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.