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)

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.

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.

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.

Stained sample of Nitrosomonas (http://filebox.vt.edu/users/chagedor/biol_4684/Microbes/nitro.html)

Make a chart of the similarities and differences between cellular respiration and photosynthesis

Cellular Respiration	Photosynthesis
Equation- C6H12O6 + 6O2 ---> 6CO2 + 6H2O + Energy (ATP + Heat)	Equation- 6CO2 + 6H2O ---> C6H12O6 + 6O2
Goes through the processes of glycolysis, Krebs Cycle, and electron transport.	Goes through light dependent reactions and the Calvin Cycle. Broken into photosystems.
Catabolic pathway in which oxygen is consumed as a reactant along with organic fuel. Occurs in the mitochondria for eukaryotic cells.	Light energy is converted into chemical energy stored in organic molecules. Occurs in chloroplasts and photosystems.
Krebs Cycle involves decomposing the derivative of pyruvate to carbon dioxide. The end products include: 2 ATP, 8 NADH, and 2 FADH2.	The Calvin Cycle involves incorporating CO2 into existing organic compounds through carbon fixation, and these compounds are reduced to form carbohydrates. It uses ATP and NADPH to convert Co2 to sugar. It turns 3 times to fix 3 molecules of CO2 to produce one molecule of glyceraldhyde.
Net amount of ATP produced: 36 ATP Glycolysis- 2 ATP, Krebs Cycle- 2 ATP, ETC- 32 ATP, NADH- 2 ATP, FADH2- 2 ATP	3 types of plants that fix carbon: C3, C4, and CAM. Each has its own mechanism that helps conserv
The Electron Transport Chain (ETC) is a collection of molecules embedded in the inner membrane of the mitochondrion. The electron excorts link glycolysis and the Krebs Cycle for oxidative phosphorylation, which uses energy released by the ETC to power ATP synthesis.	Photosystems react to photons reaching the antennae and start the process of photosynthesis.

Explain the difference between C3, C4 and CAM plants in terms of their photosynthesis

The difference between C3, C4, amd CAM plants is their process of light and dark reactions. Each type of plant uses an alternative mechanism of carbon fixation that has evolved in hot, arid climates.

In C plants, carbon dioxide enters the Calvin cycle and the first product that results form carbon fixation is 3-phosphoglycerate. C3 plants close their stomata on hot, dry days to limit water loss. In doing this, the concentration of carbon dioxide in the leaf air space falls, which causes the Calvin cycle to slow down

Examples of C3 plants: (Rice, Wheat, Soybean)

C4 plants open their stomata during the day. In C4 plants, carbon dioxide is added to a 3-carbon compound, known as PEP, with the aid of PEP carboxylase, which has a high affinity for carbon dioxide. The resulting four-carbon compound is formed in the mesophyll cells of a leaf and is transported to the bundlesheath cells tightly packed around the veins inside of a leaf. This compound is then broken down to release the carbon dioxide, creating concentrations high enough that rubisco will accept the carbon dioxide and initiate the Calvin cycle.

CAM plants open their stomata during the night. They perform the reverse of regular plants for photosynthesis. The light reactions are performed during the night while the dark reactions are carried out during the day.

Comparison of C4 and CAM plants:

What I learned about macromolecules and how does the structure of a macromolecule affect its function?

The structure of a polymeric macromolecule consists of repeating units called monomers, the building blocks of a polymer, linked into a chain. The most important factors in the structure of macromolecules is the existence of functional groups. Functional groups are the components that are most commonly involved in chemical reactions. These functional groups can affect the bonds that hold a macromolecule together. For example, the glycosidic linkages that hold together cellulose and starch differ because of a slight difference in their ring structures. The ring form of glucose for starch is in an alpha configuration while cellulose is in a beta configuration. The differences in these two configurations is dependent on the attachment of a hydroxyl group either above of below the plane of the ring. As a result, cellulose and starch serve different purposes (cellulose is a major component of plant cell walls while starch serves as a storage polysaccharide of plants.

These functional groups also affect the polarity of the bonds. The existence of polar or nonpolar bonds ultimately affect a macromolecule's ability to interact with other substances. For example The nonpolar C-H bonds in the hydrocarbon chains of a fatty acid contributes toe the hydrophobic trait of fats. Due to this trait, fats separate from water.

The structure of a macromolecule is very complex. The example shown here is the structure of a protein. The numerous loops and twists contribute to the function of that unique protein. Denaturing a protein causes the twists and loops of the protein to unravel, thus affecting its ability to perform its function. The absence of these traits can basically render a protein useless.

Another example is DNA. Its unique double-helix structure is formed by 2 polynucleotides that spiral around each other around an imaginary axis. The pattern of nucleic acids maps out the process of forming certain proteins in an organism. A mutation in this structure can cause an organism to be incapable of producing an important protein.