Week 9 Problem setslass
DUE: Next Week, beginning of class.
NOTES:
- All BIOE.80 problem sets must be completed individually unless plainly noted otherwise.
- Please turn in your completed problem sets as an electronic copy via Canvas.
- Please make sure to not go over the word limits and when appropriate show your work (e.g., calculations).
(Q1) Design and Synthesis of a Minimal Bacterial Genome (40 pts)
A key skill that you will need as bioengineers is to read, understand, and extract informationfrom research papers that are shaping and defining the frontiers of bioengineering. This is inpart due to the fast changing pace of bioengineering. We would like you to practice this skill as early as possible, to help you become better at it.
In class we started to discuss the paper “Design and synthesis of a minimal bacterial genome”. In this problem you will review the the paper to level up your ability to read and extractinformation from a research paper.
1.a. Re-read the abstract from the paper, in your own words describe what was the paper’s goal(s), what did the authors discover by working on these goal(s). (bullet points)
1.b. Take a look at Figure-1 from the paper titled: “The JCVI DBT cycle for bacterial genomes”. Think back to what you have learned during the DBT Week. Based on the figure and your prior knowledge, what tools and technologies were used to design, build, and test Syn3.0.? (bullet points)
1.c. Take a look at Figure-2 titled: “Strategy for whole-genome synthesis”. What do the red, blue, and green arrows represent? What does the orange arrow represent? Using the figure briefly explain how they went from Oligos to a whole genome? (bullet points)
1.d. Assuming $0.04 per base pair what is the minimum cost ofsynthesizing the Syn3.0 genome?
1.e. Take a look at Figure-7. Let’s compare the phenotype of Syn1.0 and Syn3.0. Describe what you see when comparing panel A and B and panel C?(bullet points) Which cellsgrow faster? ( Syn1.0 or Syn3.0.)
(Q2) Approximation and estimation - Genome Size (40 pts)
Now thatyou have examined a minimal genome have you wondered how big is a typical genome?
The E. coli MG1655 genome is 4.6 Mbp (megabasepairs) long, or approximately 4,600,000base pairs. A good rule of thumb for the length of a single DNA base pair is that it is ⅓ nm long. As another rule of thumb, let’s treat the volume of an E. coli cell as being approximately 1 μm^3 see. This is a rough, order-of-magnitude estimate.
In real life, cell size and volume willv ary based upon species, growth rate, and stage of division in addition to many other factors.
2.a. How long would the E. coli genome be as a linear strand of DNA? Provide your answerin μm. How long would the Syn3.0 genome be as as a linear strand of DNA?
2.b. The E. coli genome is actually circular. What is the radius of the genome, assuming thegenome is arranged as a perfect circle and given the linear length that you calculated above?
2.c. Consider your answers in relation to the size specifications for E. coli given above. Whatdoes this imply about the layout of DNA inside a living cell? (Two sentences).
Note: A good rule of thumb for the volume of a DNA base pair is that one base pair has avolume of approximately 1 nm^3.
2.d. How much DNA could be packed into an E. coli cell, assuming that the whole cellvolume only contains DNA? Why is this number ridiculous? (i.e., the E. coli genome issignificantly smaller: why?)
Additional resources: If you like to learn more about various genome sizes please visit this link
github source code for teaching staff