Research

I thought that hearing about professor Macosko's research was very intriguing and exciting. The different kinds of research and the vast advances in technology and knowledge that are going on around us are very exciting. I think that especially the advances that could come from cloning could be huge in the medical field for patients that would normally need a donor or artificial organ could instead have one produced in a lab through cloning techniques.

On Prof. Macosko's Research

To be honest, I thought the idea was great. The purpose is rightful, ethical and helpful in furthering the understanding of the interactions between the countless micro tubules and kinesin in each of our cells. The video he sent to us showing the fluorescent micro tubules gliding over the kinesin gave us a visual demonstration of how kinesin would "walk" along the micro tubules in actual cells. I also thought that his presentation was well-balanced, giving enough background information on the basics of DNA cloning to understand how this theoretical concept can be applied to his research. Finally, it was mind blowing to find out that one person can order "DNA" over the phone!
Overall, the presentation jump started my curiosity about research. I look forward in participating in some research field in the near future.

-Rob Gereige

Opinion on Biobotz Venture

I think that the group members are pursuing a noble cause that is very rewarding and will be even more in the long-run. The diversity of the group , each individual having their own talent and specialty contributes to the originality and creativity of the venture. However I do feel that there is an enormous profit pool that has not been tapped so far, certainly due to the fact that the venture is non-lucrative but it would not hurt to try. By doing this, I am sure that all the group members' entrepreneurship experience will triple. I look forward to contributing to the venture in this manner.

-Rob Gereige

Test to see if this is working

Dear Betsie,

I'm posting something to our blog to see if you get this in your WFU email inbox. Could you email me at my WFU address if this goes through?

Thanks!
Prof. Macosko

FYS Thoughts and Musings

“Damnit, another bad registration time,” I thought to myself after picking up my PIN number from resident Latin professor and advisor, Mary Pendergraft. I hadn’t taken the first look at the classes being offered this semester, but I knew I had to face the inevitable. It was time to pick a First Year Seminar. As soon as I reopened my Virtual Campus WIN page, I noticed the various FYS courses beginning to fill. My relaxation immediately turned to panic, and my carefree outlook on class selection suddenly became cutthroat determination. After seeing the “all we do is watch movies” FYS fill up rather quickly, I decided to settle on a course entitled “Harnessing Life’s Molecular Machines: From AIDS Tests to Hydrogen Cars.” What ensued was a semester of biology, business, presentations, and more tiny quizzes then I had in my high school Latin class.

At the beginning of the semester, I was very skeptical. I had heard the disclaimers from fellow students, but despite these warnings, I decided to continue on. The first day of class we were issued genetic code soccer ball. As I pondered why I was holding this ball I thought, “Nice and colorful. Should keep things interesting.” After learning how the ball was to be used, that simple colorful object suddenly became a complicated enigma that I still cannot quite figure out. It was also something that could be easily lost, as I also found out within the first 3 weeks of class. Losing that small soccer ball cost me roughly 1 point for every quiz we took, but this loss of points did not hold a candle to the amount of points possible we could earn in the class.

The complex breakdown of points in this class proved to be both a benefit and a burden. Reflecting back today, I still do not full understand why this particularly complicated grading system was used. I never knew how many points I had received, what constituted an “intelligent comment,” why we were forced to blog, and why we had to email the professor what we contributed in a class discussion. I felt that some things, such as intelligent comments and discussion points should be recorded by the professor, and recorded on the spot in class. To make it even easier, it could have all been lumped into the ambiguous “participation” category characteristic of college level courses. The “blogging” requirement came across as an attempt to add material to otherwise unread academic blog (let’s face it, people only want to read about sex, lies, gossip, and Brittany Spears’ crotch these days). That being said, the various components of this grading system did give students an opportunity to generate points for completing the smallest of tasks such as emailing the professor an intelligent comment. Unusual grading system aside, the class did provide with new insight into the rapidly expanding nanotechnology industry.

Being more prone towards business, I was not expecting to enjoy learning about molecular biology. We hit the ground running during the first week of class, reading a couple chapters in a dense biology book and discussing complicated molecular components in class discussions. At that point I started feeling the strain on my business oriented mind. All this talk of DNA replication, amino acids, self assembly, and Feynman made me consider assuming the fetal position with my blanket and teddy, but I kept telling myself to stick with it and persevere. Then the time came to divide up into teams. These teams would each be assigned an advisor, which turned out to be a student from the BioBotz Company, and we would have these teams until the end of the semester. The team I was assigned became known as the Power Rangers. We rocked. Our newly formed team exhibited a strong, short lived cohesion typical of newly formed groups. We were eager to learn, young, and new to the ways of bionanotechnology. After being assigned our first paper, we realized that this class was going to be far from a typical pushover FYS. The paper needed to be five pages in length (no easy task in and of itself), and it had to cover material common for biology majors. Material common for biology majors is very difficult for non biology, business majors though. Needless to say, we cranked that paper out and turned it in with an air of great accomplishment. Unfortunately, that feeling of accomplishment did not last too long. After checking the syllabus, I found out that another paper was due the next week. I believe we were supposed to meet with our student advisor more often, but I only recall meeting once or twice. There wasn’t much need for a student advisor, but regardless our advisor gave us some good insight into how the class was structured, how the grading worked, and gave a little background into the BioBotz Company. As the papers continued getting more and more difficult, our team cohesion started to change into individualism. Like a wayward group of travelers stranded on an island, it soon became everyman for himself. Because the way the class was set up, extreme team unity was not really necessary, but it could have helped with the presentations.

After hearing the BioBotz Company give their presentation during class one day, I had some mixed thoughts about the class. The nanotechnology industry is very complex, requires expensive resources, and is often difficult to enter. At first, I thought the class was promoting starting companies that really made an impact on the industry, but then I realized that some of the focus was on short term, limited vision companies such as BioBotz. While the concept of biologically inspired plush toys is appealing to small children and teachers, is there really any more potential beyond that? My skepticism towards the concept may have tainted my opinion of the company, but I still remain convinced of two things. First, there is not a high demand for such an item. Second, from the information presented by the BioBotz team, the company is limited in growth potential by the very nature of their product. Obviously, these observations may not be accurate, but the glorification of their success as being the ultimate goal of this FYS left me drowning in a pool of disillusionment. While it was a unique idea, it has about as much potential as those internet t-shirt companies that teens in a computer generation have an affinity for. Unfortunately, due to the complex and expensive nature of nanotechnology, companies like BioBotz are really the only feasible solutions for college-aged students. That being said, Professor Kuhn’s startup company involving catfish disease prevention is a company that has large profit potential and substantial demand from a decent sized industry. This type of company is the type I feel should be apotheosized in the classroom.

While the creation of a company similar to BioBotz may not have been the best goal to set for the end of the semester, the class structure in general was well put together, hands on, and effective. I can honestly state that I have never had exposure to a class taught in the same manner as this FYS. It effectively utilized the use of hands on interaction through things such as the amino acid soccer balls, enhanced strep throat detection, and community center field trip. Used in conjunction with these hands on elements, lectures, outside readings, papers, quizzes, and PowerPoint presentations were used to assist in learning new, often complicated material. Team dynamics were fostered through compulsory meetings and team presentations. The students also helped other students learn the material through their presentations on specific subjects. Through this unconventional style of teaching, I felt that difficult concepts and problems in nanotechnology were confronted, analyzed, and solved in an environment conducive to genuine learning.

Professor Macosko, I thoroughly enjoyed taking your class. Regardless of the high level of difficulty, I enjoyed every minute of it from the balloon animals to the small quizzes. It was a great experience, and I’m sure your students to come will walk away with the same appreciation and respect for life’s molecular machines that I did.

Paper 4

My Experience “Harnessing Life’s Molecular Machines”


First year seminars are required for all freshman, so I had been looking over the list of available classes since it first came out in the summer. However, I had not anticipated just how fast most of these classes would fill up. Having learned from my first semester that registration times are a major factor in deciding what classes I would take, I hoped I would get a good time. I didn’t. So when it came time to register, I didn’t have many options available. I’m very interested in science, especially biology, so the one title that stood out to me was “Harnessing Life’s Molecular Machines: From Aids Tests to Hydrogen Cars.” At that point I didn’t really know what these “molecular machines” were, but it sounded like something I would be interested in, so I took a chance and signed up.
The first day of class really sparked my interest in the subject. We watched amazing 3-D animated videos of various molecular machines which portrayed the cellular structure in a way I had never seen it before. All of these different machines worked together perfectly to do various tasks. I was surprised just how much these cellular parts really did look like the “machines” I was used to seeing. We also discussed how these machines were already being applied to solve real-world problems. We passed around various products, such as HIV tests, that used molecular machines. I was definitely interested in the class at this point.
The first few days also warned me about how challenging the course would be. We were given lists of amino acids, a huge list of complicated vocabulary terms, and of course a brightly colored genetic code soccer ball. All of this seemed overwhelming at first, but I knew that we were not the first class to take this course, so it would not be impossible. I had taken biology classes before and currently, so this class seemed to fit right in with other things I was studying. Even though I was familiar with the genetic code, it took a while for me to figure out the soccer ball, but once I did, I understood just how useful it is. I knew this class would be a challenge, but I also knew I would learn a lot.
The text book reading was a good way to gain background information on the subject of molecular machines, and to see how they could potentially be used to in consumer products. This reading described the virtues and vices of molecular machines, explaining how useful they can be and what limitations they have. Although molecular machines perform the same overall functions of traditional machines, they work in very different ways. Instead of building things out of metal and plastic, these machines are formed from proteins and other molecules, which is a strange concept to grasp at first.
When it came time to write our first paper, I was not at all sure what I was going to write about. Our team was the last to select a topic, and the genetic code was not my first choice. I was not sure just how I was going to find some interesting machine when I was confined to the genetic code. I expressed this concern in the first meeting with our consultant, and she assured me that there was plenty to write about. When I looked further into the process of how the genetic code worked, I was amazed just how many machines were involved in processes such as replication, transcription, and translation. I decided that I would write about the process of DNA replication and the machines involved.
I cracked open my biology text book and began reviewing the process of DNA replication. I made note of all the different machines involved and how they worked together to copy DNA. I then looked up more detail on each of theses machines to find out more about their structure and function in the DNA replication process. The main machines I looked at were helicase, polymerase, and ligase. Then I learned something very interesting about all of these machines: they all work together as one big machine rather than completely individual machines as I had learned previously. With so much going on in the DNA replication process, I had no problem writing the first paper.
Shortly after the first paper was finished, I had to confront the task of the fist presentation. I was not sure what kind of presentation I needed or how I was going to make a presentation on the genetic code that wouldn’t put everyone to sleep. Luckily, our group was not the first to present. After seeing the first group present and hearing people’s feedback, I had a better idea of what the presentation was supposed to be and what kind of information and visual aids I should include. Still, I was pretty nervous for my first presentation, hoping I wouldn’t forget what I was supposed to say or talk too fast. However, I prepared myself as best I could and managed to give the presentation without too much difficulty. I was relieved knowing that the first big assignment was behind me.
At this point in the semester, I was pretty well settled into the course. Readings, discussions, and daily quizzes became routine. About this time, we went on our class field trip to the community care center. I did not know what to expect of this organization coming in, but I was amazed at what it was able to do for the community. It is by far the largest and probably the most advanced free clinic in the country. Just looking around, it was hard to believe that all of the different services that the clinic provided could be given free of charge. Doctors volunteered their time and companies donated funds to help this organization provide patients with much needed care. There are no stipulations of citizenship to receive help; the patients only have to live in North Carolina. This center is a great example of the entrepreneurship that this course encourages. Although this community care center is very successful, it relies entirely on donations and good will to operate and could not be implemented on the national scale.
When it came time to write the second paper, my task was to research how molecular machines could be implemented to solve real-world problems. I decided that it would save me some work if I stuck with the machines of the genetic code, so I began to look at applications of these machines. Since I am interested in the medical field, I decided to go with machines that could possibly cure diseases. The machine that looked most interesting to me was the spliceosome, a machine involved in cutting and splicing parts of the RNA strand. It turns out that theses machines have the potential to be used in a new form of gene therapy. The more I read about this SMaRT gene therapy, the more I realized just how far we have come in being able to manipulate genes. This information was exciting and I enjoyed researching it. The second presentation was much easier than the first since I knew what to expect and how to prepare the presentation. I was not nervous this time and the presentation went well.
One novel aspect of this class is the blogging. When I first hear about this requirement, I was not sure whether or not I would like it. However, the first few classes proposed such interesting and controversial discussions that I could not help but express my opinion. I found it easier to make a well-thought-out response when I could sit down and think about the question, rather than talking on the spot in class. In some situations, I prefer to talk in class, but the blog was definitely a nice alternative.
The third paper offered a very different opportunity than I had gotten used to. Rather than researching and discussing a new molecular machine, I chose to write a children’s story about machines I had already studied. I decided that I would write about the DNA replication “factory.” I set up the story as a class field trip tour of the factory in which a knowledgeable tour guide explains the process of DNA replication in a way children can understand, using analogies and cool-looking machines. There is a conflict in the story in which the main character makes a mistake and must own up to it, creating a moral to the story as well as molecular machine education. The story ended up having a sort of “Charlie and the Chocolate Factory” feel, hopefully making it alluring and interesting to children. This paper was by far the most fun writing assignment I’ve had so far at Wake.
Overall, I’m glad I decided to take the class. Although I really didn’t know what I was getting into when I signed up for it, I am pleased with what we have done so far. While the work was challenging, it was not impossible. The class was an interesting mix of biology and entrepreneurship, something I had not experienced before. Even though I do not plan on starting my own company, it was fun learning about how groups such as the Bio Botz can get funding and connections to create such a novel business from scratch. I feel that the class was definitely worth taking.

Final Paper

An Intriguing Class

As I signed up for classes during the worst time given out for freshman, I carefully scanned the choices of freshman seminars which had been depleted greatly from the first day of registration. I narrowed my preferences between a seminar about neurological disorders or one called Harnessing Life’s Molecular Machines. Thinking that neurological disorders would be impossibly hard I chose Harnessing Life’s Molecular Machines. The title mentions hydrogen cars, and my potential major is environmental science or engineering, so I thought this first year seminar would pertain to my interests. Over Christmas break, I received an email stating that there would be specific groups that studied different molecular machines within the subject given to their group. One group in particular, global warming, ignited my excitement for the course.

The first day of class, we were shown a complex animated view of the inside of a cell. Our professor proceeded to explain multiple molecular machines and their functions as they were rapidly shown throughout the video. The fluidity and ability for so many molecular machines to work together efficiently and effectively was amazing. I was eager to learn more about the way we could use such “nanoscale” machines to our advantage and how they occur in nature. I was more anticipating expanding my knowledge on what I thought I wanted to pursue as a career, molecular machines that could be used to combat global warming.

The next class, we were assigned groups. The last two groups to be assigned a topic were my group and another with global warming up for grabs. Finally, my group generously gave up the controversial topic to the other group. So, our group was given the genetic code to research which our professor thought up at that moment. Of course the one biological topic that I have always had trouble understanding was given to us. In that same class, we were given an extensive vocabulary list of biological terms that could possibly be referred to in the course. While looking over the terms, neurological disorders started to look really good. Yet, the molecular machines had potential to become very interesting. Also, I was unaware of the entrepreneurial side of the course. I have never studied entrepreneurship so this aspect of the class kept me in it and ready for the challenge. During the previous class, our professor and a group of students created their own company. The prospect of possibly starting a business greatly effected my decision to stick with the course.

Student presentations made up a large portion of the class. Students were encouraged to read outside material which was an online book about Bionanotechnology. Our professor gave a few lectures on his research and a few other topics, but the rest of our class time was student presentations. One lecture was on how to effectively write a paper on molecular machines. Even after a lecture about what was required of us during the course, it was still vague what our professor wanted us to do. We were each given the opportunity to choose a particular molecular machine to research that was related to our group. I chose DNA polymerase not knowing much about its function except for its use in Polymerase Chain Reactions. Our professor suggested we use in our presentation different media such as movies and pictures to keep the presentations interesting. For my first presentation, I found a video on youtube.com of a music video for Polymerase Chain Reactions. After each presentation, the class commented on the student’s work so that we could improve each time.

We were also given “consultants” for our group’s benefit. These were students who had previously taken the course some of which were members of the BioBotz Inc., the company started from the first Molecular Machines first year seminar. We were to meet with our consultants one day a week. Our consultant helped us organize our presentations and determine the best topics to research. This way our group had a cohesive three presentations.

The first presentation was very difficult. I was unsure of the material I was reading about. I did not know how to effectively explain the protein structure consisting of beta sheets and alpha helices. My presentation went alright, but it was my second presentation that I actually felt comfortable with the complicated material of which I was learning. I never knew how interesting molecular machines were. Even the small DNA polymerase has an essential function of which a cell is dependent.

Our class also consisted of a few guest lectures and a field trip. It was very interesting to see real life examples in person of how molecular machines benefit mankind. Our field trip was to the Community Health Center. It is most likely the largest free health clinic in the Northeast or possibly the United States. Unfortunately some classmates took a wrong turn which caused us to lose part of our short class time so we were a little rushed. One of the head people at the clinic gave us a quick tour explaining how they are able to meet low income family’s health needs for free or little cost. We also had an enticing discussion about universal health care. The man who gave us the tour disagreed with the idea of universal health care. Dr. Ray Kuhn gave a lecture or more a guided discussion on entrepreneurship and the business he started with a few of his dedicated students. There were a few other guest lecturers scheduled in our syllabus but were either unable to come or we did not have the time for them.

Our class also had many controversial and invigorating discussions. We discussed topics from are we just machines to global warming and biases in science. We also discussed entrepreneurship and how any creative idea can spark a successful company. All one needs is the passion to create such a venture.

For every presentation we had to write a paper that corresponded with the topic being studied. The last paper we had the choice to write a children’s story about our molecular machine. I wrote an adaptation of Rumplestilskin to illustrate the function of DNA polymerase to children and explain the importance of a co-factor. Many others wrote very creative children’s stories that could possibly be used for the BioBotz inc. developed by our professor and run by a group of Wake Forest students. The company’s mission is to excite learning of molecular biology and bionanotechnology at an early age through children’s stories that explore the inside of a cell, comic books, video games, and even possibly an animated movie. It was fun to contribute something to the company that was started by this first year seminar.

Before this class, I was unaware of how a topic that had never interested me, genetic code, could become a fascinating subject. Although hard to comprehend, molecular machines play an extremely important part in everyone’s life in regards to biology or even the environment.

This freshman seminar challenged me to explore new topics in science that I never thought to research. The class was a great mélange of discussion, student presentations, guest lectures, and field trips. Groups worked together to effectively explain the intricate molecular machines present in their subtopic and the applications of the molecular machines that were researched. I was impressed with myself and other classmates of our ability to describe such complicated and difficult material. Although it was a great course, I wish there had been more lectures by the professor or guest speakers. It was great practice to present so many times. However, students’ presentations can only be so interesting for a short period of time.

Class Review

I expected the class to be a lot more biology-based, but it was actually mainly entrepreneurship. I'm not much of a business person, but seeing how biology and the study of molecular machines can lead to starting a business was incredibly interesting. I learned valuable research skills and summarizing/simplifying skills. I'm hoping to be able to carry the skills that I learned in this class throughout college and whatever career I choose.

This year

When registering for classes last semester, I wanted to put variety into my schedule, since I had taken relatively normal classes the first time. When selecting my FYS, I wanted to take something out of the box. I spotted harnessing life’s molecular machines on the page and it caught my interest. Later I would find out it would be one of my better class decisions, because I really enjoy attending class and participating in the discussions. The class structure is very relaxed and I feel comfortable expressing my opinions. Not only that, opinions are encouraged to be expressed, even when it comes to such topics as evolution and religion. These topics would have never been touched in high school, and I really liked talking about them and hearing other people talk about what they believed. Other than class discussions, I also liked the presentations given by students. It made the class much more interesting and gave it variety. In normal classes, I sit through listening to often boring and repetitive lectures. This class was definitely a good choice to take and I enjoyed it a lot.

Class Review

When I signed up for this class, I really didn't know what it was going to be about. I like biology, so "molecular machines" stood out to me on the FYS list, although it wasn't until the first class that I learned what a molecular machine actually is. At first, all the new terms, papers, and presentatios seemed overwhelming, but they got easier the more we did. I liked being able to continue discussions on the blog, since sometimes I didn't think of what I wanted to say until class was over. This class was also an interesting mix of biology and entrepreneurship. I had not thought about this particular area before, and it was cool to see how people like the Bio Botz are getting their unique company off the ground. I also enjoyed the field trip to the community care center, since it is a great entrepreneurial success, providing services some would consider impossible for a free clinic. I thought it was interesting finding out more about how these "molecular machines" work and I would recommend the class to future students.

This Class Review

When I first signed up for this class, I was expecting a much more linear outline for the course. Like most courses, read a book, attend lectures, take test. Fortunatly, this class certainly branched out from the typical lecture schedule. I really enjoyed the freedom of being able to pick and choose topics to research and have a major focus throughout your research. This sort of freedom was very beneficial to a certain extent. The field of molecular biology and the study of molecular machines is much to broad to base a single 2 hour a week class upon. There was just so much information that wasnt even tapped into in this course, which made learning knew concepts difficult. My suggestion would be to have more specific projects that students could research. For example, from reading the description of the class, I would have enjoyed looking into the details behind hydrogen cars and AIDs tests at the molecular level. I think with this knowledge it would be possible to extrapolate to new ideas and projects that could later be the basis of a company; which would have been the euntraprenuership study of this course. Although i do not expect to find the cure to cancer in my First Year Seminar I would hope to at least walk away with future ideas for studying molecular machines. I only wish there were more guidelines to speficy what exactly we are supposed to be doing in these papers. Case in point; I am a little confused as to what exactly I should be writing this last paper on. Nothing a little coffee and some time in the 24 hour room cant fix. Maybe i will turn this post into a paper...who knows.

Today we had a presentation on a children's story about Anthrax. Delicious explained how one can contract Anthrax and the proteins involved in the disease. I thought it was clever how he began the story outside the cell using a boy as the first character. Then his story moved to the inside of the body where the molecular machines became the main characters and the way Anthrax works is explained to children.

Class review

This class was different from anything that I have experienced before. I had the first impression that it was going to a very abstract class. However I learned that it had a very relevant topic, which more people should be aware about. Molecular machines are a major part of everybody's lives even though people may not know this.
I enjoyed the format of the class. It gave a lot of freedom to me and what I wanted to learn. Global warming was a topic which I was very interested in prior to the class, and I found out so much more about the topic because learned about it on the molecular level. The papers and the presentations allowed me to help other people learn about this topic too, and this is what made the class a success.
I think that the blogging could be improved though. I think that a specific topic should be given, instead of a random string of posts. Plus I think that there should have been a little more explanation on what was wanted in the first presentations. I know that the first groups that went did not really know and I think that they were put at a disadvantage. I had the opportunity to go later and I think that my presentation benefited from seeing others prior.

Paper 3

Genetic Engineering with Dorais and Friends

Ever since Jotham and Thayer were born they have been best friends. They were born on the same day, and they live across the street from each other in the city of Livingston. The town of Livingston is a small town where everybody knows everybody, so when Jotham and Thayer would walk home from school they would wave and say hello to the all of the firemen who worked at the fire station. A few of their favorite activities are to play soccer and to throw rocks off of the bridge.

One day in the middle of May, Jotham and Thayer were walking home from a long day of school. They were both looking forward to throwing rocks off the bridge, because they had two tests in school that day. To do something special to celebrate the fact that they were finished with the tests, they both decided to search for the biggest rock they could. They were looking for rocks all the way to the bridge, picking up rocks which they thought were big. They had not found a rock which was very big compared to the other rocks, until they reached the bridge. There on the side of the road was a huge rock which would make a large splash. Thayer tried to pick up the rock by himself, but he couldn’t. Jotham thought that he could pick up the rock, but after he tried, he found out that he could not lift the rock either.

Jotham then had a great idea. He said, “Why don’t we lift the rock together, and then we can throw it off the bridge into the river below together?”

Thayer replied, “That is a great idea! Ok, get into position to lift the rock. On the count of 3, lift the rock. 1…2...3 lift!!”

Together they lifted the rock and carried it over the edge of the bridge. In order to throw the rock off the bridge, they would have to throw it together. They backed up so they could get a running start to the throw the large rock. Jotham and Thayer then started to run with the rock. They were nearing the edge, when Thayer tripped on his untied shoe, and he began to stumble forward. Since they were carrying the rock together, Jotham started to stumble, too, but neither could stop because the rock was too big. The rock fell over the edge of the bridge, and along with the rock, Jotham and Thayer both fell.

For a few seconds, there was no sign of Jotham and Thayer, but then there were bubbles and Thayer’s head appeared above the surface. He gasped for air, and immediately he looked for Jotham. While looking for Jotham, Thayer pulled himself onto a tree which had fallen into the river. Then all of a sudden, Jotham appeared; he had pulled himself onto a tree also. Both of the boys knew how to swim, but the river was flowing too quickly and too violently to swim ashore.

The tree which Thayer was sitting upon was a large tree, but the tree had thorns on it. Luckily, Thayer had avoided them. The tree which Jotham was on was much smaller than Thayer’s, and it was barely staying afloat. It was falling apart in the strong current.

The two boys tried to yell for help, but the sound of the rushing water covered up their voices, so nobody could hear them. Night was quickly approaching, and the boys were starting to get scared that they would not live through the night. They were afraid that Thayer might hurt himself on the thorns and Jotham’s tree might fall apart by morning. By this time, Jotham and Thayer had managed to pull their trees together, so they were floating down the middle of the river together.

The current in the river was beginning to slow down as the river increased in size. Night set in, and the boys did not want to swim ashore in the dark. The area surrounding the river was a deep forest with lots of wild animals in it, so Jotham and Thayer could not decide what to do. At that moment, Jotham sank his face into his hands and began to cry. Thayer attempted to console his best friend, but he missed his family, and he began to cry also. The tear drops rolled down Thayer and Jotham’s checks, and it just so happened that the tears from each of the boys hit the water at the exact same time, but they did not notice this fact.

All of sudden, Jotham saw something in the water swimming next to the trees, and he pointed it out to Thayer. Thayer was startled, but he recognized the animal as a dolphin, but he was still confused. There were no dolphins that lived in the river which ran through Livingston. The dolphin then came up to breathe, and it turned and faced the boys. Jotham thought that he was seeing and hearing things when the dolphin started to talk to the boys.

“Hello, Jotham and Thayer. My name is Dorais. Don’t be afraid of me, I am going to try and help you.”

“How did you know our names, Dorais?” Thayer replied.

Dorais said, “Well, Thayer, I am no ordinary dolphin. I am the protector of this river. It is my job to make sure that all of the animals which live in and around the river live in harmony. Every day I see you and Jotham walking home from school. I know that it is your favorite activity to throw rocks into the river. However, I have to dodge the rocks every day, and the rocks are starting to scare the fish in the river. I am going to offer you a deal, if you stop throwing rocks into the river, I will make sure that both of you are safe for the night. Is it a deal?”

Thayer and Jotham looked at each other, and they knew that it was their only way of surviving. They both nodded yes.

“Ok, now let’s make sure that the tree that you are on can make it through the night. I am going to need some help from my friends to do this job, so let me get them together,” Dorais replied. She then took her flippers and clapped them together. Thayer and Jotham looked around and they saw that a robin had landed on the tree and next to it was a crab. “These are my friends” she pointed to the robin and said, “This is Elizabeth, and the crab is Renya.”

Then Elizabeth and Renya both nodded toward the boys. Dorais then chirped in, “So now, they are going to make you a new raft. Don’t get scared, but Elizabeth is going to fly around the trees to find out where they are going to cut the trees.”

“What? You are going to make both of our rafts smaller? That does not make sense,” Thayer responded.

Dorais said, “Don’t worry, Thayer; Elizabeth is going to find where to cut the trees so that we can take the best parts of each tree, and then we are going to cut those parts out. Then Renya is going to take the good parts of the trees, and she is going to use her claws to make one raft which both you and Jotham can float on safely. Elizabeth’s job is very specific. She must find the exact location where to cut. She must find a place in the wood that has the same shape every time. Then she will very carefully cut the wood. She is very good at her job, and is right almost 100% of the time. She is going to look for and then cut the same shape of wood for both of the trees. This way Renya can use her powerful claws to combine the wood and make a tree which is better that your trees. While they are working you both can ride on my back.”

Both of the boys climbed onto Dorais’ back, and then Elizabeth began to fly around the trees. Then as soon as she found the right shape she began to peck at the wood, and then the wood was then separated from the rest of the tree. She did this for both of the trees, but the shapes of the trees were very special.

Dorais explained, “She must find the right shape because that shape is what tells the rest of the tree to look like. For example, she is looking for the part of the tree which Thayer was on which would make the thorns go away, and the shape which would make the tree not fall apart from Jotham’s tree. But remember, Elizabeth must cut the shapes in the right place to make sure that Renya can join the two pieces together.”

Elizabeth successfully cut the wood in the right place, and then Renya used her powerful claws to join the wood from Thayer’s tree to the wood from Jotham’s tree. The new piece of wood which Renya made was perfect. It had all of the good characteristics from Thayer’s and Jotham’s tree, which meant that there were no thorns, and the wood was not falling apart. The boys then jumped back onto the wood.

“There you go, we are all finished. Now both of you should get some sleep, it is way past your bedtime. I will swim with you all night making sure that nothing happens to you. But remember our deal.” Dorais told the boys.

“Anything. Thank you so much. We could not have lived without you and your friends. We promise never to throw rocks into the river ever again.” Jotham replied.

Soon both of the boys were fast asleep on their new piece of wood. Neither of the boys woke up until they were on the bank of the river. When they woke up, they realized that they were surrounded by people, and then they both found their parents. They hugged their parents and they asked how they found them. Jotham’s parents responded that the firemen who they normally wave to on their walk home became worried when they did not show up, so they began to search for them.

They tried to explain what happened with Dorais, but their parents never believed them, so they just kept it a secret, which they would never tell. However, from that day forward, Jotham and Thayer never threw a rock into the river, just like Dorais had asked.

Delicious' Story
I really like the outline of the story. It was definetly an interesting way one may obtain the anthrax disease. I am a little confused about the characters in the stories and the relationship to the different molecular machines he is talking about. I am sure some of this is played out in detail in the story but maybe a little more explanation during the presentation would be helpful. Also, I do remember his presentation a few weeks ago about anthrax but some more background on anthrax and the different molecular machines would be useful. I like the different illistrations in the powerpoint. I am wondering if these were included in the story. If so than children who will read this story will enjoy it more and use the pictures as guidelines throughout the story. Good Job


Tommy

Mi papelito

Scott Dalgliesh

Prof. Macosko

FYS

Children’s Story

There was once a small bacterium called Denny Radio. He was a great bacterium, and had lots of friends and family. Normally, he spent his time hanging out with his bacteria friends, Shelly and Paul. They had great times together hanging out whenever and wherever they wanted to. The special thing about these bacteria was that they were very strong and could do lots of thing that we couldn’t do. This let them hang out in some pretty disgusting places, like contaminated water and areas with hazardous material. They didn’t enjoy going to these areas though and their favorite spot by far to hang out was the lake. What made them strong and healthy was a little man inside of them, and his name was Ricky RecA. He was a funny looking guy, and even smaller than Denny, Shelly, or Paul. Since Ricky had lots of brothers, they all lived and swam around inside of the three keeping them in tip top shape.

One day Denny was hanging out with Shelly and Paul, when he noticed some very nasty looking water in a puddle next to a lake.

He said, “Hey guys, lets go over and check that place out.”

Shelly said, “No Denny, that water looks really dirty I don’t think we should go over there.”

But sure enough Denny went anyways. When he got into the water it stung a bit and didn’t smell very good. Denny thought to himself, “Wow, there must be some pretty bad stuff in this water.”

As he was thinking this Ricky and all his brothers were working very hard inside of Denny. Ricky has the special job of helping Denny and the others stay healthy. While they were playing around in the contaminated water, he and his brothers were fixing broken parts of them inside their bacteria bodies. These parts are called DNA, which are very important to the healthiness of not only Denny, Shelly, and Paul, but us as well. The Ricky’s that live inside our bodies work much slower though, so we can not go into places like they were.

While Ricky was fixing Denny’s DNA, Denny had a sudden thought. He said to himself, “This contaminated pool really isn’t that nice, I hope the water from here doesn’t end up in the lake.”

He went back to where Shelly and Paul were standing and said, “We should do something to stop this water from getting into the lake.”

The three began to brainstorm, but they just could not think of anything they could do by themselves to clean up the water. Denny came back to his house but he could not get the lake off of his mind. Suddenly, he realized he could call his friend, Munchy. Munchy was always very hungry, and he could eat anything. Maybe he could help Denny and his friends.

On his way over to see Munchy, Denny walked by the lake, but he noticed something different about it. The water looked dark with algae and there were a few dead fish floating on top of the water. Also, it appeared the trees and bushes around the water had shriveled up and fallen over. Denny began looking around, and sure enough the contaminated water had seeped into the beautiful lake. He ran to get Shelly and Paul, and they could not believe it either. The lake was one of their favorite places to hang out at, and they knew they must get Munchy to see if he could clean it up.

When Denny got to Munchies house, he told him, “I need you help over at the lake we have a serious problem.”

Munchy joined Denny to come down to the lake, but once he got there, he was hesitant to go in the contaminated lake, because he was scared that the water might hurt him. He said, “Denny, there’s no way I’m going in there, that water is way too dirty.”

Denny was confused by this because he never had a problem going into the dirty water before. But he trusted his friend Munchy and they both went home for the night. The next morning, Denny went down to the lake again, but he could not figure out how he could clean it up by himself. He called Munchy again and told him to come down to the lake. Munchy was once again hesitant, but Denny’s reassurance made him more confident to go down.

When he got there, Denny told him of his new idea to help clean up the lake. Denny’s plan was for Munchy to climb on his back while he swam around in the polluted water. While he was swimming, the very hungry Munchy could eat up all the pollutants stuff in the lake. Once again, Munchy was a little hesitant, telling Denny, “I’m not sure whether I should do this that water looks way too dirty for me.”

Denny said, “You don’t have to worry if you’re on my back, because my quick working Ricky and his brothers will help you stay safe.”

With this in mind, Munchy hopped on his back and climbed into the water with him. Once again, the water stung a little bit for Denny and Munchy, but soon enough they became used to it. As Denny swam around, Munchy began eating all the pollutants in the lake. Stuff like Mercury, Toluene, and Radiated Hydrocarbons all tasted great to Munchy. He said, “Wow Denny, this isn’t that bad at all, and this stuff is delicious!”

Denny exclaimed, “I told you so Munchy, just think we can go around to all the dirty places now and clean them up, just like this lake.”

They were both very excited and after the lake they ran back to their house to tell Paul and Shelly about it. Neither of them could believe it and they next day, they followed Denny and Munchy down to the lake. Paul and Shelly were astonished at the progress they had made. The water looked clean, animals were beginning to come back, and the plants were reestablishing themselves around the shoreline.

The next morning while Denny was still sleeping, Shelly and Paul went to go wake up the very full, but still very hungry Munchy. The three decided to go down to the waste dump, which was next to their other favorite place to hang out, the river. Munchy hopped on Shelly’s back just like he had for Denny and they began to swim around.

Of course Paul wanted to try too, and the three went around all day cleaning the dump next to the river. At the end of the afternoon, the tired trio went back and fell fast asleep after their long day cleaning. They had cleaned up the lake, and tomorrow, they knew they could go and have a blast in the newly cleaned water. Also, they knew if in the future the lake or any other place became contaminated, they could use their new strategy so everyone can enjoy the outdoors.

Here is my second paper that i forgot to upload to the blog. Enjoy


The Tale of the Mitosis-R-Us

In the cells of every human being there is something called DNA which acts as the blueprints for the make-up for the body. Essentially, DNA is the chemical instruction manual for the construction of each part of the body. The brain, eyes, arms, internal organs, and other physical features are all determined by the chemical composition of DNA. However, like some instructions, there are mistakes. These mistakes, called mutations when talking about DNA, give the body false orders when creating the different parts of the body. Sometimes these mutations have no severe negative effects of the body make-up. However, it is common that these mutations, if not fixed, can cause severe damages to the body. Some of these damages could be fatal if not taken care of immediately.
DNA replication takes an enormous role in the process of cell multiplication of body formation. When cells divide, which is essential in the beginning stages of growth, the DNA needs to be copied exactly. If this DNA is not copied exactly, the mutations described above occur which could have severe effects. The main components of the DNA replication are molecular machines. Molecular machines carry out the basic mechanical functions that drive the most important physiological functions. When it comes to DNA copying, the molecular machine that plays an important in this process is DNA polymerase. This enzyme is responsible for binding to one half of the DNA and adding corresponding nucleotides to form a double helix. If the DNA polymerase does its job well and copies the DNA strand perfectly, the ribosome, another molecular machine involved in DNA replication, will be able to produce the correct amino acids to create the proper protein. If the DNA is copied with mutations, an incorrect protein will be created, which would have obvious negative effects. This process of DNA copying is paralleled with workers in a toy factory creating toys based on the instructions given.
There once was a factory called Mitosis-R-Us that was responsible for making various toys for the kids in Cell, which is a small town outside the major city, Body. In this factory, there were hundreds of workers responsible for different jobs in the making of these toys. There was Henry the helicase, who was responsible for splitting the blueprints prior to copying. Next was Danny the DNA polymerase who was responsible for exactly translating each specific part of the blueprint so it can be read by other workers. Basically, Danny took one part of the instructions that Henry would separate and add corresponding instructions. For example, there were specific codes that needed to be read by and translated by Danny. Danny was the only person who was able to translate these codes. Once the codes were completed they were given to Ryan the RNA which was a messenger who passed them onto to Ron the Ribosome. Ron the ribosome could not understand the instructions without Danny’s specific translations. Once Danny carried out his job, Ron was able to assemble the specific parts to make small portions of the toy. Eventually, after other DNA polymerases and other ribosomes finished their jobs, the entire toy was completed.
Mitosis-R-Us was a very efficient factory where each individual did their job quickly and correctly. Toys were flooding the homes of Cell and each and every kid was happy. Danny loved his job and he was very good at what he did. He almost never messed up the instructions and each toy was made to perfection. He realized that his job was pretty easy. All he had to do was use his advantages of being able to decipher the codes that the initial instructions had. His job was very similar to a translator who communicated between a Spanish speaking person and an English speaking person. The English person would have no clue what the Spanish speaking person was saying without the help of the translator. What seemed like a hard job to Ron was a lot easier with his translator friend, Danny.
One morning, as Danny entered the factory ready for yet another successful day copying toy instructions, he noticed something peculiar. Nick the nucleus, who was his original boss, was no longer there. He stopped what he was doing to find out where his noble boss was. As he entered Nick’s office, he laid his eyes on someone he had never seen before. A tall gray man stood in front of Nick’s desk with a dominating presence. A little wary of this unsuspecting individual, he began to worry about what was going on. He nervously asked, “Excuse me sir, do you know where Nick is?”
With a sly chuckle the mysterious man replied, “Ha ha, Nick is gone”.
“What do you mean gone?”
“Nick will no longer be your supervisor in this factory”, replied the man to the worried factory worker. “He has been…removed from his commanding position.” Danny gave a blank stare in utter disbelief. “I am your new Boss! My name is Kyle Cancer. I will be taking that pathetic minion’s position as your commander.”
Danny’s stomach fell to his feet as he listened to this man tell him he will no longer work for his boss. He had no idea what to think. He comes in on a normal day only to see his boss has been replaced by some over powering evil being, with no real explanation. He was certainly nervous for the company if this man was in control of the entire factory. Although reprehensive, Danny had no idea what was soon about to happen.
As Danny returned to his work position, the loud speaker came on. The eerie, deep voice of his new boss flooded the factory with a new message to all workers. “Attention workers!” says the voice, “I am your new boss and there will be some major changes around here. First and most importantly, Nick is no longer your supervisor. I have assumed his position as your boss and you are under my command. Second of all, I have devised some new blueprints for a new type of toy and you are all instructed to comply.” The new set of instructions reached Danny and he quickly noticed a major problem. He realized that these instructions did not code for the production of their normal toys! Instead they were instructions for a different toy, a mutated toy that Danny didn’t recognize. He had a feeling, though, that this toy would only be harmful to the kids of the Cell. He soon realized that the instructions called for a toy that had violent and negative influences on kids and that this toy could not be sent out to the town of Cell.
With no real solution to this problem, Danny quickly became worried for kids all around. There was no way he could make up his own instructions for the proper toy, there were just too many details and it was almost impossible to be made from scratch. There was also no way he would be able to go through the entire instructions to find the tiny details that were changed in order to fix the problem. Just as he thought there was no way to stop the evil Kyle cancer from distributing these violent toys all around town, he thought of someone who might be able to help. Beth the DNA polymerase beta was like Danny in the sense that she was able to translate the instructions but she had a different ability. She was able to correct mistakes made in the instructions.
Danny quickly left his post and went to the closest phone in order to call his friend. He got her on the phone and explained what happened. He told her how Kyle cancer has taken over the factory, changed the instructions to the toys, and started making evil toys that could be very harmful for the kids of Cell. In complete disbelieve, Beth wasted no time in getting over to the factory to help save the company.
She arrives within minutes, before too many toys had been assembled. Without wasting too much time, Beth quickly positioned herself at Danny’s work station and vigorously scanned the instructions as they were handed to her. Thousands and thousands of codes ran by her every minute as she quickly looked for the mutation that Kyle cancer had implemented. After twenty minutes of scanning, she came across a peculiar strand of codes that she recognized as the problem causing part of the instructions. She quickly removed the mutated instructions and implemented the correct form. She then hustled the new and improved instructions over to Ryan the RNA, who then quickly rushed them to Ronny the ribosome and told him to start building by these instructions rather than those that Kyle had previously implanted. Eventually, new and safe toys began being assembled by the hundreds. Before Kyle new it, his planned had failed miserably.
After Kyle’s plan had been destroyed by Beth’s ability to read and fix his mutations, order was finally restored in the factory. Kyle Cancer was quickly run out of town by the angry parents and factory workers, never to be seen again. The next day, Danny came to work to see that Nick the nucleus had finally resumed his position as boss of Mitosis-R-Us. Thanks to the help of Danny and Beth the DNA polymerase beta, the toy instructions were fixed and the people of Cell were able to live happily and peacefully.

Here is my paper on Clathrin

Tommy Kelsey
FYS: Harnessing Life’s Molecular Machines
Paper 3

Clathrin

Molecular machines are the basic mechanical models that drive some of the most important physiological functions. The abilities of the eye to see and the muscle to flex are both physiological responses to the work of millions of molecular machines. Molecular machines are simply molecular compounds that are designed to carry out various forms of mechanical movement. For example, the actin in the muscle fibers are pulled closer together as a result of shape change in the myosin fibers of the muscle. With the understanding of these molecular machines that run the biological processes of organisms, enormous advances can be made in the fight against viruses such as the JC and simian viruses. Each cell has thousands of molecular machines that are responsible for many different tasks, such as DNA replication, particle transport, and intracellular communication. Clathrin is a molecular machine that is important for allowing foreign substances to enter the cell.
Clathrin is a protein that is responsible for creating coated pits and vesicles that are necessary for bringing substances into and out of the cell and bypassing the cellular membrane. This process, called endocytosis, is responsible for transporting molecules, such as large polar proteins, past the hydrophobic cellular membrane. Clathrin assists this process by forming a coated pit on the inner surface of the plasma membrane. This vesicle then buds off and forms a relatively large vesicle on the inner part of the cell membrane. This vesicle brings with is not only the wanted substance but also a small volume of extracellular fluid. These coated pits and vesicles were first observed by Thomas Roth and Keith Porter in 1964.
Clathrin molecules are brought together on the portion of the cell membrane that is to become a vesicle by adaptor molecules. An example of this is the creation of a synaptic vesicle in the neuron using the protein AP180. This protein promotes polymerization of clathrin and also recruits them to one destination. Once the clathrin molecules are brought together on a specific part of the membrane, they begin to form a soccer ball shaped bubble with flat hexagons and pentagons as the borders. To understand how this structure is built by this molecular machine it is important to understand the structure of clathrin.
http://www.rcsb.org/
Figure 1
The clathrin has a triskelion structure with three long and skinny arms. Triskelion simply means that this machine has three main arms branching off its main central body (Figure 1). These arms come into play later on when forming the bubble necessary for transportation. At the end of each of the legs, is a foot that is the main component in binding to the adaptor proteins. These legs are flexible enough to form a soccer ball like sphere with flat hexagons and pentagons as the border. This hollow sphere is then able to encase the desired package and bring it into the cell. The full capsule ends up being much larger than the proteins being carried which is the reason why extra cellular fluid is also brought into the cell. If clathrin molecules are isolated and incubated at the correct temperature, they would spontaneously assemble into the spherical soccer ball shape.
As shown in Figure 1, the legs of clathrin consist of a series of 10 alpha helix repeats joined by hairpin turns, seven of which make up one leg of the protein. These segments are formally known as clathrin heavy-chain repeats. Each repeat consists of two faces of helices that is involved in the interaction of other helix faces of another clathrin protein. This may be the way in which the clathrin molecules are able to attach to each other to make the spherical vesicle. This can be supported by the finding of similar helices faces in other proteins that are involved in the formation of vacuoles.
Endocytosis is a process that allows for the uptake of external materials by cells and utilizes receptors to prevent uptake of unwanted materials. A specific receptor protein is embedded in the membrane of the cell and binds to the extracellular molecule, also known as the ligand. The receptor’s chemical structure allows it to “recognize” the specific macromolecule which prevents the internalization of unwanted foreign substances. After the receptor binds the recognized macromolecule, that portion of the cellular membrane undergoes endocytosis. Clathrin molecules are dispersed evenly on the internal side of the plasma membrane. Accessory proteins are responsible for clathrin recruitment. As clathrin converge near the receptor protein and the desired macromolecule, the inner portion of the membrane is drawn in as well, as shown in Figure 2. As more and more clathrin are drawn inward, a vesicle is formed with the bonded clathrin molecules that outer shell and that portion of the membrane is the inner part of the vesicle. The receptor proteins and their binded “cargo” are on the inner part of the vesicle.
Figure 2
http://www.cytochemistry.net/Cell-biology/recend.htm#clathrin

Accessory proteins, such as AP 180 and epsin, are responsible for the recruitment polymerization of the clathrin molecules, and membrane bending. Different accessory proteins are responsible for determining how many clathrin molecules are to be brought together to form the vesicle. Essentially, the accessory proteins are involved in determining the size of the vesicle. This is due to the size of the “cargo” that the vesicle is transporting. Adaptor proteins, AP 2 being the most well known, link the membrane cargo to the clathrin coat. Once the cargo is loaded, another protein called dynamin enacts scission of the clathrin and separates the vesicle from the membrane. Once the vesicle breaks off the membrane, the clathrin molecules disperse and continue to carry out the same process. The clathrin are then recycled and used again in the same process later.
Although this process is used to transport necessary products through the cell membrane into the cell, viruses and other harmful molecules can be transported into the cell via endocytosis. An example of this is JC virus which is a demylinating disease that occurs in immunosupressed patients, such as aids and cancer patients. Experiments have shown that these virions entered the cell through vesicles that form during routine endocytosis. Another virus known as simian virus 40 (SV 40) showed similar internalization kinetics as the JC virus. However, when agents were added that suppressed clathrin dependent endocytosis had no effect on SV 40 but inhibited the internalization of the JC virus. It is clear that clathrin dependent endocytosis had a major effect on the JC virus’s ability to enter cells.
Another experiment studied the effects of inhibiting clathrin dependent endocytosis using anti-clathrin antibodies and the effects on the Semliki Forest virus. After introducing an anti-clathrin inhibitor, clathrin cumulated in the cytoplasm of the cell rather than near the cellular membrane. In effect, the number of coated pits and vesicles formed in the membrane were reduced significantly. It had been previously proven that Semliki Forest virus entered the cell by clathrin dependent endocytosis. Since the number of vesicles and coated pits drastically decreased, the Semliki Forest virus could not enter the cell through its usual route. The uptake of the virus by the cell decreased by 40-50% which is a very significant difference. Again, it can be concluded that inhibiting the clathrin dependent endocytosis using anti-clathrin antibodies had a significant effect on viral uptake (Figure 3). Another experiment, using different methods to inhibit budding and formation of clathrin vesicles, showed that FV, Sindbis virus, and human rhinovirus depended on the clathrin endocytosis pathway for cell entry.
Figure 3
www.britannica.com/ebc/art-698

From each of these experiments it is shown that some viruses can be prevented, or at least minimized by the utilization of clathrin endocytosis. In each case it was evident that the viruses entered the cell through the vesicles formed by the clathrin molecule. Once endocytosis was subdued using anti-clathrin antibodies and other budding inhibitors, the uptake of the viruses was significantly decreased. This phenomenon could be very important for future research in virus prevention.

antibodies-ricky presentation

This presentation was an adaptation of tylers past story about ricky the RecA. It is almost the same as tylers old story except he added another main character antonio antibody(with an accent). Antonio is important because he flood freddy flu to destroy him. He carries a straw and a backpack around with him, and no one understands, it leads to a lot of suspense in the story. when antonio defeats freddy flu he puts the straw inside of him and pumps water in with his backpackj and lyces him like you would lyce a flu. The rest of the story pans out and the body goes back to normal, everything swims around in the bloodstream while new proteins are made and tommy is really pissed at jordan for getting him sick.

Wednesday's class was another good day of presentations. I particularly liked Nick's presentation of chemokines. It helps that he repeated some of his material from previous presentations that way we were all caught up when we moved on to new material. After three of his presentations I think I really have a good grasp of how chemokines work. Looking back at his presentation the future looks bright regarding new advances in medicine and virology. I loved the candid pic of Zane, too. That was hilarious. The other presentations on clathrin and antibodies were good as well.

First Paper I forgot to upload

Corinne Schuele

Professor Macosko

FYS: Molecular Machines

Nucleotides

February 13, 2008

Taq DNA Polymerase

Polymerase Chain Reaction was developed by Kary Mullis in 1983. Kary Mullis is not the typical scientist accrediting the drug LSD for his discovery. PCR functions as a way to amplify short sequences of DNA usually coding for a specific gene. Polymerase Chain Reaction is like a super fast and efficient copy machine. This genetic copier can create multiple duplicates of the template strand in a short amount of time. According to http://www.dnalc.org/ddnalc/resources/shockwave/pcranwhole.html, the process only takes a few hours to make millions of copies of DNA. It is most widely known for its role in DNA testing for forensic scientists. PCR was famously used to amplify the small amounts of DNA evidence found on the bloody glove in the O.J. Simpson case in 1994. PCR was also used in the mapping of the Human Genome Project. The main molecular machine used in a Polymerase Chain Reaction is DNA polymerase which is an enzyme that aids in the replication.

The solution for a Polymerase Chain Reaction contains a large supply of the four nucleotides, large number of the primer sequence, and DNA polymerase. Using an original piece of DNA as a template, DNA polymerase creates a new DNA strand. DNA polymerase is essentially an enzyme that binds to the template strand of DNA and providing an environment that is suitable for the nucleotides to bind to the template strand. DNA polymerase encapsulates the template strand as if it were a hand grasping it. It then catalyzes the reaction of the nucleotides bonding with the template strand. In Polymerase Chain Reactions, a heat stable polymerase, which was isolated from bacteria living in hot springs, called Tag polymerase is most commonly used to create new strands from short template strands of DNA.

The first step in a Polymerase Chain Reaction is to heat the DNA between 94 – 96 degrees Celsius to unravel the double helix and separate the strands. Heating the DNA to this level dissembles the DNA backbone and denatures the hydrogen bonds between the paired bases. Helicases in nature divide the strands. They are the enzyme that essentially “unzips” the DNA strand. Yet, helicases are not a part of Polymerase Chain Reactions. The heating process replaces the need for this enzyme and uses thermal energy to split the DNA strand. Then, short primer strands are annealed to the single stranded DNA templates. DNA polymerases cannot copy DNA without an oligonucleotide primer coding for the beginning of a replication site. Oligonucleotide primers are just short sequences of certain nucleotides that code for the beginning of DNA synthesis for DNA polymerase. As seen on the previous page on the bottom, this is the stage in which the primers can attach themselves to the correct corresponding sites on the DNA template strands. The temperature is lowered so that the primer can create stable hydrogen bonds with the complementary nucleotides. The DNA polymerase then attaches itself to the DNA template and proceeds to copy the DNA.

The temperature is then raised again to create an ideal environment for the enzyme to catalyze the binding of nucleotides to form a complementary DNA strand. If the process was started with one strand of DNA, by this step there would be two new DNA strands.

The temperature is then lowered a final time. The process is then repeated several times to create multiple new strands of the same DNA. Once millions of strands have been created, there is enough mass to run the results of the Polymerase Chain Reaction on electrophoresis gel. PCR allows the small fragment of DNA, usually representing a certain gene, to have enough mass to move through the electrophoresis gel. DNA is slightly, negatively charged. DNA fragments are separated by length when they move slowly through the agarose gel which sits in a buffer so that a slight positive charge can be applied. The agarose gel is finely porous material. The fragments of DNA move along where the shorter move faster because they fit through the holes better. There is always a DNA ladder added where the fragments are of known amount of base pairs. It is used to approximate the size of the unknown DNA. The figure above from http://commons.wikimedia.org/wiki/Image:DNA-Leiter.jpg is the result of a electrophoresis gel. The furthest column to the left is the DNA ladder with known amount of base pairs.

Thermostable Taq polymerase as seen in the picture above is most commonly used for polymerase chain reactions. The DNA is held in the center along with the nucleotides. The reaction is then catalyzed lowering the activation energy required to bind the nucleotides to the template strand of DNA. Taq polymerase is extracted from the bacteria thermus aquaticus. Because if its thermophilic nature, it operates best in high temperatures. It can withstand the denaturation step of PCR in which the solution is heated to extremely high temperatures. With the use of Taq polymerase, new DNA polymerase does not have to be added each time one wants to copy DNA. Kary Mullis discovered the important use of this enzyme and therefore was accredited the discovery of Polymerase Chain Reactions although many others were involved in the discovery.

Taq polymerase lacks a 3’ – 5’ exonuclease. One component of most DNA polymerases is that they possess the ability to correct their mistakes made during the copying of DNA. Molecular machines called exonuclease rectify these mistakes by moving up and down the template strand finding the mutations and eliminating them. Because Taq polymerase lacks this element, it has a high error rate approximately 1 x 10^-4 to 2 x 10^-5 errors per base pair. This could potentially cause damaged results when ran on an electrophoresis gel.

DNA polymerases vary very little between different species. They all essentially have the same function as a molecular machine helping in the replication of DNA. Taq polymerase is derived from a bacterium, yet functions the same by copying human or any other specie’s DNA. This evidence may be used to show that all living beings have one common ancestor. Because DNA polymerase is a necessary and simple enzyme used in every living organism that requires DNA, it shows that a simple common ancestor possessing the same qualities may have existed. When a complex human genome can be replicated just the same with a bacteria’s DNA polymerase as the human’s DNA polymerase, it suggests the possibility of a simple organism that supplied the basis for all organisms.

DNA polymerase is an essential molecular machine for the genetic code. It provides an ideal environment so nucleotides can bond to DNA fast making copying of DNA a simple and quick process. It also can correct its mistakes which could be detrimental to our health. Without it, our cells would not be able to copy their DNA in an efficient manner.

. "http://en.wikipedia.org/wiki/."

. "http://gaolab.chem.uh.edu/res6.htm."

. "http://www.accessexcellence.org/RC/AB/IE/PCR_Xeroxing_DNA.html."

. "http://www.dnalc.org/ddnalc/resources/shockwave/pcranwhole.html."

. "http://www.genome.gov/10000207."

. "http://www.pcrstation.com/pcr-primer/."

. "http://www.vivo.colostate.edu/hbooks/genetics/biotech/enzymes/hotpolys.html."

. "http://commons.wikimedia.org/wiki/Image:DNA-Leiter.jpg"