By Sandra Tabata
Prior to entering Pygmy 2000, the micro-mobile, remember to have your ticket stub ready, take any motion-sickness preventions necessary, and please, ladies and gentlemen, use the restroom! It is going to be a very long, bumpy ride, and there are no bathrooms on board. Before we leave, there are a few basic safety rules to go over: 1) Stay seated with your pressure helmets on throughout the ìshrinking cycleî 2) Do not pound on, kick, hit, or do anything to the walls and windows of the micro-craft that could cause damage; if any passengers fall out into the cell, they will be lost forever. 3) Anybody on board who has heart trouble, is pregnant, or cannot handle extremely fast speeds, quick jerks, and monstrous drops is strongly urged to exit immediately. Even the fastest, most thrilling roller coaster in the world does not even compare to the ride you will be experiencing.... Other than that, ladies and gentlemen, fasten your seat belts and enjoy the ride.
(A passengerís record)
My heart is still thumping rapidly after going through the ìshrinking cycleî. In less than one minute, we ( passengers, and crew of the ) went from being jet-sized to being as small as a molecule. Nothing in the world could have prepared me for that! Since we are now smaller than microscopic, we are injected into a human being by a syringe.
Cells are everywhere and too numerous for even the largest calculator to count. We will choose one to explore. All of a sudden, a molecule bumps into us and we are instantaneously diffused into the cell before we can decide which cell to enter. Oh well. Diffusion is the movement of particles from a concentrated area to a less concentrated area. It is caused by the random collision of molecules due to kinetic energy. Because the cell membrane is selectively permeable (only allowing some substances to pass through) and we are so small, it was likely that we would be knocked in. The cell membrane itself is made up of phospholipids and carrier proteins. We went through the phospholipids to get through the cell membrane. Phospholipids reminded me of jellyfish, for they had sphere-like heads, called phosphates, and hydrophobic tentacles made up of fat called lipids. The phospholipids paired up so that their tentacles faced each other (like a mirror image), and the pairs are lined up side by side. Proteins carry out facilitate transport, where they make a channel pushing a molecule into the cell. With a protein every once in a while, and literally hundreds of thousands of phospholipids, a blanket is formed which ultimately forms the cell membrane. Both proteins and phospholipids are made of one of the three functional groups. A functional group gives a family of molecules distinctive properties. The three functional groups are aminos, carboxyls, and hydroxyls.
Right outside a nearby mitochondria, a sugar is broken in two parts, forming two pyruvic acids. The energy released in this chemical reaction is stored in the molecule ATP. Next, the pyruvic acids enter the mitochondria and will go through the citric acid cycle. Curious about the citric acid cycle, we sneak in . Upon its entry into the mitochondria, a pyruvic acid is connected to citric acid by a carrier protein which repeats over and over again. Carbons of the pyruvic acid are separated one by one. When all of the carbons have been released, and the citric acids once again alone, it repeats the process. Meanwhile, the carbons are used to form carbon dioxide. The carbon dioxide diffuses out of the cell as a waste product. What becomes of the energy released by the carbon bonds being broken? It is stored in high energy electrons of a coenzyme. The coenzyme helps release energy from electrons by connecting ADP(adenosine diphosphate) with a phosphate to form adenosine triphosphate, or ATP. Mitochondria are one of the most vital components of the cell because they produce the energy that every single cell function uses.
The Citric Acid Cycle
Respiration is dependent on oxygen, the waste product of photosynthesis, while photosynthesis needs carbon dioxide, the waste product of respiration. Although this is an animal cell, Iíll explain its codependent, photosynthesis, the major source for plantsí energy. Photosynthesis is the production of sugar using energy from the sun, and occurs in the chloroplasts. Plant cells carry out respiration, but do not get as much energy from it they do from photosynthesis. As sunlight hits the chloroplasts, it is absorbed by the pigment chlorophyll, and electrons get excited. The excited electrons go one of two ways. In Path 1, coenzymes receive the energy from the electrons and store it by putting ADP and P together to form ATP. The non-energized electron now goes back to get excited again. During Path 2, the excited electron is given to high energy electron carriers: NADPH. These two paths make up the light reaction part of photosynthesis. The dark reaction, also known as the Calvin Cycle, is much different, yet just as important as the light reaction. It starts out with a five-carbon sugar contained in the stroma (RuBP). This molecule combines with carbon dioxide to form a six-carbon molecule. Because it is so unstable, the six-carbon immediately breaks apart and forms (2) three-carbon acids called PGA. PGA is combined with the high energy electrons from the light reaction as well as the ATP made by the light reaction to form a larger molecule called PGAL. PGAL is converted back to 4-, 5-, and 6- carbon sugar phosphates. The five-carbon is eventually converted back to RuBP, and the cycle is complete.
How does the cell know to carry out these functions? Proteins make up much of cells as well as make possible and carry out chemical reactions. The shape of proteins determines what their function is. To find this out, we will travel to the nucleus.
The view of a nucleus from a microscope may give you the impression that it is merely a small dot inside the cell. However, looks can be deceiving, for this is probably the most complex yet fascinating aspect of the cell. In spite of the cell having a membrane, the nucleus is so special, it gets its own private membrane. Actually, it has double membrane called the nuclear envelope. The inner portion fits tightly around the nucleus itself, while the outer portion fits loosely around the inner portion, and in a few spots, they fuse together. This is very important, for when the two fuse together, they form pores which are essential in the transport of RNA and other material flowing in and out of the nucleus.
Inside the nucleus, you will find long strands of a material called chromatin. Chromatin is simply the plural form of chromosomes, and chromosomes are simply pairs of wound-up DNA around proteins. Each human being has twenty-three of these pairs. In the center of each of these pairs is a protein called the centromere. Another section of the nucleus in which the chromatin appears darker is called the nucleolus, the site of ribosomal RNA manufacturing.
Deoxyribonucleic acid, more commonly known as DNA, is a vital, amazing structure within the cell. It contains the all the cellís information, and every protein the cell will make is determined by DNA. At first sight, DNA is a large clump, but when unwound, DNA forms a double helix, resembling a ladder. The rungs of this ladder are made up of different combinations of nitrogen base pairs. Four nitrogen bases can be found in DNA: adenine, cytosine, guanine, and thymine. Itís important to note that the base pairs are complementary meaning that adenine always matches up with thymine, and cytosine always hooks up with guanine.
Each individual nitrogen base is connected to a five-carbon sugar called deoxyribose, and a phosphate, which make it appear to have a tail. Together, the nitrogen base, sugar, and phosphate form a nucleotide.
As long as the suitable partners are together, meaning adenine(A) with thymine(T) and guanine(G) with cytosine(C), the nitrogen base pairs can stack on top of each other in any possible pattern. What if the cell needs to make more DNA? If a new cell is going to function correctly, it must have a complete set of instructions. Therefore, every time a cell divides, it must ensure that both new cells have exact copies of the instructions (the DNA). In order to give them this, DNA replication must take place. During DNA replication, a strand of DNA will be unzipped, xeroxed, and turned into two strands of the same thing. Pretty amazing, huh? Letís see how this happens: First off, a big strong protein called Mr. Unzipper along with his friends Slash, Mr. Cleaver, Ripper, The Divider, and Tear (among others), come along, attach themselves to the DNA, and begin tearing apart the nitrogen base pairs. Mr. Unzipper and his posse are rather violent, but after they are finished mutilating the DNA (which is now completely torn in two strands), he goes away, and is replaced by another protein. The new guy, Dr. Fix-It along with the club called The Unifying Team, some of the members being Patch, Mr. Bond, Link, Matchmaker, and Seal, come to the rescue. They immediately go to work grabbing free-floating nitrogen bases and attaching them to the lonely ones on the two half-strands of DNA, always keeping in mind that A. is with T., and G. is with C. When The Unifying Team has matched up all the single nitrogen bases, there are two lovely strands of identical DNA. Each group of three nucleotide bases is how DNA carries the code for amino acids.
Without a system for having its information interpreted and put to use, DNA would be meaningless. In all actuality, all DNA is, is information about genes and what proteins the cell is to make. Remember, proteins are what make up much of cells and carry out their functions. That is where RNA comes into the picture. Ribonucleic acid(RNA), is a molecule which acts as a copy of DNA and travels out of the nucleus to ribosomes, making proteins. There are three kinds of RNA. Messenger RNA, or mRNA, carries the data for the proteins to be made. Transfer RNA, or tRNA, acts like a honey bee, attaching to free floating amino acids and carrying them to ribosomes. Ribosomal RNA, or rRNA, along with proteins are what actually make up ribosomes, and are thought to be involved in the actual bonding of amino acid chains.
Transcription is the process of copying the DNA code onto a strand of RNA. First, a special enzyme just like Mr. Unzipper and his gang come along and unzip the DNA strand, just as they would do in DNA Replication. After they go away, another group of enzymes called The Cousins of the Unifying Team, come along and match up complements of the nucleotides. Because these enzymes serve a different purpose than the DNA replicators, they match adenine with a molecule called uracil in lieu of thymine, yet do not alter the guanine-cytocine partnership. In addition, the sugar which would be deoxyribose in DNA is replaced by the sugar ribose. Another important difference is that the enzymes only transcribe one side of the double helix called the sense strand. Naturally, the other strand, which may be involved in stopping the sense strand, is called the antisense strand. After the enzymes are through pairing together complementary bases, the phosphate on each nucleotide is bonded to the sugar end of the nucleotide right next to it. This forms another double helix, but not for long. When a terminator on the DNA strand is reached, the new RNA separates from the DNA and goes out into the cytoplasm through a nuclear pore. At the same time of the RNAís departure, each half of the DNA reunites with the other half. Keep in mind that being a substitute for the DNA means that the RNA carries the code for amino acids in groups of three nucleotides. This nucleotide sequence in RNA is called in called a codon.
Because itís on its own now, the RNA looks for opportunities. It searches for a ribosome. Ribosomes are made up of rRNA and proteins, and when the mRNA reaches its destination, the ribosome moves along until it finds the initiation codon, AUG. This signals the beginning of translation.
The ribosome is now reading the mRNA. As it reads each codon, it finds a tRNA that has the necessary anticodon. An anticodon is a loop of tRNA containing three nucleotides which determines which one of the twenty amino acids will stick on top of the tRNA. The codon and anticodon unite. The ribosome does this for every codon of the mRNA. Whenever two anticodons are side by side, the amino acids on top form a bond. As soon as that happens, the tRNA that was there first drops off to seek another amino acid in the cytoplasm. This continues until a termination codon is reached, signaling the end. The amino acid chain, now complete, naturally curls up and forms a coil. The coil then curls itself up and makes what seems to be a twisted tangle. Following, the tangle unites with several other tangles by covalent bonds, and there emerges... what do you know- a protein!
This may seem like a lot of effort for just one protein to be made, but to speed the process up, mRNA often attaches to several ribosomes at a time. This fast and effective alternative results in the production of a polysome, a group of ribosomes attached to a single molecule of mRNA. Not only that, but there are many, many ribosomes, mRNA, and tRNA making different proteins constantly. The mRNA could continue to jump from ribosome to ribosome, or may be eaten up, its parts eventually diffusing back into the nucleus.
Several of the cellís ribosomes can be found on its endoplasmic reticulum, or ER. If there is a combination of ribosomes and ER, it is rough ER, and if there are no ribosomes on it, it is called smooth ER. Rough and smooth ER are often continuous with each other. When a crude protein is released from a ribosome located on the endoplasmic reticulum, it travels through it until it reaches the smooth ER, where a small portion of the smooth ER forms a bubble around the protein. As this bubble breaks away from the ER, and the structure is now a vessicle, or membrane-bound sack.
The vessicle now gives the protein a ride to a structure called the golgi apparatus for it to be processed further. Here, the protein will be refined, packaged, and shipped. As the vessicle touches the golgi apparatus, their membranes fuse together. The protein is then sucked inside the golgi apparatus to undergo chemical changes, such as the addition of carbohydrates or the removal of water. While these changes are occurring, the protein is moving from one side of the golgi apparatus to another where it will once more separate and form another vessicle. This vessicle carries the protein to either the plasma membrane or another organelle, depending on which protein it is, of course. Lysosomes are the recycling centers in the cells. Enzymes within the lysosomes break down large molecules from worn or damaged structures and make them available for use once more; they restore. If a lysosome were to encounter a worn molecule of RNA, it would likely break the RNA down into individual nucleotides, and the nucleotides would diffuse back into the nucleus. Organelles do not float freely in the cytoplasm, as you may believe. Instead, they have an internal support system called the cytoskeleton. This is made up of microtubules and other microscopic structures. The cytoskeleton also gives the cell its shape. Microtubules also create pathways for the movement of organelles throughout the cell. A protein calle kinesin attaches to the microtubule and the organelle. The kinesin molecule moves along the microtubule, pulling the organelle with it .
Vacuoles are the cellsí refrigerators. They mostly contain water. Most plentiful in plants, vacuoles in plant cells also contain salts or pigments. They are formed when cells complete endocytosis. Endocytosis is the active transport of material in and out of cells. First the cell locates what it will consume. Next it engulfs the food by surrounding it and changing shape. Finally a vacuole is put around the food, and the cell digests it. The two forms of active transport are called phagocytosis(for digestion of solids) and pinocytosis(for digestion of liquids, including fats).
We now find ourselves back at the cell membrane, and have seen enough, so we decide to get out of the cell, this time a different way than we came in. Weíll exit the cell by a process similar to facilitate transport. It differs because it requires energy from an ATP molecule, and it moves against ion diffusion. Now out of the cell, there is just one more aspect we have not yet covered: cell division, or mitosis. The cell we have been visiting was in interphase, the period of growth in between cell division. It is during this phase that cells make proteins and duplicate DNA, and is not part of mitosis. Weíre in luck, however, for a nearby cell is about to undergo mitosis momentarily. Though we will not be entering, we still will be able to witness the phenomenon, for the cell has a thin, translucent membrane. Currently at prophase, three significant things are occurring in the cell: the centriole splits and is forming spindle fibers, the nuclear membrane breaks down, and all chromosomes are lining up in the middle of the cell.
Now the chromosomes are lining up in the middle of the cell like the line set during a football game. Spindle fibers attach to both sides of the line, trailing off like streamers.
The savage spindle fibers are now pulling apart the chromosomes at the centromeres. This is violent behavior is the anaphase level of mitosis.
Finally, sanity is established once more in the cell as two new nuclear membranes start to form around the separated chromosomes. Telophase is the name of this period. As the spindle fibers break down, the middle of the cell forms a furrow. Cytokinesis(cytoplasm splitting) is now taking place; the cell is branching off, the two halves going their separate ways in the world. Telophase can be thought of as the opposite of prophase. Now the two cells have completely severed their ties, and two small cells remain.
As I sit down in my seat, buckle my seatbelt, and put on my pressure helmet, I recall all of the adventureís sights. Truely, I am overwhelmed. I think to myself, all life really is, is a miraculous series of reactions. Too many thoughts and questions lie in my head to even think about it, so while the people on board the Pygmy 2,000 prepare to return to normal size, I prepare for the second-most thrilling ride of my life-the trip back...