Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Does the option: Option 1 Option 2 Option 3 Enhance Biosecurity • By preventing incidents 1 2 NA • By helping respond 3 NA NA Foster Lab Safety • By preventing incident 3 1 NA • By helping respond NA 1 NA Protect the environment • By preventing incidents NA 1 NA • By helping respond NA 2 NA Other considerations • Minimizing costs and burdens to stakeholders 2 2 3 • Feasibility? 2 1 3 • Not impede research 3 1 1 • Promote constructive applications 1 1 1
Homework Questions from Professor Jacobson DNA Polymerase Error Rates and the Human Genome Error Rate of Polymerase: In biological synthesis, error-correcting polymerase has an error rate of approximately $1:106$. This is significantly more accurate than raw chemical synthesis, which has an error rate of roughly $1:102$. Comparison to the Human Genome: The human genome is approximately 3 billion base pairs ($3 \times 109$) in length. At an error rate of $1:106$, copying the entire human genome would result in roughly 3,000 errors per replication cycle. How Biology Deals with the Discrepancy: Biology utilizes specific enzymatic functions to manage and correct these errors to ensure genomic integrity. This includes 3’-5’ proofreading exonuclease activity and 5’-3’ error-correcting exonuclease functions that work alongside template-dependent primer extension to identify and remove incorrect bases. Coding for Human Proteins Ways to Code for an Average Human Protein: The average human protein is 1,036 base pairs long. Because the genetic code is redundant (multiple different codons can code for the same amino acid), there are an astronomical number of possible DNA sequences that can result in the same protein sequence. The sources highlight that biology must find a balance between this codon redundancy and diversity to maintain “fabricational complexity”. Reasons Some Codes Do Not Work: In practice, many DNA sequences that technically code for the correct protein are “impossible” or difficult to use for synthesis or expression due to several biological and mechanical factors: Secondary Structures: Sequences that form hairpins or inverted repeats can interfere with replication and transcription machinery. Extreme GC Content: Regions with very high (≥90%) or very low (≤10%) GC content are often unstable or difficult for polymerase to navigate. Repetitive Sequences: Long terminal repeats, tandem repeats, or clusters of repeats can lead to “slippage” and errors during synthesis. Homopolymers: Long runs of an identical base (e.g., more than 30bp of A) are particularly prone to errors. RNA Cleavage and Stability: Certain nucleotide combinations may inadvertently trigger RNA cleavage rules (such as targets for RNase III), leading to the degradation of the mRNA before it can be translated. Codon Optimization: Not all redundant codons are treated equally by the cell’s translational machinery; choosing the “wrong” codons can lead to inefficient protein production. Homework Questions from Dr. LeProust
Week 2 HW: DNA read write and edit
Part 3. Chose Protein I chose glucokinase (GCK) because in my biochemistry classes I found it to be a very interesting enzyme due to its unique functions and its critical role as a glucose sensor. According to the sources, what makes this enzyme particularly fascinating is that, unlike other members of the hexokinase family, it is not inhibited by its product(glucose-6-phosphate). This allows the enzyme to remain active even when glucose is abundant in the system.
PART 1.  artistic design using the GUI LINK: https://opentrons-art.rcdonovan.com/?id=98conne30870554 PART 2. ARTICLE “An Automated Versatile Diagnostic Workflow for Infectious Disease Detection in Low-Resource Settings” DOI: https://doi.org/10.3390/mi15060708 The article highlights how implementing Opentrons for automated workflows in hospital and clinical settings helps significantly reduce turnaround times and accelerates overall logistics. By increasing sample throughput and enabling the simultaneous processing of multiple samples, the system greatly enhances operational efficiency. Furthermore, automation reduces the risk of human error inherent in manual repetitive tasks and minimizes the possibility of sample contamination or compromising the diagnostic process, ensuring more reliable results.