Unit 5 Reflection

This unit was about the relation between DNA and physical traits. Some of the themes were the double helix, antiparallel shape of DNA; semi-conservative DNA replication, the process of creating two identical strands of DNA from a single one, each ending up with half of the original strand; transcription, how RNA is created in the nucleus; translation, how ribosomes read RNA to create proteins; the types of mutations: point mutations, frameshift mutations like insertion and deletion, inversion, and translocation; and how genes are regulated within an operon.



My strengths this unit were understanding semi-conservative DNA replication, transcription and translation, the different types of mutations, and the lac operon. I found these processes logical and easy to follow. My weaknesses this unit were understanding the antiparallel structure of DNA, doing transcription and translation by hand, and understanding DNA structure's influence of gene expression. I didn't understand antiparallel at first because it didn't make sense, but now I do. I struggled doing transcription and translation by hand because I am easily distracted. Originally, the topic of DNA structure and its influence on gene expression seemed very complicated, but now I realize it is pretty simple.



I would like to learn more about why DNA is shaped as it is, and why ribosomes can't just read DNA in the nucleus inside of the copied RNA. I am also curious about what would happen to the rest of the RNA if the ribosome was told to stop near the beginning of the RNA sequence. I would also like to learn about the probability for each mutation, and how efficient gene regulation truly is.

I am growing as a student by studying in a more effective way. I have begun creating flashcards and looking at more diagrams in order to study. This is an effective method to study for me because, according to the VARK Questionnaire, I have high visual, kinesthetic, and reading/writing scores. The flashcards are helpful because of my reading/writing score, while the diagrams are helpful due to my visual score. I have not yet found a way to incorporate my kinesthetic abilities into studying.

Protein Synthesis Lab Analysis

There are two main steps to make a protein: transcription and translation. In transcription, a section of DNA is copied, producing messenger RNA. In translation, the RNA reaches a ribosome. The ribosome reads bases 3 at a time. Each 3-base sequence corresponds to an amino acid, which the ribosome adds to the protein it is creating. After that, the amino acid chain folds and becomes a protein.



There were three different types of mutations we tested: substitution, insertion, and deletion. Substitution either caused a great change or a very small change. Sometimes, it caused no change at all. Substitution was only an effective mutation when it was placed in a strategic position. Insertion and deletion both caused major changes when done at the beginning of a sequence. However, towards the end of a sequence, insertion and deletion caused much smaller changes.



During this lab, I was allowed to choose a mutation of my own to test. I chose to test substitution, because after looking at the bases of the gene I was given, I realized I could easily substitute strategic nucleotides in order to get a drastically different result. I substituted two nucleotides in the beginning of the sequence, turning TAC into ATC. This changed the resulting RNA sequence from AUG to UAG. Basically, I changed the start codon to the stop codon. As you can imagine, the amino acids of the resulting protein were very much changed. Instead of the protein Met-Tyr-Lys-His-Val-Ile-Asn-Cys-Ile, there was no protein at all. This mutation changed more amino acids than any other tested. Obviously, placement did matter; if I just substituted bases at random, I would not have gotten the same result.



Mutations could affect our lives in many ways. An example of a mutation is Huntington disease. According to the U.S. National Library of Medicine's Genetic Home Reference, Huntington disease is caused by a mutation in the HTT gene, which provides instructions to make the huntingtin protein. Usually, in this gene, the sequence of cytosine, adenine, and guanine is repeated 10 to 35 times. However, within those with Huntington disease, this sequence is repeated much more, making the mutation an insertion. The length of the sequence of cytosine, adenine, and guanine creates very long huntingtin proteins, which are cut apart and bind together. This eventually causes neurons to die. Huntington disease is inherited with an autosomal dominant pattern.

DNA Extraction Lab Analysis

In this lab, we asked the question, "How can DNA be separated from cheek cells in order to study it?" We found that DNA can be separated from cheek cells by adding Gatorade, salt, detergent, pineapple juice, and isopropanol alcohol, in that order. This process is a legitimate way to extract DNA because after we completed this procedure, we were all able to see at least some bits of DNA in our test tubes. We also noticed clumps in our mixtures throughout the process, and those clumps turned out to be pieces of DNA. Each step of our procedure stems from scientific research. DNA is usually extracted through a three-step process including homogenization, lysis, and precipitation. Gatorade was added because it is a polar liquid, able to homogenize cells. Salt was added so that the DNA would move closer to itself, and detergent was added to break down the cell membranes. Pineapple juice contains catabolic proteases, enzymes that break down molecules. It was added to break down histones, which are proteins that DNA wraps around. Isopropanol alcohol is nonpolar; we layered it on top of the mixture so that the DNA would become visible as a precipitate. Our data supports our claim because if we were able to see DNA after following our procedure, then we must have extracted DNA through the procedure. The scientific ideas support our claim because each step of our procedure is supported by scientific evidence, and the end results of both are extracted DNA.

My DNA falls out as a precipitate during the last step of our process.

While our hypothesis was supported by our data, there could have been errors due to how the cheek cells were gathered. In order to gather cheek cells, we chewed at our cheeks and spit into cups. However, we were unsure how long or how much to chew at our cheeks, so we may have not chewed enough. This would explain why some people only had small pieces of DNA in their test tubes. Also, instead of mixing the cheek cells, Gatorade, salt, detergent, and pineapple juice together in a test tube, we mixed them in cups instead. This did not impact our result a lot, but it made the lab a little messier, and we were worried that the cups might start to leak. Due to these errors, in future experiments I would recommend gathering cheek cells by scratching the inside of your cheeks using a toothpick. I would also recommend telling students a few hints on the procedure if they get stuck.

This lab was done to demonstrate how to extract DNA. During this lab, we learned the three basic steps to extract DNA, and the ingredients that could be used for each of these steps. From this lab, I learned about the structure of cells and which enzymes are able to break down those structures, which helps me understand the concept of where DNA is stored in a cell and how important it is. Based on my experience from this lab, I could extract DNA from nearly anything, which would be useful if I wanted to become a geneticist. I could also compare different DNA to see if I could find any similarities or differences. Also, if I had a microscope, I could use it to look at DNA and learn more about what it looks like. I also know more vocab words due to this experiment, which will help me later in science classes.

Unit 4 Reflection

At the end of our unit, we did a lab known as the Coin Sex Lab. In this lab, we flipped coins to predict the genes of the offspring of a cross. Each coin represented a gene, and the heads and tails sides of the coins represented the two different alleles. Each person was given the coin(s) of one of the parents, and one person flipping their coins represented meiosis. When the outcomes of all coin flips were put together, that represented recombination.

We simulated many different crosses. For nearly all of our simulations, our expected results were similar to our actual results. In our first experiment, a monohybrid cross, we were testing the sex chromosomes of the offspring of a male and a female. We found we had a ratio of 3 males : 2 females, which is very close to the 1:1 expected ratio. Our second experiment was also a monohybrid cross, and it had to do with autosomal inheritance of bipolar disorder. While the ratio should have been 1:1, our ratio was actually 1 bipolar child : 4 normal children. Our third experiment was another monohybrid cross, but it tested X-linked inheritance. In this experiment, our ratio of 4 normal females : 1 carrier female (or a heterozygous female) : 2 normal males : 3 colorblind males was approximately the expected ratio of 1:1:1:1. In our last experiment, a dihybrid cross involving autosomal inheritance, our ratio of 10 brown haired and brown eyed (double homozgous dominant) : 2 brown haired and blue eyed : 4 blond haired and brown eyed : 0 blond haired and blue eyed (double homozygous recessive) was close to the expected 9:3:3:1 ratio.



Probability cannot always be used to predict offspring's traits because the traits of offspring do not always follow probability. Although an offspring may have a higher chance of having brown eyes, the offspring may be born with blue eyes instead. Also, if the probability is split 50-50, it is impossible to predict which outcome is more likely.

The Coin Sex Lab relates to me in real life because I now know more about inheritance. This can help me figure out my genetics. For example, my parents blood types are B and O, but I don't know what mine is. Because of this, I know that my blood type is either B or O. Furthermore, I can find out that, depending on whether the B blood type is homozygous or heterozygous, the probability of my blood type being B is 50% or 25%, respectively. I can also use this process to figure out my other traits. In addition, if I had children, I could figure out the probability of them having certain traits.

This unit was about sex, inheritance, and genetics. Some themes were mitosis and meiosis, asexual and sexual reproduction, chromosomes versus genes versus alleles, traits, genotypes and phenotypes, homozygous and heterozygous, dominant vs recessive, the Law of Segregation, the Law of Independent Assortment, Punnet squares, autosomal and x-linked inheritance, codominance, incomplete dominance, gene linkage, epistasis, multifactorial disorders, and polygenic traits.

My strengths this unit were Punnet squares and genetics. My weaknesses were, at the beginning, the steps of meiosis and the Law of Segregation and the Law of Independent Assortment.



At first, I didn't really understand genetics. I didn't understand the differences between genes and alleles, or the difference between sister chromatids and homologous chromosomes. While doing the genetics infographic, I began to understand these things by doing outside research. Now, I fully understand all concepts presented in the infographic.

I would like to learn more about genetic exceptions and complications. Why are some genes dominant and recessive when others are incompletely dominant or codominant? Is it common to have incompletely dominant, codominant, linked, or epistatic genes? How common are multifactorial disorders?

My preferred learning styles, as shown by the VARK Questionnaire, were:

• Visual: 10
• Aural: 2
• Read/Write: 8
• Kinesthetic: 10

I expected these results, as I have done similar questionnaires in the past. In order to use these style strengths to prepare for my test, I will draw lots of diagrams and maybe create a model. I will also test myself with flashcards.

Sex Infographic

Also viewable online.

Is sex important?

Sex is not important. While there are benefits to sex, there are more benefits to asexual reproduction, or cloning. With enough luck in mutations and through travelling, asexually reproducing species such as the bdelloid rotifer can reap all the benefits of asexual reproduction while avoiding the repercussions.

Organisms that engage in sexual reproduction have, on average, lived longer than those who do not. This is due to the fact that sexually reproducing organisms do not rely only on mutations, which can be harmful. Also, sexually reproducing organisms are less vulnerable to disease, as they have different DNA, which will make it harder for disease to spread.

However, sex requires a lot of effort. As Olivia Judson explains in her book, Dr. Tatiana's Sex Advice to All Creation, "a male flower who wishes to be a Lothario and have his pollen strewn to as many mates as possible must seduce not female flowers but bees... other creatures must wear gaudy costumes, be they fancy feathers or frivolous fins; they must sing and dance for hours and hours; they must perform prodigious feats, building and rebuilding nests and bowers" (2).

Finding a mate requires an enormous amount of energy, and is rather inefficient. There are many flaws to the process, too. Even if there is an organism with a trait that would revolutionize the species, if that organism cannot have sex, the trait will die with them, and the species will never be able to benefit from the organism's trait. Also, sex may interfere with survival. Traits that attract mates are bold so that they can be seen by possible mates, but those traits can also be seen by predators, making them easier prey. Finally, organisms that reproduce sexually must compete with others of their species for mates, as it often takes a while for organisms to decide who to mate with.

Asexual reproduction, however, is much more efficient. Organisms that reproduce asexually have no need to expend large amounts of energy in order to find a mate. Also, asexually reproducing organisms have twice as many offspring as sexually reproducing organisms. "If females [of a sexually reproducing species] have fewer than two children, the population shrinks; more than two, and the population grows," says Judson. "In an asexual population, however, each female needs to have only one child for the population to remain the same size. More than one, and the population will grow" (215).

On the flip side, organisms that engage in asexual reproduction usually die out after a short amount of time either because of harmful mutations or viruses. According to Muller's ratchet, one of the theories attempting to explain why species that reproduce asexually tend to die out quickly, asexually reproducing populations die out because the number of harmful mutations will inevitably grow. Kondrashov's hatchet, another one of these theories, disagrees. It says that each individual can hold some amount of slightly harmful mutations until they die. Because sexually reproducing populations shuffle genes, the unlucky organisms with too many harmful mutations die. However, in asexually reproducing populations, many organisms will die due to bad mutations, as their only way to change their genes is mutation. Because asexually reproducing organisms mostly have the same genes as each other, it is easy for them to be killed by viruses. This is known as the Red Queen.

Something that confused me was Muller's ratchet and Kondrashov's hatchet. They both seem to have the same point. Also, why does Muller's ratchet need assumptions to be met when Kondrashov's hatchet does not? I want to learn about how scientists found out that there are two different types of reproduction, and if it's possible to control mutations.

Unit 3 Reflection

This unit was about cells. Specifically, it was about the different types of cells, and their purposes and functions. A few themes and essential understandings were the cell theory, the types of cells (prokaryotes, eukaryotes, autotrophs, and heterotrophs), the organelles of eukaryotic cells, osmosis, cell history, the endosymbiotic theory, photosynthesis, and cellular respiration.

This unit went by rather well. Although some topics, like photosynthesis and cellular respiration, were a bit hard to understand the first time through, they began to make more sense after re-reading notes. Another topic I found confusing at first was the tonicity of solutions, but I understood that after re-watching the vodcast discussing tonicity. Some of my strengths during this unit were organelle functions and osmosis, as I found both logical and easy to understand.

From these experiences, I learned about the cells that make up all living things. I learned how the cells in our bodies maintain balance, how plants grow, and what happens when we exercise. I also learned that drawing diagrams is a good way to study, and that color-coding your notes helps if you are a visual learner.

I want to learn more about how the three steps of cellular respiration happen. I am also curious about the workings of chlorophyll. I wonder how plants know to do photosynthesis, and how animals know how to do cellular respiration.

Photosynthesis Virtual Labs

Lab 1: Glencoe Photosynthesis Lab http://www.glencoe.com/sites/common_assets/science/virtual_labs/LS12/LS12.html 

Analysis Questions

1. Make a hypothesis about which color in the visible spectrum causes the most plant growth and which color in the visible spectrum causes the least plant growth?

If chlorophyll, which is found in plants, is best at absorbing red and blue light, then purple light will cause the most plant growth. If plants are green because the color of an object is the color of the light that is reflected off of that object, and plants require light energy for photosynthesis, then green light will cause the least plant growth.

2. How did you test your hypothesis? Which variables did you control in your experiment and which variable did you change in order to compare your growth results?

I grew three spinach plants, three radish plants, and three lettuce plants under each color of light, and I measured their height to see which ones grew the tallest. I controlled the type of plant and time spent in the light. I changed the color of light.



3. Analyze the results of your experiment. Did your data support your hypothesis? Explain. If you conducted tests with more than one type of seed, explain any differences or similarities you found among types of seeds.

My data supported half of my hypothesis. While I hypothesized that purple light would cause the most plant growth, it was actually blue light that caused the most plant growth. However, I was correct in that green light caused the least plant growth. The results for the different seed types were mostly the same. Spinach grew taller than radish, and radish grew taller than lettuce. Lettuce grew the most out of the three in green light, despite growing less than the others in all other types of light. All three seed types grew the tallest in blue light and the least in green light.

4. What conclusions can you draw about which color in the visible spectrum causes the most plant growth? The color in the visible spectrum that causes the most plant growth is blue.

5. Given that white light contains all colors of the spectrum, what growth results would you expect under white light?

You should expect an average level of growth, because white light includes a multitude of different colors of light. For example, it includes blue light, which causes high levels of growth, and green light, which causes low levels of growth, therefore, white light should cause an average amount of growth.

Site 2: Photolab 
http://www.kscience.co.uk/animations/photolab.swf 

This simulation allows you to manipulate many variables. You already observed how light colors will affect the growth of a plant, in this simulation you can directly measure the rate of photosynthesis by counting the number of bubbles of oxygen that are released.

There are 3 other potential variables you could test with this simulation: amount of carbon dioxide, light intensity, and temperature.

Choose one variable and design and experiment that would test how this factor affects the rate of photosynthesis. Remember, that when designing an experiment, you need to keep all variables constant except the one you are testing. Collect data and write a lab report of your findings that includes:

• Question 
• Hypothesis 
• Experimental parameters (in other words, what is the dependent variable, independent variable, constants, and control?) 
• Data table 
• Conclusion (Just 1st and 3rd paragraphs since there's no way to make errors in a virtual lab) 

*Type your question, hypothesis, etc. below. When done, submit this document via Canvas. You may also copy and paste it into your blog.

Question

What is the optimal temperature for photosynthesis?

Hypothesis

If photosynthesis involves an enzyme called ATP synthase, and most enzymes do well in conditions that are neither hot nor cold, then the optimal temperature for photosynthesis is 25℃.

Experimental Parameters 

The dependent variable is the amount of bubbles produced by the plant in a minute. The independent variable is the temperature of the water that surrounds the plant. The constants are the light intensity percentage and the amount of dissolved CO₂. The control is the plant at 25℃.



Conclusion

In this lab, I asked the question, “what is the optimal temperature for photosynthesis?” I found that the optimal temperature for photosynthesis is 25℃. At a temperature of 25℃, the plant produced 34 bubbles in 30 seconds, which is more bubbles than the plant produced at either 10℃ or 40℃. Since oxygen is produced during photosynthesis, and the bubbles are oxygen rising to the surface, the plant photosynthesized quicker at a temperature of 25℃. Also, it is known that the enzyme ATP synthase is used in photosynthesis, and that enzymes have medium optimal temperatures. The first piece of data supports my claim because it shows that plants are faster at photosynthesis when they are in a temperature of 25℃. The second piece of data supports my claim because the enzyme did the best in a medium temperature.

This lab was done to demonstrate that there is an optimal temperature for photosynthesis. From this lab I learned about the factors that can affect the speed of photosynthesis, which helps me understand the concept of the reactants needed for photosynthesis. Based on my experience from this lab, I am a better botanist because now I know the temperature for which plants will grow better in.

Microscopic Organisms Lab Analysis

Power: 400. This skeletal muscle tissue cell is unique because it has many nuclei. I observe that this cell seems to be made of many "pieces," or striations, that make up a bigger "piece," or muscle fiber. This cell is eukaryotic and heterotrophic.

Power: 400. This slide of a ligustrum plant is unique because it is the cross section of the plant, which allows it to show multiple cell types. I observe that these cells are hard to distinguish from each other because they are mostly colorless. This cell is eukaryotic and autotrophic.

Power: 400. This spirogyra cell is unique because its cells are rather rectangular and connected to each other in a chain. I observe that the chloroplasts are arranged inside the cells in a spiral chain. This cell is eukaryotic and autotrophic.

Power: 400. These bacteria cells are unique because of their size. They are quite small compared to other cells. I observe that the bacillus bacteria are darker in color than the coccus and spirillum bacteria. These cells are prokaryotic and autotrophic.

Power: 400. This cell is unique because it doesn't have a chloroplast. Cyanobacteria don't have chloroplasts because they are the ancestors of chloroplasts. I observe that these cells tend to clump together in rings. These cells are prokaryotic and autotrophic.

Power: 400. These euglena cells are unique because they can be either heterotrophic or autotrophic. I observe that they are small and hard to see with the microscope. These cells are eukaryotic and either heterotrophic or autotrophic.

Power: 400. These amoebas are unique because they use their cytoskeleton and cytoplasm to move. I observe that there are many amoebas of different colors on the same slide. These cells are eukaryotic and heterotrophic,

In this lab, we used microscopes in order to observe six different slides: skeletal muscle tissue, ligustrum, spirogyra, cyanobacteria, euglena, and amoeba. We did this in order to distinguish different organelles inside these cells. We also did this to see what features are common between eukaryotic, prokaryoti, autotrophic, or heterotrophc cells.

I was able to identify...
Muscle cell: nucleus, muscle fiber, and striations
Ligustrum: chloroplast, epidermis cell, and vein
Spirogyra: cell wall, chloroplast, and cytoplasm
Bacteria: coccus, bacillus, and spirillum
Cyanobacteria: cell
Euglena: nucleus and chloroplast
Amoeba: nucelus, cell membrane, and pseudopods

The autotrophs either had visible chloroplasts or were incredibly small. The heterotrophs mostly didn't have chloroplasts, and had visible nuclei. The eukaryotes mostly had visible nuclei and were larger than the prokaryotes. The prokaryotes mostly did not have nuclei and were smaller than the eukaryotes.

Egg Diffusion Lab Analysis

When the sugar concentration of the solution the egg was placed in increased, the mass and circumference of the egg both became smaller. This change was caused by the passive diffusion of water. In the solution of sugar water, sugar is the solute, and water is the solvent. The sugar water had a higher concentration of solute to solvent than the egg. Solutes like sugar are too big to diffuse across the egg's membrane, but solvents can passively diffuse across the egg membrane. Since diffusion's goal is to reach equilibrium, or the point when the concentrations of solute to solvent are equal, solvent molecules moved out of the egg's membrane in order to dilute the sugar water outside of the egg. Because water left the egg in sugar water, the egg shrank.

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

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

A cell's internal environment changes as it's external environment changes because of diffusion. Because cells want to reach equilibrium with their surrounding solutions, they either shrink or grow, depending on their environment. When the egg was placed in vinegar, it lost its shell because vinegar is acidic. When the egg was placed in water, it grew, because the egg has more solutes than water, since pure water has no solutes. And when the egg was placed in sugar water, it shrank because the sugar water had more solutes than the egg.

This lab demonstrates the biological principal of osmosis. Osmosis is the diffusion of water across a selectively permeable membrane. This membrane refers to the egg's membrane. Because osmosis is a type of diffusion, the water will attempt to go from a low concentration of solute to a high concentration of solute in order to reach equilibrium. This is the process that happens when the egg is placed in sugar water. This lab also demonstrates the biological principal of tonicity, which is the ability of a surrounding solution to cause a cell to gain or lose water. The sugar water was a hypertonic solution, meaning the solute concentration in the sugar water was more than that inside of the egg. The deionized water was a hypotonic solution, meaning the solute concentration in the egg was more than that in the surrounding solution.

Fresh vegetables are sprinkled with water at markets because the vegetables have less water, or solvent, and more solute. Because the cells of the vegetables have more solute than their surrounding, hypotonic solution of water, the vegetables will gain water, keeping them fresh for longer. When roads are salted to melt ice, plants along the roadside may wilt. When the ice melts, the resulting water combines with the salt to form a salt water solution. Since the cells of plants have less salt than the salt water, which is hypertonic compared to the plant cells, the plants lose water, causing them to wilt.

Based on this experiment, I would like to test the tonicity of other solutions. I would like to do this so I can find solutions that are isotonic to an egg cell. I would also like to test this with different cells, but since the changes in mass and circumference would be much harder to measure, I would probably test this with different types of eggs.