Unit 5 Reflection

In unit 5, we learned about how our genetic code determined who we are and the great importance of our DNA. Deoxyribonucleic acid, or DNA, is the basis of all life and is made up of millions of nucleotides, which are made of a nitrogen base, a phosphate group, and a sugar(deoxyribose). In 1953, Francis Watson and James Crick discovered the structure of DNA: a double helix. This double helix shape helps the DNA pack together tightly and supports the structure as well. Each nucleotide bonds covalently with each other, creating an antiparallel structure, meaning the 5' and 3' carbons go in opposite directions. Nitrogen bases with double rings are called purines, adenine and guanine, and single rings are called pyrimidines, thymine and cytosine. This basic genetic code is a simple system that allows individuals have special qualities and unique features
. The process of replicating DNA is a simple concept, where helicase unzips the DNA and DNA polymerase adds the matching nucleotides to the unwound strands creating two new genetically identical cells.

One of the most important concepts of our DNA is the central dogma of biology. The central dogma of biology is the process from DNA to protein, where DNA is transcribed into RNA and RNA is translated into amino acids and eventually into proteins. During transcription, the DNA unzips and RNA polymerase creates a complementary RNA strand and once finished mRNA exits the nucleus into the cytoplasm. During transcription, ribosomes read the mRNA three bases at a time, in codons, and turns them into amino acids and eventually protein. This process is especially important, because without it would be impossible for life to thrive. One of the most important subjects in genetics is gene expression and regulation. All cells in our body have the same DNA, and yet they only use the minimum amount of DNA that they specialize in for one reason: to save energy. This is the reason why you don't have ears on your chest and why fingers aren't on legs because the appropriate genes are only turned on at the appropriate times.

Although unit 5 was short, I grew a lot as a student. The main thing that usually helps me with the unit is understanding the concepts and applying it to the real world. For example, in protein synthesis section I applied it into real life, as proteins are everywhere and help us get through life every day. Last unit we took the VARK questionnaire, and I learned that I learn best visually over any other method. After thinking about this a little bit, I realized that I was a very artistic person, therefore a visual learner as well. Overall, in this unit I learned a lot about genetics as well as myself.

Protein Synthesis Lab Conclusion

The process, or procedure, of creating protein from DNA is called protein synthesis and requires several steps. First, the DNA unzips and the RNA polymerase begins to read the DNA, creating a complementary strand of RNA. Once the RNA is created, the mRNA exits the nucleus for the cytoplasm, and eventually bonds with a ribosome. The ribosome then starts to read the mRNA three bases at a time, called codons, creating amino acids for the corresponding codons. Finally, once the ribosome finishes reading the mRNA and creates the amino acid chain, the amino acids begin to fold into the final protein. The end result is a unique protein made of several amino acids.

Mutations can range from being lethal to very lethal, especially if the DNA is changed drastically. There are several ways that DNA can be altered, and some are more lethal than others. The least lethal, or least effective is a substitution, where one base is substituted for another, and the most it can alter is one codon, barely affecting the protein. The next two are frameshift mutations and can affect the DNA sequence drastically. The first is an insertion, where one or more bases are inserted into the DNA, and the second is a deletion, where one or more bases are taken out of the DNA. Both these mutations will shift every base after them and are more lethal if the insertion or deletion is at the beginning of the DNA sequence.

In step 7 I chose to do a deletion of two bases, which turned out to be very effective. The protein was affected drastically, as a result of the deletion of only two bases, the entire protein was deleted because the first codon was a stop codon, rendering the protein non-existent. The bases that were deleted were in the front of the DNA sequence, therefore causing more damage because it shifted almost all of the bases, changing the protein in the process.

Proteins make our body work, but it there is a mutation in the protein, the effects could be drastic. A good example is progeria, a rare disease that causes accelerated aging. People affected by this disease can die at the age of 13 but can live up to their twenties, and only about one in eight million are affected by this disease. The disease is caused by a mutation in the LMNA, a protein that supports to the cell nucleus, and shows the horrible effects that just one protein can cause.

Citations:
http://io9.gizmodo.com/10-unusual-genetic-mutations-in-humans-470843733
https://commons.wikimedia.org/wiki/File:Ribosome_mRNA_translation_en.svg
https://commons.wikimedia.org/wiki/File:Missense_Mutation_Example.jpg
https://simple.wikipedia.org/wiki/Progeria

DNA Extraction Lab Conclusion

In this lab we asked the question: How can DNA be separated from cheek cells in order to study it? We found that this could be achieved through a series of steps that extracted cheek cells and separated the DNA, making it observable. The first thing we did was we homogenized cell tissue with a polar liquid, which in our case was Gatorade, which we swished around our mouths, extracting the cell from the inside of our cheeks. After taking the Gatorade/saliva mixture and mixing salt into it, we added soap into it, in order to lyse, or rupture, the cell membrane, in effect releasing the contents of the cell into the mixture. Next, we used catabolic proteases found in pineapple juice to further break down proteins in the DNA called histones. Finally, we layered alcohol over our mixture, and because alcohol is nonpolar whereas the DNA is polar, the DNA falls out of the solution as a precipitate right in between the layers, eventually floating to the top. This data supports our claim because it shows that DNA can be in fact extracted and separated from cheek cells, using scientific methods to retrieve safely and easily.

While our hypothesis was supported by our data, there could have been errors in several parts of our experiment. First, when we were pouring the pineapple juice into our solutions, bubbles were formed at the top of the solution, which could have affected the yield of DNA that ended up having. In addition, during the addition of alcohol over our Gatorade mixtures, some of my other group mates poured the alcohol in too fast, therefore causing the two layers to mix, and affecting the yield and the outcome of their DNA. Due to these errors, in future experiments I would recommend having an easier method in transferring over solutions, such as using small graduated cylinders to measure and pour solutions over carefully and accurately. Furthermore, for pouring in alcohol, or any solution into a small test tube, funnels could be used to prevent spills.

This lab was done to demonstrate the concept of DNA and how it can be found anywhere in your body. From this lab I learned how to extract and separate DNA from the inside of an organism's cheek, which helps me understand the concept of DNA and its abundance inside the human body, while also giving me a physical observation of DNA. Based on my experience from this lab, I could use these methods of extracting DNA to do other things, such as extracting other organism's DNA or studying the effects of DNA and how
it is important to the scientific world.

Unit 4 Reflection

Recently, we performed the Coin Sex Lab, which demonstrated relationship between genetics and inheritance. We used the flipping of coins to model the process of meiosis and the randomness of the splitting of chromosomes and recombination of genes, in order to try to get an accurate representation of inheritance. One of the scenarios we tested was a dihybrid cross, where we crossed two dihybrid heterozygous genes, and the expected results was a phenotypic ratio of 9:3:3:1, our results almost matching with a ratio of  8:4:2:2. I think our results supported the expected results, excluding the minor discrepancies of 1 additional or less result. This is because when crossing two dihybrid heterozygous genes the dominant alleles are apparent and therefore this is also more likely to be apparent in their offspring. For example, if the dominant alleles are brown hair and brown eyes, then the offspring are more likely to get brown hair blue eyes, and it is very rare to get the recessive alleles to be apparent in traditional dominance. Although probability can get give us an educated guess of what results will be, it cannot predict an offspring's traits exactly because in the end genes will combine randomly and unpredictably, overruling any use of probability. Knowing how genetics and inheritance relate to our lives is important, and can help us understand more about ourselves and our entire family, including our ancestors and even our potential children in the future.

In Unit 4, we learned all about genetics and inheritance. In the beginning, we learned about the cell cycle and the process of mitosis During mitosis, there are several steps, including interphase, prophase, metaphase, anaphase, telophase, and cytokinesis, where the cell grows, duplicates DNA and splits into two physically and genetically identical cells. Then we began building on the subject of genetics and reproduction, and asked the question: Why is Sex so great? We learned that there were two main methods of reproduction, asexual and sexual reproduction, both with there costs and benefits. On one hand there was asexual reproduction, where there is one "parent" that splits, or creates, two genetically identical organisms. Although asexual reproduction is quick and easy, it is very difficult for species that use this method to survive because a simple virus or parasite could come along and wipe out the entire population. On the other hand there is sexual reproduction, where there are two parents that each contribute half of the offspring's DNA through sex cells, producing genetically variant offspring. Sexual reproduction has some costs to because it takes a lot of time and energy, exposes the parents to parasites and STDs, creates genetic combinations that are bad, and creates competition over mates. Diving deeper into the subject of sex, we found that sex was determined by a pair of sex chromosomes (XX is female, XY is male), carried in sex cells called gametes, and other traits were determined 22 other non-sex chromosomes, called autosomes. Gametes are created in a process called meiosis, which similar to mitosis splits, but splits twice in order to form 4 daughter cells, containing sister chromatids. Next we learned about Gregor Mendel's discoveries and his revelation about how great sex is. He discovered that traits were determined by two copies of a gene, and he also found that genes come in different versions, called alleles some more dominant over others, which are either homozygous or heterozygous. In addition, he found that you could predict the phenotype, the physical trait, using the genotype, the alleles, of an organism. He also had two important conclusions, first, the law of segregation, which states that gene pairs split during meiosis, and second, the law of independent assortment, which states that gene pairs split randomly during meiosis. Finally, in inheritance, there are several complications, includiong incomplete dominance, which is the blending of alleles, codominance, where both alleles are apparent, gene linkage, epistasis, multifactorial disorders, and polygenetics.

During Unit 4, I learned how genetics and inheritance were an important part in biology and in my life. Using genetics, I could predict the traits that my children and grandchildren would have, and even trace my own traits back to my ancestors. Inheritance can tell us what the costs of having a child could be, including STDs and passing diseases onto offspring, but in addition it could also tell us the benefits of having a child and the amazing traits that could potentially be passed onto the next generation. In addition, in this unit we created infographics that we used to show the important concepts in genetics, and also gave me a new way to express information creatively and clearly. Overall, during this unit I learned a lot about genetics and inheritance, my own traits and gene pool, and more about what biology offers.

Is Sexual Reproduction Important?

In today's world, producing offspring sexually is very important to the survival of a species, and there are several advantages of sexual reproduction. First, sexual reproduction helps reduce the chance of mutations. In an analogy, there is a manuscript that has been copied over and over by monks in two distant monasteries, leaving more chance for mistake, whereas having sex is like two monasteries copying each other regularly and frequently replacing their versions of the manuscripts. Mutations can be very harmful to species who don't produce sexually, suppose there is a threshold of harmful mutations an individual can carry, in sex the mixing of genes gives some creatures harmful mutations, and these creatures are quickly killed off, leaving the population safe, but if there was no shuffling of genes, the population would be overwhelmed by harmful mutations, therefore going extinct. In addition, over time organisms that don't produce sexually will, over time, be lead to several mutations, and if the last individual, that is not mutated, does not produce offspring then the population eventually goes extinct. Finally, since organisms that do't produce sexually have very similar genes, parasites and viruses, can easily infiltrate their defenses, killing them of, but sexual reproduction helps by mixing genes and making harder for parasites to kill of the species, creating a moving target. Although sexual reproduction is important and necessary, could it be possible for asexuals to thrive and grow, or would it be impossible in the conditions of today's world?

Unit 3 Reflection

In Unit 3, we learned about the function, structure, and importance of the cell. There are two main types of cells, prokaryotes, a simple cell with no nucleus only one chromosome, usually bacteria, and eukaryotes, multi-organelled, nucleus-containing, complex cells. The cell has many different structures that have specialized functions and work together to help sustain life. For example, the nucleus gives the instructions to the cell, the ribosomes assemble the proteins, the endoplasmic reticulum synthesizes the proteins, and the golgi apparatus ships proteins via vesicles throughout the cell. In addition, we learned about osmosis and diffusion, where molecules diffuse from a high concentration to low concentration until equilibrium. During osmosis, water, a solvent, diffuses through the cell towards the higher solute concentration, in order to create an equilibrium. Isotonic solutions have equal solute concentration inside and outside of the cell, hypertonic solutions have a higher concentration of solutes outside of the cell, and hypotonic solutions have a higher solute concentration inside the cell. In the beginning there was a prokaryote, but then there came autotrophs, which could make their own food. Soon, heterotrophs came into play, which could consume its food, and some bacteria survived when eaten by a cell, turning into the first eukaryote, the cell provided protection for the bacteria, while the bacteria provided food for the cell. This became known as the endosymbiotic theory.



Autotrophs use light to create food using photosynthesis, a process that occurs in the leaf of a plant. Inside the leaf chlorophyll contains stacks of thylakoids called granum. There are two main processes in photosynthesis, light dependent reactions, where light is absorbed in the thylakoids an produces NADPH and ATP, by ATP Synthase, and water is split, releasing oxygen and pumping hydrogen ions into the thylakoid membrane, and light independent reactions(Calvin Cycle) in the stroma, where sugar, or glucose, is produced using carbon dioxide, ATP, and NADPH from light reactions. Both heterotrophs and autotrophs do cellular respiration, which is divided into three steps, glycolysis, which occurs in the cytoplasm and creates two ATP and pyruvic acid, the Krebs Cycle, which converts molecules from glycolysis into 2 ATP, carbon dioxide, and NADH and FADH2, and the electron transport chain, which uses oxygen, NADH, and FADH2 to convert ADP into ATP. In total 36 ATP is produced from one glucose molecule.

During the unit, I felt that I understood the material well, but the concepts, at times, could be very tricky to grasp. The number of organelles and their specialized jobs could be confusing and the osmosis and diffusion concept was sometimes vague in my mind. When we got to the photosynthesis and cellular respiration section, the concepts were confusing, but as we did more things to help reinforce the ideas, such as drawing diagrams and reviewing photosynthesis and cellular respiration, I could begin to see the puzzle pieces being put together. Unfortunately, we missed out on some labs because of safety issues, which was a setback and a disappointment, but it was a good lesson about the consequences of not being safe and organized. Despite the setbacks, I felt that I was successful in learning about the cell and how life was created because of this extraordinary thing.

Egg Diffusion Lab

1) When the the sugar concentration increased in the solution, the egg's circumference decreased. This was because the sugar was hypertonic, where the solute concentration(the sugar) was higher, therefore the water inside the cell diffused through the membrane from the high concentration to the low concentration to form an equilibrium. 
2) As the external environment changed, the cell's internal environment changed because of the change of the solute concentration. In the vinegar, the solute concentration was less than the egg, so the solvent, the water, entered the cell, passively diffusing through the membrane, in order to create an equilibrium. Then, in the sugar the solute concentration was higher, therefore the water exited the egg, to form an equilibrium.
3) The biological represented in this lab was osmosis, which is a type of diffusion. Osmosis is when water diffuses in and out depending on the solute concentration outside of the cell. When there is a hypertonic solution the solute concentration is higher than the cell's solute concentration, then the cell will shrink due to loss of water. When there is a hypotonic solution the solute concentration is lower than the cell's solute concentration, then the cell grows due to the gain of water.
4) When vegetables are sprinkled with water, they are kept ripe, because the water makes the vegetables isotonic, so that they do not lose water and turn dry. Salt melts the ice because it is hypertonic, so it makes the ice lose water, and melt. When, roadside plants are salted they lose water, due to the hyertonicity,of the salt, making them wither and die.
5) Based on this test I would like to test the results of growing plants with sugar water and vinegar. The vinegar is hypotonic and the sugar is hypertonic, so which one is better for growing plants, and which one would have a worse affect on the plants?

Egg Macromolecules Analysis

     In this lab, we asked the question: Can macromolecules be identified in an egg cell? We found that it was indeed true that macromolecules could be found in the different parts of an egg. In the egg membrane, we found that it contained lipids because the Sudan 3, when mixed with the egg membrane, turned from a red color into an bright orange color, and on a scale from 1-10 we rated it a "10" for the color change. In a cell, the membrane contains lipids because it made out of phosophoipids, a type of lipid, which help the cell defend from outside substances, contain organelles, and lets molecules in and out. Then, in the egg white, we found that there were proteins contained in it. Testing for proteins, we used biuret to test for the presence of proteins, and once the biuret was mixed with the egg white it turned from blue to a light purple color. We rated it a "7" in a scale from 1-10 for the color change. This is because the cytoplasm in a cell, represented by the egg white, contains proteins and enzymes that break down amino acids in the cell. Finally, we found that there were also lipids in the egg yolk, which we used Sudan 3 for the test. In the solution, the egg yolk turned red to a bright orange, indicating lipids, and on a scale from 1-10 we gave it an "8" for the quantitative amount of the macromolecules. The egg white, or the nucleus of the cell, contains lipids because of the membrane which functions as a barrier, container, and lets things in and out of the nucleus, such as RNA.
     One possible error in lab, was the fact that the the amount of the solution could have been altered when we were putting it in. For example, when dropping in 3 to 5 drops of Sudan 3 someone could have accidentally put 6 to 8 drops, therefore altering the color of the solution and the results of the experiment. This problem could be easily fixed be using graduated cylinders to measure the exact amount of the solution to put in. Furthermore, the color of the solution could have been interpreted differently, such as, for the biuret solution used for proteins, there could have been a different interpretation for the purple color, where one person thinks light purple is 7 o a scale from 1 to 10 but another thinks it is a 9. This problem could be fixed by one person interpreting the color, such as the teacher, for everyone so that the results will be more accurate.
    The purpose of this lab was to find the macromolecules that are found in the different part of the cell. In class we learned that there are lipids in the membranes of organelles, protein in the cytoplasm, and carbohydrates in the mitochondria. The macromolecules can be found everywhere in the cell and are important to the function of the cell and the body, and without macromolecules life could not form. These same macromolecules that can be found in a tiny cell, can be found in the different parts of the cell. If one macromolecule was not existent then the cell could not function, and life could not thrive.

Unit 2 Reflection

During Unit 2, we learned about four main macromolecules: carbohydrates, lipids, proteins, and nucleic acids. Carbohydrates are rings of carbon, oxygen, and hydrogen which bond to create sugars, such as monosaccharides, disaccharides, and polysaccharides, and is used by plants and a main source of energy for humans. Lipids are large molecules such as fats and oils which contain long chains of carbon and hydrogen called fatty acid, containing a hydrophilic head and a hydrophobic tail. They are used to store energy, break bonds, and used to make up cell membranes. Proteins are made of amino acids, that are chained together, and support the human body and speed up chemical reactions.
There are two types of proteins, structural proteins that make up our body such as kerratin and collagen, and enzymes that speed up chemical processes up in your body, being a catalyst and lowers activation energy in order to get more product in less time. Finally, nucleic acids are made up of thousands of nucleotides that are made of three components: sugar, phosphate and a nitrogen base. DNA, a nucleic acid, serves as a blueprint for making proteins. All these macromolecules work together in order to create and sustain life, to create a happy and healthy organism.

Sweetness Lab Analysis

1. We found that sugars that were monosaccharides were especially sweet, disaccharides were moderately sweet, and polysaccharides were not sweet at all. During the experiment, we taste tested a variety of sugars, and found that fructose a monosaccharide was the sweetest sugar with a score of 175, 100 being the standard sweetness on a scale from 0-200. Tasting maltose, a sugar found in beer, we found that it was semi-sweet at about a 75 to 100 sweetness. Finally, when tasting cellulose, a polysaccharide, there was no sweetness at all, and it came up with a score of 0. This data shows that proves our claim because the monosaccharides proved to be the sweetest and the polysaccharides were the least sweet.




2. Usually, monosaccharides are found in liquids or juices such as fructose, found in honey and fruits, and galactose which is found in milk. These are usually used as a source of energy for cells and organisms because they are the easiest to break down. Disaccharides are similarly mainly used for for energy because they are easy to break down, and are found in milk(lactose) and maltose(beer). Polysaccharides are used for energy storage in plants, and in humans they are used for energy and take a longer time to digest.

3. There are a couple of reasons why each taster could have given a different sweetness ratings for the same sugar. One is because of the way each persons taste buds are physically different from each others and react to foods a different way. Another reason is the fact that some people like the taste better than others and this caused them to put a different sweetness level. The final reason is that the person may grade on a different scale, for example, one person could have said that 150 was sweet while someone else claims that 150 was super sweet instead.



4. Taste isn't just "taste" its also smell, texture, and even temperature. These factors, the smell and texture, could be factors in why different people taste sugars differently. Another reason, is the fact that are tongues have different structure altogether. A common myth about the tongue is that there are different zones that taste different things, but this is completely wrong. Although this my this myth is not true, the side of the tongue can taste better than the middle. So, if someones tongue tastes something better or worse, it could alter the rating of the sweetness of the sugar drastically.

What is Biology? Collage

Jean Lab

In this lab we asked the question: What concentration of bleach is the best to fade color out of new denim material in 10 minutes without visible damage to the fabric. We found that the the best concentration of bleach was 50%, which provided the best fade of color without damaging the fabric. There was a significant color change in the 50% bleach, but didn't drain the color completely, and in addition did not damage the material very much. The 100% bleach drained the color completely while the 25% and 12.5% did not drain the color significantly. This data support our claim because it shows the perfect amount of bleach concentration in order to get the perfect color fade without damaging the denim.

While our hypothesis supported the data there could have been errors in our procedure. While we were bleaching all our denim squares at the same time, we could not take them all out at the same time, creating possible errors in the procedure. At the same time had some timer problems and we had to reconfigure to give us the right time to submerge the denim squares, therefore the squares may have been submerged a little to long or short. Due these errors, in future experiments I would recommend a more accurate timer and submerge less denim squares at a time, in order to get more accurate measurements.

This lab was done to demonstrate the scientific method and how we could use the scientific method in a real lab. From this lab I learned each step of the scientific method and what to do in each step in order to get an accurate and verifiable result, which helps me understand overall the concept of the scientific method. Based on my experience from this lab, I learned how to use and apply the components of the scientific method in an experiment to achieve accurate, verifiable results.