Title, Purpose, Hypothesis, Introduction, and methods:
Nuclei and DNA
Purpose: To understand DNA, how it can replicate its self and all the factors involved in transcription and translation.

Hypothesis: If the DNA is hydrolisized, then the DNA will not wrap around the glass rod due to the shortness of the strands.
If the DNA is denatured, then the DNA will wrap around it because the two strands were separated and they are very long.

Introduction:
Transcription is a process in which genetic material (DNA) gene is the template for the synthesis of mRNA (messenger RNA). A gene is a section of DNA within a chromosome that codes for the synthesis of one protein. The TATA box assists in directing RNA polymerase to the initiation site on DNA. The DNA sequence is enzymatically copied by RNA polymerase to make a complementary polynucleotide RNA strand. The RNA polymerase binds at a specific sequence called the promoter. This is known was initiation.
Next is elongation. This is the covalent addition of nucleotides to the 3’ end of the growing polynucleotide chain. Last, is termination. This is the recognition of the transcription termination sequence. When RNA polymerase recognizes it, it releases and ends the chain.
The mRNA is transported to the rough endoplasmic reticulum. It is then fed through ribosomes which in turn produce a protein out of this mRNA. There are many other enzymes involved in this process.
Initiation of the mRNA is formed by the assembly of ribosomal subunits and the initiator tRNA at the start of the codon on the mRNA. These ribosome subunits start at the 5’ end. When the ribosomes find the AUG start codon and the tRNA comes, the initiator binds to the P site on the ribosome.
In elongation, the elongation factors help the amino acids form a peptide bond while the initiation factor keeps moving down the mRNA. As the initiation factor moves down, the tRNA will release from the p site and a new one will arrive almost simultaneously. This is what makes the proteins out of mRNA.
In termination, the STOP codon is reached. There are no tRNA molecules with anticodons for the stop codon. The protein release factors notice these codons and the polypeptide is release from the ribosome. The ribosome then splits into sub units which later may assemble for another protein synthesis.  
DNA (deoxyribose nucleic acid) is a genetic material found in the nucleus. It is a double helix with two polynucleotide chains twisted together. It can direct its own exact replication within each nucleus in cell division. It is made out of a 5-carbon sugar backbone, a nitrogenous base, and a phosphate covalently attached. Nucleotides are the structural units of DNA and RNA, and are very important.
The nitrogenous bases differ from one another. The nucleotide consists of adenine (A) and guanine (G), which are purines. The smaller ones are called cytosine (C) and thymine (T) which are pyrimidines. The A-T only goes together by hydrogen bonding and same with C-G. Nucleotides are the monomers of nucleic acids. Three or more bonding together make a nucleic acid.

Methods: Microscopic observation of calf thymus cells
A blunt end of a toothpick is used to scrape the cut surface of a piece of calf thymus gland to remove cells. The cells are then smeared onto the center of a clean glass microscope slide and allowed to dry. Two- to three drops of ice-cold ethyl alcohol is placed onto the slide and is given two minutes.
The alcohol is carefully rinsed off by using a water dropper. Three to five drops of methylene blue dye is placed onto the preparation and allowed to stain for about five minutes. The preparation is then carefully rinsed again with a dropper bottle until no further stain rinses out. The slide is left to air dry for at least ten minutes. Then a drop of water is added and a cover slips.
The thymus cell is observed under the low power and then the high power of the microscope. The appearance is recorded. The cytoplasm nuclei and the nucleoli appearance is recorded also. The slide is saved for later comparison to the nuclei.
Isolation of nuclei
A piece of thymus tissue is obtained, about a 20 mm square. A sharp razor blade is used and the tissue is cut into 10 to 12 smaller pieces in a plastic Petri dish. About twenty-five ml of cold Nuclear Buffer is obtained in a centrifuge tube and kept on ice. The buffer is 10 mM Tris, 5 mM MGCl2, 40mM NaCl, and .5 percent NP – 40.
The tissue is ground using an ice cold mortar and pestle. The thymus is rapidly smashed until the liquid is quite cloudy. The homogenate is then filtered through two layers of cheese cloth back into the plastic centrifuge tube and kept cold. It is centrifuged at a setting number 20 for five minutes. The supernatant is poured off and carefully discarded. Ten ml of nuclear buffer is added to the pellet. It is briefly vortexed to disperse. Preparation is kept on ice.
Microscopic observation of nuclei
A small drop of the nuclear preparation is placed on a clean microscope slide. A small drop of methylene blue due is added as well, the slide is then mixed. The material is coversliped without fixing, rinsing, or drying. It is observed with the microscope and compare directly to the slide of whole thymus gland cells.
Isolation of DNA
The dispersed nuclear pellet material is divided into approximately equally into three small glass vials. It is allowed to come to room temperature. One glass vial is labeled native, one denatured, and one hydrolisized. 1.5 ml of 10% SDS is added to each of the three vials. The contents are mixed in the vials with very gently shaking or rotation. Any observable changes are noted and recorded.
When the preparation has been in the presence of the SDS for at least five minutes, cold ethyl alcohol is added to the native DNA vial only. The native DNA is spooled onto a glass rod. The resulting DNA is described. After all the spoolable DNA is removed, the alcohol and water in the vial is vigorously mixed. Observations and conclusions are given.
Denaturation of DNA
A small amount of water is placed into a beaker on a hot plate. When the temperature of the water reaches eighty degrees the SDS treated DNA vial labeled denatured is placed into this hot water bath and watched carefully.
The vial is removed from the heat just before the water bath comes to a full boil, which should be about three minutes. The denatured DNA is quickly cooled by placing it on ice. Any changes are noted in the viscosity after the treatment. Cold ethyl alcohol is added to the sample following the directions for the last step. The denatured DNA is attempted to spool onto a glass rod following the directions above. The alcohol and water mixture is shaken thoroughly as before to observe any precipitation. All valid conclusions concerning the effects of the denaturation on the physical properties of DNA are written out.
Hydrolysis of DNA
Four N HCl is added to the last SDS treated DNA sample, the one labeled hydrolyzed. The volume added should be approximately equal to the volume of the original sample. The vial is placed in boiling water on a hot plate for ten minutes or more to complete the acid hydrolysis. It is cooled on ice and any changes are noted. After the sample is cooled, the cold alcohol is added according to the previous procedure. The DNA is attempted to be spooled as before. The contents are finally shaken thoroughly to observe precipitation.

Discussion
Enzymology

Results: See attached

Discussion: In the experiment where the effect of enzyme concentration was tested, my group found that as the amount of enzyme increased, the absorbance and rate of reaction increased as well. These results happened because increasing the amount of enzyme increases the amount of active sites that can convert substrates into products. It’s like having more people to do a job helps in getting more done. These results indicate that the more enzyme available, the more substrates can be converted. This does support this part of my hypothesis and therefore this part can be accepted. In the same manner, the more substrate that was added to the solution, the absorbance and reaction rate increased.  The results in this experiment happened because when there is more substrate more can be done. In this section of my hypothesis, I thought that we would reach equilibrium, but we did not. However, it did support part of my educated guess in saying that the more substrates available, the more reactions can take place. Eventually, in a perfect setting, the enzymes would become saturated and be working as fast as they could but they would not be able to work any faster. In the experiment with temperature, the reaction rate increased from 10 degrees to 20 degrees, but then remained the same at 30 degrees. Then at 40 degrees, it appears something in the experiment went wrong because the reaction rate drops down, but jumps back up at 50 degrees. At 60 degrees, the reaction rate drops down again. One would expect results from an experiment like this to show an optimal functioning level for the enzyme reactions and then when it gets too hot the proteins denature. However, our results seem to be incorrect. This could have been from allowing the solution to get too hot or too cold before measuring the reaction rate, by which time the proteins had denatured. This data does not support my hypothesis, but this data is more than likely incorrect. In the experiment with the pH levels, the reaction rate peaks at 5.42 and then decreases. This shows an optimal pH level for this enzyme. These results happened because pH levels effect the way enzymes function. Most enzymes function best in the areas they are located with the pH levels found there. This evidence does support my hypothesis, when I said that an optimum pH level would be the peak for reaction rates then there would be a decrease. Therefore, I can accept more of my hypothesis.
These experiments are important because they show what and how different situations affect enzymes. It proves that enzymes have optimal levels for functioning and reaction rates are directly affected when dealing with temperature, pH, substrates, and enzymes.
There were many problems that contributed to our classes experiments. There was one tool that we used improperly. There are two levels that draw up a substance and we were supposed to stop when it reached the first level. However, we accidently went to the second one and sucked up more solution than we needed. This threw off a lot of our data, but we didn’t know we were doing it incorrectly until the experiment was completed. It is clear that there was a mistake made in the temperature experiment. This could have come from inaccurate readings dealing with the thermometer. If the group did not stick the thermometer deep enough into the solution the reading may have been warmer than the parts at the bottom.