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.

Photosynthesis dry lab

In this lab we didn't actually do it, we just did a write up. Doing this you realize that it's pretty had to to a lab without actually doing it. In this lab the facts were:

• Carbon dioxide in water produces carbonic acid
• BTB is a blue green liquid which changes to a yellow color in acid and back to blue green when returned to a neutral pH.
• Carbon dioxide and water yields star and oxygen when chlorophyll and sunlight are present
• animals respire
• Green plants photosynthesize in the light and respire all the time. 
• Sugar and oxygen yields carbon dioxide and water and energy.
• Elodea is in the kingdom planate and is a producer.

     Interpreting the observations, i got that

1. water + BTB----> neutral pH-----> blue green. This means that if you have water plus BTB, it is a neutral pH, which keeps you at a blue green color.
2. Fish----> respire -----> sugar + O2 + CO2 + H2O----> CO2 in H2O----> acid----> yellow. This means that the fish respires and gives off sugar and oxygen, carbon dioxide and water. The carbon dioxide and water all make an acid which makes the color yellow.
3. In this one lodes is in kingdom planate and is a producer. Green plants photosynthesize in light and respire all the time. Which makes carbon dioxide and water yield and sugar and oxygen wen chlorophyll and sunlight are present.  BTB is blue green liquid which changes to a yellow color in acid and back to blue green when neutral.  So it is blue green in light and yellow when left in the dark for 3 hours. 
4. Elodea is pale blue green in light and yellow when left in the dark for 3 hours. The animal is doing desperation, giving off carbon dioxide and giving off BTB acid making it yellow. The plant does something different though. The plant picks up the carbon dioxide and stays blue green, not making any acid. 

Brown Recluse Spider

     The Brown Recluse Spider is a venomous spider. It can cause significant cutaneous injury with tissue loss and necrosis. You can find the Brown Recluse in the United States from the east to west coast, and sometimes in the south. The Black Recluse is different from most spiders because instead of having 8 eyes, it only has 6 eyes that are arranged in pairs. One pair is on front and another pair on either side. It usually has a shy and nonaggressive behavior, but occasionally bites humans because they share the same habitat. It usually just bites when it is being disturbed. They roam at night and hide during they day. They can survive six months without food or water. It bites when it is caught between a part of the body and another surface like when children are playing under house furniture, while a person is sleeping and rolls on to where it is, or when getting dressed with clothes or shoes where the spider has hidden itself.
     The Brown Recluse Spider's venom in extremely poisonous, even more than a rattlesnake, but when they bite, they cause less disease than rattlesnakes. The venom from this spider is toxic to cells and tissues. There are some secondary results that are very rare, but can still happen. The destruction of red blood cells, low platelet count, blood clots in the capillaries and loss of ability to form clots where needed, acute renal failure (kidney damage), coma, and death.  The  symptoms of Brown Recluse spider bites are severe pain at the bite about 4 hours later, severe itching, nausea, vomiting, fever, and muscle pain. The bite is usually red upon close inspection and may reveal fang marks. Most commonly, the bite will become hard and heal with a little scaring over the next few weeks or days. Occasionally, the local reaction will be more severe with erythema and blistering, sometimes leading to blue discoloration, and ultimately leading to a necrotic lesion and scarring. Signs that may be present are blistering, death of skin and subcutaneous fat, and severe destructive necrotic lesions with deep wide borders.
    So researching the Brown Recluse Spider, i can conclude that this spider isn't very common where we live, but if you get bit by one, it can be very serious and dangerous.

http://www.emedicinehealth.com/spider_bite_brown_recluse_spider_bite/page3_em.htm

Enzymes action

     In this lab we tested the action of enzymes and for the enzymes we used yeast. We added the yeast to a test tube with 3 milliliters of water (H2O) and 3 milliliters of peroxide (H2O2). After adding these things together we mixed them a little and put the pressure cork on top of the test tube to trap in all the pressure. As the cork was in the tube, it was hooked up to a tube that recorded the data on the computer making a graph that showed the pressure of each tube.
    We did 3 different little labs, and in each one a few things changed. In the first lab we did concentration. We took the 3 milliliters of both water and peroxide and put them in the first test tube, then added 20 drops of yeast. The second tube we did the same thing but with 30 drops, the next with 40, and the fourth and final tube we added 50 drops. We put the pressure cork on all of the tubes after adding the different concentrations of yeast and the data recorded.

     The second lab that we did was temperature. We added the 3 milliliters of both water and peroxide and added 30 drops of yeast to the four test tubes that we had. The first tube that we tested was water and peroxide with 30 drops of yeast that was room temperature. The second tube that we tested was water and peroxide that had been held in an ice bath for a few minutes with the 30 drops of yeast. The third tube was stuck in a hot water bath with the water and peroxide with 30 drops. The fourth and final test tube was stuck in a warm water bath with the 30 drops of yeast.

     The hire and final lab that we did was with different pH levels. We kept everything the same, except for the peroxide. We mixed 30 milliliters of water with 30 milliliters of the different pH buffers and added 30 drops of yeast to them. The first test tube that we did was the water with the pink level 4 pH buffer, and the 30 drops of yeast. The second test tube was water with the blue level 10 pH buffer, and the 30 drops of yeast. The third and final tube we tested in this lab was the yellow level 7 pH buffer, and added to it was the 30 drops of yeast.

     In these labs, as you can see, some of the different things we tested, reacted better and had more pressure than others with the yeast.

Plant Cell Structure

     You pass by a flower shop, or see pretty flowers planted in a yard, or meadow. The flowers you see, and all the plants you get your vegetables from all have a "heart". Every plant is broken down, and all start with  a plant cell. Plant cells are important to cells because they are the basic units of life. There are many parts involved in a cell. All of them are important too, but there is one place where everything starts. The nucleus. The nucleus is en closed in a double membrane and communicates with the surrounding cytosol in numerous nuclear pores. In the nucleus is the DNA,which is responsible for providing the cell with its one of a kind characteristics. The DNA is similar in every of every body, but depending on the cell type, some genes may be turned on and off. This is why a liver cell is different from a muscle cell (giving an example). when a cell divides, the nuclear chromatin condenses into chromosomes that can be seen easily by a microscope.

     The Nucleolus. The Nucleolus is the first thing you notice in the nucleus, it is the most obvious structure. The nucleolus produces ribosomes, which move out of the nucleus and position themselves on the rough endoplasmic reticulum where they are very important in protein synthesis.
     The Cytosol. The Cytosol is what they call the "soup" where all the other cells organelles reside and where most of the metabolism occurs. Mostly through water, the cytosol is full of proteins that control cell metabolism including signal transduction pathways, glycolysis, intracellular receptors, and transcription factors.

     The Cytoplasm. The Cytoplasm is just a collective term for the cytosol, plus the organelles suspended within the cytosol.

     The Centrosome. The centrosome of MTOC (Microtubule Organizing Center) is the area in the cell where microtubules are produced. Plant and animal cell centrosomes play similar roles in the division of cells. Both of them include collections of microtubules, but the plant cell centrsome is simpler and does not have centrioles. 

     The Golgi. The Golgi is a membrane-bound structure with a single membrane. It is actually a stack of membrane-bound vesicles important in packaging macromolecules for transport somewhere else in the cell. The stack of larger vesicles is surrounded by many smaller vesicles having those packaged macromolecules. The enzymatic or hormonal contents of lysosomes, peroxisomes and secretory vesicles are packaged in membrane-bound vesicles at the periphery of the Golgi. 

     The Lysosome. Lysosomes contain hydrolytic enzymes that are necessary for intracellular digestion. They are mostly seen in animal cells, but sometimes in plant cells. Hydrolytic enzymes of plant cells are usually found in the Vacuole. 

     The Peroxisome. Peroxisomes are membrane-bound packets of oxidative enzymes. With plant cells, they play  many roles like converting fatty acids to sugar and guiding chloroplasts in photorespiratioin. Oxidative enzymes in peroxisomes break down hydrogen peroxide into oxygen and water.

     Secretory Vesicle are cell secretions of e.g. hormones, neurotransmitters secured in secretory vesicles in the Golgi. The secretory vesicles are then transported to the cell surface for release.

     The Cell Membrane. All cells are enclosed in a membrane, a double layer of phospholipids. The exposed heads of hte bilayer are hydrophillic, which means that they are compatible with water both in they cytosol and outside of the cell. But the tails of the phospholipids are hydrophibic, so the cell membrane acts as a protective barrier to the flow of water that is uncontrolled. The membrane is more complex by the presence of many protiens that are very important to the activity of the cell. These protiens include receptors for odors, tastes and hormones, and pores responsibole for controlled enter and exit of ions like sodium, potassium, calcium, and chloride.

      The Mitochondria. Mitochondria provide energy a cell needs to move, divide, make secretory products contract- in short, these are the power centers of the cell. They are small, like the size of bacteria, but can have different shapes depending on the cell type. They are membrane-bound orangelles, and have a double membrane, like the nucleus. The outter membrane is smooth. But the inner membrane is highly convoluted. The cristae increase the inner membrane's surface area. It's on these cristae that food is combined with oxygen to produce ATP, which is the primary energy source for the cell.  

    The Vacuole. A vacuole is a membrane-bound sac that plays roles in intracellular digestion and the output of cellular waste. Vacuoles play a big part in plant cells. They play several roles like storing nutrients and waste products, helping increase cell size during the growth process. They even act like lysosomes in animal cells. It also regulates tug or pressure on the cell. Water collects in cell molecules, pressing out against the cell wall producing rigidity in the plant. Without sufficient water, turgor pressure drops and the plant will wilt.

     The Cell wall. The cell is in plant cells only. Plant cells have a rigid, protective cell wall made of polysaccharides. In bigger planet cells, the polysaccharide is mostly cellulose.  The cell wall provides and helps keep the shape of the cells and serves as a protective barrier. Fluid collects in the the vacuole and pushes out against the cell wall. This turgor pressure is responsible for the fresh vegetables crispness. 

     The Chloroplast. Chloroplast is in plant cells only also. Chloroplasts are organelles found in all higher plant cells. These organelles contain the plant cell's chlorophyll which makes the plants green like they are. Chloroplasts have a double outer membrane. In the stroma are other membrane structures like thylakoids. Thylakoids show up in stacks called grand. 

     The Smooth Endoplasmic Reticulum. Throughout the eukaryotic cell, especially those responsible for the production of hormones and other secretory products, is a large network of membrane-bound vesicles and tubules called the Endoplasmic reticulum. The ER is a continuation of the outer nuclear membrane and its functions vary and suggest the complexity of the eukaryotic cell. The Smooth ER has its name because it is shown as smooth by electron microscopy. The Smooth ER plays different functions depending on the specific cell type.

     Rough Endoplasmic Reticulum. The Rough ER shows to be pebbled by electron microscopy due to the presence of many ribosomes on its surface. Proteins synthesized on these ribosomes collect in the ER for transport throughout the cell. 

     Ribosomes. Ribosomes are packets of RNA and protein that play a very important role in both prokaryotic and eukaryotic cells. They are the site of protein synthesis. Each ribosome comprises two parts, a large submit and a small submit. Messenger RNA from the nucleus is moved along the ribosome where transfer RNA adds individual amino acid molecules to the protein chain.

    The Cytoskeleton. The cytoskeleton helps maintain the cells shape. The importance of the cytoskeleton is cell motility. The internal movement of the organelles, as well as the cell locomotion could not take place without the cytoskeleton. The cytoskeleton is an organized network of three primary protein filaments such as microtubules, actin filaments, and intermediate fibers.

     

Cystic Fibrosis

Cystic Fibrosis is an inherited chronic disease that affects the lungs and digestive system of many people in the United States. A defective gene and its protein product cause your body to produce thick, sticky like mucus that clogs the lungs and leads to lung infections, it obstructs the pancreas and stops enzymes from helping your body absorb and break down food. The symptoms and signs of Cystic Fibrosis are: salty tasting skin, persistent coughing with phlegm, frequent lung infections, wheezing or shortness of breath, poor growth, weight gain in spite of a good appetite, and greasy, bulky stools or difficulty in your bowel movements. Today, medical treatments have further enhanced and extended life for children and adults with CF (Cystic Fibrosis). People with the disease can now usually live into their 30s, 40s, and even longer. This disease has about 1,000 new cases of CF diagnosed each year. More than 70% of patients are diagnosed with disease by the young age of 2. A little less than half of the CF patient population have an age of 18 or older. The age predicted to live by CF patients is 30 years old.  Not everyone who has the mutant gene can get CF. You can have 1 perfect copy of that gene, but it takes 2 perfect copies to get it.
      The function of the protein that is defective in CF is usually in the epithelial cells lining the airways of the lung. There are channels in the lining cells where ions can pass. Usually the movement of ions brings water to the surface of the airway and keeps the mucus from getting dry, and staying moist. The gene that is defective blocks the channels, and causes the mucus to dry out. Then it makes it difficult  for somebody to sift the mucus, which becomes prone to infection by bacteria. In the lining of a person with CF, the vital chloride channel is blocked. so there is no movement of chloride ions in the mucus. Having no ionic gradient, theres is no water that moves towards the surface, and the mucus ends up drying out. Sometimes the protein may be present in the cell membrane, but may not function the way it is supposed to.
    There are a few ways that you can treat having the disease of CF and 3 of those ways are; Antibiotics, mucus-thinning drugs, and bronchodilators. The drugs with antibiotics are used to treat and prevent lung infections. They may come in pill form, inhaled in a mist, or delivered intravenously. The mucus-thining drugs are drugs that reduce the sticky mucus that you get, and makes it easier to cough it up, which improves the function of your lungs. Bronchodilators are medications such as albuterol that can be used as inhalers, or nebulizers. They help you keep your airways open by relaxing the muscles around your bronchial tubes. People who have CF have to go through a lot, and you may experience many emotions, but especially anger and fear. They are most common in teens, but openly talking about it can help a lot. IIt would also help to talk to other people with the same problem as you. If you have a child with CF, you can join support groups, or meet with other parents on your own time that also have children with CF. Psychologists are also another a good thing to consider. They can help the children as the grow into their teen years. CF can be a very serious thing that you have to live with throughout your life time.

Cell Membrane Structure

A Cell is composed of two distinctive environments: Hydrophilic aqueous cytoplasm and hydrophobic lipid membranes. Lipid environment is defined by the family of molecules that are characterized by their hydrophobic nature and their common metabolic origin. Lipid molecules are slightly soluble to insoluble in water. Lipids are hydrophobic because the molecules consist of long, 16-18 carbon, hydrocarbon backbones with only a small amount of oxygen containing groups. Serve many functions in organisms. Major components of waxes, pigments, steroid hormones, and cell membranes. Fats are synthesizes from two different classes of molecules: fatty acids attached to the alcohol glycerol. Fatty acids are usually 16-22 carbons long. There are 2 different types of fatty acids, saturated and unsaturated. Saturated fatty acids have no carbon- carbon double bonds, while unsaturated fatty acids have one to three double bonds along the backbone carbon chain. Double bonds introduce kinks in the carbon chain that have important consequences on the fluid nature of lipid membranes. Unsaturated fatty acids have lower melting points than saturated fatty acids. To construct a fat, 3 fatty acid molecules are attatched to the glycerol through an ester bond between the carboxyl group of the fatty acids and the three alchohol groups of a glycerol molecule.  A fat molecule can be composeed of1-3 different types of fatty acids each of which can be saturated or unsaturated. Saturated Fatty acids are usually 16-22 carbons long. Fat stores energy and insulates molecules. Saturated fats don't have any.
     Phospholipids contain two fatty acids attached to the glycerol head. A third alcohol of the glycerol forms an ester bond. Being a triprotic acid, the phosphate head has the potential to form ester links with a variety of other types of molecules like amino acids or carbohydrates.

    This a poster of a Fluid Mosaic Model that i drew with another person in my class, it shows how membranes are structured in a very simple/ cartoonish way.

    Protien channels also play a huge role in your body. Protien channels are trans-membrane proteins found in the phospholipid bilayer membranes in our bodies. These channel proteins allow specific molecules to pass through, crossing the membrane. When you want to move your finger, the protein channels send a message to your brain and nerves to move that finger. The same with any other thing that you move in your body.

                                                                   Diffusion and Osmosis Lab
       We did a diffusion and osmosis lab in our class. In this lab we had a solution of glucose and starch and placed it inside a bag of dialysis tubing. In a cup  outside of the tube, we had water and iodine mixed together. Then we put the tube of glucose and starch mixture inside of the cup with iodine and water, but first tied off the ends tight to make sure they wouldn't mix. After about 30 minutes passed we checked the glucose level of the water in the cup and it came out negative. Over the weekend we let the membrane tube sit in the cup, and the results were that the fluid inside the membrane tube leaked into the cup with iodine and water. The iodine from outside the dialysis tubing also leaked in, because it urned it a different color from mixing with the starch. When we tested both the liquid in the cup and membrane tube, the both had a high glucose level, that was definitely way positive.

     We decided to do another version of the lab and weigh the substances so we could see what left and went into the dialysis tubing. We did four different cups with the substances and water mixed in the dialysis tubing. The four different substances were Corn syrup, Sodium acetate, Antacid tablets, and Sodium bicarbonate. We weighed them three different times to see the results that would come out. The first time we weighed them, we weighed before we put them in the cup of water and cup one with antacid tablets weighed 13.43g. Cup two with the sodium acetate weighed 13.74g. The third cup with corn syrup weighed 11.93g, and the 4th cup with sodium bicarbonate weighed 11.66 g. An hour later we weighed them again, and the 1st cup weighed14.74g, the 2nd cup weighed 23.09g, the 3rd cup weighed 15.88g, and the 4th cup weighed 12.09g. We also did the same thing the day later. Cup one was 14.23g, the second cup was 16.23g,  the third cup was 8.47g, and the fourth was 11.46g. As you can see when we weighed them the hour later, they were at their highest, because thats the time when the water goes through all the little pores in the dialysis tubing, and water moves very quickly because it doesn't have very big molecules, so that is what made that possible. Over night and part of the next day is when the other substances started coming out slowly, because they have bigger molecules than the water and are more dense, so it takes longer for them to go through the tubing. The sodium acetate collected the most water out of all of them, because the molecules of the acetate went through the pores in the membrane easier than all of the substances. Now that we did the lab again in a different way, we really the saw the diffusion and Osmosis come out in the experiments.

Here is a Graph of the data we found out in our lab: