Unit 5 Reflection

In this unit, we learned about the central dogma. The central dogma says that information travels from the DNA to the RNA to the proteins, which make up the physical traits that we have. This process can be broken down even further into two steps: transcription and translation. Transcription is the process in which DNA unzips and RNA is made to match the spare nucleotides to make messenger RNA (mRNA). In translation, mRNA arrives at the ribosomes, where the codons are translated into a code for proteins, which are produced and make up our physical traits. There are also mutations and different things that can regulate gene expression, but those are rather slightly less relevant to the central idea of the unit.

One of my main strengths in this unit was that I was able to easily translate and transcribe different DNA pairing, RNA sequences, and going from codon to protein, This made the protein synthesis lab quite easy for me, as I was done in less than 10 minutes. However, one of my weaknesses was not being able to visualize things. When Mr. Orre called on students to walk up to the board to label the different items related to regulating gene expression, I was not even able to identify a single one. Thank goodness I wasn't called up!

Yet still, I have many questions. Mr. Orre said that this unit would bridge the gap between how our chromosomes affected our traits, but I still don't quite get how different alleles correspond to different base pair codes and how the types of proteins can create so many different combinations that affect our physical traits.

As a student, I feel like I have definitely grown after this unit. DNA had always been one of the most puzzling concepts for me that I couldn't quite grasp. However, I feel that after this unit, especially after creating the DNA model, my understanding of the structure and function of DNA has definitely expanded. Also, my learning skills have definitely improved. I used to rush through my vodcasts with haste, focusing more on completing the task rather than actually trying to learn more as a biology student. Now, I listen carefully and try to pick up on as much detail as possible, even referencing the textbook when the vodcast is unclear. I feel like this time, unlike the others, I will not be cram-studying the night before the test because I think I already have ample knowledge to do well on the final. I might study a little bit here and there and review my peer study guides, but I will definitely be getting a good night's sleep this time.   

Protein Synthesis Lab

In this lab, we asked the question: "how does the body produce proteins?" In the process of protein synthesis, RNA polymerase reads the DNA and transcribes it into a code for the messenger RNA (mRNA). Then, the RNA travels to the ribosomes. They bond, and the mRNA is read, each codon representing a specific protein. Finally, the protein is made based on the code read from the mRNA.

Frameshift mutation seemed to have the greatest effect on the proteins, and yes, it does matter where the mutation because an insertion or deletion near the beginning of the sequence can offset the entire rest of it, but one of these at the end might not do much. If the T was at the end, it would not have affected the sequence before it. However, in some cases, substitution can cause a huge change in protein as well.

In step 7, the mutation I chose was a simple substitution on the 6th base. A substitution at the end of a codon may seem like nothing at first, but the change was actually pretty massive. This simple substitution caused the second codon to go from a Tyr protein to a Stop protein. So effectively, the new sequence literally became just start-stop. Quite a difference with such a small substitution. And yes, of course, like always, the spot where the mutation occurs definitely matters when choosing the mutation that will create the biggest or smallest change.

Mutations can affect our lives because if a section of our DNA is deleted, inserted, or substituted for, it could cause a drastic change in the protein that is made, and in some cases, will cause some pretty significant changes in our phenotype. A mutation on a section of DNA that controls the proteins that make up eye color can cause heterochromia. In heterochromia, spots of irregular shape appear around the pupil that are a different color than the circular ring that is around it. Perhaps a mutation on the DNA caused a different protein to be made in the eye cells, which caused this variance in color. 

Human DNA Extraction Lab

In this lab, we asked the question: How can DNA be separated from cheek cells in order to be studied? During our research, we learned that the protocol for DNA extraction involved three basic steps: homogenization, lysis, and precipitation. We found that it was made possible by means of scraping our cheek cells with our teeth in the presence of Gatorade, adding salt, soap, and pineapple juice, and then finally applying a layer of cold alcohol at the top. The DNA floated to the alcohol with ease.

In order to break down the cell walls/membranes, plasma membranes, and nuclear material in the first step homogenization, the cell tissue must be submerged in a polar liquid, which in our case, was Gatorade. Inside the mixture of our saliva, Gatorade, and cheek cells, we could see the DNA a little bit better because of the breaking down of the cell membranes, plasma, and nuclear material. After adding soap, salt, and pineapple juice to the mixture, 95 percent isopropanol alcohol is layered carefully to the top of the mixture, and since alcohol is nonpolar and DNA is polar, the DNA falls out of the solution as a precipitate at the interface of the two solutions. After pulling it out of the alcohol layer, our DNA has been extracted.

While our hypothesis may have been supported by our data, there could have been possible errors due to the fact that many of the steps didn't have exact amounts of materials we were supposed to add. This could have affected the results because if we didn't have the right amount of something to add to the solution, the DNA may have not been able to be extracted properly. Also, we were supposed to come up with the procedures by ourselves, so if we did something that was not in the correct order, that could have messed up the process of extracting the DNA properly. I think that next time, maybe more precise amounts should be added to the procedure and the students should actually get the full procedures to prevent the possibility of just wasting materials by not being able to do the actual procedures.

This lab was done to demonstrate how DNA could be extracted from cheek cells and that DNA is not as complicated and unreachable as we may think. From this lab, I learned about concepts such as homogenization, lysis, and precipitation, which helps me better understand the concept of DNA as a whole. Based on my experience in the lab, if cloning is invented, I would definitely know how to extract my DNA to create a clone.

Unit 4 Reflection

In the coin sex lab, we simulated gamete formation by flipping coins to determine which of the two in the allele pair would make it to the sex cell. Then, we simulated sex, by adjoining the results of the coins to determine the genotype of the offspring. The expected result in our double heterozygous dihybrid cross was two have two double homozygous babies. One of which would be double homozygous dominant and the other recessive. However, it turns out that in this dihybrid cross, we got none of these. We can attribute these results to the working of random chance; even as the expected result is for two, we still cannot predict what the genes of the actual outcome will be. This is the limit of using probability to predict our offspring's traits. We can determine the possible traits they will have and their likelihoods, but we can never know for sure. In life, there are many things which we can estimate the probability of, but in the end, we can never predict for sure.

This unit in general was about sex and how great it is. It creates offspring that are part of the new generation so that species don't die out and go extinct. Some essential themes included that alleles would randomly separate during meiosis and join during fertilization for recombination, making the genotype of the offspring completely random and unpredictable. However, it is possible to determine the possibilities and the probability of those possibilities. In a monohybrid cross, there are only four squares in the Punnet square, making the results very limited and easy to find the probability of. We also learned that there are two different types of inheritance: X-linked inheritance and autosomal inheritance. Since I'm pretty good at math, one of my main successes was being really quick at finding the probabilities of certain outcomes when there were crosses.

Before these previous experiences, I had always had built in impressions that inheritance was both straightforward and intuitive. However, after learning about the different possible complications, incompletions, and exceptions, it is not quite as straightforward as I thought. However, it feels like the possibilities with genetics are endless and this was definitely one of the funner units.

Even after this unit, I still have many questions. What are the causes behind these different mutations and complications? I was almost aborted because my parents thought I had Down Syndrome, but in the end, they still decided to keep me and I turned out to be a normal, healthy baby, which makes me wonder: Is it just by random chance that we are born? If everything is just random chance, what's the point. I wonder about this often and I have never found an answer.

Here is a link to an infographic I created on genetics: https://magic.piktochart.com/output/17957312-why-is-sex-so-great

Is sex important?

There are definitely many benefits to reproducing sexually. One of the benefits is that sexual reproduction shuffles the genes of individuals from those of their parents, making the entire species as a whole less susceptible to mass extinction by a disease or mutation, as stated by the armadillo. However, there are also some downsides to sexual reproduction as well. Trying to survive the dangers of predators in the while makes it hard for an organism to find a mate at the same time, as said by Olivia Judson. It is often hard to impress the opposite gender, making successful sexual reproduction quite difficult.

There are also some benefits and costs of producing asexually like the E. Coli. Producing asexually only requires female organisms, eliminating the need for males, argued Miss Philodina. Also, unlike in sexual reproduction, where it takes two children to balance the population, asexual reproduction only needs one offspring to equalize population. However, one of the downsides of asexual reproduction is that all organisms have the same DNA, so anything like a disease can wipe out an entire species, and also, mutations will be passed onto future generations, causing more and more of the population to be mutated.

I don't have many questions regarding this topic, but I guess my one burning question would have to be: What causes us to be so eager to mate?

Unit 3 Reflection

In a nutcell (nutshell), this unit was about cell structure and function, photosynthesis, and cellular respiration. Some of the themes included the process by which a protein is created, a tour of the cell, the reactants and products of both photosynthesis and cellular respiration, etc.

Although many of the concepts and skills required in this unit were already fairly familiar to me, I had quite a bit of trouble memorizing and fully grasping all of the structures and functions of all the organelles within a cell as well as many of the complex steps in the reaction of cellular respiration.

I am definitely a better student now than I was at the beginning of the unit. I have learned many new skills such as focusing a microscope on the specimen much more quickly, I also learned how to make cool labels on Google Drawing. But most importantly, I started to get more accommodated to working with my tablemates and getting to know them better, making our labs much more efficient and at the same time, fun.

Photosynthesis Virtual Labs

Photosynthesis Virtual Labs.

Lab 1: Glencoe Photosynthesis Lab

http://www.glencoe.com/sites/common_assets/science/virtual_labs/LS12/LS12.html

Analysis Questions

1. Make a hypothesis about which color in the visible spectrum causes the most plant growth and which color in the visible spectrum causes the least plant growth?

Since in the vodcasts, it said that plants grow best under red or blue light, my hypothesis is that if a plant is that if a plant is put under red or blue light, then it will have the most plant growth.

Also, plants reflect green light, so my hypothesis is that when put under green light, plants will have the least growth.

2. How did you test your hypothesis? Which variables did you control in your experiment and which variable did you change in order to compare your growth results?

I tested my hypothesis by putting the same plant under different wavelengths (colors) of light. For my control, I used white light, as it contains all the different colors and acts as a good base measurement of how much the plant should grow. The variable I changed was the color on the left side, so I could compare it to normal while light and see what would happen.

Results:

Filter Color	Spinach Avg. Height (cm)	Radish Avg. Height (cm)	Lettuce Avg. Height (cm)
Red	18	13	11
Orange	14	8	6
Green	2	1	3
Blue	19	14	12
Violet	16	10	8

3. Analyze the results of your experiment. Did your data support your hypothesis? Explain. If you conducted tests with more than one type of seed, explain any differences or similarities you found among types of seeds.

My data definitely supported my hypothesis. All the seeds that grew under the same color of light ended up having pretty consistent heights. The plants that grew under the blue lights and red lights were always significantly and consistently taller than those that grew under violet or green light.

4. What conclusions can you draw about which color in the visible spectrum causes the most plant growth?

The color in the visible spectrum that causes the most plant growth is without a doubt blue. The height of the plants that grew under blue light always exceeded the height of those that grew under other colors.

5. Given that white light contains all colors of the spectrum, what growth results would you expect under white light?

I think that when the plants are placed under white light, which contains all the colors of the spectrum, the growth of the plants would be similar to that of the plants that grew under violet light--not quite as tall as plants under blue or red light, but taller than those that grew under orange or green light.

Site 2: Photolab

http://www.kscience.co.uk/animations/photolab.swf

This simulation allows you to manipulate many variables. You already observed how light colors will affect the growth of a plant, in this simulation you can directly measure the rate of photosynthesis by counting the number of bubbles of oxygen that are released.

There are 3 other potential variables you could test with this simulation: amount of carbon dioxide, light intensity, and temperature.

Choose one variable and design and experiment that would test how this factor affects the rate of photosynthesis. Remember, that when designing an experiment, you need to keep all variables constant except the one you are testing. Collect data and write a lab report of your findings that includes:

• Question
• Hypothesis
• Experimental parameters (in other words, what is the dependent variable, independent variable, constants, and control?)
• Data table
• Conclusion (Just 1st and 3rd paragraphs since there's no way to make errors in a virtual lab)

*Type your question, hypothesis, etc. below.  When done, submit this document via Canvas.  You may also copy and paste it into your blog.

Question: How does the amount of carbon dioxide in system contribute to the amount of oxygen produced by photosynthesis?

Hypothesis: If carbon dioxide is required for a photosynthesis reaction to happen, then more carbon dioxide will cause more photosynthesis and therefore produce more oxygen.

Experimental Parameters: The independent variable is the amount of carbon dioxide and the dependent variable is the amount of oxygen produced. Some constants include the amount of light, color of light, the amount of water, the type of plant, the amount of time, and the temperature. The control was no carbon dioxide.   

Amount of Carbon Dioxide	Trial 1 (bubbles in 20 sec)	Trial 2	Trial 3	Average
None added	16	16	16	16
Some added	28	28	28	28

Conclusion: In this lab, I asked the question: How does the amount of carbon dioxide in system contribute to the amount of oxygen produced by photosynthesis? I found that it greatly increases the amount of oxygen bubbles created, almost doubling the amount without carbon dioxide. When I didn’t add any extra carbon dioxide to the system, only 16 oxygen bubbles were produced in 30 seconds while in the system with extra carbon dioxide, there were 28 oxygen bubbles. This is likely because of the fact that carbon dioxide is required to start a photosynthetic reaction. Adding more carbon dioxide gives the plant more reactant to work with, which is most likely the cause of why there is way more product.

This lab was done to demonstrate how different environmental factors affect the process of photosynthesis. From this lab, I learned that more carbon dioxide produced more oxygen, which helps me better understand the concept of the chemical reaction behind photosynthesis. Based on my experience from this lab, if I am a botanist in the future, I might leave my plants in an area with higher concentrations of carbon dioxide to help them grow better.

Microscopic Organism Analysis

Amoeba: We were able to identify the nucleus, the cell membrane, and the pseudopods. This was examining while the power was at 400x. What was unique about the cell was that it had two nuclei and an observation we made was that it was very pink and skinny. The cell is eukaryotic.

Cyanobacteria: We were able to identify the occurrences of a single cell.

Euglena: We were able to identify the nucleus and chloroplasts. The power on the microscope we were using was at 400x. Unlike the circular cell that most of us are used to, the shape of this one was more like a dash, which made it pretty unique. Some observations we made included that it was light blue with dark blue dots which were probably the nuclei. The cell is eukaryotic, as it has a nucleus.

Bacteria cell: We were able to identify the coccus, bacillus, and spirilum.

Ligustrum: We were able to identify the chloroplasts, the epidermis cell, and the vein. This was with the microscope power at 400x. What is unique about this cell is that there are many circles seemingly chained together, giving it an almost artistic design. We observed that there was no nucleus, meaning it is a prokaryotic cell, and therefore, an autotroph.

Muscle Cell: We were able to identify the Striations and the Nucleus. This was with the microscope power at 400x. What is unique about the cell is that there seem to be many organelles clumped together. We observed that it even looks like real muscles, which is pretty intuitive. The muscle cell is eukaryotic and is heterotrophic.

Spirogyra: We were able to identify the cell wall, the chloroplasts, and the pyronoid. This picture was taken with the power on the microscope at 400x. What's unique about this cell is that it is very, very green. Also, it looks kind of like a caterpillar. This plant cell is eukaryotic and is autrophic because it provides for itself its own energy using photosynthesis.

Questions:

In this lab, we examined many different types of cells under the microscope and compared and contrasted the differences between the characteristics that cells belonging to different groups had. We compared and contrasted those which were eukaryotic or prokaryotic and those that were autotrophic of heterotrophic. Some common characteristics among the autotrophs included that they were mostly green and were plant cells. Some characteristics of the heterotrophs were that they were not green, and were usually animal cells with nuclei. They were mainly eukaryotic. The eukaryotic cells were usually the cells in which we were able to identify the nucleus. This is most likely because of the fact that all eukaryotic cells have a nucleus, while prokaryotic cells don't. The prokaryotic cells usually had pretty odd shapes that were very different from the eukaryotic cells. For example, the ligustrum was made of many multicolored rings and the bacteria cells had many floaty squiggly things known as spirillum.

Egg Diffusion Lab

1) The mass and circumference of the egg radically decreased when the egg was placed in sugar water for 24 hours. This is because in an effort to balance out the solute concentration, water came out of the egg to balance out the ratio of solute to solvent. The sugar water is a hypertonic solution, as there is a higher concentration of solute outside of the egg cell. In order to lower this high concentration, water had to flow out of the egg cell to equalize the concentrations.

2) A cell's internal environment changes in many ways in reaction to its external environment. Losing or gaining water by means of diffusion is just one of the ways a cell changes in reaction to its environment. Also, when we soaked the egg in vinegar for 48 hours, the egg's membrane was softened and slightly separated from the white and yolk.

3) This lab demonstrates the principal of osmosis and diffusion. The places where there was a lot of solvent but not enough solute went into the areas of higher solute concentration. In the case with the egg cells, water from within the egg flowed out to balance out the high concentration of sugar, causing it to shrink, while when it was placed in pure water, there was actually a higher solute concentration within the egg, causing water from outside to rush into the egg.

4) Fresh vegetables are sprinkled with water at markets because they want diffusion to occur. When diffusion occurs, the water will soak into the vegetables, keeping them juicy and yummy. Roads are salted to melt ice because when there is a higher concentration of solute (salt) outside of the ice, water will rush out to balance out the concentrations, making the melting point of the ice much lower, so that it is easier to drive during the winter.

5) After this experiment, I want to see if the same diffusion process applies for other cells, not just an egg cell. For example, I might test this kind of experiment on a growing plant. Most likely, we will see the same general idea of changes. The cell will probably shrink in sugar water and grow in pure water.

Egg Macromolecules Lab

In this lab, we asked the question: Can macromolecules be identified in an egg cell? We found that indeed there was a testable way to determine whether or not the specified macromolecules were present in that part of the egg cell. We found that there was a pretty large amount of proteins in the egg white, as the sodium hydroxide and copper sulfate turned a dark purple, signaling a large presence of protein in that area. This is most likely true because according to the nutrition facts, 85% of calories in an egg white come from proteins. This data supports our claim because it shows that there is a lot of protein in an egg white and indeed that this hypothesis was testable.

Part of our data contradicts the expected results because in our tests for monosaccharides and polysaccharides, there was little presence of those. This is most likely because in a rush to finish the lab, we didn't wait long enough for the Benedict's solution or the iodine to sink in and change color. Also, while this part of our hypothesis was supported by our data, there could have been errors due to human perception of color. Especially for the protein tests, the colors looked very similar, so we could only approximate numbers that the whole group agreed which could have skewed the actual results. I recommend that next time, we get more time for the lab, so the window of opportunity for the solutions to change color is larger. Also, I recommend that next time, we should have more bottles of the solutions so that there aren't just a bunch of people waiting in line to add the solution into their test tubes.

This lab was done to demonstrate the presence of macromolecules in cells, like an egg cell for example. Most of what we have learned so far about macromolecules seems pretty abstract, but now that we know more about the practical uses and being able to find these macromolecules in a real life object, it enhances the learning process. From this lab, I learned more about the basic structure of a cell and what macromolecules may appear in these parts of the cell. It helps me better understand the concept of the different functions that different organelles have within cells. Based on my experience from the lab, maybe for a future experiment, we could examine a plant cell and see the differences between the two different types of cells and the macromolecules present in them. Also, with this new information, I now know better how to "dissect" an egg, which could possibly help with later dissections, such as the pig dissection.

Unit 2 Reflection

This unit was titled the Chemistry of Life. As one can probably tell from the title, the unit was about the basic chemistry necessary for learning biology. In this unit, we learned about the properties of water, different types of chemical bonds, and the four different macromolecules along with their uses and structures. Some labs we did include the sweetness lab, the enzyme virtual lab, and the cheese lab. The sweetness lab demonstrated the relationship between the structure of a carbohydrate and the taste. Both the cheese and enzyme virtual labs gave us an idea of the conditions in which enzymes work best. We were pretty successful with our sweetness lab and enzyme lab, but the cheese lab had quite a few setbacks. We had a pretty severe time restraint, so if the milk didn't curdle within 15 minutes, we had to call it a Did Not Curdle. Also, there was a lot of ambiguity surrounding what the word "curdle" actually meant. It was hard to tell how much curdling would actually count as "curdling" because of this ambiguity.
From this unit, I definitely learned a lot of content as well as skills. I learned, contrary to my previous intuition, that not all sugars are that sweet. Also, I had assumed in the past that since acids were good at breaking things down, enzymes would be most effective in an acidic environment. However, I was clearly wrong, and I now know that enzymes work best in a neutral pH and at room temperature. I also never knew that a pipette had markings for volume, but now that I do know this, I will put it to good use to make my measurements much more accurate in the future.
However, I still have many unanswered questions and more I want to learn about. Like for I example, I know that enzymes work best in a neutral pH and room temperature, but when it comes to curdling milk, how come they are more effective in a warm, acidic environment? Also, as we did do experiments regarding carbohydrates and proteins, I am still curious to see if we will work with lipids and nucleic acids, the two macromolecules that we haven't touched on much outside of the vodcasts. Sometimes, these experiments make me think about my own diet, and I still feel like there are many foods that don't fall into any of those categories. However, maybe as I learn more in the future, those burning questions will finally be answered.

Sweetness Lab

In this lab, we asked the question: How does the structure of a carbohydrate affect its taste (sweetness)? We found that monosaccharides and disaccharides tended to be on the sweeter side while the polysaccharides were pretty plain tasting. Monosaccharides were very sweet, disaccharides were medium-sweet, and the polysaccharides were tasteless. The average degree of sweetness among the monosaccharides was about 123. For the disaccharides, it was 45, and for the polysaccharides, it was 0. This data supported my claim because I predicted that fructose (a monosaccharide) would be very sweet. Indeed. it was the very sweetest.

Carbohydrate structure and the amount of rings could affect how they are used by organisms. A more simple carbohydrate would be broken down very quickly, but have a smaller energy release while a more complex carbohydrate might take longer to be broken down, but have quite a bit of energy released.

The testers didn't give each sample the same rating. Of course, this makes sense because different people haven't different senses of taste. For example, Marie rated many of the sugars with a higher degree of sweetness than I did. This is most likely because I have a dull sense of taste, since a I eat a lot of spicy stuff. Marie, on the other hand, doesn't eat spicy foods.

Taste buds cause humans to taste sweetness as well as other flavors. However, the amount of taste buds varies from person to person. The more taste buds a person has, the more sensitive their sense of taste is. In the example above, it would be logical to conclude that Marie has more taste buds than me.

What Is Biology?

Jean Lab

                    In this lab, we asked the question: What concentration of bleach is best to fade the color out of new denim material in 10 minutes without visible damage to the fabric? We found that unless the concentration was at least 50%, the solution would literally do nothing. As seen in the data table, all trials for fabric damage and color change resulted in 0's for concentrations less than 50%. Since 50% had a pretty subtle change (average 1) and 100% had a bit of fabric damage, we can conclude that the right concentration is probably somewhere between the two concentration. Our hypothesis was right because indeed there does exist a concentration of bleach that can fade jeans perfectly.  

                   While our hypothesis was supported by our data, there could have been errors due to inexact timing of submerging and washing out of bleach. These timing errors could've affected the results because some samples that were submerged longer would be more faded than others. Also, we noticed that our bleach was a lot less yellow than other bleaches so maybe our bleach was not pure. This could've affected our results by making the jeans a lot less faded than they should've been. In the future, we could have everyone in the class start at the same time and maybe we could have everybody use bleach from the same bleach bottle.

                   This lab was done to demonstrate how difference concentrations of bleach could yield different results on the color and quality of denim jeans. Also, as the very first lab of the year, the lab was probably also for helping students understand how an experiment is carried out. I can relate this experiment to one time when I was doing the laundry, I used too much bleach. The results were not pretty. Based on my experience from this lab, I now know how to bleach my jeans. Although this experiment isn't very applicable to biology, it still helped me understand the steps of executing an experiment.