Unit 5 Reflection

This unit was about our genetic code, how it replicates, how it is used to make proteins, errors that can occur, and how organisms control how traits are expressed. Our DNA is unique because it is wound up in a tight double helix. When it replicates, it unzips, and complementary bases join to form 2 strands of the DNA. DNA is made of A, T, C, and G. However, when it replicates, errors, or mutations can occur. While some may be as simple as a substitution, others, like insertion and deletion can completely change the protein that is being coded for and possibly be fatal. DNA contains instructions for the cell to make proteins. This process of making proteins based on DNA happens in multiple steps. First, DNA is transcribed into mRNA, adding the complementary bases, but with uracil instead of thymine, and is also single stranded. Then, the mRNA travels to the ribosome, where it is translated into amino acids by every 3 bases (codons). The amino acids form a chain, which twists and folds to form proteins. The final main idea from this unit is that although every cell contains the genetic code for all proteins, only certain genes are actually expressed. This is called regulation, so that the cell doesn't waste energy making all of these proteins it doesn't even need. For example, there is the lac operon. The DNA is transcribed based on the repressor, and whether it fits on the operon. Also, in order for DNA to fit into such tight spaces, it is wrapped around proteins called histones, forming nucleosomes. This is what makes up the chromosomes.

I mostly struggled with gene expression and regulation, because it was a new idea. The lac operon was a bit confusing at first too. I enjoyed learning about actually walking the dogma. I learned a lot more about the connection between what a cell does, and how it knows to do that. I also enjoyed looking up random, weird mutations that people have and learning about what causes them (see my previous blog post for a video of a family that walks on all fours and behaves like prehistoric hominids). I think I am getting better at not getting discouraged when I don't get something in a vodcast. Now, I am more confident, and even if I don't get it the first time, I know I will understand after recapping and some studying.


I want to learn more about stem cells. I think its very interesting that they can morph into different kinds of cells. I also want to learn more about tumors and cancers, and how they can be caused. Lastly, I want to learn about expression and regulation in humans. 

Protein Synthesis Lab Conclusion

Proteins are made in different steps that occur in different places in the cell. First, in the nucleus, DNA is transcripted into mRNA by the enzyme, RNA Polymerase. Then the mRNA is transported through the cytoplasm, to the ribosome. Then, each codon, or set of 3 bases, is translated into protein language, or amino acids. Amino acids join to form a chain, called a polypeptide. The chain then bends, folds, and twists, eventually forming a protein.

Based on the results, substitution made the least difference, but frameshift mutations like insertion and deletion made the most flawed proteins. When a substitution happens, there is still a chance that the same amino acid will form, or there will just be one small error. But insertion and deletions towards the beginning of the sequence, completely changed the rest, starting from the mutation, onwards.

The mutation that had the absolute greatest effect was insertion or deletion of one of the first 3 bases of the sequence. This meant that the first amino acid, "MET", was altered, therefore there was no start codon. This means that there would be no protein because the translation never even started! This type of insertion that happened at the beginning affected the protein the most.

Many mutations could be in my genes, yet I don't even know it. Because some of them have little to no effect, but others can be fatal, you never know what mutations might exist in you. An example of a disease caused by a mutation is Uner Tan Syndrome. People with this disorder walk on all fours and behave like apes. Its like going backwards through evolution almost! Below is a documentary featured on BBC2 in 2006  about a Turkish family with this disorder, called "The Family that Walks on All Fours."

Unit 4 Reflection

One of the labs we recently did was the "Coin Sex Lab". In this lab, we simulated sex by flipping coins with different alleles on each side, to see what traits our 'children' would have. Coins serve as a model for genetics because traits are random, and the side that a coin will land on is random as well. In the dihybrid cross, we expected 9 kids to have brown hair and brown eyes, 3 to have brown and blue, 3 to have blonde and brown, and 1 to have blonde and blue. Our results were very similar to our prediction as the numbers, respectively, were 10, 3, 1, and 2. This is based on chance and probability. We can use probability to see how likely our offspring will be to get certain traits, but can't predict exactly. This relates to my life because now I understand how I could've gotten my traits.

In this unit, we learned about the topic of Why Sex Is So Great. We learned about the Cell Cycle and Mitosis Vs. Meiosis. Mitosis had one divisions, and went from diploid to diploid, while meiosis had 2 divisions and went from 2n to n. We also learned about Gregor Mendel's experiments with pea plants and how he came to realize certain traits dominated over others. Traits come in different versions, called alleles. Mendel came up with 2 laws, the Law Of Segregation, and the Law Of Independent Assortment. The Law of Segregation stated that chromatids split apart during meiosis. Independent Assortment meant that genes assorted randomly. There are also complications to genetics, such as codominance, where 2 traits both show up fully, incomplete dominance where neither trait completely dominates over the other, and epistasis, and polygenism. We also learned how to do crosses such as monohybrid and dihybrid crosses.

The basic genetics were easy for me and made sense. I remembered dominant and recessive from seventh grade, and Punnett Squares, but crosses were a bit confusing. Dihybrid crosses took some practice to get the hang of, but eventually, it became easy. The infographic also helped me organize what I learned in the unit, and I knew what information was most important to know, because if it was super important, I'd include it there. I want to learn more about polygenic traits and epistasis, generally the genetic exceptions. They seemed really interesting to me. Overall, this unit helped me understand about myself, how I could've gotten my traits, and I am now curious about traits more.

DNA Extraction Lab Conclusion

In this lab we asked the question,"How can DNA be separated from cheek cells in order to study it?" We found that by homogenization, lysis, and precipitation, DNA can be distracted. After carrying out these processes and adding alcohol, DNA formed as a precipitate on the test tubes and was visible to the naked eye. This worked because homogenization mixed the DNA and Gatorade, and lysis destroyed the membranes protecting the DNA. Finally, the alcohol being non polar, caused the DNA to form as a precipitate on the tube. This data supports our claim because the precipitate formed, so the DNA was extracted.

While our hypothesis was supported by our data, there could have been errors due to adding too much Gatorade (there was no exact measurement), or too much of any ingredient, diluting the solution. Another error that could've occurred was when pouring the alcohol. If you poured it in all at once, it would mix with the solution and not allow DNA to form. Due to these errors, in future experiments, I would recommend providing exact measurements on the instruction sheet for the lab, and pouring the alcohol slower and from the side.

This lab was done to demonstrate that DNA can be distracted, and which scientific principles are used in the process. From this lab, I learned about homogenization, lysis, and precipitation. This helped me understand the concept of polarity, and membranes in the cell. Based on my experience from this lab, I know how to extract DNA, so I would try to modify the experiment by using different ingredients to get the same result. For example, water instead of Gatorade, and papaya juice instead of pineapple juice, different types of soap, etc.

Is Sex Important?

The excerpt of Olivia Judson's Dr Tatiana's Sex Advice to all Creation describes the evolution of organisms that reproduce sexually and those that reproduce asexually. It is a debate about whether sex is necessary for a species to survive and thrive.

Based on the evidence in this excerpt, I think that a species can survive and thrive by reproducing asexually. First of all, cloning (reproducing asexually) is way more efficient than sex. "All else being equal, an asexual female who appears in a population should have twice as many offspring as her sexual counterpart."(215). An argument people would make about why sex is necessary is that diseases can spread very easily among clones. A solution to that is that asexual creatures can just move somewhere new. A third reason is that this has worked for 85 million years with the species of bdelloid rotifers, which shows that it can indeed be successful. Asexual reproduction is also way faster and more efficient because sex takes a lot of time and effort. Cloning doesn't even require a mate so reproduction can keep happening.

It was confusing whether sex is really necessary. In the text, there were equal arguments for both sides. In conclusion, sex may be necessary, but asexual reproduction is faster and more practical.

Unit 3 Reflection

This unit was about the cell, the organelles inside, how they came to be, and the processes that occur in it. Macromolecules make up many parts of the cell in structural support, reactions, and transport. The cell theory states that cells are the basic unit of living organisms, cells come from pre-existing cells, and all organisms are made of one or more cells. cells make up tissues, organs, organ systems, organisms. Membranes are usually made of a phospholipid bilayer and can either be a barrier, container, or a bouncer. This includes the nuclear lysosomes, er, etc.  Membranes are selectively permeable so some things go through, but not everything. Transport is either passive (diffusion) or active (using ATP). Osmosis is diffusion by water through a selectively permeable membrane. The solutions can be hypertonic, hypotonic, and isotonic. Turgor pressure is the pressure between the cell wall and the membrane when the cell swells. The main job of a cell is to make proteins. This starts with the blueprints in the DNA and then goes through the ribosomes, the er, vesicles, and elsewhere. Cells can be eukaryotic or prokaryotic. They all have nucleic materials. Some of the other organelles are the cytoskeleton, centrioles, lysosomes, vacuole, mitochondria. The endosymbiotic theory states that ancient cells ate other cells with capabilities to make their own food or convert glucose into ATP by phagocytosis, and came to an endosymbiotic relationship. That is how those cells are now. Photosynthesis occurs in the chloroplasts of autotrophs and has the light dependent reactions and the calvin cycle. Cellular respiration is the opposite of photosynthesis and goes through glycolysis, krebs cycle, and electron transport chain. 36 ATP is produced.


Animal Cell

The hard parts of this unit was mostly photosynthesis. Knowing what goes in and comes out of each reaction is hard to remember and understand the process. I learned most in the osmosis chapter when we did the egg diffusion lab. I never quite understood the practical applications there, but now I do. I also learned how mitochondria and chloroplasts used to be separate cells and the evidence for that. It helps me understand why there are DNA fragments in the mitochondria. I want to learn more about the endosymbiotic theory and diffusion because that was the most interesting part of the unit to me. 

Egg Diffusion Lab

In this lab, we placed 2 eggs that were previously soaked in vinegar in different solutions for 48 hours. One was placed into deionized water and the other was placed into sugar water.

When the sugar concentration in the water was greater, the mass and the circumference decreased by an average of 45.9% and 22.1% respectively. This was because it was hypertonic and there was a higher concentration of the solute (sugar) outside the egg than inside the egg. This caused the water inside the egg to diffuse out of the membrane to dilute the sugar water outside. The loss of fluid made the egg have a lower mass and circumference.

Deionized Water Class Data

GROUP #	1	3	6	8	AVG
% Change in Mass	-0.95%	0.4%	-0.38%	-0.84%	-0.44%
% Change in Circumference	5.88%	0.6%	25.9%	0%	7.78%

Sugar Water Class Data

GROUP #	2	4	5	7	AVG
% Change in Mass	-47.15%	-44.25%	-46.08%	-46.89%	-45.9%
% Change in Circumference	-24.24%	-17.64%	-18.75%	-27.8%	-22.1%

The cell's internal conditions changed throughout this experiment because it wanted to maintain equilibrium with the solutions outside of the cell. Putting the egg in vinegar probably made the membrane of the egg have some vinegar on it. So when the egg was placed in water, it lost some of its mass because of the egg trying to maintain equilibrium by diluting the vinegar water. However, since there wasn't much vinegar, it just lost an average of 0.44% of its mass and 7.78% of its circumference.

This lab demonstrates passive transport where the sugar tried to move from high to low concentration, but was not small enough to go through the membrane, so the water moved to dilute the sugar instead.

A real life application of this is when water is sprinkled on vegetables to keep them fresh. The solution inside the vegetable is a mixture of water and fructose or fruit sugars. The sugar attempts to move outside the vegetable but can't, so instead, the water from outside diffuses inside and makes the vegetable more juicy. Another example is when icy roads are salted to melt all of the ice. This is because the salt is at a greater concentration outside the ice cubes. So the ice melts to dilute the salt. This is a fast and simple way to melt the ice.

Based on this experiment, I would now want to test this with different kinds of fruits and vegetables with different amounts of sugar in them. Based on the growth or shrinking of the vegetables you would be able to tell which ones have the highest sugar content.

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

Egg Macromolecules Lab

In this lab we asked the question: Can macromolecules be identified in an egg cell? In which portion of the egg will they be found? We found that the membranes consisted of channel proteins. When we were testing for proteins, we found that the membrane turned purple in the biruit solution. Membranes have channel proteins as part of its selectively permeable membrane, in order to let in bigger molecules that is needs. This data supports our claim because the membrane tested positive for proteins. We also found that the egg whites had protein in them. The whites also turned purple and got a ranking of 10 for brightness in the solution. This is because in a cell, proteins and enzymes are found in the cytoplasm in organelles. This data supports our claim because the whites also tested positive for proteins. We also saw that the yolk contained lipids. The yolks turned orange and got a ranking of nine, showing that the macromolecule was present. This is because the yolk is where the baby chicken is born and uses lipids as a form of energy. This data supports our claim because yolks tested positively for lipids.

While our hypothesis was supported by our data, there could have been errors due to contamination of the samples. For example, some of the yolk remained on the membrane, which could've made the membrane test positive for more macromolecules then it actually had. The samples all could have been contaminated by the vinegar as well. Another possible error could've been not mixing in enough of the solution to test if the macromolecule was present. This could have been the reason why for some reason the membrane didn't test positive for lipids. Due to these errors, in future experiments I would recommend straining the membranes to make sure the yolk was gone, and washing the egg first to get the vinegar out. I would also keep track of the amount of the solution to mix in.

This lab was done to demonstrate where macromolecules are located in cells. From this lab I learned that an egg is similar to cell which helps me understand the locations of each macromolecule specifically in the cell or egg. I know that the membranes have proteins which are most likely channel proteins. I also learned that the yolks have lipids, because they are the fatty part of the egg and are likely to contain fatty acids. I also learned that the whites had proteins, which are the enzymes in the cytoplasm. Based on my experience from this lab, I could be able to predict where else in other foods or items these macromolecules would be present in.

Unit 2 Reflection

            In this unit, we learned about the important chemistry that biologists need to know and the 4 macro molecules.
            Bonds between atoms can happen in 3 different ways. There are ionic bonds, which happen when an atom gains or loses an electron, covalent bonds, when electrons are shared between atoms, and Hydrogen bonds, where positive charges attract to the negative charges. Water is a unique substance because it is polar (charged), cohesive and adhesive, and the solvent for many solutions. Acids and bases are measure on the pH scale from 0-14.

The 4 macro molecules are carbohydrates, lipids, proteins, and nucleic acids. Carbohydrates are made of rings of C, H, and O. They can be mono, di, or poly saccharides. Lipids are fatty molecules that make up membranes and store energy. They are chains of fatty acids (C&H). Phospholipids have heads that are hydrophilic, and hydrophobic tails. Proteins are made of amino acids, and there are two main types: structural proteins and enzymes. Enzymes speed up the reactions that occur inside a body, reducing the activation energy, by taking in a substrate into the active site, and returning a product. Changes in pH and temperature can cause an enzyme to denature, or deteriorate. Nucleic acids such as DNA (2 stranded) and RNA (single stranded) are made of nucleotides, which consist of a nitrogen base, a sugar, and a phosphate group. Overall, we learned the main molecules that help our bodies function, why they are important, and what they are used for.

            Through the cheese lab, I learned how to adjust conditions in a substance to see how well the enzyme works. This helped me realize how a good experiment is planned and designed, and how enzymes can be denatured by pH and temperature. In the sweetness lab, I learned how depending on the amount of rings a sugar has, it can taste really sweet or really bland.

            I want to learn more about denaturation. What really happens to the enzyme and where does it go? Is it just a dead enzyme that remains in your body? I also didn't fully understand polarity and how polar and non polar substances interact with each other.

Not All Sugar is Sweet! Sweetness Lab

In this lab we asked the question: how does the structure of a carbohydrate affect its taste (sweetness)? We found that the monosaccharides (1 ring) were the sweetest, the disaccharides (2 rings) were a little less sweet, and the polysaccharides (3+ rings) were the most bland tasting. On a sweetness scale of 0-200, 200 being the sweetest, we found that glucose and fructose, which are both monosaccharides, got the highest rankings of 120 and 170. The disaccharides were a bit less sweet, and the polysaccharides got a rating of 10. According to the lecture notes, the less rings that a sugar has, the sweeter it is. This data supports our claim because the sugars with one ring were the sweetest, and the more rings the sugar had, the more bland the taste.

While our hypothesis was supported by our data, there could have been errors due to contamination between samples. As the petri dishes were shared between classes, there easily could've been minor spills or mishaps. The spoon may have also collected other sugar and contaminated certain samples, affecting the sweetness of the sample. Another error could've been not waiting enough time to 'reset' our taste before trying the next sample. Due to these errors, in future experiments I would recommend wiping away the spoon each time between samples, and waiting and significant amount of time between tasting each sample, or drinking water.

This lab was done to demonstrate the varying tastes between different carbohydrates of different structures, and how these sugars are used by humans. From this lab, I learned how we use many of these sugars commercially and in our bodies for different purposes. I also learned that the taste of different carbs can vary immensely based on the number of rings it is made up of. This helps me understand the concept of monosaccharides, disaccharides, and polysaccharides, as well as their uses, and what they're made of. Based on my experience from this lab, when I taste food, based on the sweetness, I can infer what kind of sugar is in it. I also will now look out for labels of fructose being in foods, and try to avoid it as much as possible.

The more rings a carbohydrate has might be used more for energy storage rather than immediate use in a cell. All testers did not give the same ratings. We might have gotten slightly different samples unintentionally. We might also have a different perception of what is sweet and what isn't. We also might not have waited long enough between samples and tried them in a different order. People may also have a different amount of taste buds in their tongues that perceive sweetness and therefore rank it differently.

What Is Biology Collage

Jean Lab

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          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 no matter what concentration of bleach we used, there was no significant visible damage to the fabric, however the color did change. The rankings of color removal were significantly higher for the larger concentration of bleach than those with a lower concentration. But, unlike what we expected, there was no visible damage to any of the fabric. Bleach is already known to break down substances and make them a lighter color. This data supports our claim because the jeans with a larger concentration of bleach got lighter.
         Our data was unexpected because of some errors we made. We accidentally kept the wrong time by a few seconds for the soaking time and drying time. We also didn't label correctly all the time and got confused as to which jeans were with which concentration of bleach. We also accidentally soaked one batch in bleach instead of water for a few seconds until we realized. This all probably affected the outcome of the lab. In future experiments, we will read the directions carefully and be organized with our labeling.
        This lab was done to demonstrate the scientific method, how it works, and how to use it effectively. From this lab I learned to make a hypothesis based on known information, which helps me understand the concept of the scientific method. Based on my experience from this lab, I now know how to solve problems   using the scientific method and can apply this to even more problems.