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Standard 8 4th quarter

Remembering: What I did in Biology was:

1. PIG DISSECTION 
2. TRASFORMATION LAB
3. EXPLORING MOLECULAR EVOLUTION
4. DNA FINGER PRINTING
5. Old School DNA and GATTACA

What is important about it:
Each blog was really need to write and to engage myself into something new. My favorites would be learning about DNA and its functions, Evolution, Watching Gattaca and the Pig Dissection. I would say my all time favorite is the pig dissection because I really enjoy learning about the body and for some reason cutting the pig an doing it hands on made it stick in my mind much easier than reading and writing 
Applying:
I do happen to apply Biology in everyday life because I have a Biology class but in the future I'm looking into the medical field but Im not sure if I want to be a Nurse Practitioner or a Physician Assent for an OBGYN clinic.  
Evaluating:
This 4th quarter I think I did well with my blogs they became are in-depth and detailed. Some even had really good pictures. This 4th quarter I think I did a lot more group work intend of individual work and I don't really like working in groups because I don't learn exactly what is being taught. So my blogs weren't  as detailed and 3rd or 2nd quarter but I did try really hard this last quarter with my work.  I would give my self an A for effort.
Creating:
This quarter was more difficult than the last 3 we did more labs which means more partners but I do think I did pretty good for doing a lot of labs. I didn't reach my goal of putting more videos or outside resources on my blogs but I do think I did go more in detail of writing my blogs. 

Trasformation Lab

This is a prezi about making bacteria cells glow with a +glo solution. We baked them in a incubator for 24 hours and tested out results the next day.

Pig Dissection

Well I got a 100% on my test of the parts :) whoop whoop!!! I trained my brian to learn all 64!!

EXPLORING MOLECULAR EVOLUTION

STUDENT WORKSHEET

Results of your pairwise alignment comparing the beta globin gene in humans and in chimps:

1. Data about the alignment can be found below the blue/black alignment chart. How many nucleotides are there in the beta globin gene for:
1. The chimp? 600 bp

2. The human? 626 bp

2. A blue asterix indicates that the nucleotides in both sequences are the same, we say they are conserved. What percentage of the beta globin sequence is conserved in chimps and humans? (Don’t include the insertion at the beginning of the human gene). This percentage is often reported as a similarity “score” below the alignment.

99%

3. Would you expect the protein structure to be highly similar or markedly different in the chimp and the human? Explain.

I think similar because we have some similarities to chimps like hands and ears. So maybe the protein that has hands and ears in chips are the same in humans.

RETURN TO BIOLOGY WORKBENCH INSTRUCTIONS

Results of your pairwise alignment comparing the beta globin gene in humans and in chickens:

1. What is the percentage of sequence conservation between the beta globin gene in chickens and humans?

Humans and chickens have DNA sequence that is 57% alike to one another.

2. Looking at the two pairwise alignments you have performed, would you expect the beta globin protein found in humans to be more similar to that found in chickens or that found in chimps? Explain.

The beta goblin protein that is found in chickens, humans and chimps are similar. Its not surprising that the chimp and human are more similar than the chicken and the humans just by the difference in visual appearance I would expect for the human and the chimp to be more similar.

3. Do the results achieved by running these alignments support the results on evolutionary relationships determined by scientists using anatomical homology (similarities)? Explain.  

The results in the alignments supported the part of evolution that states humans are most alike to chimps and come from a line of apre ancestry. if it was stated that humans came from a line of chickens it would be less supported because only about half of the sequence were aligned.

RETURN TO BIOLOGY WORKBENCH INSTRUCTIONS

Results of your multiple sequence alignment comparing the beta globin gene in a variety of animal species:

1. Examine the Unrooted Tree produced.  

Record the species at the end of each branch on the unrooted tree shown below.

2. Based on the information in the unrooted tree:

1. Which two species appear to be most closely related to each other? Explain your choice.

Chimp and Human because the two branches are the closest together.

2. Which two species seem to be the least closely related to each other? Explain your choice.

Human and Goldfish because the two are on the other side of the tree.

3. Comparative evolutionary distance between species is indicated by the length of the clades they are on. Give the comparative evolutionary distance (by percentage similarity “score”) between:

1. The mouse and human: 79%

2. The wallaby and the human 61%

3. The chimp and the human 99%

Comment on the significance of these results given your knowledge of mammalian groups.

The mouse and human are extremely different because a mouse is gross but a mouse has whiskers, a tail, claws, and fur. Humans on the other hand don’t have any of those things which is why I’m confused about the percentage it has. The wallaby I don't know much about which is hard to compare the two. But if I had to guess humans jump so that might be a similarity. The chimp and human well they have hands we have hands cool, but they also have ears which are similar and the lips they have and also the teeth with the same facial structure and they walk and act they use their limbs like humans.

RETURN TO BIOLOGY WORKBENCH INSTRUCTIONS

Results of your Rooted Phylogenetic Tree:

1. Examine your Rooted Phylogenetic Tree and record the species at the end of each

2. Based on this tree diagram, which species is/are most closely related to:

1. The goldfish: chicken

2. The mouse: human and chimp

3. Homology is a term used to refer to a feature in two or more species that is similar because of descent; it evolved from the same feature in the last common ancestor of the species. Hence, similarity in DNA or protein sequences between individuals of the same species or among different species is referred to as sequence homology. Which two species in the tree above share greatest homology with respect to the beta globin gene? Human and chimp

4. A node is a branch point representing a divergence event from a common ancestor. Which two species have the most ancestral nodes (divergence events) in the tree above? Explain your answer giving the number of nodes leading to these species. The human and the chimp because they have a long line from the starting point, containing three nodes.

5. Looking at the phylogentic tree above, which two organisms:

1. Diverged from their common ancestor most recently?

Humans and chimps

2. Diverged from their common ancestor least recently?

Chicken and Goldfish

6. Draw a modified phylogenetic tree to show how the tree above might change if the beta globin gene for a kangaroo was added to the multiple sequence alignment.

The kangaroo would be connected to the wallaby.  the tree might change showing how the other animals are different than the kangaroo.

7. It is important to understand that the phylogenetic trees you generated using bioinformatics tools are based on sequence data alone. While sequence relatedness can be very powerful as a predictor of the relatedness of species, other methods must be used in addition to sequence homology, to determine evolutionary relationships. Briefly describe 3 other methods that you think might be used to determine evolutionary relationships.

•  Scientists could also look at the physical appearance of the organisms.

•  They could see where the animals are located.

•  They could also look at fossils found in that region to see what the past animals looked like.
  
  

DNA FINGER PRINTING

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.


In your opinion, what role (if any) did newspaper stories and editorials have in the outcome of the original trial of Dr. Sam Sheppard? I think they really had a big role in the outcome of the original trial because they were telling the wrong facts about what happened in the crime, and this caused some people to believe false information.

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:


What is the function of the restriction enzymes in DNA fingerprinting?
First DNA fingerprinting needs the DNA to be cut into small pieces. Then Restriction enzymes are used.


What is the function of the agarose gel electrophoresis step?
The point of this step is to separate the DNA based on the length. After this is put into the gel and is turned on, you wait until all the DNA has moved from wherever it was placed and this gives you a banded pattern that is your DNA fingerprint.


Why is a nylon membrane used to blot the DNA?
People use nylon to blot the DNA because the gel is very hard to handle.


What does a dark spot on the X-ray film indicate?
It shows where the probes attached to the DNA and gives the DNA Fingerprint.



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:


What evidence was initially used to convict Cotton?
An eyewitness was used. 


What did the DNA evidence show?
It showed that Cotton was innocent and that the eyewitness was wrong.


How could DNA fingerprinting be used to prevent a false conviction if a case like this was being tried today?
DNA finger printing would have helped out because  DNA means their would be eyewitnesses and their would be no mistake about who the convector would be. 


What percentage of convicts are unjustly convicted of sexual assault cases, according to Neufeld and Scheck?
25% of convicts are unjustly convicted of sexual assault cases. 

Genetic Testing: Would You Want to Know?

This was a very touching article and video. I would do the same thing that Kristen did, if I was to lose my mother to a disease. I think this testing is very important especially at this day and age. If I have a really bad disease that can cause retardation I would't have a child. Not because I couldn't handle it or financially handle it but what happens to my child when I die? Also I have seen children like that struggle in life battling the non-use of their brian or limbs and they don't have a chance in life to survive. As a parent that would KILL me to see them pass away so young. It doesn't have to be retardation that I would want to know I would want to know everything. If they have would have cancer later on in life maybe I wouldn't have a child because I know that all they would be doing is suffering and just sick. If I could keep someone from suffering that is all I would want in my adult years.

In the article Kristen gets tested so that she won't hurt her children or her future family because Huntington's disease is a very serious disease and it is just so hard to see family members with that type of illness. Kristen lived with her mom having that disease note that she didn't know that but she knew that something was wrong with her mom. As a daughter you are very close to your mom and to see her in so much pain that hurts you and you will do anything to stop the pain even if it means that you as a woman and daughter not have children. Kristen makes a point of what kind of spose would want a wife with a disease where you would need constant attention?

So in my opinion yes I would want to be tested so I would know if I am safe and so that my future family would be safe. Also if I would have to tell my spose if I so chose that you will need to take care of me for the rest of my life and yours. I couldn't do that. I am the type of person who likes to plan every single detail in life. I am planning my future house, job, dog, even typical supper ill have when I have as a family. But if I have the chance to see what types of harm I carry I would love to stop that to save the pain of my family and my self.

http://usatoday30.usatoday.com/news/health/story/2012-04-09/genetic-testing-huntingtons-disease/54475708/1

Old School DNA and GATTACA

We stated looking at DNA in  biology this last quarter and WOW is it crazy! We started looking at "old school DNA". What Old School DNA is getting this paper to sequence DNA which is basically finding were G,A,T,C goes. The picture below shows the dna in colloms of dna. We took a paper and counded the line across from left to right for each person. Then put the codons(

Three-base sequence in messenger RNA that causes the insertion of a particular amino acid into a protein, or termination of translation)

on the back of the paper in a graph and compaired to a normal DNA sequence. Easy lab but extrealmy hard to do.

These are the 4 people we could DNA for. Norm is the normal control guy and the last 3 have something wrong with them. They have at least one codon messed up. In their sequence of DNA. 

This is the paper that we put the codons on and compared them to Norm our normal guy. And we found out that Abby had 1 codon messed up, Bob had 1, and Carol had 7. She is one messed up lady.

This picture above are some notes I took about DNA. It explains what the codes are C-cytosine and G-Guamine are a pair and will always pair up the the sequence of DNA. The last two are A-adenine and T-thyme and they pair up in the sequence of DNA.

Next in biology we watch GATTACA. This movie is amazing and I really hope this doesnt happen in realy life tho.  Below are the question that analyze the movie. Which I would suggest to any person to watch.

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

degenerate and invalid?

         De-gene-erate- is a person who hasn't been tested/ elected to be the perfect child.

         In-valid- A person who isn't part of the elite crowd.

         Borrowed Ladder- it is the same as a de-gene-erate and its a term for the shape of DNA.

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?
Because he thought that side he beast Anton in the race he can go on to GATTACA and become a spaceman. 

Anton is the elite brother who was always better than Vincent and Vincent wants to beat Anton so he can finally be a man.

3. Describe the relationship between Vincent and Anton.

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?
They won't look Jerome because he is the elite personal and Vincent isn't which makes him an easy target to be the blaimed person. In life police won't expect that the goody touches did the crime they go after the lesser of people. 

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 person is Vincent because he was cute and he had good drive to do him dream job and be apart of GATTACA. I wouldn't want to be him because he could have got in a lot of trouble and probably killed. 

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?

Because he said that his son had a dream but couldnt do anything because he was invalid. I would have let Vincent go because he was a good person.

7. The technology to do what was done in the movie is definitely possible within the next

fifty years. Do you think that Vincent’s world could eventually happen in America? Why?

I think it could becuase America is always looking for the elite people.

 

8. What do you think is wrong with the society portrayed in "GATTACA"? What is right?
The dividing people because they are not "valid" is wrong but the science is pretty cool.
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?

People always wont the best and will do anything to get it. The 12 fingered pionest was very weird but now days we are getting pretty close to getting it done.

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?

I would want a smart kid who wont have a proplem learing something, athletic so they could have fun and im not sure what other things I could wan't I guess.

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 worl

If I was Vincent I would just except the fact that Im not "valid" and just live a sad life.

d as them?