Exploring Molecular Evolution

Exploring Molecular Evolution

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

1. Each line in this alignment contains 60 nucleotides. How many nucleotides are there in the beta globin gene for:

1. The chimp

1. 600

1. The human

1. 626

1. 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.

1. 99%

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

1. I would expect the protein structure between a chimp and a human to be very similar because of the 99% identical genes

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

        1. What is the percentage of sequence conservation between the beta glob in gene in chickens and humans? Work this out using the second line of nucleotides only.

                      57%

1. 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

1. I would expect the beta globin protein found in humans to be more similar of a chimp.

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

1. Yes because scientists can tell how close something is related to another when the two things are compared with each other.

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  Results of your multiple sequence alignment comparing the beta glob in 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.

1. Based on the information in the unrooted tree:

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

                               - Humans and chimps based on the unrooted tree appear to be more closely related to each other. When you look at a hmans dna and a chimps dna they are 99% similar.

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

                           -Two species that are least closely related to each other are a chicken and human.

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

1. The mouse and human

1.  79%

1. The wallaby and the human

1. 75%

1. The chimp and the human

                         1.   99%

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

           

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Results of your Rooted Phylogenetic Tree:

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

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

1. The goldfish: Chicken and Wallaby
2. The mouse: Human and Chimp

1. 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?

1. Humans and chimps

1. 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.

1. Human and Chicken with 4 nodes

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

1. Diverged from their common ancestor most recently?

                                               1.  Wallaby

1. Diverged from their common ancestor least recently?

                                               1.    Human

1. 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 alignm

1. 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.

• Anatomy/structure
• Fossils
• Biogeography

Bacterial I.D Lab

Bacterial I.D Lab

1. To grow bacterial colonies in a solid medium culture dish.
2. To prepare the DNA, we got a bacterial colony, and put it in a micro centrifuge tube then got some digestive buffer and put it in the tube with the bacteria. We then let the tube sit for a while and then put it in a water bath at 100 degrees celcius for a while then it in a centrifuge for a while and put the bacteria from the micro centrifuge tube into a PCR tube.
3. PCR is used to make copies of DNA sequences by annealing the primer to the template, and the synthesis of new strands. This takes less than 2 minutes. Each step is carried out in the same vial.  At the end of a cycle, each piece of DNA in the vial has been duplicated. The cycle can be repeated 30 or more times and each newly synthesized DNA acts a new template. 
4. First set up the micro concentrator column. You add buffer to the column and then add the PCR to the column. You then place the tubes in ice, and then next into the centrifuge. Then you don't need the column anymore, so you can get rid of it. 
5. They identify you by copies/ sequences of DNA being produced. 
6. They end up stopping the sequence at a certain point and then go on to the section. They repeat this same process many, many times.
7. Blast stands for Basic Local Alignment Search Tool.
8. It was pretty easy to find the things mutated in the DNA, and yes it had Bartonella Henselae.

GATTACA Questions

Watching the movie GATTACA was pretty cool! I didn't get to finish all of it, but i think i only missed like 5 minutes of it. From what i saw it was different than most movies but it's crazy how the things that happened in the that movie happened.
Questions:

1. A Degenerate is someone that has lost moral, physical, or mental qualities. In the movie, Vincent was considered "invalid" because he had heart problems and he was not the same as everyone else that worked where he wanted to. Vincent was a borrowed ladder with Jerome, because he took over his profile to be able to live his dream.
2. I think he might have left his family, because Anton was definitely the "favorite" of the family, because he was "normal". Even in the beginning of the movie the mom wanted to name him Anton, but the dad said Vincent, and saved Anton for the "good" son.
3. The relationship between Vincent was kind of shaky. Vincent was into other stuff than Anton, and  I think that was one of the things that set them apart. Vincent wasn't "normal" like Anton was, and he wasn't as in good of condition. He was a very strong guy though, that always tried coming out stronger, wanting to prove Anton wrong.
4. When he said that, he meant that they werent looking for the Vincent/ Jerome that he now was, they were looking for the Vincent that he was. Untill his brother showed up,nobody had ever suspected of thought anyhting of it.
5. I would have to say that my favorite character was Jerome Morrow. He was a very strong man, and didn't want people to feel bad for him just because he was in a wheel chair. He was not ashamed of being how he was. He had to draw blood from himself everyday, and urine too. He liked to have a drink every once in a while too, but he couldn't because it would come out with acohol in his urine. He had to sacrifice things he liked to do too. If you think, he might of had to do everything by himself before Vincent was there to help him do things. If i had to tell him something, i would tell him that i look up to him for being as strong of a man as he was.
6. The doctor went along with the fraud, because his son was consodered as "invalid" too and he thought it was great that he was still going for his dreams just because he was considered "different". His son wanted to work at GATACCA and do what Vincent did. If i was the doctor i would have played along with it, because i believe that anyone should follow their dreams no matter how "invalid" they are considered.
7. Thinking about it, America will probably end up with that type of technology some day in the future. We already use many different types of technology like that like with all of the many crimes that they have today. Technology like that is used every day in America now.

DNA Structure

This is the front and back of a worksheet that we did in class that really helped me understand the structure of DNA.

      When you think of DNA you probably get confused right? I know i did, but once you learn about it and learn a little about the structure of it, it's really not too bad. It's pretty much just a pattern made up of four different parts which are called nucleotides. Each of the nucleotides is made up of a sugar or deoxyribose bound on one side to a phosphate group and bound on the other side to a nitrogenous base. The two classes of bases of nitrogen are called purines, and pyrimidines. The four bases that are in the DNA's alphabet are A which stands for adenine, C which stands for cytosine, G with stands for guanine, and T which stands for thyme. If there is one thing that i remember about all of this, it is that C and G always go together, and A and T always go together. DNA has two sides. These two sides are twisted together like a ladder, called the double helix. The hydrogen bonds between the phosphates is what causes the DNA strands to twist.  First of all DNA stands for Deoxyribonucleic acid. It forms chains of genetic material organized into chromosomes and gets passed from one generation to the other. DNA guides the cell in making new routines that determine all of our biological traits. So the reason you look the way you do, is because of your DNA, which we get from our parents.











<--------This is a picture of a DNA model that we made. It's pretty cool to be able to have the hands on experience on making one, and actually learning the parts of it and getting the hang of it.

This is a picture of a DNA model that drew while we were learning the structure of DNA and getting familiar with all of the parts that are in a DNA model. -----> 

DNA Extraction Lab

I had no clue it was this easy to extract DNA from something! It was a very quick and easy lab that didn't take long at all. First we measured out 1 gram of raw wheat germ into a 50 ml test tube. Then we got 20 ml of hot water and added it to the tube with the wheat  germ and stirred it constantly for about 3 minutes or so. Next we added about 1/4 teaspoon of detergent and stirred it about every minute for 5 minutes, without creating any foam. We then had to add 14 ml of alcohol very slowly at an angle into the test tube so that it would form kind of a separate layer on top of the detergent-water-wheat mix. After setting for a few minutes the DNA started rising and forming into clumpy, stringy, snot like strands in the alcohol level. At the top of the detergent and bottom of the alcohol level is where the DNA started to grow. The detergent did the job of busting up the cells, and as i said before, the alcohol brought up the DNA. DNA dissolves in water, but gets clumpy in alcohol and doesn't really dissolve, so that is why the DNA came up into the alcohol level.

Eugenics

When i first heard about Eugenics i thought what the heck is that? I bet there are a lot more people who are thinking the same thing right about now too. But after reading and researching about it a little, i found out that Eugenics pretty much means people should control what their kids will look like, all the way from the color of eyes to the color of their hair. Eugenic origins first started after the Civil War. America was pretty racist and anti- minority during that time, and Eugenics reflected on that.  It was a pretty crazy time for everyone. People started moving and losing jobs so one brilliant man proposed the survival of the fittest, but there was a problem with that and the problem was that the "rich were having a problem with reproduction, and the "poor" people were in a baby boom! So since the more wealthy people had the money to do things with that's where eugenics helped them out a lot.

      The word Eugenics was brought up by a man very into science, Francis Galton. In 1883, this is how they could take over genetics and control what kids looked like, kind of like what we now call segregation. This is where medicine came in and really impacted the study of Eugenics because they needed the different medicanes. This is also where pedigrees came in, so they could look at family history of people to help them have a better understanding  of things. 

     Eugenic's first major challenge was made in 1915 by Thomas Hurt Morgan. He showed Genetic mutation outside of inheritance involving the finding of birth of a fruit fly with white eyes coming from a family of red- eyed flies. He had said that this showed that major genetic changes occurred outside of inheritance and that the concept of eugenics based on genetic inheritance being severely flawed. Seeing the results of the fruit fly gave him an idea of what all this was about. 

      To this day, it is a horrible movement that has inflicted massive human rights violations of millions and millions of people. There are many things engaged in eugenicists involving violations of privacy, attacks on people's reputations, violations of the right to life, to found a family, to freedom from discrimination are all classified as violations of human right today. It is a thing hated by many people, but  then again there are people out there that like it. 

     In my opinion, i think that Eugenics is a very wrong thing. It's not the right thing at all in my eyes.  Let your offspring come out the way they are supposed to. God has people come out the way they are supposed to for a reason. I know people would like to choose the way that their kids come out, but i think they should come out naturally the way they're supposed to come out, not the way you choose for them to come out. 

Paper Tasting project

In this project, we got little pieces of paper that you taste and see if you taste anything. When i tried it it tasted really bitter and really gross. It's kind of a hard thing to explain? But i have to go home and the relatives that are living her close to me, have them taste it and then come back to school and fill out my pedigree chart on whether they tasted it or not. It's kind of a cool little experiment to see who all can taste it and who can't.

     I went to my family with these little paper tasting test strips to see who could taste them and there weren't many of us who could. Only me, my mom, and my sister could taste the weird taste on the paper.  When my sister tasted it she took it out of her mouth right away and said whatever it was that she tasted was gross. My brother it on his tongue and asked what it was that he was supposed to be tasting because he tasted nothing. My mom was in the shower at the time and i needed to go so i had her stick her tongue out and taste it. She definitely tasted it because she started gagging and asked me what it was. My grandma from my moms side taste nothing too. My grandma and grandpa from my dads side(not blood related)  tasted nothing also. So i guess not everyone tastes things the same as other people.

Genetics

      I really liked that we went over this stuff, because i like learning about genetics and things like that. It interests me, because those things really happen when you have a kid. It's really neat to think about what your child will look like when they are born depending on your looks, and when you meet the partner you want to be the other parent to your kid and what they look like. Doing all the activities we did like we did with the whole making the baby thing was pretty fun. To see what dominant and recessive traits your kid would get from you. DNA is the most important thing when it come to genetics, reproduction and all of the other things like that. Working on what we are now is also interesting, like learning what all of the pedigree charts mean is really cool. It's weird that one person in your family can have one trait and the other  person doesn't. Genetics has so much to do with everything. You can figure out how your offspring will be, and you can also see if you will be affected or if you may become a carrier of a certain disease.

This is a paper that we did to help us understand the concept of genetics. It was a pretty good way to teach us and for us to learn the way it works. 

Reproduction

Going over the whole period of time that we went over reproduction, i learned A LOT that i defiantly didn't know before. Reproduction is the biological process in which new life are produced from their parents. Reproduction is a feature known of all life with both animals and humans. The two main types of reproduction methods are grouped into two different types. Asexual and Sexual. Asexual reproduction is the process by which an organism makes a genetically very similar, or identical copy of itself without any genetic material from another person. Sexual reproduction is the biological progress in which organisms make descendants that have a combination of genetic material from two different members of the same species. Most animals and plants reproduce sexually. By reproducing sexually, you have different sets of genes for every trait, better known as an allele. Offspring get one allele for each trait from each one of the parents, which makes sure that the offspring will have a combination of the parents genes. A diploid is having two copies of every gene within one organism.

      In class we watched a movie type thing showing us a couple and their process of having a baby. It was very informing to me and i thought it was really cool i got to learn about the things i did. It usually happens to every single one of us, so it's nice to learn all these things so you can know what's happening when i does happen to you. Child birth can be a very rough thing to go through, but hearing from other people, it is also one of the most amazing things that an happen to you. Genetics have a lot to do with child birth too, because when the the sperm and egg get together and make the baby, the baby 23 of them moms and 23 of the dads chromosomes which makes up the DNA of the baby. It's actually kind of hard remembering the video and explaining it but i did learn a lot from it. 

In sickness and in health

In Sickness and in Health

Greg and Olga's Pedigree

1. No, they do not.
2. No, just because his mom has two siblings that have it doesn't mean he will.
3. No
4. 50% chance
5. 0% chance
___________________________________________________________________
1. Not everyone can get it, it shows up less.
2.Consanguineous means being from the same kinship as another person. Being descended from the same ancestor as another person. It is pretty much a complicated word for incest.
3. Autosomal gives men and women the equal chance of getting something, but through out the pedigree, no women have factor VIII. It's all men.
____________________________________________________________________
1. The gene that determines what sex a person will become.
2. Because he x chromosome has to come from the mom. They get the y from the dad.
3. She has to have Two copies.
4. (on pedigree)
5. There is a 25% chance that she can be a carrier. There is a 50% chance that she could pass it to her offspring. The males may be affected differently because only males in both families. Not really any women.
6. There is a 0% chance. He doesn't carry it, and he cannot pass it on to his children.

Onion root mitosis

Doing this onion mitosis lab, it was pretty interesting to see all the things that we saw. Actually seeing the different phases such as Interphase, Prophase, Metaphase, Anaphase, and Telophase was really cool. Looking at the pictures on the edmodo site compared to the actual thing was a big difference, but it was also a bug help to help recognize the cells.

   Mitosis plays a pretty big part in the onion root tips that we were looking at. Mitosis is the thing that lets the nuclei of dells to and provide the daughter cells with a full set of chromosomes during cellular division.When a cell is at rest, it is in the phase called interphase. 

	Interphase	Prophase	Metaphase	Anaphase	Telophase
number of cells	20	10	3	2	1	36
percent of cells	55.5	27.8	08.3	05.5	02.7	100%

Doing this table, the only things that were filled out were the totals on the right hand side, and the headings on the top and side. After getting help from the teacher with the table, the bottom row the total i came out with was 99.8% so i was very close to the 100% total that it was supposed to be. 

    We then looked at onion roots underneath the microscope ourselves and we had to make a table just like the one above from the things that we had observed from underneath the microscope. In the pie chart, it is a little easier to understand the different amounts found. 

	Interphase	Prophase	Metaphase	Anaphase	Telophase
number of cells	619	14	6	4	5	648
percent of cells	.96	.02	.009	.006	.008	1.003

Observing underneath the microscope we found that there were a lot of interphase cells in that root. There weren't many of the others, and on top of that, they were hard to see. Being honest, all of this mitosis stuff confuses me, and it was a little hard for me to learn, but i guess i took some of it in and learned a little. In this pie chart, you can see that the thing that took up pretty much everything was the Interphase. It was a really big part go the cells we found underneath the microscope. 

cancer

     Melanoma is the most severe, dangerous type of skin cancer, and it is the number one cause of death from skin disease. Changes in cells called melanocytes that make a skin pigment called melanin. Melanin is in charge of your skin and hair color. It can show up on your skin, or it may start as a mole or another region of your skin that has changed in the way it looks. Some birth marks eventually turning into melanomas. The four different types of melanoma are:

1. Superficial spreading melanoma, which is the most common type, usually being flat and different in shape and color. It is usually more in light skinned people.
2. Nodular melanoma, which mostly starts as a raised area that is dark, usually a black, blue, or reddish color. But sometimes they don't have any color at all.
3. Lentigo maligna melanoma, which is most common with elders. It is mostly common in skin damaged by the sun on the face, neck, and arms. Most of the time these areas are flat, large, and tan with areas of brown.
4. Acral lentiginous, which is the least common form. You usually see it form on palms, soles, or under the nails.

Melanoma is not as common as most of all of the other skin cancers but it is increasing by a lot. The risk of getting this cancer gets higher as you get older, but it is more commonly seen in younger people. Developing melanoma is more likely to develop if you: have blue or green eyes, red or blond hair, and fair skin. Live in high altitudes or a place with a sunny climate, have spent a lot if time in the sun because of jobs or other things, have had more than one blistering sunburns as a child, or use tanning devices regularly. Some other risk factors are: having close relatives with a history of melanoma, coming in contact with cancer- causing chemicals like arsenic, coal, tar, and creosote. Certain types of moles or multiple mirth marks, or a weakened immune system because disease or medication.
     Cancerous cells can spread to any part of the body at various rates, depending on how serious the melanoma is. The cells multiply by dividing and going into healthy cells. Melanoma begins as a topical skin cancer, but can turn into cancer that goes deep into the skin, lymph nodes, blood, brain, lungs, bones or the entire body. In addition, melanoma can also spread through blood and lymphatic fluids to other areas in your body. This may cause cancerous tumors to form.

-Here is a photo of melanoma cells in the body.