18/10/2010 § 1 Comment
We reached the last lecture of the unit today. Today’s class, we learned mostly about the differences between sexual reproduction and asexual reproduction. Both types of reproduction have their advantages and even some disadvantages—particularly asexual reproduction. But both types of reproduction determine the similarity an organism has to its parents.
Asexual reproduction has its advantages and disadvantages, depending on the circumstances of an organism’s environment. Reproducing asexually means that an organism produces two clones of itself (or just one. In the long run, clones are produced), and these clones are genetically and almost an exact copy of the original organism, the single parent. Only one parent is needed for asexual reproduction. Now, in a stable environment, one that doesn’t change at all and one where parasites, bacteria, and diseases simply exist and don’t adapt to their prey and learn how to penetrate their targets, asexual reproduction survives well. The environment is unchanging, therefore, the asexual organisms live easily because nothing is changing. Asexual reproduction is also very fast and effective and doesn’t take as much energy as sexual reproduction. There are numerous types of asexual reproduction, but the textbook included specific kinds like fragmentation, budding, and binary fission.
Asexual reproduction is good. It’s an efficient process if we take into account the speed, the system of the different types of asexual reproduction and the solidity of copying information and passing it on to generations and generations of organisms. But all of this is reliable in environments that are stable and unchanging. If we take an environment that is unstable and changes all the time, then the asexually reproducing organism may not be able to survive. Most likely, an organism that doesn’t have much genetic variety can die out because its DNA and information is not updated to a point where it knows how to fight parasites, diseases and such. In terms of the computer analogy, I think that asexual organisms haven’t updated their system yet, and are therefore outdated, meaning they’ll die eventually (but this is not true in real life; computers can still keep up even with systems that are a little bit outdated.)
Sexual reproduction is special. The process takes the haploid gametes from two parents (one gamete from each parent) and fuses the gametes to produce one diploid zygote or offspring. Because the offspring has two sets of DNA, (half from mom, half from dad), its own genetic information is unique and new. (Computer system’s been updated). This gives sexually reproductive species an advantage over asexual species in environments that are heterogeneous—always changing. Although sexual reproduction itself takes up more time and energy, the benefits are great. The variety of genetic diversity sex provides a species gives the species more of a chance to survive. Their enemies; parasites, bacteria, infections or diseases, may not have such an “updated system” or won’t have the type of genetic information that tells it how to attack the species. Therefore, the generation of sexual organisms survive the environment and pass on their genes to the next generation.
This advantage and the genetic variety in sexual reproduction is all due to crossing-over during Prophase I early in the process of meiosis and independent assortment and all the factors that make the outcome—the offspring—unique.
There are three kinds of sexual life cycles and involve three different groups of organisms.
Protists undergo haploid life cycles. The organisms in this group include most fungi and some algae. The majority of life in haploid life cycles is spent in as haploidy organisms. Only the zygote begins as a diploid cell and from there, produce haploid cells (through meiosis) immediately. This is the simplest life cycle there is on Earth.
Animals, like humans, go through a diploid life cycle. In contrast to haploid life cycles, the majority of the organisms’ lives are spent in a diploidy phase. Through meiosis, multicellular individuals produce haploid gametes (to later fuse, make diploid zygotes and start the process all over again). These haploid gametes are the only haploid cells during the entire life cycle.
Finally, plants undergo alternation of generations, where the organism switches between being multicellular diploids and haploid individuals. In this phase, sporophytes (which are diploid), divide to produce haploid spores. The haploid spores continue dividing through mitosis to produce multicellular gametophytes. Gametophytes then divide through mitosis again to produce haploid gametes, which fertilize to create a diploid zygote. The zygote divides by mitosis again to produce a multicellular diploid sporophyte. As we can see, organisms that alternate within generations spend a lot of time being haploidy but an equal amount of time being diploidy.
For the essay question, I’m leaning towards answering the second essay question choice: What makes children so different from their parents, and what is the advantage in the difference? Ultimately, I would be discussing meiosis and the effects of crossing-over, independent assortment (and I would take into account both of these factors) and genetic variation within sexual reproduction, in contrast to the lack of genetic variation in asexual reproduction.
I will probably also include why sexual reproduction provides such an advantage over asexual reproduction in heterogeneous environments and use the computer analogies, and other possible analogies from class that I took notes on. The test is this Friday, meaning I have three days to prepare appropriately.
16/10/2010 § 1 Comment
So, why sex? One possible answer could be: Meiosis. Because of meiosis, eukaryotic cells have the ability to switch around genes and alleles and create a source of genetic diversity within species. It as a process that is an exact reverse of mitosis. Whereas mitosis begins with one cell and ends up with two, meiosis requires two cells to make one new one. In the midst of this kind of production, a few specific details are switched to create not an identical cell from either of the first two ones but a combination of the two cells.
All eukaryotic cells go through both haploid and diploid phases in their life cycle. When a cell moves from a haploid phase to a diploid phase, they are doing mitosis, but when a diploidy cell moves to a haploidy status, then the cell is doing meiosis.
The first out of eight stages in meiosis is Prophase I. In prophase one, the chromosomes condense and are replicated. They also cross-over and exchange a piece of each other’s DNA. In this phase, homologous chromosomes also find each other and pair up. Spindle fibers and centrosomes line up during Prophase I at opposite ends of the cell and start directing the fibers towards each homologous pair. Below is a crude illustration of the chromosomes condensing and replicating during Prophase I.
In Metaphase I, the second stage out of eight, the fibers place the chromosomes lined up at the equator of the cell, positioned with their respective homolog partner. The way the homologous partners line up at the equator though, is completely up to fate and chance. Mostly chance. Maybe the maternally derived chromosome gets to be on one side of the pole and the paternally derived chromosome has to be on the other side; it’s all up to chance. This is called independent assortment and is a large part in creating genetic diversity during meiosis. The third stage of Anaphase I consists of the fibers pulling one homolog from each pair to opposite sides of the cell. From there, Telophase I and cytokinesis pulls the cell apart and produces two daughter cells, where each cell can relax, and start again.
Prophase II is when the spindle apparatus reforms in each daughter cell. In Metaphase II, similarly to Metaphase I, the spindle fibers take ahold of each chromosome’s centromere. Anaphase II is when the spindle fibers in the cell each segregate the sister chromatids from their pairs. (Each sister chromatid gets a centromere, though.) Now, in both sister cells, each chromosome (now made up of only one chromatid), move to opposite poles of their cell. In Telophase II, cytokinesis happens again, pinching into the cells and dividing them into another two cells—each. The product is four cells.
Whilst all this happened, the genetic information on all four of the cells can be different because of the cross-over way back earlier during Prophase I. Also, during both metaphases, independent assortment occurred when the chromosomes lined up at the equators in certain positions by chance. All of the organizing and arranging is neat and efficient but the details are all by chance, which makes each daughter cell unique afterwards.
This class, however confusing the topic was and as much as it was difficult to follow and keep up, explained the basics of meiosis, which occurs during sex. The process takes two parenting cells to make one new and unique baby cell. Meiosis is so unlike mitosis because of the newness of the product. Meiosis continuously creates new cells and because meiosis is the process that produces specialized cells like gametes—the reproductive cells of an organism, like the sperm cells or egg cell—and spores, the gametes can fuse together to form new offspring.
Now. Why sex? Meiosis, once again, is the source of genetic diversity in all eukaryotic cells. The diversity and changes in every cell creates variety in the species so say when the environment has to change, the species has a numerous variety of cells in their species so that natural selection won’t kill off all of them. Genetic diversity and variation is essential to the evolution of cells. The cross-over during Prophase I and the independent assortment during both Metaphases in the Meiosis process are therefore essential to genetic diversity and variety, too.
(At least, I think that’s what we were trying to get at last class.)
14/10/2010 § 1 Comment
In class, we went over the final stages of the cell cycle, finishing the sixth chapter. Today, we learned about Mitosis and Cytokinesis. We started off by reviewing chromosomes. They are made of one chromatid (before synthesis) which are made of chromatin, which are the little coils that hold nucleotides, DNA and/or information. During the G1 phase and before synthesis, the chromatin—in its coils—spread out so that it can function and make proteins for the cell and the body. To express the number of chromosomes before synthesis, we express the number with the common variable x. After synthesis, however, we know that the number of chromosomes are copied once, therefore the number is double: 2x. After mitosis, cytokinesis and telophase—after the cycle has finished, because the two chromatids of the chromosomes have split, a chromosome in either of the two daughter cells has only one chromatid each. Therefore, the quantity of DNA in a cell is divided by two (after the cell was divided by two) and the number is expressed with only an x.
The next phase after the entire interphase is mitosis. It was repeated in class, so I guess I should also repeat it on the blog. Mitosis does divide and it divides something very important to the cell: the nucleus. In mitosis, the cell itself is not divided and the two daughter cells have to wait one more phase before they can separate. During mitosis (and leading into cytokinesis), there are four mini phases that separate chromatids in the chromosomes. The first phase is the prophase. It is the longest phase of mitosis with five different steps or stages.
The first step, the chromosomes condense. Before they condensed, they were still coiled up and functioned to make proteins and through a microscope, look stringy and wispy. After they condense, the chromatids are concentrated a little, preparing for the next steps. This step is kind of like actors tensing for a performance. They become visible as they coil up.
In step two, the nucleolus disappears. This part of mitosis is described as if the lights are going out and the curtains are going up during a performance. The main act is about to start. The nucleolus disappears from around the chromosomes.
The third step dissolves the nuclear membrane of the cell, freeing the chromosomes completely.
During the fourth step, the spindle apparatus forms. Spindles are cellular structures made out of both microtubule fibers and centrioles that play a large role in moving the chromosomes. The spindle fibers grab the chromatids later and help separate them from their centromeres and 2x chromosomes.
The last step is when the centrosomes, proteins that formed during the cell’s interphase, while it was preparing for mitosis and cytokinesis. The centrosomes (in an animal cell’s case, the centrioles—which are in the centrosomes, according the textbook, p. 128) move to opposite poles of the cell, situation themselves for the next step.
Afterwards is the metaphase. The chromosomes line up along the equator (the middle) of the cell.
Next, the anaphase is the time when the chromosomes move towards opposite poles of the cell. The spindle fibers have taken hold of the centromere and pull one chromatid from the 2x chromosome to each side of the cell.
Finally, the telophase occurs as the reverse of the prophase. The cell de-condenses and kind of ‘relaxes’ to move around and spread its organelles out again. The spindle fibers disintegrates and the nucleus membrane and nucleolus reforms again. Here, the curtain goes down and lights come back on because the show has ended. What’s a little difficult to understand is when telophase starts and stops because cytokinesis also occurs at the same time.
Cytokinesis divides the cell itself and the cytoplasm. Afterwards, two identical daughter cells have been produced. Cells divide differently depending on what kind of cell they are. In an animal cell, because it grew during interphase and is large enough, the membrane pinches inward and releases to form two daughter cells. Plant cells, however, have a cell wall and can’t pinch into the membrane, therefore a new cell wall must be formed between the two daughter cells from Golgi apparatus vesicles. They form a cell plate to separate the two daughter cells.
I think today was when we really finished the cell cycle unit. If I go over this topic a little bit more and understand it better, then I can choose between topics to answer Why sex? for the essay question.
13/10/2010 § 1 Comment
If you sit atop
And chew a piece of
You’ll find colorful
brown sand, the kind that’s
rusted monkey bars,
for someone to touch.
And if you look far
dancing stalks of grass,
constant beeping of
the whisper of the
the wind fingering
all atop a ship.
Majestic clouds dare
blotting God’s divine
And if your eyes pass
hopscotch playgrounds, they
a lone tether ball.
If you sit atop
A lone tether ball,
09/10/2010 § 1 Comment
The last biology class we had on Thursday was dedicated to learning about the Cell Cycle that all eukaryotic cells go through. During the class, we discussed the five different phases of the cell cycle, learning that three of them are part of the Interphase, which contains the first three stages of the cycle. The interphase is the time of a cell’s life when the cell and its organelles do all their usual functions to contribute to the cell’s sustainment and life. We also learned about the checkpoints that are actually chemical switches that control the stops and starts of a phase during the cycle. Finally, we learned about the disease of cancer and what happens when a person has a tumor anywhere in their body.
The first phase of the cell cycle is the Growth 1 phase, more commonly referred to as the G1 phase. This is a major stage in a the cell’s life, where it spends its time growing and where each organelle performs its specialized job to contribute to the cell’s survival. This is also the phase where proteins are made, but this fact is irrelevant as our proteins are constantly making proteins to keep our bodies going. Some cells continue to grow here and proceed to the next four stages and reproduce but others—like brain cells—stay in this stage and don’t divide, therefore remaining in a phase called G1-sub-0.
The next phase is the Synthesis phase, referred to as the S phase. This is the stage where the cell begins to copy its DNA, which are in the nucleotides, which are in the chromatids, which make up a chromosome. At first, one chromosome is made up of only one chromatid, only one strand. After the synthesis phase, however, a copied chromosome is made up of two chromatid strands connected at the middle by a centromere. The new chromatid strand is the copied version of the original chromatid.
[Synthesis happens when enzymes split the weak bonds of the DNA strands and opens it up easily like a zipper. Then new and ‘empty’ DNA strands float over to copy the original information onto themselves. These new and ‘empty’ DNA strands come from the very food we put into our bodies. The information is copied efficiently because of the coding in our DNA. The letters of the code match up and copy the exact replica of the DNA. (Letter matching is Adenosine-Thymine, Guanine-Cytosine). All of this work takes up about eight hours, which makes sleep very important so that the copying of our DNA is done correctly.]
The next and final stage of the interphase is the Growth 2 phase, or G2. This stage involves even more growth, production and more proteins-being-made to prepare for the final two stages of reproduction. In comparing this whole cycle to stage production and performing a musical, the G2 phase would be preparing the stage and getting the final touches on the costume, polishing up the lines, and such. The performance is basically almost ready.
The fourth stage of the cell cycle is mitosis. In this phase, the centromere splits, leaving the two chromatids free. The nucleus divides and makes two nuclei, ready for each daughter cell. Just to be clear, mitosis only divides the nucleus of the original cell and doesn’t divide the cell just yet. The fourth phase of the cell cycle include nuclear division to ensure that the two daughter cells will get the same and accurate amount of DNA and information.
Finally, the last stage of the cell cycle is cytokinesis. Here is where the cell finally divides itself, producing two daughter cells as a result. Proteins that have situated themselves to opposite ends of the cell reach out for a chromatid each and drags it to its own side of the cell. As a personal analogy that helps me remember this stage, I imagine many Mr. Fantastic’s (Reed Richards from the Fantastic Four Marvel comic book series) saving civilians. He (the protein) reaches out for a civilian (a chromatid) with each hand and pulls them to safety (one side of the cell). During this process, the cytoplasm of the cell also divides, finally making the two daughter cells that are ready to perform their own cycle.
Amongst all this reproduction and dividing and pulling civilians to safety, there are checkpoints that happen to regulate the amount of cells that are dividing and reproducing—a that fact becomes very important later when I discuss what happens in cancer. Checkpoints are there to check the cell’s progress during the cycle to act as tests for the cell to pass. If the cell doesn’t pass the test, it means it made a mistake and there’s something wrong with its work and progress. From there, enzymes can come and fix the problem or the cell will be instructed to self-terminate itself and die. This happens so that the mistakes the cell made does not get passed on to the next generation of cells and only the successful and ‘good’ cells get to keep going. This is a strictly efficient system that assures the health of the daughter cells that will be produced.
There are three major checkpoints that we learned in class. The first checkpoint happens before G1 ends, and makes sure that the cell is large and healthy enough; prepared appropriately for the next stage, Synthesis. The next checkpoint occurs during G2, when the enzymes come and repair whatever needs fixing. Here, the DNA’s replications are checked whether or not they can proceed to the next stage. The final checkpoint occurs at the end of mitosis and tells the cell (like a streetlight would) that it can proceed to cytokinesis and then to Growth 1.
Lastly, we learned about how the disease cancer works. Cancer is one of those diseases that continues to stump doctors to this day and is a commonly known world-wide disease. Cancer occurs when there is a loss of control during the cell cycle and division and a cell no longer contributes to the survival of the body. Cells that have become cancerous no longer have any maintenance over the amount of cells that keep dividing and reproducing. Because of this, the cells eventually accumulate too much and invade the blood veins, releasing more cancerous cells into the flow of blood, which enables them to move to other parts of the body, spreading the cancer. Cancer is caused by mutated genes that fail to copy correctly during the cell cycle. Some of these mutations include 1) point mutation, when the genes instruct the cell to make a different protein and do the wrong thing for the body, 2) gene amplification, when multiple copies of genes are made, meaning multiple copies of proteins are made and even more cells grow and divide, and 3) translocation, when genes move to a different place in the DNA strands and instruct the cell to produce extra proteins and cause a constant stream of proteins which probably won’t do well for the cell.
We also learned about proto-oncogenes and tumor suppressors that both prevent the overproduction of new cells. When a proto-oncogene becomes simply an oncogene because of mutation, then it can no longer do normal cell division. When a tumor suppressor is mutated, it can no longer ‘suppress’ tumors that can grow in the body meaning a tumor will grow in the body.
So now we know how the cell actually reproduces. How a eukaryotic cell reproduces, to be specific. But why they have to reproduce this way, we don’t particularly know yet, and why there must be sex, we still kind of don’t know.
04/10/2010 § 1 Comment
The next unit of the semester has to deal with genetics, DNA, and cellular reproduction. This unit’s essay question is simple: Why sex? (Or Why is there sex?) In class, we were faced with many arguments and reasons that showed that asexual reproduction (not involving sex) works well and there’s absolutely nothing wrong with reproducing the asexual way. So why sex with another cell, for example? According to class today, sex is actually something that humans invented on the journey to discovering reproduction. I’m pretty sure our ancestors didn’t know anything about the scientific reasons behind reproduction, they just knew, oh, if you did this, in a few months, there’d be a new human being in the house. But in that, a “new human being” or, in a broader sense, in a more generalized term, sex is somewhat more important than the asexual way to reproduce because it forms something new. The result of sex is a combination of genes, not just a copy (which is what asexual reproduction gives).
One example of asexual reproduction that we studied a little in class is the bacteria’s form of asexually reproducing itself — although the prokaryote is basically just copying itself. The DNA of a prokaryotic bacteria is a simple single loop of DNA. The structure of the DNA in a bacteria is simple so that copying the information is easy during reproduction. All in all, the entire process can be finished in about 10 to 15 minutes. This process, we learned, is called binary fission.
We know that prokaryotic bacterial cells reproduce asexually through the above process—binary fission—but eukaryotic cells can produce in two ways. A human, for example, can do both so that it is able to grow, develop and repair itself and also to reproduce and copy DNA to form offspring. We can reproduce through mitosis to grow, develop and repair. This process copies the DNA to form more cells and in reality, according to the science text book, p. 118, adults can produce up to 25 million new cells per second. That’s a lot of new cells. In contrast, we can also reproduce sexually through a male’s or female’s gametes. One way or another, the DNA in our cells is copied to produce more and more cells.
One very important idea we learned in class today was the structure and length of the genes, which form into chromosomes that stretch off as far as the length to the sun and back to earth five times. That’s an estimated 20 trillion meters of DNA in our bodies. We can fit all this DNA and genes into our body because the long strands of DNA coil again and again and again and again and again and again around proteins and around each other—very much so like a fishing line into a spool—and fits into all of our cells. And after the copying of chromosomes, the chromosome ends up with two identical chromatids, which then connect on a centromere. Chromosomes are the way our 20 trillion meters of DNA is arranged into our cells and into our bodies and help the cells reproduce properly.
Now, in chromosomes, there are 46 of them in a human body, but we consider chromosomes in their separate pairs, so to speak, there are 23 pairs. The two members of a pair are homologous and are matched by their shape, size and set of genes. While humans have 46 chromosomes, other animals or organisms can have much more or much less. Orangutans actually have 48 chromosomes and plants can have more than 200. The number of chromosomes in an organism differ depending on what the organism probably needs. (Since chromosomes hold DNA which hold information that tells ribosomes what proteins need to be made for the plant). A double set of homologous chromosomes is a diploid and has to do with sexual reproduction. When the egg and sperm fuses and after the egg fertilizes, a diploid zygote is formed, the baby or offspring of the two parents. This is meiosis, producing haploid gametes, and combining them to make the diploid zygote.
Also, as a review of something we learned in eighth grade, a particular chromosome determines what gender the offspring will be. In humans, the sex chromosomes are XX (for a female) and XY (for a male). If we look at the sex chromosomes (if we look at the karyotype pictures), then we’ll see that the male’s sex chromosome has a Y-shaped chromosomes next to a longer X-shaped chromosome. A female’s sex chromosomes are different, with two X-shaped chromosomes. This gender-determining trait chromosomes have is similar in almost all organisms, except not all organisms have X and Y chromosomes. Birds, moths and butterflies, for example, don’t have a Y-chromosome and the male gender can be determined if there is only one X-chromosome.
Finally, during the process of copying DNA, chromosomes can sometimes fail to separate appropriately during meiosis. This is called non-disjunction and can cause extra copies to be made in the offspring’s chromosomes. Down syndrome is an example of meiosis-gone-wrong because of the extra copy of chromosome 21. Other changes in a chromosome’s structure have to deal with deletion, which deals with parts of DNA that is lost—deleted—, duplication, which happens when DNA is copied, perhaps in the wrong place or the wrong amount, inversion, when certain parts of the DNA structures are switched and reversed, and translocation, when parts of the DNA are moved to places they don’t belong.
Amongst all the details of cellular reproduction, I basically understand everything. Throughout the next few weeks, I hope that I can understand a slightly deeper understanding of how sex can result into much more meaningful things other than copies of DNA. Maybe it includes the passing down of information to generations, or the change and evolution of the species/organism. I know that asexual reproduction doesn’t do that: form new things. But sex does.