30/11/2010 § Leave a comment
The topic/issue my group and another group (consisting of Yurika, Natacha and Yiram) are debating is the banning of public smoking.
I am lucky to be on the positive side of this debate (I agree with banning public smoking) because I truly think that the banning of public smoking should be undertaken and spread to as many countries as possible. I hold this type of opinion because I myself would like to get rid of smoking on Rokko Island at first. I know that smoking is possibly one of the worst things to get hooked on and addicted to and I know a few people who smoke. Taking in all the information I’ve learned so far and adding it to the information I’ve learned in the last few years, the general idea I have about smoking is that it’s generally just a terrible thing to pollute your body with and it does indeed ruin your life.
In past classes in 7th and 8th grade, my health classes included a lot of talk about how smoking really just isn’t bad for your health but it can ruin your life. Even without the health classes in middle school though, I think I get enough information about smoking online, through television and through ads and billboards (mostly in the Philippines) that warn people about smoking. Through celebrities in America, (like Lindsay Lohan, for example), I’ve seen pictures, watched clips and read articles about them having to go to rehab for smoking. Sometimes, they just look like they’re in such bad health, I feel bad for them. I see celebrity smokers (who are dangerously addicted) who are thin, pale, awfully weak and always drowsy. Unfortunately, it has been turned into a stereotype but if someone smokes, everyone else could automatically think to shy away from them because maybe they smell, maybe they stink, maybe they’re unhealthy or not fully sane. However, most people definitely know to stay away from smokers as much as they can because of the smoke they emit.
Before the Health classes this year, I tried to stay away from smokers because of their smell but now I know that the smoke that they emit is so much worse than I thought. The mainstream, side-stream and second-hand smoke (which is probably the worst, being a combination of both) that cigarettes emit and that smokers exhale are also dangerous. Smoking in public releases that type of poison into the atmosphere and into the air that innocent babies, children or non-smokers have to breathe.
Around Japan or even in the Philippines, I’ve seen people smoking then coughing immediately. I’ve seen mothers sit next to their babies in their carriages and smoke freely, not even minding that their children are breathing the smoke they’re exhaling. I’ve watched kids walk past some smoker who carelessly blows smoke right in front them, polluting the kids’ lungs, not just his/her own. I myself have walked in crowds of smokers and it is just plain nasty, not only poisoning the smokers, but also their environment and everyone else around them.
16/11/2010 § 1 Comment
Although it was a small part of the textbook, we learned in class about which parts of genes are expressed and which sections actually intervene the genes that will later be used to code for proteins. Sections of a gene that do get expressed are exons and sections of a gene that do not get expressed are introns. Exons will get spliced together while introns simply get removed, kicked out of the sequence and will be reabsorbed as new nucleotides. After splicing, the length of genes obviously gets shorter and only the exons are existent in the RNA (this all happens during protein synthesis—transcription or translation) that will be used for translation.
Since introns don’t even get used at all, it seems that they are absolutely unnecessary for genetics in an organism, but sometimes they can be very useful in the reshuffling of exons and introns that happen in the Research & Development section of our genes. The sections of genes that are introns help shuffle exons around and make new sequences in the genes. Usually this doesn’t always work out because of natural selection. Nature doesn’t just agree with what will be a new set of genes. Sometimes though—even if it rarely happens—a new shuffle of genes just happens to work and it provides such a great leap on an organism’s road of evolution.
We also learned a bit about mutations in class. Although they are also quite rare—only one in a billion+ nucleotides have a mutation—the changes can either have a large effect or have no effect at all. Substitution mutations replace one nucleotide with a different one. Sometimes this may have no effect because certain amino acids are coded by more than one codon. (So changing UCU to UGC for cysteine makes no difference. It will still be cysteine.) Some substitutions also change the amino acid itself, depending on what codon is changed. This can lead to a protein deficiency, not having enough of a protein, but does not always make too much of a difference.
Other mutations can make all the difference in the organism’s cells. Either insertion or deletion can make a huge change in a cell’s genes. Insertion adds another nucleotide somewhere in the sequence of nucleotides and sometimes changes all of the amino acids that follow it. Deletion does the same but through another way. During deletion, a nucleotide is removed and the nucleotides that follow it are also changed because one nucleotide has been removed and all the other bases shift up, changing the coding sequence for amino acids. Basically, mutations change the meaning of DNA and provide a new meaning—sometimes not one the organism would understand.
Also, in order for scientists to identify treatable genetic disorders and in order to treat them, they had to map out the entire DNA sequence of a typical human. In the Human Genome Project (where billions of dollars were used), scientists researched human genes, found which gene was on which chromosome and what it was used for. Later they also compared human genes to that of laboratory mice or rats or other non-human organisms. The reason for doing all this—which was stated above—was to totally map out the human DNA sequence so that when a person has a treatable genetic disorder that isn’t helping them and actually slows them down in life, the disorder can be found in their genetic sequence and can be fixed.
The essay question was: How does information produce meaning? Mutations provide an example of how meaning is changed and shuffling introns also support how meaning is changed. For me, I easily understand the essay question if I use protein synthesis (transcription & translation) with RNAs and DNA molecules to explain how information, nucleotides, becomes meaning, proteins.
11/11/2010 § 1 Comment
In both prokaryotes and eukaryotes, not all of the genes on DNA are transcribed and translated (expressed). If all of the genes were expressed and all the amino acids gathered and all of the proteins coded in the DNA were made, then obviously a lot of energy would be used but in the end, not every single one of the proteins would be used (because typically, only the proteins needed at the time would be used). Therefore, energy, materials and time into making the proteins would be wasted.
Prokaryotes’ way of managing which genes are expressed and which are not at certain times involves using enzymes. In one bacterium called Escherichia coli, the genes that make proteins that digest lactose are not apparent when lactose nutrients are not and a protein called a repressor is involved with the regulation of the genes. Usually, the repressor is bound to a site on the DNA called an operator, the section of genes that serves as an on-off area.
With the repressor bound to the operator, the RNA polymerase that does transcription and forms mRNA is blocked from continuing the process and not all of the coded proteins are made yet. When lactose is present, however, they attach themselves to the repressor and change its shape so that it is no longer in the RNA polymerase’s way. Once the genes have been transcribed and later translated into proteins or enzymes, in this case, the enzymes eat away the lactose—even the one attached to the repressor. This restores the repressor’s original shape.
This process of regulating genetic information controls the lactose in the bacterium because if there is too much lactose in it, it’ll probably die. If there is lactose, the bacteria makes lactase to take it away. If there isn’t any, then there’s no point of making lactase (the enzyme).
We were already beginning to run out of time in class but eukaryotes’ ways of controlling protein synthesis in eukaryotes is much more complex than those of prokaryotic cells. An RNA polymerase needs other proteins to help it transcribe the DNA molecule. These are called transcription factors. Activators activate transcription between DNA and RNA molecules and attach to regions of DNA called enhancers. The DNA curls up a little and only then can the RNA polymerase continue transcribing the genetic information. Therefore, transcription only begins when the complete group of transcription factors, including activators and enhancers together, are present for the gene that will be used for protein synthesis.
08/11/2010 § 1 Comment
During today’s class, we started learning about RNA and protein and how these molecules transcribe and translate the information from DNA and produce meaning out of it. In this section of the textbook, we started getting closer to our essay question, which was not discussed in my last blog. As a refresher, our essay question was: How does information produce meaning?
At one point in class, we were able to translate the question and replace the words information and meaning. Another word for “information” can be “nucleotides” and “meaning” can be “proteins.” So if we switch around these words, the essay question can be reworded to: How do nucleotides produce proteins? This makes sense in terms of our original essay question because nucleotides contain nitrogen bases which code for amino acids that make proteins. Proteins, in turn, are responsible for many things in an organism. Some responsibilities they have include structural capabilities (determining someone’s eye color, hair color, everything that makes them look as they do), being able to fight off infections or bacteria, moving muscles to enable an organism to move, and many other tasks.
So in a way, the reworded essay question still makes sense.
In class, we learned that both transcription and translation contain three important stages: Initiation, Elongation and Termination. In transcription, an RNA polymerase binds to a DNA molecule’s promoter region, which is around the front of the gene and where transcription starts. The RNA unwinds and unzips the DNA. This is initiation. Elongation is when the RNA polymerase begins adding nucleotides via the complementary base pairing rule (A=U, G=C). Behind the polymerase, immediately after it adds a corresponding nucleotide to the lengthening mRNA, the DNA molecule zips up again and rewinds. Elongation and the matching of nucleotides continue until termination. This is when the mRNA that is being made reaches a stopping codon; a termination sequence. When transcription is completed, the mRNA is simply released to find a ribosome to do translation.
During translation, all the action happens inside ribosomes (which are made of ribosomal RNA and lots of proteins). The process of translation can be thought of as taxis dropping off guests at a party in Sannomiya. (Or wherever). First, the ribosome (kind of like the bellboy and the parking lot at the same time), mRNA (the guest list that determines who gets to come to the … party) and tRNA (tRNA are all taxis)—carrying the amino acid for the anticodon that corresponds to the start codon—all bind together. The tRNA carrying the start anticodon binds to the P site. Another tRNA comes along with the right anticodon and matching amino acid for the next codon shown on the mRNA. It attaches to the A-site. The two amino acids now link together with a peptide bond made by the ribosome. Then the [now empty] tRNA in the P-site leaves and the tRNA that was on the A-site moves to take its spot. A new tRNA comes in to fill the A-site and more amino acids are added to the growing chain. This process is continued until a stop codon is reached and the protein is finished and released to be used in the cell.
Going back to the essay question, we just used nitrogen bases (nucleotides) and genetic information to make proteins that will work around the cells and in an organism’s body to form its structure, help it move, enable it to think, feel, and do many more things. Clearly, proteins help an organism mean something. In the processes of transcription and translation, we kind of just figured out how information helps make meaning.
07/11/2010 § 1 Comment
DNA needs to replicate with continuity and fidelity, meaning that it must copy without change. (That’s just a rule of life.)
Firstly, if we remember the structure of DNA, we can recall that the separate subunits are held together by covalent bonds and hydrogen bonds. The covalent bonds are strong enough to hold the phosphorus and sugar subunits together and the hydrogen bonds are also strong collectively (as a group of hydrogen bonds) but individually, can be unzipped easily. This enables the DNA molecules to be replicated easily, too. An enzyme called a DNA helicase is responsible for unwinding and unzipping the DNA. In this process, the helicase produces a replication fork, which is an area where the double helix has separated (replication forks are shaped as Y’s, like forks are). Both of a DNA molecule’s strands are copied at the same time by another enzyme called the DNA polymerase.
The polymerases use the open individual DNA strands as a template and add the complimentary nitrogen base to form a new strand. The enzymes continue to do this until the entire strand of DNA has been replicated. The product is two identical copies of DNA where each DNA molecule has one parent strand and one daughter strand each. This shows that DNA replicates semiconservatively and the result of replication is always the same information on half-new DNA molecules (1/2 parent strand, 1/2 daughter strand).
The polymerases also check for errors in the DNA and sort of proofread the nitrogen bases that they’ve already added. If the newly synthesized base does not match with the template’s original base, then the polymerase backtracks and replaces the incorrect base with the correct base. This reduces mistakes in replication (reduces mutations) at a rate of 1 mistake per 1 billion nucleotides.
Enzymes play a large role in breaking the hydrogen bonds to copy the DNA’s information and one the correct bases have been synthesized, create new hydrogen bonds to put the DNA molecules back together. As enzymes—in general—speed up multiple different processes in organisms, they also speed up the process of DNA replication, making eukaryotic replication an 8 hour process (for humans) when it could have taken almost a month to copy one DNA molecule.
04/11/2010 § 1 Comment
A molecule of life (DNA) has to have a few characteristics in order to sustain the organism that holds it. These characteristics include: stability, complexity (which means that DNA can code information), the abilities to self-duplicate, change, modify itself, and store a lot of information.
The structure of DNA was recorded and finalized years ago by James Watson and Francis Crick (who were two very different men, but had the same goal). They knew (from past research experiments and reports written by people like Alfred Hershey, Martha Chase and Oswalt Avery) that DNA is responsible for carrying the genetic information that codes for an organism. They then asked further questions like how is DNA structured, what does DNA look like, how does DNA code itself and how does DNA copy information?
DNA is made out of three important subunits. A DNA molecule is made of a phosphate group, a five-carbon sugar and a base. A sugar and a phosphate make a sugar-phosphate, but if a sugar and base combine, a nucleoside is made. When we add the last subunit, the phosphate group, to the nucleoside then we get a nucleotide. (The phosphate group, sugar and base combined.)
The phosphate group and sugars are simply structural subunits that primarily hold the strands of DNA together. They are like the side rails of the DNA ladder. (Because the structure of DNA is like a spiraling ladder.) The patterns of phosphate-sugar-phosphate-sugar and on and on make the long chains or links that make DNA molecules very long and are held by covalent bonds. The bases, on the other hand, are like the rungs of the ladder and are the structures that code for an organism’s genetic information. There are five types of bases, all of which appear in DNA with the exception of uracil. The main four (that are in DNA) are adenine, guanine, cytosine and thymine. Adenine and guanine are purines, which are double-ringed structures. Cytosine and thymine are pyrimidines, structures that are single-ringed. Bases on two DNA strands are held by hydrogen bonds, which enable the DNA molecule to be “unzipped” and the information copied when necessary. As mentioned just previously, DNA has bases A, G, C and T but not U. RNA, on the other hand, has A, G, C, but replaces T with U. These bases code for the information an organism needs to make the appropriate proteins.
Prior to the findings of Watson’s and Crick’s DNA-model, Ervin Chargaff had first discovered (but had not noticed its importance immediately) that in DNA, somehow, the amount of adenine would always equal the amount of thymine and the amount of cytosine would always equal the amount of guanine. This important rule (known as Chargaff’s Rule) applies to all organisms, not just humans and animals. Ultimately, in all types of DNA universally, adenine = thymine and cytosine = guanine. This is complementary base pairing, meaning that each DNA strand is complementary to each other and holds the same information.
Watson and Crick also used measurements from Rosalind Franklin’s and Maurice Wilkin’s X-Ray images. With the measurements (a .34nm distance between two nucleotides and a 3.4nm distance for one full turn of the helix), Watson and Crick concluded that there must be 10 nucleotides per helix turn. Fitting one purine (adenine or guanine) to its matching pyrimidine (thymine or cytosine), they were able to build their spiraling ladder.
In class, we also started to talk about how the bases (after RNA has copied the information), can tell ribosomes what proteins to make. Later, we should learn that the possibilities of bases in their positions all codes for types of amino acids that later make the proteins, which will lead us to understanding our essay question: How does information produce meaning?
03/11/2010 § 1 Comment
Last class, we started our new unit about what’s inside DNA and how it hold the information that makes a cell’s proteins and ultimately commands a cell to do this and that. Our essay question this unit sounds like a difficult one: How does information produce meaning? I think that scientifically, this question relates all the way to the core of the unit: DNA. I will have to learn primarily what’s inside DNA and then how that material makes information and later, how this information means something to the cell. This might mean that we could possibly learn about how exactly RNA retrieves information and decodes the genetic information to tell the ribosomes inside the rest of the cell.
On Monday’s class, we learned about Frederick Griffith’s experiments in the 1920s. He used bacteria that caused pneumonia for this experiment. He took two different samples (strains). One was an S-strain, meaning that this type of virus had a smooth edge and had a capsule. The second strain was R-strain, R standing for rough, representing the virus’ rough edge. This strain did not have a capsule.
When Griffith injected the S-strain into his subjects (mice), the mouse would die. But when he injected the R-strain into a mouse, it would be fine and would continue to live. So at first, Griffith must have known that his S-strain samples were virulent, meaning that they caused disease, while his R-strain samples were avirulent and didn’t cause disease. Now, when Griffith heated the smooth strain under fire and killed the bacteria, and when he tested the heat-killed strain on the mice, the bacteria proved to be avirulent. However, when he mixed the heat-killed S-strain (avirulent) and the R-strain (also avirulent), the result proved to be fatal and the mouse died. So typically, Griffiths wondered what caused the change and named this change transformation.
To find out, more experiments were made using lots of different enzymes that took away either proteins, carbohydrates, RNA and DNA. With every stage, one by one, the other factors were taken away and still the R-strain would change into S-strain. (The samples were still R-strain substances and S-strain substances.) When the DNA material was finally taken away, there was no transformation, therefore it became known that the genetic material was DNA.
So when we speed through time a little bit, up to 1952 (according to the textbook), Alfred Hersey and Martha Chase prove this by using a substance of radioactive sulfur to follow the path of a virus’s proteins and another substance of radioactive phosphorus to follow the path of the virus’s DNA. During the first run, when Hersey and Chase followed the path of radioactive sulfur (protein), they noticed that the new viruses that grew in the bacteria were normal viruses, meaning protein didn’t have any effect on the type of virus or its information. However, when Hersey and Chase found that the new viruses that grew inside the bacteria was radioactive because of the DNA.
These experiments basically proved that DNA is the genetic material in cells and organisms, and although it took a lot of time, DNA is what holds information for a cell.