BME $201$ Homework $5$

Due on Canvas on Wednesday $2/21/24$

On Canvas you will find a file named "BME$201\_$HW$5\_$Spring$2024.$mlx$".$ It is broken up into three

sections, each one modeling a different aspect of molecular biology: DNA replication, transcription, and

translation. Follow the instructions in the code to analyze the DNA sequence from the human insulin

gene $($found in the file insulinDNAseq.txt$).$

Throughout the code, there are lines that require you to answer questions and lines that require you to

modify$/$add your own code $($denoted by square brackets $[]).$

A couple of notes:

$1.)$ If the code takes more than $3$ seconds to run, you're probably stuck in an infinite loop. Use ctrl$+$C to

stop the code if this happens. I highly recommend you Google how to use breakpoints in MATLAB to

make sure you only run the code up until the point you care about. If you let it run beyond the lines

you've worked on$,$ you'll almost definitely run into problems. It also might be helpful to use the 'Run

Section' button $($which just runs the current section of code$)$ rather than 'Run'.

$2.)$ Troubleshooting hint: If you're running into problems, copy and paste each line in order in the

command window. Make sure each line is doing what you want it to do$.$ If you're troubleshooting a for

loop, first type $i=1$ in the command window.

Use the schematics below to help interpret the input and output for each section. Hint: use the

sequences below to confirm that your output looks correct for each step!

DNA Replication

$3\text{'}$ tcggga

$.$tggtcg $5^{\text{'}}=$ given template sequence $($input$)$

$5\text{'}$ agccct

$.$accagc $3^{\text{'}}=$ synthesized strand sequence $($output$)$

Transcription

$3\text{'}$ tcggga

tggtcg $5^{\text{'}}=$ antisense strand $($input$)$

$5\text{'}$ agcccu

accagc $3^{\text{'}}=$ synthesized RNA strand $($output$)$

Translation

$5\text{'}$ agcccu....aug gcc cug....ccagc $3^{\text{'}}=$ RNA strand $($input$)$

$5\text{'}$ aug gcc cug....ccagc $3^{\text{'}}=$ ORF $($intermediate$)$

M$-$A$-$L amino acid sequence $($output$)$

I need help with this please