Week 2 HW
Part 1: Benchling & Gel Art
Benchling Lambda DNA Gel with various enzymes
Benchling Lambda DNA Linear Map with various enzymes
Benchling Lambda DNA Art!!! XXXX put art screenshot here XXXX
Part 2: In person lab - N/A
Part 3: DNA design challenge
3.1. Choose your protein. I chose myoglobin
- Myoglobin is a protein that transports oxygen around skeletal and cardiac muscles, and scavenges nitric oxide.
- I found myoglobin interesting because of it’s prevalence in mammals that dive in water, like whales and dolphins, where in there muscles, higher concentrations of myoglobin can be found.
NCBI protein sequence for myoglobin (specifically: myoglobin isoform 1 [Homo sapiens])
- NCBI Reference Sequence: NP_001369738.1
- MGLSDGEWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGATVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLQSKHPGDFGADAQGAMNKALELFRKDMASNYKELGFQG
ex from HGTAA:
sp|P03609|LYS_BPMS2 Lysis protein OS=Escherichia phage MS2 OX=12022 PE=2 SV=1 METRFPQQSQQTPASTNRRRPFKHEDYPCRRQQRSSTLYVLIFLAIFLSKFTNQLLLSLL EAVIRTVTTLQQLLT
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 translation result using bioinformatics.com
- reverse translation -> most likely codons atgggcctgagcgatggcgaatggcagctggtgctgaacgtgtggggcaaagtggaagcggatattccgggccatggccaggaagtgctgattcgcctgtttaaaggccatccggaaaccctggaaaaatttgataaatttaaacatctgaaaagcgaagatgaaatgaaagcgagcgaagatctgaaaaaacatggcgcgaccgtgctgaccgcgctgggcggcattctgaaaaaaaaaggccatcatgaagcggaaattaaaccgctggcgcagagccatgcgaccaaacataaaattccggtgaaatatctggaatttattagcgaatgcattattcaggtgctgcagagcaaacatccgggcgattttggcgcggatgcgcagggcgcgatgaacaaagcgctggaactgtttcgcaaagatatggcgagcaactataaagaactgggctttcagggc
reverse translation -> consensus codons atgggnytnwsngayggngartggcarytngtnytnaaygtntggggnaargtngargcngayathccnggncayggncargargtnytnathmgnytnttyaarggncayccngaracnytngaraarttygayaarttyaarcayytnaarwsngargaygaratgaargcnwsngargayytnaaraarcayggngcnacngtnytnacngcnytnggnggnathytnaaraaraarggncaycaygargcngarathaarccnytngcncarwsncaygcnacnaarcayaarathccngtnaartayytngarttyathwsngartgyathathcargtnytncarwsnaarcayccnggngayttyggngcngaygcncarggngcnatgaayaargcnytngarytnttymgnaargayatggcnwsnaaytayaargarytnggnttycarggn
[Example: Get to the original sequence of phage MS2 L-protein from its genome phage MS2 genome - Nucleotide - NCBI]