Unit 5 Reflection

     This unit focused on four main concepts: DNA replication, protein synthesis, mutations, and gene expression/regulation. DNA has to be replicated identically because all cells have the same DNA. It has to unzip and fill in the bases missing in the base pairs. This is done by the DNA Polymerase, and now there are two identical strands of DNA. Protein synthesis is the process of making a protein. RNA is heavily involved in this process. The synthesis starts with transcription. DNA is unzipped again and this time, the RNA Polymerase copies the gene to mRNA (messengerRNA). Thymine is replaced with uracil, and after this is over, the mRNA goes to a ribosome. Now, translation can begin. The ribosome, or rRNA, reads the mRNA three bases at a time. These three bases are called a codon. One codon translates to one amino acid, and the animo acids formed are chained together by the ribosome. The chain folds and becomes a protein. This whole process can also be referred to as "walking the dogma". Mutations can be harmful or helpful to organisms and there are different types. Point mutations only affect one or two bases at a time. Substitution switches one base for another. Framshift mutations, like insertion and deletion, can add or subtract one or two bases in a sequence. Also, inversion and translocation involves DNA or chromosomes breaking and bonding with itself or other chromosomes. Finally, gene expression is the process of DNA being used to produce a phenotype. Gene expression has to be regulated, otherwise, ears would grow from your stomach, or eyes could grow on the top of your head. In prokaryotes, a operon, with a promoter, operator, and other parts, is used to regulate the expression of genes. Eukaryotic regulation uses proteins (called transcription factors) to control transcription. After that, the DNA is separated into exons, used DNA, and introns, unused DNA. DNA can wrap around proteins called histones to form nucleosomes.

https://c2.staticflickr.com/8/7447/9488926466_9116099def_z.jpg

https://upload.wikimedia.org/wikipedia/commons/0/0c/Lac-operon.jpeg

     My strengths were completing the vodcasts on time and basically understanding the concepts by the time I got to class. During class, I was able to completely understand the concepts with Do Nows, recapping the vodcast, and labs. I think that I can do better on labs and not make mistakes I can avoid. During the DNA extraction lab, for example, I was not able to extract DNA, probably because of an error I had made during the process. Also, I should do my textbook notes early and not procrastinate on them until the last minute.
     I am a better student than I was before because I have gotten better at managing the class over time. I can now follow along with the vodcast and pause less often. It is now easier for me to write Relate and Reviews, and I realize that they help a lot, especially now studying for the final. I believe that I am a good student because I do my work, understand the concepts taught to me, and be efficient and thorough with my work. I took the VARK questionnaire, and it said that I have a multimodal learning preference, and I wasn't sure what to do with that result. In conclusion, I am getting through the class, but I can always get better than I am now.

Protein Synthesis Lab

     The process of making a protein has two main steps. DNA is replicated by an enzyme, but the copy is RNA, specifically called mRNA. The mRNA is different from the DNA because it contains uracil (U) instead of thymine (T). The mRNA then leaves the nucleus to get to a ribosome. At the ribosome, the mRNA is translated into amino acids (which make up proteins) by separating three bases at a times. One three base combination is called a codon, and each codon creates a specific amino acid. As they are made, the amino acids are chained together to make a protein.

https://upload.wikimedia.org/wikipedia/commons/thumb/5/5b/Central_dogma_of_molecular_biology.svg/1259px-Central_dogma_of_molecular_biology.svg.png 

     All mutations can have an effect on a gene, but some specific mutations can make a big difference in the DNA sequence. Deletion or insertion (both frameshift mutations) at the beginning of a sequence seem to affect the whole sequence the most because it changes all of the amino acids after it. Also, it can even cause the translating not to start at all. The mutation that has the least effect was substitution because it only changes one amino acid out of the whole chain. 

https://upload.wikimedia.org/wikipedia/commons/6/69/Point_mutations-en.png

     I chose deletion for my own mutation because I thought that it would cause the most change (damage) to the chain of amino acids. It changed many of the amino acids after it. By placing this mutation at the beginning of the sequence, it changed all the amino acids as a result. Because of this change in all of the amino acids, the protein would probably not do what it is supposed to do, and it wouldn't function correctly.

     Progeria causes accelerated aging. It is caused by a mutation in the LMNA gene, a protein which provides support to the nucleus of a cell. Most people who have progeria die by the age of 13, due to age-related health problems. Progeria interests scientists who are trying to connect certain genes with aging.

(LMNA Gene)

https://upload.wikimedia.org/wikipedia/commons/1/16/Protein_LMNA_PDB_1ifr.png 

Human DNA Extraction Lab

     In this lab, we asked the question, "Can DNA be separated from cheek cells, and if so at what point do you predict you will be able to see the DNA?". We found that you could, if you follow the process correctly, after a process called lysis and during precipitation. I was not able to extract DNA possibly because of an error during the experiment, but others did extract their own DNA. The DNA came out as a precipitate into a layer of cold alcohol. This occurred because the alcohol is nonpolar and the DNA is polar. This data supports my claim because this occurs after lysis, during precipitation. Lysis is the disintegration of a cell by rupture of the cell membrane.
     Our data contradicts the expected results because DNA was not extracted. This could have been because while the isopropanol alcohol was poured into the solution too quickly and not from the right angle. Also, during the stage of homogenization (preparation of a suspension of cell constituents from tissue by physical treatment by a liquid, the liquid being Gatorade), too much Gatorade or detergent (used for lysis) could have been measured in too large or small quantities, which could have changed the process or made it not work. One recommendation that I have is to measure quantities carefully and accurately. Another is that all actions done in the lab, like pouring alcohol, should be done in the proper way.
     This lab was done to demonstrate how DNA is extracted and when you extract it. From this lab, I learned about homogenization, lysis, and precipitation, which helps me understand the concept of DNA extraction and the structure of DNA. Based on my experience in this lab, if my or someone else's DNA is needed in a situation, I understand how to extract it from human cells.

Unit 4 Reflection

     In this lab, we flipped coins to simulate sex, which of course leads to the offspring obtaining traits. Each side of the coin represented one possible allele (for the genotype using two genes). We tested and compared different experiments (including mono- and dihybrid punnett squares that made predictions about the offspring's traits) and saw if the results matched our predictions. Some of the traits were autosomal and some were X-linked. The coins and the flipping represents segregation and independent assortment because of their randomness. The results of the dihybrid cross didn't match with the prediction because most of the resulting genotypes were heterozygous dominant, while there were no homozygous recessive genotypes. We predicted that there would be three phenotypes of blonde hair with brown eyes, but there were only two of them. Probability can be predicted, but it isn't always accurate. The results predicted by the punnett square cannot be and aren't correct at all times. This understanding can be used in the event that I have a child, and its traits can be predicted using genetic tests and punnett squares.

     The overall theme of the entire unit was genetics. The main ideas of the unit started with the cell cycle, or mitosis. Then, we were introduced to meiosis and were able to compare and contrast between the two. Later, we learned about what happens before sex, and we re-learned the basics of traditional dominance discovered by the scientist Gregor Mendel. In addition, asexual and sexual reproduction were compared and contrasted, and the laws of  segregation and independent assortment were taught to us. There are many exceptions to the traditional expections of genetics, including incomplete dominance, codominance, and polygenic traits. Lastly, we learned about how probability ties together with punnett squares and how punnett squares are drawn and used.
     My strengths were re-learning the basics of the genetics discovered by Gregor Mendel and the process of meiosis. I was able to understand the major concepts and main ideas of this unit. One weakness I have is applying my knowledge of genotypes and punnett squares (with monohybrid and dihybrid crosses) to questions about the inheritance of traits. Sometimes, it gets confusing to put together all the possible genotypes and draw the punnett square to predict the probability of a trait. I was able to manage the class by completing all of my vodcasts and other homework on time. I now have more knowledge about genetics and how to apply it to certain situations. By doing the infographic, I learned that writing words on paper isn't the only way to keep and remember information. The use of pictures and graphics helps to make certain concepts easier to understnad and apply. Infogrpahics are a good way to learn in general and are interesting to study. I am a better student now because I know more and can do vodcasts and labs better because of more practice. In the future, I would like to learn more about the exceptions of genetics and how exactly they work and create so much genetic variation in the world.

INFOGRAPHIC

https://magic.piktochart.com/output/17967650-genetics

Is Sexual Reproduction Important?

      In Chapter 13 of Dr. Tatiana's Sex Advice to All Creation, a TV show called Under the Microscope--A Deviant Lifestyle! is described, in which a Philodina roseola, the bdelloid rotifer, is interviewed and questioned by many other animals. She claims that her species has not used sexual reproduction since 85 million years ago, when the dinosaurs were on Earth. Her species has produced asexually, in other words, they cloned themselves. After all the arguments and events that occur during the show, the rotifer finally explains that secret to her species living for this long without sexual reproduction.

     A benefit of reproducing asexually is that it is very efficient. As written in the article, "...an asexual female who appears in a population should have twice as many offspring as her sexual counterpart." (215) Plus, you don't need a mate, so you don't have to spend time/energy trying to get one.  The rotifer continues and explains that over the years, genes in her species have changed through one process: mutation. She is able to proves that there are no male bdelloid rotifers in the world. A mouse then explains, "...if you don't have sex, you can't adapt to the future?" (224) The Philodina says that her species kept adapting and they live in many different areas and places. Another animal asks how the rotifers get rid of harmful mutations, but the Philodina counters that most mutations are neutral, that they change an organism's DNA sequence, but doesn't change that organism itself. 

     Then the host of the show steps in, and explains the three most important theories about mutation. In Muller's ratchet, named after Hermann Muller, harmful mutations will stay in asexual species and the number of mutations will ratchet up after periods of time. After some time, the species will go extinct. and the sexual organisms will survive because the shuffling of genes will have some organisms with few mutations. However, this theory relies on the fact that the population of the asexual species is small, and that could sometimes not be the case. In Kondrashov's hatchet, there is a threshold number of harmful mutations an organism can have before it dies. The shuffling of genes in sexual organisms prevents this, but asexual organisms have no way to stop it, and "...if the mutation rate is high enough, there is no way to survive without sex." (227)
     The last theory is the Red Queen, and it has to do with infectious diseases. Sexual organisms change their genes, so the parasites cannot stay fully adapted to their hosts. However, in asexual organisms, the genes don't change, so parasites can infect them. Written in the article, it reads "...you have to change to stay where you are." (229) Finally, a nine-banded armadillo talks and reveals to everyone how asexual organisms can survive. Sexual reproduction gives organisms an advantage because it makes them rare. However, the bdelliod rotifers have been traveling, both in space and time. They take part in a process called anhydrobiosis, rendering themselves in suspended animation. When you come to a new place, you are now a unique species, the armadillo explains. Sexual reproduction enables mammals to survive because right now, there is no way for mammals to reproduce asexually. In conclusion, sexual reproduction is important to many organisms because it allows genetic variations, including mutations, competition between organisms, new genetic traits, and parents to care for their young, but it has limitations such usage of time/energy, exposure to STDs/parasites, competition, and bad genetic combinations.

Unit 3 Reflection

     The over-arching topic of this units was cells. A few themes were the structure of cells and photosynthesis vs. cellular respiration. We had to understand that the cell is a basic unit of life and the cells' functions. Specifically, we learned how we got to today's eukaryotic cells from the earliest prokaryotes. We got a basic overview of how cells were discovered. Later on, we got to the structure of cells, specifically membranes. These include vesicles, lysosomes, the endoplasmic reticulum (ER), and of course the cell membrane itself. It led onto the vodacast about diffusion, the passing of objects through the cell membrane requiring no energy. This continued to the topic of osmosis, the diffusion of water through the membrane due to differences in concentration of a solute. After that, we learned about how cells make proteins with its organelles, and by the next vodcast, we learned about the organelles in a cell, like the centriole, choloroplasts, and mitochondria. 

     

     Finally, we learned how photosynthesis works inside a chloroplast with the stroma and grana. It involves the electron transport chain (ECT) , the ATP Synthase, and the Calvin Cycle. The final vodcast of the unit explains cellular respiration, which occurs in the mitochondria. It has three steps: Glycolysis, the Krebs Cycle, and the ECT. Photosynthesis and cellular respiration tie together and are essentially opposites.

My strengths are the parts of a cell and how eukaryotic cells came to be (through evolution). I understand how the cell works and what it does. Photosynthesis and cellular respiration are a bit more complicated. I understand the basic steps, but I will go over them and then understand the specifics and the details, because they are both multi-step processes. My successes are the labs that we have completed and that I have completed and wrote a conclusion on. A setback was the fact that we could not complete the Microscopic Organism Lab, and we had to complete a packet instead. I am a better student now because I have learned from this unit. I am now thorough in the subject of cells and their functions. Two things I want to learn more about are photosynthesis and cellular. They are much more complicated than what we have learned. I wonder how complex these processes actually are. This unit has helped me learn and grow as a student.

     

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 plants are tested with different colors of the light spectrum, red and blue light will cause the plant to grow the most in height.

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?

Using different color wavelengths on different plants to see amount of growth over a span of time

Controls = type of soil, moisture, seed, amount of light, heat conditions, etc.

Changed Variable (Independent) = color (wavelength) of the light spectrum

Results:

Filter Color	Spinach Avg. Height (cm)	Radish Avg. Height (cm)	Lettuce Avg. Height (cm)
Red	16.87	12.82	11.12
Orange	13.5	8.33	6.67
Green	2.17	1.42	3.3
Blue	19.33	14.5	12.42
Violet	16.23	10.75	8.75

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 does support my hypothesis. Red and blue wavelengths do cause the most growth in plants. The plants grown under these colors were the tallest. With all of the three different seeds tested (spinach, radish, and lettuce), the blue wavelengths got the best results (tallest heights), with red and violet being the close seconds.

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

The color blue wavelength causes the most plant growth compared to all the others in the visible spectrum.

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

I would expect average plant growth in plants grown with white light because not only are red and blue wavelengths included, but also green and yellow wavelengths, which cause less growth.

Site 2: Photolab

http://www.kscience.co.uk/animations/photolab.swf

Lab Report - Photolab

How will varying light intensities affect plant growth?

If a plant is tested with varying amounts of light intensity, then the highest light intensity, 50, will make the plant grow the fastest.

Variables:

Independent Variable - Light Intensity

Dependent Variable - Plant Growth

Constants - Amount of dissolved carbon dioxide (high), temperature (25 degrees Celsius), angle of light, light bulb, amount of water, type of plant, time for # of bubbles (30 seconds)

Control - Light Intensity set at 0

Data Table

Light Intensity	Rate of Photosynthesis (number of oxygen bubbles)
0	0 bubbles
10	12 bubbles
25	17 bubbles
40	19 bubbles
50	20 bubbles

In this lab, I asked the question “How will varying light intensities affect plant growth?” I found that higher amounts of light intensity caused more growth in the plant. For the light intensity of 0, the rate of photosynthesis (the number of bubbles sent out from the plants) was 0. From 0 to 10, the number of bubbles increased by 12.  From the light intensity of 10 going up to 40, the number became 19. Finally, at the intensity of 20, the number of bubbles was 20. This result would naturally occur because more sunlight would result in a higher rate of photosynthesis. Generally speaking, if the amount of a reactant increases (in the chemical equation of photosynthesis), the amount of product will increase. This data supports my claim because when the light intensity, in the experiment, increased, more bubbles are “exhaled” from the plant in water

This lab was done to demonstrate how different amount of light on a plant will affect its growth. From this lab, I learned that a higher light intensity will cause more growth in a plant, which helps me understand the concept of a chemical equation. When an amount on one side of the equation increases, the other side has to increase as well. Based on my experience with this lab, this concept of increasing reactants leading to increasing products can be applied to other labs similar to this one and others having to do with a chemical equation.

Egg Diffusion Lab

In this lab, we tested 2 eggs that had been soaked in vinegar for a couple of days. We then put one egg in deionized (pure) water and another egg in a sugar solution. After two days, we came back to see what had happened to the eggs. When the sugar concentration the egg was in increased, the mass of the egg decreased by 45.9% on average. The circumference decreased by an average of 22.1%. The sugar in the solution, which is the solute, has a high concentration outside the cell and a low concentration inside the cell. So, as a result, the solvent in the cell moves outside of the cell and the cell shrinks. The more sugar that was present outside the cell, the more the cell decreases in size. Cells respond to their changing external environment internally due to different basic cell processes, like osmosis for example. The cells themselves change because they need to function a normal rate at all times for the whole body to keep working. If they didn't change, the cells wouldn't function properly. This lab relates to diffusion, the movement of molecules across a concentration gradient through the membrane, specifically osmosis, the passive diffusion of water. Depending on the solute concentration in certain areas (inside/outside), the solutions (deionized water and sugar), were hypotonic or hypertonic. The pure water was hypotonic and made the cell grow, while the sugar was hypertonic and made the cell shrink. Vegetables at markets are sprinkled with water because they need to be preserved. Roads with ice on them are salted because the salt shrinks the cells of the solid water and as that happens, the ice melts. Salt water on vegetables prevents them from spoiling and takes out water from their cells. Based off of this lab, I would want to test an egg the exact same way except with salt water to see how this data will differs from the results obtained while testing with the sugar solution. The egg will probably shrink in that case because the solution itself, with salt as the solute is hypertonic.

Control: Deionized Water
Group #	1	3	6	8	AVG
% Change in Mass	-0.95%	0.40%	-0.38%	-0.84%	-0.44%
% Change in Circumference	5.88%	0.60%	25.90%	0.00%	7.78%
Sugar Water
Group #	2	4	5	7	AVG
% Change in Mass	-47.15%	-44.25%	-46.08%	-46.89%	-45.90%
% Change in Circumference	-24.24%	-17.64%	-18.76%	-27.80%	-22.10%

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 a egg cell?" We found that there are different macromolecules in different parts of the egg. In the egg membrane, the protein test using copper sulfate tested positive. The quantity of proteins in the membrane itself was 3 out of 10. The color of the membrane solution changed from blue to purple. The reason why proteins are present in the membrane is because a part of membranes is the transport proteins. These proteins transport molecules in and out of the cell during facilitated diffusion. For the egg white, lipids were one of the molecules tested for with Sudan III. This test tested positive. The color of the solution changed from red to orange. The amount of lipids in the white was 3 out of 10. Lipids are in the egg white because lipid molecules are in different organelles. The organelles in the egg are spread out throughout the egg white. Lastly, the egg yolk tested positive for polysaccharides. The test was done using iodine. The rating of the test was 1 out of 10. The color of the solution changed from yellow to orange. Polysaccharides would be found in the cell because a polysaccharide, like starch, would be in a egg in the form of sugar. It would, or course, be a complex carbohydrate that humans can consume,
     An error that could have happened during this lab is the measurement of parts of the egg and chemicals used to test the egg. While our hypothesis was supported by our data, this error could have changed the results of the lab. Depending on how much chemical solution or how much of the egg was tested, the rating for how much of molecule is in the yolk, white, or membrane could have gone up or down. Also, different parts of the egg could have gotten mixed together. If so, it was probably in very small quantities. This could have changed the results of the test by showing a molecule is in the egg part, but without the error, it wouldn't. A way to solve this problem could be to have a better way to split the egg. To solve the first problem, students just have to be more careful while doing lab work, particularly with the measurements.
     This lab was done to see what macromolecules are in an egg, specifically the different parts (yolk, membrane, white). The four molecules that the parts were being tested for were proteins, polysaccharides, monosaccharides, and nucleic acids. From this lab, I learned more about macromolecules, which helps me understand the concept of what molecules are in what parts of the cell. Based on my experience from this lab, I can know what parts of an egg I want to eat. If I need proteins, I'll eat the egg white because it has the most protein in it. If I need fats, I'll eat the yolk because it has the most lipids in it. This lab will also help later in biology when we are learning more about macromolecules.

Unit 2 Reflection

     This unit was about three different subjects: the properties of water, the 4 main macromolecules, and enzymes. We went over the basics: the periodic table, atoms, and elements. Then, we learned about three different bonds: ionic (atoms giving up electrons), covalent (atoms sharing electrons), and hydrogen (only applies to water, positive regions are attracted to negative regions). Also, we learned about different properties of water. Polarity is the unequal distribution of charges between H and O. Cohesion is when water bonds with water, adhesion is when water bonds with something else, and capillary action is when the force of the H-bonds are stronger than the force of gravity. 

     Next, we learned about carbohydrates, which are made of sugar rings and provide energy. Lipids are fats, phosolipids, oils, etc. and they store energy. Proteins are structural and are enzymes, and they provide support to the body. Nucleic acids are made up nucleotides stranded together, and they are a source of information. Finally, enzymes are proteins that speed up chemical reaction by lowering the activation energy needed. They can be affected by pH and temperature and can become denatured, which means they won't work. I also learned more about sugars, factors that affect enzymes, and enzymes themselves.

     I had success in understanding most of the content that was represented to me. I did all of the vodcasts, and what I didn't understand was answered in class. Most of the things I learned in this unit were things I already knew about, but I got more information and explanations about them. This unit was good for expanding on what I already knew before. One setback I had was the part of the labs, because I think our group could have made some errors on steps of the procedures. I think that when we do labs, we can all follow the procedures better, and try not to make errors that would affect our results. I am better from what I was at the beginning of the unit because now I know more and will do better work now that I understand how everything works.
     I want to learn more about some of the macromolecules. What we learned about the 4 different molecules did not really talk about how different molecules affect the macromolecules. Also, I want to know how it all works together in one system. Hopefully as we go on in this school year, I will understand and know more about this subject. 
     

Sweetness Lab

     The purpose of this lab was to find how the structure of a carbohydrate changes how it tastes. So the question for this lab was, "How does the structure of a carbohydrate affect its taste (sweetness)?" So, my hypothesis was, "If fructose is tasted, it will be very sweet because it is a monosaccharide. On my data table, which was filled out after the taste test, has the sweetness level of fructose at 150, which was 50 points higher than the second-most sweet substance, which was sucrose at 100. In fact, the sweetness level of monosaccharides were higher than that of disaccharides and polysaccharides. The polysaccharides were the least sweet of the group and were rated at an average of 20 on the sweetness scale. Disaccharides however, were much sweeter, but still on the low side, at an average of 65. As the saccharides gained more rings they became less and less sweeter. It's possible that more rings on the sugar cause the sugar to be less sweet. The sugars, as they got more complex, got less sweet. All of this evidence supports my claim because monosaccharides are the sweetest out of all the different sugars tested in this experiment. All of the other sugars were not as sweet and some, like cellulose and starch, were not sweet at all, and tasted more bitter. All in all, fructose was the sweetest because it is a monosaccharide.
     The saccharides with less rings are more likely to be used for energy. The polysaccharides are used for structure in organisms and can also store energy. The disaccharides in the middle of the group can be in both food for energy and structure in the body of an organism. The monosaccharides are produced as the result of photosynthesis. Different saccharides with different structures serve different purposes.
     Not all testers put the same rating for each sugar. One reason for that could be that people didn't discuss and agree on one rating. Also, a mistake could have been made in placing the sugars on the paper. For example, two sugars could have mixed. Lastly, all people taste things differently, so one person wouldn't taste something the exact same way another person did. According to the U.S. National Library of Medicine, taste can be determined by a variety of different factors (texture, temperature, smell, etc.). Of course, these factors will not be the same for every single taster in this lab. Also, different peoples' taste bud sense different things and send different signals to the brain. This is why one taster could rank the sweetness of different sugars differently than others.