Unit 5 Reflection

Unit 5, named Walking the Dogma, described and went in depth to the function and processes surrounding the DNA in each and every one of our cells. The unit started when we learned about the structure and function of DNA and its code- which was very easy to grasp for me because it was extremely practical. The steps were logical and I felt like watching the videos of the RNA making proteins helped me see what I was learning. DNA expression and regulation, since I could relate it to our bodies, were easy to understand. I think of expression like “that is why it is there” for example having two eyes, and regulation like the opposite, why we don’t have 37 eyes. Though this is a simple example, it helped me relate the science to life. For me, the mutations vodcast was confusing because there were a ton of mutations and things that could go haywire in a DNA. I didn’t know that these all things could happen so it was a bit overwhelming! But, after doing the mutations lab, the concepts made perfect sense and were easy because I tried doing the mutations myself. What made this unit easy was that it was very convenient to try things out and figure out the processes like base pairings and mutations ourselves. And doing the DNA extraction lab towards the end of the unit was also cool and informative to another DNA process. Overall Unit 5 was short and sweet!

Protein Synthesis Lab

To start making a protein, the DNA is transcribed to RNA in the nucleus. Then it is converted into messenger RNA (mRNA) which is sent out of the nucleus to a ribosome. RNA Polymerase pairs the corresponding nucleotides with a RNA strand. In the ribosome, the RNA reads three bases at a time to form codons which code for amino acids. These amino acids are joined together to form a protein. 

In this lab we tested different kinds of mutations that could potentially occur while DNA is being transcribed and their affect on the protein structure. The mutation that caused the least damage to the protein was substitution. This mutation had the least effect on the protein because though the amino acids changed, it was still a complete protein.  The frameshift mutations caused much more damage to the protein because most amino acids were changed and there were extra incomplete codons in the end.


In the lab, after trying different mutation, we were asked to chose the one that would be the most harmful to the protein. I chose deletion, because not only does it change entire amino acids, the end codon is left incomplete. I decided to take out the first C in the DNA sequence, and was left with a completely altered RNA, as expected. 

A mutation that I didn't know stemmed from the genes is sickle cell anemia. It is the result of a point mutation, where one nucleotide is changed for hemoglobin. This causes the hemoglobin in red blood cells to change into a distorted shape and clog the capillaries, cutting off circulation.

DNA Extraction Lab

Conclusion

     In this lab we asked the question, "How can DNA be separated from cheek cells in order to study it?" We found that this procedure involved three steps including homogenization, lysis, and precipitation. We carried this out by mixing our cells in a polar liquid. This breaks down the cell and nuclear membranes of the cheek cell, homogenizing it. Afterwards we added soap to the mixture, initiating lysis which disintegrated the membrane. We used pineapple juice to break down histones found in DNA, causing it to uncoil. This was possible because pineapple juice, like a few other liquids, has catabolic proteases and  enzymes, that help to break down the histones. Finally, we poured cold isopropanol alcohol into our test tube and due to its non-polarity combined with the polarity of the DNA, the DNA became a precipitate and rose to the top of the isopropanol alcohol layer.  This data supported our procedure because, to put it simply, it worked!
     While our hypothesis was supported by our data, there was one vital error that we carried out. After adding pineapple juice and soap, we were supposed to gently invert the test tube 6 times and we chose to do this step after adding the alcohol, so the two layers got mixed. Out of the four people in our group, two people's DNA were ruined because of this. This error happened because we created our own procedure without a more educated approval to tell us when to put each step. Another hypothetical error could have been the time factors. If one gargled gatorade for more or less than thirty seconds or observed for more or less than five minutes, results might be changed though the effect isn't drastic. To minimize these rather small to extremely important details, get a teacher's approval before starting and keep a timer handy!
      This lab was done to demonstrate the process of extracting DNA from a cell. From this lab I learnt how to remove DNA from its original position in a cell which helps me understand the concept of DNA and its structure. Based on my experience from this lab I applied the concepts around DNA and I now have a
 sample of my own!








      

Unit 4 Reflection

This unit was about how things from cells to organisms reproduce. Mitosis and Meiosis along with asexual and sexual reproduction were big concepts and what helped me learn these was the infographic. I understood the process of mitosis so understanding meiosis was quite easy because it was just double the steps with a slightly altered end result. Again, many terms were difficult to memorize but learning them in related bits categorized them in my mind. The infographic helped me study because I went over all the information one last time before taking the test. Check out my Infographic here: https://magic.piktochart.com/output/9417972- biology-infographic Also at the end of the unit, we took a VARK questionare to see what type of learner we are. I got a 12 in kinesthetic and Read/Write learning, and a 10 in both Visual and Aural learner. This surprised me because I thought I was a visual learner but I’m a little bit of everything. That was cool and so was this unit.

Coin Sex Lab Relate and Review

In this lab, we used coins and a partner to simulate the assortment of alleles resulting in different genotypes and phenotypes during sex. The flipping of the coin represented the random combining to create new genes and the probability of a certain type appearing was 50%. The results we got followed the trend of the dihybrid cross simulation but obviously wasn’t exactly the same because real life isn’t probable. We can use probability to state what the possible alleles could be after meiosis or gene segregation, when cells are recombined, and to understand the number of homozygous or heterozygous individuals after a monohybrid cross. In my life, if I had a disease, whether autosomal or X-linked, I could see the possibility of my child going through the same disease by using probability.

Genetics Infographic

Below is a picture of my infographic but it is really tiny so if you don't want to kill your vision, click the link! 

https://magic.piktochart.com/output/9417972-biology-infographic

Unit 3 Reflection

Unit 3 was about generally about cells. First we learnt of different parts of an animal and plant cell, followed by learning two cell processes, photosynthesis and cellular respiration. This unit was difficult for me because I am really bad at memorizing things and there were a ton of terms. But what helped me was learning the terms as I learnt the processes so I was doing two things that I benefitted from at once. I understood cells in depth during this unit and as a class, it was interesting to dig deeper into specific cell processes. I want to learn more about how plants that live in the ocean where it is hard for sunlight to reach photosynthesize. For the test next week I plan to study by doing the regular reviews with vodcast and textbook notes but this time I will review the questions I got wrong in the CFU quizzes as a new strategy. Hopefully it will help me!

Egg Diffusion Lab

10-7-15

In this lab, we tested eggs to demonstrate how a cell’s internal and external environment changes. First we soaked two eggs in vinegar, which dissolved the egg shell so we could look into the membrane. After measuring their initial circumferences and masses, we placed one egg in deionized water and the other in sugar water. After 2 days we looked at the eggs again and most of the eggs in water burst while the eggs in sugar water shriveled up.

According to the class data, the egg in sugar water became significantly smaller the mass shrinking by about 50%  and the circumference shrinking by about 20%. The reason this happened was because the water that was inside the cell went out of it to dilute the sugar that was surrounding the egg. The solvent in this solution was the water and the solute was the sugar.

When a cell’s environment changes it either grows; like in a hypertonic solution, or shrivels up; like in a hypotonic solution. When the egg was in vinegar, it disintegrated the shell and but the egg stayed the same size since it was in an isotonic environment. When the egg was in water it also grew since the water diffused into the egg. While the egg was in the sugar water it shriveled up and shrunk significantly since it sat in a hypotonic solution for so long. The water inside each cell passively diffused across the membrane, from an area of high to low concentration.

This lab mainly helped demonstrate the differences between isotonic, hypotonic, and hypertonic solutions. We experienced an isotonic solution with the vinegar, hypertonic with water, and hypotonic with the sugar.

In life, these applications are used daily by different people. Fresh vegetables are drizzled with water to keep them hydrated and healthy. The water goes inside the cells of the vegetables keeping them big and juicy. Salt is used to de-ice roads because the salts cause the water to diffuse out of the ice, leaving behind a driveable road. But, if there are plants alongside the same road it could do harm to them because the salt will suck out the water it needs to grow and flourish since salt and water is a hypotonic solution.

Based off this experiment I would want to dig deeper to the cellular level and test individual cells under a microscope in these solutions. I would want to see how each organelle is affected rather than a whole egg.

Class Data: Control (DI water)                            %change

Group#	1	2	3	4	5	6	7	AVG
Mass	N/A*	N/A*	.74	.37	.45	N/A*	6.95	1.8
Circumference	N/A*	N/A*	1.2	1.7	0	N/A*	14.37	4.3

*Egg burst

Class Data: Sugar Water                            %change

Group#	1	2	3	4	5	6	7
Mass	-46.70	-52.80	-52.60	-49.70	-41.71	-39.58	-47.70	-47.25
Circumference	-22.40	-18.75	-26.30	-26.60	-32.35	-21.21	-13.00	-22.94

Egg Macromolecules Lab Conclusions

In this lab we asked the question, “Can macromolecules be identified in an egg cell?” After testing the egg membrane, we found all the macromolecules we tested for, including lipids, proteins, monosaccharides, and polysaccharides. In the yolk we found lipids and the egg white we again contained lipids, proteins, and monosaccharides. On a scale of one to ten, monosaccharides’ existence were a 5 in the membrane and a 2 in the egg white. We knew this because the solution of the egg part and benedicts turned green. Polysaccharides in the membrane were a 7 out of 10 because the color of the iodine mixture turned from light to dark brown. Proteins were a 5 in the membrane and scored a 3 in the egg white because the sodium hydroxide copper sulfate changed from blue to pink/purple. Finally lipids were found in all of the egg, being a 6 in the membrane, 4 in the yolk, and 2 in the egg white. We knew this after the Sudan III color changed from red to  pink/orange. 
One error that may have caused deterred results was the egg not mixing well with the solution used to test its presence. In some directions it said to mix them and in others it didn’t specify. If this happened, some solutions may have a brighter or lighter color and may be interpreted wrong. Another thing that could’ve gone wrong was putting too much or little solution into the egg filled test tubes which could cause too much or too little color, again leading to misinterpreted results. One way to avoid this is to specifically state in the directions the exact amount of drops to put in and whether to stir or not. Another recommendation would be to have more than one test for each egg part just to make sure the results are true. 
This lab was done to model the existence of macromolecules in cells. From this lab I applied the information we learnt in class to real cells which helped me visualize the concepts. By seeing lipids, proteins, and mono/polysaccharides in the cells I took the information from the vodcasts and textbook about macromolecules and related it to cells in eggs and many other areas and how they exist everywhere. Based on my experience from this lab, I was provided with an application of these foundational concepts, which will help me when the class goes deeper into the structure and function of cells.

20 Questions

     Even though it is not the game 20 questions that we all love to play when we are bored out of our minds, the 20 big questions of science are called big for a reason. Even though all of these inquiries are very interesting, I think the question "Can we live forever?" is something that, if answered "yes!", will probably be disastrous! I was intrigued by this question because if it is something that can happen, it will change everyone's life because they can live until the sun blows up. But after that, will they keep on living? I thought this question was interesting because it leads to so many more thoughts! One hypothesis for this question could be, If bodies stop expanding, then humans or other species can live forever. Though this is a very loose statement, scientists have used this concept to come very close to an answer.

20 of the many questions I think about are listed here:

1. How did we develop complex emotions?
2. Why do we see in color?
3. Will we ever be able to live on Mars?
4. Why do people cry?
5. Why does hair curl?
6. How do muscles remember how to do things? (referring to "muscle memory)
7. Why do people look different?
8. Is "natural born talent" actually real?
9. How do airplanes fly?
10. What in our body lets us sing?
11. Can you survive without sleep?
12. Why do some things taste like a smell?
13. Why are expressions in dance so hard to master?
14. Why do people lose and gain flexibility?
15. Why do we still have so much hair in some places of the body and very less in other places?
16. Why is it bad to look straight at the sun?
17. How much longer will the earth exist?
18. Is it possible to revive dead people?
19. What causes us to make bad choices?
20. Why is math so complicated?

Identifying Questions and Hypotheses

     The Good Samaritan Experiment, carried out in 1978, tested the helping behavior of humans while placed in different circumstances. The set up of this experiment includes many adolescents in a room learning about religion. Then once the lesson was over, the children were asked to move from one building to another. Some were given many minutes to pass to the next classroom and others were told to move locations in a haste. While walking to the next building, the students would see an "injured" man and the experiment would essentially test whether the students would help or not.
     The full experiment can be found at https://explorable.com/helping-behavior
     The main question of the study was to find out if students would be a Good Samaritan and help out an injured man, under various circumstances. They tried this experiment and used variables like lack or length of time and the effect of religious or nonreligious values.
     The experiment tested three hypotheses. The first one was, If people are thinking about religion and higher principles, they would be no more inclined to show helping behavior than laymen (a non religious person). The second one held as, if people are in a rush, then they would be much less likely to show helping behavior. And finally, If people are religious for personal gain, then they would be less likely to help than people who are religious because they want to gain some spiritual and personal insights into the meaning of life.
     These hypotheses were based on prior knowledge on human behavior. The first one argued that people who are religious and non religious can have the same values to help others out, which is true in many cases because people who aren't god-fearing, usually help because they have good morals. The second one stated that people who are in a rush won't help out, which can be accurate because when a person has some work to finish, they will put themselves first. But this statement may not hold true in all cases, which is why they took the experiment. The last hypothesis hints that people who are religious for personal gain are selfish, which may have been true in 1978 but where we live today- being religious will not give you more gain in society than others.

Cheese Lab

9-21-15

Analysis

In this lab we asked the question, “What are the optimal conditions and curdling agents for making cheese?” We made the claim that if a cow’s stomach, where renin is found, is warm and acidic, then renin will contribute to the making of cheese best in a warm environment with a pH lower than 7. We found that renin caused the fastest curdling time but chymosin was the most consistent, making curdles in almost every situation. For example, renin curdled the milk by 5 minutes in the hot and acidic environments but didn’t curdle at all when the milk was in basic and cold areas. But, the chymosin, curdled at the same rates and more, having curdles by 20 minutes in the basic environment. The reason the milk curdled quicker in the acidic and hotter environments were because these factors denatured the enzymes quicker. This data supports our claim because the enzymes chymosin and renin, were affected by the pH and temperature, to curdle faster.

While our hypothesis was supported by our data, there could’ve been errors due to inconsistency in checking for curdles. We checked in five minute increments, but the fastest curdling agents and environments could have curdled in four, three, two, one, or even less than one minute. This error is pretty unavoidable because every time we checked, we would have to take the experiment out of its environment but I think checking more often would result in more accurate data. Another hypothetical error could’ve been forgetting to invert the test tube 3 times after adding the curdling agent, something our group almost forgot to do. This could’ve ruined the data accuracy because the curdling agent would me more concentrated in some places more than others. To avoid this error, simply follow directions! One suggestion for the next lab would be to have one hot and cold station per group to reduce the risk of getting test tubes mixed up or broken while walking across the room.

This lab was done to demonstrate the different factors including changing pH, temperature, and curdling agents, that can influence enzymes in milk. We applied what we learned in class about changing substrates, which in this lab were the renin, chymosin, and buttermilk, or pH and temperature, to have faster or slower results. From this lab I learned about changing the activation energy by using different variables which helped me understand the concept of the chemical reactions we covered this unit. Based on my experience from this lab, I applied that when baking, the food will be made quicker under hotter circumstances because the temperature speeds up the chemical reaction.

Class Data	Time to Curdle	(minutes)
Curdling Agent:	chymosin	rennin	buttermilk
Acid	5	5	5
Base	20
pH control	15	10
Cold
Hot	5	5
temp control	10	10

Unit 2 Reflection

     In the beginning of Unit two, we touched some basic chemistry for biologists which included a review of atom structure and solutions and we learnt about polarity, cohesion, and adhesion. Then we were introduced to many concepts surrounding macro-molecules, which are carbohydrates, lipids, proteins, and nucleic acids. Carbohydrates are sugars that provide energy and are usually made of 1, 2, and 3 or more rings. Lipids are made of long chains of carbon and hydrogen and they store energy. Nucleic Acids are made of repeating nucleotides and they store information, while proteins are made of amino acids and they support our bodies and speed up chemical reactions. The hardest part for me in this unit was remembering all of these definitions and separating their unique structures and purposes. We also learnt about chemical reactions and components that can speed up or slow down these processes. Enzymes speed up chemical reactions by lowering the activation energy, and they are the machines of the body, also known as catalysts. In class we demonstrated this lab by curdling milk into cheese, but using different components to speed up or slow down the curdling time. I thought this was a great way to apply the information learnt in class and you can read a full analysis on my blog, skmbiologyp6.blogspot.com. Attached below are two pictures, one showing the structures of the four macro-molecules and the other provided as a visual representation of an enzyme lowering the activation energy of a chemical reaction. Overall, this unit was very informative and I learnt a lot, and I look forward to learn more around these topics.

http://www.biology101.org/images/macromolecules.jpg

http://academic.pgcc.edu/~kroberts/Lecture/Chapter%205/05-05_CatalystGraph_L.jpg