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There are two categories of enzymes based on kinetic features, Michaelis Menten enzymes and allosteric enzymes. Michaelis Menten enzymes will display a hyperbolic curve when initial rate is plotted against the concentration of the substrate. They also have kinetic parameters that are often studied. The Km is the subtrate concentration when the rate is half the maximum rate. This value indicates how quickly an enzyme reaches max activity, and it can be considered a measure of affinity for a particular substrate. On the other hand, Kcat is the turnover number that tells how quickly an enzyme catalyzes a reaction after it bind substrates. It is determined in saturating conditions of an enzyme, and it is particular to specific substrates. The higher the Kcat, the faster the enzyme changes substrate to product once bound. These two value are then compared to determine the specificity constant, Kcat/Km. This is the measure of an enzyme's overall catalytic efficiency. It takes into account both subtrate binding and speed of product formation, so even if an enzyme's Kcat is low, if its Km is low, its catalytic efficiency can still be decent. These kinetic parameters provide information about an enzyme's function and can be used to compare various enzymes. 

Once genomic DNA is extracted, PCR can be performed to amplify a specific region of the DNA. PCR reactions can be set up by preparing a master mix of reactants to be added to the DNA. This master mix includes sterile water, polymerase buffer, a dNTP nucleotide mix, two primers for either end of the selected fragment, and Taq polymerase. The Taq polymerase is always added to the mix last and is treated with care to prevent denaturation of the protein. The master mix and DNA are then added to PCR tubes, which are small and typically only hold about 2 milliliters of liquid at maximum. The tubes are placed in a PCR machine that will cycle through a set protocol of specific temperatures at specific times. Different temperatures are required to repeatedly denature the double stranded DNA, anneal the primers to the DNA, and extend the DNA with the polymerase. Once PCR is complete, which usually takes 2-3 hours, the PCR products can be run on a gel to verify the fragment and separate the DNA from the contaminants in the PCR reaction. Agarose gel electrophoresis is completed, loading the gel wells with a DNA ladder and each sample mixed with loading dye. Once the gel has been run, the DNA can be visualized using UV light. There should be a distinct band that represents your DNA. 

The rate of a reaction is measured as the change in concentration of product(s) per unit time. For most biological mechanisms, product increases too slowly to be effective. Enzymes are needed, which speed up the reaction rate. In the presence of enzymes, the concentration of products increases fastest at the beginning and then decreases over time as substrates are used. The rate of the reaction eventually levels off and remains constant when the mechanism reaches an equilibrium. Kinetic experiments assess the initial velocity/rate of a reaction because this is when the concentration of subtrates is approximately constant, there are minimal product(s), and the enzyme-substrate complex is most rapidly formed. The initial velocity of a reaction can be found by determining the initial slope of a [products]/time graph. To analyze an enzyme's activity, the initial velocity at different subtrate concentrations is measured, keeping the amount of enzyme constant throughout. The initial velocities of these reactions are plotted against the concentration of subtrate. It can usually be seen that the change in initial velocity increases the fastest at the beginning and levels off as the concentration of subtrate increases. This is because when the concentration of subtrate reaches a certain concentration, the enzymes are saturated, and the reaction is going the fastest it can go. This is known as the maximum velocity. 

My friend is sitting across from me and is on her phone. Her thumbs move rapidly, jabbing the brightly lit screen. She has three sliver rings on her left hand on her thumb, index, and middle fingers. She has two rings on her right hand on her middle and ring fingers, one of which has a green stone in the center of it. She raises one hand to her face, resting it on her chin as her right hand continues to support her phone. Her right thumb slides upward on the screen repeatedly. After a while, she places her phone down and flips up the screen of her laptop, which has a marble cover on it. Her forearms rest on the wooden table as her fingers dart across the laptop keyboard. She is wearing a long-sleeve gray zip-up hoodie with a heathered gray tank top underneath. The majority of her long, wavy dark brown hair falls to the right side of her face, which is angled downward to face her laptop screen. Her eyes are pointed downward at the screen, and her eyelids are exposed. She has brown eyeshadow on her lids. Her mouth is agape slightly, her lips close to a centimeter apart. She looks up as someone walks through the front door of the cafe. Her eyebrows angle slightly upward, and her mouth changes to a grin as she waves at her friend who just entered. Within seconds, her eyes fall back to her laptop screen. Now both of her hands are placed on her lap, and she raises her right hand to her mouth. She bites the nail of her right index finger while she stares at the screen. She rests her right elbow on the table, her forearm overlapping her phone, which is face-up on the table surface. Her phone screen lights up suddenly, and she quickly picks up the phone with her right hand. She stares at the screen for a second and places the phone back down, moving her hand back on the laptop keyboard. She hits the space bar and lifts both her hands to her head. She combs her fingers through her hair as she straightens out her back and takes a deep breath. 

Symbiosis is often mistaken to mean a mutually beneficial relationship, but it is actually a general interaction between two organisms. Symbiosis includes  mutualism, along with commensalism and parasitism. Mutualism is an interaction in which both organisms benefit. An example of mutualism is oxpeckers and zebras. Oxpeckers perch on the backs of zebras and eat ticks off of them. The zebras benefit because they are rid of pests, and the oxpeckers benefit by eating. Commensalism is an interaction in which one organism benefits and the other is fairly unaffected. An example of commensalism is trees and lichens. Lichens grow on the trunks of trees, using them for support, while the trees are not affected. The trees are not benefited or hurt. On the other hand, parasitism is an interaction in which one organism is benefited and the other is harmed. Examples include all parasites and their hosts. Just one example is the common head lice and humans. Lice attach to people's heads and feed on human blood, harming them. 

The photographic differences between figures 1A and 2A and figures 1B and 2B are because the photos in figure 2 were taken at a further distance. This is because the location of the top of the steps were misinterpreted for photo A, and the distance at which photo B was taken was not specified in a detailed manner. The differences in tree exposure in figures 1C and 2C were also due to the photos in figure 2 being taken at a further distance. The description for where photo C was taken was relative to the distance at which photo B was taken, which was already taken further than in the original. The lichen in figure 2C was also not centered because that was not specified in the Methods, and the angle at which the photo was taken was also not discussed. The car in the background of figure 2C, which was not present in figure 1C, is because the tree is on a busy street with constantly changing conditions, and the blue tint in the photo was probably due to the sunlight being shaded at the moment the photo was taken.

Lastly, the difference in font for the boxed letters was because the Methods specified for the default font settings, which may be different on different computers. The instructions for the figure layout must have been relatively clearer than the instructions for the photography because the layouts between the figures were nearly identical.

There were some photographic differences between the two figures. Figure 2A showed more of the tree and foreground than shown in figure 1A. Figure 2B also showed more bark than in figure 1B, and the lichen in figure 1B occupied half of the photographed space, while the lichen in figure 2B occupied only one tenth of the space. Figure 2C also showed the full width and more length of the tree trunk compared to figure 1C. Additionally, in figure 1C the lichen is centered horizontally and vertically, while in figure 2C the lichen is located in the lower right region of the photograph. Figure 2C also has a red car in the background, along with an overall blue tint throughout the whole photo.

In terms of the figure layout, the dimensions and relative locations of the photos are identical. The white boxes in the upper left corners of each photo are also identical, except for a difference in font between the letters.

Exergonic reactions are spontaneous, while endergonic reactions are not; however, it is not the free energy change that determines the rate of a reaction. The rate of a reaction is determined by the activation energy, which is the energy needed to reach the transition state between reactants and products. Reactions with higher activation energies have slower rates because fewer molecules have enough energy to reach the transition state. When the activation energy is lower, more molecules can easily reach the transition state, accelerating the reaction. Enzymes speed up reactions by lowering activation energies. They do so by stabilizing the structure of the transition state, which then requires less energy to be reached. Enzymes do not affect the free energies of the substrates or products, and they do not alter the equilibrium of a reaction. They simply allow equilibrium to be reached faster. Enzymes can enhance the rate of a reaction in many ways: forming favorable interactions in its active site, orienting two substrates to react, directly participating in the reaction, or strain the substrate bonds. Enzymes usually use more than one of these strategies to stabilize the transition state, lower the activation energy, and speed up a mechanism.

The Methods Project has three goals: to practice writing the Methods section of a research paper, which is used by scientists to replicate the research described, to differentiate observations from inferences by writing the Results and Discussion sections, and to identify controls needed for an experiment. For my figure, I will depict the interspecific interaction between a tree and a lichen, an example of commensalism that is often overlooked in everyday life. The specific tree and lichen I will portray are on a busy street in Amherst Center, one that is walked past by students frequently.

In order to maintain strict consistency between the photos in both the original and replicated figures, I will have to set several controls described in the methods. I will control the time at which the photos are taken, in order to keep the lighting uniform, and the relative distance at which the photos are taken. I will also control the instructions for combining and labeling the photos to create the final multi-panel figure, specifying dimensions and coordinates.

Exergonic reactions are spontaneous, while endergonic reactions are not. However, it is not the free energy change that determines the rate of a reaction. The rate of a reaction is determined by the activation energy instead. An exergonic reaction can be slow, while an endergonic reaction is fast. The activation energy is the energy needed to reach the transition state between reactants and products, and all reactions require activation energy, even exergonic reactions. Reactions with smaller activation energies have faster rates than those with larger activation energies. With a high activation energy, fewer moleules have enough energy to reach the transition state, causing the reaction to proceed slower. When the activation energy is lower, more molecules can easily reach the transition state, accelerating the reaction. This is precisely how enzymes work to speed up a reaction: They lower the activation energy of the reaction. They do so by stabilizing the structure of the transition state, which then requires less energy to be reached. Enzymes do not affect the free energies of the substrates or products, and they do not alter the equilibrium of a reaction. They simply allow equilibrium to be reached quicker. Enzymes can enhance the rate of a reaction in many ways. They can form favorable interactions with the transition state in its active site. It can also orient two subtrates to react easier. An enzyme can also directly participate in the reaction, or it can strain the bonds in the reactant(s). Enzymes usually use more than one of these strategies to stabilize the transition state, lower the activation energy, and speed up a mechanism.