Epigenetics 2/4

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Epigenetics is the study of changes in organisms caused by modification of gene expression rather than alteration of the genetic code itself. It is simply the change of an organism's phenotype, yet not it's genotype which in turn effects how cells read the genes. But what is a phenotype and genotype? If you didn't already know, a phenotype is a visible trait of an individual or a set of observable characteristics of an individual. In addition, a genotype is the pair of alleles or each form of a gene or the genetic constitution of an individual organism. Epigenetic change is a regular and natural occurrence. However it can also be influenced by several factors including age, the environment/lifestyle, and disease state. So how can traits be passed down from generations if it doesn't effect an organism's DNA? The reason why is because when the offspring inherits the DNA, the way the code is read and used is what makes the organism obtain the same characteristics as their parents. How does this happen? Well in every cell biological machinery constantly translates DNA into the proteins needed to carry out vital processes. Chemicals that are attached to the DNA turn genes on or off, telling which proteins to produce and in what quantities. These switches are called Epigenetic Tags are responsible for why a kidney cell looks and acts different then a skin or nerve cell. Even though all three cells have identical DNA. 

S&EP - SP7: Engaging in argument from evidence

I used evidence to defend my explanation. I took some notes on Epigenetics providing the video we watched in class as evidence. I formulated evidence based on solid data when I stated that Epigenetics change the organism's phenotype, yet not it's genotype using the video that was provided to me in class, a website that I personally researched as evidence, and the fact that the physical DNA strand isn't effected by Epigenetics, just how the DNA is read and used. I examined my own understanding in light of the evidence. I used to think that the reason why experiences of previous generations effected new generations or offspring was because it physically changed the DNA strand that was inherited, but because of the video that my classmates and I watched in class and a website that I researched now I think that it doesn't affect the genotype or DNA strand. Instead the chemicals attached to the DNA called Epigenetic Tags turn the genes on the DNA strand on or off, telling them which proteins to produce and in what quantities. I collaborated with my peers in searching for the best explanation. I did some research on Epigenetics and how it works which I discussed with my table group. Together we figured out how we would determine what our superhero's child would look like and act like.

XCC: Cause and Effect

The cause and effect relationship that occurs in Epigenetics is between the Epigenetic Tags and how the DNA is read and used. As you may know, Epigenetics doesn't physically effect the genotype of an organism but the phenotype. Epigenetic Tags just effect how the DNA is read and used by switching or turning the genes on and off on the DNA, which tell them which proteins to produce and how many. More specifically, the Epigenetic Tags determine and control what characteristics the offspring obtain and how these genes are read. In other words, the traits or characteristics that the next generations obtain depend on which genes the Epigenetic Tags switch on or off. A real example that displays how this relationship works is how a kidney cell looks and acts different then a skin or nerve cell. Even though all three cells have identical DNA. I can use this relationship to answer questions about what characteristics a certain organism may have based off of what genes in their inherited DNA is turned off or on. In addition, this relationship can help me "take over the world" by helping me in future education of Genetics. Especially if I choose to specialize in a career that deals with Epigenetics specifically when I grow up. This relationship gives me certain knowledge about the topic of Epigenetics, such as how Epigenetics works and how the Epigenetic Tags control what traits and characteristics the offspring will inherit.

Mutations 1/29

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Have you ever wondered how superheroes got their powers? Maybe you've heard some theories, yet never really understood the concept of it all. Well then you're in luck because I'm going to explain one way superheroes usually get their powers. Organisms can obtain special abilities by a reaction in their DNA called a mutation. Mutation is the change in nucleic acids. Mutations can be caused by either external factors or internal factors. For example, some external factors that can cause mutation are chemicals and radiation. When these factors are in contact with your body, they can effect your body by possibly creating a mutation. One example of an internal factor that can cause a mutation is DNA replication. DNA replication is the process in which a double-stranded DNA molecule is copied to produce two identical DNA molecules. A common mistake people make is thinking that mutations happen on purpose, but something most don't know is that mutations are random. Meaning they can't be controlled and can happen at anytime. There are three different types of mutations; helpful, harmful, and neutral. However, mutations that are helpful are incredibly rare and don't happen as often as the rest. In addition there are gene mutations and chromosomes mutations. The three different gene mutations are substitution, insertion, and deletion. Substitution happens when a base is substituted with other bases in DNA that don't match with each other. Insertion happens when an additional base is added to the DNA strand. Lastly, deletion happens when a base in DNA is simply removed from the DNA strand. The four different chromosome bases are duplication, deletions, inversion, and translocation. Duplication happens when extra copies of genes are produced. Deletions happen when there are missing parts in the chromosome and inversion happens when the parts are reversed. Finally, translocation happens when the chromosomes are put in the wrong location and are not where they are supposed to be.

S&EP - SP7: Engaging in argument from evidence

I used evidence to defend my explanation. I wrote down some notes in my binder providing the video we had watched in class as evidence. I formulated evidence based on solid data when I stated that helpful mutations are very rare and occur less often than the other types of mutation. Using the fact that there is a ten percent chance that mutation can occur and that less than a third of this ten percent will be a helpful or beneficial mutation as evidence. I examined my own understanding in light of the evidence. I used to think that you can make a mutation happen to an organism on purpose, but because of the video that was provided to us in class now I think that mutations are random and can happen to anytime. I collaborated with my peers in searching for the best explanation. I did some research on mutations and how they occur which I discussed with my table group. Together we figured out that if we were going to make our superhero obtain powers by a mutation it would have to be unintentional. As well as we discussed how we would also have to choose from one of the different mutation situations to explain how our superhero got special abilities.

XCC: Cause and Effect

The cause and effect relationship that occurs in mutation is between the order or format of the DNA or chromosome and what form of mutation will happen to the organism. More specifically, the formation in which the DNA bases are in the DNA strand or location of chromosome parts, control the form of mutation the organism might obtain. Basically, the particular form that happens to the organism depends on the location of the DNA bases or chromosome parts in the body. One example of this cause and effect relationship is if a DNA base is substituted with other bases in DNA that don't match with each other, this means that the organism will most likely have a substitution gene mutation. Such as, if the base A matched with C instead of T. Or if the base G matched with T instead of C. Another example of this cause and effect relationship is if a base in DNA is simply removed/missing from the DNA strand or if there are missing parts in the chromosome, this means that the deletion gene mutation or deletions chromosome mutation will most likely happen to the organism. I suppose that this theory could possibly be tested by purposely changing a particular formation in an organism's DNA strand or chromosome to see if it will result in the desired gene or chromosome mutation.

Genetic Modification 1/15

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Have you ever heard of the superheroes Spider man or Dead pool? Maybe you've heard about their origin stories (how they became who they are, how they obtained those certain powers and abilities) before and don't quite understand the process. Or maybe you haven't heard of their stories at all and wonder if they just woke up one morning with special powers that resemble a certain organism. If you fit into any of these categories, then read on because I'm going to explain how these superheroes and many others usually came to be, while hopefully fixing your confusion. The most common way a superhero can acquire unique abilities is by a process called Genetic Modification or otherwise known as Genetic Engineering. This process is the direct manipulation of an organism's genome using biotechnology. It is a set of technologies used to change the genetic makeup of cells, including the transfer of genes within and across species to produce improved organisms. When Genetic Modification is performed or experimented on organisms it is known as GMO, standing for Genetically Modified Organisms. So how is Genetic Modification specifically? The process starts by choosing the certain organism that you want to take the abilities from and extracting those specific genes from the organism's DNA. Next a small piece of circular DNA called plasmid is extracted from a bacterial cell. This short piece of DNA is capable of replicating on its own when inside a bacterial cell. After a small section of the circular plasmid is cut out by restriction enzymes, otherwise known as molecular scissors. Then the gene DNA of interest is inserted into the gap of the plasmid. The ends of the two sequences are stitched together by a DNA ligase. The bacterial cell is put in large fermentation vessels to allow growth and duplication. This cell should divide rapidly. The process is basically done, the bacterial cells just need to be inserted in the human. However, this doesn't mean that only superheroes are used as GMOs, many other organisms such as plants, fruits, vegetables, animals, and humans with certain diseases are also commonly Genetically modified.

S&EP - SP7: Engage in argument from evidence

I used evidence to defend my explanation. I took notes on how scientists specifically perform Genetic Modification on organisms providing the several sources I researched as evidence. I formulated evidence based on solid data when I stated that the bacterial cell were put into the fermentation vessels to allow growth and duplication using the fact that bacterial cells divide rapidly inside the fermentation vessels as evidence. I examined my own understanding in light of the evidence. I used to think that the DNA of interest from the certain organism could be inserted into the gap of the plasmid and then the plasmid is inserted in the bacterial cell as is, but because of researching a little bit deeper throughout websites now I think that the ends of the two sequences of the DNA and plasmid have to be stitched together by a DNA ligase first, before it is inserted into the bacterial cell. I collaborated with my peers in searching for the best explanation. I did some research on this process of genetically modifying organisms which I discussed with other students who were researching the same process. Together we figured out that Genetic Modification is a complicated process that has to be performed carefully.

XCC: Cause and Effect

The cause and effect relationship in Genetic Modification is between what the steps the scientist does in the process and the end result of the organism's abilities. What happens to the organism after the experiment depends on how the scientist genetically modifies the DNA of the organism. The scientist basically controls what will happen to the organism in the end. More specifically, if the scientist modifies the DNA so that the organism has certain abilities, it effects the organism by allowing it to obtain those special abilities. For example, if the scientist added in genes that portray the power of flying into the gap of the plasmid before inserting it inside the bacterial cell, as a result this would effect the organism after the process is done by allowing it to have the power of flying. However, if the scientist makes a mistake or messes up anywhere in the process, it can greatly effect the organism by probably causing a negative reaction in its DNA. This might lead to a malfunction in the organism. This information that I contain in my knowledge about the specific relationship in Genetic Modification can help me "take over the world" by allowing me to have certain details n my knowledge about the effects of genetic modification. Which can help me especially in the future if I choose to become a scientist that specializes in GMO. Particularly in the genetic modification in food, resources, and humans with certain diseases.

Punnet Squares 1/8

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Currently in science class, we've been using punnet squares to declare what traits our superhero's baby will have. If you didn't already know a punnet square is a 2 x 2 array, but instead of being filled out with numbers it is filled out with genotype combinations. This diagram is used to predict the outcome of a particular cross breeding experiment. More specifically, it is used by biologists to determine the probability of an offspring having a particular genotype. Punnet squares were named after Reginald C. Punnet, who devised the approach. So how do you set up and fill out a punnet square? To do this, you put the genotype that one parent passed on to the offspring, above the diagram. Lining each letter above each individual box of the array. As well as, you put the genotype that the other parent passed on to the left side of the diagram. The same set up applies accept you put each letter to the left side of each individual box. To fill out a punnet square, you start at the first box and look at the letter to the left of it and the letter above it. Then you write both of these letters in the box. Keep in mind to always put the dominant letter before the recessive letter. After, you will continue this process to fill out all of the four boxes.

S&EP - SP4: Analyzing and interpreting data

I used a diagram to display and analyze data to predict the outcome of a particular cross breeding experiment. I created punnet squares to determine the probability of an offspring having a particular genotype. I recognized patterns in data and see relationships between variables. For example, I observed that if there is only one dominant allele in a genotype combination, the hybrid genotype will always count as the dominant trait. As well as if both the alleles are dominant, the purebred genotype will always count as dominant. For purebred recessive genotype combinations, it will always count as recessive. I revised my initial hypothesis when the data doesn’t support it. My original hypothesis was that my superhero's baby would have echolocation since that trait is dominant, but my new hypothesis is that there is an equal chance that the baby will or will not have echolocation. This is because the dominant genotype is a hybrid combination, meaning that it has one dominant allele and one recessive allele. After filling out the punnet square, the outcome showed a 50% chance.

XCC: Cause and effect

The cause and effect relationship that punnet squares create is between the genotype that each parent passes on and the traits the offspring will have. The certain genotype combinations that the parents pass on help determine the probability of an offspring having a particular genotype. Which helps biologists predict the outcome of a particular cross breeding experiment. For instance, if the dominant genotype is a hybrid and contains one dominant allele and one recessive, this means that the offspring has a 50% chance of having the dominant trait. If the dominant genotype is purebred and contains two dominant alleles, this means that the offspring will definitely have the dominant trait. This information helps me better predict what traits the offspring will have, as well as the percentage of the offspring having a particular trait.

Genetics Vocabulary Test Corrections 12/13

Explanation: I completed the quiz and rushed to submit it right as we needed to move on. However when I looked back up to my computer it didn't load properly. So I reloaded the page and found that the answers were blank and it had erased all of the work I had done. Seeing that I couldn't redo the work because we had moved on to something different, I decided to le
ave it and do a regrade.

*For the first question, the exact definitions that were originally provided weren't there when I went over the quiz results so my definitions will not be the exact same as the original definitions.

1. Match the vocabulary words with the correct definitions

a. Genotype:  A genotype is the pair of alleles or each form of a gene.
b. Phenotype: A phenotype is a visible trait or characteristic of an individual organism.
c. Allele: An allele is each form of a gene.
d. Homozygous: Homozygous is a term that describes having two of the same allele for a trait.
e. Heterozygous: Heterozygous is a term that describes having two different alleles for a trait.
f. Dominant Trait: A dominant trait is when a single copy of its gene is inherited.
g. Recessive Trait: A recessive trait is when a copy of the recessive gene form is inherited from each parent.

2. Mendel concluded that the alleles for tall stems in pea plants are dominant. Thus, in crossing a purebred tall pea plant with a purebred short pea plant should result in

A. All tall plants
B. All short plants
C. All medium height plants
D. Half short and half tall plants

I chose A. because when the alleles for tall stem in pea plants are dominant, it doesn't matter what is in crossing with a purebred tall pea plant because the offspring will always be tall. In this situation, the short purebred effects will not be seen in the heterozygous offspring. In order for the pea plant offspring to be tall, it can either have one tall allele or two tall alleles in its genes because the tall trait is dominant. For the plant to be short, it would require two short alleles because it is recessive. Since the alleles of all of the offspring will be something like Tt, the offspring are guaranteed to be tall.

Charity Fair 12/11

(Image from drive)

Summary

         During the annual Charity Fair project, I learned many things from most of my classes. In math, I learned how to calculate the cost and profit of my group's product. I learned how to calculate how much all the materials would cost altogether to make 5 products, 10 products, 100 products, and 1000 products. As well as I learned how to calculate how much money would be given to the actual charity after paying for all of the expenses. In addition, I learned how to find the statistics of my group's chosen charity. To do this, I would have to look through the organization's tax forms for several different years. I learned what line the revenue or how much the charity earned was listed and what line showed the charity's administrative costs. We would have to subtract the administrative costs by the revenue to get how much the organization actually gives to the cause. In Science, I learned how to put together an instructable that gave the step by step process of how to create my group's product. In Social Science, I learned the correct way of choosing an organization to support and how to research that certain organization. In Language Arts, I learned how to create an Ignite presentation to convince the audience to vote for the charity my group chose to support. Lastly in Elective, I learned together a tri-fold to present while selling our product.

Backward-Looking

           Since I was fortunate enough to be apart of the Adventure stem program last year, I had the opportunity to experience what Charity Fair is like. Having the chance to participate in Charity Fair a year ahead really encouraged me to get better at this type of work. I believe I improved my presentation as well as my product. For example, I think I improved my presentation because I now understand how to properly put together and present an ignite presentation. I now know that an ignite presentation should strictly only be pictures, should only limit to one picture each slide, and should be only fifteen seconds long. Last year, I made the mistake of having bullet points and multiple images and lines on one slide. However this year, I only put single images on each slide so the audience could focus easily on each slide and didn't have to look at so many images. In addition, I didn't put any text on any of e slides and limited to a few lines for each slide so it would fit the fifteen seconds. For my product, I learned that the customers mainly bought items that were related to the current season. By making my product Christmas related, I sold a lot more items than last year.

Inward-Looking

          I feel that this piece of work my group and I put together was great. We did everything perfectly as planned and made little mistakes. I particularly like creating our product because I thought that it was really creative and unlike anybody else's products. As well as my group and I had a lot of fun putting together the jars since they were all different themes. The only thing I disliked about the outcome of the Charity Fair project was the ignite presentation. This is because I felt that our ignite presentation had too many lines for each slide. When reading our script while presenting we had to rush a bit. This made it hard for the audience to understand and take in what we were saying. In addition I believe that we could have put more heart felt images that would really make the audience think about our charity in a whole other level.

Outward-Looking

        My group and I didn't do some aspects of the project the way other groups did theirs. For instance, we did our presentation and product differently. Our presentation was different than others because we chose to support a charity that no other groups chose and chose to support a topic no other groups supported, which was women equality. In addition, we didn't put the exact same information on our presentation and we obviously included different pictures than others. For our product, we made something no other group made. We made mini ecosystems. These ecosystems were sold in mason jars and came in four different themes. Including a winter/snow ecosystem, an ocean ecosystem, a forest ecosystem, and a fall ecosystem. 

Forward-Looking 

         If I had the chance to do this project over again, I would change our presentation. The reason being is that I felt we had too many lines for each slide. I would change this by cutting the amount of words we had to say so we didn't have to rush when reading our script. As well as I felt we could have put better images on each slide. I think we could have put more heart felt images that would make the audience really think about our charity. Other than this, I wouldn't have changed anything else because I believe that the other aspects of the project went smoothly.

Genetics and DNA 12/4

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Have you ever wondered why you and your mom or dad share the same features? The factor that makes you and your parents act and look alike is genetics. Genetics is the name for the directions for only one trait of a living thing. You might be wondering how genetics is able to affect you, this is because of DNA. DNA is the directions an organism's cells follow that tell the living thing how to grow and what it will do. DNA contain nucleic acids which are four molecules you require to survive; Cytosine, Thymine, Adenine, and Guanine. They are instructions that make all organisms appear and behave a certain way. These nucleic acids make up the layers or "steps of the ladder" of DNA. The two structures that hold them together are composed of phosphate and deoxyribose.

S&EP - SP7: Engaging in argument from evidence

I used evidence to defend my explanation. I answered a packet of questions about DNA and genetics, providing a documentary that my class watched as evidence. I formulated evidence based on solid data when I stated that Tay-Sachs disease is caused by only one bad letter in a baby's DNA using the information that scientists researched about DNA and Tay-Sachs disease as evidence. I examined my own understanding in light of the evidence. I used to think that DNA was simple to research, but because of the video now I think that DNA could take decades to research without modern technology. I collaborated with my peers in searching for the best explanation. I did some research on the subject in which the packet was based on which I discussed with my table group. Together we figured out that the answers to the questions on the packet.

XCC: Structure and Function

The structure of DNA greatly affects the function of how cells decipher the DNA and how the organism will develop and behave. This is because our cells decipher the nitrogenous bases of our DNA to know exactly how and what to construct. This means that if there is one small problem in a single letter of our DNA, it can greatly affect the function of the organism. For example, in Tay-Sachs disease, it only takes one malfunction in one letter of a baby's DNA to cause the baby to slowly become brain dead.