lpotter's blog

We worked with a really cool bacteria in lab today called streptomyces it is in all of the soil. In fact the streptomyces is what gives the soil its characteristic smell. This earthy dirt smell is caused by geosmins that the streptomyces produce. These bacteria need oxygen to breathe and can use a lot of nutrients from the soil that they are in. One of the main reasons I chose to write about them is because of how cool they look when they are plated. They are white colonies that are sort of leathery. They stick to the agar and are almost impossible to get off, we have to restreak them which took a while. They sort of look dried out but they aren’t, the white part of the colonies are the spores that are produced by the streptomyces. When you restreak them the white usually rubs off of the colonies first, this is because you have only collected the spores. The streptomyces look kind of grey and drab, but this is the part that sticks to the agar so it is really hard to remove. I can’t wait to observe them under a microscope and see what they look like up close.

Again I am studying for a biochemistry test and as anyone reading this would notice the exam is this week and I am using my 30 minutes of daily writing to help me dive in to concepts with words rather than images or equations. There is many ways to express the activity of enzymes and one way is with the rules that Michaelis and Menten have laid out. They make three assumptions. The first being that there is no k-2. This means that any amount of enzyme product complex is negligible so it isn’t counted, it also means that free enzymes and products will never complete a reverse reaction to return to the enzyme substrate complex. The second assumption is that the concentration of the enzyme substrate complex remains constant when measuring the initial velocity. The third assumption is that Vmax can always be reached, this means that you can always react the most available enzymes with the most available substrates. Putting all of these assumptions together you can fully understand the equation. E+S<->ES<->E+P. E is enzyme, S is substrate, P is product, ES is enzyme substrate complex. You can go back and forth between the free enzymes and free substrates state and the enzyme substrate complex. The rate at which the enzyme substrate complex is formed remains constant. Once you pass the enzyme substrate complex to the free enzyme and product you can no longer return to the enzyme substrate complex. When graphed you can always relate the substrate concentration to the velocity. This is where you can derive the relation Km=[substrate] at ½ Vmax.

Enzymes are relatively complex. They can function in many different ways. There are many enzymes however they are almost all meant to interact with just one substrate. The main point to enzymes is that they lower activation energy of a reaction, whether or not that reaction is exergonic or endergonic. Enzymes only affect the free energy of the transition state, this means that enzymes only have the ability to lower the activation energy of a specific reaction in which they can bind to that substrate. Enzymes don’t affect the free energy of either the products or the reactants, this is what makes them so complicated. It only affects the energy it takes to get the reactants to the product stage. The start and end state of the reaction will always be the same regardless of an enzyme being present. Additionally enzymes don’t affect the concentration of products or reactants. What this means is that the concentration of products and reactants will always be the same no matter if there is an enzyme present in the reaction. What all of this information means is that enzymes can’t affect the favorability of a reaction, it can’t make it more or less favorable, it can only speed up the reaction in order to get all reactants to be products.

Thermodynamics is a complex topic. One way that equilibrium is noted is with the letter “k”. K is the equilibrium constant, this metric is used to show the concentration of products in relation to the concentration of reactants at equilibrium. If k=1 at equilibrium then the concentration of products equals that of the reactants. Equilibrium means that the forward and reverse reactions are occuring at the same rate, it does not necessarily mean that the concentration of the products and the concentration of reactants are equal to each other. When k is greater than 1 that means that the concentration of products is higher than the concentration of reactants at equilibrium. Additionally, this means that products are favored when at equilibrium, this favor is not referring to what direction the reaction will move rather just what side of the reaction has a higher concentration. In order to determine which way a reaction will move you will also need to consider the metric Q. This is a different topic that I will talk about later on however it is related because you need it to fully assess a thermodynamic reaction. When k is less than one the concentration of products is less than that of reactants at equilibrium, meaning that the reactants are favored at equilibrium. K is only used when discussing a reaction at equilibrium.

Metabolism is not as simple of a term as many people may think. Metabolism is essentially a complex energy pathway within the body. It works in a series of short contained reactions in order to efficiently capture and use energy. The small chemical reactions have low activation energies, since there are many small reactions in a pathway the energy can be captured and stored way more efficiently than if you had one large activation energy and completed the pathway in just one big chemical reaction. There are two main types of metabolism. Anabolism is the part of the metabolism that builds simple molecules into bigger complex molecules. This process requires the input of energy from the body. This energy input comes in the form of ATP. Anabolism is how things like proteins, nucleic acids, membranes, etc. are made. Another main component of metabolism is catabolism. This is the break down of big complex molecules into smaller more simple molecules. Catabolism breaks down things like sugars, lipids, proteins, etc. and in doing so creates ATP. This creation of ATP is the release of energy associated with catabolism. The main takeaway of metabolism is that it functions in such a way that all reactions have very small activation energies making the capture and release of energy way more efficient than completing the reaction in one big step.

An exergonic reaction is a reaction where there is a net negative change in free energy. This type of reaction is considered to be spontaneous, meaning that no energy has to be put into the system for a reaction to occur. This type of a reaction is favored because it releases energy that can be used by the cell. You can relate this concept to catabolism. Catabolic reactions start with reactants that have a high free energy and end with products that have a low free energy. Catabolism is the type of process in which ATP is generated. An endergonic reaction is a reaction in which there is a net positive change in free energy. This type of a reaction is not spontaneous and requires the input of energy to proceed. You can relate this concept to anabolism. Anabolism starts with reactants that have a low free energy and end with products that have a high free energy. This process take ATP to complete and for that reason is not favorable for the cell to carry out. A trick that I use to remember whether the reaction uses ATP is that anabolism and ATP both start with the letter A.

Vaccines work in a complex way. The human immune system is broken into two parts, the innate immune system and the adaptive immune system. The innate immune system is made up of components such as skin, mucus, and macrophages that engulf cells to destroy them. The innate immune system is something that all humans have. Vaccines work with the adaptive immune system. This part of the immune system can remember antigens by producing antibodies that bind to them. Vaccines expose the adaptive immune system to weakened or dead antigens. The adaptive immune system builds antibodies against the weakened or dead antigen so that when a live version of that antigen invades the body an immune response can be triggered immediately. Without the adaptive immune system the innate immune system would be overwhelmed and the host human would experience symptoms of disease.

Vaccines work in a very complex way. The human immune system is broken into two parts, the innate immune system and the adaptive immune system. The innate immune system is made up of components like skin, mucus, and macrophages that engulf cells to destroy them. The innate immune system is something that all humans have. Vaccines work with the adaptive immune system. This part of the immune system can remember antigens by producing antibodies that bind to them. Vaccines expose the adaptive immune system to weakened or dead antigens. The adaptive immune system builds antibodies against the weakened or dead antigen so that when a live version of that antigen invades the body an immune response can be triggered immediately. Without the adaptive immune system the innate immune system would be overwhelmed and the host human would experience symptoms of disease.

I work in a research lab on campus. We work with anaerobic bacteria, meaning that they don’t require oxygen to make energy, in fact that bacteria that we use in my lab will die in the presence of oxygen. When we make media to put the bacteria in we must gas out the media. We typically do it by using a blend of nitrogen and CO2. To seal the bottle containing the media we place an air tight cap on called a bung. The bung must be place on the jar while the cannula (which is putting gas in the media) is still in the bottle. This task is incredibly hard to do considering the fact the bottle opening is barely big enough for the bung itself. In putting the bungs on I tore all the skin off the top of my middle finger. The wound is still healing almost one week later. It has a gross yellow scab which has grown over the top of it. The scab has begun to split and a slight hint of fresh blood has been coming out for the last couple days. I really need more calluses to form and I need them to form fast because everytime I create an environment for these bacteria to live in I will have to do this process.  

This is the write up for my microbial growth experiment.

Expected Results:

To do a viable count a serial dilution was done using E. coli. The original broth containing E. coli was diluted 8 times. It was expected that as the broth was more diluted less cells would grow on each subsequent plate. To test cell density E. coli was inoculated in 4 tubes of TSB and kept at different temperatures, 27, 37, 45, and 55 degrees celsius. The most optimal temperature for E. coli growth was expected to be 37 degrees celsius, this is because E. coli are adapted to live within the digestive tracts of humans and humans maintain a constant body temperature of 37 degrees celsius. The way cell density was measured was with a spectrophotometer. It was expected that the E. coli being incubated at 37 degrees celsius would have the biggest change in cell density. Additionally it was expected that E. coli would have the lowest cell density at 55 degrees celsius, this is because it is too hot for the cells to live at this temperature.

Observed Results:

The10-1and 10-2dilution plates produced lawns and the colonies were too numerous to count (TNTC). The 10-3dilution plate had 62 colonies on it, giving a density of 6.2*105CFU/mL. The 10-4dilution plate had less than 30 colonies which is too few to count. The 10-5, 10-6, 10-7, and 10-8dilution plates had no colony growth. The cell density over time experiment yielded expected results. The E. coli had most increased cell density at 37 degrees celsius and the least increase in density at 55 degrees celsius. The k value (number of generations per time period) and g value (generation time) were calculated for E. coli at all 4 tested temperatures. At 27 degrees celsius the E. coli had a k value of 0.013 and a g value of 75. At 37 degrees celsius the E. coli had a k value of 0.02 and a g value of 48.825. At 45 degrees celsius the E. coli had a k value of 0.012 and a g value of 82.748. At 55 degrees celsius the E. coli had a k value of 0.001 and a g value of 763.85.