Chapter 1 of Genome looks into the "word" that builds up the world. Ridley points out that many would mistaken DNA as this word when in reality, the word is RNA. He describes RNA as a kind of bridge between DNA and proteins worlds. Its presence is extremely necessary in the most primitive and basic functions of a cell, acting as catalyst or replication device. Another important topic brought up in the chapter was the discussion on LUCA, the Last Universal Common Ancestor. LUCA is first described as an organism that looked like a bacterium that lived in a warm pond, possibly near a hot spring. However, it is later revealed that LUCA was most likely a protozoan.
The reason I believe this chapter is titled "Life" is that it still amazes us how our lives are basically determined by genetic code. Our lives literally hang by a thread of four letters put into specific sequences that map out our appearance and ability to carry out vital processes.
Sunday, February 12, 2012
Tuesday, February 7, 2012
Double Fertilization
Double fertilization is an essential characteristic in the sexual reproduction of angiosperms. In sexual reproduction, a haploid sperm cell fuses with a haploid egg cell, forming a diploid zygote that soon develops into an embryo. Following this fertilization process is a second event that involves another sperm cell and a second cell found in the female's reproductive tissue creating a triploid cell as a product. This product develops into what would be the embryo's food supply. Without double fertilization, angiosperms would be incapable of successfully reproducing due to an inability to fertilize and a lack of resources for the embryo.
Fertilization starts between sperm cells, which are transferred through pollen grains produced in the anthers, and two cells within an ovule, the reproductive organ of the female. The reproductive cell found in the ovule is a diploid (2n) megaspore mother cell, which eventually undergoes meiosis to produce four haploid (n) megaspores. Only one of the four megaspores remain in most species while the other three degenerate. The surviving megaspore goes through three rounds of mitosis to form eight haploid nuclei that share the same cytoplasm, forming the embryo sac. Cell walls form between the nuclei to form three antipodal cells opposite the micropyle and near the micropyle; the ones near the micropyle are distinguished as two synergids and an egg. The two remaining nuclei, called polar nuclei, remain together in a single large central cell.
Before the two polar nuclei can take place in double fertilization, the sperm must travel within the female's reproductive organs to the cells. A pollen grain lands on the stigma and begins to germinate, sending a long pollen tube through the style and ovary. The generative cell, a haploid, travels down the pollen tube behind the tube nucleus and divides by mitosis to form two haploid sperm cells.
After the pollen tube reaches the micropyle and makes its way into one of the synergids, the sperms cells are released, which degenerates the synergid and sends one of the two sperm cells to fertilize the egg cell. The second sperm cell fuses with both of the polar nuclei, forming a triploid cell. This cell develops into the endosperm and serves as the embryo's food supply as the zygote develops into an embryo.
Fertilization starts between sperm cells, which are transferred through pollen grains produced in the anthers, and two cells within an ovule, the reproductive organ of the female. The reproductive cell found in the ovule is a diploid (2n) megaspore mother cell, which eventually undergoes meiosis to produce four haploid (n) megaspores. Only one of the four megaspores remain in most species while the other three degenerate. The surviving megaspore goes through three rounds of mitosis to form eight haploid nuclei that share the same cytoplasm, forming the embryo sac. Cell walls form between the nuclei to form three antipodal cells opposite the micropyle and near the micropyle; the ones near the micropyle are distinguished as two synergids and an egg. The two remaining nuclei, called polar nuclei, remain together in a single large central cell.
Before the two polar nuclei can take place in double fertilization, the sperm must travel within the female's reproductive organs to the cells. A pollen grain lands on the stigma and begins to germinate, sending a long pollen tube through the style and ovary. The generative cell, a haploid, travels down the pollen tube behind the tube nucleus and divides by mitosis to form two haploid sperm cells.
After the pollen tube reaches the micropyle and makes its way into one of the synergids, the sperms cells are released, which degenerates the synergid and sends one of the two sperm cells to fertilize the egg cell. The second sperm cell fuses with both of the polar nuclei, forming a triploid cell. This cell develops into the endosperm and serves as the embryo's food supply as the zygote develops into an embryo.
Sunday, February 5, 2012
Genome Chapter 4- Fate
This chapter of Genome focused on chromosome 4. Chromosome 4 is linked to degenerative diseases such as Wolf-Hirschhorn syndrome and the notorious Huntington's disease. Both of these diseases are caused by a gene that contains the repetition of the "word" CAG (glutamine). The chapter focuses mainly around Huntington's disease, which is caused by a mutation of the previously mentioned gene. Usually the longer the repetition, the more prone you are to the disease. The Huntington gene was actually located quite recently by a woman named Nancy Wexler. Finding the gene was compared to "looking for a needle in a haystack the size of America" but Wexler pushed herself to locate that needle.
Going back to the disease itself, Huntington's disease is known to strike at earlier ages in people with longer repetitions of glutamine. The disease is extremely destructive, causing a loss of muscle control and, inevitably, control of your mind. Symptoms as usually not apparent until it is too late. The inevitable result: Death. No case of Huntington's has been cured at the moment.
The chapter is titled "Fate" for a very obvious reason. It is constantly repeated that no one can escape their fate even if what will happen is known. The Greek allusion to Tiresias, the blind seer, caught my attention. The allusion spoke the fact that knowing the future (or fate) is truly not a gift since nothing can be done to change it. In this case, a person who has Huntington's disease knows that he/she has the inescapable fate of a slow but premature death, whether it be by their own hand or by the disease itself.
The chapter is titled "Fate" for a very obvious reason. It is constantly repeated that no one can escape their fate even if what will happen is known. The Greek allusion to Tiresias, the blind seer, caught my attention. The allusion spoke the fact that knowing the future (or fate) is truly not a gift since nothing can be done to change it. In this case, a person who has Huntington's disease knows that he/she has the inescapable fate of a slow but premature death, whether it be by their own hand or by the disease itself.
Thursday, January 12, 2012
Extreme Organism: Acetobacter aceti (Acidophile)
An acidophilic organism can thrive in environments of extremely low pH (usually of a pH of 2.0 or below). These organisms have evolved highly efficient mechanisms to help pump protons out of the intracellular space in order to maintain a pH that is near or at neutral pH. This mechanism is what allows acidophilic organisms to tolerate being in such highly acidic conditions. Additionally, the intracellular proteins are not required to develop acid stability due to this evolved mechanism.
Acidophiles can be found in conditions of acidic pH. Pictured here is an acidic mud pot in Yellowstone Park, which contains the acidophile Sulfolobus acidocaldarius. Found on http://www.daviddarling.info/encyclopedia/A/acidophile.html
Acetobacter aceti is an example of an acidophile that has proteins that have been forced to develop acid stability. This organism has an acidified cytoplasm which forces the proteins to evolve this way. Acetobacter species have the ability to convert ethanol to acetic acid in the presence of oxygen. It's commercial uses can vary. Acetobacter species are known to be used in the production of vinegar, during which ethanol is intentionally converted into acetic acid in wine, and the maturation of certain beers, during which they are intentionally used to acidify beer. However, acetobacter have the potential to destroy wine they infect by producing an overabundance of acetic acid or ethyl acetate, both of which can cause the wine to be unpalatable.
Acetobacter used to produce vinegar and the acid in beer. Found on http://indokombucha.wordpress.com/2009/12/29/scoby/
Sources:
http://en.wikipedia.org/wiki/Acetobacter
http://microbewiki.kenyon.edu/index.php/Acetobacter
http://library.thinkquest.org/CR0212089/acid.htm
http://en.wikipedia.org/wiki/Acidophile_(organisms)
Acidophiles can be found in conditions of acidic pH. Pictured here is an acidic mud pot in Yellowstone Park, which contains the acidophile Sulfolobus acidocaldarius. Found on http://www.daviddarling.info/encyclopedia/A/acidophile.html
Acetobacter aceti is an example of an acidophile that has proteins that have been forced to develop acid stability. This organism has an acidified cytoplasm which forces the proteins to evolve this way. Acetobacter species have the ability to convert ethanol to acetic acid in the presence of oxygen. It's commercial uses can vary. Acetobacter species are known to be used in the production of vinegar, during which ethanol is intentionally converted into acetic acid in wine, and the maturation of certain beers, during which they are intentionally used to acidify beer. However, acetobacter have the potential to destroy wine they infect by producing an overabundance of acetic acid or ethyl acetate, both of which can cause the wine to be unpalatable.
Acetobacter used to produce vinegar and the acid in beer. Found on http://indokombucha.wordpress.com/2009/12/29/scoby/
Sources:
http://en.wikipedia.org/wiki/Acetobacter
http://microbewiki.kenyon.edu/index.php/Acetobacter
http://library.thinkquest.org/CR0212089/acid.htm
http://en.wikipedia.org/wiki/Acidophile_(organisms)
Saturday, January 7, 2012
Cell Metabolism Wordle
http://www.wordle.net/show/wrdl/4642806/Cell_Metabolism
The key terms I chose in this wordle were terms that I found to break down the basic concept of metabolism. Metabolism can follow one of two pathways: catabolic, which involves the release of energy by breaking down complex molecules to simple compounds, and anabolic, in which energy is consumed to build complicated molecules from simpler ones. Energy is a very important term due to the fact that all metabolic processes depend on energy. Energy comes in different forms: kinetic energy, which is the energy of motion; potential energy, which is the stored energy matter possesses because of its location or structure; and chemical energy, which is a form of potential energy stored in molecules as a result of the arrangement of atoms in those molecules. Energy can also be described in terms of free energy, which is the portion of a system's energy that can perform work when there is a uniform temperature in the system, or activation energy, which is the energy required to start a reaction.
The laws of thermodynamics explains the limits of energy transformation. The first law of thermodynamics explains that energy is constant and cannot be created or destroyed. The second law of thermodynamics every energy transfer or transformation increases the entropy, a measure of disorder or randomness, of the universe. Chemical reactions can either be endergonic or exergonic. In an endergonic reaction, free energy is absorbed from the surrounding environment. In contrast, an exergonic reaction involves a net release of free energy.
Another important factor in metabolic processes is the use of a catalyst or enzyme. Catalysts are chemical agents that changes the rate of a reaction without being used up in the process. Catalysts help lower the amount of activation energy needed to start a reaction. Enzymes are a type of catalytic protein. They function in a similar manner to that of a key and a lock; the enzyme binds to its substrate in a region known as the active site, which is typically a pocket or groove on the surface of the protein. The fit must be compatible in order for the reaction to be carried out. The enzyme can manipulate its shape so that the active site fits around the substrate. This is known as an induced fit.
The key terms I chose in this wordle were terms that I found to break down the basic concept of metabolism. Metabolism can follow one of two pathways: catabolic, which involves the release of energy by breaking down complex molecules to simple compounds, and anabolic, in which energy is consumed to build complicated molecules from simpler ones. Energy is a very important term due to the fact that all metabolic processes depend on energy. Energy comes in different forms: kinetic energy, which is the energy of motion; potential energy, which is the stored energy matter possesses because of its location or structure; and chemical energy, which is a form of potential energy stored in molecules as a result of the arrangement of atoms in those molecules. Energy can also be described in terms of free energy, which is the portion of a system's energy that can perform work when there is a uniform temperature in the system, or activation energy, which is the energy required to start a reaction.
The laws of thermodynamics explains the limits of energy transformation. The first law of thermodynamics explains that energy is constant and cannot be created or destroyed. The second law of thermodynamics every energy transfer or transformation increases the entropy, a measure of disorder or randomness, of the universe. Chemical reactions can either be endergonic or exergonic. In an endergonic reaction, free energy is absorbed from the surrounding environment. In contrast, an exergonic reaction involves a net release of free energy.
Another important factor in metabolic processes is the use of a catalyst or enzyme. Catalysts are chemical agents that changes the rate of a reaction without being used up in the process. Catalysts help lower the amount of activation energy needed to start a reaction. Enzymes are a type of catalytic protein. They function in a similar manner to that of a key and a lock; the enzyme binds to its substrate in a region known as the active site, which is typically a pocket or groove on the surface of the protein. The fit must be compatible in order for the reaction to be carried out. The enzyme can manipulate its shape so that the active site fits around the substrate. This is known as an induced fit.
Sunday, December 18, 2011
Bacterial Transformation (Helped by Michelle Tan)
During the process of transformation, bacteria are "transformed" when they take up DNA from a different strain. As demonstrated in the slide show, the bacteria were transformed into virulence when taking DNA from a virulent strain. This was accomplished through a process known as heat shock since natural transformation is rare occurrence. Lowering the temperature congeals the lipid membrane and stabilizes the negatively charged phosphates found on the lipids and in the DNA plasmid. The temperature imbalance created by the process of heat shock creates an "ionic shield" that allows the plasmid DNA to pass through the adhesion zone in the plasma membrane. In other words, this technique induces the bacteria to take in plasmid DNA and transform by integrating this DNA into their own. The resulting transformed bacteria contained both tetracyline and kanamycin genes (both are antibiotics) and could thrive in the presence of antibiotics.
Thursday, December 8, 2011
3 Beneficial Bacteria (Helped by Michelle Tan)
Lactobacillus
Lactobacillus is a bacterium that can digest lactose. It converts lactose and other sugars into lactic acid. Many studies have shown that lactic acid bacteria have the ability to inhibit the growth of Helicobacter pylori, a pathogen that can cause Type B gastritis, peptic ulcers, and gastric cancer. Lactobacillus has also proven to treat and prevent diarrhea in children. Other potential benefits of this bacterium is the prevention of colon cancer, lowering cholesterol and blood pressure, and inflammation reduction.
View of Lactobacillus bulgaricus (http://microbewiki.kenyon.edu/index.php/Lactobacillus)
Escherichia Coli
Normally found in the lower intestine of warm-blooded animals, e. coli is known to benefit their hosts by producing vitamin K2 and preventing the establishment of pathogenic bacteria in the intestine. E. Coli strains are relatively harmless but there are some forms that can cause food poisoning in humans. This bacterium is also used in drugs produced to treat and cure illnesses. These drugs include synthetic insulin or antibiotics.
E. Coli Specimen (http://www.freedrinkingwater.com/water-contamination/ecoli-bacteria-removal-water.htm)
Nitrosomonas
Nitrosomonas is an obligate chemolithotrophic bacterium. It is normally found in areas of sewage, soil, fresh water, and marine ecosystems. It functions as a nitrifying bacterium that oxidizes ammonia into nitrate. Nitrosomonas are very useful in the treatment of industrial and sewage waste with the process of bioremediation. Their absence can cause a huge disruption in the nitrogen cycle and the process of carbon fixation.
Lactobacillus is a bacterium that can digest lactose. It converts lactose and other sugars into lactic acid. Many studies have shown that lactic acid bacteria have the ability to inhibit the growth of Helicobacter pylori, a pathogen that can cause Type B gastritis, peptic ulcers, and gastric cancer. Lactobacillus has also proven to treat and prevent diarrhea in children. Other potential benefits of this bacterium is the prevention of colon cancer, lowering cholesterol and blood pressure, and inflammation reduction.
View of Lactobacillus bulgaricus (http://microbewiki.kenyon.edu/index.php/Lactobacillus)
Escherichia Coli
Normally found in the lower intestine of warm-blooded animals, e. coli is known to benefit their hosts by producing vitamin K2 and preventing the establishment of pathogenic bacteria in the intestine. E. Coli strains are relatively harmless but there are some forms that can cause food poisoning in humans. This bacterium is also used in drugs produced to treat and cure illnesses. These drugs include synthetic insulin or antibiotics.
E. Coli Specimen (http://www.freedrinkingwater.com/water-contamination/ecoli-bacteria-removal-water.htm)
Nitrosomonas
Nitrosomonas is an obligate chemolithotrophic bacterium. It is normally found in areas of sewage, soil, fresh water, and marine ecosystems. It functions as a nitrifying bacterium that oxidizes ammonia into nitrate. Nitrosomonas are very useful in the treatment of industrial and sewage waste with the process of bioremediation. Their absence can cause a huge disruption in the nitrogen cycle and the process of carbon fixation.
Stained sample of Nitrosomonas (http://filebox.vt.edu/users/chagedor/biol_4684/Microbes/nitro.html)
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