Protein Synthesis Lab Analysis/Conclusion

In order for the body to make proteins, first the DNA must be transcribed into RNA in the nucleus. It is then converted into messenger RNA (mRNA) and sent out of the nucleus to a ribosome. Instead of thymine (T) though, RNA, single stranded, has the base pair uracil (U). The RNA Polymerase pairs the corresponding nucleotides when it is transcribing DNA into RNA. In the ribosome, the RNA is translated from nucleotide "language" into amino acid "language." The RNA is read three letters at a time, called a codon. Each codon codes for an amino acid. These amino acids are joined together to form a protein.

In the lab we experimented with different kinds of mutations that could potentially occur while DNA is being transcribed into RNA. One example of a mutation we tried is a substitution, where one base pair is substituted for another. This mutation had the littlest effect on the final protein. In the worst possible cases it could change just one amino acid, in many cases it could have no effect. The frameshift mutations had a much greater effect, particularly insertion. Almost all of the amino acids were changed when a base pair was inserted, therefore changing the protein entirely. The mutation is worse if a base pair is inserted at the beginning, because more amino acids are changed. 

I chose an insertion when we were asked to choose our own mutation that would make the greatest difference, therefore the greatest damage to the protein. I chose to insert a G directly after the start codon. Inserting a base pair at the beginning made a huge difference to the protein, because it changed all amino acids in the protein except for Met. My mutation changed the protein the most out of all the ones I tried in the lab. This was because the mutation occurred at the earliest time possible. An insertion also changes the amino acids completely. 

An example of a mutation that occurs in humans is Tay-Sachs disease. It is very rare but depending on the onset can be deadly. The autosomal recessive genetic disorder destroys nerve cells in the brain. Gangliosides are fatty substances which are necessary for development of the brain. Normally, gangliosides are broken down, but people who have Tay-Sachs disease lack the enzyme that breaks them down. This destroys the functioning of the nerve cells. There is a mutation on the Hex A gene that causes Tay-Sachs. 

Human DNA Extraction Lab Conclusion

In this lab, we asked how DNA can be separated from cheek cells in order for it to be seen and studied? We found that in order to extract DNA from cheek cells, three steps must be followed: homogenization, lysis, and precipitation. We accomplished this by homogenizing the cell's tissue with polar liquid. This breaks down the cell membrane and nuclear membrane of the cheek cell. We scraped off some of our cheek cells with our teeth, then swiveled it around in our mouths for 30 seconds. Afterwards we added soap, which was involved in lysis (the disintegration of the cell membrane). We used pineapple juice to break down histones found in DNA that the DNA wraps itself around. This is because pineapple juice, like a few other liquids, has catabolic proteases, enzymes, that help to break down the histones. Then we poured cold isopropanol alchohol onto the test tube and due to the nonpolarity and the polarity of the DNA the DNA became a precipitate and rose to the top of the isopropanol alchohol layer. This data support our claim because in order for DNA inside the nucleus to be seen, first the cell membranes, plasma membranes, and nuclear material must be broken down.

While our hypothesis was supported by our data, there could have been possible errors due to gargling the Gatorade for less than exactly 30 seconds. This would have affected the experiment in that all of the cheek cells would not have been caught in the solution. Also when we left the test tubes in the rack for observation, we did not time the 5 minutes exactly and this may have not allowed the solution to settle enough. I think our group should have used timers for both the gargling of Gatorade and the test tube 5 minute observation to make the experiment more accurate.

This lab was done to demonstrate our understanding of DNA and the process of extracting DNA out of a cell. From this lab I was able to understand how DNA is located in the cell, and that all the membranes that must be broken down differently in order to see the DNA. Based on my experience in this lab, I can apply this same process to extracting DNA from any cells and understand how the process works.

Unit 4 Reflection

This unit focuses on genetics and why individuals have the traits that they have. We started the unit by studying the cell cycle, the way that our body cells formed and the way that many asexually reproducing species reproduce. The cell cycle consists of interphase (the copying of DNA), mitosis (DNA and organelles split), and cytokinesis (the cell officially divides in two). This was one of my strengths; I was able to understand the different phases and the purpose of the cell cycle. We also learnt about asexual and sexual reproduction, and the pros and cons of both. Asexual reproduction yields tons of offspring and is possible without a mate, but there is no genetic variation and the species will not stand the test of time. Sexual reproduction has lots of genetic variation and creates competition for mates, but it requires time and energy and exposes you to parasites. I felt that this topic was fairly straightforward. Meiosis is the process in which gametes (sex cells) are formed. In humans, these are the sperm and egg cells. They are haploid, meaning that they have half the normal number of chromosomes. This is so that during recombination, the new zygote cell will be diploid. I felt strong on this topic. I feel that determining incomplete dominance from codominance as well as looking at dominant and recessive alleles in punnett squares is one of my strengths.

The Law of Segregation and the Law of Independent Assortment are definitely my weak areas. I think that if I try to draw meiosis from memory with the different alleles on each chromosome, I will be able to conceptualize the laws better. I understand the basic definitions, but don't know whether I'll be able to apply them to a specific scenario yet.

I definitely have a better understanding of genetics, punnett squares, and I feel like I am more knowledgeable about why individuals look and are the way they are. I have learnt a lot from doing the infographic; it helped me understand the concepts better when I did research and created my own graphics and diagrams. I would like to learn more about the common human genes that are more complicated than basic dominance and recessiveness. I am also interested in learning more about genetic disorders.

My VARK learning style is multimodal. My scores were visual 7, aural 6, speech/writing 5, kinesthetic 4.  Kinesthetic is my lowest, because I don't tend to learn from simulations as much. These are the scores I would have expected, because diagrams and charts tend to stick in my mind. I will focus on learning and understanding diagrams from the vodcasts and the textbook; during tests I often find myself trying to visualize those.

Coin Sex Lab Relate and Review

         In this lab we looked at how the probability of having a child with a certain trait was related to actually predicting how many children would actually have that trait. In order to illustrate how genes separate during meiosis, we used coins as props. We determined what possible genotypes we had by looking at our phenotypes; for example if a person had a phenotype of brown hair their genotype could be either BB (homozygous dominant) or Bb. One each side of the coin we wrote one allele (if an individual was heterozygous for brown hair they would write "B" on one side of the coin and "b" on the other.) When we dropped the coins onto the table, it was random which allele landed face side up. This is a simulation of meiosis. When we subsequently paired our coin with our partner's coin to find out the offspring's genotype, we simulated sexual recombination.
         We did a dihybrid cross--we looked at the gene for having brown vs. blonde hair, and the gene for having brown vs. eyes at the same time. We crossed two individuals who were double heterozygous. Their genotypes were BbEe (B=brown hair, b=blonde hair, E=brown eyes, e=blue eyes). The expected phenotypic ratio was 9 brown hair brown eyes: 3 brown hair blue eyes: 3 blonde hair brown eyes: 1 blonde hair blue eyes. Our results were 8 brown hair brown eyes: 3 brown hair blue eyes: 4 blonde hair brown eyes: 1 blonde hair blue eyes. Probability says how likely something is to happen, but the certainty of something actually happening is different. Our results were close to the expected, but slightly different.

Probability is a prediction of the likelihood of an event occurring. If thousands of trials were to be done, the law of averages would ensure that the probability of getting a certain trait was met. However, if a person were to flip a coin 5 times, it is entirely possible that they could flip 10 heads in a row, even though the probability of flipping a head is 50%. Most humans don't have that many offspring compared to other species, and often times probability is inaccurate in predicting offspring's traits.

Genetics can be seen everywhere in our life. Genes are the reason why people have certain traits and the reason why people look the way that they do. I have wondered in the past why some children have completely different traits, such as blonde hair or blue eyes (autosomal inheritance), than their parents do. Now, with the knowledge of punnett squares and different alleles, I can answer that question. Also, knowing how X-linked inheritance works, I can understand why certain people I know are colorblind, even if neither of their parents are.

Genetics Infographic

https://magic.piktochart.com/output/9381881-genetics-infographic

Unit 3 Reflection

Throughout this unit, there were a variety of topics some of which I found to be fairly straightforward, and some which I found difficult. Coming fresh off of the macromolecules unit, I found it helpful to see some of the ways in which carbohydrates, lipids, and proteins are found in cells. Carbohydrates are found in chains around the cell membrane, the cell membrane is made up of phospholipids. Channel proteins as well as proteins made by ribosomes that are found inside the cell.
We also discussed the different parts of a cell; we likened the cell to a factory. There are many organelles that have very specialized jobs: the nucleus holds the DNA that contains instructions for all the cell's activities; the mitochondria are the "powerhouses" and carry out cellular respiration; the ribosomes do protein-synthesis; the ER packages and completes protein-making...etc. I found this topic to be one of my strengths because the different functions of how each organelle works is easy to remember by comparing it to a job in a factory; such as comparing the Golgi Apparatus to a UPS.
We also studied how the cell membrane is selectively permeable, and only some substances can pass through. I felt as though diffusion was definitely one of my strengths: understanding how particles move from a high concentration to a low concentration until equilibrium is reached, at which point particles move back and forth in every direction. I feel as if I have a grasp on the differences between osmosis, diffusion, and facilitated diffusion. Active transport requires energy to be put in from the cell, whereas passive transport does not.

Photosynthesis and respiration were very detailed and went far beyond what I had learnt in the past about them, and in this unit we learnt a lot more about the chemistry behind the basic reactions. Photosynthesis was difficult to understand at first, but with more drawings and with reading the information from multiple sources, I began to grasp it. Inside the mesophyll cells, inside the chloroplasts, photosynthesis occurs. The "photo" part of the reaction happens in the thylakoids of the granum, and the "synthesis" part happens in the stroma of the chloroplast. I feel that I still do not have a full understanding of cellular respiration, although I basically understand that it takes place in the mitochondria and that the three stages are glycolysis, the Krebs cycle, and the electron transport chain. I think with more practice and more re-reading of the topic, I will be able to strengthen this weak area.

From this unit, I learnt that drawing diagrams (and color coding them) is extremely helpful and is great for really understanding the information. I learnt how to properly focus a microscope and reinforced the do's and don't's of how to use it. I learnt more about the structure and function of cells as well.  I want to learn more in the future about the chemistry behind the Krebs Cycle and the Calvin Cycle. I wonder how the first scientists even imagined that cells could exist, and I think it is fascinating how they designed the microscopes. In order to study, I am going to re-draw the diagrams and look at unlabeled diagrams to try and name all the parts.

Egg Diffusion Lab

In this lab we wanted to further explore how diffusion works, and we wanted to find out how and why a cell's internal environment changes when its external environment changes? We first took two eggs and soaked them in vinegar for 24-48 hours. After this amount of time, the calcium carbonate shell had been dissolved by the acetic acid. After washing and recording the mass and circumference of the eggs, one egg was placed in deionized water and the other was placed in sugar water. We let the eggs sit for 24-48 hours, and then recorded the new circumference and mass.

When the sugar concentration of the solution increased, the mass and circumference of the egg decreased, and the egg began to look shriveled up. The mass of the egg in sugar water decreased on average by 47.25% and the circumference decreased on average by 22.94%. In the egg that was placed in deionized water, the sugar in the macromolecules were the solute inside of the egg and water was the solvent outside. From a desire to reach equilibrium, the solvent wanted to move by diffusion from a low concentration of solute (outside cell) to a high concentration of solute (inside cell). Therefore, the cell gained water and grew. This is an example of a hypertonic solution.

It is desirable for cells to have an equal concentration of solute and solvent inside and outside of the cell. The cell membrane is semi-permeable and does not allow for the solute to leave the cell or enter the cell. The conditions of the cell are only changed by the movement of solvent. This is an example of passive diffusion. The cell expanded when put in vinegar, it shrunk when put in sugar water, and it grew when put in water.
In class we have learned about molecules which move from a high concentration to low concentration when there is an unequal concentration of solute or solvent.

Since cells grow when they are put in water, fresh vegetables in markets will be sprinkled with water to keep them fresh and help them to not shrivel up. Salt is sometimes sprinkled on roads to melt ice because since salt is a solute, the ice (which is water and is a solvent) the solvent will move outside and in order for it to do this it must melt. However, if the salt is sprinkled along the roadside where there are plants, the plants will die. This is because the plant cells will shrink when exposed to too much salt, and when they shrink, they will not function as well.

I would like to see the effect of putting salt on plants in action and other such experiments that illustrate cells shrinking due to too much solvent. Also, I would like to know if the shriveled up egg was placed back in deionized water, how long would it take to be revived?

Data Table for Eggs in Deionized and Sugar Water

Top: Egg that was placed in sugar water
Bottom: Egg that was placed in deionized water