Midterm_Answers - BioE 140L SynBio Bootcamp Midterm Exam...

Info iconThis preview shows pages 1–2. Sign up to view the full content.

View Full Document Right Arrow Icon
BioE 140L SynBio Bootcamp Midterm Exam Due: March 19, 2009 Your name: <yournamehere> This exam is independent work! You may ask questions of your TAs or Prof for clarification, but you may not work together nor discuss the questions with each other. It is open powerpoint, open notes, open videos, open Wikipedia, open pubmed, and open internet. Put your answers into this word document in black and send it back through bspace (as a word file). Grading: each question is worth an equal number of points. The penalty for late submission is 15% per day unless an alternate due date is arranged at least 5 days in advance. For each question requiring an explanation, your explanation should be under 100 words (less is more ). Qapla'! 1) Design a construction file for making a BglBricks basic part (with start and stop codons, the {part} style) for the Prochlorococcus marinus str. AS9601 phosphatase (YP_001009829.1). Your template for PCR is Prochlorococcus marinus str. AS9601 genomic DNA. A simple construction file, no internal sites. 2) Design a construction file for making a BglBricks basic part (with start and stop codons, the {part} style) for the Legionella pneumophila alanyl tRNA synthetase(AJ277756). Your template for PCR is Legionella pneumophila genomic DNA. GenBank: AJ277756.1. In the annotation, there is something funky with the stop codon, so check that a complete ORF is in the part. 3) Design a construction file for making a BglBricks basic part of the {<part>} style (no start, no stop) for the leucine zipper peptide: YGGIEAKIEAIEAKAEAIEAKIEAIEAKIEA Should be a wobble. Check assembly, check frame, check translation 4) Design a construction file for making a BglBricks basic part of the {<part>} style (no start, no stop) for the RGD peptide: RGD Should be an EIPCR. Check assembly, check frame, check translation 5) Using the PCA method for gene synthesis, design the oligos you’d need to synthesize a BglBricks basic part of the {<part>} style (no start, no stop) for the codon-optimized Tev protease described in accession number DQ516974. There probably is an oligo assembly tool somewhere on the web to make this easier to re- assemble. It may also be that everyone’s oligos are the same and you can compare one student to another. 6) Using the LCA method for gene synthesis, design the oligos you’d need to make the same Tev protease part described in question 5. You should be able to easily concatenate their oligos into the full length product 7) Design oligos to change the Trp58 residue of RFP in plasmid pBca9145-Bca1089 to Alanine using Quikchange There should be two oligos between 40 and 50 bp in length 8) pGFPuv was digested with EcoRI in buffer containing polymerase buffer and dNTPs and blunted with T4 DNA polymerase. After a Zymo cleanup, the material was digested with XbaI and then separated on a gel. The smaller band was gel purified. Meanwhile, plasmid pBca1020-J23100 was digested with PstI and Mung Bean Nuclease. After a Zymo cleanup, the material was digested with SpeI and then loaded on an agarose gel. The larger of two bands was purified.
Background image of page 1

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Image of page 2
This is the end of the preview. Sign up to access the rest of the document.

This note was uploaded on 01/21/2012 for the course BIOE 116 taught by Professor Various during the Fall '10 term at University of California, Berkeley.

Page1 / 6

Midterm_Answers - BioE 140L SynBio Bootcamp Midterm Exam...

This preview shows document pages 1 - 2. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online