BIOL 240 - UW - FINAL LATEST
EXAM
What proportion of E Coli's genome would be predicted to have
"unknown function"? - ANSWERS-30%
If you care about high quality gene sequences more than you care about
high throughput, which technology might you choose? - ANSWERS-
Sanger is a bit dated but it is still the one we reach for because it is has
very low error rates
If you already have illumine sequences for your genome and your
genome still has gaps, how might you collect long reads to help bridge
the gaps, without primer walking? - ANSWERS-PacBio and Nanopores
would work
In involving a streptomycin-sensitive wild type Hfr donor and an F-
recipient that uses a streptomycin resistant leucine auxotroph (leu-) an
appropriate selection for leu+ recombinants would be... - ANSWERS-
Defined medium lacking leucine but with streptomycin
Transcriptome - ANSWERS-Collection of transcribed mRNA molecules
in a cell
END OF
PAGE 1
, BIOL 240 - UW - FINAL LATEST
EXAM
Transcriptomics - ANSWERS-A library of the expressed mRNA
molecules of a cell can be formed as a cDNA library using reverse
transcriptase. Can be sequenced directly, or analyzed by microarrays
RNA Sequencing - ANSWERS-Performed by conversion of extracted
mRNA into cDNA by reverse transcriptase. cDNA is then sequenced
using rapid automated methods. Has been used successfully to study
Saccharomyces cerevisiae and other organisms. Look at the
transcriptomes of MANY organisms beyond yeast too. Will continue to
evolve in speed and benefit in tandem with DNA sequencing and
analysis methods. You sequence a million reads from one cDNA and
another to see the statistically significant difference
Microarrays - ANSWERS-A method for examining transcriptional
activity of all genes in a cell simultaneously. Comparing different
treatments of cells. Probe DNA fragments are amplified by PCR and
placed on a glass slide in a known pattern. Maybe make three probes to
each gene in the genome, you will put them all in a grid like pattern and
then you take the cDNA that you prepared (with an added florescent
label) and add it. Each label is different. Total cell mRNA is converted
to cDNA by reverse transcriptase, labeled with a fluorescent molecule,
and passed over the microarray slide. The more intensely a "spot" on the
microarray lights up, the more cDNA is present
END OF
PAGE 2
, BIOL 240 - UW - FINAL LATEST
EXAM
Microarray Uses - ANSWERS-Global gene expression (expression of
specific gene classes under different conditions: regulons. Including
mutant strains), expression of genes with unknown function, yield clues
to function, comparison of gene content in related organisms (label the
DNA and compare that to another organism), species identification
Proteome Analysis - ANSWERS-Can be studied by multiple methods
such as 2D-polyacrylamide gel electrophoresis (PAGE), Mass
spectrometry, x-ray crystallography, Nuclear magnetic resonance
(NMR)
Proteome - ANSWERS-The collection of expressed proteins in a cell
2D-Page - ANSWERS-Allows separation of proteins on a gel based on
isoelectric point (i.e. charge, pH where the protein has no charge). Mass
spectrometry can determine amino acid sequences of the polypeptides
from 2D-PAGE. Comparison of sequence to known protein sequences
can help determine identity
2D PAGE Analysis - ANSWERS-Across the top of the gel you spread
your proteins based on their pH. They move through the gel until they
reach a point where they become neutral, isoelectric point. Small
proteins move further down than the larger proteins
END OF
PAGE 3
, BIOL 240 - UW - FINAL LATEST
EXAM
X-ray Crystallography - ANSWERS-X-ray beam shot at crystallized
protein. Diffraction pattern used to discern protein shape. You can get
really high resolution 3D shapes
Nuclear Magnetic Resonance (NMR) - ANSWERS-Measures distances
between atomic nuclei. Can measure proteins in solution. Limited to
proteins of about 30 kDa. As long as your protein is small you will be
able to get the shape
Metagenomics - ANSWERS-Involves construction and analysis of gene
libraries from DNA extracted directly from complex microbial
communities. This field is changing our understanding of life on Earth,
finding evidence for newly discovered organisms in very diverse and
challenging locations (acid mine drainage, deep sea thermal vents,
wastewater treatment). Some of the genes discovered have possible
applications in biotechnology and nanotechnology
Metagenomics Steps - ANSWERS-Obtain DNA from area of interest,
Sequence, and Analyze (eliminate known sequences to then find new
genes, potentially from new organisms)
END OF
PAGE 4
EXAM
What proportion of E Coli's genome would be predicted to have
"unknown function"? - ANSWERS-30%
If you care about high quality gene sequences more than you care about
high throughput, which technology might you choose? - ANSWERS-
Sanger is a bit dated but it is still the one we reach for because it is has
very low error rates
If you already have illumine sequences for your genome and your
genome still has gaps, how might you collect long reads to help bridge
the gaps, without primer walking? - ANSWERS-PacBio and Nanopores
would work
In involving a streptomycin-sensitive wild type Hfr donor and an F-
recipient that uses a streptomycin resistant leucine auxotroph (leu-) an
appropriate selection for leu+ recombinants would be... - ANSWERS-
Defined medium lacking leucine but with streptomycin
Transcriptome - ANSWERS-Collection of transcribed mRNA molecules
in a cell
END OF
PAGE 1
, BIOL 240 - UW - FINAL LATEST
EXAM
Transcriptomics - ANSWERS-A library of the expressed mRNA
molecules of a cell can be formed as a cDNA library using reverse
transcriptase. Can be sequenced directly, or analyzed by microarrays
RNA Sequencing - ANSWERS-Performed by conversion of extracted
mRNA into cDNA by reverse transcriptase. cDNA is then sequenced
using rapid automated methods. Has been used successfully to study
Saccharomyces cerevisiae and other organisms. Look at the
transcriptomes of MANY organisms beyond yeast too. Will continue to
evolve in speed and benefit in tandem with DNA sequencing and
analysis methods. You sequence a million reads from one cDNA and
another to see the statistically significant difference
Microarrays - ANSWERS-A method for examining transcriptional
activity of all genes in a cell simultaneously. Comparing different
treatments of cells. Probe DNA fragments are amplified by PCR and
placed on a glass slide in a known pattern. Maybe make three probes to
each gene in the genome, you will put them all in a grid like pattern and
then you take the cDNA that you prepared (with an added florescent
label) and add it. Each label is different. Total cell mRNA is converted
to cDNA by reverse transcriptase, labeled with a fluorescent molecule,
and passed over the microarray slide. The more intensely a "spot" on the
microarray lights up, the more cDNA is present
END OF
PAGE 2
, BIOL 240 - UW - FINAL LATEST
EXAM
Microarray Uses - ANSWERS-Global gene expression (expression of
specific gene classes under different conditions: regulons. Including
mutant strains), expression of genes with unknown function, yield clues
to function, comparison of gene content in related organisms (label the
DNA and compare that to another organism), species identification
Proteome Analysis - ANSWERS-Can be studied by multiple methods
such as 2D-polyacrylamide gel electrophoresis (PAGE), Mass
spectrometry, x-ray crystallography, Nuclear magnetic resonance
(NMR)
Proteome - ANSWERS-The collection of expressed proteins in a cell
2D-Page - ANSWERS-Allows separation of proteins on a gel based on
isoelectric point (i.e. charge, pH where the protein has no charge). Mass
spectrometry can determine amino acid sequences of the polypeptides
from 2D-PAGE. Comparison of sequence to known protein sequences
can help determine identity
2D PAGE Analysis - ANSWERS-Across the top of the gel you spread
your proteins based on their pH. They move through the gel until they
reach a point where they become neutral, isoelectric point. Small
proteins move further down than the larger proteins
END OF
PAGE 3
, BIOL 240 - UW - FINAL LATEST
EXAM
X-ray Crystallography - ANSWERS-X-ray beam shot at crystallized
protein. Diffraction pattern used to discern protein shape. You can get
really high resolution 3D shapes
Nuclear Magnetic Resonance (NMR) - ANSWERS-Measures distances
between atomic nuclei. Can measure proteins in solution. Limited to
proteins of about 30 kDa. As long as your protein is small you will be
able to get the shape
Metagenomics - ANSWERS-Involves construction and analysis of gene
libraries from DNA extracted directly from complex microbial
communities. This field is changing our understanding of life on Earth,
finding evidence for newly discovered organisms in very diverse and
challenging locations (acid mine drainage, deep sea thermal vents,
wastewater treatment). Some of the genes discovered have possible
applications in biotechnology and nanotechnology
Metagenomics Steps - ANSWERS-Obtain DNA from area of interest,
Sequence, and Analyze (eliminate known sequences to then find new
genes, potentially from new organisms)
END OF
PAGE 4
