BIOL 309 Midterm
Friday October 8, 2021
9 AM (EST)
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By submitting my answers to this midterm, I promise:
I have not communicated with others during the test via any means and not consulted an
unauthorized aid (notes, textbooks, internet, social learning groups etc.)
These answers are entirely my own work.
I will accept a disciplinary penalty if evidence arises that I have broken my promise.
I have entered my name and student ID below to document my agreement with these statements:
Name:Cary
ID: 20894264
1. Complete the following statements with the correct information: (12 marks)
a. Biological replicates reveal whether certain trait is determined by gene or something epigenetical.(or
whether is totally determined by gene or not)
b. two critical factors in creating a fusion protein are:
1) structure tolerance of the reporter and the original(will not disturb each other very deeply)
2)choosing the right site and method to insert the part(like gene for GFP), make sure its mRNA won’t be cut
while being spliced.
c. Conventionally, DNA sequences are presented in what polarity?
5’ to 3’ direction
d. A PCR requires the following 4 distinct components in addition to sterile water:
1)(DNA) primer(region selective, forward and reverse)
2)dNTPs in buffer solution
2)thermostable DNA polymerase (such as Taq)
4)the mould(original DNA to be replicated)
e. Immunolocalization requires a secondary antibody that is conjugated to
both primary antibody and marker(enzyme or colored luminescent or fluorescent product)
f. It is an advantage for a model organism to have a low amount of repetitive DNA because it will be easy to
locate something in its genome such as a mutation or allele(it makes the search smaller and easier)
g. The difference between a screen versus a selection is screen will let all survive but only indicate and find
part of the organisms while selection will kill the part that is not selected
h. A 30 mL reaction mix should contain __6__ mL of a 5X buffer.
1
0.5
0.5)
yes, things that can be included for fusion proteins, but what critically do you need to consider about the gene sequences when creating a fusion protein?
best referred to as a DNA template here 🙂
think more with respect to the experimental methods you might use, e.g. probes/primers, how would this be affected by more repetitive sequences
2. Distinguish between the following and include an example of each (2 marks each)
a. Selectable marker versus reporter gene
Selectable marker is used in selection, which usually will kill the unselected (transformation not successful).
Selectable marker: ampicillin resistant gene;
reporter gene will show the selected(transformation successful), but will do nothing to the unselected.
reporter gene: GFP gene
b. Targeted versus untargeted studies
Targeted studies has a pre-determined target and this sometimes leads to easiness in the process, untargeted
studies does not have one. However, sometimes we use it to inspire our thinking and the study may soon
become with a target.
c. Antibody versus antibiotic
Antibody is something formed by immune system. It comes from the B cells and is a result of immune reaction
to antigen(many of which are pathogen).
antibiotics is something that suppress the grow of bacteria, it originally comes from other microbes and now
can be chemically produced.
3. What does it mean to do the following? (1 mark each)
a. elute a protein from a column
use large amount of solvent to flush the protein out from the gel compounds of a column
b. to design a gene-specific probe
design a probe that consist of complementary gene and other reporter, for a known gene
c. design a positive control for an experiment
add certain factor in the one of groups of the controlled experiment
d. study a transcriptome of an organ
to search into the transcription product of an organ
4. Why? (8 marks)
a. Why must we use a supercoiled plasmid of known concentration rather than a ligation mix to measure the
competency of cells? (2)
supercoiled plasmid is the real stable and effective form for a gene to “ride on”. An easy ligation mix might be
easily degraded and it hardly makes the target gene express effective and rightly.
2
0.5/2
when linear DNA in ligation mix is degraded, we do not know the total amount of DNA present; but with supercoiled DNA, none of it degrades, so we know the total amount of DNA cells take up
2/2
answer needs to be more specific
0.5/2
1/2
missing examples
1/1
wording is unclear
how to make gene-specific?
0/1
answer is vague, misunderstanding the concept
0/1
what are the transcription products?
0.5/1
b. A cosmid is packaged into lambda particles. What do cells infected with these lambda particles create when
plated? Explain why this is the case. (2)
after about a cycle of lambda’s period. not immediately because the bacteriophage has a lysogenic part in its
life period.
c. Studying proteins is more complicated than studying nucleic acids. Why? (2 marks)
1 proteins has 20(or sometimes more) amino acids(aa) while there’s only 4 nucleotides in one RNA or DNA.
2 the aa series is a result of selective transcription and translation and there’s a lot of modifications in between
3 the proteins form dimers(and or even more) and has complicated 3D structures(and that of DNA is far easier)
d. Why do some researchers use non-model organisms for their research? (Provide two different possible
reasons) (2 marks)
1 model organism does not have the certain needed trait(very special) to be studied
2 model organism does not have the similar system of life(maybe non-model organisms have something much
more complicated and it could not be transferred or inferred from other organisms, like pandora virus)
5. How do I do this? – only a sentence or two is needed for each answer. (2 marks each)
a. Determine the size of a polypeptide using an SDS polyacrylamide gel.
extract a sample containing the needed protein, process with SDS and do a PAGE electrophoresis
b. Determine the Tm of a DNA fragment experimentally.
repetitively change temperature and measure molecules(number or mass both do)at the temperature, make a
fine series of temperature and do the measurement
c. Change a PCR primer so it binds more specifically to its target.
check the nucleotide series of target and interference, re-determine the series and length of the primer
6. Consider this recent, true research result (4 marks)
Scientists have identified 14 genes that can cause, and three that can prevent, weight gain. They RNAi
screened 293 genes in C. elegans subjected to two different feeding regimens: (1) regular diet, and (2) high-
fructose diet, which they developed as an invertebrate model of diet-induced obesity (DIO).
a. Did this research involve a forward or reverse genetic approach in their study? Explain (2 marks)
forward genetic and reverse genetic
we first know obesity than gene lead to it and we are trying to find the reason, that is trait to gene
and then came to verify it, this is gene to trait
3
0/2
2/2
2/2
0/2
missing critical details
0.5/2
increase temperature to denature DNA, all the while measuring absorbance
0.5/2
add more nucleotides to primer to elongate it
Sorry, you had to make a decision – you had to indicate whether the experiment that was done was forrward or reverse?
0.5/2 BM
b. What experiment would you be interested to do next if you were on this research team? Explain your
reasoning. (There is no one correct answer to this -please provide your thoughtful suggestion.) (2 marks)
search into the interactions of these known genes
because the genes does not effect alone and the interactions and how they form the DIO system may give us
more useful information
4
But these genes do have an effect alone.. fine to look for interactions but no explanation as to how to do that…1/2 BM