Protein Synthesis Lab

          This process is call protein synthesis. A copy is made of one side of the DNA (called the mRNA) where the gene is located. This copy is transferred to the cytoplasm. Then mRNA then leaves the DNA and travels to the ribosome. The segment is fed through the ribosome. The mRNA bonds with a ribosome, which will make a protein. The ribosome reads the first three bases of the whole sequence where the ribosome translates the amino acid (it will repeat this action through). The mRNA bonds with a ribosome, which will make a protein.

          When a mutation occurs it can either be a mutation that makes a small difference or a big difference. A small problem occurs when a mutation effect the amino acid sequence but in total the mutation does not make the base a different one. A big difference is when a base is added or pulled out and the amino acid changes. There are two main topic kinds of mutation. Substitution which is when a nucleotide is substituted for another. The other, frameshift mutation - a frameshift mutation breaks into two separate parts. Those two parts are called insertion (when an extra base pair is put into the code) and deletion (when a base pair is left out of the code). If a T was inserted into the code at the end versus the beginning it would do less damage to the sequence. This is because the mistake acts like a chain effect. 

           In my own sequence on for the lab I chose to add in a frameshift mutation because I though this would make the biggest effect. I inserted an extra base in the very beginning, specifically the fourth base. This then effected the rest of sequence. It matters where the mutation occurs because it can either effect the whole rest of the sequence or only some of it.  

          Amino acids can really effect you life. For example there is one mutation that happened and its called Apert syndrome. Apert syndrome s a genetic disorder characterized by the premature fusion of certain skull bones and sometimes even fuses fingers and toes together. Almost all cases of Apert syndrome result from new mutations in the gene, and occur in people with no history of the disorder in their family. Although if one has Apert syndrome they may pass this on to there newborns.

Unit 5 Reflection 

This unit was about coping DNA, and translating it. It is called walking the dogma. We talked about the difference between DNA and RNA. RNA is single stranded and has ribose - not deoxyribose, and RNA contains unracil instead of thymine. Mutions was also brought up and we look at the different kinds of mutations, there were two main of mutations. One of which is called substitution, this is when one nucleotide is substituted for another. The second kind is called a frameshift mutation and in a frameshift mutation there are two kinds that branch off. Insertion (when an extra base pair is added to the code) and deletion (is when a base pair is left out of the code). I think my strength was based around mutations because I liked learning about how much a mutation could really effect you. Usually when I enjoy something I excel at it. We brushed over the topic as to why we should care about mutations. We said that it changes DNA - more specifically it changes proteins which are essential to life. Some diseases are caused by a change of a single base! Mutations in DNA can lead to cancer and they can create new genetic variation giving population new traits for natural selection to act on. We looked at gene expression and regulation. Gene expression is the process of a gene begin used to produce a gene project or phenotype. A gene regulation is a mechanism used by cells to increase or decrease the expression of a gene. This is where I ran into trouble as I feel it go a

lot harder trailing off into promoter, operons, and operaters. I learned that I am usually better at something that I enjoy and can ask a lot of questions, after I watch the vodcast I usually find myself pondering over questions i've asked myself. I think that I have grown as I biology student but I have also learned a lot more about myself and my learning style.

Human DNA Extraction Lab

        In this lab we asked the question: "How can DNA be separated from cheek cells in order to study it?" In this lab we found that you can separate DNA from your cheek in order to study it. I found that in this experiment you can see DNA when you follow three basic steps: homogenization, lysis, and preciptiation. You can see the DNA when you add detergent, salt, enzyme and cold alcohol to create a gatorade solution. I observed that my DNA floated to the top once I had added the cold alcohol. I looked as though bubbles carried it to the top. This observation helped me strengthen my thinking and thoughts that came out of notes and vodcasts I watched. This data supports my claim because DNA extraction is the process of homogenizing (to combine two unlike things), lysis (a process of disintegration or dissolution (as of cells)), prectiptaion. When the protease (the enzyme) was added to the gatorade solution outcame a faint reaction and the DNA was in the making, but when the layer of alcohol was added the DNA was made visible in the test tube.
         While my hypothesis was supported by my data, there could have been errors due to me not scraping my cheek enough when I was swishing plain gatorate in my mouth. I know this was an issue because group member who had kept the gatorade in there mouth longer and scraped there cheeks more effectively had more DNA. In order to eliminate this error next time I would scrap my cheeks more to break off the cells. A second error that could have affected my experiment was adding too much gatorade to the solution and not enough alcohol. Adding to much gatorade also makes the DNA less concentrated and could have affected the over all process. To prevent this from happening again I would use less gatorade to balance out the amount of alcohol that was added. Due to these errors, in future experiments I would follow my recommendations in order to avoid anything affect your experiment.
         This lab was done to demonstrate that DNA could be separated from cheek cells in order to study and observe it. From this lab I learned and what an enzyme help create a reaction an eventually some DNA, this helps me understand how a enzyme works on a larger scale. Based on my experience from this lab, I could apply this knowledge to another situation if I were to maybe look at DNA on more of a molecular level, and needed to re-create someones DNA in that kind of form.

Egg Lab Conclusion 

             In this lab we asked the question: Can macromolecules be identified in an egg cell? 

Our claim/answer to the question was that, yes they can but they may not be identified in all macromolecules. Also, in the egg membrane the macromolecules that were present were polysacchrides, lipids, and proteins. In the egg white the macromolecules that were present were proteins, polysacchrides, and monosacchrides. In the egg yolk the macromolecules that were present were the lipids, proteins, monosacchrides, and polysacchrides. Each test had a chemical added to it, for us to see if the macromolecules were present. There were four different indicators; Benedict Solution, Iodine, Sudan III/IV and Sodium Hydroxide with Copper Sulfate. Evidence that supports our claim is as follows: In each test we would know if the macromolecules were present because the test would change to a darker color. We were asked to rate how present the macromolecules were out of 10. We found out that the membrane has polysaccharides because the solution turned black and it's found on the surface of the cell membrane, I rated this a 5/10. The membrane also has lipids, the solution turned orange, and the membrane is made of phospholipids, which is a lipid, so this makes sense. I rated this a 2/10. Lastly, the membrane showed the macromolecule; proteins, and in effect the solution turned dark purple. I rated this a 6/10. All in all, the egg membrane showed the macromolecules, polysaccharides, lipids, and proteins. We also found out that the egg white has polysaccharides(3/10), monosaccharides(7/10) and lipids(4/10) for energy growth and development. The egg white contains proteins for two purposes, first one is for growth and development, but also as enzymes, to protect it from bacterias. We know that the macromolecules were present because when we did the different tests the colors of the indicators because darker, just as the egg membrane test. Lastly, the egg yolk contains all four macromolecules, it contains monosaccharides(3/10), water(8/10), polysaccharides(4/10) and lipids(7/10) as energy, but also to make up the cell's internal membrane, which is covering the yolk. Again, the indicators colors turned a darker color to show that the macromolecules. The Benedict solution turned a darker navy blue. The Iodine turned a dark brown/purple. The Sudan III/IV turned a dark red/orange. Lastly, the the copper sulfate turned a dark royal blue. This data supports our claim because it one figure out which macromolecules are present in the different parts of the egg.

          Some possible errors that could have happened are the amount of drops of each solution where dropped into the different tests. My group dropped in 1-2 drops. This could have effected the outcome depending on whether my group members dropped in 1 or 2 drops this could have effected the outcome by a little. Another possible error is the amount of ml (the parts of the egg we tested. which were in the test tubes, they may have not been the right amount and it may have affected the color. To improve this lab, I would first have a perfectly controlled and tested experiment where only one person does everything so you know how many drops to do, or just tell your group mates to use the same amount of drops. To solve the second problem,  I would have used another tool to get the 1 ml of water, white, yolk and membrane, to be more precise.

           The purpose of the lab was to demonstrate that different macromolecules are present in the different part of the eggs. From this lab, I learned that certain macromolecules were only present in certain parts of the cell and that they had different uses depending on where they were, which helps me understand the concept of macromolecules and their functions. Based on my experience from this lab,  I may be able to do more experiments with eggs, and solutions such as the indicators that we used in the lab. Taking other food items and adding indicators to the different parts and seeing whether or not it has any macromolecules.

The 20 Big Questions in Science

Are we alone in the universe?

The question that I am most interested is: Are we alone in the universe?
I'm most interested in this question because I often ponder upon this question on my own time. Sometimes daydreaming and coming out with some solution and sometimes ending with more questions.
My hypothesis is: If we are not alone on this universe, then one day humans will either find us or life will find us.

My 20 Big Questions:

1) Is there another word for synonym?

2)If a turtle is doesn't have a shell then is it considered homeless?

3)What color would a chameleon was put in a room full of mirrors and the room magically contained light?

4)Why is a building called a building if it is already build?

5) What do dinosaurs really sound like? 

6) Why don't most fish blink?

7) Why can't you breathe out of your mouth and nose at the same time?

8) What does water taste like?

9)Who invented school?

10) When did dogs become a social norm to have as a pet?

11)Why do so many people like pizza?

12)Who was the first person to classify something as funny?

13)Who created the concept of money?

14) What would the world look like if no laws were in place?

16)Who is the smartest person in the world? 

17)Why do people have to eat, sleep, and drink?

18)I wonder what life would be like if we did not have school?

19) I wonder what life would be like if we did not invent computer?

20) What does "slow down" and "slow up" mean the same thing?

Identifying Questions and Hypotheses

The study I have found asks the question: Are viruses alive? 
The hypothesis of the study is: that viruses are living entities that share a long evolutionary history with cells.
This study offers offers the a reliable method that traces viral evolution back in time when neither viruses nor cells existed in the forms recognized today, the researches say.
Link: http://www.sciencedaily.com/releases/2015/09/150925142658.htm 
Prior Knowledge: Viruses can be difficult to classify. I did not know much about viruses but I did know, that they are an invective molecule which consists of nucleic acid, and is too small to be seen microscopy, and is able to to multiply within the living cells of the host.  

Unit 2 Reflection

Unit 2 was about topics like enzymes, element, molecules, the big 4 Macro Molecules, amino acids etc.

Molecules are made up of protons which have a positive charge, electrons which have a negative charge. We also learned how milk curdles. This happens by taking a substrate (casein) and an enzyme to speed up that process (rennin) and then you create a hot condition and the milk curdles, then you stick the curdles together to make cheese. There are 3 types of carbohydrates monosacchides (which means 1), disacchrides (which means 2), and polysacchrides (which means 3 or more). There function is to store energy. The second macro molecule is lipids and they are essentially long chains that contain carbon and hydrogen called fatty acids. There function is to store energy. The third one is protein. Proteins are build with amino acids and look a little like chains. There are 20 different kinds of amino acids, each with different purpose. Changing one amino acid actual changes the type of protein the object become. The last one is nucleic acids they are large molecules composed of up to thousands of repeating nucleatides.  

My strengths were learning about the proteins and molecules and the process of making cheese. I fully understood this mostly because we touched base on it during class through labs and discussions. I think that one of my weaknesses would be       

Cheese Lab Conclusion

In this lab we asked the question: What are the optimal conditions and curdling agents for making cheese? This experiment was conducted to take a closer look at different factors that affect the curdling  of milk (the curdling agent and the and the optimal conditions). My claim is that there were two factors that affected the process the most and they were heat and the acid. The solution to the problem was that both curdled the milk within a good 5-7 minutes faster than our other factors. My evidence gathered supports the claim because cow’s stomach is both hot and acidic. A cow’s stomach is the best place to curdle cheese. Cheese is made by coagulating milk to produce curds (solids) and whey (liquid). More of my evidence proves my claim because the hot and cold temperature took quite a while to curdle with chymosin or rennin, along with the regular milk that had no testing no agent.  In fact when the milk was tested with a cold condition it reached max time (35 mins) without curdling.

There were at least two major errors that took effect in this lab. The first error was that when testing the temperature for HOT, the water that the tubes of milk were put in were colder than the temperature WARM was supposed to be in. In fact, the milk that had the WARM condition curdled in 9 minutes, yet the HOT condition curdled in 20 minutes. So this messed with the results a little because the HOT condition was supposed to curdle faster than the warm condition. The second error that took effect on this lab was a little more hypothetical. In the bucket of ice that was used as the cold condition there was a lot of cold water and some ice. From time to time I had to add in extra ice into the bucket. That may have affected the temperature. Therefore, affecting the end results, the curdle.

There are two recommendations that I would give so that the errors above could either be removed or minimized. My first suggestion would be to check the temperature of the HOT condition and check the temperature of the WARM condition and make sure that the temperature of the HOT condition is hotter that the WARM condition. Regularly check both condition to make sure that the temperature stays consistent. The second recommendation would be to start of with a full bucket of ice and leave it to melt as time goes by without adding extra ice the bucket. This will keep the temperature more likely to become consistent, ending with more consistent results.

The purpose of this lab was to demonstrate how cheese is made. More specifically how cheese is curdled with a substrate and and enzyme. This labs relates to something in class because before the lab began Mr. Orre demonstrated on the board that in order for milk to curdle you must first have a substrate and mix it with an enzyme. In the lab we used this information given in class by using a substrate (EX. Casein) and a enzyme (EX. rennin). I can apply this knowledge in future experiment with enzymes and create the best environment for them to function.

         

Sweetness Lab

          The question of this lab was: How does the structure of a carbohydrate affect its taste (sweetness)?  Monosaccharides were sweeter than the disaccharides and the polysaccharides having three different tests. The first test was fructose I rated this a 100 on a scale of 0-100. Fructose is white and has a granular texture, it melts rather than dissolves in your mouth quite fast. The second monosaccharide that was tested was glucose. Now glucose was not as sweet as fructose but still rated a staggering 90 on the scale of 100. Now glucose was had the same texture (granular) and color (white). I noticed that glucose tasted like an artificial sweetener, kind of like splenda. The third and final monosaccharide was galactose, I rated this a 60 out of 100 which was a lot less sweeter than the other monosaccharides, but it was still one of the higher sugars. I observed the texture of the of this sugar and it felt like powder. Sugared powder. The sugar was also white. The disaccharides were a little different. Most of them were not as sweet as the monosacharides. Sucrose was the only one to rate 100 out of 100 and that had a white granular texture. This dissolved in my mouth really fast. The next disaccharide was Maltose. Maltose did not taste like most sugars and had a powdery texture. I rated it a 40. It did not taste like most sugars, it was more like a maple syrup. The final disaccharide was lactose. Lactose is the sugar in milk and what makes the milk a little sweet, so I was it expecting it to be sweet, but I ended up rating it a 10 on the scale. It had a powdery texture and was white. The lactose also did not melt nicely it just stayed in my mouth and eventually started tasting like paper. Finally, the polysaccharides. To me these did not taste like sugars. There were two and I rated both a 0. Starch and cellulose were both white, both powdery, and neither of them tasted like anything, not even paper.

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          My data states that monosacchrides were the sweetest kind of carbohydrates. This may be because monosacchrides are the smallest kind of structure, and the taste cells on our tongue may prefer single cell structures (monosacchrides) versus multiple cell structures (polysacchrides). The way we measured the sweetness lab had possible error. Everyone has a different conception of what not-very-sweet mean and what very-sweet means. The second error happened because each testers taste cells are different and respond differently to different levels of sweetness. The third and final error would be that maybe not all of the tester could have drank water between tests to clean their palate.

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          Not all tester gave the same rating for all the sugars, especially lactose. Lactose is the sugar in milk, and I rated lactose pretty low. A 10 out of 100. I spoke to some people that rated this 40-60. These people drink a lot of milk and enjoy the sweet taste. Now me personally do not drink mil that has lactose  in it (my mother is lactose free and we just drink her milk). When I was younger I had a problem with dairy products and so from a young age never really enjoyed regular milk. So I think a difference here could be people who like milk and people who do not. I think another difference could simply be that people just had a different thought of what sweetness level 40-60 should be. My 10 could have been another person 40. Lastly, there was a common difference between the sweetness level between sucrose and fructose. For me personally both sucrose and fructose were the same level of sweetness. Only difference was that sucrose melted in your mouth faster than fructose. For other people there could be the problem of have a different definition of sweetness that me on the scale of 0-100.

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          Humans can taste sweetness because of our taste buds. We can taste anything because of our taste buds. Taste buds are sensory organ found on one's tongue. If you were to look at your tongue in the mirror right now you would be able to spot dots/small lumps. Those are called papilla and most of them contain your taste buds. In one's tongue we average to have about 10,000 taste buds that get replaced every 2 weeks. According to KidsHealth while you are chewing the food releases chemicals that travel up your nose.  The chemicals trigger of the olfactory receptors inside your nose. They work together with your taste buds to create the flavor of what your eating. Everyone tastes differently because they have different tastes. This may because some testers have more cells and then they may experience more flavor.

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Jean Lab Conclusion

In this lab we asked the question, What concentration of bleach is best to fade the color out of the new denim material in 10 minutes without visible damage to the fabric? My group found out that 50% concentration of bleach is the best to wash out the color of the denim square. When the 50% bleach was tested its color removal was not as significant as the solution with 100% bleach, but averaged a 3.5 on a scale of 1-10. Taking a look at fabric damage for the 50% bleach solution, the average came up to be 1 on the scale. When we tested the 100% bleach, the color removals averaged to be a 8, but the denim damage was a 2, which was higher than the solution with 50%.  other sentence

While our hypothesis was supported our data,... that the 50% bleach solution was the best, there could have been errors due to having a slight delay in time. The fact that we had a slight delay in time was because we started with the wrong procedure. After we figured out that we had started the with the wrong procedure, my team and I cleaned up and started new. Two of my lab partners went and got clean materials (i.e. jean squares, petri dishes), and my other one and I filled up the beakers with the correct amount of bleach and water.

The lab was done to demonstrate how solutions with bleach and/or water can effect a piece of denim by the amount of color it washes and how much damage creates. By taking part in this lab I learned that both bleach is a very strong chemical and can get out stains and make denim white but it is also very damaging. Based on my experience from this lab i could apply this to real life situations, keeping in mind how strong of a chemical bleach is and how it can damage my clothes.

Concentration % Bleach	Average Color Removal	Average Fabric Damage
100	8	2
50	3.5	1
25	3	0.5
12.5	2	0.5
0	0	0