Unit 5 Reflection

This unit was all about how DNA and RNA helps our body make proteins that help it function. This process is called protein synthesis. In this process, DNA first replicates itself into a one stranded copy called mRNA, which replaces base T with base U. This process of making RNA is called transcription. Next, the mRNA leaves the nucleus and goes to the ribosomes. Here, the ribosomes take groups of three base pairs called codons, and make amino acids. All the amino acids that the ribosomes make are chained together to form the protein. These proteins help our body work. Here is a visual example of protein synthesis.

 I also learned how mutations in this process affect our bodies. The most dangerous mutations are probably the frameshift mutations, either insertion or deletion. These either change the protein completely, or don't make the protein at all. Any mutation, either frameshift or substitution at the beginning of a sequence really causes damage to the end protein. Here is a visual representation of how mutations affect the protein.

The protein synthesis lab really helped me understand this topic, and I think at first, I was at a 3 on a scale of 1-5, and now I am at a 5. If there was one topic from this unit that I had to work on, I think it would be gene expression and regulation. Was that vodcast just an extension of the protein synthesis vodcast? In the last unit, I took a survey and learned that I learn best with hands on activities. This unit, I did the lab conclusions very carefully and thoroughly, and learned a lot from the DNA extraction lab and protein synthesis lab. In all, I am a better student than I was at the beginning at the unit, both content based and skil based. 

Protein Synthesis Lab

Protein synthesis has three different steps. The first one is transcription where DNA is copied into a mRNA, which is where uracil is substituted for thymine and it is a single strand. The mRNA then leaves nucleus and travels to the cytoplasm. The next step is called translation, where the actual protein is made. In this step, the mRNA attaches to the ribosome, and the ribosome matches each codon to an amino acid. After translation is finished, the amino acids fold up to make a protein!

The mutations that seemed to be harmless or very in affective seemed to be the small substitution mutations. When taking out a letter and replacing it with the other, the protein did not change at all. However when DNA had a letter added the effects were obvious. Even when the strand was deleted the protein turn out to be a disaster. However, I wanted to see what would happen if we affected the beginning of the sequence, so I used substitution at the begging, and there was no start codon, so there was no protein. I think that any mutation, either frameshift mutations (insertion or deletion) or just substitution to the start or end of a sequence would completely change the end result. In the middle, these mutations aren't quite as harmful, especially with substitution. This is why the location of the mutation matters.

To make a mutation with maximum effect I substituted one of the base pairs in the first codon. I chose this because it would change the start codon, which would prevent the ribosome from making a protein at all. Substitution has to occur in the start of the sequence for it to have a major effect, otherwise it's effect will be very minor, like what we saw with our first substitution, where the protein didn't change at all.  

Proteins normally help us carry oxygen in our blood and digest food, so mutations can damage these processes or even stop them completely! And it's not only these things that mutations could affect, it could affect any other phenotype which humans should have. Uner Tan syndrome is a genetic disorder caused by a mutation in the DNA, and it causes people to walk on all fours. These are one in many ways mutations can affect our lives.

DNA Extraction Lab

The question of the lab was, "How can DNA be separated from cheek cells in order to study it?". We claimed that DNA can be extracted through three different steps, homogenization, lysis, and precipitation, which is where the DNA first becomes visible. Homogenization was when we swished Gatorade in our mouth and spit out cheeck cells, and let the Gatorade break them down. Lysis was when we added salt, detergent, and then the pineapple juice as the protease  to destroy the cell membrane or wall. Precipitation was when we added alcohol and the DNA became visible at the top because the Gatorade is nonpolar and the alcohol is polar. After our procedure was completed, we were able to see small strands of white lines in our alcohol solution which was DNA and after completing the procedure twice we got the same result. This shows that DNA can be extracted from cells and can be seen if following the right procedures.

While our hypothesis was supported by our data, there could have been a few errors. First, the alcohol could have mixed with the Gatorade if you poured it too hard. That would cause the DNA to remain unseen because it would not rise to the top. Second, there could have been too much  Gatorade and/or too little cheek cells . That could have caused the DNA to not show up or not float up to the alcohol during precipitation. Due to these errors, in future experiments, I would recommend to have a measured amount of Gatorade and wipe the inside of the cheek with cotton around ten times. To solve the Gatorade and alcohol mixing, you should tilt the Gatorade test tube and let the alcohol trickle in. 

  This lab was done to demonstrate that DNA could be separated from cheek cells in order to study and observe it. From this lab I learned and what an enzyme help create a reaction an eventually some DNA, this helps me understand how a enzyme works on a larger scale. Based on my experience from this lab, I could apply this knowledge to another situation if I were to maybe look at DNA on more of a molecular level, and needed to re-create someones DNA in that kind of form.

Unit 4 Reflection

This unit was all about sex and why it's so great and interesting! I learned a lot about myself and what helps me learn. In the VARK questionnaire, my visual score was a 7, my aural score was a 9, my reading and writing score was a 2, and my kinesthetic score was a 10. I learned I learn better with hands on activities, and in the case of biology, I learn the best with labs. The Passing on My Genes Mini-Lab and the Coin Sex Lab really helped me understand how new combinations of alleles are made and how they are passed on. My second best learning style is hearing. these are the two things I will use to study for the test. For the kinesthetic part, I will try to find online labs relating to what we learned this unit, specifically on mitosis and miosis. For the hearing part, I will listen to Mr.Orre's vodcasts again and try to take in the information. The themes about this unit was all about the cell cycle and Mendel's laws in genetics. We also learned about genetics and the difference between mitosis and meiosis. My strengths were using Punnett squares to predict what offspring would look like and the autosomal and x linked inheritance. Some things I need to work on are mitosis and meiosis, and how they are different. I learned a lot from the infographic because the infographic made me understand the different topics that were covered in the unit. Pictures and the information brought everything together for me. I am indeed a much better student than I was before this unit started!

Coin Sex Lab

In this lab, we learned how to use punnet squares to predict what our offspring will look like and what traits they will have. The coins served as genes and the two sides of the coins served as alleles. The flipping of the coin modeled meiosis and putting them together modeled recombination, or in other words, sex. The coins also showed how probability of something happening can be different from what actually happens. We did multiple autosomal crosses, where the sex chromosomes are not involved, and one x-linked cross, which is when the sex chromosome are involved. We used two sets of a coin each to represent a monohybrid cross, and two sets of two coins each to represent a dihybrid cross. In a few of our tests we labeled both sides of the coin the same letter to represent a homozygous trait, but in others we labeled the two sides differently to represent a heterozygous trait. When we preformed the di-hybrid cross, we got results that were slightly different than what was expected. The punnet square gave us a phenotype ratio of:

9 Brown Hair, and Brown eyes : 3 Blond Hair, and Brown eyes : 3 Brown Hair, and blue eyes :

1 Blond Hair, and Blue eyes

Our experiment had slightly different results, and gave us the phenotypic ratio of:

8 Brown Hair, and Brown eyes : 4 Blond Hair, and Brown eyes : 2 Brown Hair, and blue eyes :

2 Blond Hair, and Blue eyes

The slight difference between the probability, and what actually happened is due to the fact that probability is not always what is going to happen. It is possible to cross two heterozygotes, and get two recessive alleles in all ten offspring just like you can flip a coin ten times and get heads every time. This lab demonstrated the limits of probability. Probability can give you odds on what can happen, but until the event occurs there is no guarantee it will happen. Relating back to the coin, the probability of getting heads two times in a row is a 25% chance, but until you flip the coin twice you can't know if you will get two heads.

This lab relates to me because if/when I have children, then I can use probability to predict what they might be like, but I have no way to know for sure what traits they will have, until they are born.what traits they might have gotten until they are actually born.

Genetics Infographic

Because this infographic is too small, click for a larger version here

Unit 3 Reflection

This unit was about cells, their structure, and their function. It was also about the concepts of photosynthesis and cellular respiration. My strengths are the function of cells and all their parts. I know the organelles by heart (ribosomes, nucleus, ER, Golgi body, mitochondria, cell wall, cell membrane, cytoplasm, lysosome, chloroplast, etc.) I know the functions of all these organelles and how they complement each other. At first I didn't understand diffusion at all, but the egg diffusion lab really helped me understand it better. I got a wider understanding of hypertonic and hypotonic solutions. I really learned how diffusion affects a cell's size. I understand photosynthesis a little better after Mr. Orre explained it in detail with the diagrams in class. However, my weakness in this unit is cellular respiration. I get the products and reactants, but I don't understand the details of it yet. Maybe to study, I will watch Mr. Orre's vodcast again and draw diagrams without my notes and label them. The lab with the microscope was really fascinating to me because I got to see some organelles up close with different cells. I am still curious about what ribosomes look like, although they are very hard to see with our microscopes. I want to learn more about the process of photosynthesis because it really fascinates me. I look forward to the next unit.

Egg Diffusion Lab

The purpose of this lab was to find out how a cell's internal environment changes as its external environment changes. We took two eggs that were both dissolved in vinegar to dissolve the shell and expose the membrane, and we put one of them in deionized water and one of them in sugar water. We took the mass and circumference of each egg before we placed them in the solutions, and took the same measurements after we put them in the solutions. Them we knew if the cell shrunk or grew in the different solutions, so we would have a conclusion for our question. 

Our class data showed that the mass and circumference decreased as the sugar concentration increased. Because the cell had more water(solvent) in it than the outside and passive diffusion goes from high concentration to low concentration, or in other words, the sugar water was a hypertonic solution, the water diffused out of the cell, and as a result, the cell shrunk.  

A cell's internal environment as its external environment changes. If the external environment has many solutes in  it, then the water will diffuse out of the internal environment of the cell and make the cell shrink. Meanwhile, if there a little or no solutes in the external conditions, then the water diffuses into the internal environment of the cell and makes the cell grow. This is all because of the concept of diffusion and the different types of solutions. Vinegar is a hypotonic solution, where there was more water outside than inside the cell, so the egg grew from when it had its cell.   

This lab demonstrated the concentration of diffusion, which we also learned in class. We learned that when its a hypertonic solution, water diffuses out and the cell shrinks, and when it is hypotonic, the water diffuses in and the cell grows. 

This lab can also relate to real life.Fresh vegetables are sprinkled with water because the water is hypotonic, so the vegetable becomes bigger which makes it more appealing. Salt along roadsides kill plants because salt is hypertonic, which will make the plant cells shrink. When they shrink, they can't function which also means the plant can't function. 

If I were to test another thing based on this, I would test the affect on salt water on the body. I would want to see what exactly happens to the human cell. 

Egg Macromolecules Lab

For this lab, we asked the question, " Can macromolecules be identified in an egg cell?" We found that in an egg yolk and an egg membrane, monosaccharides were present. Lastly, we found out that in an egg white, proteins are present. In the monosaccharide test, both egg yolk and the egg membrane tested positive. In the egg yolk test, it turned blue, but also with a hint of green. With the membrane, it turned to almost complete blue. This evidence supports our claim because for a monosaccharide to be present, the solution had to turn blue, and for those two parts, it did. In the polysaccharide test, the egg white tested positive. The solution turned to a darker blue and almost purple color. This supports our evidence because for it to have proteins, it had to turn form blue to purple, and it did.

One possible error in this experiment could have been the perception of color from different eyes. If I thought that a dark blue was not close enough to purple, I could have said that proteins were not present in the egg yolk, but if someone else decides that it is basically purple, they can say that proteins are present in an egg yolk, which would lead to two different results. One way to fix this error is to possibly have a scale and compare your solution to that one. This will lead to more consistent results throughout the class. Another error that could have occurred is that egg was not separated properly into the different test tubes. For example, the egg membrane could have mixed with the yolk and when the solution was added there could have been an extra color change. This could tell the analyzer that there is a specific macromolecule in the yolk, when the macromolecule was not supposed to be found there. One recommendation is when you are separating the egg yolk, you can use a strainer to get only the yolk.

The purpose of this lab was to find out what macromolecules are in the different parts of an egg cell. In class, we learned about the different macromolecules and their function, and this lab tells us where they are located in an egg cell. We now know what types of macromolecules we are getting when we eat an egg. This could be applied in putting macromolecules in other foods that have egg contents. I look forward to learning more about macromolecules in the future. 

20 Questions

Question: Is time travel possible?
I am interested in this topic because I have always wondered what the past or future might have or will look like. I always wanted to see dinosaurs from the past or robots from the future. This topic might give me the answer of whether it is possible. The current hypothesis is that time travelers already walk among us through astronauts.

My 20 Questions

1. Can dinosaurs come back into the world?

2. When will the world end?

3. Is it possible to leave the galaxy?

4. Will we ever see aliens in outer space?

5. Does being skinnier make you fitter?

6. Why do you get dizzy when you spin?

7. When will the sun explode?

8. When the sun explodes, will we explode too?

9. What is the best diet?

10. Can we mutate a human with an animal?

11. Is there anyone with the same fingerprints of someone else?

12. What happens when you become subatomic?

13. What is it like to be in a black hole?

14. When will we reach peak oil?

15. What will happen when the world becomes too hot?

16. Why does crying make you feel better?

17. Can humanity live on Mars?

18. What are other planets like?

19. Why do people get sore after exercise?

20. What is the maximum age someone can live?

Identifying Questions and Hypotheses

Question: Will the amount of sugar used in a recipe affect the size of the bread loaf? Hypothesis: If more sugar is added, then the bread will rise higher. He based it on research he did from the internet and his teacher, and his if statement was certain to be true

https://www.youtube.com/watch?v=kJ01TMt0XJk

Unit 2 Reflection

This unit was about the chemistry that is involved in biology and life itself. We learned about the basic units of matter including atoms, and we also learned about the 4 macromolecules, proteins, lipids, carbohydrates, and nucleic acids. Lastly, we learned specifically about enzymes and their functions. My strengths form the unit are probably about macromolecules, because that is the one thing I think I can explain to someone if they ask me. Carbohydrates are made of rings of carbon, hydrogen, and oxygen. They provide energy for many animals. Proteins are made up of small molecules called amino acids. They help store energy as well as control the rate of chemical reactions. Nucleic acids are made up of molecules called nucleotides, and they help store and transfer genetic or hereditary information. A nucleotide has 3 parts: sugar, a phosphate, and a base. Lipids contain fats, oils, and waxes. They are made up of chains of carbon and hydrogen called fatty acids. They also store energy while also making up part of a cell membrane. My weaknesses from this unit are probably the type of bonds and enzymes. With bonds, I usually get mixed up between covalent, ionic, and hydrogen bonding. For enzymes, I still get confused with the concept of activation energy and how it works. I think I have still improved in those regions, particuarly with the enzyme part through the cheese lab. I now understand the concept of denaturing and how pH and temperature affects the time of the reaction. It also helped with my weakness of activation energy. It showed me that when a pH or temperature gets affected, the activation energy goes up. The activation energy do now also helped with this concept. At first, I didn't really get the structure of carbohydrates, and the idea of a monosaccharide, a disaccharide, and a polysaccharide, but the sweetness lab really reinforced this. We learned that monosaccharides taste the sweetest out of all the carbohydrates, disaccharides taste the next sweetest, and polysaccharides taste the least sweet. I learned how a cabohydrate's shape or structure affects its function. Another thing I learned about was the basic units of matter. The most basic units are atoms, which are made of protons, neutrons, and electrons. Protons have a positive charge, electrons have a negative charge, and neutrons have a neutral charge. There are the same number of protons as there are electrons in an atom. Atoms of the same element that differ in the number of neutrons are known as isotopes. I think matter is another strength of mine from this unit. I feel like I am a much better student today than I was at the start of the unit. I have learned the importance of chemistry, even though I used to think that chemistry is not needed for biology. I want to learn more about atoms and learn more in depth about chemistry. I have really grown as a student from the beginning to the end of this unit, and I look forward to learning more. 

Cheese Lab

The question of this lab was what the optimal conditions and curdling agents for making cheese? Through our experiment, we found out that acidic and hot conditions are the optimal conditions for curdling agents, and that chymosin is the best curdling agent. In our data, neither buttermilk ther control of milk with no curdling agent curdled at all. However, both chymosin and rennin did curdle. In an acidic pH, both of them took 5 minutes to curdle, while in basic pH, there were no curdles at all. In a neutral pH, the milk did curdle, but it took 15 minutes. This supports our claim because in our claim, we stated that acidic was the optimal pH for milk to curdle, and in our experiment, an acidic condition only took 5 minutes. When we made it basic, the enzyme denatured and it increased activation energy. The neutral conditions curdled slower, but because it just turned a little less acidic, it still curdled. In hot conditions, chymosin took 5 minutes and rennin took 10 minutes to curdle. Meanwhile, in cold conditions, no curdling was visible, while in a neutral temperature, it again took 15 minutes to curdle. This supports our claim because it shows that a hot temperature is the best temperature because it took the least amount of time to curdle. Also, chymosin curdled faster than rennin, which supports our claim that chymosin is the best curdling agent. This is because we wanted to see which curdling agent would curdle the fastest, and the data from hot conditions shows that chymosin does that.

While our hypothesis was supported by our data, there could have also been a few errors that affected the results of the experiment. Firstly, our data says that in an acidic pH, chymosin and rennin curdle at exactly the same time, but this is probably not true. This could affect our results by not specifying which curdling agent took the least time, so we wouldn’t know which one is the best curdling agent if we just tested an acidic pH. The issue repeats in the neutral temperature as well, with both chymosin and rennin being 15 minutes. Also, in hot conditions, we don’t know if it is a closer difference between chymosin and rennin because the curdling is checked every 5 minutes. A way to eliminate this mistake would be to check for curdling every thirty seconds to a minute to give us more accurate data. Secondly, everyone’s armpit has a different temperature. This could affect our results by the curdling being off by a minute or two. One armpit may have been a little cooler than others, so by the time we checked at 5 minutes, there was no curdling. The next time that we checked would have been at 10 minutes, while it may have curdled earlier, so our data wouldn’t be as accurate.  A way to fix this is to find a more constant place to put the test tube, like maybe just outside in the sun.

The purpose of this lab was to find out what the optimal conditions and curdling agents for curdling milk and making cheese are. This lab helped strengthen my understanding of enzymes denaturing and activation energy, while also reinforcing how pH and temperature affects the rate of a chemical reaction. Based on my experience from this lab, I can explain enzymes to others while also teaching others how to make cheese. I hope this experiment will help you make your new cheese.

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

Sweetness Lab

 The purpose of this lab was to see how the structure of a carbohydrate affect its sweetness. Through our evidence, we think that monosaccharides taste sweeter than disccharides and polysaccharides, and disaccharides taste sweeter than polysaccharides. In our experiment, we gave each sugar a degree of sweetness from a scale of 0-200. We gave fructose a degree of 200,we gave glucose a degree, and we gave galactose a degree of 75. These support our claim because these are the three monosaccharides, and they have the highest degree of sweetness out of all the other sugars. Also, the two polysaccharides(starch and cellulose) both had a degree of 0, which supports our claim because that is the lowest degree of sweetness and we stated that polysaccharides had the least amount of sweetness. Sucrose had a sweetness degree of 100, maltose had a degree of 50, and Lactose had a degree of 10. These were the disaccharides in our experiment, and they support our claim because all those degrees are less then the two monosaccharides but more than the two polysaccharides.

The structure of the carbohydrate might affect how they are used by cells or organisms. I think that the more rings there are, the more energy will be provided for the cell or organism.

In this experiment, the rating for each sample differed from person to person. Different tasters have different taste buds. If I thought maltose was fifty degrees, someone else may have thought that it is was a 75 just because everyone tastes things differently. Secondly, the amount of carbohydrate that someone tastes might affect their rating of the sweetness. If someone takes an extremely small amount of fructose in their hand, it might taste less sweet. If someone takes a decent amount of fructose in their hand, then they might think it is more sweet than the person who took very little fructose. The person who took a small amount might give it a 170, while the person who took a decent amount might give it a 200. Lastly, the amount of time in between tastings could affect the way someone tastes a carbohydrate. If someone tastes galactose right after they taste fructose, their rating might be different than someone who takes about twenty seconds between the tasting. If they taste galactose right after they taste fructose, they might give it a rating of 100 because the taste of fructose may have stayed in their mouth. The person who takes twenty seconds to taste galactose might give a rating of 75  because the taste of fructose may have faded away. For these reasons, the results in this experiment could have varied.

Popular Science states that the bumps on our tongue, or taste buds in other words, help determine how we taste not only sweetness, but also the other four kinds of tastes. According to Popular Science, "Although our brains can recognize the same five tastes—bitter, sweet, salty, sour and umami (savory)—the suite of chemicals that can trigger those signals varies from one person to the next." This means that people's taste buds that were tasting these carbohydrates might have responded differently to the sweetness of it, therefore making a wide range of ranking possible. I thought that cellulose was a zero, probably because my taste buds don't react to cellulose like someone else's might have. If I gave cellulose a zero, then someone else might have given it a 10 because their taste buds react to cellulose better. 

Biology Collage

Fading Jeans

What concentration of bleach is best to fade the color out of new denim material in 10 minutes without visible damage to the fabric? Through the experiment, we have concluded that the higher the concentration of bleach, the better the color fades. When full strength bleach was used, the average color removal was eight. After that, the color average kept going down. At fifty percent concentration of bleach, the average was five and two-thirds. When it reached zero percent concentration of bleach, there was no color removal at all. For all the concentrations of bleach, there were no visible signs of damage. This evidence proved that higher concentration of bleach provides more color fade.

Concentration(% bleach)	Average Color Removal (Scale 1-10)	Average Fabric Damage (Scale 1-10)
100	8	0
50	5.66	0
25	3.66	0
12.5	0.66	0
0	0	0

While our hypothesis was supported by our data, there could have been errors that affected our result. Firstly, the measurements that we made could have been slightly off. When we were supposed to measure thirty milliliters of bleach, we could have measured twenty eight or thirty three. When we were supposed to measure twenty milliliters of water, we could have done eighteen or twenty three. These few milliliters could always make a difference in the color of the jeans or how much the jeans are rinsed. This problem can’t be completely taken away, but to control it, all you have to do is be more careful and pay attention to your measurements. A second error could have been that the color of the jeans weren't completely constant. Some squares of jeans were just a little darker or a little lighter than the others. This could have maybe brought the average of full strength bleach down to seven or even up to ten. While it is likely that the conclusion would have remained the same, the data in the experiment might not have been completely accurate. To control this, you can find completely dark jeans which have the same color throughout to find more accurate results.

The purpose of this lab was to find a way to fade out the color of jeans. Through this experiment, we actually got to use the scientific method first hand and learn how to create a high quality scientific study. This experiment could be a simple way to teach students about the scientific method, or it could be used in the real world for people who like fading out their jeans.

Works Cited