Unit 5 Reflection

        In this unit, I learned about processes involved with the essential nucleic acids: DNA and RNA. I learned about how DNA has an antiparallel, double helix structure made of nucleotides. These nucleotides have nitrogenous bases, which include the purines adenine and guanine, and the pyrimidines cytosine and thymine.

Structure of DNA

They pair to make a code, which can be replicated through semi-conservative replication during interphase, or be transcribed by helicase and RNA polymerase to create mRNA used in protein synthesis. The mRNA is translated into amino acids in a ribosome, and the resulting protein is sent to use in the cell or body. However, mutations can cause significant changes in DNA that lead to radically different proteins being produce, and this can interfere with processes. Additionally, gene expression is regulated by transcription factors and repressors, keeping certain genes from being read by RNA polymerase. This controls the production of certain proteins, such as lactose, from being produced unless they are needed. In general, much of this was a review for me, but there were also times where I took longer to understand new concepts that were presented, such as how operators work in gene expression and regulation. On the other hand, the structure of DNA and protein synthesis were not too challenging to grasp, especially since I had encountered them before in science classes, though the practice was very helpful.

DNA extracted during the DNA extraction lab

        Throughout the unit, I found that I learn better when asking questions and clarifying more complex parts of the content. I discovered that for topics like gene regulation and expression, I tended to understand the material and process much better after the in-class discussion the next day. As a student, I would consider myself having improved, as I learned how to garner more information and skills from what is presented; in essence, I am not only smarter now than a month (or the duration of the unit) ago, but I have improved at improving. (Δ(Δk)?) I think the strategy of physically typing and creating a study guide is an effective one: through writing down the material, one is reviewing and remembering perhaps nuances that were forgotten over the course of a few months. Next semester, I will try to utilize this method to synthesize material better and continue to learn more. (and learn more about learning)

Protein Synthesis Lab

        In this lab, we modeled the processes involved in protein synthesis. To make a protein, on goes through transcription and translation. First of all, we copied down the DNA strand and transcribed it into mRNA, replacing thymine with uracil. This is what RNA polymerase does in the nucleus. Then, we translated the mRNA by splitting it into codons and finding the corresponding amino acid for each codon. This process, representing the tRNA's work in the ribosome, produced the primary structure of the protein.

Diagram of protein synthesis
https://commons.wikimedia.org/wiki/File:0328_Transcription-translation_Summary.jpg

        The mutations that seemed to have the greatest effect were the frameshift mutations, insertion and deletion, while the mutation that seemed to have the least effect was substitution. For the frameshift mutations, the location of the mutation was also very influential: a mutation near the beginning of the sequence would alter (shift over) almost every codon, while one at the end would change very little. This is due to frameshift mutations affecting every codon after it.

Some possible mutations in DNA
https://en.wikipedia.org/wiki/File:Chromosomes_mutations-en.svg

        I chose the frameshift mutation as what my data indicated would cause the most damage to the gene. This mutation, unlike other mutations we tested, had a chain reaction effect that rippled across and changed the frames of every codon after it. This could lead to devastating consequences, such as a stop codon in the beginning or completely different amino acids. As mentioned earlier, this effect is especially predominant if the mutation is at the beginning, as it would change everything after it.

Effect of a frameshift mutation (insertion)
https://www.flickr.com/photos/yourgenome/26855221022

        Because of the direct connection between DNA and proteins, and the influence proteins have in the body, dangerous DNA mutations can wreak havoc and create abnormalities in daily processes such as blood flow, digestion, and respiration. For example, cystic fibrosis is caused by a mutation in the CFTR gene. These mutations prevent chloride ion channels from functioning properly, and unusually thick mucus is produced, which clogs airways.

Diagram of cystic fibrosis
https://www.flickr.com/photos/yourgenome/26855222462

Human DNA Extraction Lab

        In this lab, we asked how DNA can be separated from cheek cells to study. We found that significant amounts of DNA can be extracted as a visible precipitate. The thread-like structure could be seen suspended in the isopropanol alcohol, after the layer of nonpolar alcohol was added on top of the solution with DNA. It has been proven that through homogenization, lysis, and precipitation, one can extract DNA. This is done through breaking down the membranes and nuclear material with polar liquid, lysing the membranes, emulsifying the proteins and lipids, and breaking down the histones in the DNA. Then, by adding a polar substance as a layer, the DNA will fall out of solution at the interface and become a precipitate. Our data supports this claim and is the result of such a process, using salt as a precipation facilitator, detergent as a disruptor, and pineapple juice as a catabolic protease to help break down different structures in the cell and free the DNA.

DNA precipitates into the ispropanol alcohol

        Some errors people in our lab group made led to alcohol and solution mixing, thus precluding the DNA from becoming a precipitate. In one experiment, the inversion to mix detergent with the solution was done too quickly and violently, thus leading to bubbles forming and disrupting the liquid surface. This would have kept the DNA from successfully precipitating at the interface, and could have mixed up or damaged the DNA strands in the solution. Another error was not measuring very precisely, which lead to a variety of results, some unsuccessful. We simply estimated amounts (e.g. pinch of salt), which may have led to imprecise measurement and thus a failed extraction with a certain substance being too dilute or concentrated. In a future experiment, I would suggest making sure to mix slowly, which would keep the solution from forming many bubbles. Additionally, keeping measurements precise, such as using measuring spoons and graduated cylinders, would give less variation and a higher success rate in general.

Precipitation is unsuccessful due to violent inversion

        This lab was done to demonstrate how DNA can be extracted from inside the nucleus of a cell. Moreover, I also learned how the membranes, histones, and nuclear material must all be broken down before the DNA can be extracted. This helped me understand how much protection the DNA has, due to it holding the genetic information. Not only does it never leave the nucleus (mRNA copies and leaves instead), there are many layers of membranes to keep it from being damaged by substances outside the cell. Outside of these concepts, based on my experience from this lab, I also now know how one might break down cell membranes to access, not only the DNA, but any organelle one might be studying using the techniques of homogenization, lysis, and precipitation.

Coin Sex Lab and Unit 4 Reflection

        In the coin sex lab, we simulated the inheritance of traits on different genes through crosses. This effectively models genetic concepts, as the flipping of coins represents the random recombination of alleles, and thus creates plausible results that conform to the combinations found in a punnett square. We tested a cross with sex chromosomes, autosomal inheritance, x-linked inheritance, monohybrid crosses, and a dihybrid cross. Across the board, though our results and ratios did not always completely match the expected results, such a discrepancy can easily be explained by the small sample sizes (10-16 flips), and our results all fit within the possible genotypes from meiosis. Using probability to predict offsprings' traits is limited in that in the real world, as the results often vary from both randomness and environmental traits (here factors that affect the flip result).

Data for dihybrid cross

        As expected, the X-linked colorblindness cross yielded mostly affected males, and the dihybrid cross yielded different genotypes with more double heterozygous and few double homozygous. In the dihybrid cross, BbEe brown haired, brown eyed individuals were crossed, which is expected to produce 9:3:3:1 phenotypic ratio. Our results produced a 14:1:1:0 ratio, which is close to expected, and this high brown-brown expected value is due to there being more combinations that result in it. Dominant alleles dominate others, so the double dominant genotype would be much more common. This understanding can be directly related to life, as dominant traits are observed much more in the phenotypes than recessive ones, and this can be used to understand how recessive traits such as blue eyes or blond hair are passed down through generations even if masked. This can explain where people around you attained such unique characteristics as the ones they have.

        In this unit, we explored concepts like these, such as the cell cycle (interphase, mitosis, cytokinesis), the process of meiosis, how asexual and sexual reproduction each have their costs and benefits, the difference between haploid and diploid cells, Mendel's experiments with pea plants, the principle of inheritance, Mendel's Laws of Segregation and Independent Assortment, genotypes and phenotypes of traits, how dominant alleles mask recessive alleles, the usage of Punnett squares, incomplete dominance and codominance, how genes affect one another through epistasis, and the multiple genes that contribute to polygenic traits.

Diagram and punnett square of a dihybrid cross

        Some of this material was a bit challenging and confusing to understand, such as the complex probabilities of X-linked traits. However, after practicing and learning about how these alleles are passed along differently in males and females that guarantee certain things, I have grasped a better understanding of it. After lectures and completing the labs and infographic, I could make more connections between the different aspects of genetics, and understood better how Mendel's laws make the principles and complications possible. In addition, I would like to explore some of the more convoluted processes a bit more. For example, how do the spindle fibers in meiosis work? How are they produced and how do they extend and latch onto chromosomes to pull them apart? Also, in DNA replication, how exactly are the strands replicated? Are the leading and lagging strands copied differently due to their direction?

Reproduction: Is sex important?

        For a population of organisms to survive, they depend on either sexual or asexual reproduction. Both of these methods have their benefits and costs, and neither is perfect for the survival of the organisms. Sexual reproduction can help spread positive genetic traits and even the dissemination of disease or parasite resistance, as the genes from each parent are naturally selected to benefit the offspring. The nine-banded armadillo benefits from this genetic variety, which helps it become unique and resist disease. However, sexual reproduction takes more time and energy, and competition can be detrimental to the population. Furthermore, asexual reproduction is simple and does not require a mate, but it often results in swift extinction due to clones being genetically identical and vulnerable to the same threats. Philodina utilize asexual reproduction to propagate all over the planet, using anhydrobiosis to travel long distances. This helps overcome vulnerability as a mass, and takes advantage of the benefits of asexual reproduction. Furthermore, the Atta colombica ant travels with disease-free fungus, which helps protect the asexually reproducing fungus gardens against outbreaks of parasites. E. coli can cope with the problems of asexual reproduction by picking up loose DNA from the environment, viruses, animals and dead bacteria.
        After reading about these organisms and methods from the article ("Dr. Tatiana's Sex Advice to All Creation"), several questions still remain: how are eggs fertilized? How does asexual reproduction (e.g. binary fission) occur? And how exactly do these mutations occur during meiosis? I look forward to finding some answers in this unit.

Unit 3 Reflection

        In this unit, we explored cells and their processes of photosynthesis and cellular respiration. While prokaryotic, autotrophic cells were the original ones, after cyanobacteria evolved, there was enough oxygen for heterotrophs to prosper. According to the endocytotic theory, eukaryotes with different organelles evolved as a result of heterotrophs consuming smaller autotrophs and cyanobacteria through phagocytosis, and the consumed bacteria surviving and living in symbiosis, creating the organelles we see today. These organelles include many membrane-bound structures, including the nucleus, lysosomes, ribosomes, mitochondria, and chloroplasts. The cell membrane has also evolved to be semipermeable and to allow protein-facilitated transport. A similar method of transport--diffusion--plays an important role in the osmosis of water, which not only helps maintain equilibrium, but also makes processes such as photosynthesis and cellular respiration possible.

The organelles of a eukaryotic animal cell

        Photosynthesis uses carbon dioxide, water, and light in a series of light dependent reactions, diffusing the H+ ions from water across the thylakoid, and producing NADPH and ATP to be used in the Calvin cycle. The Calvin cycle produces sugar from carbon dioxide and the molecules formed in the light independent reactions. Cellular respiration does the opposite, breaking down glucose to form ATP for energy storage through glycolysis, the Krebs cycle, and the electron transport chain. This yields 36 ATP in total from 6 glucose and 6 oxygen molecules.
        In general, I found understanding the processes of photosynthesis and cellular respiration a big jump from the relatively simple concepts that we covered earlier. In addition, though I found diffusion natural, the complex tonicities of osmosis were confusing when I was first exposed to them. However, after completing several labs and going through the steps of the processes, I found all of these concepts much easier to grasp. The egg diffusion lab helped me understand the impact of hyper- or hypotonic solutions on the movement of water across a membrane, and the photosynthesis virtual lab helped me better correlate each factor of photosynthesis with its rate and output.

The egg diffusion lab showed the effects of tonicity with a semipermeable membrane

        I still feel that the cellular processes of energy are extremely complex with details, and I would like to explore the different steps, such as glycolysis and the Calvin cycle, more in depth. This would provide a better understanding of how exactly each molecule is formed and used throughout the process.

Egg Diffusion Lab

      In the egg diffusion lab, we tested how osmosis in different solutions of water would affect the cell. Using eggs to represent cells, we submerged them in corn syrup and deionized water, and recorded the circumference and mass of the eggs before and after the submersion. Overall, the eggs in the sugar water decreased in mass about 46.1%, and decreased in circumference about 22.1%. This was caused by the presence of a hypertonic solution, as the high concentration of solute (sugar) led to water diffusing out of the egg to decrease its mass and circumference.

Class data tables for deionized and sugar water

      A cell attempts to maintain equilibrium, and thus water diffuses in or out of the cell when the solute concentration changes due to the solute molecules being to large to diffuse through the cell membrane. For example, when the egg was in the vinegar bath, the tonicity was hypertonic, and thus water left the cell. When the egg was submerged in water, the tonicity was hypotonic, and so water entered the cell. Lastly, putting the egg in sugar water made the tonicity hypertonic again, causing water to diffuse out of the cell once more.
      This lab demonstrates the law of diffusion that occurs naturally: substances diffuse from areas of high concentration to low concentration. Also, when solutes are unable to diffuse through a membrane, water instead diffuses in the process of osmosis. The different solutions that the egg was exposed to showed the diffusion of water to maintain equilibrium, including solutions that were hypertonic or hypotonic.
      The sprinkling of water on vegetables prevents the diffusion of water out of the vegetables, and even leads to some water diffusing in due to the hypotonic nature. This preserves the "freshness" of the vegetables keeping them hydrated. In addition, the salting of roads to lower the melting point of ice can adversely affect plants nearby to put out water (and shrivel) due to the hypertonic solution of salt in the water.
      After this experiment, I would want to further explore the osmosis of water in cells by testing an extremely hypotonic solution. The opposite of the hypertonic solution, I would want to see if cells might swell and possibly pop due to having too low of solute concentration in the solution outside (like water in bloodstream).

Egg Macromolecules Lab

      In the egg macromolecules lab, we asked if monosacchardies are present in the cell nucleus, represented by the egg yolk. We found that they indeed were present in the egg yolk, as a chemical test involving benedicts solution produced a color change from blue to green (rated a 7/10 on our scale compared to the 0/10 of water). This indicated the presence of monosaccharides, in this case glucose, present in the cell nucleus to provide energy, and supports our claim by showing how they can be found in the egg yolk in our experiment.

Monosaccharide test results
(control, egg white, egg yolk, egg membrane from left to right)

      Furthermore, we also asked if proteins can be found in the egg white, representing the cytoplasm. Here, we found that they were present, and the CuSO4 compound we introduced produced a color change from dark blue to light purple. This was a 9/l0 on our scale, and was supported by the presence of enzymes and structural proteins throughout the cytoplasm. Thus, this supports the claim with proteins.

Protein test results
(control, egg white, egg yolk, egg membrane from left to right)

      In addition, we asked whether lipids are present in the egg membrane. We found that lipids are in the cell membrane, as the Sudan III test yielded positive results of a color change from red to brownish orange (7/10). This supports the claim and can be explained by the presence of lipids as phospholipids making up the cell membrane.

Some macromolecule data tables

      While our hypothesis was supported by our data, several errors may have occured and thus skewed the results. For example, we may not have added the correct amount of test substance for each macromolecule test. This potentially incorrect drop amount may have caused the color and scale rating to be lower than the actual amount, due to having less test substance to create a noticeable effect; more care on correct dropper measurement would prevent this. Furthermore, the amount of test sample could have changed our results as well, and made the data lower due to a more diluted exposure to the testing substance. Standardizing this in some way could improve and negate this error; for example, setting a specific measure for each part of the egg, such as a mass measure, could make it more even across tests. These errors may have affected several of the tests, as every group member used a different (estimated) amount of egg membrane, yolk, or white to test.

      Lastly, this lab was done in order to identify macromolecules in different parts of the cell. This taught me the concept of macromolecules being the building blocks behind many of the cell parts and organelles. I learned how glucose can be found in the cell nucleus, how lipids make up the cell membrane as phospholipids, and how structural proteins are found throughout the cell, including in organelles. All in all, based on my experience from this lab, I would also be able to identify the presence of various macromolecules in different types of cells, regardless of their type or origin, even without much knowledge of the cell itself.

Unit 2 Reflection

        Unit two encompassed macromolecules such as carbohydrates, lipids, proteins, and nucleic acids, as well as molecular properties. Carbohydrates are saccharides, atoms of carbon, hydrogen, and oxygen formed into rings. Lipids include phospholipids that make up cell membranes, as well as fatty acids in food that can be saturated or unsaturated. Proteins include enzymes, which facilitate the chemical reactions of substrates into products, and structural proteins, which make up different parts of the body. Nucleic acids are composed of nucleotides, which combine at the bases and phosphate groups to form long chains of DNA or RNA, and also include ATP, which is broken down to acquire energy. In addition, polar molecules such as water have properties like cohesion and adhesion, which allow them to be attracted to other molecules of the same or different substance. These properties allow water to be very useful in making solutions, usually as the solvent. Another type of mixture that water is often found in is a suspension, such as blood or cytosol, where undissolved materials fail to settle out. This attraction is called a hydrogen bond, where oppositely charged regions attract; other bonds include ionic bonds, in which atoms gain or lose an electron, and covalent bond, in which electrons are shared.

Nucleic acids include DNA, or deoxyribonucleic acid

        We also completed a number of different labs in this unit, including the sweetness lab and the cheese lab. These experiments provided further insight into various topics, showing how a higher number of rings leads to less sweet sugar, and how a hot, acidic chymosin solution gave the optimal environment for cheese curdling in milk, respectively. The sweetness lab was mostly a success, aside from a subjective analysis providing slightly contrasting results, but the cheese lab data was skewed by having to clean up early, and some groups not incubating the samples for the full length of time. This led to a somewhat longer curdling time, but the results were still conclusive. In general, however, the labs proved a success in supporting certain concepts and hypotheses and grantng insight, aside from the minor setbacks due to user error.

The sweetness lab compared the sweetnesses of different saccharides

        All in all, I attained from this unit an abundance of both information and experience, and I look forward to learning more in-depth about the processes and makeup of enzymes and ATP, and finding out the nuances and complex aspects of how our body functions.

Sweetness Lab

        In the sweetness lab, we looked at the sweetness of different sugars, including sucrose, galactose, maltose, lactose, and starch: we found that in general, monosaccharides were the sweetest and polysaccharides were the most bland. This was supported by our high ratings (with 100 being the base sweetness of sucrose) of 150 and 70 for glucose and fructose, respectively, and our low ratings of 0 for starch and cellulose; monosaccharides averaged about an 83.3 on our scale, disaccharides a 45, and polysaccharides a 0. This data supports our claim, as the differences between the different sugar types were both significant and consistent. The carbohydrate structures of the different sugars likely affected their sweetness; our results also supported this, with the monosaccharides with the least rings and bonds being much sweeter than the polysaccharides with the most.

The sugar samples in order of sweetness

The different sugars tested

       As with any experiment, the sweetness lab results were not without flaws or inconsistencies. The testers often gave different ratings for the samples, which probably resulted from various taste sensitivities of the testers or slightly varying samples. In addition, as subjective ratings made up most of the experiment, many testers likely had contrasting impressions of the sweetness of the sugars. Even the amounts of sugar in each sample were arbitrary, which could have led to a skewed perception. According to the U.S. National Library of Medicine, taste is linked to smell, and different taste buds on the tongue have varying degrees of sensitivity to different tastes. This could have further influenced testers to record contrasting results. All in all, the sweetness of different sugars are affected by many factors, some of which are very difficult to control.

Sweetness lab results

Biology Collage

Jean Fading Lab

       In this lab, we asked what concentration of bleach would be best to fade the color out of new denim material; we found that about a 25% concentration was most effective, as the 25%-bleach-soaked-denim had less fabric damage but still yielded a reasonable amount of fading. We rated those jean samples an average of 2 out of 10 for fabric damage, and an average of 3 out of 10 for color removal. A Chlorox article claims about a 5.9% concentration of bleach being effective, but their more concentrated and potent bleach solution would mean this would be somewhat higher with generic bleach. This data supports our claim because the final concentrations are comparable to an extent. (especially taking into account some possible errors below)

The varied effects of different concentrations of bleach on denim

        The data partly supports the expected results, but yielded a higher successful percentage of bleach due to the partial submerging of the fabric. This incomplete submerging was a result of the small petri dishes and stacking of the fabric, and would have made a higher concentration of bleach necessary with the limited contact. The jeans stacking together covered some area that would ideally also be in contact with the bleach. Also, not all of the denim was submerged, because the petri dishes were insufficient in height; another centimeter of height would probably be more effective. For future executions of this lab, a larger container (with more solution) and a simple separation of the fabric samples would help the denim be more fully submerged and show a more accurate representation of the effects of the bleach concentration on the jean pieces.

Results show significant variation across different jean samples

        This lab was done to demonstrate the proper execution of the scientific method and the process that must be undergone in an experiment. We learned how a proper hypothesis is formed, and also how different variables and constants are utilized in an experiment. This helped me understand and experience firsthand the correct procedure of a scientific experiment. Furthermore, based on my experience from this lab, I now understand how 25% is an effective percentage of bleach to use with jean fading.

25% bleach, 75% water: the optimal concentration for jean fading