Unit 5 Reflection

In this unit, we learned about the central dogma of molecular biology. We studied the structure of DNA and its antiparallelness. We also learned about how the enzymes helicase and DNA polymerase are used to copy DNA. In addition to DNA, we also learned about RNA and proteins. We were taught the main types of mutations and their effects on proteins. The labs we did in this module involved extracting our own DNA and simulating the process of going from DNA to RNA to Protein.

I feel that I was able to understand the DNA copying, the Dogma, and mutations vodcasts very well. I am already familiar with the information taught in the dogma and mutations vodcast, but not the copy machine one. Although the enzymes involved in DNA replication were new to me, I think that their roles were quite basic. This probably explains why that set of vodcasts felt extremely easy. However, the gene expression vodcast was slightly tougher than the other ones. This is probably because I am not very familiar with how the operon and gene regulation work. After reviewing the diagram a couple of times though, I had a pretty good grasp of the concept.

I am glad that I learned a lot of new material in this unit. In other units, the number of new concepts were close to zero and weren't very interesting. However, the enzymes and mechanisms involved in the replication, transcription, and regulation of genes I learned about in Unit 5 were really cool. I definitely think I am a better student today than at the start of this unit. This is because for this unit, I really had to try to understand some of the concepts, compared to other areas we have learned about that I was already too familiar with to apply studying methods.

I want to learn more about the operon and gene regulation. I still have questions involving gene regulation in eukaryotes. I might research these processes for the 20 time project, but I am not sure.

For this unit, I learned more about the operon by searching up other diagrams that felt more descriptive to me. This helped because I am a multimodal learner (mostly visual and reading), and the images were labeled diagrams.


DNA floating on top of alcohol from-DNA Extraction Lab

a deletion mutation from-Protein Synthesis Lab

Protein Synthesis Lab Conclusion

     In order to make protein, the a gene found on DNA must me copied into mRNA (transcription). This involves RNA Polymerase, which constructs an mRNA strand complementary to the DNA sequence being scanned. Also, instead of using Thymine, RNA uses another pyrimidine: Uracil. This strand of mRNA then exits the nucleus and arrives at a ribosome (translation). Here, tRNA molecules carrying the amino acid corresponding to each codon, a set of 3 bases, connect the amino acids in the dictated order. Once the polypeptide chain has formed, it folds and gets packaged in the Golgi Apparatus. This protein is then used either inside or outside the cell for a variety of purposes.



     In my opinion, insertions and deletions of 1 or 2 bases at the start of a sequence and the start of a codon make the largest difference. It makes a major difference when it is 1 or 2 bases because that creates a frameshift. If 3 were inserted, then a new amino acid would be produced but the rest would remain the same. It makes a large change when at the start of the sequence because then Methionine may not be read, and all of the following codons are frameshifted. It is also important for it to be at the start of the codon, because sometimes if the base change is at the end of a codon, it may not change the amino acid that is made. The mutations that makes the least change are frameshift mutations of 3 bases, frameshift mutations near the end of a gene, and substitutions of the last base in a codon. The first one makes a small difference because if 3 are inserted/deleted, it just adds/removes an amino acid. The second mutation makes a minor difference because if the frameshift is near the end of a gene, it doesn't frameshift that many codons. Also, substitutions of the last base in a codon don't make much of a difference because often the produced amino acid is not different.

^A lot of these hemoglobin variants are caused by a single base substitution

    In step 5, I chose to make an insertion at the very start of the sequence. The result was that there was no "start" codon, and no "stop" codon. This is a drastic change from the other mutations because in step 5, no protein was produced at all. This frameshift mutation at the start of the gene shows that the location of the mutation is very important.


    If I had a severe mutation that affected an important protein like actin or collagen, I could have muscular or skin defects. These may have a major impact on my life, like preventing me from playing a sport or engaging in high physical stress activities. One mutation that affects collagen is called "Ehlers-Danlos Syndrome". It has a variety of levels, but usually causes hypermobility, stretchy skin, and slow skin healing time. These symptoms make sense because collagen is a structural fiber present in skin that gives skin its ability to stretch and compress.

DNA Extraction Lab Conclusion

     The problem we tried to solve in this lab is, "How can DNA be removed from a cell?". DNA can be removed from cheek cells by using 3 steps: homogenization- removing and dispersing the cells in a liquid, lysis- breaking the cell membranes and other proteins down so DNA is accessible, and precipitation- using a polar liquid to get the DNA to fall out of the solution. When we used gatorade to homogenize our epithelial tissue, soap and pineapple juice to lyse that solution, and alcohol to precipitate the DNA out of the solution, we were able to extract our DNA. The DNA floated from the gatorade solution to the top of the alcohol, and we can be quite sure that it is DNA due to its stringiness and the fact that it precipitated out of the homogenization/lysis solution. The reason why this evidence verifies my claim is that I followed the exact steps outlined in the claim and found the expected result.

    Although I can't find any possible errors in this experiment, there are a couple of things that may have prevented me from getting the optimal results. One possible mistake is that I didn't scrape my cheeks enough. This may have resulted in not getting a lot of cells and consequently not much accessible DNA. I also may have used too little soap/pineapple juice. If I didn't use the right amount of soap, I may have only broken open a few cells and only received a small amount of DNA.
     The purpose of this lab was to understand the lab process of splitting open a cell to get to the DNA. The process of DNA extraction relates to how DNA copies itself. If DNA was unable to replicate itself, then there wouldn't be so many cells with so much of it. The lack of DNA would prevent us from being able to see it (and prevent us from surviving). This skill of DNA extraction may be applied to various contexts such as jobs at genetics companies or research facilities.

In this image, the yellow material at the top of the test tube is my DNA. The clear liquid beneath it is a polar liquid used for precipitation (alcohol). The yellowish liquid under that is a combination of polar liquid for homogenization (gatorade), and liquids used for lysis (soap and pineapple juice).

Unit 4 Reflection

This unit was about cell division (meiosis/mitosis) and sexual reproduction. We also learned about Mendel's laws and what patterns he found in pea plants. Students were required to understand inheritance, the cell cycle, and basic Mendelian principles. This unit was quite easy for me and I was able to understand all the concepts quite quickly. Some things that were new included a few of the genetic "complications" like epistasis, dihybrid crosses, and x-linked inheritance. Even though they were new to me, I found making Punnett squares for things like dihybrid crosses and x-linked traits quite interesting. One setback was turning in these blog assignments. We haven't really had that many labs and blog assignments this unit so when I had 2 large ones (Coin Sex Lab and Unit 4 Reflection) at the end of this unit I was unprepared. I turned in both late and although hopefully this doesn't impact my grade too severely, the lateness will probably result in a loss of a couple points. From this experience I learned that even something relatively easy will fade in memory and skill if you don't practice it for a while. In my case this unit, the skill that I left unpracticed was typing up a blog post or conclusion about a lab. This teaches me that I should probably not leave future skills unused till the last minute when they are extremely important. One other thing that taught me an important lesson about turning assignments in on time is the infographic. I did not work on the infographic much in class so it ended up getting finished in the last two days. However, my work was surprisingly good for a last minute job and I am actually quite proud of the way my infographic turned out. This experience also teaches me that I shouldn't hold assignments off till the last minute, but I may be a good last second worker. I really want to learn more about x-linked traits, epistasis, and epigenetics. These complications interest me quite a bit and I will probably research them in my free time. I also wonder about what exactly causes dominance. I already know how an X chromosome is rendered dominant in female's cells, so I wonder if the process is similar for autosomal alleles. My numbers are as follows: Visual-10, Aural-9, Read/Write-9, Kinesthetic-7. These results are more or less what I expected. However, I thought there would be a larger difference between visual & read and aural & kinesthetic. This is because I like to make organized diagrams and do labeling. I also learn from watching videos, reading wikipedia, and understand directions best in ordered written form. I usually zone out when I'm listening to a teacher and find manipulating objects entertaining but unhelpful. To prepare for tests, I will make diagrams when applicable and write ordered lists where it seems helpful to my learning.

Coin Sex Lab Conclusion

In this lab, we flipped coins to simulate the processes of meiosis and gene recombination. The coins served as models for a variety of concepts including: sex of offspring, simple autosomal dominance, x-linked recessive alleles, and dihybrid crosses.
Coins are good analogies for genetic concepts because they can be used to visualize probability and gene inheritance. For example, flipping one coin could decide between X and Y, while another is labeled X on both sides and therefore has no probability of passin on a Y chromosome. Another good example is that if both parents are heterozygous, each coin could be labeled with "X" and "x". Four flips of each coin together would show one possible inheritance scenario.
For the dihybrid cross we had 11 brown hair brown eyes (instead of 9), 2 blond hair brown eyes (instead of 3), 3 brown hair blue eyes (same as expected 3), and 0 blond hair blue eyes (instead of 1). I'd say that these results aren't that unexpected because the maximum deviation was by 2. The reason why the results aren't the same as what the Punnett square tells us is that it is all about probability. It is completely possible, although highly unlikely, that someone has 20 kids and they all have blond hair and blue eyes. Probability would dictate that only about 1 of these kids should have those traits, but this chance is a chance; not an undeniable fact. Punnett squares serve as models for the most likely situations and genotypes that probability models, not as the genotype combination that will be present every time.
The limit of probability is that it can never tell us exactly what babies will have what traits and how many of those babies we will have. It can give us a most likely number that is found if you take an average of those crosses, but will not tell us what will always happen in our situation.
Understanding that I can predict the possibilities of my child's traits means that I can only hope that my child will have certain beneficial characteristics and won't have any disorders. If I really wanted, I could create a monohybrid punnett square for my parents and wife's parents to figure out whether we are homozygous or heterozygous. We could then do a cross of these to find the traits our child may have.

Genetics Infographic

Due to the small size of this infographic, I am including a link to the full sized picture:

Unit 3 Reflection

In unit 3, we learned about the cell and all its processes and many intricacies. We learned about the complexity of organelles and how our energy is collected. Although a wide variety of topics were covered, they all shared a common theme: the cell. I think that most of the unit was quite easy, because some of it was just a review of 7th grade biology. I even knew a little in depth information about photosynthesis and cellular respiration before learning this unit. But if one thing is the hardest to grasp in this unit, it would be cellular respiration. I think this is because it has 3 sort of overlapping parts rather than photosynthesis' 2 distinct parts. Even after watching the vodcast, I was still not completely sure about where reactants went in and products came out.

One thing that definitely helped is drawing a diagram. By illustrating the 3 pieces of CR separately and with clean sketches, I was able to understand where and why certain reactants entered CR. This taught me the important skill of drawing diagrams. A diagram is not something that would help only in biology; it could also be applied to chemistry, physics, and a variety of other topics. I do think that I'm a better student now than at the start of this unit. I have learned important studying skills as well as gained a better understanding of the way a cell works. I want to learn more about photosynthesis and cellular respiration. How exactly does ATP synthase work? What are the "in between" steps of the reactions that weren't taught in class? To study for this test, I will probably not make flash cards because I feel like I have already mastered the concept of organelles. However, I will definitely draw out the reactions of photosynthesis and 3 parts of cellular respiration. This process will help me tackle the exact processes and give me a deeper understanding on the topic.

Egg Diffusion Lab Conclusion & Analysis

In the egg diffusion lab, we took 2 eggs and placed them in 2 liquids for a few days: deionized water and corn syrup. We hypothesized that the egg in the deionized water would expand and that the egg in the corn syrup would shrink.

When the concentration of sugar (solute) in the external solution was high, water (solvent) left the egg to maintain the proportion of water to sugar. This caused the mass and circumference to decrease. This is proved by the fact that most of the groups' eggs in corn syrup decreased in mass by around 45%, which is a large difference. The change in circumference also hovered around -21%.

A cells internal environment changes depending on its external environment through a process known as "diffusion". Diffusion always moves molecules from areas of high concentration to low concentration. For example, if a large amount of water is outside of the cell, the water will enter the cell until both sides of the membrane have around the same water concentration. However, if a solute like the sugar in corn syrup is unable to pass through the membrane, then water diffuses out of the cell until the ratio of water to sugar is the same on both sides of the cell membrane.

This lab demonstrates the biological principle of diffusion. Diffusion is extremely important to cells and allows for water and nutrients to move in and out of the cell without the use of energy. By putting an egg, essentially a cell, in a hypertonic solution we investigated the effects solute concentration had on a cell.

Fresh vegetables may be sprinkled with water to counteract the natural process of water leaving the plant cells due to diffusion. If water is sprinkled on the vegetables, the concentration gradient would be less steep which would decrease the rate at which water escapes vegetable cells. This helps prevent the vegetables from wilting or becoming squishy. Salting definitely has a detrimental effect on roadside plants. When salt approaches the roots of a plant, it creates a gradient that forces water out of the root cells. This causes the plant to wilt and may eventually result in its death.

After understanding the results of this experiment, I would like to test what would happen if I removed some of the egg white from another egg and injected it with a hypertonic sugar fluid. This egg would then be placed in a beaker of deionized water. I hypothesize that this egg would absorb water until it bursts. If this hypothesis is correct, it would prove that the membrane is semipermeable from both sides.

Egg Cell Macromolecules Conclusion & Analysis

What macromolecules are present in the cell and where are they?

     The membrane contains polysaccharides. When we put the membrane in an iodine solution to test for polysaccharides, it turned black. The membrane contains this because it uses polysaccharides to communicate with other cells. The egg white had proteins floating around in it. We know this because when the separated egg white was dropped in copper sulfate, a chemical that tests for peptide bonds, the solution turned purplish. The egg white may contain proteins for helping the developing chicken embryo grow. The proteins would provide nourishment and vital ingredients for life.The egg yolk was composed of lipids. This was learned when the broken down yolk was put in a solution of Sudan IV. Soon, it turned a shade of orange. The yolk probably contains lipids because it is actually a cell. Cells have phospholipid membranes, so this is the most likely reason for a positive lipid test.

     One possible error is that a sample was contaminated. If one sample was accidentally mixed with the one being tested, it may show positive results when in reality the macromolecule is only present in the contaminant. If this happened, then the macromolecules that the evidence proved may not normally be present. Another mistake that could have occurred is if an inadequate amount of testing substance was used. In the procedure, it only said how many drops should be added. This is not a very accurate measurement and people may have also miscounted the amount of drops of a chemical they added. This may cause no results to be displayed even when a part of the cell contains a certain macromolecule. These inaccuracies can be remedied in the future by assigning each table a certain part of the egg rather than having each group test every single part of the egg. This new procedure would reduce the chance of contamination. The amount of testing chemical should also be changed from "drops" to "milliliters". This is a more standard and widely accepted measurement unit and would help prevent not using enough testing solution.

     The purpose of this lab was to learn about the function and location of macromolecules in the cell. This relates to an activity I did in seventh grade where we made a chart of the macromolecules and wrote facts about what they did and where in the cell they are found. What I learned in this lab can be applied to situations where I may need to retrieve a certain macromolecule from the cell. With this information, it will be easier to know where the molecule is and how to isolate it.


Monosaccharide Test tubes- From the left: water, membrane, white, yolk

Inquiry Hour 1.1: Identifying Questions and Hypotheses

The question was, "Do monkeys and humans perceive optical illusions in the same way?". The hypothesis was that the monkeys would perceive the pictures as illusions. This is because in a similar study executed previously, the tested monkeys saw perceived the size of circles incorrectly: a purpose of the optical illusion.

The study used a type of illusion called a Delboeuf illusion. These consist of a thin circle with a large filled in dot in the center. The size of the center dots stay the same, but the thin surrounding circle's size changes. This creates the illusion that dots in smaller circles are larger than dots in bigger circles. To test whether the monkeys saw the images as an illusion, the researchers trained monkeys to use joysticks and computer monitors. Both the monkeys and humans were asked to classify dots as large or small. When they answered correctly, humans were given a written reward and monkeys were given a banana flavored pellet.

http://www.sciencedaily.com/releases/2015/09/150928083116.htm

"What is consciousness?", and another 20 Questions

I really like most all of the questions in the article, especially the first few near the top. But if I had to choose one, I'd say my favorite question is, "What is consciousness?". I think this question appeals to me because we hardly know anything about our brain and nervous system. And even though we know all about the physiological processes, we are nowhere close to comprehending our ability to understand language and picturing images in our mind.
The consciousness is one of these mysterious things about the brain that I don't think anyone really understands. In reality, our body is just a means of receiving and exporting information. The brain is the real thing controlling, preparing and processing this information.
I also believe that our understanding of "what we are" has changed over time. Originally, we assumed that this body was "me", and later we were able to grasp the concept that we are actually just a lump of neurons sitting in this body's head. Soon, I think we may be able to fully comprehend the fact that our consciousness is just a bunch electrochemical messages constantly being relayed between a few billion neurons inside of our skull.
The main hypothesis on what our consciousness is, is that as we sift through so much information in our lifetime, we quickly are able to tell what is real and what is not. We learn that the things we imagine and dream are all in our mind, but the real world is something that others also perceive and that everyone knows is true.
My Big 20 Questions: 

1. What causes self-awareness?
2. Do we have biological free will from our brains?
3. What allows us to see things in our mind? What allows the mind's eye?
4. Is medical progress hindering human evolution?
5. Why are plant cells usually larger than animal cells?
6. How much energy does my phone use per minute?
7. Who will win the 2016 presidential election?
8. Because our government uses the electoral college, is the USA really a democracy?
9. How can I know that the universe didn't begin just a few minutes ago and that all my memories were implanted?
10. Is Obama and any of our federal government real? I've only seen them on TV.
11. How much longer will we continue to find and use fossil fuels?
12. Is solar power ever going to become practical?
13. When will the human race master interstellar space travel?
14. Will socialism ever become the global government norm?
15. Will humans slowly degrade mentally and physically due to our laziness and stupidity?
16. Will humans ever become a purely mental race which only interacts psychologically rather than physically?
17. If time travel is possible, then where are the visitors hiding?
18. Why does my ring finger also bend when I bend my pinky?
19. Could humans function with only 2 or 3 fingers and an opposable thumb?
20. Can gravity truly be quantized and if so will we be able to harness its potential as an energy source?

Unit 2 Reflection

The general purpose of this unit was to understand the chemistry involved in biology. Themes included understanding basic atomic structure, intermolecular forces, macromolecules, and how enzymes worked. I think I was able to understand everything in this chapter and some of my favorite parts included the macromolecules and how enzymes function. However, one part I didn't find too interesting was the pH scale. This is because I've already learned about it many times for various reasons, and some of the information seemed inaccurate.
In this unit I learned about how atoms form bonds, how biological systems use enzymes to do their work, and what causes the meniscus in a graduated cylinder. One skill I learned in this chapter was how to use data tables to make graphs in google sheets.
I think I am a better student now than at the start of this chapter, because although I knew a large portion of the content I didn't fully understand how they worked. I also wasn't aware of the extremely intricate structure of enzymes. I would like to learn more about enzymes and proteins. This is because proteins and enzymes are like microscopic biological machines that have a large potential for scientific use.

Cheese Lab Conclusion

What are the optimal conditions and curdling agents for making cheese?

CER: The best curdling agent to use is Chymosin in a hot, acidic environment. In the lab, Chymosin curdled the milk in 5 out of the 6 conditions. This shows that the milk may continue to curdle even if something happens to the machine that keeps the enzyme’s environment in check. The environment should be hot because in the lab, the hot environment produced curdling in 5 minutes for Chymosin. Also, the environment should be acidic because during testing, chymosin produced curds in 5 minutes when it was in an acid. If hot and acidic make the enzyme produce curds faster, then a hot and acidic environment would be best from a manufacturing perspective because cheese could be produced very fast.

Possible Errors: Some possible errors may result from different people’s armpits, and accidents during timing the incubation. The temperature of the underarm varies slightly from person to person and some groups didn’t even put the test tube in their armpit. The effect of this may be that the enzymes in some tubes may have been more active than others and would eventually result in inconsistencies in the time for curdling. When I ended the the 10 minute timer for one of the incubation rounds, I forgot to immediately restart it. This means that the timing of that round was slightly off. If everyone made small mistakes like these, then overall it could create a large timing difference which would skew the results. To prevent inaccuracies in time from occurring, I would alter the procedure of this experiment in 2 ways. One thing I would do is put all of the test tubes in an incubator with a steady temperature to prevent differences from underarm to underarm. Another thing I would change is the way we time. I think that the timer should run for 10 minutes, then have a 10 second pause to check for curds, and then restart its 10 minute cycle. This would prevent the humans from forgetting to restart the timer.

Practical Applications: The purpose of this experiment was to understand how different factors such as pH and temperature can affect the activity of enzymes. This relates to what I’ve learned in class because in 8th grade we learned about pH and hydronium ion concentration. This makes me think about why and how hydronium can affect enzymes. The results of this lab could be applied to making cheese at home. I have already made cheese at home many times, but only used buttermilk. Now I know that if I want the quickest outcome, I could purchase some chymosin or rennin.

	Chymosin	Rennin	Buttermilk	Milk (Control)
Acid	5	5	5
Base	20
pH Control	15	10
Cold
Hot	5	5
temp. Control	10	10

Sweetness Lab Analysis & Conclusion

How does the structure of a carbohydrate affect its sweetness?

CER: The fewer saccharides bonded together in a carbohydrate, the sweeter it is. When the sweetness numbers for the monosaccharides were averaged out, it gave a whopping 125 on our arbitrary sweetness scale. When disaccharide sweetness was averaged, it was only 35. And the average of the polysaccharides was 0. Polysaccharides had the most chained monosaccharide molecules and lowest sweetness. Monosaccharides were not chained at all and were the most sweet. This shows that as the amount of saccharide molecules in a chain decreased, the sweetness increased.

2. The larger carbohydrates such as starch can be broken up to produce a large amount of energy. This makes them good for storage. However, smaller monosaccharides and disaccharides are much more portable and can be moved around easier.

3. No. The rating varied from tester to tester. (1)This may be because the testers have a background of eating sweeter foods or less sweet foods. If they ate sweeter foods in general, then they may not think that a sample is very sweet and rate it lower. (2)Another reason is that the testers may take different amounts. The amount of carbohydrates that was ingested was not measured which means that if one tester took a large amount of sugar, they might find it sweeter and rate it high. (3)Also, results may vary because of genetics. Some people have a large number of papillae in their mouth which would give them high sensitivity to sweetness. Others may have genes which could reduce their sensation of sweet.

4. Human taste is perceived by taste buds on the tongue, soft palate, and throat. These taste buds come in small groups called papillae which look like bumps. When taste buds sense certain chemicals, they send information to the gustatory cortex where the data is interpreted as taste. This mechanism would allow taste rating to vary because the amount of papillae in a person's mouth can be different in each individual. Also, the way a person's brain interprets the taste can vary because of their genetics.

Characteristics of Life Collage

Jean Lab Conclusion

Claim Evidence Reasoning:

Higher concentrations of bleach do make jeans fade more than lower concentrations. However, there is no correlation between fabric damage and bleach. When the jeans were put in the 100% bleach for 1 minute, it became very faded and a yellowish color. This was rated as an 8.5/10 on our fading scale. When a half-bleach half-water solution was used on the jeans for the same amount of time, it was rated as a 7 out of 10. The ¼ bleach solution gave a 4.5 for fading, while the 12.5% bleach only faded 2.5/10 according to our scale. This shows a clear downward trend of fading with decreasing bleach concentrations. That means that the more bleach used, the more the denim fades, thus proving the claim.

Possible Errors:

Although our data supports the hypothesis, errors could have happened because of time differences and prior color differences. One possible error could be the slight time separation that occurred when we put the denim into the bleach and when we took it out. This is because there were 5 denim squares and not enough tweezers so we couldn’t take them all out at the same time. Due to this inconsistency in timing, some of the fabric may have sat in bleach longer than the others. The second error may have happened when we chose our jeans. There were jeans of a wide variety of shades of blue, so we can’t be a hundred percent sure whether the color difference was there from the start, or because of the bleaching. In the future, these problems could be solved by making every group choose fabric from a single pair of jeans. This would make all the squares about the same color. To fix the timing inaccuracy, we could have 5 tweezers at each table so that all of the jeans could be pulled out at the same time.

Practical Applications:

This lab was done to demonstrate how bleach affected the color of fabrics. From this lab I learned how to carry out an unbiased, procedural, scientific experiment that gave accurate results. This helps me understand the larger concept of using the Scientific Method to answer questions. Based on my experience from this lab, I now have the knowledge to execute professional experiments that use the scientific method in its full power.

Concentration (% Bleach)	Average (Color Fading out of 10)
100	8.5
50	7
25	4.5
12.5	2.5
0	0

Concentration (% Bleach)	Average (Fabric Damage out of 10)
100	1
50	2
25	3
12.5	1
0	0