This details the molecular biology lab in AP Biology. Best grade in class.
The AMGEN Lab that we have been doing for the past two weeks consisted of
two parts; Plasmid Fusion and PCR. Each one is a complicated procedure of genetic
engineering, with our own cheek cells and E.Coli supplied by AMGEN. I will start by
explaining the Plasmid Fusion lab.
The Plasmid Fusion lab consisted of four major parts; plasmid digestion, gel
electrophoresis, restriction enzyme inactivation and ligation, and the final step, plating
out.
But, before I get into that I should define some parts of the lab. The main pieces of
genetic
information we will be working with are plasmids. Plasmids are gene sequences found in
a
loop outside of the main chromosome. Their main purpose is to code enzymes that digest
antibiotic enzymes. Antibiotics are chemicals that kill bacteria or interfere with their
growth or metabolism. Cells that have antibiotic resistance have an advantage because
they are able to grow in places that other cells can not.
Our main purpose in this lab is to give an E.Coli cell immunity to the antibacterials,
Ampicillin and Chloramphenicol by genetically doctoring its plasmids. The first step in
doing this is to "cut" the plasmids so that we can ligate the new pieces on later. The DNA
will be cut once twice or not at all because the process does not work all of the time with
all DNA. The part that makes the resistance enzyme will be left in tact and separated into
a
smaller section of DNA. We do this so that we can isolate the genome so that we can
later
attach other sections of DNA to it. The next step involves checking to see if the
Restriction Enzymes did their job by a process called Electrophoresis. First we suspend
the DNA in a solution of Agarose. Then an electric is applied, one end is "+" and the
other
"-". DNA forms ions, like most substances that dissolve in water. It separates into H+ and
DNA-. The DNA will move toward the + end through the Agarose. Since the Agarose
will stop many of the bigger pieces but the pieces that were cut will pass through because
they are smaller. Using a chemical called Ethidium Bromide (EtBr) and UV light we can
see how far our DNA made the journey. The farther it went the smaller the pieces and the
smaller the pieces the better the Restriction Enzymes worked. The next step involves
three
chemicals; the two separated plasmids and a T4 ligator. Mixing these three together
should form one final strand. The two pieces will be ligated to form the correct genome.
The next step is to put the new resistant strand of DNA back into the E.Coli. This process
involves mainly hot and cold water. The DNA will be put in a iced solution with the
cells.
The cells should have small holes in them to let the plasmid back in. They will then be
shocked by putting them in a hot water bath for two minutes and then put back into the
ice. The shock should open up the cell long enough for the plasmids to get through. If the
plasmid makes it through, the cell should accept the new plasmid and start producing the
resistance enzyme to Chloraphenicol and Ampicillin. The next and final part of the
experiment is referred to as plating out. The process involves four petri dishes, each
divided in half. Each petri dish contains a different substance. There is a Luria Broth
(LB)
plate( Luria Broth is a excellent nutrient source for the E.Coli), a Chloraphenicol
plate(CAM), an Ampicillin plate(AMP) and a Chloraphenicol and Ampicillin
plate(CAM+AMP). We spread our new E.Coli over each plate and let it stand for 36
hours. The following results took place.
LB
AMP
CAM
CAM/AMP
growth = +
+
++
+none = little = +What these results mean is the following: Since there is growth on the Luria
Broth
solution the cells are still alive and are able to reproduce; Since only two very tiny
colonies
grew on the AMP plate we can assume that only a very few gained the Ampicillin
resistance; Since there was growth all over the Chloraphenicol we can assume that the
cells have been altered and that they can now grow in a antibacterial environment that
would have once killed them; Since there was only very little growth on the Ampicillin
and
Chloraphenicol plate I will have to assume that the plate had either too much Ampicillin
or
that just the presence of it in cell growth will kill cells.
The PCR lab was the second lab we did. PCR which stands for Polymerase chain
reaction. The main purpose of this lab was to extract our own DNA from our cheek cells,
prepare in for the PCR and then put it in the PCR machine. What PCR does and allows us
to do is make indefinite copies of DNA. Not just the whole strand, nature does that for us,
but we can copy just part of the DNA for intense studies.
The first part of the lab is to extract our own cells for the project. We did this by
gargling with a saline solution for one minute while we bit our cheeks. I was incredibly
sick with a fever at the time so this might have affected my results. The next part is to get
the cells ready for the machine . To do this we mixed the cells in a micropipeter with a
substance called Chelex. We then mixed our buccal cells with two compounds called
Master Mix I and Master Mix II. Now is the most important part, the thermalcycler. The
thermalcycler's main purpose is to break down the DNA in to small parts. The hydrogen
bonds around the base pairs break apart and the DNA is suspended in the solution. The
next and final step in the lab is to run a gel electrophoresis on the sample. After adding
the
loading buffer you can run the gel.
The expected results should be that the well in which we loaded the solution into
is
now a bright glowing color and the band start bright and eventually fade into black. What
the lab actually tested was the presence of a genome called tPA-25-ALU. tPA-25-ALU is
a gene inside the tPA gene(which everyone has a copy of) which is not found in all
people
since it is an inherited trait. We have either 2,1 or 0 copies of it in our body. The reason
that that specific part of the gene was targeted was the different Primers we used. The
primer selects the certain gene in want to copy by it's nucleotide sequence. It then saves
that part and replicates it because it is the only strand in the entire PCR mix to reproduce.
I think that the fact that the wells were glowing means that the PCR did work and that the
glowing product in the wells is the product of the PCR experiment. This is because in the
PCR machine all the DNA is separated and jumbled, the primer helps to form the only
full
DNA structure so when we added the yellow loading buffer it could only bond with the
full DNA which was the tPA-25-ALU.
Keywords:
this details molecular biology biology best grade class amgen that have been doing past
weeks consisted parts plasmid fusion each complicated procedure genetic engineering
with cheek cells coli supplied amgen will start explaining plasmid fusion plasmid fusion
consisted four major parts digestion electrophoresis restriction enzyme inactivation
ligation final step plating before into that should define some parts main pieces genetic
information will working with plasmids plasmids gene sequences found loop outside
main chromosome their main purpose code enzymes that digest antibiotic enzymes
antibiotics chemicals kill bacteria interfere with their growth metabolism cells have
antibiotic resistance have advantage because they able grow places other cells purpose
this give coli cell immunity antibacterials ampicillin chloramphenicol genetically
doctoring plasmids first step doing this ligate pieces later will once twice because process
does work time part makes resistance enzyme left tact separated into smaller section
isolate genome later attach other sections next step involves checking restriction enzymes
their process called electrophoresis first suspend solution agarose then electric applied
other forms ions like most substances dissolve water separates into move toward through
agarose since agarose stop many bigger pieces were pass through because they smaller
using chemical called ethidium bromide etbr light made journey farther went smaller
better restriction worked next involves three chemicals separated ligator mixing these
three together should form final strand ligated form correct genome next resistant strand
back coli process involves mainly cold water iced solution should small holes them back
they then shocked putting them water bath minutes then back shock open cell long
enough through makes cell accept start producing resistance enzyme chloraphenicol
ampicillin final part experiment referred plating four petri dishes each divided half each
petri dish contains different substance there luria broth plate luria broth excellent nutrient
source chloraphenicol plate ampicillin plate chloraphenicol spread over stand hours
following results took place growth none little what these results mean following since
there growth luria broth solution still alive able reproduce since only very tiny colonies
grew assume only very gained there over assume been altered grow antibacterial
environment would once killed them only very little assume either much just presence
kill second which stands polymerase chain reaction purpose extract from cheek prepare
machine what does allows make indefinite copies just whole strand nature does copy just
part intense studies first extract project gargling saline minute while cheeks incredibly
sick fever time might affected results ready machine mixed micropipeter substance called
chelex mixed buccal compounds master master most important thermalcycler
thermalcycler break down small hydrogen bonds around base pairs break apart suspended
electrophoresis sample after adding loading buffer expected well which loaded bright
glowing color band start bright eventually fade black what actually tested presence
genome gene inside gene which everyone copy found people inherited trait either copies
body reason specific targeted different primers used primer selects certain want copy
nucleotide sequence saves replicates entire reproduce think fact wells were glowing
means work glowing product wells product experiment machine separated jumbled
primer helps form full structure when added yellow loading buffer could bond full
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