Unit 5 Reflection

        Throughout our unit, we learned an immense amount on DNA, and its role and function in the body. At first, everything was understandable, the content being fairly straightforward, when we learned about DNA replication and Protein synthesis. During DNA replication, the DNA is unzipped into two single strands, and then interpreted with proteins in order to make two identical DNA strands. This unzipping process is also used in protein synthesis, being the first step of DNA being converted into RNA in the nucleus. Soon after, the RNA moves to a ribosome, and is converted into amino acid code, eventually naturing into a brand new protein.

        This, however, does not mean that DNA is flawless. Occasionally, DNA can get mutations from mutagens, changing the genetic code in a positive or negative way. For example, some mutations can help lower cholesterol. On the other hand, some mutations can kill embryos within minutes, or put someone's life at constant risk. Mutations can also change nothing in the genetic code however. In general, there are three main types of mutation, being substitution, a mutation replacing one nucleotide with another one, insertion, where a nucleotide is added into the genetic code, shifting the rest of the nucleotides one way, and deletion, where a nucleotide is taken out of the genetic code, shifting the rest of the nucleotides another way. This is not to say that there are not other types of mutations though. For example, inversion, a mutation that reverses the nucleotides, exists, as well as many others.

        However, as the Unit progressed, I found myself getting confused more often, especially when the lesson on operons was shown. With some studying, I now know that operons are gene sets that are expressed through gene regulation in order to make proteins. Gene regulation is highly reliant on operators, using them as roadblocks in order to express or not express genes, which have the code to make proteins.

        I believe that I learned a lot during this Unit, not only in content, but in learning procedure as well. While learning about operons, I would  consistently look at diagrams, and see if I could label them myself, effectively quizzing myself on my knowledge. This has allowed me to better retain information taught in class and at home, and has made me a better student.

Protein Synthesis Lab

        Throughout this lab, I have discovered that protein molecules are made in two steps; translation and transcription. In translation, DNA is converted to RNA in the  nucleus, making a temporary copy of the genome. The RNA is then transferred to a ribosome, in which amino acids are made in a new sequence of codons. Finally, the newly formed amino acids nature themselves into a protein molecule.
        As I progressed in the lab, I began to realize that mutations are found in proteins, coming in many different forms that effect the protein production process. Main mutations include substitution, where a single nucleotide is replaced with another, insertion, where a nucleotide is added to the code, and deletion, where a nucleotide is taken out of the code. These mutations can cause harmless, destructive, or positive genes, killing an organism or allowing it to thrive. Out of the three main mutations, I believe that deletion is the most destructive, as two nucleotides are left out of the processing code. However, I also believe that substitution is the most harmless mutation, with only one nucleotide being changed. If additional information is given, however, the destructive power of a mutation can alter.

        In the final part of the lab, I was given the task of using a mutation to test its destructive capabilities if it was used in a different way. I chose substitution, switching the two nucleotides in the front into different genes. This created a stop codon, forcing the ribosome to make no protein at all. This is important because it influences the idea that the place of a mutation in the gene matters.
        Mutations can effect life dramatically, but have the potential to cause positive traits as well. For example, a mutation located in Italy named "Apo-AIM" is a stronger version of Apo AI, which works to help cholesterol flow throughout the body. This gene also acts as a antioxidant, which helps to reduce inflammation in the arteriesclerosis.

Human DNA Extraction Lab Write-up

        In this lab, our group asked the question, "How can DNA be separated from cheek cells in order to study it?" Through experimentation with DNA, we have come to the conclusion that cheek cells are separated through. homegenization, lysis, and precipitation. This is shown from are lab data, evidently showing that DNA molecules were extracted from in between our solution. In fact, when the mixture of saliva solution was mixed with the cold rubbing alcohol, DNA began to precipitate in between the two liquids. Because of this, cheek cells were obviously shown in the liquid substances.

        At the start of the lab, our group grabbed cups, pouring gatorade into them, and swishing the gatorade around in our mouths in order to mix cheek cells into our substance. Once spitting the liquid mixture out,
we added soap detergent in order to lyse the cells, effectively splitting open the cell membrane in our cells. Once the DNA was floating in the mixture exposed, salt was added by our group in order to clump the DNA together. Pineapple juice, a catabolic protease, was then added to completely break down any proteins, or histones, that the DNA wraps itself around. However, once the cells are burst and the DNA is clumped up, isopropanol alcohol is then layered on top of the gatorade saliva mixture, making the DNA precipitate,
as DNA is polar, while the alcohol is not. this allowed for collectable DNA.

        During the lab, some errors occurred, but did not affect the lab drastically. For example, our group specifically did not add enough salt into our mixture, resulting in less visible DNA clumps. Another error occurred when our group slightly mixed the alcohol with the
gatorade saliva mixture, but had little, if any affect on the DNA clump. These errors could be fixed if instead of grabbing a pinch of salt, actually measuring the salt in order to reduce having too little or too much salt. The alcohol mixture error can be fixed if instead of having us carefully hold the tube to the side, having a wood post which holds it, so that human malfunction is nearly impossible.
        This lab was done in order to help us understand the properties of DNA, and how it reacts to certain substances. The outcome of this lab is essential to DNA extraction, and can be applied to the field of Biotechnology, as gene splicing is done in order to process traits in the DNA helix, and used tin order to breed and create hybrid creatures.

Unit 4 Reflection

        Our group started the "Coin Sex" Lab off by looking at different genes in humans, and then proceeded to flip coins, randomly determining these traits, then looking at data tables after multiple coin flips, determining the averages for each possibility, such as the chance of two heterozygous parents having an albino child. Most of the results that our group had matched the amount of possible offspring through the dihybrid cross simulation. Even so, the limit of using probability to predict offspring is quite big, as you are not predicting the exact traits of the child, but possibly millions of different genotypes for a child.
        This follows into our main unit, explaining that how even though probability is not exact, genetic variety is created from this, allowing for adaptations to the environment, including disease immunity. These possibilities are furthered even more so when genetic mutation comes into play, allowing for an infinite amount of different genotypes and phenotypes in a single offspring. In fact, the infographic project highlights this by not only having us research variety further, but grading each other's infographics, which allows us to be taught the content even more.

Why is Sex so Great? : Infographic

Is Sexual Reproduction Important?

        During the reading "Dr. Tatiana's Sex Advice to All Creation", Olivia Judson explains how many things in nature would not be existent if sexual reproduction did not exist. This includes how crickets chirp at night, and how the mighty horns of deer antlers grow. The reading also pointed out that the only way genes are mixed is through sexual reproduction. Mutations are an exception, however, creating completely new genes not possible anywhere else, for good or for bad. The reading specifically pointed out that sexual reproduction was the only way to adapt to the environment. This means that when a sexually reproductive species evolves into one that is asexually reproductive, it flourishes until the environment changes, but becomes extinct suddenly due to the lack of variety in the species. This means that the genes heavily influence the rate of survival and reproduction in a species. Another point given shows that a balance between the two needed things in the wild are very hard to balance out. For example, some birds can have huge, long tails in order to seduce females, but die to predators in lack of survival instinct. The opposite effect can happen in a similar manner. Along with this, the reading suggests that ways to seduce other organisms in a species are much more varied than the predictable amount of ways in order to avoid predators. This is only kept varied with mutations, which the book states are raw evolution which help vary any species, asexual or sexual. Much, however, is kept unclear in the reading, such as the question of how frequently mutations occur, or what type of species have used mutations to survive asexually, if at all.

Unit 3 Reflection

Throughout Unit 3, I came to realize how the Unit emphasizes the main functions of the cell, and how it came to be. As I progressed through this unit, I have acknowledged that the process of Photosynthesis and Cellular Respiration bothered me at first, but have eventually become more clear with repeated study and collaboration with my group. From this, most of this content is easy to understand for me, and I have not struggled with too many topics, excluding Photosynthesis and Cellular respiration.

As I understood most content from this unit, I have learned that cells contain multiple organelles, which all help the cell to function in some way, varying from membranes which filter things in and out of the cell, to mitochondria, which provide energy for the cell. I have also learned that cells have evolved from cyanobacteria, becoming heterotrophs which ate cyanobacteria, eventually folding in membranes to allow symbiosis between the bacteria, which made energy for the heterotroph, in order to recieve protection from the heterotroph. Autotrophs, however, make their own energy.

From this Unit, I am inclined to learn about the Calvin cycle and the Citric Acid Cycle, as they were not explained in depth in class and during the vodcasts. This is only explained in context of its role in photosynthesis and cellular respiration. Other from this, I have little questions on the unit and have understood most of the content in the unit.

Photolab: Virtual Lab 2

At the beginning of the virtual lab, we asked the question “How does Carbon Dioxide affect the speed of photosynthesis?” Through evidence, we found that a higher concentration of Carbon Dioxide increases the speed of photosynthesis. This is shown in the data table, indicating that a high concentration of Carbon Dioxide results in an increase of 11 Bubbles, with the low concentration producing 18 Bubbles, while the high concentration resulted in 29 Bubbles. This data supports our claim because the bubbles are filled with oxygen a waste product of photosynthesis, which indicates that the reaction took place.

This lab was done to explain to us how photosynthesis works, and what is used in photosynthesis, as well as what is produced with photosynthesis. From this lab, I learned that Carbon Dioxide is needed for photosynthesis, even speeding up the process, which helps me understand the concept of photosynthesis in general. Based on my experience from this lab, I can now utilize what I have learned to start an indoor garden, using more Carbon Dioxide in an enclosed space.

Amount of CO2	Bubbles Produced (In 30 seconds)
High Amount of CO2:	29 Bubbles
Low Amount of CO2:	18 Bubbles

Egg Diffusion Lab Analysis: 10.12.2016

      Our group asked the question "How and why does a cell's internal environment change, as its external environment changes?" Through our data, we found that a cell's environment changes because of osmosis, depending on what environment it is currently in. When taking the Egg Diffusion lab, our group left one egg in de-ionized H20, while the group we teamed up with left an egg in sugar water, measuring their circumference and mass beforehand. After one full day, our groups checked on our eggs, measuring their circumference and mass once again. With the ending of our experiment, our groups found that the egg in sugar water shrank, while the egg in de-ionized water grew, its mass shrinking -0.44%, while its circumference grew 7.78%. This came to be because of osmotic pressure, where a cell will adjust to its environment by giving up or absorbing water in order to balance out the solute.

      This change was caused from osmosis, a passive diffusion where the solvent (water) either diffuses into or out of the cell membrane in order to balance the concentration ratio of water to sugar, the solvent. This happens as the solute cannot diffuse across the cell membrane. In the case of the sugar water egg, the solvent was greater outside of the egg, and it shrank in order to balance out the ratio, making a change from low concentration to high concentration. In turn, this put the sugar water egg in a hypertonic environment, where there is more solute outside the cell.


      This lab can be related to many real life events, one of them being how your skin "prunes" up after you are in the pool for an extended period of time. Osmotic pressure makes your skin bloat up as water seeps in, making your skin look "pruned".

      From this experiment, I have better learned about the principles of osmosis, and the effects of osmotic pressure. In fact, I can make my own experiment from this, further testing this principle by putting an object relative to the egg used in the previous lab, draining its solvent in a hypertonic environment, then putting it in a hypotonic environment full of solvent, and seeing if the object grows once again.

Egg Macromolecules Lab Analysis: 10.10.2016

      In the following lab, our group asked the following question, "Can macromolecules be identified in a cell?" With our group's evidence, we discovered that macromolecules can be identified in cells. In fact, our group decided with our information that proteins are found in almost parts of the cell, shown through the identifier sodium hydroxide, which turns liquid from blue to purple on contact if they contain proteins.
      For example, proteins are found in the cell's cytoplasm. This is shown in the protein data table, where the egg example substance scored a 9 out of 10, turning light purple on contact with its identifier. This is because proteins are found in organelles, which need them in order to function.
      Our group also found that proteins are found in the nucleus of cells. This is shown in the data table for protein identification, where the egg yolk example for the nucleus scored an 8 out of 10 on contact with the identifier, turning dark purple. This may be because proteins transport RNA out of the nucleus from DNA in order to give the rest of the cell commands.
      Proteins are found in the cell membrane as well as the nucleus and the cytoplasm. This is shown in the data table, where the egg membrane example is given a score of 5 out of 10, turning indigo on contact. This is because protein channels are scattered across the cell membrane, which help transport molecules into the cell.

      This lab was done to give us a better understanding of what macromolecules are located in parts of the cell. However, some errors could have happened in the lab which could have offset the results. For example, some did not stir all of the contents of the identifier and the egg substance together, which could have lightened the color of the final substance. This is shown in the monosaccharides test, where heat is used to solidify some of the unmixed substances, and can be fixed if shown in the instructions to mix the identifier with the egg substance. Another error is shown when groups take the liquid substance in the egg as the egg white instead of the actual thicker egg white. This can completely alter the data shown, and can also be minimized with proper detailed instructions. This lab reminded me of a microscope looking at ants, inspecting every detail of it. This lab could be used to figure out what specific types of macromolecules live in other specific types of the cell.

Unit 2 Reflection: 9.28.2016

       Throughout Unit 2, lessons generally circulated around macromolecules, including specific topics such as enzymes, while describing different types of bonds. As we went through vodcasts, I found myself learning the content of this unit at a steady pace, going back every day or so to review, and quizzing myself. Although some information is still fuzzy when I am asked to remember it, most information is clear. From this, I didn't just learn about things in the unit such as hydrogen bonds or polarity, but how to review work effectively and efficiently. After trying multiple studying techniques, I found something that worked for me and studied specifically with it, learning more than I usually would in a unit.

        As I started my first vodcast for the unit, Macromolecules (Part 1), I learned about how the chapter would mainly consist of different types of macromolecules, and how they interact and help the human body. In the vodcast, I was told about the first two macromolecules, Carbohydrates and Lipids, which are used for energy storage, along with other things. In these two specific macromolecules, I learned about sugar rings in carbohydrates, along with the bland taste and massive energy storage of polyssaccharides. After, I took notes on lipids, realizing that they are, in fact, healthy, benefiting to the body greatly. This is, however, if the lipid is an unsaturated fat, found in things like avocados, to things like cell membranes, its types varying from phospolipids to fatty acids.

        Soon after, I moved onto the next vodcast, Macromolecules (Part 2), which talked about the other two macromolecules, being proteins and nucleic acids. Through this source, I discovered that proteins consisted of two main groups, being structural proteins, which consist of muscles, hair, and nails, along with enzymes, which lower activation time for chemical reactions. Of these enzymes, each has an optimal pH and temperature in which they speed up their chemical reaction.

        In my last vodcast for the section, I learned specifically about enzymes, and how much they really contributed to the human body. Going through the vodcast, I retained information, such as how enzymes are used in almost everything. For example, enzymes are used in things like laundry detergent in order to break down clothes, to things like biotech in order to transform substances into new substances.

        Throughout the Unit, I also participated in various labs, including the Sweetness lab, the Enzyme virtual lab, and the Cheese lab. These labs enhanced my awareness of different macromolecules. For example, the cheese lab emphasized enzymes for proteins, while the Sweetness lab emphasized carbohydrate function in the body.

Sweetness Lab Analysis: 9.15.2016

        In this lab my group asked the question "How does the structure of a carbohydrate affect its taste (sweetness)?" Through the experimentation of this lab, my group found that monosaccharide sugars such as glucose taste sweeter, with the exception of galactose. Going through the lab, my group and I found that sugars having only one sugar ring were more prominent in taste (sweetness) than sugars containing two or more sugar rings. In fact, through our data tables, we found that Glucose had a degree of taste (sweetness) containing 150, with 100 being the base table sugar. Many other groups' data tables showed similar evidence, with the exception of galactose, with a degree of 25. Most other sugars with multiple sugar rings had a degree of 40 or lower, with the exception of sucrose being 100. This data supports our evidence, as most monosaccharides were proven from the data tables to have a more prominent taste (sweetness) than sugars with multiple sugar rings.

        Some data was unexpected because, although there was evidence showing that monosaccharides have more prominent taste (sweetness) than disaccharides and polysaccharides, there were exceptions with glucose and sucrose. Along with this, sugars could have mixed from using one spoon, if only even a little bit. In order to fix this error, you could have multiple spoons for each sugar bowl. Another error including cross contamination of sugars includes the fact of how sugars could have mixed into each other on the same paper towel. To fix this, you would have to have multiple, ripped up paper towels, with one sugar on each.

        This lab was done to demonstrate the function of sugars, and how their properties are affected by their structure. For example, carbohydrate structured with multiple sugar rings is used more for backup energy by organisms, such as when a bear would hibernate, eating a massive amount of polysaccharides, while monossacharides are used more for short nourishment, such as when a fruit is eaten for one meal. However, taste (sweetness) is different in function based on the carbohydrate, with testers putting a roughly higher sweetness degree for monosaccharides, as all people have differently developed tongues, with different sensors for taste. This is cited in NPR, where a scientist explains how taste cells in taste buds are stimulated by different substances, channeled specifically by special ion channels in order for us to figure out how sweet something exactly is. This reminds me of a phone call, as the phone is stimulated by one person calling another. This also reminds me of how the power button stimulates a computer to turn on. Based on my experience from this lab, I could apply this to study on how the brain senses sweetness based on structure from sugar rings, and if this could apply to other types of food, like wheat.

Sources: http://www.npr.org/2011/03/11/134459338/Getting-a-Sense-of-How-We-Taste-Sweetness

What is Biology Collage: 9.7.2016

Jean Lab Analysis: 8.31.2016

Throughout the course of this experiment, my group and I asked the question "What concentration of bleach is best to fade the color out of new denim material in 10 minutes without visible damage to fabric?" I found with my group that a bleach solution with a percentage of bleach equaling 25% is the best solution to bleach jeans with, as with the other solutions of bleach equaling 100%, 50%, 12.5%, and 0% either had visible fabric damage, or did not bleach the jeans enough, if at all. In fact, much of the other group's jean fabric turned out similar when bleached with the same solutions. This data supports our cause because our result of bleaching jeans with the 25% solution was supported positively supported by multiple other experiments.

          While our hypothesis was supported by our data, there could have been errors due to the 50% solution having more twice as much solution as every other solution, as well as every beaker, while similar in mass, not being completely equal to their respective solution. This could have affected my group's results by slightly changing the color or fabric damage of the jean pieces. Due to these errors, I would recommend measuring the beaker more carefully, marking it with tape, or paying more attention to directions or stating them in class to direct the students.

          This lab was done to demonstrate the lab process done in experiments, so we can prepare for biology experiments in the future. From this lab I learned how to effectively complete labs, as well as the ability to better understand variables, which helps me understand the concept of variables in general, as well as the lab process. Based on my experience from this lab, I could use what I learned to better complete other biology labs, as well as when I study on my own. This can also be applied to when others want to bleach their jeans.