BCH5413 - Exam 1 2026 NEWEST EXAM
COMPLETE 600 QUESTIONS AND CORRECT
DETAILED ANSWERS (VERIFIED ANSWERS)
ALREADY GRADED A+ BRAND NEW!!
1. After any type of mutagenesis is complete, the additional steps of transformation, selection,
miniprep, and sequencing are needed. Explain why each is necessary to complete the
mutagenesis project. - CORRECT ANSWER: a. Transformation: Involved Bacteria uptake of
genetic material which enables it to gain a function. Then you plate the bacteria on media that
contains antibiotic and colonies that grow have that plasmid
b. Selection: In selection, you pick a colony and grow them in liquid LB with positive selection,
and let it rest overnight to grow more of the bacteria
c. Miniprep: Is used to isolate the plasmid
d. Sequencing: In this step, there is screening for the mutation, to see that the mutation actually
took effect. It is usually completed through sanger sequencing and using a chromatogram.
1. After one cycle of PCR, how many DNA fragments to you have that exactly match your target
sequence? Explain your answer. - CORRECT ANSWER: a. In the first round of PCR, DNA
polymerase does not know where to stop. Each primer copies the template beyond the target
sequence. Every fragment of DNA in the mix is longer than the target. Over time, the fragments
that start and stop and the primer sequences dilute out those longer fragments. answer would be
zero. If you have the forward primer extending past where it "needs to stop" and the reverse
primer extending past where it "needs to stop" in the opposite direction, after a single cycle of
PCR, you would end up with: (1) the two original denatured strands of template DNA (2) a 5'-to-
3' synthesized strand that has "too much" 3' end and (3) a 3'-to-5' synthesized strand that has "too
much" 5' end. Therefore you would not have ANY of the target sequence by itself after only 1
cycle.
1. Based on the carbon numbering system for the sugar (1 - 5) that makes up DNA, describe the
main component that is attached to each carbon and why it is important to the structure of DNA.
- CORRECT ANSWER: a. Carbon #1: Has the nitrogenous base attached. There are 2 groups of
nitrogenous bases: 1.) purines (2 rings; adenine and guanine) and 2.) pyrimidines (1 ring;
thymine (uracil in RNA) and cytosine). Adenine and thymine (2 hydrogen bonds) and guanine
and cytosine (3 hydrogen bonds) base pair then to form double-stranded DNA.
,b. Carbon #2: Determines if the sugar is ribose (RNA) or 2-deoxyribose (DNA). A hydroxyl (-
OH) at position #2 would indicate ribose and just a hydrogen at position #2 would indicate 2-
deoxyribose.
c. Carbon #3: Always has a hydroxyl group attached whether DNA or RNA. This hydroxyl group
participates in the reaction required to build nucleotide chains.
d. Carbon #4: Closes the ring structure of the 5-carbon sugar. Carbon #5 branches from Carbon
#4 then.
e. Carbon #5: Has the phosphate group attached. This phosphate group reacts with the Carbon #3
hydroxyl of another nucleotide to form a phosphodiester bond and link nucleotides together
(phosphate-sugar backbone). In addition, the phosphate group is negatively-charged, giving DNA
its overall negative charge.
1. Briefly describe the regions of DNA and histones that make contacts within the nucleosome
structure. - CORRECT ANSWER: When DNA wraps around the histone to form the nucleosome
it does so by having 14 sites in its minor groove (non-specific interaction) interact with the
histone arginine. -Depending upon the needs of the cell this interaction can be tightly wound up
making it inactive (less active) or looser, making it active (more active).Modifications to the
structure of the nucleosome can occur at the tail ends of the structure.
1. Choosing an E. coli protein expression system has a lot of advantages such as yield, cost and
ease. Discuss (not just list) two reasons why a researcher might not choose this type of system.
Be specific, what might their goal be and why wouldn't this system work for them? - CORRECT
ANSWER: a. The initial reason why researches may not use E.coli is because E. coli lack
sophisticated post-translational modification systems alongside a limited cDNA size (which may
limit the vector choice for preferred protein). For example, if the protein of interest is post
translationally modified in eukaryotic cells, you may not be able to study in completion the
protein function because you can miss a key step within the process (cofactors, phosphorylation,
methylation, etc.). If studying along gene regulation, cell trafficking, or cell cycle that involve
the key protein, you need to utilize a mammalian cell to study in completion to fulfill the purpose
of the experimental question.
,b. Secondly, E.coli may have a different preference of codons to create a protein, and depending
on the coding sequence needed for the protein of interest, this may pose an issue. Site directed
mutagenesis may be necessary to change a codon and use the nucleotide that E.coli prefers
without having to change the protein. This adds more steps to the purpose of the experiment, and
additional risk for skewed results.
1. Compare and contrast the method by which you detect your fragment of interest in a Southern
vs. northern vs. western blot. - CORRECT ANSWER: To detect your fragment of interest in a
Southern blot (DNA), you have to transfer the DNA fragments that are in the agarose gel to a
nylon membrane. It is done using an apparatus which allows buffer to flow upwards through gel
and to the nylon membrane. It is left overnight until the DNA of interest is in the filter, which can
then be detected by incubating with a specific probe.
The Northern blot (RNA) technique is similar to the Southern blot because we have to transfer
RNA using the capillary transfer apparatus. You probe the membrane with the labeled DNA
probe as well. The major difference of the Northern blot, in comparison to the Southern blot, is
the use of formaldehyde in the gel to denature the RNA.
The Western blot (protein) technique uses sodium dodecyl sulfate (SDS) to denature the protein
sample. The SDS-coated protein samples are loaded onto a polyacrylamide gel and an electrical
field is applied. The negatively charged proteins migrate towards the positive electrode. You
would then set up a transfer apparatus, however, you would apply another electrical field rather
than relying on capillary transfer. It's similar to Southern and Northern blots because you still
have to transfer your fragment of interest from the gel to the membrane, but doing it using
electrical fields instead.
1. Compare and contrast the method of base detection between pyrosequencing and ion torrent
sequencing. - CORRECT ANSWER: a. Both Pyrosequencing and Ion Torrent sequencing are
sequencing methods that quantify the integration of nucleotides into a DNA fragment. The
chemistry for both ways is the same. You start by preparing a DNA fragment obtained from a
DNA library and add an adapter to each end. The designed DNA fragment is then attached to a
bead and amplified. These beads are further diluted and loaded into wells of a microtiter plate.
Next, you get a primer, allow it to anneal to the DNA of interest, and then add one of four bases
A, T, G, or C. In the example, a T is added to the mix. If the T is the next base in the sequence,
then it will be integrated by DNA polymerase, and pyrophosphate is removed. Two other
enzymes use this released phosphate and ATP to produce light. If the added base was not the next
, in the sequence, no light would be produced, and apyrase would degrade the nucleotide. You
then repeat this process with each of the other bases.
b. In the case of Ion Torrent Sequencing, it starts with the same process, except that in addition to
removing pyrophosphate, it also removes Hydrogen ions. This allows for the detection of pH
changes. So, for example, you add a T, and if the pH changes, then the base is added to the
sequence. On the other hand, if there is no change in pH, then the base is not incorporated and
degraded by apyrase.
c. In summary, Pyrosequencing and Ion torrent sequencing share the same chemistry. However,
they differ in that pyrosequencing detects base integration through light production, while ion
torrent sequencing detects it through changes in pH.
1. Compare the use of DNA methylation in mammalian cells and DNA methylation in bacterial
cells. - CORRECT ANSWER: a. DNA methylation in mammalian cells inhibits transcription. In
bacterial cells, DNA methylation works as part of a bacterial immune system by preventing
digestion by their own restriction enzymes, which digests foreign DNA molecules that are not
methylated, including phage DNA molecules.
1. DAPA
a. How is it different from ChIP for determining if a protein is bound to a specific DNA
sequence? - CORRECT ANSWER: i. DAPA relies on Western blotting to further understand the
relationship between the protein and a portion of DNA, while ChIP relies on PCR as the method
to determine the pairing
1. DAPA
a. What is it? - CORRECT ANSWER: i. The DNA Affinity Purification Assay (DAPA) is a
technique used to analyze protein-DNA interactions and identify a particular protein that binds to
a specific DNA sequence. It involves the isolation and purification of DNA fragments (that have
tags added) that are bound to the protein of interest, followed by their subsequent analysis.
1. Describe how PCR can be modified to make it quantitative. - CORRECT ANSWER: a.
Modified to make quantitative to measure the amount of amplified DNA during or after PCR
process
b. Use fluorescent probes (TaqMan probe) - hydrolysis probes consisting of fluorophore and
quencher attached to each end that are designed to bind within amplified DNA and during
COMPLETE 600 QUESTIONS AND CORRECT
DETAILED ANSWERS (VERIFIED ANSWERS)
ALREADY GRADED A+ BRAND NEW!!
1. After any type of mutagenesis is complete, the additional steps of transformation, selection,
miniprep, and sequencing are needed. Explain why each is necessary to complete the
mutagenesis project. - CORRECT ANSWER: a. Transformation: Involved Bacteria uptake of
genetic material which enables it to gain a function. Then you plate the bacteria on media that
contains antibiotic and colonies that grow have that plasmid
b. Selection: In selection, you pick a colony and grow them in liquid LB with positive selection,
and let it rest overnight to grow more of the bacteria
c. Miniprep: Is used to isolate the plasmid
d. Sequencing: In this step, there is screening for the mutation, to see that the mutation actually
took effect. It is usually completed through sanger sequencing and using a chromatogram.
1. After one cycle of PCR, how many DNA fragments to you have that exactly match your target
sequence? Explain your answer. - CORRECT ANSWER: a. In the first round of PCR, DNA
polymerase does not know where to stop. Each primer copies the template beyond the target
sequence. Every fragment of DNA in the mix is longer than the target. Over time, the fragments
that start and stop and the primer sequences dilute out those longer fragments. answer would be
zero. If you have the forward primer extending past where it "needs to stop" and the reverse
primer extending past where it "needs to stop" in the opposite direction, after a single cycle of
PCR, you would end up with: (1) the two original denatured strands of template DNA (2) a 5'-to-
3' synthesized strand that has "too much" 3' end and (3) a 3'-to-5' synthesized strand that has "too
much" 5' end. Therefore you would not have ANY of the target sequence by itself after only 1
cycle.
1. Based on the carbon numbering system for the sugar (1 - 5) that makes up DNA, describe the
main component that is attached to each carbon and why it is important to the structure of DNA.
- CORRECT ANSWER: a. Carbon #1: Has the nitrogenous base attached. There are 2 groups of
nitrogenous bases: 1.) purines (2 rings; adenine and guanine) and 2.) pyrimidines (1 ring;
thymine (uracil in RNA) and cytosine). Adenine and thymine (2 hydrogen bonds) and guanine
and cytosine (3 hydrogen bonds) base pair then to form double-stranded DNA.
,b. Carbon #2: Determines if the sugar is ribose (RNA) or 2-deoxyribose (DNA). A hydroxyl (-
OH) at position #2 would indicate ribose and just a hydrogen at position #2 would indicate 2-
deoxyribose.
c. Carbon #3: Always has a hydroxyl group attached whether DNA or RNA. This hydroxyl group
participates in the reaction required to build nucleotide chains.
d. Carbon #4: Closes the ring structure of the 5-carbon sugar. Carbon #5 branches from Carbon
#4 then.
e. Carbon #5: Has the phosphate group attached. This phosphate group reacts with the Carbon #3
hydroxyl of another nucleotide to form a phosphodiester bond and link nucleotides together
(phosphate-sugar backbone). In addition, the phosphate group is negatively-charged, giving DNA
its overall negative charge.
1. Briefly describe the regions of DNA and histones that make contacts within the nucleosome
structure. - CORRECT ANSWER: When DNA wraps around the histone to form the nucleosome
it does so by having 14 sites in its minor groove (non-specific interaction) interact with the
histone arginine. -Depending upon the needs of the cell this interaction can be tightly wound up
making it inactive (less active) or looser, making it active (more active).Modifications to the
structure of the nucleosome can occur at the tail ends of the structure.
1. Choosing an E. coli protein expression system has a lot of advantages such as yield, cost and
ease. Discuss (not just list) two reasons why a researcher might not choose this type of system.
Be specific, what might their goal be and why wouldn't this system work for them? - CORRECT
ANSWER: a. The initial reason why researches may not use E.coli is because E. coli lack
sophisticated post-translational modification systems alongside a limited cDNA size (which may
limit the vector choice for preferred protein). For example, if the protein of interest is post
translationally modified in eukaryotic cells, you may not be able to study in completion the
protein function because you can miss a key step within the process (cofactors, phosphorylation,
methylation, etc.). If studying along gene regulation, cell trafficking, or cell cycle that involve
the key protein, you need to utilize a mammalian cell to study in completion to fulfill the purpose
of the experimental question.
,b. Secondly, E.coli may have a different preference of codons to create a protein, and depending
on the coding sequence needed for the protein of interest, this may pose an issue. Site directed
mutagenesis may be necessary to change a codon and use the nucleotide that E.coli prefers
without having to change the protein. This adds more steps to the purpose of the experiment, and
additional risk for skewed results.
1. Compare and contrast the method by which you detect your fragment of interest in a Southern
vs. northern vs. western blot. - CORRECT ANSWER: To detect your fragment of interest in a
Southern blot (DNA), you have to transfer the DNA fragments that are in the agarose gel to a
nylon membrane. It is done using an apparatus which allows buffer to flow upwards through gel
and to the nylon membrane. It is left overnight until the DNA of interest is in the filter, which can
then be detected by incubating with a specific probe.
The Northern blot (RNA) technique is similar to the Southern blot because we have to transfer
RNA using the capillary transfer apparatus. You probe the membrane with the labeled DNA
probe as well. The major difference of the Northern blot, in comparison to the Southern blot, is
the use of formaldehyde in the gel to denature the RNA.
The Western blot (protein) technique uses sodium dodecyl sulfate (SDS) to denature the protein
sample. The SDS-coated protein samples are loaded onto a polyacrylamide gel and an electrical
field is applied. The negatively charged proteins migrate towards the positive electrode. You
would then set up a transfer apparatus, however, you would apply another electrical field rather
than relying on capillary transfer. It's similar to Southern and Northern blots because you still
have to transfer your fragment of interest from the gel to the membrane, but doing it using
electrical fields instead.
1. Compare and contrast the method of base detection between pyrosequencing and ion torrent
sequencing. - CORRECT ANSWER: a. Both Pyrosequencing and Ion Torrent sequencing are
sequencing methods that quantify the integration of nucleotides into a DNA fragment. The
chemistry for both ways is the same. You start by preparing a DNA fragment obtained from a
DNA library and add an adapter to each end. The designed DNA fragment is then attached to a
bead and amplified. These beads are further diluted and loaded into wells of a microtiter plate.
Next, you get a primer, allow it to anneal to the DNA of interest, and then add one of four bases
A, T, G, or C. In the example, a T is added to the mix. If the T is the next base in the sequence,
then it will be integrated by DNA polymerase, and pyrophosphate is removed. Two other
enzymes use this released phosphate and ATP to produce light. If the added base was not the next
, in the sequence, no light would be produced, and apyrase would degrade the nucleotide. You
then repeat this process with each of the other bases.
b. In the case of Ion Torrent Sequencing, it starts with the same process, except that in addition to
removing pyrophosphate, it also removes Hydrogen ions. This allows for the detection of pH
changes. So, for example, you add a T, and if the pH changes, then the base is added to the
sequence. On the other hand, if there is no change in pH, then the base is not incorporated and
degraded by apyrase.
c. In summary, Pyrosequencing and Ion torrent sequencing share the same chemistry. However,
they differ in that pyrosequencing detects base integration through light production, while ion
torrent sequencing detects it through changes in pH.
1. Compare the use of DNA methylation in mammalian cells and DNA methylation in bacterial
cells. - CORRECT ANSWER: a. DNA methylation in mammalian cells inhibits transcription. In
bacterial cells, DNA methylation works as part of a bacterial immune system by preventing
digestion by their own restriction enzymes, which digests foreign DNA molecules that are not
methylated, including phage DNA molecules.
1. DAPA
a. How is it different from ChIP for determining if a protein is bound to a specific DNA
sequence? - CORRECT ANSWER: i. DAPA relies on Western blotting to further understand the
relationship between the protein and a portion of DNA, while ChIP relies on PCR as the method
to determine the pairing
1. DAPA
a. What is it? - CORRECT ANSWER: i. The DNA Affinity Purification Assay (DAPA) is a
technique used to analyze protein-DNA interactions and identify a particular protein that binds to
a specific DNA sequence. It involves the isolation and purification of DNA fragments (that have
tags added) that are bound to the protein of interest, followed by their subsequent analysis.
1. Describe how PCR can be modified to make it quantitative. - CORRECT ANSWER: a.
Modified to make quantitative to measure the amount of amplified DNA during or after PCR
process
b. Use fluorescent probes (TaqMan probe) - hydrolysis probes consisting of fluorophore and
quencher attached to each end that are designed to bind within amplified DNA and during
