PCR and Gel electrophoresis
What does PCR stand for?
Polymerase chain reaction
(slide) Using PCR & gel electrophoresis, which template and primers could you use to detect a SNP in Exon 1?
Option 1) gDNA, primers L1 and R1
Option 2) cDNA, primers L2 and R2
Neither of these options would work
Both of these options would work
Neither of these options would work
What is the name of the step that turns DNA into pre-mRNA and what synthesizes RNA from DNA?
Transcription
RNA polymerase
Name the 2 types of promoters and the genes that we used for Experiment 3:
Constitutive: Amp-R and Conditional: GFP
Scientific name of the "barley" plant that we used
Hordeum murinum
What step of PCR involves the separation of DNA strands and what temperature does it require. What is the enzyme involved in PCR?
Denaturation/ 98 C/ DNA polymerase
Which nonsynonymous mutation changes a codon to a stop codon?
Nonsense
Name one stop codon
UAA/ UAG/ UGA
What allows the GFP gene to glow?
sugar (arabinose)
Define bioinformatics
use of technology/tools like gene sequencing to understand biological data
How much agarose is required to make a 2% gel with a volume of 300 mL 1X TAE?
6 g
Calculations:
(2g/100) * 300 = 6g
(slides) What causes polymorphism shown in the image?
Transposable element
This is the term for a three-nucleotide sequence on mRNA that codes for a specific amino acid.
codon
How can a bacteria uptake plasmid?
Bacteria is turned chemically competent by weakening their cell walls through chemical washes. This allows plasmids to enter after co-incubation with bacteria on ice followed by heat shock.
Name one way to identify genetic differences in organisms
Genomic sequences
If you dilute a solution that has a volume of 300 mL and a concentration of 90 M to make a solution that has a final volume of
500 mL, what will the final concentration be and how much water will you have added?
final concentration = 54M
water volume = 200mL
c1v1 = c2v2
90M * 300mL = c2 * 500mL
final volume =(90*300)/500 = 54M
volume of water = final volume - initial volume
500 - 300 = 200mL
The mRNA sequence "AUC UAC AGC GAA UAG" codes for the amino acids "I-T-S-G-Stop". The third codon has a SNP mutation that changes the third nucleotide 'C' to an 'A': AGC --> AGA (changing the protein to A) What type of mutation would this be?
Nonsynonymous -missense
What type of RNA serves as a link for growing amino acid chain?
Transfer-RNA
(slides)
What is the activator/inducer that controls the
promoter?
Lactose
Arabinose
GFP
Ampicillin
Lactose
Name the primer used in the Actin PCR.
ITS (Internal Transcribed Spacer)
(Slide) PCR table
.....
(slides) In the sequence alignment, where is an Indel present?
Position 7 (All 4 sequences)
Position 8 (All 4 sequences)
Position 4 (All 4 sequences)
Position 8 (Sequence 1)
Position 6 (All 4 sequences)
Position 5 (All 4 sequences)
Position 3 (All 4 sequences)
(slide) Using the codon table, look at the following mRNA sequence (ACG AAA UCU CAC UAA), what would the correct string of amino acids be if the second nucleotide "C" of the third codon was deleted?
Thr Lys Phe Thr----
Transformation efficiency formula?
first calculate mass of plasmid: #ng of plasmid = volume of DNA used * concentration of DNA.
transformation efficiency: (# colonies/ #ng of plasmid) * (#total volume µl/#plated volume)
What was the Barley Project's main objective?
Identify the genetic differences among Hordeum murinum and analyze the genetic relationships through phylogenetic tree