Comparing Bacteria, Virus, Prion, and Protist

Bacteria are living things that are neither plants nor animals, but belong to a group all by themselves. They are very small individually not more than one single cell, however there are normally millions of them together, for they can multiply really fast. A few beneficial functions of bacteria are the production of food products including dairy products, such as yogurt, sauerkraut, fermented meat products such as summer sausage, and vinegar. Bacteria also help fix nitrogen in the soil and are responsible for decomposing organic materials, which returns important nutrients back to the soil. The beneficial aspects of microorganisms far outweigh their harmful effects.

Viruses occupy a special taxonomic position. they are not plants, animals, or prokaryotic bacteria (single cell organisms without defined nuclei), and they are generally placed in their own kingdom. In fact, viruses should not even be considered organisms because they are not free living; for example, they cannot reproduce and carry on metabolic processes without a host cell.

A prion is a microscopic protein particle similar to a virus but lacking
nucleic acid, thought to be the infectious agent responsible for scrapie and certain other degenerative diseases of the nervous system. Prion illnesses affect the brain and cause extensive damage to brain tissue, causing it to become spongy in appearance. Though prion illnesses are not contagious in typical fashion, introduction of infectious prions into healthy brain tissue transmits the infection.

Protists are organisms in the kingdom Protista. These organisms are eukaryotes, meaning they are made up of single or multiple cells which all contain a nucleus enclosed by a membrane. The protists are a diverse group of eukaryotes that cannot be classified as animals, plants, or fungi. Organisms in the Protista kingdom include amoebae, red algae, dinoflagellates, diatoms, euglena and slime molds.



http://www.funsci.com/fun3_en/protists/introduction.htm
http://www.ucmp.berkeley.edu/bacteria/bacteria.html
http://www.bacteriamuseum.org/cms/Bacteria/what-are-bacteria.html
http://www.news-medical.net/health/What-is-a-Virus.aspx

Extreme Organism

Thermophiles are the heat loving bacteria found near hydrothermal vents and hot springs. Many thermophiles use dissolved sulfur or other elements as their energy source and iron as a means of respiration. It is generally considered as one that maintains life or activity at temperatures above 40 degrees Celsius. Thermophilic microorganisms are able to survive because of their ability to produce thermophilic enzymes. Some thermophilic enzymes have been discovered that can maintain at least half of their specific activities at temperatures as high as 80 degrees or even higher temperature. However, enzymes might partially denature at high temperatures but have adaptive systems that allow them to renature once removed from extreme conditions.

http://serc.carleton.edu/microbelife/extreme/extremeheat/

http://www.biology.ed.ac.uk/research/groups/jdeacon/microbes/thermo.htm

Bacterial Transformation

In transformation, DNA from the environment is absorbed into the bacterial cell. In transduction, a piece of DNA is transported into the cell by a virus. As a result of incorporating new genetic material, an organism can become resistant to antibiotics. Bacterial transformation is the process by which bacterial cells take up naked DNA molecules. If the foreign DNA has an origin of replication recognized by the host cell DNA polymerases, the bacteria will replicate the foreign DNA along with their own DNA. When transformation is coupled with antibiotic selection techniques, bacteria can be induced to uptake certain DNA molecules, and those bacteria can be selected for that incorporation. Bacteria which are able to uptake DNA are called competent and are made so by treatment with calcium chloride in the early log phase of growth. The bacterial cell membrane is permeable to chloride ions, but is non-permeable to calcium ions. As the chloride ions enter the cell, water molecules accompany the charged particle. This influx of water causes the cells to swell and is necessary for the uptake of DNA. The exact mechanism of this uptake is unknown. It is known, however, that the calcium chloride treatment be followed by heat. When E. coli are subjected to 42degC heat, a set of genes are expressed which aid the bacteria in surviving at such temperatures. This set of genes are called the heat shock genes. The heat shock step is necessary for the uptake of DNA. At temperatures above 42degC, the bacteria's ability to uptake DNA becomes reduced, and at extreme temperatures the bacteria will die.

http://faculty.plattsburgh.edu/donald.slish/Transformation.html

http://www.genome.ou.edu/protocol_book/protocol_adxF.html

Photos from Google images

Beneficial Bacteria

Lactobacilli bacteria is one of the most important types of friendly bacteria found in the digestive tract, making mainly the small intestine home. Lactobacillus acidophilus is a specially stabilized type of friendly bacteria that flourishes in the small intestine. One benefit of L. acidophilus is that it inhibits bacteria and microorganisms that produce disease in the urinary tract, especially Candida albicans. Another benefit is its ability to aid in developing natural defenses against foreign intestinal bacteria and viral infections, boosting the immune system. L. acidophilus has also shown promise in the battle against Helicobacter pyloriiv, the pathogen considered to be one of the top two causes for peptic ulcers.

Bifidobacteria bacteria is friendly bacteria, colonizing mainly the large intestine, or colon. Bifidobacteria are considered extremely important to the health of the gastrointestinal tract. Bifidobacterium bifidum is especially good at enhancing the body's immune response and inhibiting harmful enzymes. It encourages resistance to intestinal infections. It has resulted in synthesis of B-complex vitamins and absorption of calcium and also helps improve symptoms of diarrhea and constipation.

Bifidobacterium longum has a high affinity for intestinal colonization, improving the intestinal environment, which leads to better regularity. Bifidobacterium longum is a bacteria that normally inhabits a healthy bowel in most mammals, including humans. It can be found in fermented foods or taken in supplement form. These beneficial bacteria thrive on plant fiber and they may assist digestion, have a protective anti-cancer effect, reduce inflammation and lower cholesterol.

http://www.betterway2health.com/florafood.htm
http://www.buzzle.com/articles/beneficial-bacteria.html
http://www.probiotic.org/Bifidobacterium-Longum.htm

Virtual Diffusion

Villi % of Cell Surface Area: 50
Radius: 1x
Cell Shape: 10:1
# of Dimples: 40
Dimple % of Cell Surface Area: 1
Highest Rate of Diffusion: 4.64(r)

The smaller the surface area, the faster the diffusion rate is, but with a bigger surface area the rate of diffusion is much slower due to a bigger cell. As molecular size(radius) increases, diffusion rate decreases, vice versa. Villi increases the surface area on the intestine which helps in the increase absorption(rate of diffusion). Finally, a cell will have the highest rate of diffusion if it is in a cylindrical shape with many villi and dimples.

http://www.mhhe.com/biosci/genbio/biolink/j_explorations/ch02expl.htm
http://www.biologymad.com/cells/diffusion.htm

Cellular Respiration Vs. Photosynthesis

Photosynthesis is the conversion of light energy into chemical energy by living organisms. The raw materials are carbon dioxide and water; the energy source is sunlight; and the end-products are oxygen and (energy rich) carbohydrates, for example sucrose and starch. This process is arguably the most important biochemical pathway, since nearly all life depends on it. It is a complex process occurring in higher plants, phytoplankton, algae, as well as bacteria such as cyanobacteria. Photosynthetic organisms are also referred to as photoautotrophs.

Cellular respiration describes the metabolic reactions and processes that take place in a cell or across the cell membrane to obtain biochemical energy from fuel molecules and the release of the cells' waste products. Energy is released by the oxidation of fuel molecules and is stored as "high-energy" carriers. The reactions involved in respiration are catabolic reactions in metabolism. Plants use photosynthesis to create the energy they need out of water, nitrogen and CO2 (carbon dioxide) and produce the waste gas oxygen. Most animals use cellular respiration to take in oxygen, and through chemical processes create ATP, then exhaling waste CO2.

Both photosynthesis and cellular respiration transform energy. Photosynthesis transforms the energy of sunlight into glucose in two phases: the light reaction and the Calvin Cycle. In cellular respiration, glucose transforms into ATP for use by the cell in two phases: glycolysis and the oxidation of pyruvic acid. An exchange of gasses is an inherent part of photosynthesis and cellular respiration. During photosynthesis, plants use carbon dioxide from the air and release oxygen as a result of the reaction. Other organisms, including humans, use that oxygen to drive cellular respiration, which in turn uses oxygen in the reaction to break down glucose, releasing carbon dioxide as a byproduct. Electron transport chains and chemiosmosis play roles in the process by which ATP is synthesized during photosynthesis and cellular respiration. 
http://www.worsleyschool.net/science/files/photosynthesis/page.html

Differences between C3, C4 and CAM plants

C3, C4, and CAM plants all carry out the same photosynthetic functions. They all have light-dependent reactions and the Calvin-Benson cycle. The major difference in C4 and CAM plants is when and where the carbon fixation initially occurs. C3 plants carry out their light-dependent and Calvin-Benson reactions in the same place at the same time: in the mesophyll cells during the day. C4 plants carry out their light-dependent and Calvin-Benson reactions at the same time, but in different places: the light reactions take place in the mesophyll cells while carbon fixation occurs in the bundle sheath cells. CAM, like C3 plants, perform their light-dependent and Calvin-Benson reactions in the same place and at the same time, but they get their carbon from a store they build up overnight.
http://tables-evo-sci.blogspot.com/2007/11/comparison-of-c-3-c-4-cam-plants.html

Macromolecule Structures

I have learned that a monosaccharides is any of the class of sugars that cannot be hydrolyzed to give a simpler sugar. Glucose, for example, is a hexose (6 carbon atoms) of the aldose type. The most stable form of glucose is a 6 atom ring or pyranose (glucopyranose). Sucrose is formed by the linkage of glucose and fructose and is a type of disaccharides. Cellulose is formed by the linkage of D-glucose molecules through glycosidic beta(1-4) bonds and is an example of polysaccharide. Saturated fats only have single bonds between carbons and the formula is H-(CH2)n-COOH. Unsaturated fats have double bonds that force the chain to bend. For example, Oleic acid is an unsaturated fat with 18 carbon atoms and a double bond between carbons 9 and 10. Triacylglycerols (triglycerides) are the result of the linkage of a glycerol molecule with 3 fatty acid molecules, equal or different. For example, 1-palmityl-2-oleyl-3-stearylglycerol.

http://biomodel.uah.es/en/model3/index.htm

Biochemistry Wordle

Chemistry is mostly about electrons and chemical bonds. Valence electron is an electron in the outer shell of an atom (valence shell) which can combine with other atoms to form molecules. For example, the valence electrons of Magnesium is 3s electrons. Electrons, protons, and neutrons are the subatomic particles that are found in an element's atom and it tells us the characteristics of that particular element. For example, Oxygen has a mass number of 16 with atomic number 8 which means there are 8 electrons and 8 protons. The number of neutrons is always equal to the mass number- the atomic number. In this case it is 16 - 8=8. There are two types of chemical bonds: Covalent Bond and Ionic Bond. Covalent Bond is a chemical bond that involves sharing a pair of electrons between atoms in a molecule. An Ionic Bond is a chemical bond in which one atom loses an electron to form a positive ion and the other atom gains an electron to form a negative ion.
http://www.wordle.net/show/wrdl/4198085/Untitled

Ecology Wordle

Ecology is mostly about how the environment affects the behavior of organisms within the ecosystem. Two of the main Biomes are Aquatic Biomes and Terrestrial Biomes. Organisms communicate with the biotic and abiotic factors around them within the community of where they live in. The area where an organism live will affect their behavior, which is a form of learning from specific experiences and communication with other factors. Various types of learning include habituation and imprinting. Once organisms have been through experiences of learning, they will have an ability (cognition) to perceive, store, process, and use information gathered by their sensory receptors. In addition, migration takes place when organisms encounter climate changes or the limitation of resources.

http://www.wordle.net/show/wrdl/4071510/Untitled

Personal Wordle

http://www.wordle.net/show/wrdl/4071528/Untitled