The View of Blue; The Use of Eliza to Determine the Health Status of an Individual

A) Since the beginning of time, the ability to differentiate between healthy and unhealthy individuals has literally saved lives. Early detection has also been a life-saver, and the use of the ELISA (Enzyme linked immunosorbent assay) test has only improved these logistics.  The Use of the Elisa test has been helpful in determining the status of individuals (healthy or unhealthy), and is important in the field of medicine today. The test is completed by adding an antigen and incubating it to allow binding to the plastic walls. The primary antibody is then added to the well and incubated to allow it to bind to the antigen. Unbound primary is washed from walls, and secondary antibody is added to wells to bind to primary antibody. Upon rinsing of unbound secondary antibody, enzyme substrate is added, and color change occurs for infected individuals, while it does not for healthy individuals.

B) The purpose of this experiment is to  discover who the "infected" members of our class are and tracing the original "infected" people. We will also get experience in the field of testing contagious diseases. If we understand the ability of the ELISA test and the possibilities of it, then we will have learned what we were supposed to, and we can take this knowledge into the real world with us.

C) As individuals, we are supposed to transfer our fluid with three other people. Upon completion of this, we are to transfer 50 micro-liters of our mixed fluid into 2 of the wells on the 12- strip well. We then wait for five minutes to allow our proteins to to bind to the plastic wells. After this objective is completed, we wash out the wells twice with wash buffer. Then the primary antibody is added into every well for about five minutes. The washing is completed twice upon completion of this objective as well. Again, more fluid is added into the wells (this time, secondary antibody). Washing with sample buffer is to occur three times after five minutes of waiting. Finally, enzyme substrate will be added, and blue coloring will appear if the individual is infected, and the solution will remain clear if the individual is healthy.

D) I predict that I will be a healthy individual, and that 15 people will be infected in my class.

Studying The Secret of Life; The Use of Proteomics In The Testing of Marketplace Sushi

A) Although life on earth is unable to function without one of the four important macromolecule (lipids, carbohydrates, proteins, and nucleic acids), Proteins are possibly the most important of the group when it comes to human life. Proteins are utilized by every organ of the human body, and carry out numerous important, specific functions which are vital to the human body. Proteins are not only linked with current human life, as they have played a large role in evolution and the past history of every species in the world. Proteomics is the study of proteins. Although the acalanes period three biotechnology class has used the process of genomics before in the classroom, they have yet to experience the use of proteomics in their studies. Proteomics can be used in the study of evolution, bodily functions, and numerous other important biological observations/experiments. The central Dogma of biology is DNA to RNA to Protein, with the main molecule being protein as it carries out vital tasks in the human body.

B) The purpose of this experiment is to analyze the muscle proteins (actin and myosin) in fish species to determine how closely related they are to each other.

C) To successfully complete this experiment, our lab table will need to complete a number of tasks. To extract the actin and myosin from the fish, we will need to grind up the muscle. Upon grinding up the muscle, we will run the proteins in a gel and visually compare them. The more similar the banding patterns of the fish, the more related they are, and the more different the banding patterns are, the less closely related the fish are to each other.

D) For this experiment, I predict that we will be successful. Although I am unsure of what fish we will be testing, and because of this I am uncertain about the results, I believe that the results will be accurate, and we will learn something new as a lab table.

Tracing Our Ancestry From Our Mitochondrial DNA Lab Discussion

A) In this experiment, our lab table was successful in completing the experiment. The gel and markings on it turned out to be fine, and the results proved our incredible success. After the errors of our last lab experiment which led to the burning of our gel (results) we worked together as a lab table to ensure that this experiment worked out and that our mitochondrial DNA was ready for sequencing after the recent extraction. All four of the visible bands were in the desired location indicating the success and glory of performing the experiment correctly.

B) Sources of Error:
- We could have ran the gel for too long and burned off our half again.
- Could have not rinsed mouth thoroughly prior to cheek cell extraction and sequenced the mitochondrial DNA of a chicken or a strawberry.
- Chelex beads missed the DNASE and the DNA was destroyed before sequencing took place.
- No cheek cells were extracted and there was not sufficient mitochondrial DNA for successful extraction.

Searching For Eve; Tracing Our Ancestry From Our Mitochondrial DNA

A) Although each cell's nucleus is generally known as the storage facility DNA, the mitochondria also contains several copies of its own genome. Inside the Nucleus is the organisms very own unique DNA (taken from the egg of the mother and the sperm from the father and created to make an entirely new sequence); however, mitochondrial DNA is taken directly from one's mother (is an exact replica of one's mother's mitochondrial DNA). The difference between these two also include: Nuclear DNA has 46 chromosomes, mitochondrial DNA has only 37 genes, and the mitochondrial DNA contains only 16,569 nucleotides. Genetic tests are done using Polymerase Chain Reaction (PCR), a process which takes small DNA sequences, uses a DNA polymerase, a primer, and nucleotides to accomplish its goal. The PCR amplifies a gene (a 440 nucleotide sequence), each from the same part of the mitochondrial DNA genome, thus, making it possible to compare each and every mitochondrial sequence allowing us to determine our relatedness, and in some cases, how long ago we shared a common ancestor.

B) The purpose of this experiment is to amplify a piece of our mitochondrial genomes for easy comparison with other students in the class. This will enable us to determine how related we are to each other, and allow us to figure out how long ago we shared a common relative.

C) To complete this experiment, our lab table will need to complete a number of tasks correctly. We will need to extract our DNA through cheek cell extrcation, which requires saline mouthwash for extraction. Upon extracting the cheek cells, they will need to be broken open which we will utilize a lysis buffer for. After breaking open the cells instagene matrix will be added to kill DNASE. Next we will utilize PCR (Polymerase Chain Reaction) to amplify the desired sequence of DNA. After PCR, we will use Gel electrophoresis. The Gel electrophoresis will allow us to determine how closely related we are to each other, and to hopefully see how we are related to Eve.

D) The objective of this experiment is to isolate our mitochondrial DNA, and to discover how closely related we are to each other and how long ago we shared our last common relative.

Disease Gene Lab Discussion

A) As it turns out, I have the genetic trait which causes the disease. Although this is not an actual disease, the process was still emotionally challenging, and I will take a long time to recover from this unfortunate diagnosis.

B) Sources of Error:

-Period 4 ran the gel for too long, so it melted thus destroying our actual results.

-We dropped the tubes after centrifuging once, and on the second time we centrifuged too much.

-We ran the gel the wrong way at first.

-We analyzed period 4's gel instead of our own, and the three of them were infact diseased instead of us.

-We analyzed the DNA of a strawberry seed instead of a cheek cell.

-We used insufficient time to vortex each sample.

More Than Meets The Eye; Identifying A Diseased Gene With PCR

A) DNA testing is when one uses science to discover more about themselves than is possible by looking at oneself. Such a test can decode one's entire genome and can thus indicates one's genetic future. Genetic tests are done using Polymerase Chain Reaction (PCR), a process which takes small DNA sequences, uses a DNA polymerase, a primer, and nucleotides to accomplish its goal. DNA tests are done for a variety of reasons, including: identifying other species, and discovering one's genetic future. PCR can be used to sequence a gene of interest and allow scientists to determine whether the gene is diseased (harmful) or not.

B) The purpose of this experiment is to determine whether each of us possess a "diseased" gene. The gene is not a real diseased gene, but it will offer insight into our evolutionary past and give us real world experience in the realm of genetic testing, thus teaching us the significance of such testing.

C) To complete this experiment, our lab table will need to complete a number of tasks correctly. We will need to extract our DNA through cheek cell extrcation, which requires saline mouthwash for extraction. Upon extracting the cheek cells, they will need to be broken open which we will utilize a lysis buffer for. After breaking open the cells instagene matrix will be added to kill DNASE. Next we will utilize PCR (Polymerase Chain Reaction) to amplify the desired sequence of DNA. After PCR, we will use Gel electrophoresis. The Gel electrophoresis will allow us to determine whether we are each individually carriers of this "disease" by visually comparing the Gel and the lanes within it to one another.

D) The objective of this experiment is to figure out whether we are the carriers of this "diseased" gene. I am unable to produce an accurate hypothesis at this moment, but if I was to attempt to do so, I would say that I am not afflicted with or a carrier of the "diseased" gene.

Genetically Modified Organism Discussion

Results: 

Our gel did not reveal the results of this test, so our experiment did not work. However, we were able to analyze the gel of fourth period table two, and the results indicated that their test food was not genetically modified. Their number three band corresponded directly with their number five band on the gel, thus indicating its organic status. Even though the test food appeared to be organic, Mr. Chugh's corn flower band (number four) corresponded with the number six band on the gel. This means that The cornflower (test food two) is genetically modified.

 

Sources of Error:

-Ran Gel for too long, so DNA and the loading dye ran off the Gel.

-Did not crush test food well enough, causing the chunks to be too big to fit into the pipette, which caused no lettuce to be analyzed by PCR or Gel Electrophoresis.

-Accidentally extracted leftover DNA from the previous class's mortar and pestle.

-Added too little loading dye, and the DNA is not visible on the gel.

-Missed the wells when adding the DNA into the gel.

Oh No GMO; Testing Our Favorite Foods To Inspect Prevalence Of GMOs In Agriculture

A) GMOs are genetically modified organisms, and their use in agriculture is increasing, and becoming harder to distinguish. Genetically modifying plants can make them more durable, as some of the traits they can gain from genetic modification include resistance to: frost, drought, disease, and insects. GMOs are made by placing a gene of interest into a tumor inducing plasmid, adding the plasmid into agro-bacteria through the method of heat shock, and infecting a plant cell with the bacteria. The plant cell will then divide and grow up into a large, healthy plant. Genetically modified organisms can be identified by taking a plant cell, and finding a specific gene sequence located in a tumor inducing plasmid inside of the plant cell. This process is made possible by Polymerase Chain Reaction (PCR), a process which takes small DNA sequences, uses a DNA polymerase, a primer, and nucleotides to accomplish its goal. The controversy behind GMOs is the possibility that they could in fact harm the public. One way is that by making plants stronger, scientists are in fact strengthening the bugs and weeds which feed on plants. For example, weeds that crossbreed with herbicide resistant crops could evolve into super-weeds, and bugs which feed on toxins in plants will no longer be susceptible to such poisons and evolve into super-bugs. Another way is the possibility of allergies or religious conflict that could arise from people unknowingly consuming plants containing proteins from an animal which is not revealed (ex. somebody allergic to fish eating frost resistant tomatoes and becoming deathly sick from the fish protein). GMOs can be a source for good, and could end world hunger and famine, yet the risks and potential dangers must be weighed before any such actions can be taken.

B) In this lab, we will be testing our various favorite foods to identify whether or not they are genetically modified. While doing this we will be policing our own food, and deciding for ourselves whether we really want to eat food which has been altered genetically. This can be applied to the population of the world, and could allow people to make this decision even if the foods are unlabelled.

C) To extract the DNA, we will be heating a hot water bath to 99 degrees Celsius. This should effectively burst the cell membrane. DNASE is a protein developed by Eukaryotic cells to kill DNA outside of the nucleus. To get around this problem, we will add Instagene. Instagene matrix beads are designed to kill DNASE, thus allowing us to perform the experiment. We will use a sequence of interest (from DNA) from the Tumor Inducing plasmid (one that would not occur naturally in the plant) through PCR, to identify if genetic modification has taken place. Special techniques that we will be using include the use of Polymerase Chain Reaction. Our controls of this experiment are the Non-GMO food control with plant primers, Non-GMO food control with GMO primers, the GMO positive control with plant primers, and the GMO positive control DNA with GMO primers. They serve as a comparison for the unknown pieces of vegetable or fruit, and also as an indicator of whether the experiment worked successfully or not. We will be using Gel Electrophoresis in this lab to visually compare the similarities and differences of GMO/Non-GMO foods with the foods that we brought in to experiment with. Depending on the food, we should have accurate results of how much food is genetically modified in our supermarket.

D) In this experiment, the main objective is to see how much of the food is genetically modified. So, the variables of this experiment will be the food we bring in to test (Test food with plant primers, and Test food with GMO Primers). My hypothesis for this experiment is that  both plants which we test will be genetically modified. I believe this because, 70% of the food in the united states is genetically modified, and odds are that both will contain some type of modification.

How To Make Your pGLO; Transformation Of Fluorescent Sea-jelly Genes Into Bacteria

A) Transformation is a genetic process which means change caused by genes, and involves the insertion of foreign DNA into an organism to change its trait. Transformation is carried out by restriction enzymes to cut plasmid DNA and insert new code in its place, and heat shock (rapidly heating and cooling cells with calcium chloride) which will move the plasmid (DNA which contains one or more genes which would be beneficial to a bacteria's survival) into the cell. It also is a key instrument of biotechnology, and is used in numerous ways, such as, bioremediation (the genetic manipulation of bacteria to digest oil from spills), and medicine (use of gene therapy to correct defective genes). Also, another use of Transformation is to make bacteria glow by inserting the Green Fluorescent Protein (from Seajellies) into bacterial cells.

B) The purpose of this experiment is to insert the GFP gene into a plasmid, and move the plasmid into bacterial cells. This will cause the cells to produce Green Fluorescent Protein, and they will glow brilliantly. We hope to have a flourishing fluorescent colony by the end of this experiment.

C) In this lab, we will have four petri dishes: +pGLO and LB/amp, -pGLO and LB/amp, -pGLO, and LB, and the +pGLO and LB/amp/ara. We will use Transformation, which is carried out by restriction enzymes to cut plasmid DNA and insert new code (GFP gene) in its place, and heat shock (rapidly heating and cooling cells with calcium chloride) which will move the plasmid (DNA which contains one or more genes which would be beneficial to a bacteria's survival) into the cell. The controls of this experiment are the -pGLO, and LB petri dishand the -pGLO and LB/amp. The variables will be +pGLO and LB/amp,and the +pGLO and LB/amp/ara. I predict that the +pGLO and LB/amp will be the only bacterial colony to exhibit fluorescent characteristics. This is because it contains the ampicillin resistance gene, and the plasmid containing the GFP gene.

Discussing The Strategic Use Of Microarrays In The Study Of Lung Cancer Genes

A) Results: From the gene chip our lab group was able to determine that: Genes 1, 2, and 5 were active in in the cancer cells, Genes 2,3, and 6 were expressed in cells obtained from healthy tissue, and also that Gene 4 was express in neither the healthy cells nor the cancerous cells. We were able to tell this becauseof the colors of each gene on the slide. Genes 1 and 5 were pink (pink means expressed only in cancer), Genes 3 and 6 were blue (blue means only expressed in healthy cells) , Gene 2 was purple (this represents expression in both healthy and cancerous), and Gene 4 was clear (expressed in neither).

B) Sources of Error:
- Not enough of the cDNA was added, and the true color of the gene was not shown.
- The genes from the gene chip were not accurate, and we tested the expression of the wrong gene.
- We pipetted too much of the cDNA, and the slide overflowed, thus we were unable to get an accurate reading of the expression of the certain gene.
- We left the gel in the pipette for too long so it hardened and less than 20 microliters was exposed to the slide.

Translating Diseases; The Strategic Use Of Microarrays In The Study Of Lung Cancer Genes

A) Microarrays have simplified how scientists study gene expression in thousands of cells. This new technology detects patterns in transcription and translation, and aids in the understanding of the normal and abnormal aspects of cell function. The process of using Microarrays to analyze/study genes involving lung cancer include: creating a DNA chip, and using the DNA chip to analyze complementary DNAs isolated from both cancerous and noncancerous tissue (the same tissue). The Microarray will then indicate the differences between the two corresponding genes. This will be an indication of the extent to which transcription occurred. Some scientists have indeed observed that some genes are not transcribed as much in cancer cells as in healthy cells, and that some genes are not transcribed as much in healthy cells as in cancer cells.

B) The purpose of this experiment is for our lab table to use Microarrays to study Genes Involved in Lung Cancer. This will hopefully give our group a better understanding of the causes of the disease on a genetic level, and thus allow us to speculate with possible methods to prevent or cure it.

C) In this experiment, our lab table will be studying six genes using a Microarray. We will prepare the Microarray by spotting six different gene sequences onto a glass slide. Then we will obtain DNA tubes from a 70 degree water bath, and spot the appropriate gene solution onto the correct areas of out slide. To hybridize the Microarray, our group will add fifteen microliters of hybridization solution to each spot. We will then wait and observe our results when they appear.

D) Although we have the six genes that we are to study, making predictions is not possible because we do not have the background knowledge to hypothesize our results. However, I am quite certain that our group will accomplish something worthwhile, and we will learn valuable facts about gene expression and the effects of cancer on this.

The Sticky Ends Justify The Means Discussion

A) During Day one of the lab, our lab table acquired the DNA of the five suspects, and the DNA found at the crime scene. The purpose of the experiment was to identify the culprit by matching the DNA found at the scene with the DNA of the five suspects using Restriction Fragment Length Polymorphism. After acquiring the DNA, we added restriction enzymes to the tubes, flicked/tapped them, and placed them in a hot water bath for 30 minutes. On Day two we ran the newly cut DNA through a gel, and visually compared the samples using loading dye to stain the DNA (make it visible), and attracting the fragments to the positive end through Gel electrophoresis. Gel electrophoresis functions by pulling fragments of DNA (negatively charged) through the gel matrix towards the red end (positive), run to red. On Day three, our group was able to compare the DNA of the five suspects with the DNA found at the crime scene. We were able to positively identify Chloe Krey as the culprit in this crime scene.

B) Possible Sources of Error:
- We did not add enough loading Dye so the DNA fragments were not visual.
- Accidentally scraped off a skin cell into a test tube, and my DNA was analyzed instead of a suspect's DNA.
- We did not add enough DNA to the tube, and thus not enough substance was present for DNA to become fully visible.
- Accidentally added the wrong suspects DNA into the wrong well, and the wrong suspect was 'proven' guilty by the DNA evidence.
- Accidentally added the food coloring in place of the Loading Dye, and the DNA was not properly stained thus leading to an inaccurate reading.

The Sticky Ends Justify The Means; The Strategic Use of Restriction Enzymes In DNA Fingerprinting

A) DNA fingerprinting has revolutionized how crimes are solved, and has also aided in other applications. Since described in 1985, Restriction Fragment Polymorphism (RFLP) has acted as the factotum for DNA fingerprinting/profiling, and currently Polymerase Chain Reaction (PCR) is in use. The Restriction Enzymes are vital to the functionality of DNA fingerprinting. Restriction Enzymes are obtained from E-Coli, and the enzymes act as a natural defense against viruses. Restriction Enzymes work by cutting DNA at palindromes. To compare the desired strands of DNA, it is ran on a gel. The DNA differences are the fragments of different lengths. Running DNA on a gel produces different results, because gel electrophoresis is the use of electricity on a gel, giving it both a positive and a negative end. DNA has a slightly negative charge, so the fragments run to red. In the case of DNA, the smaller fragments go farther and the larger fragments remain closer to the original well.

B) The purpose of this experiment is to match DNA from a crime scene. During the experiment, our lab table will be attempting to match the DNA of the suspects with the DNA found at the crime scene. We hope to analyze the DNA correctly and receive experience in the field of crime solving.

C) The use of Restriction Enzymes in this experiment is vital. To analyze the various sample of DNA, and to successfully determine the culprit we will be using six samples of DNA: one from the crime scene, and five other tubes which contain DNA samples from suspects 1-5. We will be pipetting the restriction enzymes into the different tubes. We will then make a gel  (add correct ingredients, and mix it) and run the various samples with a dye to make the fragments visible on the gel. The smaller fragments will move farther, and the success of the lab will depend on the similarities between the crime scene DNA and the DNA from one of the five sample tubes. The Variables of this experiment will be the five DNA samples, and the control will be the DNA from the crime scene. We will attempt to visually compare and identify the controls with the variables to figure out which variable most matches the control.

D) The hypothesis cannot be produced at this time, because I have no knowledge of the suspects or the crime. However, I do predict success for my lab group and I as we use DNA fingerprinting in our special CSI lab.

Prolonging Life with Life Discussion

A)  Throughout day one the lab, our group attempted to record the effectiveness and efficiency of cellobiase on an artificial substrate which represented cellobiose. One day two of the lab, our group measured the effectiveness and efficiency of edible mushroom in turning cellobiose into glucose. We measured the rate of conversion from the artificial substrate (acts as cellobiose) to glucose by adding a strong base. The strong base turns the artificial substrate yellow, and stops cellobiase. To measure reaction rate, we labeled five tubes and added a fixed amount of artificial substrate and cellobiase (day 1) and a fixed amount of artificial substrate and our mushroom (day 2)., and added the strong base at set points in time. This allowed our group to discover that both were approximately even when it came to efficiency. Overall, my hypothesis was correct. The cellobiose was converted into glucose efficiently by both the cellobiase and the mushroom solution on both day one and day two of the lab.

B) Possible Sources of Error:
- When adding the strong base, we could have added it at the wrong time messing up the correct coloration of yellow.
- Failed to grind the mushroom up enough, thus the majority of the enzymes remained unable to produce glucose.
- Not enough cellobiase was added, thus a slower conversion occurred and inaccurate readings were obtained by our group.
- The centrifuge was not spinning for long enough to fully separate the mushroom solution, not enough of the mushroom was added to accurately convert the artificial substrate.
- Too much cellobiase was added, so the artificial substrate was converted too rapidly for our group to notice a change after three minutes.

Prolonging Life With Life; Extending The Future By Exploring Possibile Benefits Of Biofuels

A) The current fuel system is subject to change. The global economy is dependent on petroleum, which is a polluting natural resource which is destined to run out. Although the future seems bleak for the global economy, there is hope in alternate fuels. Some of the most promising of the prospects to replace gasoline are biofuels. Biofuels are the classification for fuels derived from biomass. In the wall of plant cells lies a polymer with a lot of potential named cellulose. Cellulose cannot be broken down naturally by animals, and this is the reason why it's importance for energy has not become relevant until now. Cellulose is broken down by the cellulose enzyme which is present on the inside of Protists. Enzymes are beneficial to reactions because they speed up chemical reactions and are not consumed with the reaction, so they can be used again and again. The majority of enzymes are proteins, and have a specific 3-D structure. For a chemical reaction to take place, the active site (site of chemical reaction) binds to the substrate (the reactant of the enzyme catalyzed reaction). The process is sped up because the substrate is positioned in a way which allows the transition state of the reaction to become stabilized, and the activation energy is lowered to allow quicker reaction rate. However, the conditions of enzymes must be kept within an optimal range, (the right pH, the right temperature, and the right level of salinity). For centuries, termites have broken down cellulose and used its energy as fuel, and not until recently, scientists discovered how the termites were able to accomplish this feat. The termites have a protozoan called Trichonympha living inside their abdomen, and the trichonymphba has a bacterium named Rs-D17 that lives inside it and produces cellulase enzymes, including cellulase. Cellulase enzymes convert the cellulose into cellobiose, which is converted into two glucose molecules by the enzyme cellobiase. Biofuels work by using glucose (energy) obtained from cellulose to power their engines.

B) For our class, the purpose of this experiment is to measure the enzymatic activity of cellobiase, and to identify the optimal conditions for the enzyme. This also acts as a real world example of the possibilities behind enzymatic studies, and the relevance in the possible future. For industry, the research of Biofuels can offer an alternative energy which would be more sustainable than petroleum. The biofuels offer a new future for industry, one which could make life less polluting, more sustainable, and more reliable.

C) The lab will start with a one milliliter pipette of cellulose. Cellulose is broken down by bacteria, protists, and fungi, so we will use enzymes derived from these sources to convert cellulose into cellobiase. Cellobiase is composed of two glucose molecules, and will be the substrate of the experiment. Cellobiose will be placed in a test tube along with Cellobiase, an enzyme which breaks down cellobiose into single glucose molecules. To measure the effect of the cellobiase on the cellobiose, we will substitute the cellobiose with an artificial substrate. The artificial substrate will be composed of Glucose and P-Nitrophenol. At various time points, we will add a strong base to the test tube which kills cellobiase, and turns P-Nitrophenol yellow. This will allow documentation of the coloration of the test tube, and we will be able to drw a conclusion from this data. For extended exploration in this experiment, we will bring in mushrooms to test which mushrooms are better decomposers. We will grind up the mushrooms, and add them in place of the cellobiase (add them with the Glucose and P-Nitrophenol). This part of the experiment will give us a greater understanding of the cellobiase content in the foods that we eat, and also in some of the mushrooms that we see.

D) I believe that the cellobiase in Day 1 will make glucose disappear faster than the ground mushrooms which we will add in day 2. The controls of this experiment are the Cellobiase and the artificial substrate (Day 1), while the variables of the experiment will be the ground mushrooms and artificial substrate (Day 2). The cellobiase acts as the control, because cellobiase will definitely separate the artificial substrate at a quicker pace with its higher concentration. The ground mushroom acts as the variable in this case, because we are unaware of the cellobiase concentration within the organism, and we are charting the difference between cellobiase and the mushroom.

DNA Precipitation Lab Discussion

A) Discussion:
The resluts of the DNA precipitation lab were approximately what I had predicted. My earlier predictions included that I would receive a transparent little knot of precipitated DNA, and that part was true. My group and I performed every part of the procedure correctly, and precisely, which allowed each of us to obtain favorable results.

B) Possible Sources of Error:
-Ate a chicken sandwhich during brunch, and precipitated the DNA of a chicken.
-No cheek cells were extracted from mouth, so there was no DNA to precipitate.
-Lab table member accidently contaminated the lysis buffer pipette with his or her DNA by dipping pipette into their test tube.
-The inverting of the tube was not intense enough, and the lysis buffer was not thoroughly mixed in. Thus the cell membranes were not dissolved and the DNA never left the cell.
-We did not add enough Protease, and the DNASE survived to kill all of my DNA.
-The inverting of the tube with the protease was too intense, and all of he DNA stuck to the sides of the tube.
-I accidentally removed the tube from the hot water bath too soon, so the necessary chemical reactions did not occur.
-Read the directions incorrectly, and added 10 microliters instead of 10 milliliters.
-When placing the precipiataed DNA in the supercool class necklace, applied too much pressure to the glass case itself and the glass broke in my hand.

Our Own Slice Of Immortality; The Extraction and Precipitation Of Our DNA

A) For all living  organisms DNA is present, and for some, DNA is the code for life. However, not until fairly recently have scientists known DNA's genetic importance. In human beings DNA codes for such traits as hair color, eye color, height, facial features and blood type. In 1953, James Watson, Francis Crick and discovered the structure of DNA with the help of Rosalind Franklin. The scientists built a model of DNA, which was the first accurate model of its time. Their model described that DNA a double helix, connected by four nitrogenous base pairs, adenine, thymine, guanine, and cytosine. Each base is connected to a sugar and a phosphate group, which act as the backbones of the structure. The entire unit is called a nucleotide. The DNA of the cell is found in the nucleus of almost every cell of the human body (because an enzyme called DNASE evolved to kill all DNA outside of the nucleus in case the DNA was viral). The DNA is coiled up around histones (proteins) and organized into structures called chromosomes. There are 46 chromosomes in human cells, and all of the genetic information contained in the 46 chromosomes represents the genome. A gene is a section of DNA which codes for a certain trait. Humans receive their DNA from their parents, half from the father, and half from the mother.

B) The purpose of this experiment is to precipitate our own DNA. Precipitating our DNA will make it visual, and we will have the chance to view our very own DNA. This allows us to compare it, and would allow us to test it, clone it or sequence it.

C) To precipitate our DNA, the first objective we must complete is to extract our cheek cells by rinsing our mouths vigorously with a 0.9% saline (isotonic) solution. The solution will allow for quick extraction, and the cells will not burst in an isotonic solution. We will then add the lysis buffer (soap), and invert the tube several times to mix in the buffer completely. The lysis buffer will break open the cell membrane by dissolving the phospholipids in the plasma membrane. After the addition of the buffer, protease will be added and the tube inverted to spread the Protease throughout the test tube. Protease had the purpose of destroying DNASE before DNASE can kill our DNA. DNA has a negative charge, and water has a positive charge. Because of this, DNa is hydrophilic (attracted to water) and will dissolve in water. To counter this, we will add salt which will neutralize DNA's charge. Without a negative charge, DNA will become hydrophobic and non-polar. Our DNA will then be placed in a hot water bath to speed up the reaction time and break open the cell membrane. To finish this process we will add cold ethanol to precipitate the DNA. Ethanol is the preferred substance because of it's lower freezing point. It will become colder while staying a liquid.

Yogurt Lab Discussion

A) The predictions that my lab table gave were approximately what we received as results. In tube 1 (the milk), the milk never transformed into yogurt, because there was no addition of a probiotic. Tube 1 was acting as a control, a basis for what the milk was to look and smell like, and also to give the lab researcher an idea of the texture. Some of the physical properties of tube 1 include: a semi-liquid texture, a smell of slightly sour milk, a white color, and a pH of 7. In tube 2, the milk and the addition of the yogurt (the probiotic), transformed the milk and yogurt into yogurt. Tube 2 was a variable, because the results of the milk added to the yogurt could have either changed or remained the same. The purpose of a variable is to measure the transformation and possible change that a certain experiment could cause. The properties of tube 2 include: a semi-solid texture, a smell of yogurt, a white color with a transparent film at the top, and a pH of 4. Tube 3 was composed of milk, yogurt, and ampicillin. This tube was also a variable in this experiment, as we were trying to figure out if yogurt could be produced with the addition of an antibiotic. The end result was no, because the ampicillin killed the bacteria in yogurt which did not allow the transformation from milk to yogurt to occur. The physical properties of tube 3 include: a semi-liquid texture, a smell of sour milk, a white color and a pH of 7. In our final test tube, tube 4, we tried using a different type of bacteria to make yogurt. This was also a variable, because E.Coli is another type of bacteria, and our lab group was attempting to find if any type of bacteria could create yogurt. E.Coli did not produce yogurt, some of the physical properties of tube 4 are: a semi-liquid texture, an unattractive smell (bad smell), a white color and a pH of 7. The yogurt up in the front of the classroom is worthy of mentioning, as it acted a control for tube 2. The yogurt had a pH of 4, and a yogurt smell, a white color, and a semi-solid texture. Our table succeeded in creating yogurt.

B) Possible Sources of error include:
- Accidentally adding ampicillin to tube 2, which causes all the bacteria to die. Which means no yogurt is produced.
- We used the same yellow rod to add yogurt to all 4 of our tubes, and we add ampicillin to tube(s) 1, 2, or 4 on accident.
-The vortex could have shaken the tubes so violently that the ampicillin stuck to the roof of the tube and we created yogurt in tube 3.
-The hot water bath was so hot that the DNA strands in the bacteria's nucleoids denatured, thus making the process of yogurt making impossible.
- The hot water bath was not hot enough to pasteurize the yogurt, so bad bacteria survived and spoiled the milk or yogurt
- The vortex did not move enough to thoroughly mix in the contents of tube 2, tube 3, or tube 4 so either yogurt was not produced, ampicillin did not come into contact with the yogurt and yogurt was produced, or the E.Coli was just pooled at the bottom
- We dropped all of our tubes on the ground and bad bacteria entered all of the tubes and spoiled the various results

Exploring the Technological and Biological Factors in the Process of Yogurt Making

A) For hundreds or even thousands of years, Yogurt has been a delicious treat enjoyed by humans all over the planet. Yogurt is a food of mysterious origins, and has been an early example of biotechnology. However, the process of yogurt making is very different than one would think. Bacteria plays a major role in yogurt production, thus making it an important topic. Bacteria is the most populous and successful form of life on earth, and has played a large role in human history. Although only a surprising minority of bacteria is known to cause disease, pathogenic bacteria in the form of cholera, typhus, tuberculosis, and the bubonic plague have caused the suffering and death of millions. However, the bacterium that we are to be using for our yogurt is a type that is not harmful towards humans.There are many distinct shapes of bacteria, such as coccus (spherical), bacillus (rod-shaped) and spirillum (spiral). These different types of bacteria reproduce through binary fission, which allows them to divide every 15-20 minutes. The yogurt we shall be producing is a pro-biotic, meaning that it is designed to aid the helpful bacterium which reside in the stomach of humans along the stomach and small intestine.

B) Our purpose for this experiment will be to test Koch's postulate (which has four steps: find microbe present in all sick people, culture the micrrobe, inoculate a healthy subject with the microbe, culture the same microbe from the newly sick), and practice the microbial technique.

C) To make our yogurt, we will scald the milk to 80 degrees Celsius (pasteurize) to kill spoilage bacteria, then we will cool down the milk, add the yogurt and wait for 24 hours. The way this process is completed, is that the milk sugar, lactose, is converted into lactic acid. This decreases the milk protein, casein, and turns the milk from a semi-liquid to a semi-solid. This process is known as curdling.

D) The controls of this experiment will be tube 1, which is the negative control, and tube 2 which is the positive control. The variables of the experiment are tube 3 and tube 6, because tube 3 is indicating the yogurts reaction to ampicillin, and tube 6 is monitoring the growth of E-Coli. My predictions for this experiment are that tube 3 loses the benefits of a pro-biotic, and tube 6 grows into a healthy medium.