Unit 5 reflection

In this unit we learned about  how DNA gets used to create proteins, and how DNA is copied. To copy DNA it is first unzipped by the enzyme helicase, then the enzyme DNA polymarase adds the missing halves, which creates two full sets of DNA. To create proteins, DNA is first transcribed into mRNA by the enzyme RNA polymarase. The RNA is then processed to remove unnecessary parts(introns), and leave only the extrons. The mRNA then leaves the nucleus, and goes to ribosome where it is read in 3 base sections called codon, and used to create a protein. The RNA can be mutated, and there are 3 types mutations. Substitutions are when one base is swapped for another, Insertions are when a base is added, and deletion is when a base is removed. Insertions, and deletion are called frame shift mutations, and have more effect on the protein than a substitution because they effect every codon after the mutation. Finally we learned about gene regulation, which controls which genes are expressed. This is done with an operon that can have a represser attach to at, and block the RNA polymerase from copying the DNA. I am pretty solid on everything in this unit. I am slightly less sure about gene regulation, but overall this unit was one on my better ones.

https://upload.wikimedia.org/wikipedia/commons/1/11/Gene_expression_control.png

http://study.com/cimages/multimages/16/point_mutation_types.png

In this unit learned some new skills. In the DNA extraction lab, we had to create our own procedure, and were not told if we had the right procedure, and this taught me to confident in myself. I still want to know more about how DNA expression, and regulation works. I find it interesting that despite the same DNA in all cells, they are very different, and I would like to know more about how and why that happens.

Protein synthesis lab

The body produces proteins in two steps, first DNA is transcribed into mRNA by an enzyme. The mRNA then leaves the nucleus, and goes to the ribosome. It attaches to the ribosome, and the ribosome creates a protein. The ribosome reads the mRNA in the base codons, and adds an amino acid depending on the codon. Once the ribosome reaches a stop codon it stop adding amino acids, and the protein is finished.




https://upload.wikimedia.org/wikipedia/commons/1/11/Gene_expression_control.png


The type of mutation with the least effect was substitution, because it only had an effect on one codon, this mutation has a good chance of having no effect if tit occurs in the last base pair of a codon. Insertion, and deletion had the most effect, because they effect all the codons after the point where the mutation occurs. These mutations have the most effect if the are toward the beginning of an mRNA sequence.



http://study.com/cimages/multimages/16/point_mutation_types.png


To make a mutation with maximum effect I substituted one of the base pairs in the first codon. I chose this because it would change the start codon, which would prevent the ribosome from making a protein at all. This mutation has to occur in the fist codon for it to have a major effect, otherwise it's effect will be very minor.



https://upload.wikimedia.org/wikipedia/en/6/67/Different_Types_of_Mutations.png


There is a genetic disorder called progeria, which has the symptom of an increased rate of aging. This usually results in the death of the person with the disorder due to a stoke or heart attack by the age of 20.

http://api.ning.com/files/rij9YXbYphAbAgYkKuHnEMcN0EoYnljvCN3Na44C-XRZsDjNcAW7VPfQcTyhkR8Esf49kNsXhP6BMl0uPyvyWw__/1.HutchinsonGilfordProgeriaSyndrome.jpg?width=229&height=350

DNA Extraction Lab

In this lab we asked the question: "How can DNA be separated from cheek cells order to study it?" We claim that DNA can be extracted from a cheek cell through a simple procedure. First, you scrap the sides of you mouth your teeth, then you swish you mouth with Gatorade, and spit it out. This lets you spit some of your cheek cells out with the liquid, and since Gatorade is a polar liquid it begins to break down the cheek cell. You then add salt to allow the DNA to clump up. You than add soap and enzymes from pineapple juice to further break down the cell, and at the end you ad alcohol to make the DNA float to the surface

As seen in the picture above the DNA floated to the surface at the end of this procedure, which proves that DNA can be extracted from a cell using this procedure.

On possible error is that some people poured the alcohol in too fast, and it mixed with the Gatorade mixture instead of forming a separate layer. This would negate the effect of the alcohol and prevent you from seeing DNA. To fix this the procedure should say to from two layers.

Another error is that is you don't put enough alcohol, then you wont see DNA. This could be fixed by adding more alcohol. 

This lab was done to show how DNA can be extracted from cells, and then be retrieved. This related to DNA, and how it is in every cell in your body. This lab can be applied to the field of genetics. You can use a similar procedure to extract DNA and test it for certain mutations.

Unit 4 refection

This unit was about reproduction, specifically sexual reproduction. I specifically learned the differences between sexual and asexual reproduction, how sex works, and what happens before sex(meiosis, and its steps). We also learned about inheritance, This involved using punnet squares to calculate the probability of offspring having certain traits based off their parents' genotypes. We also learned about dominant, and recessive alleles, which is when one allele is shown over another. Mendel discovered the characteristics and laid down the foundations of genetics. We also learned about some more complicated topics in genetics such as gene linkage, and epistasis.

My main strengths were punnet squares,mitosis and meiosis. My weakness is that i don't quite understand some of the more complected terms yet, and could still use some review on them. Doing the info graphic helped me a lot. It help with both the content side, and the time management side. On the content is was both a test of what I knew, and a review on what I didn't. I had to explain the concepts, so I had to be solid on them, which held me accountable for knowing them.

I still want to know more about genetic mutations. Genetic mutations ave always fascinated me, and the weren't talked about muck in this unit. 

I took a VARK Questionnaire to see how I should be studying, and what type of a learner I am. The results were as I expected, I was more kinesthetic(13), and visual(11), than read/write(6) and aural(2). The useful part of the survey was the studying tips. It recommended that I find/draw diagram and that I go back over what i did in labs. I intend to try both of theses new methods of studying on the new test

Coin Sex Lab

In this lab we learned how to use punnet squares to predict what traits our offspring will have, and how these prediction can deffer from what actually will happen. In this lab we used coins to represent genes, and the two sides of the coin represent the two different alleles for the gene. The flipping of the coins represents meiosis, and the two sets of coins up represents the processes of recombination. The coins also showed how probability of something happening can be different from what actually happens. We did multiple autosomal crosses, where the sex chromosomes are not involved, and one x-linked cross, which is when the sex chromosome are involved. We used two sets of one coin each to represent monohybrid crosses, and two sets of two coins each to represent dihybrid crosses. In some of our tests we labeled both side of the coin the same way to represent a homozygous trait, but in others we labeled the two sides differently to represent a heterozygous trait.

When we preformed the di-hybrid cross, we got results that were slightly different than what was expected. The punnet square gave us a phenotype ratio of:

9 Brown Hair, and Brown eyes : 3 Blond Hair, and Brown eyes : 3 Brown Hair, and blue eyes :
1 Blond Hair, and Blue eyes

Our experiment had slightly different results, and gave us the phenotypic ratio of:

8 Brown Hair, and Brown eyes : 4 Blond Hair, and Brown eyes : 2 Brown Hair, and blue eyes :
2 Blond Hair, and Blue eyes

The slight difference between the probability, and what actually happened is due to the fact that probability, and reality do not always line up. It possible to cross two heterozygotes, and get two recessive alleles in all ten offspring for the same reasons that you can flip a coin ten times and get heads every time. This lab demonstrated the limits of probability. Probability can give you odds on what can happen, but until the event occurs you have no idea what will happen. Relating back to the coin, the probability of getting heads two heads in a row is a 25% chance, but until you flip the coin twice you can't know if you will get two heads.

This lab relates to me because if/when I have children, then I cant use probability to predict what they might be like, but I have no way to know for sure what traits they will have, until they are born.

Genetics Infographic

Because in this layout my info graphic appears very small, to view it in full size click here.

Unit 3 reflection

This unit was about what is inside a cell, and what cells do. It included photosynthesis, cellular respiration, and osmosis. This unit also mentions how cells were discovered, and how cells changed over time. The main theme of this unit was that cells are the building blocks, and the ways cell use their organelles, and processes to communicate, and survive, and create life. One other key concept was how the structure of a cell affects its function. My main strength was the organelles, and osmosis, because I feel like I really understand them, and can explain them. My main weaknesses would be photosynthesis and cellular respiration, because while I mostly understand them, there are a few details I still don't understand fully.

I learned a lot about cells, and also about good lab procedure. I learned how to find errors in an experiment, and come up with ways to fix them. I also got a little better at getting through the vodcasts without pausing. Finally I learned new ways to get through difficult material.

I still want to learn more about photosynthesis, and how it works at a deeper level. At a more broad level I find it amazing how life evolved from tiny bacteria to big multi-cellular organisms that will have the capability to learn, and study the tiny cells they are made of. I also love concept of osmosis, and how quickly a cell will change based on its surroundings. If I have time I might try duplicating one of the experiments at home, but with slight modifications.










I normally study minimally for test, but for this one I plan to at the minim review photosynthesis and cellular respiration through the CFUs, vodcast notes, and the diagrams. I will also take the CFUs again, and review any other difficult concepts based on what I get wrong.

Egg diffusion lab

In this lab we took two eggs, and put them both in vinegar to dissolve the eggshell, and expose the membrane. After two days we took them both out of the vinegar, and put them into de-ionized water for a few more days, then after measuring their mass and circumference, placed one in sugar water, and one in de-ionized water. We then waited two days, measured their mass, and circumference again.

The cell that was placed in the hypertonic solution(sugar water) shrunk. Its mass decreased by 51.7%, and its circumference decreased by 23.67%. This was caused by the water in the cell wanting to diffuse from high concentration(the cell), to low concentration(the sugar water), and the sugar wanting to defuse into the cell,but being blocked by the membrane. The cell that was placed in the hypotonic solution grew. Its mass increased by .176%, and its circumference increased by .201%. This was caused by the water in the cell wanting to passively diffuse from high concentration(the DI water), to low concentration(the cell), and the minerals wanting to defuse into the cell,but being blocked by the membrane.

A cell's internal environment changes, as its external environment changes, because it naturally wants to maintain equilibrium, and because of that the cell will try to take in everything around it , until the concentration inside, and outside of the cell is the same. It does this through diffusion.

This lab demonstrates diffusion, and how solutes, and solvents want to move along the concentration, and the effect this has on the cell. 

Fresh vegetable are sprinkled with water, because water is hypotonic, and will want to diffuse into the cells of the vegetable, which will make the vegetable bigger, which will in turn make it look better, and make more people want to buy it. Also, when road are sprinkled with salt, the plants along the side die because the salt is hypertonic, and will make the cells in the plant shrink and lose functionality.

Based of this lab, I would want to do a lab to determine the effects of salt water on a cell, versus mineral water. 

Egg Macromolecules

In this lab we looked a cell to determine which macro molecules are found in which parts of the cell. To do this we took an egg, and separated it into the yolk, white, and membrane. We then took each of these three components and used chemical identifiers to determine which macro molecules were  in which parts of the cell. We found that proteins are found in the egg white. This was shown, by when we added sodium hydroxide (NaOH) and copper sulfate (CuSO4), to the sample, and it turned a dark blue, which is an indicator that a protein is present. This makes sense, because egg whites are the food for the growing embryo, and cells need proteins to grow. The membrane contains lipids. We know this because, when we added Sudan III to the lipid it turned orange, which is a sign that a lipid is present. This data makes sense because all membranes are made of lipids. We also found lipids in the egg yoke.  We know this because, when we added Sudan III to the lipid it dark-ish orange, which is a sign that a lipid is present. This data makes sense because all membranes are made of lipids, and there is a clear membrane surrounding the egg yoke.

 One possible error in this lab was that when we tested the yoke for proteins, the sample turned green,which made it impossible to tell if it contained proteins. To remove this error I would mix the sodium hydroxide (NaOH) and copper sulfate (CuSO4) better. Another error is that when testing the membrane we cut it into one chunk. This only exposes the outside of the membrane, but not the inside. This led to us not finding proteins in the membrane, even though there were proteins in the membrane. To fix this error, I would cut the membrane into more, smaller, pieces before testing it.

This lab was done to further our understanding of macromolecules, and how they the building blocks of life. This relates to macromolecules, and also what makes up the different parts of a cell. This lab can be applied to future leaning about cells, and will allow me to make inferences about which macromolecules make up which parts of the cell.

20 big questions

One of the articles that interested me, was question about whether or not there were more universes. This was interesting, because if there are more universes out there, they might no abide by the same law of physics as us, and there may be advanced beings in them, and they might even be watching us. One hypothesis in this field is that If scientist are observing unexplained "dark flow" then other universes may exist.

My 20 big Questions:

1. What happens after death?
2. Are we the only planet with life on it?
3. Will humans ever solve their population problems?
4. Will humans ever solve energy problems?
5. How long will humans survive?
6. How did life start?
7. How did the big bang start?
8. Are humans just another being's experiment?
9. Do people have free will, or are their action pre-decided? 
10. Will humans ever live forever?
11. Will there ever be a "better" evolution of humans?
12. How does the human brain work?
13. Is there a god?
14. What will happen if a temperature reaches absolute zero?
15. Will any other animals evolve the way humans did?
16. Will time travel ever exist?
17. What will happen when the sun dies?
18. Will there ever be a nuclear was?
19. What would lift be life after a nuclear war?
20. Will computers ever reach a limit on how fast they can be?

Identifying Questions and Hypotheses

This study was about how a specific set of brain connections correspond to positive behavior traits. The scientists were asking if a specific set of brain connections correspond to behavioral traits, and if so, in which ways. They came up with the hypothesis that if a person has as connectome on one end of the scale, then the will show characteristics that are viewed as positive. The surveyed peoples brains with an MRI, and they viewed the connections in their brains (connectome), and found correlations.

Unit 2 Reflection

This unit, ¨Miniature Biology¨ was about the molecules that make up life. It focused on four main macro-molecules, Carbohydrates, lipids, proteins, and nucleic acids.

Carbohydrates, are ring and chains of rings. Their main function is energy storage. Single ring molecules are called monosaccharides, and generally taste sweet. Carbohydrates that are made up of two rings are called disaccharides. Finally polysaccharides are chains of at least three rings.

Lipids are long chains of carbon and hydrogen. Lipids are also used for energy storage. Phospholipid has hydrophyllic head, and a hydrophobic head, which allows it create a double layer in water.

Proteins are long chains of amino acids. They have many functions including supporting cell, helping cell communicate, and speeding up chemical reaction. One specific type of protein is called an enzyme, and its function is to speed up chemical reactions by lowering activation energy. It only works in a specific pH and temperature. If it goes outside of that it will denature.

Nucleic acids are a chain of neucleotide arranged into a double helix. Their primary function is to pass down information, but ATP(Adenine tri-phosphate) is used for energy transfer.

We also learned about different types of molecular bonds. One type is an ionic bond, which is when an electron gets transferred, and covalent bonds, which is when an electron is shared. There is also a hydrogen bond, which is what creates cohesion,adhesion,ad capillary action.

Cheese lab

	Time to curdle (minutes)
Curdling Agent	Chymosin	rennin	buttermilk	milk(control)
Acid	5	5
Base
pH control	15	15
Hot	5	10
Cold
Temp. Control	15	10
Avg. of controls	15	12.5

In this we asked which conditions were ideal for making cheese with enzymes. We found that the most effective conditions for making cheese were by using the curdling agent chymosin, which works best in a hot, acidic environment. Two of the curdling agents, buttermilk, and naturally occurring bacteria in milk, did not curdle in in any conditions. The other two curdling agents, rennin, and chymosin, did not curdle in basic, or cold temperatures, and curdled in under 5 minutes to curdle in an acidic environment, and under 10 minutes to curdle in a hot environment, which proves that a hot, acidic environment is ideal for curdling cheese with enzymes. Also, Chymosin is a better curdling agent than rennin because, while they both curdled in 5 minutes in an acidic environment, chymosin curdled 5 minutes faster that rennin in a hot environment. This conclusion makes sense because, chymosin is rennin that in made by fungi, and rennin is naturally found in a cow’s stomach, which is a warm, and acidic environment.

While our hypothesis was supported by our data, there may have been a few errors. One error, was that to simulate normal conditions, we put the test tube with the enzyme, and milk under our armpits, and not everybody's armpits are the same temperature. This error could have affected our data by having one curdling agent do better than another because it was in a warmer armpit. Another error was that we checked the test tubes every 5 minutes, which is very imprecise. This led to multiple tests having the same result, even though they might have been different by up to 4 minutes. To fix these errors, we should put the test tubes in lukewarm water, instead of our armpits, and checked at one minute intervals.

The purpose of this lab was the strengthen our understanding of enzymes, This lab demonstrates, a lot of stuff that we have learned in class. It show what enzymes do, and also what denaturing is, and the factors that lead to denaturation. This lab could be applied to a cheese making business that wants to find out what enzymes and and condition are most effective for cheese production.

Sweetness lab

In this lab, we asked how the structure of carbohydrates affects their taste. To test this, we the pure forms of various carbohydrates, and compared their taste. We found that monosaccharides were the sweetest carbohydrates, followed by disaccharides, which were slightly sweet, finally polysaccharides were not sweet at all. To measure this we use sucrose as a baseline of 100, and created a scale from 0 to 200, with 0 being not sweet at all, and 200 being super sweet. Our monosaccharides had an average of 140, while the disaccharides had an average of about 50, and the polysaccharides all ranked at zero. This help prove that monosaccharides are the sweetest, followed by disaccharides, and then polysaccharides. Also the highest ranked carbohydrate was Fructose, with a rank of 200, which supports our claim that monosaccharides are the sweetest carbohydrate.

This lead to my inference that the structure of carbohydrates affects the way cells use them. The simpler monosaccharides could be for when the cell needs a quick burst of energy because they are a simple ring, and can be broken down quickly. The slightly more complex disaccharides, could be for when the energy is need over a longer period of time because they are made of two rings, and will take longer to break down. Finally the polysaccharides could be used for long term energy storage because it is made up of a long chain of rings, and would take the longest to break down.

There were slight differences in the ratings different tasters gave. This could be due to many factors. One is that everybody is different, and has different opinions on how things taste. Also Different tasters spent different amounts of time between tasting different sample. Finally, Both tasters didn't take exactly the same amount of each sample.

You sense of taste is determined by your taste buds, which are scattered throughout your mouth. These taste buds each specialize in a certain basic taste(sweet, sour, bitter, etc...). Each person has a different amount of each type of taste bud in their mouth. This leads to people with more "sweet" taste buds to perceive a food to be more sweet that someone with less "sweet" taste buds would.

Carbohydrate	Type of carbohydrate	Degree of sweetness	Color	Texture	Other observations
Fructose	Monosaccharide	200	Clear Crystals	Grainy	Super sweet
Glucose	Monosaccharide	150	Clear Crystals	Grainy	sweet
Galactose	Monosaccharide	75	white	Powdery	pretty sweet
Sucrose	Disaccharide	100	white	Grainy	slightly sweet
Maltose	Disaccharide	50	tan	Hard and chunky	bitter
Lactose	Disaccharide	15	white	Powdery	slightly sweet
Starch	Polysaccharide	0	white	Powdery	tastes like flour
Cellulose	Polysaccharide	0	white	Powdery	stays on tongue