biogeno.us

Today, the class’ objective was to finish the notes of the remaining organelles which consisted of  the cytoskeleton. The teacher intricately discussed the three major protein fibers, microtubules, microfilaments, and intermediate filaments and the class analyzed the structure and the function of these different fibers.

Firstly, the class went over the details of microtubules, which are the thickest of the three fibers, measuring at about 25nm. They are also composed of protein tubulin. They are significant because they are responsible for a cell’s structure and a cell’s movement. They also move chromosomes during cell division with the use of centrioles, which organizes microtubules by guiding these chromosomes. Microtubules are also are able to move through the use of cilia and flagella. Although cilia and flagella both create movement, they function in very disparate ways. For example, cilia moves with an oar-like movement with alternating power and recovery strokes. Flagella has an undulatory movement and it allows small organisms to propel themselves through water. Also, it its important to know that the bending of cilia and flagella is a result of motor proteins such as dynein.

Another similar structure to the microtubules are the intermediate filaments which are quite smaller measuring about 8-12nm. These filaments are built from keratin proteins. Some of their functions are that they are specialized for bearing tension, and they are able to holding things in place within cells.They also reinforce the shape of the cell and they fix the organelle locations. Last of the main protein fibers are the microfilaments which are about 7nm in diameter, making them the thinnest of the three. They are often referred to as actin filaments because they consist of twisted double chains of actin subunits. They are quite essential in muscles cells and by interacting with myosin filaments, the actin filaments create muscle contraction. Actin filaments also constantly form and dissolve which makes the cytoplasm liquid or stiff during movement.

Lastly, the class watched a video that concerned the functions and the actions that occur within a cell. This video elaboarate on the true structre and movement of these organelles within cells and what functions they perform within the body. This really helped to piece together and eplain how sophicated a cell really is with the use of a visual aid.

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The two main concepts that we focused on in class today was the Mitochondria and the Chloroplasts. In overview, these two parts of a cell are the organelles that convert energy to forms that a cell can use for work. Each of these organelles do however share many similarities with each other. Both of them transform energy to generate ATP. They each have a double membrane as well as move, change shape, and divide in order to to perform the functions a cell needs. But with these similarities there are also many differences as well. The Mitochondra and Chloroplasts are very differnent in function as well as strucure.

The Mitochondria has many different functions within a cell. This includes cellular respiration, and generate ATP. It is able to generate the ATP throughout a cell from the breaksown of sugars, fats and other fuels that enter and exit the cell. Int he presence of oxygen though, the breakdown of larger molecules into smaller ones is required in order to generate energy. To generate energy in the presence of O2 is known as aerobic respiration.

The structure of the Mitochondria is made up of two membranes. In order to increase the surface area of a membrane two cells are necessary. It has a smooth outer membrane and a highly folded inner membrane . There is fluid that fills the smace between these two membranes as well which is made up of DNA ribosomes and enzymes. Almost every eukaryotic cell has a Mitochondria found inside. This number can range from one individual Mitochondira to hundreds or thousands of small individual ones. The number of Mitochondira is directly correlated with the aerobic metabolic activity inside a cell. The more activity ther is, more energy is required , which then leads to the more Mitochondia that a cell must have.

Then there is the Chloroplasts. These are found in all plant organelles. They are made up of two membranes just as the Mitochondria. This consist of one inner and one outer membrane. They also have an internal fluid filled space called a stoma which is made up of DNA, enzymes and ribosomes. They also have thylakoids which are membraneous sacs, in which ATP is made. They can also be in stacks known as grana. But the fluid outside of these thylakoids is known as the stroma.

The Chloroplasts also have closely related plant organelles known as amyloplasts which are colorless plastids that store starch in roots and tubers. There are also chromoplasts which store the pigment for fruits and flowers. But Chloroplasts themselves store Chlorophyll to function in photosynthesis. The proccess of photosynthesis occures in leavs and other green structures of plants as well as algae. This is the main function of Chloroplasts. Photosynthesis is the proccess of using solar energy and transforming it into chemical energy. It results in the production of sugars, CO2 and H20.

As mentioned before, both the Mitochiondria and the Chloroplasts differ in many ways. There organelles are both not part of an endomembrane system. They also grow and reproduce very differently from one another. These are just a few of many differences that both of these organelles do not have in common with each other. But the main point of this is to show how even very similiar organelles share many of the same qualities, each is unique in its own way.

The last thing that we discussed were the differneces between the Endosymbiosis theory and the Endosymboint theory. The Endosymbiosis theory states that the Mitochondria and the Chloroplasts were once free living bacteria  that were engulfed by an ancestrial eukaryote. But the Endosymboint theory states that a cell lives within another as ahost to create a partnership that resulted in an evolutionary advantage for both. One supplies the raw material while the other supplies the protection. These are very important theories that need to be known and studied in order to empand ones knowledge.

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My apologies on the fact that there was no post on Wednesday, September 17. Our class had some organizational issues, and it will not happen again.

Today in class, we took notes. Lots and lots of notes, resulting in a mental rush of information. I will summarize this as best I can. We began by going over our voicethreads, which are looking amazing thus far with the inclusion of the self-drawn versions of the Smooth and Rough Endoplasmic Reticulum.

Afterwards, our teacher (upon his return from the Mothership)greeted us with a plethora of notes. These notes were on Lysosomes, the “recyclers” of our bodies. We began with their structure and that they have a “membrane bud sac of hydrolytic enzymes…” We continued to learn that these lysosomes are only found in animal cells. Their function is to be the cell’s stomach by cleaning up the cell. They do this by fusing with the food vacuoles. Through the lysosomes, polymers are digested into monomers.

We soon learned that lysomal enzymes work best at pH 5, and that organelles create custom pH’s by using proteins in Lysomal membrane to pump Hydrogen from Cytosol into the lysosome because Lysosomes are very sensitive to the pH level because they are proteins and the pH affects structure.

Finally, we worked on our voicethreads while listening to some Classic Rock and discussing classic Saturday Night Live skits; such as the famous “More Cowbell” skit.

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We started today’s shortened class period reviewing what we learned last class by going around the room and naming one thing about the nucleus and one thing about ribosomes. Next we went straight to notes where we continued with Endopasmic Reticulum , Golgi Apparatus and started with lysosomes.

Today in a nutshell:
The materials follow a path starting from DNA-mRNA-Ribosomes-(make proteins)-rough ER-(tagged and folded)-Golgi Apparatus.

There are two different Endoplasmic Reticulum, Smooth and Rough. The Smooth ER synthesizes lipids, oils, phospholipids, steriods, and sex hormones. It also breaks down the glycogen that is in the liver into glucose. The smooth ER also detoxifys drugs and poisons in the liver.
The Rough ER produces proteins for export out of the cell. These proteins are “packaged” into transport vessivles.
The membrane factory makes membrane phospholipids in order to build a new membrane. So as the Endoplasmic Reticulum membrane expands, it buds off and transfeers to other parts of the cell that do need new membranes.

The Golgi Apparatus finishes, sorts and ships cell productions, it is found excessivly in cells that are specialized for secretion. The Golgi apparatus is looks like pita bread stacked on top of one another. It has two sides, cis and trans. The cis side recieves the material by fusing with the vessicles. The trans side buds off vessivles that travel to other sites(transport). The Golgi apparatus processes or modifys the products that are from the ER.

Lysosomes are a basically a bunch of enzymes that can break down macromolecules. Both the enzymes and the membrane of this lysosome are synthesized by the rough ER and are transfeered to the Golgi Apparatus. This is one of the organelles that is not found in plant cells, only animal cells. They are known as the “stomach” for the cell because thy break things apart. They are also said to clean up the cell and the question for next class is…
Why is it important that lysosomes clean up the cell?

If you want to know why glycogen is better for humans for the synthesis of sugars picture this. Take a part of a tree that branches out(glycogen) and another one that  is just straight with no extra branched portions(starch). If you hold one end, there is only one other end left on the starch stick that can be broken off symbolizing the synthesis of sugars. On the other hand the glycogen has many points because it has many more ends.

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At the start of class, our instructor handed back the chapters 1-5 test. He explained how the grading worked. 80% of our score came from the multiple choice section and 20% came from the essay itself. After declaring that the first test is usually bad, the whole class sighed in relief. He also gave us a chance to earn a curve by allowing half a point extra for every incorrect answer that we found the right answer to.

Then our instructor went over the class objectives which were to take notes on the introduction of cells and discuss the class project. He lectured about how cell size is determined by the ratio between cell’s volume to the cell’s total surface area. This is why the average bacteria cell is 1.0 to 10 microns in diameter and  the average Eukaryotic cell is 10 to 100 microns in diameter. Metabolic requirements are also what triggers cells to divide into smaller cells. In a large cell, materials necessary for the cell to survive cannot move fast enough in and out of the cell. The only way it can become bigger is by becoming a multi-cellular organism. Our instructor also talked about membranes within a cell. The bi-lipid membrane of the cell serves as a selective barrier that only allows certain materials to pass. In Eukaryotic cells, all organelles are covered by a membrane. This partitions the cell into compartments that have specific functions. The membranes themselves are specialized for their function. Some membranes allow the passing of proteins while other membranes may not. This was the last of our notes for the day.

After the class was finished taking notes, our instructor presented us with our class project. It was to be done on VoiceThread.com which he explained to us how to use the website. It was pretty much a powerpoint presentation format with slides where an individual comments on the item displayed. In our case, those items are to be the various organelles of a Eukaryotic cell. I (John) created a Google spreadsheet that lists the photo responsibilities of each student (the voice comment on each organelle must be done by every student in the class).

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Today in AP Biology, we did not get our recent tests back, but we did begin a new chapter. We took a plethora of notes on chapter 6 material. Chapter 6 describes the cell: the basic unit of life. Why do we study cells? We must understand cells in order to make sense of any other forms of life on earth through reductionism. In addition, cells account for much of the diversity and unity on earth, since everything is made from cells. The cell is the smallest organism that can perform all of the necessities of life: reproduction, growth and development, energy utilization, response to environment, and homeostasis. The class learned that cells are studied through the lenses of a microscope. There are various different kinds of microscopes that can are used for different reasons. The light microscope is used for bigger subject matters. The electron microscope is used for smaller subject matters because it can magnify objects about a 100 times greater than light microscopes. The electron microscope is capable of revealing organelles under its lens, but can only be used on dead cells. The summer reading, described the use of an electron microscope to scrutinize an Ebola virus. The electron microscope enabled the researchers to see the thread virus and its characteristic cheerio shape. The modern marvels of technology enlarges the wealth of knowledge in the science world and enables scientists to form a hypothesis and eventually an answer faster than when electron microscopes where not around. The other two electron microscopes are transmission electron microscopes, used to study the internal structures of cells, and scanning electron microscopes, used to study surface structures. The notes then discussed how organelles can be isolated. Of the isolated organelles, the nucleus is the heaviest and ribsomes are the lightest. This process is called cell fractionation using an ultracentrifuge (spins up to 130,000 rpm) and a micro centrifuge (used from biotechnology). Our teacher then showed us a working micro centrifuge and relayed his plans to purchase a bright green micro centrifuge in the future as well as a lab in which we would be using the centrifuge.

The next major section of our notes focused on cell characteristics. All cells have some fundamentals in common: they are surrounded by a plasma membrane, have a cytosol, contain chromosomes, and have ribosomes. Then the notes pointed out some differences between prokaryotic cells and eukaryotic cells. Prokaryotic cells are generally smaller and less complex than eukaryotic cells. Prokaryotic cells lack a nucleus and contain DNA in their nucleoid region. Eukaryotic cells contain specialized structures for specialized functions. Eukaryotic cells are present in the plant and animal kingdom. Next class, I’m sure that we will go into further detail regarding cells and how provide a basis for life on earth.

Today, many people hear about the importance of cells by medicine and research. Stem cell research is discussed everywhere from magazines to the news. Stem cells will inevitably lead to increased treatments and possibly cures. Understanding cells and their basic characteristics help scientists unlock new inventions and knowledge daily. For more information about cells and study tools visit this website http://www.windows.ucar.edu/tour/link=/earth/Life/cell_intro.html.

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The first thing we did in class today was see our shirts we tie dyed on Friday. Everyone’s turned out great and was happy with the way it looked except for Nick whose shirt turned out looking very girlie. Next, our instructor showed us his virtual AP Bio café which he plans top eventually make national. The virtual café was really interesting and cool to see someone’s idea shown through a computer. When our instructor was done showing us his café, we moved on to notes.
These notes were a continuation of chapter 5 about macromolecules. The first topic was lipids; before today I didn’t know lipids and fats couldn’t be used interchangeably: fats are a type of lipid.  Lipids are a long hydrocarbon chain and have 3 groups: fats, phospholipids, and steroids. Fat is a long HC chain that is non polar and hydrophobic. The two types of fats we learned about were saturated and unsaturated fats. Phospholipids consist of 2 fatty acids and PO4. The fatty acid tail is hydrophobic and the PO4 is hydrophilic. Steroids such as, cholesterol and sex hormones are 4 fused C rings.
Next we learned about Proteins which have many functions. The structure of a protein is a monomer which is an amino acid. We also learned about what determines the order of amino acids but unfortunately we didn’t have enough time to complete the lesson.

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The first task of class was to take the chapter 4, which concerned carbon and the molecular diversity of life. Afterwards, our class inspected the germination progress of the seeds. Unfortunately the seeds were  severely destroyed by the mold within the bags. This impeded the progress of the seed growth and as a result, seeds were not displaying any progress. My partner, John and I had some difficulty finding the exact number of germinated seed within each bag, but nonetheless, the experiment had to continue.

Moving on, the class learned about a site called delicious.com which finally worked after several days of difficulty. This nifty site allows computer users to have their bookmarks available on any computer.  This does allow each classmate to, dare I say have another weapon in their “technological arsenal”, but it is also a bit overwhelming since everyone has to keep track of these different tools. I suppose, in a couple weeks the everyone will become experts to all of new functions.

Lastly, our class briefly took notes on sugars and the basic properties of cellulose. He also showed to the us the structure of a cellulose molecule through the utilization of “tinker toys”. It was also important to know that celloluse is quite hydrophilic, which would be significant in the class’ experimentation in making tie-dye shirts in the near future…hopefully.

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This was the first day where our instructor was not present. The class had a substitute teacher who only supervised the class after giving instructions to open up a Google Document and work on our Seed Germination Lab. We collected our last round of data for the lab and recorded the information onto our Excel Spreadsheets.

After we collected our data, we began working on our lab reports. Our instructor shared a document with us on Google Docs which explained the step-by-step process of creating a lab report. The whole class was confused about the instructions so we made a cicle in order to work on the lab together. We even called our instructor during class because we had questions about the lab.It wasn’t long before Nick busted out his ipod and began playing Disney songs. This drew our attention and pretty soon all 9 of the students began singing along with the tunes. It started with Disney songs such as The Circle of Life (The Lion King), The Bells of Notre Dame (The Hunchback of Notre Dame), and Part of Your World (The Little Mermaid) and then the songs progressed into the Pokemon theme song and Stairway to Heaven. While the music was playing, only a miniscule amount of work was completed.

Our instructor finally made some contact with us and Nick and I (John) went out to our instructor’s red minivan to carry several water containers. Once we got back, our instructor began explaining how to set up our labs in detail. We were to write the report in this order: title, abstract (summary of the whole report), introduction, results, discussion, conclucion, and references. By the time he was done explaining everything, it was time to go which means that tomorro is tie-dye shirt and quesadilla day. YES!!!

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I will not be in class tomorrow so we have to move the lab to Friday.

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