Drafts

It's interesting that Okazaki fragment is able to not get lost in the process of DNA replication and become oriented perfectly in the newly synthesized DNA strand. There must be a series of cellular machines that keep this in the realm of possibility. However, I would assume that a good amount of the DNA errors that do occur are related to the Okazaki fragment, since the process is considerably more complex than synthesis of the leading strand (at least conceptually).  

This is really an amazing mechanism that happens within our bodies and within all other eukaryotic organisms. I wonder how the DNA polymerase is able to make the conformation shift to compare the newly synthesize strand to the original. Perhaps a ligand or even a phosphate group binding leads to the action of DNA polymerase. Also, this is far from the only proofreading mechanism that exists for DNA replication, which explains the incredible accuracy exhibited by the complex over the huge magnitude of DNA replicated.

Since this reaction requires a considerable amount of free energy to occur, it must be couple with a different process in the cell in order to be thermodynamically possible. Endothermic reactions like this need to be paired with an exothermic reaction to make the product formation favorable. All reactions need to have a negative change in free energy, the process of making that happen is called metabolic coupling.

I've read elsewhere that DNA polymerase is actually a series of enzyme subunits working together as a complex rather than a single enzyme. This makes sense when you think about it though. Considering that an enzyme typically corresponds with one reaction, there must be many involved to achieve DNA replication. DNA is a complex molecule and thus it would require a number of reactions and organization to achieve true replication.



 

Another function of helicase is to prevent the DNA in the process of replication from getting two wrapped up. Similar to how a rubber band is changed when both ends are twisted. When DNA is put into such a conformation it is unable to be copied due to the torsional strain on the molecule. Thus, it is critical that helicase performs this action as well as simultaneously working to separate the two strands of DNA.

We decided to analyze the energy expenditure of Ursus maritimus, commonly known as the polar bear. We were curious about how polar bears budget there time so we asked the question: What proportion of time is spent preforming high energy versus low energy behaviors by Ursus maritimus individuals. We wanted to know if they conserved their energy and how they spend there time. We hypothesized that Ursus maritimus individuals will spend a larger proportion of time performing low energy behaviors in order to conserve energy while active. 

Background Info:

Polar bears are a carnivorous maritime bear that resides on the arctic sea ice. They hunt primarily ringed and bearded seals because they require a high fat energy diet to survive. Polar bears have a thick layer of fur around their entire body in order to keep them warm and they also have a thick layer of blubber under their fur to provide insulation and buoyancy. They are currently listed as a threatened species due to declining populations of polar bears as a result of melting sea ice. There main food source is seals and in the summer they are in a physiological state of hibernation even though they remain active. This means they require less food because there body is feeding of the fat storages. 

The term crypsis englobes a multitude of strategies for avoiding detection by other animals by blending in with their environment. It plays an important role in predator-prey relationships, such as the interactions between crab spiders and bees. In this study we used a close relative of Misumena vatia, a crab spider widely studied for its color changing abilities, to investigate background color preferrence in swift crab spiders (Mecaphesa celer).

Like other crab spiders, Mecaphesa celer is an ambush hunter and it preys on pollinator insects by lurking in the flowers they visit. We hypothesized that in order to successfully capture its prey, Mecaphesa would choose to hide in flowers that more closely resemble its actual body coloration. In order to test our hypothesis, we designed an arena split into two different colors based in the RGB color model, and recorded to which side the spider moved after being placed in the center.

The goal of this review is to focus on selected new approaches and techniques for understanding how fish move through the water and to put these recent results into the context of classical studies of fish swimming. In particular, the review focuses on the analysis of the motion of the center of mass (COM), new approaches to imaging water flows in three dimensions (3D), and fish robotics as a means to understand the physical principles underlaying aquatic propulsion.

Changes in fin and body shape occur during fish locomotion, and can be used for studying patterns of fluid flow and developing computational fluid dynamic models of swimming fish. Undulatory swimming results in increased water velocity in the caudal region of the fish. The general form of the body wave that is produced during such movement is very similar among a diversity of fishes, such as the clown knifefish, eels, and bluegill sunfish.

There were three postulated methods of DNA replication that explained how genetic information was copied and passed down through the generations. The methods were semi-conservative, conservative and dispersive replication. Semi-conservative replication involved the double helix unwinding and each half becoming incorporated into a new strand of DNA while it served a s a template for what the other half should look like. Conservative replication suggested that the DNA double helix unwound to serve as a template for a new double helix, but that the original would wind back up and stay together and the replicated strand would be entirely new. Dispersive replication suggested that the double helix would be cut up and that the new strand would have pieces of the old strand of DNA and the newly synthesized DNA in it in no particular orientation. Meselson and Stahl investigated the idea of DNA replication and by using nitrogen markers, definitively showed that DNA replicated in a semi-conservative manner.

We watched 5 minutes of videos of polar bears, Ursus maritimus, from the Macaulay Library database to observe behaviors and we identified certain behaviors that the polar bears did. We identified a list of behaviors and divided this list into four categories based on how much energy each behavior takes. The four levels of energy were minimal energy, low energy, mid energy, and high energy. We identified minimal energy behaviors as lying down and standing still. Low energy behaviors were walking around with the nose up or nose down. We identified mid energy behaviors as walking quickly and swimming. Running, digging, diving, and shaking were high energy behaviors. We watched 30 additional minutes of videos of polar bears from the Macaulay Library database and using Jwatcher, recorded how much time each behavior occurred. We took a screenshot of each behavior and put the images into a table based on the energy level and added a description of each behavior. Each behavior in the table appears chronologically. To determine how much energy the polar bears have, we identified the location and season of when the videos were taken and we identified the food source of these particular polar bears.

I will not lie. Once I had known about my assignment for LEE-SIP internship, I was most excited at the prospect of cancer research. I expected working with petri dishes and isolated cell cultures, either human’s or mice’s. So, I was really surprised to learn that I would be working with fruit flies and mostly in-vivo. It seems as though the learning curve from working in the lab is exponential and continuous I have already learned so much, yet there is so much to run. I want to know the toxicology impacts. Not only does this research ties in with my current interest on genetics and cell and molecular biology, rather it facilitates my future interest and path as an MDPhD candidate. Experiments like what I am conducting now will dictate possible drug uses for chemotherapy patients. Or, at the very least, it will have impact on environmental science and toxicology.

2-naphthol was reacted with sodium hydroxide and n-butyl iodide via an SN2 reaction and butyl naphthyl ether was obtained in 5% yield. The product yield was very low due to incorrect use of the suction filtration machine by the student. The product was identified as butyl naphthyl ether via TLC analysis with correct data from the student’s partner, as well as from using the melting point of the small amount of product that did form. The first plate did not have applicable data because the amount of product formed was too small to make a significant difference between A, B, and C. The spots were all almost entirely equivalent to the A spot (the 2-naphthol solution) because the amount of product (C ) was so low, thus making the C spot ineffective and the B spot essentially just the same as the A spot. However, the plates of the student’s partner, which had the better ratios of hexane to EtOAc sufficed for the date for the rest of the Rf values. On plate 3, substance C travelled farther than substance A, which tells that the final product of the reaction is much less polar than the starting material. This makes sense in accordance with the reaction scheme because 2-naphthol is more polar than butyl naphthyl ether. Of the three solutions used, the best separation of substances was obtained with the solution ratio 60:40 hexanes:EtOAc. The solution with 25:75 hexanes:EtOAc was too polar to get a sufficient separation and the solution with 75:25 hexanes:EtOAc was not polar enough to get a sufficient separation of the substances present. By adding more EtOAc, the solution became more polar so that both the starting material and product had sufficient separation. The hexane composition of this solution agrees with the assumption that the product was less polar than 2-naphthol because butyl naphthyl ether is less polar than 2-naphthol The identity of the product was shown by the sample’s melting point of 33 °C, which fits with butyl naphthyl ethers melting point  of 33-35 °C.

11 mmol or 1.58 grams of isopentyl propionate was expected to be recovered from the acid-catalyzed reaction of 11 mmol of 3-methyl-1-butanol with 13 mmol of propionic acid. However, only 0.292 g of final ester product resulted in a low recovery rate: 18.5%. Low percent recovery could have been due to reflux reaction not going to completion (substantial amounts of unreacted alcohol and carboxylic acid remained in the rb flask after reflux) or loss of organic product during reaction work-up.

Isopentyl propionate had a sugary banana odor, compared to 3-methyl-1-butanol’s bittersweet licorice smell and propionic acid’s bitter vinegar smell. The odor test confirms formation of isopentyl propionate as it is known for its usage as a flavor extract: mainly fruity, ripe, banana smell.

The IR spectroscopy of isopentyl propionate also confirms the formation of an ester product, since it displays the characteristic carbonyl peak specific to esters: sharp, strong, 1740/cm. However, there is some unreacted alcohol product left in the final sample, as evidenced by the broad peak of medium intensity at 3300/cm.