or make a key and use shapes for amino acids.

d.This difference between the two proteins (if two are included) should align with the general description provided for Part 1.

e.Do not just use a squiggly line to represent the difference. Include the specific amino acid sequence (just how we did it in class).

8.Create a model that illustrates how the two proteins (or one protein, if CRISPR prevents gene expression) and resulting phenotypes are different. Consider the following:

a.This is a model and not a written summary. It is fine to include brief notes that explain your model, but a model still needs to be created. 

b.This model is not a structural representation of the proteins- that is done for the previous model. This model is regarding the name and function of the protein (e.g., hemoglobin, which carries oxygen in red blood cells), and then how that protein (before and after CRISPR) influences the organism.

c.This model will vary greatly from topic to topic, but for most topics it should illustrate the difference at multiple scales: both the cellular level and the organismal level. For instance, if it is altering cell signaling, then model which component is being altered and then model how this change in signaling affects the organism. If it is an enzyme, then show how this enzyme impacts cellular function and how that influences the organism. If it is changing structural proteins, then model it at the molecular scale and then how that change affects the organism. If you are unsure if your model is addressing different scales, then please talk with the teaching team.

d.If the CRISPR modification prevents creating the protein, then note this in the model and create a model that portrays differences in phenotype. 

Part 3: Broader Impacts

9.Write a paragraph in the worksheet that explains the broader impacts of this use of CRISPR. Consider the following:

a.Include multiple stakeholders in your explanation. 

b.What are the broader impacts of this use of CRISPR? In other words, is it supposed to reduce symptoms of diseases, prevent diseases, increase crop yield, help with conservation of a species that will then influence other species, etc.? Is it meant to give people more opportunities? 

c.What is the purpose? If it is in regard to diseases, which groups of people primarily have this disease? If it is for conservation, then where is the species from and who will benefit? If it is for agriculture, who is this supposed to help the most? 

d.Who will have access to this and who gains the most from it- financially or otherwise? Which stakeholders may be underrepresented or systematically marginalized? 

e.While looking through articles, the discussion/conclusion of the article may be most useful for this part. You might also have to do some research on the broader topic to answer this question.