BIOMG 3300 - Unit 9 Study Questions
Solved 100% Correct
Discuss how a DNA microarray (or chip) can be used to study changes in gene expression
that accompany development. Note that the microarray is probed with two samples
prepared with different fluorescent markers giving the relative abundance of the sequence
of interest in each sample.
A microarray can be prepared from a known DNA sequence. Once the DNA is attached to a
solid support, the microarray can be probed with other fluorescently labeled nucleic acids.
Here, mRNA samples are collected from cells of a frog at two different stages of development.
What can DNA microarrays also be used for?
medical diagnosis (e.g. for the detection of DNA variation known to be linked to disease)
What does CRISPR stand for?
Clustered Regulatory Interspaced Short Palindromic Repeats
What is the biological function of CRISPR / Cas in bacterial cells?
CRISPR is the immune system for prokaryotes in that when exogenous DNA that has previously
infected the prokaryotes reinfects the bacteria, the CRISPR array is transcribed and the
exogenous DNA is cleaved. If the exogenous DNA is new, then the exogenous DNA is cleaved
and a piece of the DNA is put into the CRISPR array and then is there for next time.
Use Fig. 9-24a (left, p. 343) to show how CRISPR / Cas 9 can be used to "knock out" a
gene. Use Fig. 9-24a (right, p. 343) to show how CRISPR / Cas 9 can be used to make a
specific change in a gene sequence.
For CRISPR use a Cas protein that contains two active endonuclease domains that can do a
double strand breaks. Then for the specific change in the sequence you would have to do
a single strand break so the Cas
What are micro-RNAs?
small pieces of DNA that can prevent translation, they need to associate with a (RNA Induced
Silencing Complex) RISC, when they come together, it can block translation of the mRNA, when
it is a perfect complement for the mRNA it will cause its degradation.
Explain how RNAi can be used as a gene silencing method.
, This can be used as a gene silencing mechanism as it is can degrade particular mRNA to
prevent proteins from being made, therefore, comparing these cells to other cells, you can
detect the functions of the protein based on the cell's response.
Use Fig. 8-34 (p. 303) to discuss the Sanger method for DNA sequencing.
Sanger uses a dideoxynucleoside (no 2' OR 3' hydroxyl group) in order to stop polymerization
when it reaches a particular nucleotide. It uses a mix of this nucleotide and the regular dNTPs
in order to figure out the point of every one of the bases that is used. The new version is one
entire reaction that uses every type of ddNTP and attaches them to fluorophores in order to
determine the base at every point. They are run on a gel and you can sequence it from this at
high resolution as you know that the first base is the lowest color and the second base is the
second lowest etc. The new method just uses one reaction also with dNTPs that are attached
to fluorophores and polymerized normally. This molecule is then passed through a laser and
the nucleotides are determined based on the fluorescence that they are giving off.
Draw the structure of ddATP (you may use A as an abbreviation for the structure of the base).
Explain how incorporation of a dideoxynucleoside will affect subsequent polymerization by
DNA polymerase.
IT IS JUST A REGULAR ATP WITH NO HYDROXYLS ON THE 2’ OR 3’ CARBON
How many reactions are included in a typical DNA sequencing experiment? Describe the
composition of each reaction.Review the definition of "radioactive isotope" given in the
glossary of the text book (p. G-15). How is radioactivity incorporated into the sequences?
Before the fluorescent ddNTPs were used, you did four different reactions for each nucleic acid.
With the fluorescent ddNTPs, you only need to do one reaction with all of it together. The
radioactivity is the label that is put onto each nucleic acid that is unique to the other types of
nucleic acids.
Given the sequence and primer, write the sequences that would be produced using
the dideoxy analog of dATP. Do the same for the other three dideoxy analogs.
The bands seen on the electrophoresis gel differ in length by how many nucleotides?
(in Sanger sequencing)
There will be spacing of one nucleotide between all of the bands
Do problem 17 on p. 315.
Distinguish between radioactivity and fluorescence.
The difference between radioactivity and fluorescence is what you are emitting.
Why is it possible with this method to have only a single reaction mixture?
Solved 100% Correct
Discuss how a DNA microarray (or chip) can be used to study changes in gene expression
that accompany development. Note that the microarray is probed with two samples
prepared with different fluorescent markers giving the relative abundance of the sequence
of interest in each sample.
A microarray can be prepared from a known DNA sequence. Once the DNA is attached to a
solid support, the microarray can be probed with other fluorescently labeled nucleic acids.
Here, mRNA samples are collected from cells of a frog at two different stages of development.
What can DNA microarrays also be used for?
medical diagnosis (e.g. for the detection of DNA variation known to be linked to disease)
What does CRISPR stand for?
Clustered Regulatory Interspaced Short Palindromic Repeats
What is the biological function of CRISPR / Cas in bacterial cells?
CRISPR is the immune system for prokaryotes in that when exogenous DNA that has previously
infected the prokaryotes reinfects the bacteria, the CRISPR array is transcribed and the
exogenous DNA is cleaved. If the exogenous DNA is new, then the exogenous DNA is cleaved
and a piece of the DNA is put into the CRISPR array and then is there for next time.
Use Fig. 9-24a (left, p. 343) to show how CRISPR / Cas 9 can be used to "knock out" a
gene. Use Fig. 9-24a (right, p. 343) to show how CRISPR / Cas 9 can be used to make a
specific change in a gene sequence.
For CRISPR use a Cas protein that contains two active endonuclease domains that can do a
double strand breaks. Then for the specific change in the sequence you would have to do
a single strand break so the Cas
What are micro-RNAs?
small pieces of DNA that can prevent translation, they need to associate with a (RNA Induced
Silencing Complex) RISC, when they come together, it can block translation of the mRNA, when
it is a perfect complement for the mRNA it will cause its degradation.
Explain how RNAi can be used as a gene silencing method.
, This can be used as a gene silencing mechanism as it is can degrade particular mRNA to
prevent proteins from being made, therefore, comparing these cells to other cells, you can
detect the functions of the protein based on the cell's response.
Use Fig. 8-34 (p. 303) to discuss the Sanger method for DNA sequencing.
Sanger uses a dideoxynucleoside (no 2' OR 3' hydroxyl group) in order to stop polymerization
when it reaches a particular nucleotide. It uses a mix of this nucleotide and the regular dNTPs
in order to figure out the point of every one of the bases that is used. The new version is one
entire reaction that uses every type of ddNTP and attaches them to fluorophores in order to
determine the base at every point. They are run on a gel and you can sequence it from this at
high resolution as you know that the first base is the lowest color and the second base is the
second lowest etc. The new method just uses one reaction also with dNTPs that are attached
to fluorophores and polymerized normally. This molecule is then passed through a laser and
the nucleotides are determined based on the fluorescence that they are giving off.
Draw the structure of ddATP (you may use A as an abbreviation for the structure of the base).
Explain how incorporation of a dideoxynucleoside will affect subsequent polymerization by
DNA polymerase.
IT IS JUST A REGULAR ATP WITH NO HYDROXYLS ON THE 2’ OR 3’ CARBON
How many reactions are included in a typical DNA sequencing experiment? Describe the
composition of each reaction.Review the definition of "radioactive isotope" given in the
glossary of the text book (p. G-15). How is radioactivity incorporated into the sequences?
Before the fluorescent ddNTPs were used, you did four different reactions for each nucleic acid.
With the fluorescent ddNTPs, you only need to do one reaction with all of it together. The
radioactivity is the label that is put onto each nucleic acid that is unique to the other types of
nucleic acids.
Given the sequence and primer, write the sequences that would be produced using
the dideoxy analog of dATP. Do the same for the other three dideoxy analogs.
The bands seen on the electrophoresis gel differ in length by how many nucleotides?
(in Sanger sequencing)
There will be spacing of one nucleotide between all of the bands
Do problem 17 on p. 315.
Distinguish between radioactivity and fluorescence.
The difference between radioactivity and fluorescence is what you are emitting.
Why is it possible with this method to have only a single reaction mixture?
