Lab Assignment questions

Which are the major types of sections (major portions of the text) that the two primary source papers have in common? Note: the sections may not occur in the same order in both papers, but the nature of the content should be similar. (Lab 1)
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Which are the major types of sections (major portions of the text) that the two primary source papers have in common? Note: the sections may not occur in the same order in both papers, but the nature of the content should be similar. (Lab 1)
They both have the materials and methods in common in each paper. They also have results in common that is driven from their own knowledge.
How does one distinguish primary and secondary articles? (Lab 1)
One can distinguish a role of a primary source by where the author or source got the information from. It is a primary source if it's from the source directly and not based off of another source. Next, it will be considered a secondary source if the information is coming off of another source and is pulling information from different directions.
When plotting the absorbance of the glass cuvette with water (Figure 2-8) is there a clear difference across the spectrum, even though the glass and water might appear "colorless" to the unaided eye. (Lab 2)
Yes, there was a decrease which then increased and later decreased again within the wavelength.
Explain how it is that this same pattern is not evident in Figure 2-10, even though the measurements of the dye also included the glass and the water. (lab 2)
The absorbance levels of the dye are different from the water because absorbance is associated with the color of the solution. Blue dye will absorb wavelengths that correspond too blue, water will absorb different wavelengths compared to the dye.
During this lab you were asked to demonstrate proper pipetting technique. Discuss why it is important to use proper pipetting when performing scientific experiments, and describe one problem that can arise if proper pipetting technique isn't followed (include an example of a pipetting "don't" that can lead to this problem). (Lab 2)
It is important to use the proper pipette because each pipette is labeled at a certain number of milliliters it can hold up too. One problem that can arise when not using the correct pipetting technique is that air bubbles can get contracted in the pipette. For example, when drawing up liquid from a tube. Someone may insert their pipette within the tub but won't follow the liquid down when sucking up the liquid with the pipette. This causes the air bubbles.
Describe the characteristics of the histogram you plotted in lab. What does the distribution tell you about the size of cranberry beans? (Lab 2)
1. The graph tells me that 9 cranberry beans have the same seed mass of 0.37, which is the highest number of cranberry beans in one seed mass. Also, the highest number of cranberry beans collectively is between .37 and .41 on the graph.
If you need to pipette 620.0 uL, which pipette would you use, and what would the window read (use all 3 spaces in the window; i.e. 000)? (Lab 2)
1. You would use the P 1000 and the window would read 620 micro-liters.
Explain in your own words what a solution's pH is a measure is of; explain pH in terms of the relative abundance of particles in solution, noting which particles are of consequence, and how the values of the pH scale correspond to the terms "acidic" or "basic/alkaline". (Lab 3)
The pH measures how acidic or basic a solution is and it measures the H+ compound within the solution as well. For example, H+ is acidic and OH- is basic. While looking back at the pH scale, 1 through 6 is considered acidic. Then on the pH scale comes 7, which is the neutral level. After those, there is 8 through 14, which is considered basic.
a. Describe how the pH of the water was affected (describe the change in the estimated
pH values, if any). (Lab 3)
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Search for and describe three other molecules that work well as a buffer. For each molecule, describe how it associates with an acid or a base. (Lab 3)
One molecule that can act as a buffer is citric acid. This is associated with a natural occurrence but it is a weak acid. The next molecule is ammonia. Both ammonia ions and molecules creates a buffer. Lastly, sodium acetate is a buffer. Sodium acetate is made of salts and a weak acid.
Did you observe a difference in the capacity of the 2 solvents (water and oil) to dissolve the different solutes (sucrose and margarine)? Provide an explanation for your results based upon what you know about the structure and properties of the solvents and solutes. (lab 3)Margarine is non-polar, while water is polar, this resulted in the margarine not being able to dissolve. Sugar is a polar molecule, and oil is non-polar, so sugar was also unable to dissolve in the oil.a. Describe how the pH of the MSG solution was affected (describe the change in the estimated pH values, if any). (lab 3)The pH of the MSG changed slightly comparing to the water solution. The MSG is already had some acidic properties within it. My recordings measured the pH going from 6.0 to 5.0.Describe the results of the graph in a way that someone who had not conducted the experiment would understand the patterns shown. (Lab 4)This graph shows the protein concentration of the tissues of a plant. These samples include a leaf and root soluble and a leaf and root membrane. The leaf and root soluble have a higher protein concentration. On the other hand, the leaf and root membrane have the least protein concentration.Cells occur at a range of sizes, but the components of which they are composed (biological macromolecules and other materials) do not change sizes; rather the individual molecules will be of comparable sizes whether they occur in a tiny bacterial cell or a large eukaryotic cell. Explain how this observation establishes a "lower limit" for how small living things, as we recognized them, can be. (Lab 5)The lower limit for how small living things can be is about how small the surface area to volume ratio can be. For example, the cell can never be smaller than macromolecules and other materials. It needs this in order to survive, so the cell won't shrivel up and die.There is a limit to how much "stuff" can cross a unit area of membrane in a given time, explain how this might set an upper limit on how big a single cell can be. In composing your answer, describe the relation between cell size, cell volume, and cell membrane area (Lab 5).The relationship between cell size, cell volume, and cell membrane all adjusts accordingly. A cell knows how to maintain a surface area to volume ratio. As the cell gets larger, the surface area to volume ratio must maintain a steady range in order to survive. The surface area must grow less than its volume. Lastly, the upper limit is the cell's knowing how big it can grow to maintain a proper surface area to volume ratio.Describe in full sentences how you calculate the total magnification of a microscope. With which lens do you have the ability to change magnification? (Lab 5)The total magnification of a microscope can be calculated by taking the power of the objective and multiplying it by the power of the eyepiece. For example, 4x times 10x will equal 40x magnification. The objective lens gives the ability to change the magnification.Describe how a selectively permeable membrane is involved in osmosis. Include the role that the solute concentration plays in the direction of water movement. Now think about how this process may differ between plant and animal cells. For instance, how might cell walls disrupt the role of solute concentration and cause one to refute a hypothesis for the direction of water movement based on water concentration alone? (Lab 5)The selective permeable membrane is involved in osmosis and controls how much water comes in and out of the cell. Also, the selective permeable membrane doesn't allow charged ions to cross, only non-charged ions. Solute concentration plays a role in the direction of water movement by trying to reach equilibrium. For example, if a cell was dropped in a glass of saltwater, the water from the inside of the cell would expel itself towards the saltwater. Next, between the animal and plant cells the plant cell has a cell wall and has more protection from harsh solute environments. An animal cell will shrink and shrivel compared to a plant cell. This hypothesis can be refuted not based on the water concentration alone but on the cell wall and its environment.Describe at least two differences between animal and plant cells that you observed after examining each under a microscope. (Lab 5)One difference between animal and plant cells was that the plant cell consisted of a cell membrane and a cell wall. The second difference consists of the animal cell being much bigger (150 um) than the plant cell (30 um for the elodea and 100 um for the onion).In the citric acid cycle malate is converted into oxaloacetate. Write the chemical equation for this reaction clearly labeling which components are the substrates and products. Label the enzyme that catalyzes this reaction. Which functional groups on the substrate and product are important for this reaction to take place and why? (Lab 6.1)The substrates consist of NAD+ and malate. The products consist of OAA and NADH. Also, the important functional groups on the substrate and product is the hydroxyl and carbonyl functions. These two functions are important because they involve the reduction (additional enzymes) of a carbonyl carbon to a hydroxyl group. It helps convert oxaloacetate to malate. Lastly, the enzyme that catalyzes this reaction is NAD+ and NADH.Though the cell has hundreds of enzyme activities, we might be able to use this activity assay to measure MDH specifically. We should be able to do this even in the presence of all of the other enzymes that do other reactions. How is this possible? Recall why MDH is called MDH. What about the composition of this activity assay (i.e. our chemical equation model) allows us to measure only MDH activity? (Lab 6.1)Certain reaction components, such as NADH and OAA, are specific to the enzyme activity that is being called MDH. Multiple other enzymes don't use this combination of substrates that NADH and OAA do.When all of the reaction components are combined in the presence of the enzyme, what did you see happen (what was your direct observation)? (lab 6.1)Once the reaction components were combined in the presence of the enzyme, the absorbance levels started to decrease after each recorded time slot.What do you interpret this observation to mean in terms of what is happening to the measurable feature of the reaction? What is the component of the reaction that is measurable, and what is happening to its concentration in the cuvette as the reaction progresses? (Lab 6.1)Since the absorbance is due to the NADH concentration in the cuvette, the absorbance is taken as an indicator of the amount of NADH present. Next, we interpret this to explain that the concentration of NADH in the cuvette is decreasing.Our model of the overall reaction has five parts: OAA and NADH as substrates, malate and NAD+ as products, and the enzyme itself (we will ignore the proton because they are present in solution and we do not need to add them). Explain what happens each time the enzyme uses one molecule of NADH; what happens to each of the other components? (Lab 6.1)Once an enzyme uses one molecule of NADH every time, two electrons and one single proton is taken away from NADH. Then, this creates the production of malate and NAD+. Also, OAA in this process is being consumed. Being that NADH and OAA are the substrates, OAA then becomes malate. When more enzymes are added, the faster the process is and the faster the substrates are consumed.In lab 6-1 we observed that both NADH and OAA are needed for the conversion reaction to malate. We know this because we did not see a drop in NADH absorbance in the absence of OAA. If we use absorbance changes in NADH levels to monitor the reverse reaction (Malate and NAD+ to OAA), what would you expect to happen to absorbance of NADH and why? (lab 6.2)For the reverse reaction, we can expect the NADH absorbance measurements to increase. Since in the forward reaction, we know that MDH turns OAA into malate and converts NADH to NAD+. Reversing this around, NADH will be absorb and NAD+ won't.You have demonstrated that it is possible to observe the functioning of an enzyme under different conditions. Looking at the graphs of time vs. absorbance, explain how the appearance of the graph tells us whether the enzyme is functioning more quickly or more slowly, under different conditions. (lab 6.2)Looking at the graphs of time vs. absorbance, you can tell if the enzyme is functioning more quickly or slowly. If the absorbance value decreased as the time decreased, then the enzyme is functioning more slowly. On the other hand, if the absorbance value decreases at a faster rate than the time decreases, the enzyme is functioning at a faster rate.As we examine the rate of enzyme function in vitro (that is, in the test tube or cuvette) remember that the conditions for this measurement may differ significantly from the enzyme's native environment in the cell. Identify two ways in which the cell's composition and internal environment may differ from our experimental conditions, and how these might impact the function of the enzyme (hint: think about the name of our enzyme). (Lab 6.2)Enzymes are able to increase the reaction rate without being consumed by the reaction. One different way is through the body temperature. As the body temperature increases, so do the enzyme reactions. However, if the body temperature gets too high, the enzyme can stop working. Another way is enzymes are used to break down food. They speed up chemical reactions that turn into nutrients that the digestive system can absorb. Both of those examples are two ways the cell's composition and internal environment may differ from our experimental conditions.Suppose you are a pharmacologist (a pharmacologist is a scientist who discovers or creates new pharmaceuticals and studies their function and uses) developing a treatment for a disease that results from too much MDH activity. Taking a rational approach to designing a new drug, what kind of a structure might an effective drug have; what kind of a molecule might it resemble, and how would this have the effect of reducing MDH activity? (Lab 6.2)The conversion of malate to OAA is driven by an enzyme. Once this reaction occurs, the enzyme will turn into an enclosed substrate and will have very little solvent exposure. From there, the enzyme should go to the active site where it will be converted. Minimizing the activity of MDH can be done by using a version of malate. The catalytic triad will be changed so it can bind. This is a way the activity of MDH can be reduced.Describe the optimal environment for the reaction of oxaloacetate + NADH (plus enzyme MDH) to malate + NAD+. Your description must invoke the results of the experiments to support your answer. (lab 6.2)From our experiments, the optimal environment will consist of a pH of 9 and a higher concentration of enzymes. In table 6-2, it shows that the more alkaline the pH is, the higher the absorbance rate will be. Compared to the pH levels in table 6-2, it shows that the higher the pH level is, the higher the absorbance rate is.