Wednesday, April 30, 2008
Class Review
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
Tuesday, April 29, 2008
This Class Review
Monday, April 28, 2008
Class review
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
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
“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
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
“What? You are going to make both of our rafts smaller? That does not make sense,” Thayer responded.
Dorais said, “Don’t worry, Thayer;
Both of the boys climbed onto Dorais’ back, and then
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,
“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.
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.
Sunday, April 27, 2008
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.
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.
Friday, April 25, 2008
antibodies-ricky presentation
Thursday, April 24, 2008
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
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"
Wednesday, April 23, 2008
presentations
Carey Gates
March 24, 2008
FYS paper #2
GREEN SCUM AND RED CARPETS
As the “ecomobililty provider” for the Rome Film Festival, BMW offered its 7-series Hydrogen cars to transport the VIPs from their five-star hotels to the red carpet[1]. In addition, the Virgin Atlantic transportation service will be switching to hydrogen powered limousine vehicles to carry their premium class clients, and have placed a $2.6 million dollar order for a hydrogen powered airplane engines[2]. As classy as it sounds, the fuel in these vehicles comes from the less than appealing pond algae you may have seen around the neighborhood. Its capability to produce inordinate amounts of hydrogen ions has launched massive research and application efforts of harnessing pure hydrogen fuel from the simple process of photosynthesis.
Driven by the gene expression of the hydrogenase protein, photosynthesis is an anaerobic process in green algae. The family enzymes called hydrogenase catalyze the oxidation of hydrogen as it removes the electrons from the molecule by the equilibrium reaction 2H++2e- ⇌ H2. This molecular machine was discovered in the 1930’s. Further research in the 1950’s revealed two distinct types of hydrogenase, which differ in function and in accordance with their metallic component. The diiron hydrogenase [Fe-Fe] is less prominent in nature, found in microorganisms that produce hydrogen. Nickel-Iron hydrogenase exists in those that consume hydrogen.[3]
As photosynthesis occurs, Photosystem I collects energy from the sun, and typically sends the excited electrons to another molecular machine known as ferredoxin in order to create sugar, the form of energy useful to plant cells. However if excessive electrons accumulate in Photosystem I, they are sent instead to the hydrogenase enzyme. Hydrogenase then uses this energy to split water molecules and release molecular hydrogen as a waste product of photosynthesis. This natural process does not create significantly large amounts of hydrogen, but its simplicity and renewability make it a hugely viable energy source. Scientists today are interested in artificially emulating the process and genetically altering photosynthetic organisms to facilitate hydrogen production, having already found ways to breed and multiply the algae.
The first group to ever successfully directly manufacture and harness hydrogen fuel from a hydrogenase based molecular machine was led by Japanese efforts in 2006. A hybrid enzyme, crossed between hydrogenase from β-proteobacterium and Photosystem I subunit from cyanobacterium, was engineered by removing the subunit PsaE from the Photosystem I and attaching it to the hydrogenase. When placed near each other, these two artificially fashioned molecules spontaneously fused to create a single hybrid. The hydrogenase-PsaE-Photosystem I complex was confirmed as a complete molecular machine by sugcrose-gradient ultracentrifuge and immunoblot analysis.
While the structure had the potential to produce hydrogen at a rate of 1.2 μmol H2 · mg chlorophyll-1· h-1, the maximum was not reached. Factors such as insufficient electron supply from Photosystem I allowed the direct light-to-energy conversion of at a rate of .58 μmol H2 · mg chlorophyll-1· h-1. Although it only represents half of the ideal production, the complex did accelerate the electron transfer by five times the natural rate. This research group also intends to engineer a photosynthetic organism that unites hydrogenase, Photosystem I, and Photosystem II to increase hydrogen production even more. [4]
Professor Anastasios Melis of the
With all this impressive technology, it seems ridiculous that these processes are not yet applied in the mainstream economy. Yet as with all research endeavors, there are small issues that delay or prevent major successes. One inhibitor that scientists have incurred in using hydrogenase to create hydrogen fuel is its extreme sensitivity to oxygen. As a strictly anaerobic process, it is an arduous task to provide appropriate conditions for hydrogenase to function in order to produce hydrogen. Another frustrating aspect is that the photosynthetic process prefers to use the energy for sugar production. Photosystem I more naturally sends electrons to the ferredoxin to supply energy for the Calvin-Benson-Bassham cycle. In addition to being the underdog in the competition for energy, the constant electron transfer between Photosystem I and hydrogenase has not been finessed at this juncture. While they are challenging obstacles for making hydrogen fuel efficient enough for widespread use, the direct conversion of light to energy through artificial photosynthesis is still a very high priority in the international research field. Hydrogen as a primary fuel source has even sparked competition between the
The BioSolarH2 program is funded by the Air Force Office of Scientific Research to integrate traditional science and engineering to target and resolve issues faced by the U.S. Department of Defense. Led by Dr. Charles Dismukes of
The European Union’s initiative for implementing hydrogenase in effective hydrogen production is manifest in the Solar-H networking program. It was established to promote collaboration between existing researchers to provide support and to share expertise across the field. Solar-H objectives are classified into four team goals: the first to study living cyanobacteria and to alter its metabolic rate at the genetic level; the second to determine the mechanisms of natural photosynthesis, the third to artificially simulate those mechanisms at the molecular level, and finally to physically measure the pertinent reactions.[7] The programs of the
Hydrogenase and Photosystem I are obvioulsly applicable to real world issues and are extremely useful molecular machines. In conjunction, their capabilities present a potential and promising solution to the current energy crisis. Because using solar energy is probably the best possible option for a clean, renewable, abundant alternative energy source, this type of biofuel would be an exceptionally long term solution with outstanding benefits and virtually no downfalls. In fact, resolving oxygen inhibitors is not necessary for the process to work, only for facilitated use. Even preceding this advancement, the knowledge and application of natural and artificial hydrogenase enzymes present an optimistic, confident future for the production of fuel and energy.
BIBLIOGRAPHY
Ihara, Masaki, et. Al. “Light-driven Production by a Hybrid Complex of a [Ni-Fe]-Hydrogenase and the Cyanobacterial Photosystem I.” Photochemistry and Photobiology. 2006, 82: pgs. 676-682. March 16, 2006
Jaffe, Sam. “Mutant Algae Is Hydrogen Factory.” Wired Science.com.February 23, 2006. http://www.wired.com/science/discoveries/news/2006/02/70273
Lachance, Molly. “Biofuel research could result in alternative energy source.” AFOSR Public Affairs. March 11, 2008. www.afmc.af.mil/news
Melis, Anastasios.
Navarro, Xavier. “Glamor post of the week: BMW Hydrogen 7 is official limo for Rome Film Festival.” AutoblogGreen. September 27, 2008. http://www.autobloggreen.com/2007/09/27/glamor-post-of-the-week-bmw-hydrogen-7-is-official-limo-for-rom/
“New Euro Research Program for Bio, Solar H2.” Green Car Congress. March 1, 2005 www.greencarcongress.com
“Virgin