Unit 5 Reflection

   In unit 5, we learned deeper into how and what DNA is. DNA is constantly being replicated. DNA is composed of a nitrogen base(A,T,C,G), a phosphate group, and a sugar(deoxyribose). DNA is antiparallel and is made of a two strands, double helix. A goes with T and C goes with G. We also learned about RNA, which is only one stranded. A RNA Polymerase will attach onto a DNA strand and start transcribing the DNA, then it shoots out the mRNA with the same code. In mRNA the T is switched with U. The mRNA then leaves the nucleus and goes to the ribosomes. The ribosomes then translate the code into amino acidsl, which are the ones that create the proteins. We also learned more about mutations. Mutation can be natural but mostly caused by something. There is substitution, which changes one base into another, insertion, meaning one base is inserted into the code, or there is also deletion, meaning one base is deleted from three code. The most harmful is deletion, for it is a frame-shift mutation. The more changes in the  DNA, the more there is a difference in the protein being created. Last but not least, we learned about gene expression and gene regulation. Gene expression is how one gene is expressed in different areas of your body. Gene regulation is how gene are regulated on how they are being expressed. Eukaryotic regulation are much more complicated. There are histones and nucleusomes. I did not understand how gene regulations worked very well, for the process is very complicated and there is a lot of components. My strengths were in translating the codons.

  From this unit, I have grown a lot in relation with everything that has to with DNA. With this unit and these many labs, I have learned about how and why DNA is how it is. I have also learned to challenge myself in learning more complicated subjects that take time to fully understand. The many labs we preformed have help me understand and I am also better at following and creating labs. I am a better student, for now I have worked and learned more challenging units and can now better understand and also no know how to learn subjects that I may not understand on the first try.

Protein Synthesis Lab

  To create proteins, there are two steps, transcription and translation. First the DNA is copied by an enzyme, it becomes mRNA. The mRNA will then travel out the nucleus to reach the ribosomes. mRNA bonds with the ribosome , which reads the sequence of three bases at a time, it is called a codon. Each codon is translated to an amino acids. The amino acids are bonded together to make a protein.

   By changing the bases of DNA, the protein could vary a bit from the original protein or it can be changed greatly. The mutation  with the greatest effect was deletion, for it caused the sequence to be completely changed after it being deleted. It also caused there to be no stop and the codons changed a lot from the original. In  ours, the sequence just stopped in the middle of it. Substitution tended to be the less harmful, for it only changed one codon at the most, but sometimes, it did not even change, for it translated to the same amino acids. A mutation that occurs in the beginning, if it is a deletion or insertion, will have more harmful effects, for the sequence from near the beginning will change widely from the original. One that occurs at the end, will only affect the end of the sequence. If the T was at the end, the sequence would not have changed a lot for only the end would the T have become another letter.

   We chose to test deletion another time, for it was the most harmful of all the mutations. This mutation related to the others because we specifically chose to delete to of the letters T, we mostly modified the T in the other mutations. Instead of only deleting one base, we decided to delete two of them, one near the start and one near the end of the sequence. With this, we saw that the most damage occurred directly near the beginning, this shows that where a mutation occurs, directly affects the results. The closer to the beginning, the more harmful the mutation becomes.

    Some mutation can affect our lives greatly. Though some are not harmful, some others are. A mutation could be very small and just cause some minor problems, or it could cause your body to not function correctly and make your cells not work correctly. Though there are many harmful mutations out there, an interesting and very rare mutation related disease is called Progeria. Progeria causes the child affected to seem to age a lot. Most children with Progeria die at the age of 13, but some do reach their 20's. Their cells mature very fast, and their bodies look and act like if they were an elderly person. Progeria only occurs to one out of around 80 million of children. 

 

DNA Extraction Lab

  In this lab, we asked the question," how can DNA be separated fro cheek cells in order to study it?" We found that to extract the DNA from our cheeks, we had to create three parts, homogenization, lysis, and precipitation. To accomplish homogenization, we needed to retrieve the samples using a polar liquid. We used Gatorade, which became one with the DNA. We then used that mixture for lysis, which we added salt, then soap. This caused the DNA to be completely released into the mixture. We also used pineapple juice, which contains catabolic proteases, to further break down the proteins, the juice was used as an enzyme. Lastly, we added the wiping alcohol, which ended the precipitation stage, the DNA had finally been extracted. After we added the alcohol, the DNA started to float up to where the two liquids met, for the alcohol is nonpolar while the mixture was polar. The DNA was very small and had been dyed red by the Gatorade. Like what was taught in Unit 2, polar and nonpolar mixtures separate, so the DNA floated to the middle. We also learned in Unit 5 that DNA is nonpolar. This data supported our claim because the reason why the DNA was extracted was because the of DNA's polarity and how it reacts when mixed with polar liquids/solutions.

   While our hypothesis was supported by our data, there could have been errors made due to how my group and I had to in some ways create our own procedure by rearranging the steps, so that the experiment would work out. This could have affected the results because we may not have done the experiment correctly, which could have led to no data at all. Another error that may have been made was how we may have measured each/some of the liquids wrongly. We could have accidentally put in 11 drops instead of 10 drops which could have possibly led to the experiment not working out, and no DNA being extracted. These errors could have been avoided through having been given the instructions given at the beginning and that the measurements could have been more precise and that we could have been more cautious.

    This lab was done to demonstrate how homogenization, lysis, and precipitation could be used to extract the DNA from our cheeks. We used what we had learned from the previous vodcast about DNA and all the prior knowledge we had accumulated over the past units to form an experiment and extract our own DNA. From this lab, I learned about the properties of DNA. I also learned about how scientist extract/ absorb DNA. Based on my experience from this lab,  I better understand how the properties of DNA, such as polarity, affect it.

Unit 4 Reflection

        In the Coin Sex Lab, my group and I experimented the pairing of chromosomes to find their genotypes, we also found the probability of the results prior to the lab. We preformed both monohybrid crosses and dihybrid crosses. Each letter represented a different type of gene that was either recessive or dominant. The dropping of the coins represented meiosis. Meanwhile, the coins being put together was the recombination of the alleles, also known as sex. The coins represented the chromosome, with each side representing another chromatids. Most of our expected results came very close to the actual results of the dihybrid cross stimulation. We expected, 9:3:3:1, and instead got 8:3:4:1. Because it was a dihybrid cross, we knew there would be 2 homozygous and 14 heterozygous children. One of the homozygous would have to be a homozygous recessive, meaning there could only be one of those. And the homozygous dominant would be the most common. The limit of using probability to predict our offspring's traits is that the outcomes are affected be so many factors, that not all those factors can be taken in account when finding the probability. In this lab, we learned about how autosomal inheritances and X-linked inheritances affected males and females differently. X-linked inheritances are more probable in males, while autosomal does not favor any gender. This understanding relates to our life, for with this, we could predict using probability on how likely your offspring will be and even whether he/she will have a disorder. It also becomes very important in this time period, for scientist and doctors to treat/ find whether you have any gene linked disorders.

      Overall, in Unit 4, we learned about the basis of genetics. Asexual and sexual reproduction was taught. Asexual is the the cloning of an organism while sexual reproduction requires a mate. While asexuality is more efficient, time wise, sexual reproduction is less vulnerable than asexual organisms. Meiosis is the process in which the chromosomes divide to prepare for sexual reproduction. This occurs in two stages, Meiosis I and Meiosis II. There are two types of alleles, dominant and recessive. A gene can be either heterozygous, one dominant and one recessive, or it can be homozygous, same allele in a pair. Dominant alleles will always be shown and are written as capital letters. While recessive alleles are written with lower case letters and are not shown when it is not homozygous recessive, the dominant alllele dominates the recessive allele.  Autosomal inheritances occur in one of the 22, non-sex chromosomes, while X-linked inheritances happen in the X chromosome of an individual. Men are more likely to be affected by X-linked inheritances while women are typically just carriers. Epistasis is when a gene masks another gene, so that it can not be shown in the phenotype. Epistasis is different from recessive and dominant. Codominance is when two different dominant alleles are equally expressed in both phenotype and genotype. Incomplete dominance is when one trait is not completely expressed nor is the other. Mendel was a great pioneer of genetics, he create the Law of Segregation and the Law of Independent Assortment. The Law of Independent Assortment stated that the alleles of two get sorted into gametes independently. A allele one gametes gets does not affect the other allele in the gamete. The alleles pair up with the opposite letter and one is dominant out of the pair. While the Law of Segregation is only one of the traits(dominant) gets passed down because the recessive is dominated by the dominant trait. The other trait is not passed down, but only reappears at F2. Helps us predict how one trait will be inherited. The alleles match up with the different letter but the dominants are paired together as the recessive is paired with each other. Through out this unit, my knowledge on genetics grew tremendously. Through this unit, I now understand why we are all how we are and that are genetic difference came equally from our parents' genes. In conclusion, in Unit 4, we were taught about key elements that form the basis of genetics and life. 

Here is a link to my infographic about genetics: https://magic.piktochart.com/output/17876697-new-piktochart

Is Sexual Reproduction Important?

   In the book, Dr. Tatiana's Sex Advice To All Creation by Olivia Judson, Judson explains about how different organisms reproduce. Mammals and some other organisms reproduce sexually, with a mate, while some organisms, like the Philodina, reproduce asexually. Sex is very important. The benefits of reproducing sexually is that your offspring is a bit different than both parents meaning that if there were to be a disaster, your offspring may survive because it is not identical. This means that their populations are better adapted. Some costs of reproducing sexually is that it is not very efficient, you have to try to look for a mate. According to Dr. Tatiana, herself, males dispense a lot energy to try to win over a female to mate. Asexual beings do not have to do that, so they can more efficiently reproduce (replicate).To reproduce asexually, the organism does not need a mate and the offspring will have the identical genes of the mother. In an asexual population, there are no males, just females that clone themselves. Some advantages of asexuality include how there is a better demographic of population because the female only needs to have one offspring to be balanced and more than one would be extra population. Another pro is that asexuality is much more efficient, in the sense that one can have a child anytime and does not need to depend on any other organism of its own species. According to Miss Philodina, her population is much more efficient and larger than the non-asexual populations. Miss Philodina also argued that her species has been asexual for 85 million years. Cons include the offspring not having any gene difference meaning that if something was to kill some of them , they would likely all die because they are all the same and one is not better protected than the other. According to Muller's hatchet is because the generations did not have any adaptation, it would not survive to any changes. Because of this, many asexual species tend to face extinction relatively soon after the conversion to asexuality. In this upcoming unit, I do hope to further understand why a some organisms choose to reproduce asexually if sexually is clearly better? Another question I have is, what happens to organisms that might lose any way to reproduce sexually/asexually?

Unit 3 Reflection

    In this unit, we started to learn about the cell and all its functions and types. There are two types of cells, prokaryote, no nucleus and no organelles, and eukaryotes, has a nucleus and organelles and has long chains of DNA called chromosomes. Cells are made up of all the different macromolecule.  Eukaryotic cells have nucleus, where DNA is stored it is like the brain of the cell. There are lysosomes that recycle proteins, and endoplasmic reticulum that holds proteins as they are being finished by ribosomes. The cell membrane holds all the content inside, a plant cell will also have a cell wall. The main function of a cell is to produce proteins. There are two types of transports. One of them is passive transport, requiring no energy, there is diffusion, high to low concentration that happen for small molecules, then there is facilitated diffusion which uses proteins to help larger molecules come in. The other form of transport is active transport which requires energy and is only used for the highly needed molecules. Osmosis is the diffusion of water through a lipid layer in the cell. There are autrophic cells, produce own energy, and there are heterotrophic cells, that consume other cells for energy. Photosynthesis only occurs in plant cells and it takes in CO2, water, and light and turns it into oxygen and glucose, which is kept in the cell unlike oxygen, with the help of the chloroplast, which a long time ago was a bacteria, another cell. Cellular respiration occurs in both plant and animal cells. It takes in oxygen and glucose and makes CO2, water, and ATP, energy used by cells, using the mitochondria. During this unit, some of my weaknesses were understanding how photosynthesis and cellular respiration worked, for it took time to go in depth and truly understand how it worked. A strength for me was to easily classify a cell as an eukaryote, prokaryote, autotroph, and/or heterotroph.

     In this unit, we did many labs to further our understanding of the topics. One of the labs included the egg macromolecules lab. This lab consisted in figuring out where each macromolecule was present in each part of an egg, which was used to show a cell. From these experiences, I understand the purpose and the function of the parts of the cell and the cell in a whole new way that makes a lot more sense and makes me understand the basics, so I can now try to deep further into cells. An unanswered question I still have is whether cellular respiration and photosynthesis produce and use up the same as the other produces, so that actually nothing is really being let out of the plant? I would also like to learn more about each specific organelle in a cell, and understand what they bring to a cell. For this upcoming test, I plan to go other all my vodcast notes and read the biology textbook in depth to try to further my understandings of each subject and truly know 100% of what this unit what about. In conclusion, unit 3 was a very useful unit for understanding the basis of biology and what a cell actually does and is.

Organism Lab

Euglena cell magnified at x400. It is unique because it has a flagellum. It is green and purple. It is eukaryotic and autotrophic.

Amoeba cell magnified at x400. It is unique because it has pseudopods, which consumes cells. It looks like jelly and is very colourful. It is eukaryotic and heterotrophic.

Cynobacteria magnified at 400. There no chloroplasts because it is a prokaryotic cell and is autotrophic. It has no nucleus and is green and blue. 

Bacteria cells magnified at x400. Bacteria can be shaped as coccus, bacillus, and spirilum. They are a lot smaller than the other cells. Thay are pink and purple. It is prokaryotic and autotrophic because no nucleus..

Spirogyra cell magnified at x400. It has a cell wall, cytoplasm, and nucleus it is like a strand. Looks like spirals and is blue green. It is eukaryotic and autotrophic.

Ligustrum cell magnified at 400. It is unique because it has veins. It is green and blue. Composed of many dots. It is eukaryotic and it is autotrophic.

Skeletal Muscle Tissue magnified at 400. It is unique because there are muscle fibers. It was pink/purple and had many strands of fiber. It is eukaryotic and heterotrophic.

   In this lab, we asked the question: what are the key features of autotrophs, heterotrophs, prokaryotes, and eukaryotes. We observed different samples of cells under the microscope to see the characteristics. Based on our observations, we could identify whether the cell was an autotroph or a heterotroph and whether the cell was an eukaryote or a prokaryote.  Autotrophs have a key characteristics of being plant cells and some bacteria. Because of this, they have chloroplasts ,vacoules ,and cell walls, unless they are bacteria. Heterotrophs are consumers, meaning they consume other cells to get their energy. Heterotrophs do not have vacoules, chloroplasts, and cell walls. For a cell to be an eukaryote, it must have a nucleus and a nuclei. While a eukaryote has a nucleus, prokaryotes do not have a nucleus and also have no organelles. Eukaryote cells are bacteria and other cells with no nucleus and no organelles. In conclusion, we learned about identifying cells as an autotroph or a heterotroph and whether the cell was an eukaryote or a prokaryote.

Egg Diffusion Lab

24 hour time lapse of our Egg Diffusion Lab. Egg on left in corn syrup, egg on right in DH2O pic.twitter.com/wdfujQyBXM

— Mr. Orre's Class (@OrreBiology) October 5, 2016

                                                                                     In this lab, we left two eggs in a deionized water and sugar water for 48 hours, and later observed what occurred. Based on the class data, the mass decreased and the circumference decreased as the sugar concentration increased. Because the sugar water has a lower concentration of water than the egg itself, the water in the egg diffused out of the egg from high concentration(the egg) to low concentration(the sugar water), which is known as a passive diffusion(requiring no energy). This then caused the egg to lose water, meaning a lose of mass causing the egg to shrink. On average, the egg, which stayed in sugar water, lost around 43.5% of mass and 26.16% of circumference. The solvents leave the inside of the egg to balance the amount of solutes inside and outside the egg.    

       A cell's internal environment changes as its external environment changes because diffusion causes both external and internal environments to change, for the change will occur from a molecule going in or out of the membrane, so both environments are effected. When the egg was placed in vinegar, the egg expanded as the solvent came in the egg. Both the internal and external condition changed. Then when the egg was placed in the sugar water, the egg shrunk because the water was diffused out and into the sugar water, meaning both the internal and external environments changed, they became equal in concentration.

      This lab demonstrated the biological principal of diffusion, which was taught during class. This lab showed how diffusion works in real life. Because the egg in the sugar water was hypertonic, the solvent(water) went from high concentration(the egg) to low concentration(the sugar water). This was a passive diffusion and caused a change in the internal and external environment of the egg.

       What this lab taught us can also be applied to real life. For example, fresh vegetables are sprinkled with water at markets, so that the vegetables do not diffuse the water in them. This would cause the vegetables to shrink and would be harder to sell. With the sprinkling water, the vegetables stay nice and plump with no wrinkling. Another example of diffusion in real life, is the salting of roads to melt ice. Because of this salting, the plants along the roadsides lose their water inside and either die or become less big and massive. This is caused because the salt diffuses the water out of the plants because the salt has a much lower concentration of water than plants.

     Based on the Diffusion Lab, I would want to test whether an egg that has shrunk would go back to its normal mass if placed in water. I would like to test this, so that I could know whether diffusion is a reversible process or if instead once the cell shrinks, it can never come back to how it was before.                

Egg Macromolecules Lab

   In this lab we asked the question, can macromolecules can be identified in an egg cell. We found that in the egg membrane, protein was abundant. During the test, it scored a 10 out of 10 for the presence of proteins, turning the sample a dark purple. Because the cell membrane uses protein channels to let in/out molecules, then the egg membrane will also have proteins in it. We found that in the egg whites, lipids, monosaccharides, and proteins were abundant. During all three tests, the egg white sample scored a 6/10 for the presence of lipids, monosaccharides, and proteins. Lipids are used to store energy; monosaccharides are simple sugars, which release energy; and proteins( enzymes) used to stop germs. All these macromolecules are all key for letting an embryo grow, for it needs energy, storage of energy, and needs enzymes( a sort of immune system). Last but not least, we found that proteins and polysaccharides were present in the egg yolk. The yolk scored a 8/10 in the protein test and a 7/10 in the polysaccharide test. Proteins are present because an embryo needs to have enzymes, and proteins are also used to make muscle. Polysaccharides are also present because they are complex sugars that provide stored energy needed for the embryo to start its transformation form embryo to baby chick.

 

   Our data contradicts the expected results because our group predicted that the egg yolk would test high for lipids, for the membrane of the egg yolk is mostly made of lipids. This may have happened because the egg yolk's consistency. Because of the egg's consistency, the Sudan III and NaOH+CoSO4 did not mix with the egg  well. Another error that happened was the instructions did not specify the quantity of egg membrane needed in each test tube. Due to these errors, in future experiments I would recommend to specify how to apply the agent, to find lipids, onto egg yolks, or to dilute the egg yolk in water to make it more liquid. I would also recommend to specify the quantity of egg membrane in milligrams, so that there is an exact amount in each test. 

   This lab was done to demonstrate what type of macromolecule was in each part of a cell with the metaphor of an egg. From this lab, I learned that some marcomolecules are necessary for the function of the each part of a cell, which helps me understand what each part of a cell does based on the macromolecules it needs for its function. Based on my experience from this lab, I could apply my new found knowledge towards better understanding in depth the function and structure of each part of a cell.

Unit 2 Reflection

   In this unit, we started to learn about biochemistry, but most importantly carbohydrates, lipids, proteins, and nucleic acids. There are electrons, protons and neutrons. Electrons are negative, protons are positive and are with the neutron, which has no charge, in the nucleolus. Carbohydrates are sugars that have ring structures of one, two, or three+. Our body breaks the bonds down to get energy. Lipids chains of carbon and hydrogen called fatty acids. They are nonpolar and are used in our body for storage of energy. Proteins are large molecules of smaller molecules named amino acids that are chained together. Proteins are used in our bodies to made into our protein. There also enzymes that are used to speed up chemical reactions. Enzymes turn substrates(molecule enzyme works on) into products by attaching with them at the active site. Enzymes work best where it is not too acidic or basic and also where it is not too cold or warm. Lastly, we learned about nucleic acids. These are composed of nitrogen, phosphate, and sugar. These make our DNA(two strands) or RNA(one strand).

  In the labs, we furthered our understandings of the concepts in unit 2.  We did the Cheese Lab, which furthered our understandings on how enzymes' functions are effected by temperature or pH and the curdling agent. From this lab, we learned that for making cheese, the best conditions were a warm and acidic environment. We also preformed the Sweetness Lab, which taught us about how the number of rings a carbohydrates has affects the sweetness of the carbohydrate. This lab taught us that the carbohydrates with the least rings were easier to get energy from them, for they are less dense and their bonds are easier to break. Here is the data for the Sweetness Lab.

  From these labs, I learned a lot more about carbohydrates and enzymes then I could have learned from a textbook. For example, we got to taste in person how carbohydrates are like. We learned the difference between monosaccharides(one ring), disaccharides(two rings), and polysaccharides(3 or more rings) through tasting them and tasting their differences. Another enriching lab was the Cheese Lab. With the Cheese Lab, we learned/saw how enzymes work in front of us. We saw how enzymes, with the optimal conditions, could cause milk to become cheese by speeding up the chemical reactions. In summary, the labs helped us understand more how the different macromolecules work in everyday life. 

   Last but not least, after learning Unit 2, I still have some unanswered questions. For example, do all enzymes prefer warmth and acidic conditions? Also, are nucleic acids found anywhere else than just RNA or DNA? In conclusion, Unit 2 was a very helpful unit to learn the basis of biology.

Sweetness Lab

    The structure of the carbohydrates directly affects the sweetness. Monosaccharides are the sweetest, disaccharides are not as sweet, and polysaccharides are not sweet at all. A carbohydrate's rings affect the taste, the more rings, the less sweet. For example, the monosaccharide, glucose, has a sweetness of 95/100 meanwhile the polysaccharide, cellulose, has sweetness of 0/100.

   The structure of a carbohydrate affects how a cell/organism uses it. If the carbohydrate has three or more rings, its function for a cell and organism is more complex and is also used sometimes for storage. The one ringed carbohydrates are very commonly used by humans to sweeten their food. It will be easier for organism to use a monosaccharide compared to a polysaccharide, because it is less dense and easier to break down to get its energy.

    Not every tester gave the same rating for each carbohydrate, but to have a accurate experiment, we took the average of all four ratings if one or more disagreed. Because everyone perceives taste a bit differently  while someone might have thought it was very sweet, another tester might not think of it as sweet. Another reason for having different ratings, would be that maybe the sample could have been contaminated. Last but not least, some testers might have not rinsed their mouth of the previous carbohydrate.

  Lastly, humans are able to taste sweetness by small sensory cells. There are specific cells that taste sweetness. Because sweetness is considered part of the fifth basic taste, only the sensory cells for the fifth taste can sense them. Because of this, each tester could have perceived the sweetness differently because either their sensory cells were not as sensitive or they did not have the same quantity of sensory cells for the fifth taste.

Biology Collage

Jean Lab

    In this lab, we asked the question, what concentration of bleach is the best to fade the colour out of new denim material in ten minutes without visible damage? We found that 25% was the best concentration of bleach to fade denim without excessive damage. The average for colour removal and fabric damage ,for the 100% concentration, was eight for both. Meanwhile, the 25% concentration had an average of four for fabric damage and three for colour removal. The colour of the 50% concentration became light blue, but the 100% concentration became completely faded, losing its colour. Meanwhile, the 25% concentration faded enough that it was no longer dark blue. Bleach is known to break down pigments and also damages the structure of the material. This data supports our claim because it shows that when there is too high of a bleach concentration, the material will endure severe damage and lose of its colour.

     Our data contradicts the expected results because some errors came up during the experiment. Because we did not have timers, instead we relied on the clock, the period of the jeans being soaked in the solutions were not all equivalent. Another error was that because of time constraints, not all the denim rested for nine minutes. Because of this, the 100% concentration pieces did not fully reach its most faded. To improve the lab, I would have provided the groups with a timer to time the soaks perfectly. Another improvement that could have been done, would have been to have more time to carry out the experiment.

    This lab was done to demonstrate to us how to set up and carry out labs for biology class in the future. From this lab, I learned to do an experiment with controls which helps me understand the concept of creating and doing an experiment using controls, dependent variables, independent variables, and constants. Based on my experience from this lab, I now am able to create experiments and labs for other classes but most importantly for all my science classes to come.