Part 1: Benchling & In-silico Gel Art

See the Gel Art: Restriction Digests and Gel Electrophoresis protocol for details. Overview:

• [x] Make a free account at benchling.com
• [x] Import the Lambda DNA.
• [x] Simulate Restriction Enzyme Digestion with the following Enzymes: EcoRI HindIII BamHI KpnI EcoRV SacI SalI
• [x] Create a pattern/image in the style of Paul Vanouse’s Latent Figure Protocol artworks.

3.1.     Choose your protein.

In recitation, we discussed that you will pick a protein for your homework that you find interesting. Which protein have you chosen and why? Using one of the tools described in recitation (NCBI, UniProt, google), obtain the protein sequence for the protein you chose.

I chose to work with three finger toxin protein. 3 finger toxins are among the most common toxins in venomous snakes in Kenya and other parts of the world. They are a protein superfamily of toxins that are part of the 3 finger protein domains. I choose it becasie its structure is small enough to work with and its significance in snake venom is massive.

here is the sequence

>sp|Q8QGR0|3SIM7_DENAN Muscarinic toxin 7 OS=Dendroaspis angusticeps OX=8618 PE=1 SV=1
MKTLLLTLVVVTIVCLDLGYTLTCVKSNSIWFPTSEDCPDGQNLCFKRWQYISPRMYDFT
RGCAATCPKAEYRDVINCCGTDKCNK

3.2.     Reverse Translate: Protein (amino acid) sequence to DNA (nucleotide) sequence.

The Central Dogma discussed in class and recitation describes the process in which DNA sequence becomes transcribed and translated into protein. The Central Dogma gives us the framework to work backwards from a given protein sequence and infer the DNA sequence that the protein is derived from. Using one of the tools discussed in class, NCBI or online tools (google “reverse translation tools”), determine the nucleotide sequence that corresponds to the protein sequence you chose above.

Reverse Translate results

Reverse Translate Results

3.3.     Codon optimization.

Once nucleotide sequence of your protein is determined, you need to codon optimize your sequence. You may, once again, utilize google for a “codon optimization tool”. In your own words, describe why do you need to optimize codon usage. Which organism have you chose to optimize the codon sequence for and why?

Codon optimization is very important becasue there are there are more than one codon that may have resulted in the amino acid at a particular location. In different organism,different codon are prefered as comapred to others in the process of translation and therefore its important to optimize inorder to correctly predict how the protein was formed. I have chosen the African green mamba (dendroaspis angusticepts) because this reperesents a potent cocktail of snake venom that and contains a higher percentage of 3 finger toxin than other snakes. I will compare the codon with that of its close relative the black mamba (dendroaspis polylepis).