Unit 5 Reflection

     In this unit, we learned a lot of different things. First we learned about our genetic code, DNA. DNA is made up of a 5 carbon sugar called deoxyribose, a phosphate backbone, and one of 4 nitrogenous bases, adenine, guanine, thymine, and cytosine. We also learned about the difference between pyrimidines and purines.  Adenine and Guanine are purines, meaning that they are double-ringed. On the other hand, Thymine and Cytosine are pyrimidines, meaning that they are single ringed. A always pairs with T, and G always pairs up with C. DNA is also antiparallel: it runs from the 3' to the 5' direction.

Nitrogenous bases

    In the next vodast, we learned about how DNA copies itself. First a DNA unzips itself using helicase by breaking hydrogen bonds. DNA polymerase then matches corresponding nucleotides. The result is two identical DNA molecules, each containing one of the original strand's DNA. This type of replication is called semiconservative replication. 

     The next vodcast was about protein synthesis, the central dogma of biology. First we learned about the differences between DNA and RNA. DNA is double stranded, while RNA is single stranded. RNA has ribose, while DNA has deoxyribose. Finally, RNA has the base uracil, while DNA has the base thymine. The first step of protein synthesis is transcription. DNA unzips, and RNA polymerase matches nucleotides to make an RNA strand, known as messenger RNA. mRNA goes to the ribosome. The ribosome reads a codon, 3 bases at a time. Each codon codes for one amino acid. The result is a protein.
     Next, we learned about mutations. Mutations change the DNA. Point mutations change a single base. Examples include substitution and. We also learned about frameshift mutations, which include insertions and deletions.
     Finally, we learned about gene expression and regulation. It is very hard to explain, so it is better to see a picture.

Gene Expression and Regulation




I have understood most of what was taught in this unit. For me, the most confusing things were protein synthesis and gene regulation. Through labs and Mr. Orre's explanations, I understand them better, but still need practice with them. I feel that I am a better student. I learned to be proactive and relearn things that I had trouble understanding. A lot of the previous units make more sense now. I either had to apply knowledge from a previous unit or relate this unit to something else.
I am very curious about this topic. I want to learn more about protein synthesis and what causes mutations. Last unit, I took a VARK questionnaire to see how I learned best. I tried applying these habits to my study routine not just for biology, but for other classes. For the most part, it has worked.  This unit has been very interesting, and I have learned a lot.

Protein Synthesis Lab Analysis

     In this lab, we tested how proteins are produced by our body. First, a copy of a DNA gene, called Messenger RNA, goes to the cytoplasm. Next, the mRNA bonds to a ribosome. The ribosome reads the mRNA as a codon, three bases at a time and adds an amino acid to a chain. Amino acids bond together to make the primary structure of a protein The chain twists and turns to form a protein.

Protein Synthesis

     The effects of mutations on proteins can range from none to very severe. A substitution seemed to have the least affect. In our case, it did not effect the protein sequence. The worst it could do was changing one protein of the sequence.The next worst mutation was insertion. When an extra base was inserted into the DNA, the protein changed dramatically. Every protein after the mutation was different than the original protein chain. The proteins before the mutation stayed the same. The mutation with the greatest effect was the deletion. It completely changed the structure of the protein. It coded for different proteins than the original strand after the second protein. After the fourth protein, there was a stop codon, meaning to stop translating. The resulting sequence was only four proteins long. There is an effect on where the mutation is placed. For substitution, it does not matter where the mutation is. For insertions and deletions, the closer the mutation is to the beginning of the gene, the more damage the mutation will do.

Mutations

When I got to choose my own mutation, I decided to use a deletion. I used a deletion because it had the greatest effect on the protein in the previous problems. I decided to put my mutation at the very front. The first letter of the amino acid chain was changed. The result was a completely different protein. It had the greatest effect out of all the other mutations. I chose to put the mutation in the very front to maximize the power of it. Since the mutation was in the very front, everything was changed.

My mutation

There are many different types of genetic disorders caused by mutations. An example is Tay-Sachs disease. Mutations in the Hexa gene, which provides instructions for making beta-hexosaminidase A, an enzyme responsible for critical functions in the brain and spinal cord. Symptoms of the disease include loss of motor skills, vision and hearing loss, and paralysis. Although the disease is not very common, there are still people who have it. It shows the power of mutations. 

Gene whose mutations cause Tay-Sachs disease

DNA Extraction Lab Conclusion

     In this lab, we asked the question, "how can DNA be separated from cheek cells and be studied?" We found out that through homoginazation, lysis, and precipitation, DNA can be extracted. First we swished Gatorade in our mouths, which was the homoginzation. Gatorade is a polar liquid, and it breaks down the cell membrane. Next, we added, salt, which facilitates precipitation by shielding the negative ends of the phosphates of DNA, allowing them to move closer together. Soap and pineapple juice were also added to facilitate lysis. The soap interferes with the polar interractions in the phospholipid bilayers. The pineapple juice contains catabolic proteases, which break down proteins, called histones, which the DNA wraps itself around. Finally, we added cold alcohol, which is nonpolar, while the DNA is polar. Since opposites attract, the DNA floated to the top. Once these steps were complete, we saw DNA.  The DNA looked like little white strands. The way that we extracted DNA is supported by currently held science. This data supports our claim because since we saw DNA, then our procedure had to work.

   Although our results were expected, we made some mistakes. One mistake was not getting enough cheek cells. We did not scrape our mouths enough, and as a result, not much DNA actually showed up. Another mistake that we made was that we poured the alcohol too fast. This allowed the alcohol to mix with the Gatorade mixture. As a result, less DNA floated to the surface. In order to combat these problems, we should scrape our mouths more and pour the alcohol slower.
  This lab was done to demonstrate that DNA can be extracted. This lab related to our unit on enzymes and DNA structure. We were able to understand the processes in which DNA was extracted due to what we learned in the Chemistry for Biologists unit and the unit on DNA structure. Some examples include the fat that phospholipids have a polar head and a nonpolar tail. Based on my experience with this lab, I can extract DNA from other organisms, such as strawberries.

DNA in testube

Unit 4 Reflection

   The essential question for this unit was "Why is Sex so Great?"  In this unit, we learned about the different types of sex, how gametes are formed, how chromosomes are inherited, laws of inheritance, and genetic complications. We learned about each of these in detail.
   We first learned about the cell cycle. We learned how the life cycle of a cell. Next, we learned about asexual vs sexual reproduction. They both have costs and benefits. We then learned about how gametes are made. They are made through a process called meiosis. We also learned some important terminology.
  In the following vodcasts, we learned about the work of Gregor Mendel. He was the father of genetics. He crossed pea plants together and observed the results. His results are the law of segregation and the law of independent assortment. The law of segregation states that the gene pairs for a trait separate independently of each other during meiosis. The law of independent assortment states that gene pairs separate independently of each other.
  We then learned about how sex leaves you stuck. We learned about genetic diseases. We also learned about the different types of ways a gene can be expressed. These are incomplete dominance, codominance, epistasis, gene linkage, and polygenetics. Finally, we did a bunch of crosses.
   I have grow a lot during this unit. We had a big infographic project. We got a little bit of class time to do it, but not a lot. I had to time manage it I ended up doing a little each day. A lot of the content we learned was from middle school, but in more detail. It was kind of hard to remember every detail, but the big ideas were clear.
   I did a VARK questionnaire and found out that I am slightly Kinesthetic  learning preference. This means that I prefer to experience things and read things. To learn best, I need real world examples, trial and error, and labs and field trips. To study for tests, I need to role play and write practical examples and paragraphs. I should take brief notes with case studies and real world examples.
  All in all, I really liked this unit. It was really interesting. I had fun learning the content. Genetics really explains a lot of things in life. 

Coin Sex Lab Relate and Review

     In this lab, we simulated different types of crosses by flipping coins. Coins serve as a good model for determining what alleles get passed on. Each side is one allele, and each side has an equal chance of being chosen. In the lab, we used coins to simulate crosses. First we tried to predict the the sex of an offspring. We labeled the side of one coin with "x" and the other with "y." The other coin had "x" on both sides. We flipped each coin 10 times. The results were 6 boys and 4 girls. The next cross we did was testing whether a child would inherit Bipolar disease. Bipolar disease is inherited through  autosomal inheritance. Autosomal inheritance is where the gene is on one of the 22 chromosomes that do not determine sex. On one side of a coin, I labeled "x," and on the other side, "y." The other coin was labeled "x" on both sides. I flipped each coin 10 times. The result was 5 children with bipolar disease and 5 children without it.
    Next, we looked at colorblindness. Colorblindness is inherited through X-linked inheritance. It is a recessive trait. The "mother" was a carrier and the "father" had normal color vision. One coin was labelled XB and y, and the other was labeled XB Xb. When we flipped the coins, we got 2 boys with normal vision, 4 with colorblindness, and 4 girls with regular vision. The last cross was a Dihybrid cross. A dihybrid cross is where two traits are passed on at the same time. The rest of our crosses were monohybrid crosses. I expected a 9:3:3 ratio. 10 would be homozygous and 6 would be heterozygous. Our results were a 7:4:3:2 ratio. This could have happened because this was only a guess. Probability can only take you so far. It does not tell you exactly what will happen. It is only a guess.
     I can attribute the results that I got in these labs due to meiosis and recombination. These two processes create genetic diversity. Since alleles separate independently of each other, many different combinations can be made.
    This relates to events in my life. When my aunt and uncle wanted to have children, they did a genetic test to make sure that their child would not be prone to any genetic diseases. They knew that because of genetic inheritance, their baby could have genetic diseases. There was a history of genetic disease in their family. Once the results of the genetic test came, they saw that they were not carriers of the disease. because of this, they have healthy children. 

Genetics Infographic

Because the picture is too small, click on the following link to see it in the website in which I made it, where it is full size. 

https://magic.piktochart.com/output/9061385-genetics-infograph

Photosynthesis Virtual Lab

Question:  What is the effect of temperature on the rate of photosynthesis

Hypothesis: If higher temperatures make reactions faster, then higher temperatures will increase the rate of photosynthesis.

Independent variable: temperature

Dependent variable: amount of oxygen bubble present

Control: 10 degrees centigrade

The experiment will have 30 second trials. The temperatures will be 10 degrees, and 40 degrees.  All trials will have white light, with 25 light, and 1 scoop of dissolved carbon dioxide.

Degrees ( 0C)	Amount of Bubbles (Measure of Oxygen)
	Trial 1	Trial 2	Trial 3	Average
10	9	9	9	9
25	27	28	30	28 1/3
40	22	21	22	21 2/3

Conclusion

In this lab, I asked, “What is the effect of temperature on the rate of photosynthesis.” I found out that a higher temperature does increase the rate of photosynthesis, but when the temperature increased too much, then the rate of photosynthesis decreased. I found out that at 10 degrees centigrade, the average amount of bubbles in 30 seconds., which quantifies the rate of photosynthesis, was 9. At 25 degrees centigrade, there was an average of 28 ⅓ bubbles per 30 seconds. At 40 degrees centigrade, there was an average of 21 ⅔ bubbles per 30 seconds. This was expected, because the enzymes that drive photosynthesis cannot work at too hot or too cold temperatures. If the temperature is not ideal, then the enzyme will denature, and photosynthesis will not work as fast.

This lab was done to demonstrate the effect of temperature on photosynthesis. From this lab, I reviewed the concept of enzymes and photosynthesis. The lab demonstrated how temperature can denature enzymes and slow down reactions such as photosynthesis. I also learned how to design a simple experiment and identify parts such as controls and variables. Based on my experiences with this lab, I can easily design another lab and identify its parts. I could also test a different variable, such as amount of light.

Unit 3 Reflection

    This unit was all about the cell. We first learned about the cell, then how the cell evolved, We also learned what was in a cell, movement in the cell, and photosynthesis and cellular respiration. The main idea of this unit was that the cell is the most basic unit of life.
    In the first vodcast, we earned about how the cell was discovered and the cell theory. We then learned about the levels of organization of life and the differences between prokaryotes and eukaryotes. Finally, we learned and that macromolecules are present in cells and where. In the next vodcast. we learned about membranes. We found out about their structure and function and the different methods that molecules use to get in and out of the cell. In the next vodcast, we learned about osmosis and diffusion. We reviewed some terms and learned about what happens when water leaves and enters the cell. In the following vodcast, we learned how proteins are made and other various functions of cells. We briefly talked about mitosis, cellular respiration, and photosynthesis. In the next vodcast, we toured the cell. We learned about the different functions of organelles and where they are located. We also looked at the differences between plant and animal cells. Next, we learned about the story of cells. We learned how cells gradually evolved to be more complicated. The following vodcast was about photosynthesis. We learned what photosynthesis is, its products and reactants, where it takes place, and how it is performed. Finally, we learned about cellular respiration. We learned about the exact things about it as we did for photosynthesis.
     This unit was slightly difficult because there was a lot of concepts. There were a lot of different ideas and concepts. Also, there was a lot of memorization, especially in the photosynthesis and cellular respiration vodcasts. I understand most of the concepts, but I have trouble remembering all the terms and details of them. In addition, we did a lot of labs. I learned various skills from them, such as team work and how to use a microscope. From these experiences, I can do more types of labs.
     I want to learn more about the cell. I am interested in how cells communicate with each other. I am interested in learning more about organelle functions and functions of the cell.

Plant Cell

Animal Cell 

Egg Diffusion Lab

     In this lab, we first put two eggs in vinegar and left them for 48 hours. This was to insure that that the shell of the egg broke down. Next, we measured the circumference and the mass of both eggs. We submerged one egg in dark corn syrup (sugar water) and another in deionized water. We left the eggs in their respective solutions for 48 hours. After 48 hours, we measured the circumference and the mass of both eggs.
   Looking at the class data, the mass and circumference of the egg in sugar water went down. On average, the mass decreased by 51.7% and the circumference decreased by 23.67%. This was because of diffusion. There was more solute, sugar, than solvent, water, in the outside of the egg. The opposite was true inside the egg. Diffusion involves the moving of stuff from high to low concentration. The solute cannot move through the membrane, so water from the egg had to move out. 
     A cell's membrane changes as a result of its external environment because of its semi-permeable membrane, and forces such as passive diffusion acted on it. When we put the egg in vinegar, there was no change because the egg shell prevented stuff from moving out. However, once we put the egg in deionized or sugar water, the egg shell was gone because the vinegar caused the shell to erode. When we put the egg in sugar water, water diffused out, When we put the egg in deionized water, water diffused into the egg. 
     This lab demonstrates the biological concept of diffusion. In the egg with sugar water, there was a low concentration  of water outside and a high concentration inside. The solution was hypertonic. In order to keep the concentration the same, water needed diffuse out. Since sugar cannot move through the membrane, only water could diffuse out. With the egg in deionized water, there was a high concentration outside and a low concentration inside. The water diffused in, and as a result, the egg got bigger. 
     This lab can be applied to real life solutions. Have you ever wondered why water is sprinkled on vegetables? The principles of diffusion easily explain this. Since there is less water on the outside of the cells than on the inside, through diffusion,water will move into the vegetable cells, expanding them. This creates the impression of a larger vegetable. Also, roads are sometimes salted to melt ice. Salt mixes with the water to form salt water. This effects plants on the side of the road. Since the water on the outside has salt, water diffuses out of the plant to balance it out. This results in shriveled up plants. As you can see, diffusion is everywhere.
     Based on this experiment, I would want to test whether fruits with a thin skin, such as apples perform diffusion. The shell or skin sometimes blocks diffusion, but what happens if the skin is thick. The setup would be the exact same thing. A whole apple would be placed in corn syrup and a whole apple would be placed in deionized water. 

Control (DI Water)

Group #	2	3	4	5	6	7	AVG
% Change in Mass	-0.54	-1.47	10.5	.74	-4.2	-5.1	.176
% Change in Circumference	-2.89	0	2.1	0	-12.9	-4	.201

Sugar Water

Group #	2	3	4	5	6	7	AVG
% Change in Mass	-49.77	-55	-52	-44.6	-52.4	-56.7	-51.7
% Change in Circumference	-23.6	-28	-20.6	-29.4	-37.5	-37.5	-23.6

Before

After

Egg Cell Macromolecule Lab Conclusion

           In this lab, we asked the question," Can macromolecules be identified in an egg cell? We found out that in the egg membrane, polysaccharides and lipids were found, in the egg white, polysaccharides and proteins were found, and in the egg yolk, monosaccharides, polysaccharides, and lipids were found. We figured this out through indicators. If benedicts solution and boiling water are placed in a solution containing monosaccharides, the benedicts solution will change from blue to green or orange. If iodine is placed in a solution containing polysaccharides, the the sample will change from brown to black. If Sudan III is placed in a solution containing lipids, then the sample will turn from red to orange. If sodium hydroxide and copper sulfate are mixed into a solution containing proteins, the sample will turn from blue to purple. This evidence supports my claim because when the indicator was added, the sample would turn positive for the macromolecules that I listed.
      However, our data was unexpected because some of the macromolecules that were suppost to be present were tested negative for. A possible error that could have caused this was because the indicators were not properly mixed into the different parts of the egg. For example, there was suppost to be protein in the egg yolk, but since the indicator was blue and the yolk was yellow, it looked green because they were not properly mixed. Another error was that not enough indicator was put it. This would have led to not a full color change. Since the color did not change enough on various tests, we marked them not having a particular macromolecule, while in reality they could have if more indicator was put in. In order to stop these problems, the indicator needs to be put in greater amounts and mixed better.
     The purpose of this lab was to find what macromolecules are present in the different parts of an egg. This lab relates to what we learned in class because many of the places that macromolecules we were taught that appeared also were tested positive for in the lab. For example, we were taught that lipids are formed in membranes. In the lab, the egg membrane tested positive for lipids. We essentially verified what we were taught. Finally, this lab could be applied to other labs by using the same indicators to test for macromolecules in other foods. 

20 Questions in Science

One of the 20 biggest questions in science that I have is how to beat bacteria. I am interested in this because the discovery of antibiotics greatly impacted the quality and length of human life. Now,we are being threatened by antibiotic resistant bacteria. This threatens to bring us back to times where millions of people died of bacteria causing infections every year. To combat this, people are exploring the genetic sequence of bacteria and making new antibiotics. In addition, there has been research of transplanting bacteria from fetal matter  that are good to patients who have the bad bacteria.

List of Questions in Science that I have
1.) How did bacteria evolve into humans?
2.) How advanced will the Human race become?
3.) Will we ever lived in a society with artificial intelligence?
4.) Can we stop global warming?
5.) Will we be able to manipulate what genes we pass on to our children?
6.) Can we find an effective cure for viral infections?
7.) Can we make medicine with minimal side effects?
8.) Can we travel to other galaxies?
9.) Can we find a source of energy that is cheap, reliable, renewable, and non-polluting?
10.) Can we have vaccines against cancer?
11.) Can we map an evolutionary tree that maps relationships between all species that have ever existed.
12.) Can we figure out the quality of our air?
13.) Can we figure out how fresh and how nutritious our food is?
14.) Can we easily figure out what is in our food?
15.) Can we find out how safe our water is?
16.) Can we easily make recycled paper.
17.) What are the most effective ways to use less water?
18.) How can we lower cost and improve efficiency of solar panels.?
19.)  What are the most effective ways to reduce our carbon footprint?
20.) How can we make life less susceptible to disease and climate change.