Tuesday, May 27, 2014

DISSECTION INTRODUCTION LAB

 DISSECTION LAB 

Purpose: The whole purpose and why we are doing this lab in the first place was to learn about the anatomy of different specimens. In this lab what concepts that were being tested i would assume was the idea of different specimens have different inner and outer parts that make them all different. For independent and dependent variables there were the specific inner organs that were outlined in guilds to find. Other than that there wasn't anything that we had to measure but more of the point of this lab was to observe the dissection process and demonstrate understanding.


Intro: In this lab we had to choose 4 out of the 6 specimens given to us to dissect and learn about the inner and outer parts and its functions. The specimens that we had to choose were the frog, starfish, clam, and perch which is a type of fish for people that don't know. In each specimen shown in this blog we will discuss the procedures we did and then explain the importance of body parts inside and outside of the specimen. Furthermore there will be videos and pictures of each specimen that will help walk through anyone that needs help with dissection of these certain specimens. Having said all of this let us begin with the frog which was the first specimen we dissected.

Methods: Our methods will be put into videos of breaking down the whole dissection. 

Frog (Chau):
Internal parts taken out 
Internal 
First opening showing liver


part of the frogs mouth



https://www.youtube.com/watch?v=GYYIzMHzZrQ

Video Link to frog dissection



_____________________________________________

Starfish (Gunnar):
 
External Anatomy:





External anatomy (parts with definitions):


Dorsal/aboral fin: Primary arm.

Arms: Used for general movement.

Central disc: Activity center of the starfish. Contains the mouth.

Spines: Some used to absorb oxygen. Others are used to clean the surface of the skin.


Eyespots: Used to detect light and its general direction so they have some idea of where they are going.


Mouth: Used for eating.

Soft tube feet: Used for specific movement.

Ambulacral groove: Houses/Protects the soft tube feet



Internal anatomy:







Internal anatomy (parts with definitions):


Pyloric caeca: Long digestive glands that make enzymes to digest food in the stomach.

Gonads: Used for reproduction

Ring Canal: A circular canal in which filtered water enters through the madreporite and branches out into the radiated canals.

Lateral canal: Holds the soft tube feet in place.

Ossicles: Skeletal plates for protection.

Madreporite: Allows water to enter into the water vascular system




Incision Guide (for dissection):
(Some incisions are lined in blue and may be hard to see)






Starfish Dissection Video:





Video Link:

https://www.youtube.com/watch?v=I6i1QXllUTg




_________________________________________________________________________ 
Clam (Luke):

External/Internal Diagram:




External Parts:

Dorsal Side: Back side. Contains Umbo and Hinge Ligament
      Umbo: Oldest part of the clam
      Hinge Ligament: Holds clam together

Ventral Side: Front/ Mouth of the clam

Siphon: Brings in water/food

Anterior/Posterior Sides: Right and left sides of the clam, respectively



Internal Parts:

Adductors: Hold Clam open/ Close Clam

Gill: Allows Clam access to oxygen for respiration

Foot: Muscle that the clam uses to move around and burrow





More Internal Parts:



Mantle: Soft tissue coating the inside of clam

Esophagus: Moves food to stomach

Stomach: Digests and breaks down food

Reproductive Gland: Clam uses this to produce offspring






INCISION/DISSECTION GUIDE:

In order to cut open the Clam, just cut the adductors on both sides. Marked below.



VIDEO LINK:




https://www.youtube.com/watch?v=-9dCrHeczNU










__________________________________________________________
Perch (Derek)



Incision Guide Reference

   External Anatomy

   Internal Anatomy







___________________________________________________________________________________

Conclusion: Overall the lab was engaging as we got to experiment then actually apply our knowledge in teaching others about our dissections of different specimen. Each one of us had the chance to dissect and were fascinated at the type of organs and parts of each specimen compared to another. 







Thursday, March 6, 2014

PGLO TRANSFORMATION LAB

Purpose:The purpose of the lab was to show the process of transformation. With that concepts we were testing was the the effects of ampicillian and the sugar arabinose had on the growth of the cells. The relationship between the dependent variables was that we measuring the growth of cells would differ depending which plates had the ampicillian which the pglo was resistant to. For the independent variable we had our control group as the plate with just broth and no ampicillian and the others will be the ones with the varied results. What were trying to find out the success of transforming the gene into the organism E-coli given the variables.

Introduction: The lab will be conducting a process which is known as genetic transformation caused by genes. Gene transformation will is basically inserting a trait from an organism to another. The trait that will be expressed is GFP (Green Fluorescent Protein). If the transformation is successful then the organism which is E-coli in this case will glow under ultraviolet light. For the gene to go off, the sugar arabinose is added to the cell. Cells that have transformed will grow on the plates that have lb/amp because the pglo is resistant to the antibiotic ampicillin.


Methods: During the lab, our group would carefully read out the measurements just in case to confirm, what we were doing was correct with the other lab partners.. We made sure that we recognized each plate and continued accordingly. In between tasks if we had the opportunity, we would answer the questions pertaining to the lab. It was easy to answer them because it was either still fresh in our minds or predictions about the lab. Of course we couldn't answer the end questions because we had to wait 24 hours to answer those. At the end to make sure that we were successful we went over the plates until it was covered in transformation. Overall the lab procedure was clear and simple and we adjusted to what was more convenient for us and that was to organize and break up the lab equally to be more efficient.

Data:


Graphs and Charts: (see above)

Discussion: The normal e. coli culture with no pGLO introduced had high e. coli growth on it, as would be expected; additionally, the normal culture that had been inteoduced to ampicillin had no growth due to ampicillin's role in stopping bacterial growth. These two are the control plates, so it's to be expected that they behaved the way they normally would. The transformation plates contained the most important data. With the pGLO introduced, its natural resistance to ampicillin was present, so those colonies of e. coli which were transformed by the pGLO managed to survive even with ampicillin present, resulting in a few surviving colonies. In the final culture, arabinose was added to the culture, and because arabinose stimulates the GFP to cause phosphorescence, the colonies found in that culture did glow under ultraviolet light.

Conclusion: There wasn't really a definite answer to the lab however, it was a success in having E-coli taking on the gene that made it glow green under fluorescent light. What went wrong during the lab was the outcome or in the lab stated as the efficiency of the about of cells that actually took on the trait. We had a very low outcome in the end but was successful.

References: The lab itself


Friday, December 20, 2013

Cell Communication Lab $

Purpose: The purpose of this experiment was to test the % of cells produced with an a-type, α-type, and a mixed culture. The whole concept of the lab was all about cell communication and for this lab it was the mating of yeast cells. The independent variable was the time intervals, and the dependent variable was the types of cells we measured. These cells include single/double haploid, Shmoos, single/double zygotes, and Asci.

Introduction: As explained in the purpose the concept of the lab is cell communication. So for the yeast there were two mating types a, and α and both of these create signaling molecules that bind to the opposite type of cell. The received signal is converted to a specific mating response which in this lab it is mating and the series of steps is called the signal transduction pathway. The three steps of cell signaling is reception, transduction, and response. Starting out with the first step is reception
Is basically just the detection of the signaling molecules. Once the signaling molecule is detected is binded to a receptor protein. This sets up for the last step which is the cellular response. It could be the arrangement of the cytoskeleton or genes being created in the nucleus. For the yeast the cell response was the production of more cells through mating.

Methods: In the lab we observed α-type and a-type yeast cultures, through a microscope, and how they interacted with each other after 24 hours, 24 hours + 30 minutes, and 48 hours. In a class where teamwork and efficiency is required for success, we devised a system to complete this lab with minimal problems and delays. We had two group members view the cultures that were dropped using a dropper on a slide and then covered with a cover slip. Those two members would relay how many specimen they counted, whether it was the single and budding haplodes, shmoo, single/budding zygotes, and asci, to the third group member who would record the information for later analyses (this lab). The forth group member would take the already observed slides with yeast, bring them to the 50% bleach and 50% water bucket, sanitize the slide and slide cover by soaking them in the bucket, and bring them back to the lab group so they could be used to analyze more yeast cultures. That process was repeated multiple times over multiple days.     

Data:
(Data observed from alpha-type yeast, on the left, and a-type yeast, on the right.)
(Time 1 is at 24 hours, Time 2 is 24 hours and 30 minues, and Time 3 is 48 hours.)
Graphs and Charts:



Discussion: The data we collected from our “a” and “alpha” samples showed a slight increase in single haploid and budding haploid populations, respectively. Though this was recorded this could be due to a number of reasons such as quality of sample and area observed under the microscope, as little to no increase should have been recorded. The mixed cultures, being a combination “a” of and “alpha” “marinated” in broth for 24 hours showed significant transitions of the existing single and budding haploid cells in to shmoos, zygotes, and asci. That was due to the ideal environment that they existed in during that time. The “a” type and alpha type yeast cells send out pheromones which are recognized by the opposite type. When they receive these signals, the two cells are induced to mate which results in a fusion of the two cells (which is a zygote). From there, they begin budding and reproducing.

Conclusions: The summary of the whole lab was that with more time the yeast had the more cells produced for the a-type and α-type separately however the mixed culture did not really have a huge difference in cell reproduction from our data. What we have experienced that did not go according to plan was that our initial test for the cultures did not really was seen when put under the microscope. We adjusted every thing on the microscope, but in the end there weren't any results the first day of recording data. So what we did in the end was only have 3 data points for each test on the cultures as shown on the graph.

References: N/A

A picture of a mixed yeast culture, taken through the microscope.
The microscope and the tubes containing the sample we used.

Sunday, December 8, 2013

Chromatography & Photosynthesis Lab

Purpose: The purpose of the chromatography lab was to use chromatography to separate and identify pigments and other molecules from cell extracts that contain a mixture of molecules. For the photosynthesis lab, it was to test the rate of photosynthesis in different scenarios. The concepts we were testing was photosynthesis itself and its process of how chlorophyll relates to the color change.

Introduction: Chromatography paper is special paper that is used to separate and identify pigments and other molecules from cell extracts that contain a mixture of molecules. It works by viewing how the solvent travels vertically up paper by capillary action (the attraction of solvent molecules to the paper and other solvent molecules). As the solvent moves up the paper, different pigments are carried up at different rates due to due to their differences in solubility. Photosynthesis is the conversion of solar energy to chemical energy in plants. Plants use that chemical energy to promote cell growth, consume it as a food source, and for other cellular functions. That conversion occurs in the chloroplasts plant cells. The rate at which photosynthesis occurs in chloroplasts depends on the amount of light that plants receive.

Methods: In the chromatography lab, pigments from a spinach leaf were extracted on a piece of chromatography paper and barely immersed in 1ml of solvent. Once immersed, we measured the distances the different pigments in the solvent traveled upward on chromatography paper. In the photosynthesis lab, we measured how the rates of photosynthesis were effected in four cuvettes containing different variations of chloroplasts, when exposed to light. Those variations were unboiled chloroplast (surrounded by tinfoil), unboiled chloroplast (exposed to light), boiled chloroplast (exposed to light), and no chloroplast (exposed to light). Each solution’s absorbance and % transmittance was measured before they were exposed to light. Once measured for the first time, they were placed in front of a light and were removed every five minutes, three times for each cuvette, to be tested for any change in absorbance and % transmittance.

Data:
The results of the failed attempt, measured in percent transmittance (photosynthesis lab).

The results of the successful attempt, measured in percent transmittance (photosynthesis lab).

Graphs and Charts:
The failed attempt. The time when each data point was taken is shown by color (photosynthesis lab).
The successful attempt (2nd trial). (On the x-axis, "1.0" refers to the sample of unboiled chloroplasts in darkness. "2.0" refers to the sample of unboiled chloroplasts in light. "3.0" refers to the sample of boiled chloroplasts in light. "4.0" refers to the sample without any chloroplasts). (photosynthesis lab)


Our time intervals for each cuvette  (photosynthesis lab).


Our paper chromatography separating the different pigments (chromatography lab)

Discussion: In the photosynthesis lab we had two trials hence two graphs for our data. As seen above both graphs show different results however one is more accurate than the other due to certain errors and calculations. Going into that we encountered the time for each test being a problem for the first trial as some tests did not meet the time requirements stated in the lab. As such in the 2nd trial we made sure that we had enough time to do all the tests and correctly measure as well the photosynthesis rate. The results of both trials can be contrasted by the scaling of the rate of photosynthesis and also how the 2nd trial showed more of an increase for the unboiled chloroplast in light, which was the one cuvette that should have shown the most progress as time went by. In the first trial it showed a decrease or none at all in the rate of photosynthesis of the 2nd cuvette and that is not suppose to occur. overall our 2nd trial did support what was suppose to happen as the lab stated as we learned to fix the mistakes that affected our results.

Conclusion: We found that there was a wide variety of colors displayed when the chromatography lab was in progress. As the colors showed the solubility of each was shown on the strip of paper. As for the 4b which was the photosynthesis part of the lab, we found out about what went wrong the first time we did the experiment and that was the time for the reaction to occur. Given a time limit when not enough time was given the rate of photosynthesis did not really occur in a situation that was supposed to happen. For example the unboiled chroloplast with light in our first attempt showed no response in the rate of photosynthesis. Hence why a 2nd trial was done to see if there was a huge difference and there was.

References: N/A

Sunday, November 17, 2013

Cellular Respiration Lab

Purpose: The purpose of this lab was to observe the effects of cellular respiration on different carbon dioxide concentrations, study the effects of temperature on cellular respiration, determine whether germinating or non-germinating corn respire, and compare the rates of cellular respiration between germinating and non-germinating seeds.

Introduction:  Celllular respiration is converting the chemical energy of molecules that can be used by organisms. Both plants and animals break down glucose for energy and there is a three step process cellular respiration.the first step is glycolysis which creates two pyruvates for the next step along with a net of two ATP. The pyruvates oxidation is not a huge step but creates acetyl CoA from the pyruvates. This will be fed into the citric acid cycle and generate more ATP as well as Electrons carried to the last step which is oxidative phosphorylation and chemiosmosis by NADH AND FADH2. The final step creates the most ATP in the whole process.

Methods: In the experiment, we measured how different levels of carbon dioxide affected the rate cellular respiration, for ten minutes and in a closed system, on 25 room temperature and 25 chilled germinating corn seeds, 25 non-germinating corn seeds, and 25 glass beads. We began with the germinating corn seeds. We then soaked the same 25 germinating seeds in 4°C water for about 10 minutes.  We then tested non-germinating seeds. Finally, we tested glass beads. Glass can’t perform cellular respiration, as it is non-organic. The fact that glass beads were so similar in size to the corn seeds made it the perfect control group. 

The setup.


Getting a reading from germinated seeds.

Germinated seeds getting cold.



Data:

Graphs and Charts:
y= CO2 concentration    x= time (in seconds)
(The blue line is the normal germinating seeds, and the green line is the chilled germinating seeds. The red line is the non-germinating seeds, and the purple line is the glass beads.)

Discussion: The result for the germinating seeds was a positive slope for the whole ten minutes of recording, with a final reading that was roughly 1½ times the starting concentration. This should be expected from seeds that are actively using oxygen to grow and release CO2 as a product. Since non-germinated seeds are dormant seeds, which means that they can’t perform cellular respiration, the result was a slope of nearly zero because they simply weren’t actively trying to grow, which would produce CO2. The result was similar for the cold germinating seeds: a slope of zero for the first 1½ minutes of recording, and then a positive slope for the remaining amount of time. That most likely occurred because the seeds were cooled so far below the optimal temperature that they require to perform cellular respiration, they had to warm back up to room temperature before they could begin cellular respiration. As a result, the CO2 concentration in the chamber filled with cold seeds was very similar to that of the ungerminated seeds.

Conclusion:  temperature did play a large role in the rate of respiration as all the test subjects showed the same correlation. With germinated being the fastest, germinated cold getting slower and non germinated being the slowest. We conclude that lower the temperature had a negative impact on the seeds.

References: N/A


Beware

Wednesday, November 6, 2013

Enzyme Catalysis Lab (Part 2D)

Purpose: The purpose of part 2D was to test the cenzyme-catalase. The independent variable tested was time, while the dependent variables was H202 consumed as well as KMno4 used when titrating.

Introduction: Enzymes are proteins that speed up the rate of reactions. In this lab enzymes were used on a substrate. A substrate is a solution whose rate of reaction can be catalysed, or accelerated, by the enzymes. The amount of enzymes and substrate in a solution, along with the amount of time the two are together, determine how much of the substrate is catalysed. In this portion of the lab, time was of the essence when it came to determining the amount of substrate that was decomposed by the enzyme.

Methods: In the experiment we had to determine the rate at which seven different timed trails of 10 mL of 1.5% H2O2 solution decomposed after 1 mL of enzyme-catalase was added. Once the enzyme-catalase was added we started a timer, swirled each solution for the ten seconds, and then let them sit for increasing amounts of time. The amounts of time were 10, 30, 60, 90, 120, 180, and 360 seconds. Once time was up we stopped the reactions by adding 10 mL of H2SO4. We then took 5 mL samples from each trial and titrated each one and recorded the amount of KMnO2 used to titrate the 5 mL samples.     

Data:

Graphs and Charts:


Discussion: Both the amount of KMnO4 consumed and the amount of water used started at 2.5 milliliters and ended at the same amount. Between the different cups and the amounts of time for which they were exposed to catalase, the two figures-- KMnO4 consumption and H2O use-- seem to decrease and increase in a wave-like pattern. One will decrease while the other increases proportionately, and at some point they each reach a maximum distance from their starting value and begin to move in the other direction-- one increases while the other decreases. It's normal for the KMnO4 amounts to be opposed in this way to the H2O2 amounts, but under normal circumstances, the H2O2 amounts would not decrease after increasing.

Conclusion: our question was to find out the effiency if the enzyme catalase as time being a variable that is changed. We found out that in the fist few tests that our data supported that the enzyme sped up the reaction. However as time got longer we had varied results with our time and it did not support the claim. Errors that may occur is the measurements of our substances and also the time measured might be a little off. Overall we found that most of our data was somewhat accurate.

References: N/A

Monday, October 21, 2013

Diffusion-Osmosis Lab

Chau: A
Gunnar: B
Derek: C
Luke: E

Purpose:
1A Diffusion: The purpose of this part of the lab was to test diffusion of small molecules through a selective permeable membrane. We were testing with solution color and the presence of glucose.

1B Osmosis: The purpose of the osmosis portion of the lab was to test the relationship between solute concentration and the movement of water through a selectively permeable membrane.

1C Water Potential: The purpose of this experiment was to gain an understanding of how the molarity of a solute affects the transfer of water in solutions.

1E Plasmolysis: The purpose of the Onion Plasmolysis lab was to examine how highly concentrated solutions affect diffusion and the contents of a cell.


Introduction:
1A Diffusion: The membrane allows molecules to pass through through the process of diffusion. However a selectively permeable membrane only allows some molecules to pass through but not others. Molecules go from a higher concentration to a lower concentration.

1B Osmosis: Osmosis is a process where molecules of a solvent pass through a semipermeable membrane from a less concentrated solution into a more concentrated one, thus equalizing the concentrations on each side of the membrane.

1C Water Potential: The term "water potential" refers to the tndency of water to move around from one place to another. In general, water moves from areas of high water potential to areas of low water potential.

1E Plasmolysis: A plant cell, such as the onion cell in the experiment, strives to be at a full state, so that it may retain its structure. It achieves this in a hypotonic solution, but wilts and dies in isotonic and hypertonic solutions respectively. Plasmolysis is when the cell has lost so much water that the cytoplasm inside pulls away from the cell wall and can cause the cell wall to collapse.


Methods:
1A Diffusion: we had the dialysis bag put into the solution of iodine and distilled water for diffusion to occur. before hand we had to prepare the bag using water.

1B Osmosis: We filled six dialysis bags, one with  0 M distilled water and the rest with sucrose solutions of 0.2 M, 0.4 M, 0.6 M, 0.8 M, and 1.0 M and measured the mass difference and amount of percentage change of mass after they soaked in a cup of water for 30 minutes.

1C Water Potential: We measured out equal amounts of distilled water and sucrose solutions of 0.2, 0.4, 0.6, 0.8, and 1.0 molarities into plastic cups. We then hole-boring device to cut cylindrical cores out of our potatoes, and placed four similarly sized cores in each cup. We left these cups to sit overnight so that the osmosis could reach equilibrium.

1E Plasmolysis: We placed the onion cells on a wet mount and placed them underneath a microscope. Then, using a dropper, placed 3 drops of 15% NaCl solution onto the slide, pushing it over onto our cell. After that, we followed the same procedure, only this time using fresh water instead.


Data:
1A Diffusion: The bag solution color was colorless initially and then final it was black. For the presence of glucose the bag had glucose to begin with so ended with having glucose. For the beaker the color was red initially and then lighter red in the end. For presence of glucose it had none to begin with then in the end it had glucose.

1B Osmosis: After the bags soaked in cups of water for 30 minutes they had fairly significant mass differences and thereby significant percent changes in mass. The bag with 0 M distilled water had a loss of mass and negative percent change in mass while the dialysis bags with sucrose in them from .2 M and up gained mass and increase in percent changes in mass. 

1C Water Potential: The masses of the potato cores in the distilled water increased overnight by a good amount, and the mass of the cores in the 0.2M sucrose increased as well, if less so. However, the cores in the rest of the cups saw a decrease in mass, with the severity of the mass decrease being bigger in solutions with higher concentrations.

1E Plasmolysis: before the application of the NaCl solution, the onion cells were mostly a bright pink/red color. When we used the solution, the shade of the cell grew darker, and the color retracted from the inner edges of the cell. Using the fresh water, the cell went back to its previous state.


Graphs and Charts:

1A Diffusion:

1B Osmosis:


Dialysis Bag results
Percent change in mass of dialysis bags graph












1C Water Potential:


1E Plasmolysis:
--The top layer shows the regular onion cell, while the bottom shows the plasmolyzed cell.  



Discussion:

1A Diffusion: The results concluded that iodine and glucose were the molecules that went through the process of diffusion to have equilibrium. The bag received the iodine which made its drastic color change while the beaker received glucose.

1B Osmosis: The dialysis bag containing water had a negative mass difference and negative percent change because more water exited the dialysis bag than entered. That occurred because there was a larger amount of distilled water in the bag than out of it, causing the selectively permeable membrane to transfer the distilled water out of the bag, making it lose mass. The dialysis bags with sucrose in them from .2 M and up had positive mass differences and positive percent changes in mass because more water entered the bag than exited. That occurred because there wasn't any water in the bag in the first place, causing the selectively permeable membrane to transfer water inside the bag, making the bag gain mass.

1C Water Potential: The increase in mass of the potato cores in the water and low-concentration sucrose was due to a higher water potential in those solutions. Because the water potential in the potato cores was less than that of the solutions they were submerged in, the water moved into the cores and their masses increased. When the molarity of the sucrose began to reach higher than 0.2M, however, the water potential of the cores ended up being higher than that of the solutions, so the water moved out of the cores, causing the drop in mass.

1E Plasmolysis: The application on the NaCl solution created a hypertonic environment, causing the cell to lose water and convert to a plasmolyized state. The water inside of the cell flowed out into the solution in order to balance out the NaCl to Water ratio and reach equilibrium. When we poured fresh water back into the cell, the process was reversed and a hypotonic environment was created. The cell reverted back to being full, as the greater concentration of water on the outside of the cell proceeded to flow back.


Conclusion:

1A Diffusion: We found out that starch was not one of the molecules that passed through the membrane and that glucose was the one that was allowed through the selectively permeable membrane.

1B Osmosis: In conclusion it can be determined that if water and another solution differ in concentration and are separated by a selectively permeable membrane, water will move between the membrane until both sides contain equal amounts of water.

1C Water Potential: Looking at the results of our experiment, it can be concluded that higher solute concentrations result in lower water potential, which causes the water to move into those solutions with high solute.

1E Plasmolysis: These results confirm that a hypotonic solution allows a plant cell to retain its turgidity and live, while the hypertonic solution causes it to lose water and become inneffective. DETRITUS!



References: N/A