Gel electrophoresis

Procedure 

1. First we had to make the gel substance. By doing so we had to measure the amount of agarose (gel stuff0 about three grams then add it to water. We mixed the water up and put it in the microwave to heat it up. It was just like jell-o, in order for it to become a gel substance it had to be heated up. So after it was heated we added it to the trays and let it sit there over night. Once we came back to school the next day we were able to actually start the project. There were multiple stations and we split up in to different groups. There were many tools that were sterile. So we grabbed a pipette and measured the right about of substance and put it in the little squares in the gel. While doing this we had to make sure we didn't go through the gel otherwise it would make a mess. Once you knew you were in the gel you would press down and the substance would release. This was kind of a ruff process. Afterwards we put the lid on and hooked it up to the gel electrophoresis (gel rig). We left it going for about 45 minutes.
So in the end they liquid dyes had spread out and some of them had reacted differently because the mixtures had been different.
There are pictures of the different steps I had went through and the reactions the had happened. While putting the dye I had difficulties of not going through the gel and on some of them I had. In the pictures you will see how it spread out.

DNA Detective Work

DNA DETECTIVE WORK

Unless you have a twin, no one in the world has a DNA sequence identical to yours. Although 99 percent of the DNA is the same in all humans, certain segments vary widely. Differences in these segments are detected through DNA fingerprinting. A small amount of tissue, such as blood, hair, or semen, is all that is needed to create a DNA fingerprint. The sample is cut up using enzymes and the segments are separated by size through gel electrophoresis. DNA is made visible either with radioactive probes or by staining. This reveals a pattern of bars: the DNA fingerprint. If the two DNA fingerprints match, they probably came from the same person. If they don't match, they certainly came from different individuals. In recent years, a number of people convicted of crimes have been exonerated based on DNA evidence.

Activity

In this exercise, you will learn the basics of DNA fingerprinting and consider the use of DNA in criminal investigations.

Part 1.

Use your browser to go to NOVA’s web site about “Killers Trail,”  the story behind the man who inspired the Fugitive TV series and later the movie version starring Harrison Ford:

http://www.pbs.org/wgbh/nova/sheppard/

Click on the “Chronology of a Murder” section and read about the events that led up to the murder trial of Dr. Sam Sheppard.

1. In your opinion, what role (if any) did newspaper stories and editorials have in the outcome of the original trial of Dr. Sam Sheppard?

So in my opinion, they have a huge a effect because the people believed what was put in the newspaper even if it wasn't true.

Go back to the Killers Trail homepage and select ”Create a DNA Fingerprint.”

Read about the crime and the suspects then go on to part 2. Answer the following questions about the technique as you go through the simulation:

2. What is the function of the restriction enzymes in DNA fingerprinting?

The function of the restriction enzymes in DNA fingerprinting, they work similar to scissors that cut across long DNA molecules at different locations.

3. What is the function of  the agarose gel electrophoresis step?

The function of the agarose gel electrophoresis step is that its a gel jell-o like substance that will act like a molecule strainer that allows tinier pieces of DNA to move through more easier than larger pieces.

4. Why is a nylon membrane used to blot the DNA?

Nylon membrane is used to blot the DNA because DNA transfers to the nylon.

5. What does a dark spot on the X-ray film indicate?

A dark spot on the x-ray film indicates the radioactivity from the probes.

Part 2.

Use your browser to go to Frontline's "What Jennifer Saw" at

http://www.pbs.org/wgbh/pages/frontline/shows/dna/.

The material on this site is about a man convicted of rape but later exonerated by DNA evidence. To read a summary of the case, choose the link to Ronald Cotton's wrongful conviction, then choose "Summary of Cotton's Case."

In the interviews section, read the interviews with DNA expert Peter Neufeld and lawyer Barry Scheck.

Answer the following questions:

6. What evidence was initially used to convict Cotton?

The evidence that was initially used to convict cotton was a flashlight that resembled the one used by the assailant and the rubber of the tennis shoes which was consistent with the rubber found at one of the crime scenes.

7. What did the DNA evidence show?

The DNA evidence showed no match to cotton. The results matched a convicted felon who had confessed to a crime earlier.

8. How could DNA fingerprinting be used to prevent a false conviction if a case like this was being tried today?

The DNA fingerprinting could be used to convict false convictions today by getting the correct results from evidence found on the crime scenes and match to the correct DNA from the convict.

9. What percentage of convicts are unjustly convicted of sexual assault cases, according to Neufeld and Scheck?

The percentage of convicts that are unjustly convicted of sexual assault cases is 15 percent.

10. The O.J. Simpson trial was one of the most visible trials that attempted to use DNA evidence.  In the end, the DNA evidence was not satisfying to the jury, who acquitted Simpson.  What do Neufeld and Scheck believe about the impact of the O.J. Simpson trial on the use of DNA evidence?

Neufeld and Scheck believed that the case had a lot of potential from when it had first started. Neufeld said they have to be very rigorous in the kinds controls that they exert when they utilize this tremendously powerful new technology to make sure that it's used wisely and cautiously. So the OJ trial had a big impact they believe from where DNA evidence started.

DNA Extraction Lab

Procedure:
1. Place 1 gram of raw wheat germ in a 50 ml test tube
2. Add 20 ml of hot (50-60 Celsius Degrees) tap water and mix constantly for three minutes.
3. Add 1 ml or a scant 1/4 teaspoon of detergent and mix gently every minute for 5 minutes. Try not           to create foam.
4.  Us an eye dropper, pipette, or piece of paper towel to remove any foam from the top of the solution.
5 Tilt the test tube at an angle. Slowly pout 14 ml of alcohol down the side so that it forms a layer on top of the water wheat germ/ detergent solution. Do not ix the two layers together . DNA precipitates at the water- alcohol interface (the boundary between the water and the alcohol). Therefore, it is crucial to pour the alcohol very slowly so that it forms a layer on top of the water solution. If the alcohol mixes with the water, it will become too dilute and the DNA will not precipitate.
6. Let the test tube sit for a few minutes. White, stringy, filmy DNA will begin to appear where the water and alcohol meet. You will usually see DNA precipitating from the solution at the water-alcohol interface as soon as you pour in the alcohol. If you let the preparation sit for 15 minutes or so, the DNA will float to the top of the alcohol.
7. Use a glass or a paper clip hook or a wooden stick to collect the DNA.
Observation
This is when I added alcohol and it didn't mix.

Models of DNA Structure

So my group and I created a structure of DNA on the white bored and took a picture of it. We had decided to do it differently than everyone else's. Then we answers some questions about the structure of DNA and how it kind of works.

 

Old school DNA sequencing: Sanger method

So there are many ways that you are able to record DNA. This one was the old way, which was quite difficult to do with out getting confused a little or lost with the multiple lines of coding. Back then they didn't have computer to do them automatically like we do now. I had to read the bottom to the top and make sure it was all done correctly otherwise I would either have to many letters or not enough.

From DNA to Proteins: Central Dogma Vocabulary

I created a Popplet with definitions to show the definitions and that I was able to understand them.
http://popplet.com/app/#/1781706 If you go here, it will take you to the popplet.

GATTACA Reflection Questions

Questions about GATTACA!

Choose several of the following questions to discuss in a blog post reflection on the movie GATTACA. This reflection might be used as an artifact on your portfolio page 4 and could help demonstrate your awareness of the effects of science and technology upon society.

1. The following terms were used in the movie. How do they relate to the words we use: degenerate and invalid?

        De-gene-erate

        In-valid

        Borrowed Ladder

2. Why do you think Vincent left his family, tearing his picture out of the family photo, after winning the swimming race against his brother?

So I thin Vincent left his family because they didn't support him in his dream, they thought he could never do it because he was invalid.

3. Describe the relationship between Vincent and Anton.

The relationship between Vincent and Anton is kind of difficult at times because Anton was the perfect child while Vincent was invalid. Vincent and Anton competed in swimming the furthest and every time Anton won until the last time they swam and Vincent won. In the end they still were brothers and loved one another.

4. When Jerome Morrow said to Vincent/Jerome, “They’re not looking for you. When they look at you, they only see me,” what did he mean? Can you find any parallels to this type of situation in real life?

When Jerome said that to Vincent, he meant that they don't see beyond what his information his because his information says it all. It's like what people say it's not what is on the outside but what is on the inside.

5. Choose your favorite character from the film. Explain why you choose that person. Would you want to be that person? Why? Why not?

My favorite character had to be Vincent because even when people told him he could never go to outer space he never listened but instead strived to be better and live his dream. Even though he was invalid he accomplished more than anyone could dream and he strove so hard to be better. Although I would never want to be him because those aren't my dreams at all.

6. At the end of the film, you are told that the Doctor knew about Vincent all along. Why did the Doctor go along with the fraud? What would you have done if you were the Doctor?

So in the end the doctor did knew about Vincent all along but he went along with it all this time because he to had a son with dream and problems. His son had looked up to Vincent and the doctor knew how hard he worked to get to where he was. If I were to be in the same situation as the doctor I would help Vincent accomplish his dream. I would not want to be the one to destroy his dreams. He was not causing anyone problems or putting anyone in dangerous situation because he was able to control himself.

7. The technology to do what was done in the movie is definitely possible within the next ten years. Do you think that Vincent’s world could eventually happen in America? Why?

I do think that Vincent's world could eventually happen in America because everyday in America there are people working to improve our technology. Every year the improvement to our technology is tremendous.

8. What do you think is wrong with the society portrayed in "GATTACA"? What is right?

The society in GATTACA is portrayed as the perfect people could accomplish anything they wanted to because they were not messed up or had a disease. The people who were sick or had some type of disease were automatically put at the bottom and kind of looked down upon. Vincent had a heart disease and because of that he wasn't allowed to do much. I thought of this to be very wrong because the dreams of many people were taken away without even having a fighting chance to them.

9. What were the screenwriters trying to tell us through the episode of the 12-fingered pianist? Is anything wrong with engineering children to have 12 fingers if, as a result, they will be able to make extraordinarily beautiful music?

The screen writers were trying to tell us that you can have a child with any feature or can do anything by putting the right gene together that you want them to have. I truly think that having twelve fingers is wrong just to make extraordinary music. We are not mean to have twelve fingers only ten, even if the parent want that they should not be able to go through with it.

10. You and your spouse are having a child and are at the Genetic Clinic pictured in the movie. What characteristics would you want for your child and what would you ask to be excluded? Why would you make those choices?

  If me and my spouse were to have children and go to the Genetic Clinic like in the movie, all I would ask is to have a healthy child that resembled both my spouse and I. I would love for them to play sports but I would not want them to be made for them because I would rather them make their own choices rather than them having to live up to a picture perfect future. It's not right!

11. Picture yourself as either Vincent, Jerome, or Anton. Would you have acted the same or done things differently if you were in the same world as them?

If I were to be in the same situation as Vincent and Jerome then I would do the same thing because I would want to prove everyone wrong on what they think and believe. Just because something is wrong with you doesn't mean you have to revolve your world around it.

12. How does the society portrayed in GATTACA resemble the type of society that some Americans were hoping for during the height of the Eugenics movement?

The society in GATTACA is resembled to stop all of the bad characteristics that kids can have. The healthy people or kind of put on a pedal stool while the sick or not healthiest people or put down at the bottom. They believe that only the healthy people can do stuff while the unhealthy are a inconvenience.