Unit 5 Reflection

In this Unit, we learned about the central dogma of biology, how protein is made, and about mutations. The central dogma of biology is that DNA becomes RNA which becomes proteins which eventually become a organism. But in order to make the protein it has to go through the process of transcription and translation. Transcription is the process of RNA polymerase reading and copying DNA code into a temporary mRNA copy. This mRNA then travels to the cytoplasm to be translated. Once the mRNA arrives at the ribosome, the ribosome reads the mRNA in pairs of 3 or codons to correspond to an amino acid. Once the whole sequence has been translated, there is a string of amino acids left, or a protein. However, during this process bases in the sequence can be changed, which is what we call a mutation. Some types of mutation are insertion, deletion, and substitution. Insertion means inserting another base into the sequence, deleting means deleting a base, and substitution means substituting a base pair for another base pair. 

In this unit some of my weaknesses were fully grasping the concept of translation to create a protein. It took me a while to understand why that process was needed and how to exactly translate the DNA sequence itself. However some of my strengths were learning about mutations because that was a concept I could pick up really quickly. But, for translating DNA I was able to understand it much more because of the protein synthesis lab we did. In that lab we practiced translating DNA and thoroughly understood the process of protein synthesis.

After this Unit, I think I have grown as a learner. I would classify a good learner as one that learns from his or her mistakes and grows because of it. I think I would fall into that group. In the beginning of the year, I did not have the correct strategies to learn. I would wander off during vodcasts and not really pay attention and that had bad outcomes for me. However now I actively listen and my grades have reflected that. Overall this Unit has taught me a lot and has made me a better student. 

Protein Synthesis Lab

In this lab we asked the question, How does the body produce proteins? Through this experiment we got a thorough understanding on the process of making proteins. First, a section of our DNA is copied by an enzyme which produces mRNA. Then, once the mRNA is produced it leaves the nucleus and travels to the cytoplasm. That process is called translation. The next process is transcription where the mRNA bonds with a ribosome. The ribosome then reads the sequence of the bases on the RNA 3 at a time, or in codons. Each codon corresponds with an amino acid, and to determine which amino acid goes with each codon, the codon is read by RNA polymerase. Once it is determined which amino acid goes with each codon, all the amino acids are bonded together making a protein.

However, during this process bases could be changed around which is called a mutation. There are many types of mutations such as insertion, deletion, and substitution. Insertion is when an extra base is added anywhere in the sequence. Deletion is when a base in the sequence is deleted. Finally, substitution is when a base in the sequence is substituted for something else. In the lab, we tested out the effect of these mutations in the gene, and what we have found is that insertion and deletion generally causes the most damage especially if the change happens in the beginning of the sequence. The reason it had more effect if the mutation is in the beginning of the sequence is because that one change can alter everything after it, but if the change was at the very end of the sequence there is not much to alter after it. Also substitution didn't have as big of an effect because it only changes the codon that it is part of.

In step 7 of the lab we got to choose our own mutation. The mutation I chose was the deletion of the very first base. This had a much more dramatic effect than any of the mutations I had experimented with before. This is because since the base changed was the first one, not only did it change all the codons after that, but it also caused the fourth codon to be one that coded for stop so the sequence was only 4 amino acids long. This clearly shows that where the mutation occurs has a big effect. Since my mutation was in the very beginning of the sequence, it cause a lot of damage.

This relates to my life, because there could be mutations in my body that could possibly give me a disease. Mutations can be beneficial, but they can also be detrimental. For an example, a disease caused by a mutation is Tay-Sachs. This disease occurs when there is a defective gene on chromosome 15,  causing nerve cells in the brain and spinal cord to die.

DNA Extraction Lab

In this lab we asked the question: How can DNA be separated from cheek cells in order to study it? We thought that if DNA can be separated from a solution in the form of precipitate, then when alcohol is added DNA will unwind. To test our hypothesis we first began by homogenizing our cheek cells with polar liquid, in other words we began by scraping our cheek cells and swishing it in our mouth with Gatorade. Next we added salt, and soap which lyses or breaks down the cheek cells. Then we added pineapple juice which acted as an enzyme to break down any if the proteins that the DNA was wrapped around. Finally we added cold alcohol to the mixture and let it sit for 5 minutes. When we observed it after those 5 minutes were up we saw precipitate beginning to the top of the solution. This precipitate was the DNA that had been extracted from our cheek cells. This supports my hypothesis because after alcohol was added, precipitate started to form at the top of the solution.

While our hypothesis was supported by our data, there could have been errors due to not following the instruction very carefully. One example of an error we made is adding the wrong amount of Gatorade. This is because since we didn't have a measurement of how much Gatorade we were supposed to drink, some people had more Gatorade in their solution than others. This could have effected the ratio of Gatorade to other things like pineapple juice and resulted in little to no precipitate produced. A way to eliminate this error is by having a set measurement of Gatorade so everyone ends up having the same amount. Another possible error is not doing the lab in the right order. This is because for this lab all the steps were out of order and we had to put it back in the right order. It is very possible that we may have put it back together in the wrong order. For this error the only way of eliminating it would be to give us the instructions already in the right order or when we put it together to tell us whether it is correct or not.

This lab was done to demonstrate how DNA is separated for studying purposes and that DNA can be found everywhere in your body including places like your cheek cells. From this lab I learned the process of extracting DNA and all of the new vocabulary that is associated with it such as lysis and homogenization.  Based on my experience from this lab, I now know how to extract DNA from cells if that is every required of me in the future. 

Unit 4 Reflection

In Unit 4, we did an experiment called the coin sex lab. In this lab we tried to answer the question, can probability be used to predict what our offspring will be? We used coins to simulate the different genotypes of both the parents, and flipped the coins to determine the genotype of their offspring. We used the coins to display many different genotypes such as whether the offspring would be a girl or boy, have bipolar disorder, and what color hair and eye they would have. The experiment that tested what hair and eye color the offspring will have is called a dihybrid cross. In this cross, instead of using 2 coins (one for each parent) we used 4. This simulated the two different genes (hair and eye color) for each parent. Our results from this cross was that 14 out of 16 had brown hair and brown eyes and 2 had blonde hair and brown eyes. This result was far from what we had expected ; we had expected a ratio of 9:3:3:1 which means that in our results we were missing 2 phenotypes! This definitely shows that there is a limit to predicting our offspring's traits. We can always guess the probability of how likely a trait will occur but we can not predict if that trait will actually happen. This experiment relates to my life because this helps me understand why I have traits that the rest of my family does not.

 The coin sex lab was part of the Unit, Why is Sex so Great? In this unit we learned about the basics  genetics and about reproduction. We learned about the very basics, meiosis and mitosis, asexual and sexual reproduction, Mendel's Laws, dominance, and different patterns of inheritance. One of the most challenging parts of this Unit for me was understanding Mendel's Laws. Some of the laws such as the law of segregation and independent assortment were very complex and challenging for me to understand. Also the more difficult parts of genetics that we touched on such as epistasis and polygenetic were not easy for me to grasp either. However making the infographic and the coin sex lab made it easier for me to visualize what I was learning about and definitely made the topics easier to understand. The infographic was almost like a review on the whole Unit so not only did it help me to revise topics for the test but all the research I did for the infographic definitely helped me get a deeper understanding on concepts I needed help with.

From this Unit I have learned that in order to really understand any of the topics it is essential to actively listen to the vodcast. However I have also learned that listening is not always enough and it is important to take my own time to review difficult concepts. Overall in this Unit I have learned a lot about the basics of genetics and how I can be a better student for the future. 

Is Sex Important?

Sex is important in order for a species to stay alive, and reproduce successfully. There are 2 main different of sex, asexual and sexual.  For each type of sex there are it's benefits and costs.
In the book, the author tells us about the advantages and disadvantages of different types of  sex by writing in the form of various species. For an example the bdelloid rotifer  (or Mrs. Philodina) produces asexually by cloning. She says that this has been a big advantage for her species, "Sex may be fun, but cloning is much more efficient...In an asexual population, however, each female needs to have only one child for the population to remain the same size." Another asexual reproducer the E.Coli bacteria states that asexual reproduction is good for them because, " sex- by which I mean that acquisition of extra genes - is something we reap the benefits throughout their lives. If humans could do this, which they can't, it would be like suddenly adding a few genes for longer legs or bluer eyes."

However, sexual reproduction has it's advantages as well. For an example according to Muller's ratchet and Kondrasov's hatchet, " asexuals are driven extinct by the accumulation of harmful mutations- in other words, asexuals eventually die of genetic diseases." So being a sexual reproducer can ultimately keep your species alive for a much longer time, which is the ultimate goal. Another benefit of sexual reproduction is that they can avoid parasites unlike asexuals. "Since asexuals keep the same genes (give or take a mutation or two) from one generation to the next, parasites can easily evolve to infiltrate their defenses, annihilating clones.

In the end sexual reproduction is the best way of reproducing. This is because although it has it's own costs and benefits, the benefits outweigh the costs.

            

Unit 3 Reflection

Unit 3 was all about cells and how they function. Chapter 7 was mainly about the cell's structure and how it functions. We learned about the different parts of the cell, how they function, how they were discovered and about things like osmosis and diffusion. We learned about the 4 macromolecules of the cell, carbohydrates, proteins, lipids, and nucleic acid and what they do. Some parts of the cell are the nucleus, ribosomes, vacuole, mitochondria, and endoplasmic reticulum. We also learned about the 4 main types of cells prokaryotes who don't have a nucleus, eukaryotes who have a nucleus, autotrophs who make their own food, and heterotrophs who don't. Chapter 8 expanded and went into great depth about the process of photosynthesis which we touched on in middle and elementary school. We learned that photosynthesis which occurs inside chloroplasts is the process of taking water, carbon dioxide, and light energy to make glucose and oxygen. This occurs in 2 main parts the light dependent reactions and the light independent reactions (the Calvin Cycle). We also learned about the very important concept of ATP which and energy carrying molecule which is vital for the cell to function. The last chapter we learned about, Chapter 9 was all about cellular respiration. Cellular respiration is the exact opposite of photosynthesis, taking glucose and oxygen and turning it into water, carbon dioxide and ATP. Cellular respiration occurs in 3 different stages, glycolysis which takes place in the cytoplasm, Krebs Cycle which takes place in the mitochondria, and the electron transport chain which takes place in the inner membrane of the mitochondria.

Definitely one of the most challenging parts of this Unit was fully understanding the processes involved in both photosynthesis and cellular respiration. Cellular Respiration and Photosynthesis are both extremely complex processes so it was difficult for me to grasp what was going on in each individual part, and how that related to each other. However labs were really helpful in expanding my knowledge of different concepts such as the different cell types. With the microscope lab I was able too look at real cells with my own eyes and see how different types of cells are structured. For an example, after the lab i was able to easily recognize which cells were eukaryotic, prokaryotic, autotrophic, and heterotrophic.

What I have learned from this Unit is that making sure I go over the vodcasts a second time really helps. I realized during this Unit that with watching it one time I don't fully grasp the concept, leaving me confused for the next few days. However when I did take the time to watch it twice, I ended up with a pretty good understanding of what was taught.  Overall I think this Unit has taught me a lot only about cells, good studying habits that I should keep up with, and has made me a better student. 

Photosynthesis Virtual Lab

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?

If blue light shines on the plants, then there will be more plant growth. If green light shines on the plant, then there will be less plant 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 each type of plant under each color of light to test what the effects were. The control variables in this experiment were the amount of water, soil, and the viability of each seed. The variables I changed in this experiment were the colors of light.

Results:

Filter Color	Spinach Avg. Height (cm)	Radish Avg. Height (cm)	Lettuce Avg. Height (cm)
Red	18.33	13	11
Orange	15	8.33	6
Green	3	1.66	3
Blue	19	14	12.5
Violet	16	30	8.33

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 supported my hypothesis because as I suspected, blue was the color that produced the most plant growth and green was the color that created the least. I conducted tests with 3 different plants, radish, spinach, and lettuce. Across all of them green had the lowest height and blue the tallest. However there were some difference between the plants, for an example the lettuce did not grow as tall as the radish or spinach did.

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

I can conclude that the color green produces the least amount of plant growth, and blue light produces the most.

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

I expect an average of all the colors put together to be the effect of white light on a plant. Since, white light contains all of the colors, it makes sense to me that white light should be not as good as blue but not as bad as green.

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: Will increased amounts of carbon dioxide increase the rate of photosynthesis?

Hypothesis: If the level of carbon dioxide surrounding the plant is increased, photosynthesis will take place more rapidly.

Independent Variable: Amount of carbon dioxide

Dependent Variable: Number of bubble produced

Control: Plant

Data Table:

	Water	Carbon dioxide + water
Amount of bubbles in 1 min.	0	0

Conclusion:

In this lab we asked the question, will an increased amount of carbon dioxide added to the plant’s surroundings make photosynthesis occur more rapidly? Before performing the experiment I thought that it would increase the rate of photosynthesis, however after conducting the experiment I found that an added amount of CO2 does not have any affect on the plant. In one minute without adding any water, the amount of bubbles produced was 0 and with the carbon dioxide, the amount of bubbles was also 0.

This lab was done to demonstrate how changes in a plant’s environment affects how much oxygen it produces. From this lab I learned that even if more carbon is added to the atmosphere (something plants need) it doesn't necessarily mean that the plant will thrive. This lab deepened my understanding of photosynthesis because previous to this lab, I thought more carbon dioxide meant more photosynthesis. Based on my experience from this lab, if I ever decide to grow a garden I know the proper conditions to have a healthy plant.

Microscope Organism Lab

In this lab, we looked at different cells under the microscope and observed their characteristics. We learned how to properly use a microscope in this lab, and we got a hands on view of what real cells look like. 

After observing different cells under the microscope, I was able to find the differences and similarities between different types of cells. For an example, I found that all autotrophic cells (Spirogyra, Cynaobacteria, and Euglena) had a blue-green tint in them. Autotrophs are organisms  that make their own food, or producers. The reason why they all have a green tint on them is from the chlorophyll which is used to soak up light energy in order to make food. 
Heterotrophic cells (Animal Cell and Amoeba)  are cells that get their food and energy by consuming other cells. I classified that the muscle cells were heterotrophic since they had multiple nuclei and I classified amoebas as heterotrophic because they had pseudopods to consume other cells. 
The defining characteristic of a eukaryotic cells is that they contain a nucleus. Using this characteristic I classified the Animal cell, ligustrum, Spirogyra, Euglena, and Amoeba to be eukaryotic. In all of these cells I identified a nucleus which made me absolutely certain that it was a eukaryote cell. 
Prokaryote cells are single celled and without a nucleus. In this lab I found that the bacteria cells (Coccus, Bacillus, and Spirillum), and the cyanobacteria are all prokaryotic. Generally, almost all bacteria are classified as prokaryotic which was one of the reasons it let me to believe these cells were prokaryotes too. The other reason was that there was no identifiable nucleus. 

Spirogyra at 100X                    
Organelles Identified: Cell wall, Chloroplasts, Cytoplasm
Unique: Visible spirals in individual strands
Observation: Green streaks are formed by chloroplasts
Eukaryotic and Autotrophic

Ligusgtrum at 400X
Organelles Identified: Chloroplast, Epidermis cell, vein
Unique: Chlorplasts are extremely visible 
Observation: Visible holes within the individual circles
Eukaryotic and Autotrophic

Animal Cell at 400X
Organelles Identified: Nucleus, Muscle Fiber
Unique: Many nuclei visible as black dots
Observations: Individual striations are visible 
Eukaryotic and Heterotrophic

Cyanobacteria at 400X
Organelles Identified: One single cell
Unique: Individual cells are visible
Observations: Colors are various shades of blue green and purple
Prokaryotic and Autotrophic

Euglena at 400X
Organelles identified: Chloropast, Nucleus
Unique: Oval shaped cell is very clearly visible
Observations: Has a teal-blue pigment
Eukaryotic and Autotrophic

Ameoba at 400X
Organelles identified: Cell Membrane, Pseudopods
Unique: Many food vacuoles can be seen
Observations: Can see the pseudopods where the amoeba captures it's food
Eukaryotic and Heterotrophic

Bacteria Cells: General Shapes
Identified: Bacillus, Spirillum, Coccus
Unique: Bacteria are exteremely tiny compared to the rest of the cells
Observation: Compared to the other bacteria, coccus is the smallest
Prokaryotic and Heterotrophic