Unit 5 Reflection

    This unit was about DNA, replication, protein synthesis, and mutations. We learned how DNA is made of a nitrogenous base, a phosphate group, and a sugar, as well as other details about the structure of DNA. In replication, DNA is split into two strands. Each of those two strands are used as templates for making the new DNA strands. Proteins are made when DNA goes through transcription and translation. There are many different types of mutations, including insertion, deletion, and substitution. One of my strengths were understanding the concepts taught. I also worked with my current group better. One setback was that I did not follow the directions for making the DNA correctly, so it turned into a "slide". I'd like to learn more about gene expression and regulation. I wonder about how it is amazing that processes happen quickly in the cell.

     I have grown as a student, as I learned how to cooperate with my peers better. I participate more with group discussions. I also learned how to focus better when studying. Mr. Orre taught us a process of "active studying", which I found very "useful." A good student means that he or she focuses in class and while studying, and participates in discussions. A good student should also use their time efficiently. The end affect of being a good student is getting good grades. I feel like I am not a completely good student and can try a bit harder, although I am satisfied with my grades right now. I am a better student than I was yesterday, because I learned how to manage my time efficiently, as I need to study for finals as well as not sleeping too late. I also have built on my previous biology knowledge. I tried to do the things that were easier for me, and I guess it helped a bit in my studying.

Protein Synthesis

    Proteins are made starting with DNA, or deoxyribonucleic acid. The first step of the process is transcription, where one strand of the double helix is used as a template to make mRNA, or messenger RNA. All of this takes place in the nucleus, as DNA cannot exit it. The mRNA then travels to a ribosome, and goes through the process of translation. In this process, every three bases in the RNA sequence, called a codon, is coded for an amino acid. After the strand of mRNA is finished translating, the amino acid chain is twisted and folded into a protein.

Transcription and Translation. Digital image. Wikipedia. N.p., n.d. Web. 12 Dec. 2016.

    The insertion and deletion mutations, also known as frame-shift mutations, are more impactful than substitution mutations. The mutations are also more impactful if they are located near the start of the sequence. If the mutation was near the front of the sequence, then all the amino acids after the mutation would be affected. But if it were located near the end, only a few amino acids would be changed.

Point Mutations. Digital image. Wikipedia. N.p., n.d. Web. 12 Dec. 2016.

    I chose insertion as my mutation because it is a frame-shift mutation and is very impactful. This was more damaging than other mutations, since it forced the sequence to not even be able to be translated. I mutated the very beginning of the sequence so that the mutation would do the most damage. Putting the mutation in the back would not have done as much damage.

Insertion. Digital image. Wikipedia. N.p., n.d. Web. 12 Dec. 2016.

     Mutations could affect my life by making me do some things that "normal" people wouldn't do. For example, I might have mental retardation, which would make me think like a child for the rest of my life. My body might also not work properly, which may lead to sickness, or even death. Phenylketonuria is a disease caused by a mutation on the PAH gene, located on chromosome 12. It can lead to intellectual disability, seizures, behavioral problems, and mental disorder.

Structure of L-phenylalanine. Digital image. Wikipedia. N.p., n.d. Web. 12 Dec. 2016.

Human DNA Extraction Lab

    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 extracted by going through a three-step process: homogenization, lysis, and precipitation. We took cheek cells from our mouths and broke down the nuclear material of the cells with detergent, a polar liquid. We added salt to facilitate the precipitation and soap to lyse the cell membranes and emulsify the lipids and proteins. Then, we used catabolic proteases to break down proteins called histones that the DNA wrapped around. Finally, alcohol, a nonpolar substance, was added after mixing the solution to form the precipitate, DNA. This process of extracting DNA is confirmed with textbook information as well as other "articles". This data supports our claim because it shows that extracting DNA can be done in the way shown.
    While our hypothesis was supported by our data, there could have been errors due to the fact that we shook the test tube a little after the alcohol was put in, causing the alcohol and Gatorade solution to mix a little. This would affect our results, as the DNA would go back into the Gatorade solution. Another error is that we did not let the solution sit for long enough. This would impact our results, as the processes may not have been fully complete. Due to these errors, in future experiments I recommend that the experimenters should carefully follow the procedure given to them and have a good timer.
   This lab was done to demonstrate the process of DNA extraction. From this lab, I learned that polar liquids can help break down nuclear material, the different materials to help with different processes, and other similar concepts. I also learned how DNA extraction works. Based on my experience from this lab, I could can use the process described above the extract other materials from other substances.

Unit 4 Reflection

    In the coin sex lab, I drew out Punnet squares to calculate probabilities of offspring having some trait, and then I flipped coins to randomly generate outcomes. The coins served as a model for the Law of Segregation. My results for the dihybrid cross were exactly the same as the predicted results in terms of phenotype, but not genotype. The probabilities for the different phenotypes are accurate, since my results were very similar to the predicted results. Probability may fail when you test gene-linked chromosomes, since they have a larger possibility of being inherited together. My understanding in life of this is that there are people with one set of traits and people with another set of traits, but not much mix between those two sets of traits. Other sets of traits, however, are completely randomly distributed among people.
    This unit was about the different parts of genetics. There was a chapter on the "Introduction to Genetics", which talked about Gregor Mendel and his laws, genes and dominance, Punnet squares, and meiosis. There was also a chapter on "The Human Genome", which talked about human genes, chromosomes, x-linked traits, and other similar concepts. The big ideas to focus on were information and heredity, and science, technology, and society. One of my strengths in this chapter was working out the Punnet squares. A weakness was understanding the many different types of inheritances, dominances, and other similar things. One new thing in this unit was that I was put into a group with three people, so I had to partner with people in other groups many times.
    From these experiences, I learned that genes and chromosomes are very complex, and that the inheritance of traits was determined through many different rules. From the infographic, I learned how infographics look like, and how to format one. I also learned how to effectively organize what I learned in the unit. Working with many different people helped me organize myself better, since I needed to switch back and forth.
    I would like to learn about the other concepts in the unit in the textbook which were not covered in the vodcasts. I am not so sure about how to read a pedigree and how it works. I wonder about how people survive with disorders on the dominant alleles.

Genetics Infographic

Why is Sex so Great?

The selected reading was about the good and bad parts about sexual and asexual reproduction. In the note from Dr. Tatiana, she talked about how sex was such an important aspect of life. In the chapter "Wholly Virgin", the author gives reasons about how asexual reproduction is good or bad, and also compares it to sexual reproduction.

Sex is important, since without sex, everything that is beautiful in nature would exist. This is because the organisms would have to try to attract mates by "wearing costumes". It is also important for survival and reproduction. The mixing of genes during sex will help with the process of natural selection and mutations.

One benefit of sex is that sex mixes genes from different individuals. It is an internal shuffling of each chromosome, so it produces a different genetic combination than each of its parents. This shuffling can also keep the amount of harmful mutations down, which will increase the survival rate of the species. Another benefit of the shuffling is that diseases will have a harder time infecting the species, as the species will evolve to resist the disease. Although sexual production has many benefits, it also has some costs. For example, the species will not be able to produce as quickly or easily as asexual organisms.

 Asexual reproducing organisms, such as the Philodina and E. coli, are benefited since asexual production is more efficient than sexual reproduction, as it produces twice as much offspring. It is also easier to do, since it does not require the participation of a male organism. A cost of asexually reproducing is that it is a evolutionary dead end and usually quickly leads to extinction. There are many ways to extinction, including harmful mutations and diseases. These problems can be sidestepped with effort, for example, a species can have a very large population, which will help the amount of organisms without harmful mutations to grow. They can also go through anhydrobiosis, which will stop the disease problem, although not all organisms will survive the process.

The difference between Muller's ratchet and Kondrashov's hatchet was kind of confusing, as they were pretty similar. I would like to learn more about viruses and how they work. 

Unit 3 Reflection

    This unit was about many different aspects of cells. It talked about different parts of the cell, and their functions. The process of how a protein was made in a cell was described. Different ways for a molecule of any sort to pass through a cell membrane was discussed. The process of photosynthesis, which takes place in chloroplasts, and the process of cellular respiration, which takes place in mitochondria, were described in a lot of detail. It walked us through the steps of both of the processes. The big ideas of this unit were the cellular basis of life and matter and energy.

    This unit went along decently well. I am getting more used to the classroom and how Mr. Orre teaches. I can make myself be more concentrated and more productive. Despite this, I also have some setbacks. For example, I do not like my current group as much as I liked my previous group. Half of the time, one person was missing, and there is also a person who keeps talking and is kind of dictatorial. The photosynthesis and cellular respiration processes were kind of hard to understand and memorize. 

    From these experiences, I learned that I can take advantage of the knowledge of the patterns of how Mr. Orre assigns things and can do predict that some things will happen and do them ahead of time. I can also learn how to cooperate better with my classmates. I can also use what I learned in class to do things related to cells in better ways, such as taking better care of plants.

    I want to learn more details about photosynthesis and cellular respiration, since we did not cover much of that in class. That is practically all that I am unsure about. I wonder about how amazing the world of cells is.

• What do you want to learn more about? What unanswered questions do you have? What do you wonder about?

Photolab

Hypothesis: If the temperature increases, then the amount of oxygen bubbles being released will decrease.

The number of oxygen bubbles being released, the dependent variable, will depend on the temperature of the plant’s surroundings, the independent variable. The amount of carbon dioxide, light intensity, light color, and time tested will be constants.

Amount of CO2: Increased
Light Intensity: 40
Light Color: White
Data Table:

Temperature (in o)	10	25	40
# of Bubbles/ 10 sec.	11	9	4

Conclusion:
    In this lab, we asked the question, “How does temperature affect the number of oxygen being released from a plant?” We found that the plant produced the most bubbles when the surrounding temperature was at 10o. It produced 11 bubbles in 10 seconds at 10o, 9 bubbles in 10 seconds at 25o, and 4 bubbles in 10 seconds at 40o. This supports our hypothesis because the plant produced bubbles at a lesser rate as the temperature was raised.
    This lab was done to show how the temperature impacted the amount of oxygen produced by a plant. From this lab, I clarified my understanding of how temperature affects photosynthesis, helping me to also understand photosynthesis, as we learned in class. Based on the experiences of this lab, I can treat my plants with better care, and I can apply some of my knowledge of photosynthesis to other labs in the future.

Microscopic Organism Lab

Animal Cell: Skeletal Muscle Tissue
Power: 400
Has strations separting cell chains
Many chains of cells separated with some lines
Eukaryotic, Heterotrophic
Identified: Nucleus, Strations, Muscle Fiber

 

Plant: Ligustrum
Power: 400
Has many layers of cells of different sizes
The plant leaf is a long strip containing many cells in it
Eukaryotic, Autotrophic
Identified: Chloroplast, Epidermis Cell, Vein

Plant Cell: Spirogyra
Power: 100
Forms long chains
Has a lot of chloroplasts
Eukaryotic, Autotrophic
Identified: Cell Wall, Chloroplast, Cytoplasm

Bacteria Cells: General Shapes
Power: N/A
Extremely small
Not much detail in the cells
Prokaryotic, (Autotrophic or Heterotrophic)
Identified: Coccus, Bacillus, Spirilum

Cyanobacteria (Blue Green Algae)
Power: 400
Made life possible for us
Contains chains of circular cells
Prokaryotic, Autotrophic
Identified: 1 Cell

Euglena
Power: 400
Large with obvious inside elements
Flagellum is very thin and unnoticeable
Eukaryotic, Autotrophic
Identified: Nucleus, Chloroplast, Flagellum

Amoeba
Power: 100
Many different colors for the cell
Many pseudopods sticking out of the cells
Eukaryotic, Heterotrophic
Identified: Nucleus, Cell Membrane, Pseudopods

In the lab, we took a look at different types of cells, and their components, using a microscope. We found out what was unique for each cell, did some observations on each cell, determined if the cells were eukaryotic or prokaryotic, and autotrophic or heterotrophic. We also identified some different parts of each cell. The autotrophs made their own food. Some of them had chloroplasts and some of them were located inside cells. The heterotrophs obtained energy through other means. None of them had chloroplasts and some had pseudopods to bring in things from outside the cell. The eukaryotes are not extremely ancient, and they all contained nuclei. The prokaryotes were ancient, and were extremely small.

Egg Diffusion Lab

    When the sugar concentration increased, the mass and circumference of the egg decreased. This is because the egg was placed in a hypertonic solution. The sugar is the solute and the water is the solvent. The water molecules diffused through the membrane through passive diffusion from the low concentration of the sugar to the high concentration, so the egg shrunk.

    The cell's internal environment changes as its external environment changes, since the cell is pressured to keep the sides in equilibrium. The egg grew when it was placed in the vinegar, as the vinegar had a lower concentration of sugar than the egg. The egg grew even more when it was placed in water, but it shrunk when it was placed in sugar water.

    This lab demonstrates the biological principal that everything wants to reach equilibrium. The solvent diffuses through the membrane to make both sides of the membrane have the same concentration of sugar.

    Fresh water is sprinkled with water so that the water on the vegetable evaporates before the internal water evaporates. This will keep the vegetable fresher for a longer time. Putting salt on roads will "draw the water out of their iced form", making it melt faster. This salt also extracts the water out of the plants on the roadside, making the plants more dry. This is because the water moves from the less concentrated solution on the interior of the plant cells to the outside with the salt.

    Based on this experiment, I would want to test putting eggs in more types of solutions. This is because I am not sure if the egg only shrinks in the the corn syrup or if it shrinks in all high-sugar solutions.

Egg Macromolecules Lab

    In this lab, we asked the question "Can macromolecules be identified in an egg cell?" We found that monsaccharides, polysaccharides, proteins, and lipids were all located in the cell. We found that there were monosaccharides in the egg white, and lipids in the egg yolk and egg membrane. This information is also in the biology textbook and in the background information article that was given to us. It talks about the functions of the nucleus, cytoplasm, and cell membrane. We can infer what macromolecules each part contains through these observations. This data supports our claim in the following ways. The nucleus has a membrane, and all membranes contain lipids bilayers, so the egg yolk will contain lipids. The cell membrane also is a membrane, so it will also contain lipids. The background information stated that the cytoplasm contained monosaccharides, which supported our claim, as it the egg white tested positive for monosaccharides.
    While our hypothesis was supported by our data, there could have been errors due to the fact that we may have put too much or too little solution in our tests. This could have impacted our results because the amount of solution may have changed the final color of the solution, making it more like the original solution color, or something like that. Another error might have been that our samples of the different parts of the egg may have been contaminated with other parts of the egg. For example, the some of the egg white may have went into the egg yolk part. This will have impacted the final results, since the different parts of the solution have different amounts of the macromolecules we were testing for. This would yield colors that are not for the part we are testing for. Due to these errors, in future experiments I would recommend that the scientists should be careful to correctly separate the different parts of the egg in the beginning and also carefully measure the amount of solution you put in the tests.
    This lab was done to demonstrate which types of macromolecules are contained in each part of the egg, or cell. From this lab, I learned how the different functions of organelles function impacts what macromolecules are in it, which helps me understand the concept of the parts of a cell and what we learned in class. Based on my experience on this lab, I can learn the concepts of biology better.

Unit 2 Reflection

    This unit's theme was Miniature Biology. We learned about the properties of water, the structures and the functions of the four main types of macromolecules, and how enzymes work. We demonstrated some of these principles in labs. In the Sweetness Lab, we demonstrated how different structures of carbohydrates lead to different sweetness levels. In the Messing with Enzymes lab, we demonstrated that different factors affected the production of molecules for the enzymes. In the Cheese lab, we demonstrated how different factors affected the curdling speed for the curdling agents.
    In this unit, the information on the four types of macromolecules was hard to memorize, but the rest was pretty straight forward. We discussed and made a shared agreement about how we were going to treat each other. We agreed that we would be engaged and focused, give respect, and not give negative consequences for mistakes. I developed a more cooperative personality with my new table group. 
    From this unit, I experienced how to be more helpful in a group while working on an experiment. I am better than I was yesterday in that I know different factors that impact different things. I'd like to learn more detail about the macromolecules, such as each of the 20 different types of amino acids. I do not have any unanswered questions. I wonder about how learning about this will impact my life.

Sweetness Lab

In this lab, we found that the monosaccharides are the sweetest, the disaccharides were less sweet, and the polysaccharides almost had no flavor. The monosaccharides have one ring, and are used more than the disaccharides and the polysaccharides in food. Some are primary sources of energy, some are used for food enhancement, and some are used in cellular control. The disaccharides have two rings, and are used in less sweet foods. Some are used in plants for photosynthesis, some is present in germinating grain, and some are the main source of carbohydrates for infants. The polysaccharides have multiple rings, and are not digestible, not used in foods, or something similar to that. Some are used in staple foods.This data supports our claim because it shows that the carbohydrates that are used more in food are more sweet.

    All the testers had a similar rating of degree of sweetness for the carbohydrates. The rating could have been different for the testers due to the accuracy of their taste buds, which may have lead to incorrect rating of the sweetness of the carbohydrates.Another reason that the ratings may have been different is that their carbohydrates may have been contaminated with other carbohydrates, which could have altered their final results by making the ratings higher or lower. Also, the testers may have tasted different amounts of the carbohydrates.

    Humans taste sweetness by the taste buds on their tongues. The bumps on the tongue are called papillae, and most of them contain taste buds. Usually, taste buds get replaced, but as people age, some taste buds don't get replaced, so some people may taste differently making the testers rank the same samples differently.

"What is Biology?" Collage

Jean Lab

    In this lab we 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 the fabric?" We found that the 50 percent bleach was the best at doing this job. It was the highest concentration of bleach where the curling of the fabric was not obvious. It had the highest amount of color removal out of those without fabric damage, with an average color removal of 4. This data supports our claim because we used the scientific method to devise an hypothesis and test it with an experiment.

    While our hypothesis was supported by our data, there could have been errors due to the timing, since the squares of jeans were not all exactly soaked for one minute. This may have lead to incorrect color removal amount or visible damage. Another error might have been that the water that was used may have been contaminated with bleach or other things could have altered the final results. Also, the  bleach might not have been evenly distributed through the mixture. Due to these errors, in future experiments I would recommend an exact timer and pure water.

    This lab was done to demonstrate how some bleach concentrations can have better results than others. From this lab I learned that you can not only concentrate on just one aspect of the result, such as color removal, but all of the aspects, to decide which is the best. This helps me understand the concept of the scientific method, as I went through its process. Based on my experience from this lab, I can have a better sense of what is good next time I try something similar.