Unit 5 Reflection

      This unit was about how information flows from DNA to RNA and then to proteins. We learned how DNA codes for all of our traits and the process of protein synthesis and how ribosomes read RNA, which gives us the phenotypes we have, and even mutations, of which there are two types, point and frameshift. The processes involved in this "central dogma" of biology include protein synthesis, which is a two part process of transcription and translation where DNA is copied and the nitrogen bases are read, semi-conservative DNA replication, where the two new strands contain half of the original strand, and DNA regulation, which determines which genes are expressed and which aren't.

http://thebiologyprimer.com/transcription-rna-processing-and-translation/

       In my opinion, the majority of the concepts in this unit was easy to understand. I really understood the process of protein synthesis and how amino acids are made. I also know the different kinds of mutations fairly well, as the protein synthesis lab really helped me understand what exactly happens to the DNA and the resulting protein. Some concepts were a little more vague at first to me, like the gene regulation and expression in. Now I understand the process of gene regulation in prokaryotic cells, but I still need to review how it works in eukaryotic cells. I want to learn more in detail about protein synthesis and why the nitrogen bases in DNA pair up the way that they do. 

      I think that I am understanding the concepts even more than I did last unit. I am definitely putting in more effort into trying to understand what we learn, rather than just blindly memorizing facts like I used to do. According to the VARK questionnaire that I took last unit, I learn best by reading and writing, so I took the approach of reading over my notes and writing my own notes on what I think that I need to study for the test. I remember things better if I physically write them with my own hands, so that is how I've started to prepare for the final exam. I think in the future I still need to work on my time management in terms of studying, as I usually try and cram in the last few days before a test.

Protein Synthesis Lab

      In this lab we asked the question, "how does the body produce proteins?". Protein synthesis has two stages, transcription and translation. Transcription happens first in the nucleus. First, a copy of a section of DNA is made, called RNA, and the base thymine is replaced with uracil. Then the RNA moves to the cytoplasm, where translation happens. In the cytoplasm, a ribosome reads three base pairs at a time, this is called a codon. Each codon codes for a different amino acid. The amino acids bond together to form a long chain, which become a protein.

http://www.yourgenome.org/facts/what-is-a-mutation

      A mutation is any change in the sequence of the DNA. There are point mutations and frameshift mutations. A substitution is a point mutation that substitutes one base pair for another. For frameshift mutations, insertion is where an extra base pair is inserted, and deletion is where a base pair is removed. From the experience with the lab, the frameshift mutations seemed to have a greater effect than substitution. With substitution, only one of the amino acids is changed, but with insertion and deletion, the whole sequence is shifted, which can completely change the codons and they amino acids produced. Also if the mutation is earlier in the sequence, then it has a greater effect, as the rest of the sequence after the mutation is shifted, resulting in more change. However if a mutation happens later in the code, than it only effects the DNA after, which is a smaller amount.

http://study.com/academy/lesson/insertion-mutation-diseases-examples-quiz.html

      When I chose my mutation, I chose to do a substitution to see if it could have a huge effect like a frameshift mutation. I changed the DNA at the very beginning, resulting in the absence of a start codon, so there was no protein. I think having the mutation towards the beginning of the code has a higher chance of making a bigger change to the amino acid sequence.

      Mutations are very common and they can have little to no effect, or they could have a very dangerous or even fatal effect. Mutations effect the amino acids in proteins, so they could possible alter how your body functions, and cause diseases etc. Hutchinson-Gilford Progeria Syndrome is a very rare disorder caused by a mutation on the LMNA gene which produces the Lamin A protein. Progeria caused rapid aging in children, and children usually die of heart disease at around age 14. Symptoms can include aged skin, loss of body hair, stiff joints, and more. 

https://www.sciencenews.org/article/family-takes-progeria-%E2%80%98life-according-sam%E2%80%99

DNA Extraction Lab

      In this lab we asked the question: How can DNA be separated from cheek cells in order to study it? We found that we can extract DNA through a three step procedure of homogenization, lysis, and precipitation. We collected the cells with gatorade and added salt. We then added soap to lyse, or rupture, the cell membrane so all the contents of the cells released into the gatorade. We then added pineapple juice, which is a protease that breaks down the histones (proteins) that the DNA wraps itself around. Lastly we added a nonpolar liquid, alcohol, which made the polar DNA separate from the gatorade solution, successfully extracting DNA from our cheek cells.

     

      While our observations supported our hypothesis, there could be possible errors due to failure of properly inverted the test tube to mix the contents. If the tube was inverted too quickly, then air bubbles could have formed, and according the information about DNA extraction, air bubbles can get caught in the double helix structure. In the procedures I recommend saying to invert the tube slowly. Failure to add the alcohol in could also cause errors. If the alcohol was added too quickly, than it would mix with the gatorade, which would not allow for the DNA to separate out into a polar solution. I recommend to hold the test tube at as much of as angle as possible and to pour the alcohol very carefully and slowly.

      This lab was done to demonstrate the process of DNA extraction and what happens to the DNA through this process. From this lab I learned how to extract DNA with materials that anyone has access to. Based on my experience from this lab, if I ever entered a field like genetics or forensic science, I could use this procedure to extract DNA from important or useful sources.

A clump of DNA

Unit 4 Reflection

     In the coin sex lab, we used coins to demonstrate the recombination of alleles. It also demonstrated how probability comes into play when determining an individuals genes, as just like you can't be completely sure if a coin will land heads or tails, you can't be completely sure what the genotype of your offspring will be. This lab showed Mendel's law of Segregation when the different alleles of genes were separated randomly, as they do during meiosis. We first used a monohybrid cross of a male and female to test the probability of having a male or female child, and we also crossed a homozygous non-bipolar person with a heterozygous carrier of bipolar disorder. These were both examples of autosomal inheritance. We also crossed two individuals to see if the offspring would be color blind, and x-linked recessive trait. Males are most likely to be color blind as females have a second X chromosome to mask the recessive allele. Last we did a dihybrid cross to see the hair and eye color of the offspring, and the expected phentoype was 9:3:3:1, and ours was similar with 10:3:2:1. We can see the probability of our offspring having a specific trait in real life, but we can't make a sold prediction, as according to Mendel's laws, the separation and recombination of alleles is random.

      This unit was all about sex and genetics.We learned about processes like mitosis and meiosis and the different types of reproduction. We also learned about different components of genetics, including how genes and alleles work and their significance. I personally enjoyed learning about genes, alleles, and punnett squares. It was more confusing for me to remember the details about mitosis and meiosis, so I need to take more time to study those concepts.

      I learned many new and interesting things over the course of this unit. Some of the concepts, like dominance, were a review, but other topics, like the different types of inheritance, were new. This unit definitely related to the real world/ daily life a lot, as many our traits are determined by genetics and processes learned in this unit, like meiosis. Doing the infographic also enforced a lot of these concepts and helped me have a broader understanding of all of them. It helped me recognize the main concepts of the unit. In the future I would like to learn more about the specifics of each chromosomes, and other cases like genetic mutation, which we didn't really touch on.

      After taking the VARK Questionnaire, these were my scores.

• Visual 1
• Aural 4
• Read/Write 7
• Kinesthetic 4

      I was really surprised with these results because I always thought that I was more of a visual learner, however according to my results, I learn the least visually. When studying for the upcoming test, I am going to take a more written approach than a visual one. I remember information that I see written down or that I write myself, so I might make some flashcards.

Why is Sex so Great?

     Sex is a driving force of life, and it is essential to help species thrive. While asexual reproduction has its benefits, sexual reproduction is more efficient and advantageous.With asexual reproduction, each female only needs to have one offspring for the population to stay the same, however with sexual reproduction, two offspring are needed. Asexual reproduction also has disadvantages. Since all asexual organisms like the philodina have very similar genes, it is easier for disease to take them over, as they are all almost the same.

     In "Wholly Virgin," it is said that the Philoldina Roseola has reproduced asexually for the past 85 million years without meiosis. The chaetonotid gastrotrichs is a species that seemed to be asexual at first, but it was found that they actually thrived by hiding the males in the roots of the weeds. Bacteria also reproduce asexually by dividing, while eukaryotic organisms like the moose reproduce sexually through meiosis after the fusion of sperm and egg.

      In this unit I want to learn exactly how mutations happen and what the exact process is for asexual reproduction.

Unit 3 Reflection

     Unit 3 was about cells and the processes that take place in them. We learned about the different parts of the cells and their functions, and processes like osmosis, photosynthesis, and cellular respiration. We started with the basic functions and types of cells, and then we went into more detail about all the complicated things that happen inside of cells. Overall, this unit was very interesting and packed with information. Most of the general information, like the different organelles and functions were easy for me to understand. I also had an easy time understanding the processes of osmosis and diffusion, and how they take place. It was a little more difficult for me to remember the details of photosynthesis and cellular respiration, as they are both very complicated and detailed.

      Throughout this unit I learned that visual components, such as pictures really help me grasp a concept even better than just reading about it. For photosynthesis, the diagrams that we copied down in class really helped me understand the process better. I also learned that I have learned a lot about these concepts before, and the vodcasts just help me revive and enrich the knowledge I already have.

     In the future, I want to learn more about the smaller details of cells that were not covered in the vodcasts. I would also like to learn more about how all the organelles in cells work together. I also wonder about the huge variety of cells that exist and what makes them all unique. For the test I plan on studying the diagrams and pictures more than I did for previous tests.

Egg Diffusion Lab

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

     In this lab we placed two different eggs of about the same size in deionized water and corn syrup to see the effects on the circumfrence and mass of the eggs. Both the eggs had their shells dissolved off in vinegar, so substances could leave and enter the egg.

     According to the class data, when the sugar concentration increased, both the mass and the circumfrence of the egg decreased. This is because the corn syrup is a hypertonic solution. There is more sugar, which is a solute, outside of the egg than inside of the egg, so water and solvents from inside the egg leave, making the egg smaller in size. According to www.exploratorium.edu egg white is about 90% water and corn syrup is about 25% water. Due to this the water moves from an area of high concentration to an area of low concentration to create equilibrium with the solute. This is an example of passive diffusion.

     As the external environment of the egg changed in terms of concentration of water and solute, the interal conditions of the cell changed as well. When the outside of the cell was highly concentrated with solute, the water diffused out from inside the cell, and when there was less solute outside (deionized water) the water diffused into the egg. And when the egg was put in vinegar, the shell was dissolved off, leaving only the membrane.

     The lab demonstrated the biological of diffusion, which we learned in class. The lab was a good way of showing how the concentration gradient can really affect the size of the cell. We learned how cell membranes don't allow large solute molecules through, which was shown to be true by the lab, as the corn syrup didn't enter the egg, only water came out.

      Fresh vegetables are sprayed with water at markets, to prevent them from drying out. The water gets absorbed into the vegetable, as there is probably more solute in its cells. When salt is sprinkled onto the road, plants along the road are dried out and dehydrated. Salt is a solute and since, there is a higher concentration of salt outside of the plant, water diffuses out of the plant cells, drying out the plant.

     Based on this experiment, I would like to test how much water a cell can hold before popping. I would also want to find a way to maximize the amount of water it can hold, or maximize the amount that the cell can shrink as water diffused out. 

Egg Cell Macromolecules Lab

      In this lab we asked the question: Can macromolecules be identified in an egg cell? We identifies which macromolecule was present in each part of the egg. We found that the egg membrane tested positive for lipids because it turned from red to orange in Sudan III. Lipids are found in egg membranes, because cell membranes, which are the equivalent of egg membranes, are made of phospholipid bilayers. We also found that the egg white contains protein because it turned the blue biuret solution purple. The egg white would contain protein because it is like the cytoplasm of a cell, which contains many proteins and ezymes, which are a type of protein. Finally, the egg yolk tested positive for protein because it turned the biuret solution purple. This is because the yolk is like the nucleus of the cell, which contains structural proteins.

     A possible error that could have occurred was two parts of the eggs accidentally mixing together. For example, if some of the egg white got into the beaker with the yolk, then the yolk may have tested positive for a macromolecule that was actually in the egg white. Another error could have been that there was not enough of each substance in the test tubes, so the color change may have been less drastic or obvious. This could make it seem like there was a smaller presence of the macromolecule, even when there was a lot of it. Due to these errors, I recommend devising an easier way to separate the different parts of the egg, and maybe have students put a larger amount of each part in the test tubes.

     This lab was done to demonstrate that different macromolecules are found in different parts of cells. This lab enforced the knowledge of where different macromolecules are found in the cell, which was taught in the vodcasts. For example, we found that the egg membrane had lipids in it, which was explained in the vodcast. This knowledge can help people know what they are getting from eggs. For example, body builders need protein to build muscle, so they can eat the yolk. 

Unit 2 Reflection

      In this unit we learned about biological units on the smaller scale and how they interact with each other. First, we learned about properties of atoms and molecules, including adhesion to other substances, cohesion to itself, and how polar molecules attract to each other. We then learned about the 4 main large molecules (macromolecules) which are carbohydrates, lipids, proteins, and nucleic acids. Carbohydrates are the main source of energy for consumers, lipids store energy, proteins serve many different functions such as cell walls and enzymes for chemical , and nucleic acids serve as sources of information.

   

     This unit was interesting, and overall I think it went very well. I was able to understand the information presented with little difficulty or confusion. I learned that reviewing over the notes right after watching the vodcasts helped me retain the material even better. Throughout this unit, I learned a lot about how the topics taught are relevant to our daily life, for example, how the carbohydrate, fructose, is present in a large amount of the foods we eat everyday.

     Some of the information I learned was enforced through the sweetness lab and the cheese lab. In the sweetness lab, I learned how the different ringed structures of carbohydrates can effect the sweetness of a sugar. I found out that the monosaccharides, or the carbohydrates with one ring, are sweeter than the polysaccharides, or the multi-ringed carbohydrates. In the cheese lab I saw a real life example of how enzymes can be affected. The enzymes of rennin and chymosin worked different different paces under different temperatures and pH's, which showed how an enzyme can be denatured. The enzyme virtual lab was also a fun way of demonstrating how a drastic change in pH and temperature can decrease the amount of product created by an enzyme.

     A topic that I want to learned more about is DNA and RNA. I would like to learn more about the difference and their different functions. I am also curious as to how the string of DNA is translated into characteristics like eye color and height.

Sweetness Lab

     This lab was done to find the relationship of a carbohydrates structure to its sweetness. According to results from the experiment, monosaccharides are the sweetest, and polysaccharides are not sweet, however, they are bland or slightly bitter. In our experiment, we found that fructose was the sweetest along with sucrose and glucose, and according to the information collected in step 2, these are all monosaccharides. In addition, cellulose and starch were the most bitter and least sweet, and according to the information collected, they are polysaccharides. Galactose, maltose, and lactose, which are disaccharides, were all towards the middle of the sweetness scale, which further supports the claim that monosaccharides are sweet and polysaccharides aren't, as disaccharides are in the middle.

     A carbohydrate's structure may affect how it interacts with other molecules in the body such as lipids and nucleic acids. The monosaccharides, which are the smaller carbohydrates, may interact on the smaller scale, such as with cells, and serve smaller functions. The larger polysaccharides, may serve larger functions, like storing energy.

    The testers within my group did not give all the samples the same ratings. This could possibly due to a difference in the way our taste buds work. If someone is used to tasting really sweet things, then they may not thing a sample is very sweet, while someone else could think its very sweet. Also, if one person tasted the sample for longer than another, they may have a different experience tasting the sample.

     According to PubMed Health the tongue contains many taste buds and taste papillae, which help perceive the dominant tastes of sweet, sour, bitter, and salty. The article states that on average, adults have about 2,000 to 4,000 taste buds. Our perception of the sweetness of the different sugars could have been due to a different amount of taste buds on our tongues. The 4 dominant tastes have can be tasted most strongly on different areas of the tongue. The location where we tasted the sample on our tongue could have also affected the way we tasted the sugar.

What is Biology?

Jean Lab

     In this lab we asked the question, what concentration of bleach is best to fade the color out of new denim material in 10 minutes without visible damage to the fabric? We found that that a higher concentration of bleach leads to more color fading without visible fabric damage. The average color removal of 100% concentration bleach was 6.3, while the 12.5% concentration had and average of 1. The color of the 100% concentration was also far lighter than the control and the 12.5% concentration. According to UCSB Science Line , bleach, oxidizes pigment, making it reflect all colors of light, meaning it emits white light. This supports our claim, because if pigment is oxidized by bleach, then a higher concentration should make a pigment appear lighter.

     While our hypothesis was supported by our data, there could have been errors due to the fact that we bleached one of the 100% jean square and one 50% jean squares by themselves, instead of 3 at a time. This could have affected our results, since they were in the bleach by themselves, the bleach could have absorbed more of the pigment. This shows in out results because one of the 100% squares was slightly lighter than the rest. Also, we had many different timers going on at the same time, so some of our timing may have been off, resulting in some squares being in the bleach longer than others. Due these errors, in future experiments I would recommend making sure directions are written thoroughly, and to read instructions with an eye for detail, so there are no misunderstandings when executing the experiment. In the future, it would also be helpful to have a method for timing how long the squares have been in the bleach that would help avoid confusion and disorganization.

     This lab was done to demonstrate our understanding of the scientific method. Although, the lab wasn't related to biology, it allowed us to use the different steps of the scientific method. During this lab, I practiced identifying controls, constants, and independent and dependent variables in and experiment, which was discussed in the scientific method vodcasts. I also applied the concept of the metric system, which was also talked about in a vodcast when I measured out the bleach and water in milliliters. Based on my experience from this lab, this experiment can have a variety of practical, real world applications. For example, if I ever had a stain in something white/light, like clothing or carpet, I could use bleach to fade the stain, just like it faded the pigment in the jeans.