Drafts

Once isolated colonies had been grown on the CDC agar plate, the next step of the experiment was to test them for their ability to eliminate two reactive oxygen intermediates (ROIs), hydrogen peroxide and singlet oxygen. To test for the bacteria’s ability to degrade hydrogen peroxide, a catalase test was done. It was expected that the anaerobic bacteria would contain the enzyme catalase and be able to degrade hydrogen peroxide. It was expected that when these bacteria were exposed to hydrogen peroxide, a chemical reaction would take place and small bubbles would form indicating that catalase was present and able to degrade hydrogen peroxide into water and gaseous oxygen. Staphylococcus epidermidis was used as a positive control for the catalase test, as this organism is known to have the catalase enzyme. It was expected that bubbles would form when S. epidermidis was exposed to hydrogen peroxide. Streptococcus agalactiae was used as a negative control for the catalase test, and was expected to show no bubbling when exposed to hydrogen peroxide due to the absence of catalase.

Wild type C. violaceum will produces a purple colored antibiotic called violacein. Violacein production is regulated by quorum sensing. C. violaceum’s AHL synthase gene, CviI, synthesizes the signal molecule C6-HSL which then binds to the regulator protein CviR. The CviR/C6-HSL complex regulates an operon responsible for violacein production. On the Petri plate streaked with wild type C. violaceum, it was expected that the heavy band of inoculum at the top quarter of the plate would turn completely purple. The wild type strain was expected to produce violacein because the AHL synthase and regulator protein were not mutated. Thus, this strain could produce its own signal molecule and receptor to activate the operon responsible for violacein production.

Discussion:
The starting materials were reacted using conditions specific to the reaction being performed and the
target product was obtained in a good yield. The reaction mixture began to boil fairly quickly. The
organic phase started collecting after about 20 minutes of the first reflux. The second reflux happened
more quickly. The third reflux was slow, and the final product yielded a relatively low amount of water
in the side-arm. The % yield of crude product was 65%. The % yield of the distilled product was 20%.
Assumptions about the procedure that were made can include that the compounds were all relatively
pure and did not contain impurities in the separation. The IR spectroscopy showed peaks at 4000, 2000,
and 1500 (1/cm). There was a large wide peak from 2800-1800. The peak around 4000 can be connected
to the IR absorption of water O-H, which is a strong, broad peak around 3700. There is no sharp peak
around 1740 to signal the presence of an ester. The large broad peak between 2800 and 1800 can not
be identified for any functional group. The IR spectroscopy showed that the ester separation was not
100% perfect and therefore, it can be assumed that the esterification of propyl propionate was not
100% successful.
There were multiple assumptions made for this experiment. To start, it was assumed that the right
amount of propanoic acid and 1-propanol was calculated and placed in the round-bottomed flask at the
beginning of the experiment. If this was wrong, the entire experiment would have been thrown off and
could have yielded completely different results. A second assumption that was made, was that there

was a complete separation of water during the three refluxes that occurred during the experiment
which would have indicated that the reaction went to completion. However, there was in fact very little
water collected in the side-arm and some of the water that was collected could have been poured back
into the round-bottomed flask during the cooling of one of the refluxes. This also could have affected
the separation and reaction. If the experiment were to be redone, the right amount of 1-propanol and
propanoic acid should be calculated properly and measured out more carefully. Furthermore, there
should be a more affective reflux method so that there can be a higher guarantee of the separation of
water. Also, a maximum time limit should be kept on the reflux so that the reaction does not change to
what is preferred.
Changes in the catalyst would not change the chemical parts of the reaction. A catalyst is an agent that
is introduced in a reaction to speed up the reaction and nothing else. It does not undergo any
permanent chemical change and merely affects the rate of the reaction without any outside influence.
This could however, produce more molecules of the final product in a shorter amount of time.
In general, by increasing the concentration of the reactants, the rate of the reaction should also
increase. Similarly, as the temperature increases, the rate of the reaction should also increase as well.
By decreasing the temperature, the rate of the reaction would slow down. Side products would be
formed. Furthermore, unstable reagents could result in a lower than expected yield. This is because
with unstable reagents, there is room for side reactions and other things to occur that are not wanted in
the end product. With unstable reagents, there are other components that can be formed or taken off
by heat or reaction which would end up with a lower than expected yield. Overall, the identity and
purity of the product was assessed.

Post-Lab Questions:
1.) On Pre-Lab Attached
2.) In this experiment, equimolar amount of carboxylic acid and alcohol are not used. There is more
propanoic acid used in a molar amount. Approximately 0.013 mol of propanoic acid was used and
approximately 0.011 mol of isopentyl alcohol was used. This would produce a higher percent yield of
ester.
3.) In esterification, the purpose of the sulfuric acid is that it is used as a catalyst for the experiment to
proceed more quickly.
4.) Most of the carboxylic acid was removed during the part of the experiment when the reaction
mixture was in the centrifuge tube.
5.) During distillation, pure product is collected when there is a temperature range plateau within a few
degrees of each other. For example, a first drop could be recorded at 55 °C during a distillation, but the
pure product may not be collected until the temperature plateau which could be something around 59-
61 °C.

Purpose: The purpose of this lab is to remove water from a reaction mixture to form an ester. As water
is removed, the equilibrium is upset. The ester that is being prepared in this experiment is n-propyl
propionate.
Reaction:

Experimental Procedure:
The structural C formulas were written out for the formula of alcohol and the carboxylic acid. Using
densities, the proper amounts of carboxylic acid and alcohol were determined. The proper amounts of
0.974 mL of propanoic acid and 0.823 mL of 1-propanol were determined to be used for the experiment.
The volume of the propanoic acid and 1-propanol were measured and placed into a 5 mL round-
bottomed flask. While swirling, 2 drops of sulfuric acid was added. Then, 3 boiling chips were added for
a heating. A distillation apparatus was set up which involved a distillation column, condenser, and side-
arm. The flask was heated to a gentle boil, then refluxed for 15 minutes.
The round-bottomed flask was raised from reflux to cool after 15 minutes. The apparatus was also
allowed to cool and the apparatus was then tilted allowing the water and other distillate to drain back
into the round-bottomed flask. Due to the density of the water, while the round-bottomed flask was
cooling, the distillate in the side-arm was separated in the water. Before being refluxed again, the
distillate was drained back into the round-bottomed flask, while the water stay in the side-arm. The
round-bottomed flask was lowered back into the sand bath and allowed to reflux for an additional 15
minutes.
After 15 minutes of a second reflux the same cooling and tilting process was performed as in the first
reflux. For a third time, the round-bottomed flask was lowered and allowed to reflux for a final 15
minutes. The apparatus was allowed to cool. This time however, everything in the side-arm, water and
distillate, was drained in the round-bottomed flask. This is because the reaction should have gone to

O

H
O
H+

Propyl Propionate
O

Water

O

OH
Propanoic
Acid

+

OH
1-Propanol

O
O
OHOH

Sulfuric Acid

completion, and water should not have affected the final distillate that was now contained in the round-
bottomed flask.
The ester contained in the round-bottomed flask was carefully pipetted into a centrifuge tube, and 1 mL
of water was added. The mixture in the centrifuge tube was mixed using a pipet for a few minutes. The
aqueous layer was allowed to settle and was carefully removed and placed into a beaker for later
disposal. About 1 mL of sodium bicarbonate was added into the centrifuge tube and the mixture was
mixed again for a few minutes. The reaction mixture was allowed to settle and the aqueous layer was
again carefully removed into a waste beaker for later disposal. For a last time, the extraction was
repeated with about 1 mL of sodium chloride. The reaction mixture was mixed with a pipet for a few
minutes, allowed to settle, and the aqueous layer was carefully removed into a waste beaker for later
disposal. The organic layer that remained in the centrifuge tube was carefully transferred via pipet into
a clean and dry collection vial.
Once transferred, anhydrous spheres of calcium chloride were added to the liquid and swirled. More
spheres were added until the spheres did not clump together anymore which meant that the mixture
had been dehydrated. After, the mixture was allowed to settle for a few minutes with occasional
swirling to make sure that the anhydrous calcium chloride spheres did not clump together.
Using a pipet, the liquid in the collection vial was carefully transferred into a clean and dry tared 5 mL
round-bottomed flask. A small amount of distillate was saved in case a successful distillation could not
be performed. The round-bottomed flask was attached to a distillation column and the lowered into the
sand bath and a distillation was performed. The temperature of the first drop and the collected
distillate was recorded.

Both the steel slag and cement offer a potential sink to store carbon in and both processes involve a form of ion extraction, usually calcium, to combine with the carbon dioxide to form the carbonate material. As was explained in the steel slag pilot plant facility, a solvent was necessary to promote this migration of calcium ions in the solid steel slag to a more reactive state that could combine with the carbon dioxide. However, other solvents are available to perform similar functions, just not in the context of steel slags. Other such solvents are sodium based and have been tested to see their practicality when used with a feedstock of the magnesium rich serpentinite.

US:

• HIV was prevalent in US for of years prior to the first known case of AIDS

• First recognized in NY and NJ in 1971, made its way to Cali and Georgia by 1979

• 1980:

  • From October 1980 to May 1981 five homosexual men were treated for biopsy tested Pneumocystis carini pneumonia at THREE different hospitals, two had died

  • Reported by MS Gottlieb, MD, HM Schanker, MD, PT Fan, MD, A Saxon, MD, JD Weisman, DO, Div of Clinical Immunology-Allergy; Dept of Medicine, UCLA School of Medicine; I Pozalski, MD, Cedars-Mt. Siani Hospital, Los Angeles; Field services Div, Epidemiology Program Office, CDC.

• 1981:

  • By July 1981, 41 cases of aggressive Kaposi Sarcoma (rare form of relatively benign cancer found in the elderly) among homosexual men in New York and California

  • 8 victims died in 24 months or less

  • https://www.nytimes.com/1981/07/03/us/rare-cancer-seen-in-41-homosexuals.html

  • By the end of 1981 121 people had died

• 1983:

  • 3,064 cases of AIDS were diagnosed

  • 1,292 People had died from complications to the disease

  • Government does nothing to acknowledge it

• 1984:

  • 4,251 people had died

  • US Health and Human Services Secretary Margaret Heckler announced that Dr. Robert Gallo of the NCI had isolated AIDS virus -HTLV-III

  • Heckler-"We hope to have a vaccine [against AIDS] ready for testing in about two years.“ … "yet another terrible disease is about to yield to patience, persistence and outright genius

  • Government still does not acknowledge the existence of AIDS

• 1985:

  • 5,636 people had died from AIDS

  • PRESIDENT FINALLY ACKNOWLEDGES AIDS

• In total, 13,309 people died from complications to AIDS before it was recognized by the US government system as an issue to be tended too

We choose to observe the presence of wing bars, if the bird had a short or long beak, the color of the throat, eye ring color, belly color, feet color, the presence of yellow feathers, the presence of bright colored feathers, rump coloration, the presence of a curved beak, if the bird had more than two feather colors, and if the crown was a different color than the body. We observed the photographs and the skin museum to observe each species and categorize the plumage characteristics. We wrote the color of each plumage feature in the table and we used “1” and “0” for traits that didn’t specify a color. The presence of wing bars, yellow feathers, bright colored feathers, more than two feather colors, and a matching crown were indicated by a 1 for yes and a 0 indicated no. A short beak was categorized by a 0 and a long beak was categorized by a 1. After evaluating each of the 33 species of Warblers for the set of characteristics determined, four of the patterns were chosen to apply to a phylogenetic tree. We choose the presence of wingbars, the presence of yellow feathers, foot coloration, and the presence of a matching crown color. We indicated the absence of wing bars with a black line on the taxa of the phylogenetic tree.

I was a little surprised to see that 64% of the public supports the use of gene editing for both somatic and germline cells for therapeutic purposes but not for enhancement. I feel like most of the public don’t fully understand how genetics works in general, especially how gene editing would work. I appreciate that there are several regulatory organizations to help inform the public as well as figure out how to regulate gene editing, but what do they share with the public and how do we know these organizatons will make the best choices for everyone involved? Ethically, I feel like the use of somatic genome editing is better than germ-line genome editing becaue you can get consent from the person getting their genome edited. With germ-line gene editing, it is within the embryo, which cannot speak for itself and there is also a high risk to benefit ratio. Additionally, I am curious to know how a germ-line genome edited individual would reproduce and pass down their genes. I feel like the process of replication and passing down genes may be affected or harmed from genome editing.

Figure 3 shows the effect of thinning Aspen in its early successional stage. Before the thinning of the aspen the morality percent of aspen and fir were both about 5%. After the thinning of the aspen the morality of aspen increased slightly to about 6%. This is not the same for the fir, which instead jumped up to almost 21%. We know the aspen is the early arriving species, and without it fir do worse. This shows a facilitation relationship between the two species. 

The mechanism controlling the interaction between Populus remuloides (aspen) and Abies laslocarpa (fir) is that of a facilitation relationship. Figure 3 shows that when there is less aspen, fir die significantly more.  One reason may be due to fir being able to take over the stands much faster than they would be able to in the normal successional cycle. If fir are taking over faster, and more often then the case of fires is going to occur more. With more fires the cycle will begin again after both species get burnt down. Aspen will then arrive first, and if re-thinned will get taken over by fir again very quickly resulting in more frequent fires and a higher mortality rate for fir. The Aspen morality rate does not increase by a lot because by the time the fire occurs the plot is already overtaken by fir.