Unit 5 Reflection

This unit was about DNA and what it does.  DNA contains the code for all life. It is made of a double helix that is connected by nucleotides. The nitrogen bases are purines (Adenine and Guanine), and pyrimidines (Thymine and Cytosine). Adenine (A) pairs up with thymine (T). Cytosine (C) and guanine (G) pair up.
DNA is unzipped by enzymes. DNA polymerase uses one of the strands as a template to add matching nucleotides to it. DNA codes for proteins. First, DNA is made into mRNA by RNA polymerase that matches spare nucleotides to make single stranded RNA. This is transcription. Second is translation. mRNA arrives at the ribosomes, which read codons to make amino acids which become proteins.
Sometimes there can be mutations. Point mutations change one or two bases. They can be substituted, inserted, or deleted. If the mutation occurs at the start then it is likely to be more harmful.
We also learned about gene regulation. The genes can be turned on or off based on when it needs to. It is extremely complex in human cells. In bacteria for lactose, a repressor molecule is attached to the operator to stop RNA polymerase from working. However, when lactose is present the repressor is detached and the gene for making lactase to break down lactose is created.
I found this unit to be relatively short and easy, however gene regulation is a little complicated and confusing. I tried using reading to learn by re writing key points on flashcards and quizzing myself. It worked quite well. I am a better student today because I understand more about previous unites, especially unit 4 and 3 which had to do with genetics and cells. I have a bunch of unanswered questions. Can we change someones DNA? How does the mRNA get to the ribosome? How do the ribosomes make the amino acids from the codons? What happens to the other DNA strand that does not take place in making mRNA?  Can we ever clone humans? \

A picture of extracted DNA 

DNA replication 

https://commons.wikimedia.org/wiki/File:0323_DNA_Replication.jpg

Protein synthesis conclusion

There are two major steps to make protein. First, transcription occurs. In this step, DNA is unzipped, and RNA matches the nucleotides to make a single stranded mRNA. Uracil replaces thymine. The mRNA leaves the nucleus for the cytoplasm. Second, translation occurs. The mRNA binds with a ribosome. The ribosome reads 3 bases (codons) at a time and determines with amino acid corresponds to that codon. The amino acids link together and eventually become a protein.

The mutation that causes the most harm is frameshift mutation. Substitution can be deadly, but rarely, because it only changes one amino acid and sometimes it may not change it at all. Where the mutation occurs is very important. If a deletion or insertion is made in the beginning, then all the codons in the DNA sequence after it will be moved forward or backwards. If the mutation happens towards the end, then only the codons after it will be affected. If the T we removed was near the end, then more codons would have been coded, and less would be affected. However, it was near the start, so many more codons were not coded.

The mutation I chose in step seven was a frameshift mutation, deletion, that took away the first codon.  This mutation affected the proteins the most out of all the mutations, because it took away the start codon, Met (AUG). None of the proteins were made because the ribosome(s) did not start to read them. It was really important that it was near the start. If it was near the middle, all codons would be read, but some would not necessarily be the right ones. If it was near the end, then all codons would be read, and a few would be the wrong ones.

A single mutation can greatly affect a person's life. Tay-Sachs disease is a rare inherited disorder that eventually destroys nerve cells in the brain and spinal cord. The most common form of Tay-Sachs disease is shown during infancy. Infants with this disorder usually appear normal until the age of 3 to 6 months, and their development slows and the muscles used for movement weaken. These infants lose necessary skills such as turning over, sitting, and crawling. They also experience intellectual disability and seizures. Children with this form of the disorder usually die during early childhood. 

Picture Links: 

http://www.bing.com/images/search?q=Baby+Boy+Crawling&view=detailv2&&id=28632541ED07699F5E9AF6849BE8531E657F9C69&selectedIndex=0&ccid=j9GcfQ24&simid=608050263347168714&thid=OIP.M8fd19c7d0db89dde16f628e748e24c18o0&ajaxhist=0

https://commons.wikimedia.org/wiki/File:Missense_Mutation_Example.jpg

DNA extraction

In this lab, we asked the question: How DNA be separated from cheek cells in order to study it? We found that DNA becomes visible during precipitation, when we gently poured alcohol into the Gatorade, it rises up from the Gatorade into the alcohol. First, we swished Gatorade in our mouth, after we gently scrapped the inside of our mouths, which was homogenization. Then, we spit it into the cup and added an enzyme (pineapple juice) and soap, which was lysis. Then precipitation occurred once we slowly poured cold alcohol into the Gatorade. Since DNA is polar and so is water, the DNA was dissolved in the water. Once it came in contact with the non polar alcohol, it was able to form into visible stringy clumps with oxygen. This supports our hypothesis, because we predicted the DNA would become visible during precipitation.

While our hypothesis was supported by our data, there could have been a few errors. First, the alcohol could have mixed with the Gatorade if you poured it too hard. That would cause the DNA to remain unseen because it would not rise to the top. Second, there could have been too much  Gatorade and/or too little cheek cells . That could have caused the DNA to not show up or not float up to the alcohol during precipitation. Due to these errors, in future experiments, I would recommend to have a measured amount of Gatorade and wipe the inside of the cheek with cotton around ten times. To solve the Gatorade and alcohol mixing, you should tilt the Gatorade test tube and let the alcohol trickle in.

This lab was done to demonstrate that DNA is found in all cells, and it is possible to make it visible during precipitation. From this lab I learnt that the protocol for DNA involves three steps: homogenization (where we added a protease and enzyme), lysis, and precipitation, which helps me understand the concept of DNA extraction that many scientists use. Based on my experience from this lab, I understand the basic methods scientists use to extract DNA, and a LOT or DNA is inside cells.

Unit 4 Reflection

Units 4 essential question was "Why is sex so great?" The themes were meiosis vs. mitosis and Mendel's laws. We also discussed the different types of alleles and how we can predict the genotypes of offspring. Sexual and asexual reproduction were also introduced. I think I understood most of the topics quite well. It is a little difficult for me to understand monohybrid and dihybrid crosses, especially if the individuals are heterozygous. Epistasis can also be very confusing sometimes.

From the infogrpahic, I realized how important it is to learn how to include only vital information and make it look presentable and interesting for someone to actually take in information well. I understand some of the complicated genetic concepts now, although I have A LOT of unanswered questions. I wonder what traits are hereditary? How much does genotype determine about a person?  Will we ever be able to change a persons genotype? Can we clone humans?  and of course WHY is the ratio of men to woman 101:100???etc. 

According to the questionnaire, I am a multimodal learner and prefer all different methods: 

• Visual 8
• Aural 11
• Read/Write 10
• Kinesthetic 12

 Personally, I am surprised that I got such a high score for kinesthetic. I personally prefer reading/writing and aural methods. Usually, I just read all the important terms out loud, or have someone quiz me. To prepare for the test this time, I will make flashcards, write a question and answer, have someone ask me the questions and answer them, and then re-write the ones I got wrong. I might even make some little hand motions to clear up confusing concepts. 

Coin Sex Lab

In this lab, we flipped coins to simulate sex and determine the probability of what alleles multiple offspring will receive. Coins serve as a model for genetics concepts where genes randomly segregate during meiosis and come together during recombination. We determined the sex of offspring, chances of having bipolar disorder, an autosomal (non sex) and monohybrid (only one pair of alleles) trait, and chances of being colorblind, an X linked recessive trait.

In the di-hybrid cross simulation, we looked at the alleles on the genes for hair and eye color of the offspring of two double heterozygous individuals. We hypothesized that the probability of them having a child with blonde hair and blue eyes is 1/16. The expected results were 9 with brown hair and eyes, 3 with brown hair blue eyes, 3 with blonde hair brown eyes, and 1 offspring with blonde hair and blue eyes who would be homologous recessive. However, we got 7 brown hair/ eyes, 3 brown hair/ blue eyes, 4 with blonde hair/ brown eyes, and TWO with blonde hair and blue eyes. Unlikely things happened. We did not get the expected ratio of 9:3:3:1, but instead got 7:3:4:2. This could be because it was probable but it happened to lean towards the unlikely side. Also, because of the law of averages, the more trials the closer the probability, and if we had done more trials it would have been much closer.

The limit of using probability to predict our offspring is that sometimes we may not know the genotypes of the parents to predict the traits of the offspring. We also do not know what exact pairs of alleles the offspring may receive.

It made me more aware of the risk my own children may be at of having disorders or the chances they have to receive certain traits. For example, my offspring may have bipolar disorder, even though I do not have it, but my spouse does. This made me more aware of disorders and traits that can happen.

Genetics Infographic

In case it doesnt work, or its too small, here is the link to my original  

https://magic.piktochart.com/output/9417023-genetics-inforgraphic

Unit 3 Reflection

In this unit, we learned about cells. First, we learned about the cell theory. It states that all living things are made up of cells,cells are the basic unit of life, and that new cells come form previously existing cells. We also learned about prokaryotic cells vs. eukaryotic cells. Eukaryotic cells have nuclei and many cell organelles. All of these organelles have different, important functions. Nucleus contains the DNA. Ribosomes, rough ER, and the Golgi apparatus all help in producing proteins. The mitochondria help in producing ATP. The chloroplasts (only in plant cells) are where photosynthesis occurs. The cell wall provides support. The cell membrane is a selectively permeable lipid bilayer that allows only certain molecules to pass through using protein channels, osmosis, and diffusion. Diffusion is the movement of cells from areas of high to low concentration. Osmosis is the diffusion of water. Another thing we learned about was photosynthesis and cellular respiration. 

For me, the topic of cell organelles and their functions is the easiest and the best understood. Diffusion and osmosis is understood but a little confusing. The topics of photosynthesis and cellular respiration confuse me the most, and were the more difficult to learn because they have so many steps and molecules involved. I wonder how cells evolved. I really want to learn more about photosynthesis and the nucleus, like how does the DNA inside give the instructions? 

Egg Diffusion lab

In this lab, we put one egg in sugar water and the other in deionized water, to see how a cell's internal environment changes as its external environment changes.
When the sugar concentration increased, the mass and circumference decreased. The cell's mass changed by an average of -47.25% and the circumference changed by an average of -22.94%. The sugar solution is a hypertonic solution because there is more solute outside the cell. Now, there is high solute concentration (sugar) and low solvent concentration (water) outside the cell than inside the cell. To balance the concentration, the water inside the cell diffused to the area outside the cell where there was a low concentration of water. The sugar could not go inside the cell, because the cell membrane is semipermeable and does not allow solutes to pass through since they are too big.

A cell's internal environment changes as the external environment changes to maintain homeostasis. Sometimes, the cell can grow and shrink using diffusion to maintain the concentration gradient. When we put the cell in vinegar, it grew because the solvent concentration outside the cell was high, and in the water it grew even more. However, when we put it in the sugar water, it shrunk because all the water diffused out.

We learned a lot about diffusion, solvents, and solutes and how they help a cell live. One major biological principle we learned in class was passive diffusion and the concentration gradient. This concept is used a lot in real life as well. When roads are salted to melt the ice, it can sometimes cause the plants to shrivel up because there is a lot more solute outside the plants' cells now, so the water inside the cells will leave the cell, causing it to shrink.
One experiment I want to do is to see if all cells will react the same way. I could see if fresh fruits and vegetables react the same way when they are put in sugar water or deionized water.

Eggcellent experiment- Egg Macromolecules Lab

In this lab, we asked the question can macromolecules be identified in an egg cell?
We found that egg yolk tested positive for lipids. When Sudan III was added to the yolk it turned from red to orange, and it turned a very dark orange, indicating that egg yolk has many lipids. Egg yolk may have lipids because lipids make up the thin membrane surrounding the yolk, and is used for energy for growth and development.
Egg white tested positive for proteins and monosaccharides. When tested for proteins, it turned purple, and when tested for monosaccharides, it turned greenish blue. Monosaccharides are used for energy and development. Proteins contain the enzymes needed to break down the carbohydrates for energy, and it can also be used for growth and a last line of immunity.
Egg membrane tested positive for polysaccharides, proteins, and lipids. When tested for polysaccharides it turned a very dark brown. When tested for proteins, it turned purple. When tested for lipids it turned a light orange. Polysaccharides are found on the surface of cells to communicate. Proteins are used as transport proteins in the cell membrane. Lipids (phospholipids) make up the membrane.

There could have been some errors due to difficulty of separating the eggs parts and bias towards the color. It was very difficult to separate the different egg parts completely. The yolk and the egg membrane mixed a little, so the egg white tested positive for some macromolecules that should not have been there, such as monosaccharides. The bias towards color could have also resulted in some errors. Our data said that certain parts tested positive because they turned a certain color, but it could have been a different color, but someone thought it was another color, or a deeper/ lighter shade. For example, with the polysaccharides it was hard to determine what turned "black" and what was "brown". I would recommend having a better way to separate the egg, rather than poking it open, such as rinsing the egg membrane to wash off any yolk/white that is on it, and gently separating the yolk and white. To eliminate the bias, more than two or more people should determine the color, or there is already a sample of a macromolecule that has been tested to compare our sample to.

The purpose of this lab was to identify the different macromolecules avaliable in certain parts of a cell. In class, we learned about the different macromolecules and cell organelles and how the are related, and we re-enforced that concept with this lab. Based on my experience from this lab, I know understand more about how cells work, and why eggs have the layers and macromolecules that they do.

Identifying questions and hypothesis

I found a study saying that many people are missing certain genes, and the variation depends on what part of the world that person comes from.The question is: Do people all have the same genes, and if not then is it problematic? The hypothesis is: If several people around the globe can have over 200 missing genes, then it is not problematic.

To read the ful article click here:
http://www.sciencedaily.com/releases/2015/10/151001094723.htm

Inquiry hour 1.2

The most interesting science question is: Is time travel possible? There have been several photographs of people in the past using technology from our time or ahead and having a sense of fashion that seems a bit too modern. Not only is time travel a fascinating science-fiction idea that has been around for decades, but making time travel possible might just help us solve many other scientific questions. For example, time travel can be used to see: how life began, how the universe came into being, will robots take over in the future, will we ever solve global warming?  A current hypothesis for this could be-  if physicists have already planned how to travel back in time and astronauts in the international space station experience time ticking slower, then time travel is possible.

Some questions I have:
How did the universe come into being?
Will the universe ever end? If so, when and how?
Can anything live forever?
Will time ever end?
Will humans ever live on another planet/moon?
For how much longer will the earth be habitable?
How did DNA evolve?
Why are hammer head sharks shaped the way they are?
How did the dionsaurs become extinct?
What will humans evolve into in another 2000 years?
Why can't we remember our dreams?
Why can't we manufacture water?
Why are some people superstitiuos?
Why don't we use up our entire brain?
How did humans become the dominant species?
What would have been the dominant species if humans didnt evolve well?
Will robots ever take over the world?
Can diabetes be cured?
Can stress be a good thing?
How do dogs learn human languages?

Unit 2 Reflection

In this unit, we learned about the chemistry of life. The first thing we learned about was atoms. The three subatomic parts are neutrons,protons, and electrons. Neutrons and protons make up the nucleus at the center of the atom, and the electrons revolve around it. Material made out of one type of atom is called an element. Two or more elements come together to form a compound. Atoms also form bonds. Ionic bonds are formed when electrons are transferred from one atom to another. Double ionic bonds are formed when two electrons are shared. Covalent bonds are formed when atoms are shared between two atoms.

Water works well due to it polarity or unequal distribution of electrons. Its oxygen has a negative charge, but the two hydrogen have a positive charge. Water also is very cohesive, meaning it has a strong attraction with molecules of the same substance. It is also very adhesive, meaning it also has a strong attraction with molecules of different substances. Because of these properties, water makes a great solvent. A solution is a mixture of equal components. A solute is what is being dissolved and a solvent is what the solute is dissolved in. Suspensions have an unequal distribution of the substances. Different substances can also have different levels of acid or bases. The pH scale is used to measure that. The more H+ ions, the more acidic something is. The less H+ ions, the more basic something is. 7 on the pH scale is neutral. Anything lower than 7, from 0 to 6 is acidic. Anything higher than seven, 8-14 is basic.

Four main macro molecules make organic compounds- carbohydrates, lipids, proteins, and nucleic acids. Carbohydrates are sugars. They are made up of rings of carbon, hydrogen, and oxygen. Producers use it to store energy and consumers use it as a source. Monosaccharides are one ring of sugar, disaccharides are two, and polysaccharides are three rings or more. Lipids are long chains of carbon and hydrogen and most are nonpolar. They are used for energy storage, make up cell membranes,and make hormones. There are two types- saturated fats and unsaturated fats. Proteins are used for structure. Nucleic acids are used mainly for carrying out and passing out genetic information. Enzymes are catalysts that help reaction go faster by lowering activation energy. They work best in certain pH and temperature or else they become denatures/deformed.

The themes were mainly the four macro molecules, their structure and function. Enzymes were pretty important as well. I think this unit went pretty well, the only confusing part was the different structures and functions of the macromolecules because there were so many. I think I would like to learn more about nucleic acids. We focused A LOT on carbohydrates, proteins, lipids, and enzymes which mostly have to do with energy and structure of organisms. However, we talked very little about nucleic acids. How exactly do they write the genetic code? How do they carry it out? How can the information for a whole organism be written by a few nucleic acids? What is the structure of DNA?

Cheese Lab

In this lab, we asked the question: what are the optimal conditions and curdling agents for making cheese? We found that warm and acidic conditions are optimal and chymosin is the best curdling agent. Chymosin, rennin, and buttermilk all curdled the milk in five minutes or less in a more acidic environment. Chymosin and rennin showed some signs of curdling in five minutes or less in the heat. Nothing curdled in a colder environment within the time we had. Chymosin was the only enzyme that curdled the milk within the time we had with a time of 20 minutes in a more basic environment. The warm and acidic conditions had the fastest times for all the different enzymes. Since chymosin curdled the milk in almost every condition except the cold, it was the optimal curdling agent. While rennin still curdled milk a little quicker in the pH control, we decided chymosin was better because it curdled the milk in more conditions.

While our hypothesis was supported by our data, there could have been errors due to timing and the control/heat. There could be errors due to timing because our instructions told us to check for curds every five minutes. However, the curds could have appeared after four or even three minutes. So while the data says that milk with chymosin, rennin, or buttermilk under acidic conditions curdled in exactly five minutes, the times could actually be quicker. Another was with the control because the temperature of everyone’s armpit could be different. Some people had jackets on and some did not. This could have an effect on the curdling time as well, because as we can see, warm conditions are better for the reactions to happen. Everyone has a slightly different body temperature, so the cooler people would have slower reactions, and the warmer people would have faster reactions. Due to these errors, in future experiments I would recommend two changes. One, check the curds every minute instead of every five minutes. This will reduce the margin of error. Two, put the mixtures in an environment with a similar temperature to the human body, but make all of them exactly the same temperature.

This lab was done to demonstrate how enzymes work at their best when they are in favorable pH and temperature conditions. From this lab I learned that enzymes work best in certain conditions and not very well in others, which helps me understand the concept of denaturation and activation energy. Based on my experience from this lab, I will be able to change the conditions if I want a reaction with an enzyme to occur faster.

Curdling Agent:	chymosin	rennin	buttermilk	milk (control)
Acid	5	5	5
Base	20
pH control	15	10
Cold
Hot	5	5
Temp control	10	10

Sweetness Lab

In this lab, we asked the question: how does the structure of a carbohydrate affect its sweetness. We found that the monosaccharides are very sweet, and polysaccharides are quite bland; therefore, the fewer the rings, the sweeter the carbohydrate. The monosaccharides fructose and glucose and the disaccharide sucrose were the top three sweetest carbohydrates. Sucrose was used as the standard sweetness at 100. Fructose had a sweetness degree of 115 and glucose had a sweetness degree of 90. The polysaccharides starch and cellulose were extremely bland. Starch had a sweetness degree of 10, and cellulose had no sweetness degree. Since the sweetest carbohydrates were monosaccharides and the blandest were polysaccharides, a carbohydrate is sweeter when it has less rings of carbon, hydrogen, and oxygen.  

Monosaccharides and disaccharides are mainly used as sources of energy for the cell. This is because they are easier to break up since not many rings are bonded together. The polysaccharides are mostly used for forming the cell wall since there are more rings bonded together it is more resistant and cannot be broken apart so easily.  

Not all of the tasters gave the exact same rating. One reason could be that different testers are used to eating different sweetness levels, so someone who eats a lot of sugar will need more sugar for the carbohydrate to be sweet and someone who is accustomed to less sugar needs less for the carbohydrate to taste sweet. Another reason could be that some people are genetically inclined to have more taste buds on their tongue. Therefore, the more tastebuds they have the more flavor they can detect. A third reason is ability smell. It is possible that one person had a cold and a blocked nose, so he or she could not smell very well. Smell helps in identifying flavor.

According to Dr. Robert Magolskee on NPR, the taste bud contains about 50 or 100 taste cells, and maybe a quarter of them are responding to sweetness, and a different percentage of them will respond to salty and sour and bitter. Sweet receptor protein and the sugar encounter each other, they excite the sweet taste cell, and that sends a signal to the brain, to particular centers of the central nervous system that respond to sweetness. In particular for common types of sweet compounds such as sucrose and glucose and fructose, the monosaccharide and disaccharide sweeteners, there are extra pathways, extra mechanisms that allow us to taste something as being sweet. These are sugar transporters and special ion channels, potassium ion channels. The number of tastebuds could play a role in tasters ranking the same samples differently because the more taste buds, the more sweet receptor proteins. Some people will have more proteins to taste all the sweetness.

Sources:

"Getting a Sense of How We Taste Sweetness." NPR. NPR,  Mar. 11  2011. Web.Sept. 16 2015. <http://www.npr.org/2011/03/11/134459338/Getting-a-Sense-of-How-We-Taste-Sweetness>

Carbohydrate	Type of Carbohydrate	Degree of Sweetness	Color	Texture	Other Observations
Sucrose	Disaccharide	100	white	granular	sugar
Glucose	Monosaccharide	90	transparent white	granular	granulated sugar
Fructose	Monosaccharide	115	white	granular	granulated sugar
Galactose	Monosaccharide	50	brownish yellow	powder	powdered sugar
Maltose	Disaccharide	110	white	soft	brown sugar
Lactose	Disaccharide	20	white	soft powder	powdered milk
Starch	Polysaccharide	10	white	sticky powder	potato/corn
Cellulose	Polysaccharide	0	white	soft and sticky	paper

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 ten minutes without visible damage to the fabric. We found that using 100% concentration of bleach is the most effective way to give a faded look to new denim material. Using one hundred percent concentrated bleach reduced color by an average of 80% and had almost no visible fabric damage with an average of 10% visible damage. There were no holes, tears, or extreme weakening of the fabric and the dark blue jeans became a blueish white. It is widely known that bleach is a disinfectant that removes color so more bleach will remove more color. Since more amounts of bleach removes more color from clothes, 100% concentration of bleach removes the most color. It also had little to none damage, and the most extreme case had been damaged by only 10%, making it the most efficient way to fade new jeans.

While our hypothesis was supported by our data, there could have been two possible errors. The first possible error was that each of the denim squares was subjected to the bleach for different amounts of time. Since we submerged the denim squares one at a time, we could not track the exact time they were in the bleach, lying on the table, and in the water to wash away the bleach. The squares that were submerged in the bleach for longer and washed for shorter amounts of time were exposed to the bleach for longer amounts of time, so they would possibly have a more faded look. Those that were in the bleach for a shorter amount of time and washed for a longer amount of time had less time for the bleach to fade the color. Also, we did not use fresh water to rinse the material each time so some bleach may have been left behind in the rinsing water. The second error was that each square of denim material was a different color. Some of the squares were a very dark blue and some were already slightly faded. Since we did not track which ones were dark or light in the beginning, the dark jeans would not have looked as faded and the lighter jeans would have looked a lot more faded. Due to these errors, in future experiments I would recommend to use the same color of denim material, time more accurately, and to use fresh water for every rinse.  

This lab was done to demonstrate the process of the scientific method. From this lab, I learned the different parts of the Scientific Method which helps me understand how to solve different questions and answers with a scientific procedure. Based on my experience from this lab, I know how to form a good hypothesis, design an experiment with controls and variables, and present my data.I can use this to solve scientific problems/ questions in the future.

Concentration (% bleach)	Average Color Removal (scale 1-10)	Average Fabric Damage (scale 1-10)
100	8	1
50	5	0.50
25	2.33	0
12.5	1	0
0	0	0