The Power Tool of the Future: Biofuels

     A basic overview of the process and understanding of biofuels: the Biofuel Enzyme kit measures the activity level and optimal condition cases of the enzyme cellobiase, which breaks down cellobiose, which is crucial to the process of making cellulosic ethanol. This cellulosic ethanol is an alternative replacement for petroleum.

     Enzymes, which speed up reaction rates of various processes, work again and again because they are not actually involved in the reaction. Long live the enzyme! In an enzyme catalyzed chemical reaction, the reactant is called the substrate. The substrate fits into the enzyme at the active site, which is a cleft in the protein and the substrate's chemical groups are attracted to the enzyme's amino acids facing the substrate. Different enzymes have different capabilities of maintaining their internal environment, even with changes in salinity, pH and temperature. Most enzymes have a decreased effectiveness when these are changed. Enzymes usually function best at moderate tempuratures (20-40 C). The concentration of enzymes present and the concentration of substrate present alters the reaction aswell. The more enzymes for that specific reaction, the faster it will take place. The more substrate, the increased amount of product production rises. Conditions to which enzymes preform under different reactions depends on the way they are found in nature. In other words, the behavior of enzymes in a reaction depends on what the enzyme is "used to", if you will, in nature. For example, the enzymes in a person's stomach work best under conditions with a significantly low pH.

     Cell walls in plant cells are very hard to break down. The enzyme callulase, breaks down cellulose like a chram. Cellulose is the main structural component in a plan'ts cell wall. Animals such as cows that eat grass, have to break down cellulose. They contain a bacterium know as Bacteroide Succinogene which digests the plants cows consume, and produces cellulase. Why is it important to break down the cellulose in plants? The breakdown of cellulose, which is catalyzed by cellulase, is converted to glucose, one of the main food molecules for a huge majority of different cells.

     How does glucose convert to a fuel, ethanol, that can power our present day automobiles? The process is quite simple. Cellulose (with cellulase to speed up the reaction) is made up of long strands of glucose, held together by cellobiose. The cellobiose is broken down by cellobiase, which then ultimately leaves single glucose molecules. The energy from the glucose molecules is used to make ethanol, or the alternate source of fuel. However, in the process, glucose is practically invisible, so glucose is mixed with P-Nitrophenol as the alternative substrate. Then, a stop solution (strong base) is added and this kills enzymes (such as cellobiase) and turns the p-nitro yellow, and the glucose is now visible.

     We are doing this lab because it is important in our world today to further study the possibilities of advancement of alternative biofuels. The biofuels will help replace depleting fossil fuels and other unreliable sources. My opinion is that more scientists from around the world should work together and compare results to create an effective method of producing the selective breed of biofuel that is more effective in production than the others.

     DNA, Deoxyribonucleic Acid is the hereditary material for life itself. It is unique in every single person, bacteria, plant, or other cell species. Who we are and why is the fundamental understanding of this nucleic acid. DNA nowadays can be used to help cure diseases, making better products to help people in all different areas from biological sources, and maybe one day to extend life itself. The DNA molecule is constructed of a sugar-phosphate backbone, with the four bases, Thymine with Adenine and Guanine with Cytosine. The sugar, Deoxyribose, and the Phosphates make the backbone strong. The shape of DNA is a double helix and the sides run in opposite directions (figured out by Francis Crick). The bases are organized to make messages that are delivered to cells called genes. These genes contain the information to make proteins, which lead to the body's structures and functions. DNA are arranged in chromosomes, or long strands of DNA tightly coiled around a protein. Chromosomes are split apart and copied in cell replication. All 46 chromosomes in the human body make up one's genome. Even though DNA contains the directions for protein synthesis, it does not carry it out. The templates for protein synthesis is mRNA, which carry the instruction to ribosomes, which manufacture the proteins. The ribosome decodes the information and links amino acids together in specific orders to make up the proteins.
     The purpose of the DNA necklace lab is to understand more about the structure and function of DNA, help explain its importance in life, understand the genetic combinations that could occur within our bodies, and how to extract DNA from cells using chemical reactions and certain steps.
     The purpose of the chemicals and their steps in our lab was to extract the DNA from their nuclei in cells. They broke down the plasma membranes, helped maintain pH, killing DNase, which is found "out in the world" beyond the cells that break down DNA. The use of the cold alcohol is to precipitate the DNA so we can put it in our necklaces, and so its visible. The use of the micropipette allows us to use precise measures when preforming our experiments.
    

Yogurt: Bacteria you can eat

       Microbial diseases have been on the minds of scientists for the past 200 years. Until Robert Koch, studying them has been but a mystery to the many scientists on their tail. Bacteria are probably the most abundant life forms on earth, and come in various sizes, shapes, characteristics and natures. Bacteria as pathogens can cause harmful and sometimes fatal sicknesses, such as scarlet fever, tuberculosis, and brucellosis, but many forms are extremely beneficial to health. Bacteria divide very rapidly and grow their colony size quickly to a visible level. The shapes of the colonies under a microscope can include circular, irregular, or branching. Using enzymes, or large proteins that quicken reactions by lowering activation energy, bacteria break down sugars chemically into other molecules. This process is called fermentation, and is their main food source. Specifically, Yogurt forming bacteria break down lactose to pyruvic acid, then to lactic acid , which lowers the pH of the milk. Lower pH levels allow the milk's proteins to curdle and become denaturized to give it the more solid texture we call yogurt. Like other beneficial Bacteria, yogurt helps break down organic waste material the body digests when it consumes food. Other types, like Intestinal bacteria, synthesize nutrients and break down indigestible material.Bacteria are very important in maintaining a healthy lifestyle, not that we can do anything about the billions that live within us.
       Specifically, yogurt is made by fermenting milk which contains specific strains of bacteria, all under controlled temperatures. The Bacteria feed on the natural milk sugars, passing on lactic acid as a waste product, lowering milk's pH levels. This increased acidity leads to entanglement, or denaturation, of milk's most common protein, casein. This gives yogurt its texture. In our lab, we will be using Koch's postulates to grow and test our yogurt bacteria, as well as ampicillin. Koch's postulates include first, describe the symptoms shown. Second, isolating the pathogen and establish a pure culture, then infect a healthy species to identify if the same symptoms occur. Finally, be sure that the pathogen is the same as the first.
       Our lab will be starting from Koch's third step, since we already know the bacteria causes yogurtness. This basic procedure will summarize how bacteria is used in some common foods we eat today. It will also explain the nature of  some common bacteria.

       My prediction is that, without any error or improper technique, the yogurt bacteria will create a well established yogurt texture in the milk. When working will E. coli, I will have to be very important in using sterile technique because it can be dangerous. I predict the nature of the E. coli will act much differently then the Yogurt bacteria visibly and what the actual bacteria consumes and produces.
       A summarization of the Procedure starts with explaining the key steps of the lab. After all of the test tubes were labeled, we have to make sure we not only stir well the different bacteria into the milk, but that we put the right bacteria into the right test tube. Proceeding the contamination of the bacteria to the milk, we have to place the test tubes into the incubator for  the correct environment for growth of the bacteria types.
       When we mixed the bacteria into the milk, there was no immediate effect, unlike a chemical reaction. As for the results the following day, here is the list. Test Tube 1, the positive control of just milk, smelled like sour milk, and had the same texture as before, liquid. Test Tube 2, the negative control or the yogurt in milk, transformed into a yogurt texture at the bottom half of the tube, and it smelled like regular milk. Test Tube 3, the yogurt + ampicillin, had the same results as Test Tube 1, same smell and texture. The E. Coli in Test Tube 4, had the same results, with a slight alteration in the smell. It didn't smell sour. As for color and pH, the milk, yogurt+ampicillin, and the E. Coli test tubes all were off-white with a pH of around 6-7. The yogurt had a more solid color and a lower pH of about 4.5.
       The reason the yogurt test tube was more solidified, and a more white color was because the bacteria of yogurt fed on the milk sugar, casein overnight and broke down the proteins, causing them to denature and spread apart (curdle). The ampicillin nuetrilized the yogurt bacteria, the E. coli bacteria has its own nature and doesn't feed on milk sugar, and the regular milk just maintained its color texture and pH. The reason the pH drops for the yogurt is because the bacteria can only properly ferment under those conditions, so the bacteria lower the level.
       The possible sources of error could have resulted from many things. These could include mixing the wrong bacteria into the right test tube, not labeling them in a color we would remember so we could find it in the incubator the following day, or mixing up the litmus paper when we took the pH's, which could have confused our results.