Active Transport

23/09/2010 § 1 Comment

For the second time, the class faced their final lecture before a test. Today’ s lecture was about the opposite of passive transport: active transport. Active transport is the movement of a substance against its concentration gradient, which requires energy from the cell, usually in the form of ATP. This type of transport of a substance or of molecules requires energy because instead of moving from high concentrated areas to low concentrated areas, the systems of transport are required to pump or ‘push’ the substances from their area of low concentration to an area of high concentration. The way this was explained was using the kids-in-a-closet analogy. In passive transport, I would simply have to leave the door open (if I were a channel protein and a non-gated one that let kindergarteners through), and in no time at all, all the children would be spread out either in that closet or outside and around in the classroom. From an area of high concentration, we spread out the ‘solutes’ and ‘molecules,’ in this case, the kids. In active transport, however, the process would consist of me trying to push a few kids into the closet; from an area of low resolution (the classroom), to an area of high resolution (the closet). Because the molecules or substances that we’re trying to move are energetic, always bouncing off walls or other solids and always active, it will take some energy to get kindergarteners into the closet.

The first idea of active transportation we learned in class was the sodium-potassium pump, a carrier protein. Imagining the Superman picture we were shown in class, we remember that sodium-potassium pumps (SP pumps, for short here) require the energy of one phosphate in the triphosphate part of ATP (adenosine triphosphate). Since I can’t really draw the entire scheme of the SP pump, the graph below shows how it basically works.
Figure 1: The Steps of the Sodium-Potassium Pump

The first step that happens is the binding of three sodium molecules from inside of the cell (in the beginning of the process, the SP pump’s original shape is open towards the inside of the cell, to be able to receive sodium, Na+, molecules). Then an ATP molecule comes along and gives off one of its phosphate molecules for energy. This interaction between the pump and the phosphate group cause a change in the pump’s shape. Now, the opening is not towards the inside of the cell but outside the cell. The three sodium molecules are then released to the area outside the cell, where it is more concentrated with more sodium molecules. Meanwhile, two potassium molecules sneak into the still-open opening (?) of the SP pump.

Backing up a little, we remember that there is still the phosphate group from the ATP molecule that helped make all this happen in the first place. In the first shape, the pump itself are primarily attracted to the sodium molecules. After the sodium molecules are released, however, and the new potassium molecules bind to the pump, the pump loses its affinity for particular molecules, in this case, the sodium molecules. The phosphate group is then released, therefore the pump takes back its original shape, where the opening is pointed towards the inside of the cell. (Without the phosphate group to power the change of the pump’s shape, the pump stays in its original shape).

Our bodies do this all day and we don’t even know it, which is partly why I chose this topic to explain for the essay question. The sodium-potassium pump is a daily, hourly, minutely and secondly process that we human beings perform individually and we don’t even understand it completely. (I say that because people are still discovering more about it and winning Noble Prizes in its honor.) I also chose this subject for the essay question because I understand this concept to a point where if someone gave me a pen and a piece of paper (A4), I could draw the whole process for them and explain what’s going on and maybe touch on why the sodium and potassium molecules are moving to where they’re moving. At that note, I do believe that the pump moves sodium molecules out and potassium molecules in so that there’s a charge around the membrane of the cell, as you can see in the far right of Figure 1. There is a positive sodium charge and a negative potassium charge outside the cell (and vice versa for inside. Positive potassium, negative sodium charges inside the cell.) This charge helps us think and concentrate, which makes the SP pump something all animals need or we wouldn’t be able to function at all.

The next process is relatively simple, and involves a lot of pinching into and fusing with the membrane. Endocytosis and exocytosis are ways to get substances moved into or out of a cell via transport vesicles. In endocytosis (in general, although there are specific kinds of transport that we touched upon in class), the substance fuses against the membrane and a vesicle pinches off the membrane to surround the substance, thus become able to be brought around the cell, as seen in Figure 2.

Figure 2

Figure 3

Exocytosis is just the opposite, shown in Figure 3, where there are already vesicles holding substances (maybe proteins or other molecules needed around the body) and those vesicles again fuse against the membrane (from the inside of the cell) and almost explode, releasing the substance into the blood and around our body, at least, out of the cell. The way I remember this is “endocytosis” is “IN-docytosis” and “exocytosis” is “EXIT-cytosis”.

Finally,  we learned about receptor proteins, proteins that pick up signals from signal molecules so that the cell knows what’s going on in its environment and so it knows how to respond properly. An example of signal molecules are neurotransmitters or hormones. Receptor proteins and signal molecules work in three ways: 1) They activate a channel protein and allow certain ions or substances into or out of the cell. 2) They trigger the formation of a second messenger, which are AMPs, adenosine monophosphate with one phosphate group, which acts as a signal molecule inside the cell. 3) They act like an enzyme and amplify the signal molecule’s signal, producing millions of molecules and speeding up chemical processes.

After this blog, I feel a bit more solid with my essay question and describing how the function of sodium-potassium pumps sort of rely on the shape of the pump. (Of course, in reality, they also rely fully on the energy from ATP.) This unit was interesting, maybe not as easy to follow as last unit, but there were definitely multiple concepts that I understood well (sodium-potassium pump, anyone?). I didn’t receive satisfying grades during the last test but this blog has eased some of my nerves and I now understand the relationship of function and structure in cells, organelles and around cells.

Passive Transport

20/09/2010 § 1 Comment

In our second-to-last lecture before the unit test, the class learned about passive transport in cells. This type of transport lacks the need to use any energy from the cell and depends mainly on the random movement of each molecule or substance. Substances and molecules that move and transport themselves (without energy from the cell) do so to move from a high concentrated area to a low concentrated area. In the textbook, the whole act of moving from high to low, which in scientific terms is called diffusion, was described as numerous never-ending bouncy balls in two rooms connected by an open doorway. Where there are more balls (in Room A, say), because they just keep bouncing, it’s more likely that some balls will eventually move to Room B and later find an equal number of balls in each room. In biology, this describes molecules and substances trying to find homeostasis within a cell. Passive transport and the transportation of substances and molecules happen so that the individual cell finds a balance within it. It tries to find some sort of equilibrium.

In class, we started looking through osmosis and the types of transportation water performs to get around the cell; into or out of one. As review, osmosis is the diffusion of water through selectively permeable membranes. (The phrase “selectively permeable,” I had to look up, means that a membrane allows only certain liquids, gases or substances go through it. In osmosis, we can basically imagine a U-Tube (not YouTube.) which is basically a glass tube that’s been curved into a perfect U. In the curve of the U, we also have to imagine a selectively permeable membrane that only lets molecules smaller than glucose to go through it.

So now, in the U-Tube, there’s a membrane, there’s water in it and we pour a little bit of glucose on one opening (side B) and even less glucose on the other opening (side A). There is then less glucose particles in side A and more glucose in side B. Now, remember that the membrane prevents any of the glucose from moving so the glucose particles themselves can’t move to find equilibrium in the U-Tube. Instead, to find homeostasis, the water moves from a hypotonic environment (side A) to a hypertonic environment. Personally, I think that this happens so that the glucose molecules can be more spread out and more even in the U-Tube. All in all, that might be the general idea of diffusion and osmosis; finding that equilibrium.

Just for the sake of restating the main idea of the previous paragraph: The osmotic potential is greater than gravity, so in a U-Tube, the water (since there is a membrane and certain substances can’t get through), from the hypotonic solution moves into the hypertonic solution to even out the balance of oxygen molecules. Another example of this is in our very own bodies. When human beings exercise, we sweat, and the water that we release (a characteristic we learned last unit) takes the heat and drains us of our H20. When we lose this water, our bodies have more solutes and less water, becoming hypertonic. To find homeostasis in our bodies, we drink water, consume water and dump water over our heads to gain back the water we lost, to find an isotonic state. (When the body, in this example, has found a balance and is neither hypertonic or hypotonic.)

Substances and particles that cells are exposed to also can diffuse through ion channels. These channels are basically transport proteins that allow certain ions and certain substances through. These channels are scattered all over the membrane of any cell and maintain what kind of things go into the cell. Channels help transport molecules and are little holes. Sometimes they have gates that only open when encountering the right stimuli. (For example, the gate could be triggered by an atom, a smaller molecule or an ion, etc.) Of course, when the gate opens, the molecules with the appropriate size are able to enter the cell.

Carrier proteins, are another form of transportation (that don’t include energy from the cell). They are proteins that only specific substances can bind to. After ‘binding’ together, the carrier proteins are like a revolving door. When the molecule attaches to the carrier protein in shape A, the molecule and the carrier protein interact. After the interaction, the protein is no longer attracted to the molecule and shape-shifts into shape B, allowing the molecule to leave on the other side; whether into the cell or the other side of the cell.

To clear things up a little, molecules try to find homeostasis not because they just want to but because of the frequency of their collisions. More collisions in a space obviously have more concentration. From there, molecules then just automatically bounce around until they’re all eventually spread out evenly throughout a certain space. Diffusion moves down the concentration gradient, which is the difference in concentration of a substance across a space.

In terms of my essay question, (Within the context of cellular structure and function, describe and explain how form relates to function) I think I can explain form’s relation to function by using membranes and phospholipids and how they form protective walls. Or, I could explain everything I’d just explained, except recollect the drawings and sketches of transportation I put in my notebook into the essay question and label and describe what’s going on in the sketches. (Since I’m not very much of an artist, it’ll be easier to just sketch the drawing and explain from there all of the labels.) I’m planning on practicing describing equilibrium and diffusion tomorrow and also practicing my sketches to make sure I have the concept down to a pat. Or at least, as much “to a pat” as I can.

Cell Organelles

16/09/2010 § 1 Comment

In today’s class, I re-learned the basics of organelles and inner structures inside a cell. By ‘relearn’, I mean that I’ve learned of mitochondria, Golgi apparatuses, ERs, and other internal characteristics of eukaryotic and prokaryotic cells. Of course, I began studying it back in 6th grade so the level we’re studying cells right now is much higher.

In any case, firstly, prokaryotes are the smallest and most basic form of life there is. They like to “keep things simple”, don’t have nuclei and don’t have any organelles, either. But we didn’t really discuss prokaryotes as much this class as we did eukaryotes. Eukaryotes are the ‘cars’ we talked about last class. For some people, a prokaryote is a bicycle that helps them get to school (if they live on the island, like me) but the eukaryote is the Lexus that brings them to Sannomiya and back with style. In general, a eukaryote is obviously more advanced and can do much more than a prokaryotic cell can. This is because of the many smaller compartments that a eukaryotic cell has inside its structure.

Now, there are probably multiple reasons why a cell needs a various amount of smaller compartments but the main reason is that the smaller compartments are needed to do its own individual specialized function to help sustain the cell. In class, this cooperative relationship between all the organelles in a cell was described as the economy. Many jobs help supply the economic market (and all other types of markets) and keeps the economy alive and working. The same goes for all cells out there. The multiple organelles (cell membrane, nucleus, lysosomes, ER, etc.) all work together to keep the cell alive and working.

First, the  membrane has a rather important role in keeping the cell and its organelles safe from unfamiliar substances and bacteria, too. The membrane itself and the proteins attached to it lets in certain substances and keeps other out. Nearly all organelles have membranes around them and they are all the same. All membranes are made of phospholipid bilayers except for protein membranes, which will vary depending on the type of protein.

The nucleus, as we’ve repeatedly mentioned in class, holds all of the information living creatures inherit from their parents. This information tells our cells what kind of proteins to make and then from there, the proteins do the rest, distributing themselves throughout the cell or even out of the cell. The sequence of nucleotides in DNA directs the sequence of amino acids, which make proteins in ribosomes.

Next, the endoplasmic reticulum is like the inner highway of a cell because they are some proteins’ means of transportation and also help the rest of the proteins get around the cell. There are two parts of the endoplasmic reticulum (ER, for short). The rough ER is considered rough because it is the part of the ER that has many ribosomes attached to the surface and under an electron microscope, the exterior looks rough and bumpy. Obviously with all those ribosomes, the rough ER is where many proteins are made. In reality, the ribosomes on the surface are always working and producing proteins and is very similar to a 24/7 factory; always making things. In contrast, the smooth ER has no ribosomes attached to its exterior (and is therefore smooth) and instead processes molecules inside its tubes.

The function of the ER can be seen through its form (which relates to the essay question!) because of its many folds that form passageways (like hallways, almost) that the proteins can weave through. So for example, the proteins that have already been made by the rough ER are then sent inside the ER to move through the highway, later packing the proteins into vesicles.

Afterwards, the proteins are sent to Golgi apparatuses, where the proteins encounter what could be called the post office. The proteins in the vesicles are taken and chemically modified, then repacked. (Like in a post office. The package is taken, examined, repacked and relabeled.)  The proteins are put into new vacuoles are released from the Golgi apparatus to be distributed to other organelles (they are distributed by exploding, literally) or outside of the cell.

Also, lysosomes go around the cells to break down food. They are membrane-bound organelles. These organelles have very violent and rough characteristics and, though we haven’t really studied their structures a lot, they function by cutting things down to very small bits. (A very good example was the destruction of bacteria when one is sick). Lysosomes also break down old organelles that no longer function efficiently enough for the cell.

Finally, the mitochondrion is the organelle that’s like the powerhouse of the cell. It harvests energy from the nutrients and foods an organism eats and turns it into ATP, our energy currency.

All of the previous organelles are all in animal cells and are also in plant cells but plant cells have three different organelles that animal cells don’t have. They have chloroplasts, which are the organelles that use the energy harvested from sunlight to make carbohydrates with carbon-dioxide and oxygen. These organelles are vital providers of energy for the cell.

Plant cells also have cell walls that are rigid and surround the cell membrane. It is thick and made of proteins and carbohydrates, supporting the shape of the plant and protecting the cell from damage.

Finally, the central vacuole is a large shape (also membrane-bound) that stores water and other substances. These vacuoles, when a plant is being nourished and watered, puffer up and enlarge with the water it’s storing. The fullness of the vacuole helps the plant stand rigidly and when the plant is being malnourished, the vacuole is not full enough, therefore causes the plant to wilt.

So now I know many types of organelles and their functions and also have a general idea of how their structure helps their functions and jobs. Some examples of this would be the ER, central vacuoles in a plant and even membranes. One could even take the subject of phospholipid bilayers and use them to explain how their form relates to their function.

Cell Features

13/09/2010 § 1 Comment

To state it very frankly, cells are one-one-hundredth of a millimeter. 1/100. Of a millimeter. The cells that make our bodies, the cells that form every single living organism on this earth are very small and they are puny in size for a reason.

When we say our bodies need nutrients, in reality, the cells need nutrients and the food we consume so that they can turn it into energy. I think that basically, our cells do all the work for us. We as humans in spirit and soul … don’t do much and the cells are the ones who are chemically changing everything we put in our bodies into energy for them to use.

To get these nutrients, however, the cells have to be small so that food and nutrients don’t have a difficult time to get around the surface area of each individual cells and won’t have a hard time entering the cell. In class, we watched an animation of a small cell obtaining the necessary demand of nutrients because it had a large surface area – volume ratio.

Now, if an object has a large surface-area – volume ratio, it means that the surface area is larger than its volume. I think, because I’m not so clear with this part of the lecture, this means that many nutrients have a lot of space and many chances to get inside the cell, but because of the small volume, it’s very easy for them to get to the middle of the cell. I mean, that’s how I think about it in terms of the Peter-in-the-classroom and Peter-in-the-gym analogy. Peter can get into the class through the wide windows, through the many doors and if he wanted, he could break through the floor or the ceiling but because the volume isn’t as large as the gym, the classroom’s surface-area – volume is greater than the gym’s. It’ll be easier for him to get to the middle of the classroom because there isn’t as much space he’ll have to travel.

[It’s like the cube. There are 6 sides on the cube. The surface area for one side is 1, let’s say. This means that (if my math is correct), the total surface area is 6 units. If one side is 1 unit in length, then the volume must be (1 x 1 x 1) 1. The ratio is then (surface area ÷ volume) 6. (6 ÷ 1 = 6). Whereas if the cube is bigger and one face is 4 units in area, then the total surface area is 24 units. Then, the volume (lwh) is 4³ = 64. So, the ratio is (24 ÷ 64) 0.375. That’s very small.]

Basically, if the cell is too big, then it’s hard for the nutrients and substances to get to the middle of the cell, to be given to the ribosomes, mitochondria and other organelles that need them.

We also learned about prokaryotes and eukaryotes and were told that we could compare the two to bicycles and cars. Prokaryotes which are the oldest types of cells, are single-celled, don’t have nuclei and membrane-bound organelles, and are only about 1 to 10 µm in size, are the bicycles. They are of older class and are somehow more antique and limited.

Eukaryotes however, are the cars. They do have nuclei, they have many organelles and can go up to 1000 µm in size. They can be compared to cars because they’re more advanced, they’re bigger, do more than just ring a bell on the pavement while the user pedals, and can travel a lot faster.

We learned a little bit about bacteria and how they’ve evolved throughout the ages. (The ones that survived antibiotics are the ones that go on and continue their genetics.) We also learned that bacteria multiplies by using binary fission and can multiply by thousands in an hour.

Finally, we were reintroduced to the concept of phospholipids (a type of lipid made out of one phosphate group and two fatty acids, and as a result, they make little jelly-fish-looking lipids) acting as an important role in a cell’s structure. They form the cell’s cell membrane. I think, throughout the entire class, this was probably the most vital information to relate to our essay question. The phospholipids have double personalities. One side, the phosphate side (the head, say), actually likes water and is polar. The other, the fatty acids, are hydrophobic and the result of these two different preferences cause the phospholipids to act like magnet, forming walls that look like this (very roughly like this):


Basically. And I think this type of structure can actually show you that they make a kind of boundary, like a castle’s wall and keeps unwanted things and substances out of the castle or cell. Also, the many proteins that cover the cell membrane are like the knights who manage what goes in and goes out of the castle or cell, making sure only the right substances and right nutrients come in. All in all, I can see that from what I can see in the phospholipids’ structure, because they form a wall, I know that that’s part of their function, to act as a protective wall for a cell.

What Other People Should Do

11/09/2010 § 1 Comment

You know what I’d like other people to do to their blogs?

Make it theirs.

This is the second time I’ve changed my blog to make it look the way I want it to look. I haven’t really looked at everyone else’s blogs but I’m pretty sure I’m one of the only people who did something special to their blog.

I mean, come on. It’s easy to change the appearance and stuff.

So why don’t people just … click a few buttons and … spice up their page?

And they should post their own stuff, too. Their own posts, I mean. The blog isn’t ONLY for Biology, right? xD It is your blog. Under your name, your email, and all that stuff. You do have your own mind and your own will….

But whatever. It’s just what I think other people should do to their blogs.

Make it theirs.

Looking at Cells

11/09/2010 § Leave a comment

Having finished the first unit (Biochemistry), our class immediately started our next unit, which is Cell Organization. For this unit, our essay question relates a cell’s structure to its function: Within the context of cellular structure and function, describe and explain how form relates to function. In terms of what we’ll learn this unit, we’ll have to describe how something’s structure tells us something about what it does. To state a very tentative and vague example; if we look at the cells of heart organ, we should be able to tell that the cell helps the heart in some way by its structure.

Or something like that.

I’m pretty sure that that’s the idea of the essay question for this unit but I can’t be sure. We’ve only started the lesson of Looking at Cells and nothing much else.

We (scientists, students and teachers) look at cells through magnificent instruments called microscopes. This is basically what we learned about through-out the entire class. The history of microscopes start somewhere during the middle of the 17th century (circa 1650s). The people of the time discovered that if they curved a piece of glass and looked through that curved piece of glass, they would find that what they were looking at was magnified. Maybe the specimen wasn’t magnified as much as specimens are magnified today but they could see the object much larger than it is in reality. Robert Hooke was the first to look at a cork under the light of a flame (since there was no electricity back then). By the time the 19th century arrived, microscopes got much better and scientists could actually see all the cells that make up organ and organisms.

Then the class learned that there are two kinds of microscopes used today: light and electron microscopes.

Light microscopes and electron microscopes have their separate advantages and disadvantages. For example, light microscopes have something of a greater advantage because they show the specimens in color. With color, scientists (or students, in our case) have a factor or characteristic to add to their observations and sometimes, color is very important in a study. Plus, experiments where color is involved help greatly, too.

Light microscopes are also much cheaper than electron microscopes and are easy to move around; they’re portable. Light microscopes also magnify up to 2000x and resolve to 200nm. They also have a bigger field view and can observe living organisms. In observing living organisms (as we witnessed in our most recent lab experiment), we can watch their behavior and make note of what the organisms do every day.

Ayushi then asked after Mr. Ferguson pointed out all of the advantages of a light microscope: “Then what’s the point of buying an electron microscope when light microscopes are so good?” Actually, electron microscopes also have their advantages. Although they’re incredibly large, barely portable and hugely expensive, (not to mention that they don’t even show the organisms alive nor in color), these microscopes can magnify a specimen up to 200,000x and can resolve the image to 1nm, meaning the observer will be seeing the specimen very clearly. If the resolution is not very good, then it is low and things will look as if they’re attached. But if they’re resolution is high, like in an electron microscope, then things will look separate, as they’re supposed to and an observer will see light between each specimen.

Although I’m not very solid with this part of the lecture, light waves, which are about 400-700 nanometers in size/length (depending on how powerful the light wave is, I think), are too big to flow through some specimen, so the electron microscope instead uses electrons (which use electricity) to bounce off the metal-covered-specimen and give off shapes and the general outline of the specimen. All in all, this process works so well that it’s as if a scientist is looking at a magnified specimen perfectly.

There are also 3D versions of the electron microscope, which is the SEM (scanning electron microscope), and the specimen is tilted so that an observer would be able to see all parts of the specimen, even if it’s dead.

So, basically, right now we’ve only been introduced to the entire unit but I’m sure that in a while, I’ll be able to make more connections for our essay question: How does form relate to function? (basically).

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