Unit 5 Reflction

In this unit, we focused on the subject of genetic code. We learned about DNA. It is a double helix spiral that contains all the information to make  proteins and all of us. DNA has two complementary parts, the 3 5 and the 5 3 which there are purines and pyrimidines which pare up with each other A T and G C. The four bases are adenine, cytosine, guanine, thymine. The sides alternate between phosphate and sugar. DNA is semi conservative replication which means that half of the DNA remains original. DNA polymerase breaks the bonds of DNA and unzips it and a new strand forms on each original strand. The Central Dogma says that it starts at DNA and then goes to RNA and then goes to ribosome. The DNA is transcribed into RNA by making a complementary strand of the DNA and replacing Thymine bases with Uracil. You then Translate it from genetic code to protein code in the ribosome. Each three bases, a codon, maps to an amino acid. These are assembled and these long amino acid chains become proteins. Mutations are also very important because they are changes in the genetic code. If they are small changes they rarely do anything but if they are big changes they can be very harmful. Two types of mutations are frameshift mutations and substitution. Substitution replaces one pair and doesn't cause many problems especially if it doesn't change the amino acid. A frameshift mutation, however changes every amino acid after the mutation and causes huge changes. There are two types of frameshift mutations: insertion and deletion. Gene expression and Regulation is very important because it determines which genes are expressed. If there was no gene regulation, there would be no cell differentiation and all the cell will be able to do the work of all the cells, but it will take it more time and energy which could cause death in the organism.
     I believe my strengths in this unit was the understanding of DNA and RNA because it built upon things I'd learnt in previous years. My weakness was in gene expression and regulation because I was unfamiliar with the topic. One of the setbacks was being sick which caused me to not be in class for the day we were supposed to go over the gene expression and regulation vodacast. I want to learn more about gene expression and gene regulation because that is my weakest point. I would like to know how understanding it could help us understand certain diseases like cancer which are cause by no cell apoptosis which leads to cells being replicated more times than a normal cell should. I think I became better at studying over this unit because of the upcoming final. I started to apply the studying techniques such as writing into memory and self assessment. Not having the vodcast notes for two of the vodacasts made them take longer than just filling them out on the printed paper, but it made it easier to remember many of the details.

Protein Synthesis Lab

     Protein is made by reading the DNA instructions. You start with a strand of DNA that contains the code to create protein. The DNA is unwounded by the RNA polymerase and it is turned into single stranded RNA. The RNA is the complimentary strand of the DNA copied and all Thymine bases are turned into Uracil. mRNA goes to the ribosome where the protein is assembled. tRNA takes 3 bases, or a codon, and matches it to a amino acid which the ribosome attaches to the amino acid strand. This forms an amino acid strand which turns into a protein.

    In our lab, we found that substitution causes the least effect. Only one letter of one codon was changed which at most could change one amino acid but it didn't in our lab. Deletion of the T caused the biggest effect on the protein in our experiment. Every amino acid after the error was changed. It does not matter where the substitution takes place because it will always cause little error. The level of change caused by insertion and deletion depend on where there position was. If the deletion of the T was near the end, it wouldn't have changed as much.

    I added 2 deletions and one insertion near the beginning to create the biggest change. Frameshift mutations like deletions and insertions create the most changes. Having them close to the beginning created the most changes because everything after the mutation changes. I had 2 deletions because they showed the most diversity in the lab. I didn't have three of the same mutation because it has a chance of not changing all the acids after the mutation.

    Mutations are very important because they have the potential to cause life threatening changes or potentially helpful traits. One example of a harmful mutation is proteus syndrome. One mutation in the AKT1 gene causes this disorder. It causes body parts, specifically the limbs and head, to become very big. This could potentially cause premature death do to deep vein thrombosis and your neck not being able to support the weight of your head if it affects your head.

DNA Extraction Lab

In this lab, we wanted to see whether we could extract DNA from our cheek. We found that we could could do this in a 3 step process: homogenization, lysis, and precipitation. This was proven by our experiment where we saw the DNA that we collected between the gatorade and alcohol. This meant that the procedure we followed was correct and we had arrived at the correct result. This also makes sense because the procedure fore DNA extraction involves homogenization, lysis, and precipitation and we used this guide to find the correct procedure. These processes breakdown the cell and separate DNA from the rest of the cell. We grouped the steps into one of the three categories and rearranged those steps into what seemed intuitively correct based on the definition of the step.
There were many possible errors that could have affected the results of this experiment. One possible error is that we mixed up certain steps because we weren't given the actual order of steps for the experiment. Another possible error is that we might have gotten food or other materials inside the gatorade while rinsing. Finally, the end result might not have been DNA and it could have been another substance because we never tested to see what it was. All these errors could cause this experiment to be invalid because what we observed might not be DNA. There are many things we can do to prevent the errors we encountered in this experiment. One thing we can do to prevent food getting into out sample is rinsing our mouth before the experiment. Another thing we can do is get more information about DNA extraction before doing the lab because we had a very faint idea of what we were doing, and some of it was just guessing where the steps were instead of understanding why each step is in its order. Another thing we can do is test the DNA we have to see whether it is actually DNA.
The purpose of this lab is to test whether we can extract DNA from our cheek. This lab helped us better understand the process of DNA extraction. We specifically learned of the processes such as homogenization, lysis, and precipitation, which are used to breakdown a cell and histones and to separate DNA from the rest of the substance. This experiment taught us stuff that has a lot of practical applications. This process can be used in crime labs to check the DNA of a criminal. It could also be used by Doctors who want to sequence someone's DNA. Biologists can use this on animals to check their DNA for research purposes. This also taught us about how to figure out how to go about accomplishing an experiment, and how to manage our time in a project that has a limited time frame.

Unit 4 Reflection

In this lab, we modelled the passing of traits to offspring through sexual reproduction with coins. Each side of the coin represents one of the alleles of the parents and flipping two of the coins shows the resulting genotype. For modelling the gender of the offspring, one of the coins would have an X on both side to show the female's alleles. The other coin has an X on one side and a Y on the other. Flipping both coins simultaneously will result in either XX for female or XY for male. In the Dihybrid cross, we had a 4 coins. Two of the coins had A on one side and a on the other side. The other two coins had B on one side and b on the other side. Flipping all of them simultaneously represent a dihybrid cross. There was a margin of error from the results from the coin flipping and the predicted results from the punnet square. This is because probability isn't certain and probability is the chance something will happen. Even though the ratio between male and female offspring is 1:1, it does not mean that exactly half of the offspring is male or female. There is a limit to predicting offsprings' traits because they are often influenced my multiple genes and factors and are hard to predict with simple probability. This could relate to our lives because we could predict the traits of someone's offspring or whether they will get a disease or not. An example would be the probability of whether a child will get colorblindness which can be modelled through a punnet square showing X-linked inheritance. The main topics in this unit were the cellular processes of sexual reproduction and the patterns of inheritance. We learned about mitosis and asexual reproduction in which a cell creates a clone of itself. We then learned about meiosis and sexual reproduction. Next, we learned about Mendel's discoveries that would make the field of genetics and his laws of inheritance. We then learned about more complex patterns of inheritance that are what most traits are determined by. Some examples are X-linked inheritance, polygenic inheritance, multifactorial disorders, codominance, incomplete dominance, gene linkage, and epistasis. We finished the unit by learning in detail the notable types of crosses such as a heterozygous dihybrid cross and their phenotypic ratios such as the 9:3:3:1 ratio. My strength in this unit was punnet squares and the types of inheritance because I learned some of the topics in 7th grade biology. My weakness was in the process of meiosis and mitosis because it was complicated and we did not spend as much time on it as genetic inheritance. The genetic infographic at times helped or hurt my progress on the unit. It hurt my progress sometimes because we would spend the class doing the infographic rather than doing something that would cement the information learnt in the vodcasts. However, it also helped because we would have a general idea of a topic before learning it in the vodcast which made it easier to understand. Click here to visit my genetic infographic. By having to do the infographic, we learned a lot in doing projects. One thing we had to learn to do was create a diagram of the infographic before making it. This planning was essential because without it, we would have no plan in the infographic and it would take forever to create a result and it would make the project seem overwhelming. These were the main things that we focused on while completing this unit. Thank you for reading.

Genetic Infographic

Go here to get a better view for my infographic

Photosynthesis Virtual Lab

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 absorb light through chlorophyll and chlorophyll absorbs the most violet light and the least green light, then the plants with green light will grow the least and the plants with violet light will increase the most.

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?

We tested our hypothesis by changing the color of the light and measuring how much the plant grew. We repeated it three times with different plants.

Results:

Filter Color	Spinach Avg. Height (cm)	Radish Avg. Height (cm)	Lettuce Avg. Height (cm)
Red	18	13	11
Orange	15	8	7
Green	2	1	3
Blue	19	14	13
Violet	17	11	9

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.

Our data both supported and refuted our hypothesis. It supported our claim the green would grow the least. We found however that instead of violet light causing the most growth, it was blue light that caused the most growth. We also found that spinach grew most and lettuce and radish grew about equally less than spinach.

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

We concluded that blue light causes the most growth in plants. The blue light had the highest plant height in the end of the 30 days. We also found green light caused the least amount growth because all the plants with green light were very short in the end of the 30 days.

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

We would expect that it would grow more than anything else because all colors of the light spectrum are being added up. It would have the effects of all the best lights combined.  

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: How does carbon dioxide affect the rate of oxygen produced by the plant?

Hypothesis: If carbon dioxide is essential to photosynthesis and oxygen is a byproduct of photosynthesis, then the more carbon dioxide added to the water, the more oxygen is produced.

Experiment: The variables that remained constant in the experiment were the temperature of the water at 25 degrees, light intensity at power 50, and light color as white. The independent variable in this experiment was the amount of carbon dioxide in the water. The dependent variable was the amount of bubbles produced in 30 seconds. The control is when no carbon dioxide is added. The two levels are no carbon dioxide and half a bottle of carbon dioxide.

	No Carbon Dioxide	Half Bottle of Carbon Dioxide
Trial 1	19	33
Trial 2	19	33
Trial 3	19	33
Average	19	33

Conclusion:

In this lab, we asked the question of how carbon dioxide affects the amount of oxygen produced by the plant. I found that the more carbon dioxide added to the water, the more oxygen produced by the plant. We measured this in how many bubbles were produced in 30 seconds. We found that on average, the water without carbon dioxide added produced 19 oxygen bubbles in 30 seconds while the water with carbon dioxide produced 33 oxygen bubbles in 30 seconds. This makes sense because photosynthesis requires carbon dioxide and oxygen is a byproduct of photosynthesis. This data supports our claim that the more carbon dioxide added to the water, the more oxygen is produced by the plant.

We did this lab to demonstrate how carbon dioxide affects the production of oxygen in plants. This helped me better understand the process of photosynthesis and what are the products and reactants of photosynthesis. This could be applied to other real world situations such as having an ideal amount of carbon dioxide in a greenhouse.

Microscope Lab

We used 400 power to take a picture of this spiryoga. It is unique because it is unique because it is all in a very straight column. We observed that the cell looked very rigid and straight. This is a autotrophic eukaryote. 

We used 400 power to take a picture of this cyanobacteria. It is unique because it was one of the first bacteria and it changed the Earth by making oxygen. We observed they were like beads that were connected. It is a prokaryotic eukaryote.

We used 100 power to view this amoeba. It is unique because of its pseudopods which make it look like a ¨blob.¨ We noticed that it was very big because this picture only used 100 magnification when most of the others required 400. It is a eukartyotic heterotroph.

We used 400 power to observe this Euglena cell. We noticed it is very tiny. We could not see the chloroplast and we could barely see the flagellum. It is both autotrophic and heterotrophic and it is eukaryotic. 

We used 400 power to see this ligustrum. It is unique because there are a lot of cells clumped up. We noticed there was a red center which was a vein. It is a eukaryotic autotrophic cell.

This picture of bacteria was taken with 400 power. It is unique because it is very abundant and there are countless bacteria everywhere. We observed that the bacteria looked like small squiggles. It is a prokaryotic heterotroph.

We used 400 power microscope to capture this picture of the animal tissue. It is unique in that it is made in bands of fibers known as striations. We observed that the cells were long and thin. We determined that this was a heterotrophic eukaryotic cell.

In this lab, we observed microscopic organisms under a microscope and labelled their parts. We were able to see most things except for the flagellum of protists. The autotrophs had chloroplasts and were usually smaller than their heterotroph counterparts. The heterotroph were usually eukaryotic. The eukaryotes were much bigger than prokaryotes.

Diffusion Lab

The purpose of the Diffusion Lab was to see what happens to eggs through the process of diffusion. We did this by putting 2 eggs in different cups, one containing corn syrup and one containing deionized water. We first measured both eggs in their circumference (the short way) and their weight. We then put the eggs in their cups and left them their over the long weekend. We then carefully took out the eggs from their containers and measured their sizes to see whether the circumference and weight had changed. We found that the eggs placed in the corn syrup had deflated and lost weight. On average, they lost about 42.17% of their mass and had a 19.68% decrease in circumference. This happened through the process of diffusion. The sugar in this case was the solute and the water was the solvent. There was more solute (sugar) on the outside of the cell so it tried to get in but it can because its to big so instead the water from inside the egg comes out where there is less water. Cells change in response to their environment because of diffusion. Putting them in the water would cause the egg to inflate because their is more solvent (water) outside the egg and more solute inside the egg. When you put it in the sugar water, it will deflate and water will be taken out of it.
This lab helped demonstrate the process of diffusion. It showed the effects of diffusion on eggs and these can be applied to actual cells. It shows what happens when you put a cell in certain conditions such as having too much or too little solute. Fresh vegetables are sprayed with water so that they don inflate and remain rigid. Salting effects the plants by causing them to wilt.  This is because there will be water coming out of the plant cells because of so much solute outside. This will stop the turgor pressure and wilt the plant. We can make a new experiment seeing the same thing except having salt and not sugar. We can see the different effects of this.

Egg Macromolecules Lab Conclusion

The purpose of the Egg macromolecules lab was to identify specific macromolecules in an egg. We did this by adding a solution to specific parts of the egg and depending on whether on not they changed color, we could determine whether the macromolecules was present. We rated the amount of the macromolecules present from a scale from 0 to 10, 0 meaning we did not find any of the macromolecules and 10 meaning we found a lot of macromolecules present. If lipids are known to make the cell membrane, then we should expect to find lipids in the cell membrane. If yolk is where the chick if formed and it needs structural proteins to grow, then we cane expect to see proteins in the yolk. If proteins are found in the cytoplasm of the cell, then we can expect that we will find proteins in the egg white. We found that there are a lot of lipids present in the cell membrane. When adding a chemical known as Sudan III to the parts of the egg, it is supposed to be red if lipids are not present, and red to orange if lipids are present. When we added Sudan III to the egg membrane, it became very orange. We rated this a 7 on the macromolecules scale. This makes sense because the cell membrane is mostly made of lipids. When adding copper sulfate and sodium hydroxide to the parts of the egg, it should turn from blue to purple if proteins are present, and stay blue if proteins are not present. When we added copper sulfate and sodium hydroxide to the yolk, it became purple. We rated it a 5 on the macromolecules scale. This makes sense because proteins would be needed in the yolk of the cell where the chick is developing. We also found that doing the same test to the egg white would bring similar results. We also rated it a 5 on the scale. This makes sense because the cytoplasm is where a lot of protein is found. Also, eggs usually have their proteins in the egg white so that the chick will develop.
While our hypothesis was supported by our data, there could have been errors due to many reasons. On contradiction was that some of the lab partners reported seeing colors from the test that should not have been seen. One example is in the monosaccharides test where we found the color purple in the membrane even though it is only supposed to turn blue green and orange. Another problem we found was that many of the numbers seemed off compared to the color observed. The color it was supposed to turn might not be found but it was still given a high rating on the scale. One example was the protein lab where egg white got the color murky white but it was given a 5 on the scale. It should have turned either blue if it was not present or purple if it was. Another problem was that the rating from 1 to 10 is subjective because the numbers are not relative to anything. One recommendation I have is to have multiple people work together to eliminate errors like the ones mentioned above. Another recommendation I have is to have the scale relative to something like showing a picture example of what would be a 0 and what would be a 10.
We did this lab to see what macromolecules we would identify in the egg. We learned from this lab what macromolecules are found in certain parts of the cell. It helps reinforce your understanding of macromolecules and their use in the cell. You can make assumptions for why you found certain macromolecules in certain parts of the cells. This could be applied to other situations. You could use this to find the most nutritional parts of the cell such as the yolk and egg white because they have the most protein. It could also be used for real cells found in plants and animals to better understand how their cells work.

Sweetness Lab

We did a Sweetness Lab in class so that we could determine how the structure of a carbohydrate affects its taste. Based on the evidence collected in this experiment, I think that the less complex a sugar is, the sweeter it gets. This means that monosaccharides are the sweetest type of sugar and the polysaccharides are less sweet. This is proven by the results of our experiment. Glucose and Fructose, which are monosaccharides scored the highest on the sweetness scale. Polysaccharides such as Cellulose and Starch, scored lowest on sweetness scale. This proves that the less complex a sugar is, the sweeter it is.

There are three classes of carbohydrates: monosaccharides, disaccharides, and polysaccharides. The monosaccharides are used for short term energy because they are easier to break down into energy. Disaccharides are harder to break down but still relatively fast. Polysaccharides are used for longer term energy and they take longer to break down. As a result, it can be used for energy longer than monosaccharides and disaccharides.
Not all the testers got the same result as me. This is probably because we all are different and perceive taste differently. Rating them by a number system is difficult because the numbers are opinions. The scale we used for this experiment was 0 - 200 with sucrose being 100. One tester 180 could be another testers 140. Taste is a qualitative observation that we try to convert to a quantitative observation, so it is difficult to get accurate results.
According to the Public Medical Health Records, "Taste was a sense that aided us in testing the food we were consuming." Foods that are sweet are sweet because they have sugar. Sugar used to be less common so when one obtained sugar, they would wan more of it. This is why sweet is a very pleasant taste compared to bitter which indicates possible poison. This is also why we perceive taste differently. It depends on how much sugar the body thinks it needs. It makes it sweeter so we are more tempted to eat it.

Jean Lab

We did our first lab of the year in which we tried to find what composition of water and bleach, faded jeans the best. We concluded from our experiment that 12.5% bleach was the best option because it had the best fade with the least fabric damage. We rated the fabric damage and the color removal from a scale from 1 to 10. We had three jean squares and we rated each and took the average. We used the following concentrations: 0% (control), 12.5%, 25%, 50%, 100%. We chose the 12.5% because it had a good color removal number and the lowest fabric damage other than water. We also had to qualitatively see which one was the best and the 12.5% had a really good fade.

Although we reached a reasonable conclusion from the data, it had many errors in it that could have influenced the result. One was that are timing was pretty bad and we changed how we counted time from the beginning to the end. The main one was that we only started the clock when it was completely submerged in the bleach. We didn't do this in the beginning but we started doing this which increased the time and probably influenced our results. This might be one reason why the 100% bleach didn't have a good fade even though it should have been the strongest. Another major problem with our experiment was that we didn't use the same type of jeans so some of them were already darker and lighter than each other. This definitely impacted our results because some of the data is very inconsistent and doesn't make sense like the stronger bleaches having less of an effect because the jeans were darker. The final error that was probably made during this experiment was that all of it is personal opinion. The number we assign each pair of jeans isn't based on anything so if another group were try this again, they would get different numbers and a different result even if the experiment was replicated perfectly. If someone else were to do this experiment, I would have two recommendations. My first recommendation is to  plan the timing ahead of time so that you know what to do when you are doing the experiment and changing anything while the experiment is going on. My second recommendation would be to use the same pair of jeans for all the jean squares so that everything is consistent. Also you should take pictures as a before and after. 

The purpose of the experiment is to find the best composition of water and bleach to fade pants without resulting in too much damage. I learned that having a constant environment is very important to science experiments which helps better helps me understand how to have a good lab. This lab could actually be used in real every day life if I wanted to fade my jeans. This is a popular fashion trend so people could know the best ratio of water to bleach when fading their jeans. In conclusion, even though this lab was a success, we had many variables that we didn't control which could have affected the experiment. We learned a lot from this experiment and this will help us for the next time we do a lab.