Unit 5 Reflection

Unit 5 was about protein synthesis, mutations, and how genes are regulated.

For this section, I had to look into my notes, but only to see how to spell some words so that doesn't count! Protein synthesis is how proteins are created from DNA. RNA polymerase makes a copy of the DNA, which is deoxyribose nucleic acid. DNA is made from a sugar, the deoxyribose, a phosphate group, and a nitrogen base, which can be either Adenine, Thymine, Guanine, or Cytosine. DNA has two strands, and twists into a double helix shape, with bases matching together. The bases match with each other, Cytosine with Guanine, and Adenine with Thymine. The copy is called RNA, which is very similar, except Thymine is replaced with Uracil, and it is single stranded instead of double stranded. This is messenger RNA. It goes out of the nucleus and to a ribosome, where it is read. Each codon, which is 3 bases, codes for one amino acid. An amino acid can be coded for by several different codons. Transfer RNA brings the amino acid to the ribosome to build the protein, and matching base pairs for the messenger RNA.


Mutations are changes in DNA. They can be deadly, or do nothing at all, which is called a silent mutation. One type of mutation is a point mutation, where a single base pair is changed. One type of point mutation is a substitution, where one base pair is substituted for another one. This type of mutation causes little to no damage, because some amino acids can be coded for in several ways, and if it does change the amino acid, it only changes one of them, which will have a small effect. The other type of point mutation is a frameshift mutation, where one base pair is added or removed. This has a large effect, and can completely ruin a protein because  in addition to changing the current codon, it shifts over all following codons, which can cause a completely different protein to be made, or cause no protein to be made at all. There are other mutations that aren't point mutations, such as inversions, which cause a piece of DNA to become unattached, and reattach backwards. Translocations are when DNA from one chromosomes attaches to a different chromosome. Mutations are caused by mutagens, such as UV, (checks notes for other mutagens) nuclear radiation, X-rays, and toxins(closes notebook).

Example of a mutation.

Gene regulation was probably the most complex part of the unit, so I will obviously be referring to my notes for this paragraph. All cells have DNA for all genes, but they don't express all genes at all times because cells don't want to waste energy by over expressing genes. A group of genes that work together is called an operon. A good example of gene regulation is the Lac Operon. The RNA attaches to the part of the DNA called the operator, and copies the gene from there. But, in Lac Operon, there is a repressor, which is like a road block, attached to the promoter. The repressor is removed when lactose appears, and attaches to it. Then, the gene can be read to create the enzyme lactase, which breaks down lactose for food. In eukaryotes, the process is more complex, and several proteins can bind before a gene. After RNA copies a gene, sections called introns, which don't code for anything, are cut out, leaving the exons, which are expressed.

1: RNA polymerase. 2: Repressor. 3: Operator. 4: Promoter. 5: Lactose

That's all we covered in unit 5. The only part I really need to study is gene regulation, and the spellings of thymine, adenine, guanine, and cytosine.

Protein Synthesis Conclusion

Proteins are created in the process of protein synthesis. It starts with DNA being copied into RNA by a molecule called RNA polymerase. The RNA then exits the nucleus and goes to a ribosome, where it is read. Each codon, or three base pairs, in RNA codes for one amino acid. An amino acid can be coded for by several codons. Transfer RNA brings the amino acids to the ribosome. At the end of the RNA strand is a STOP codon, which tells the ribosome that the protein is complete.



When DNA bases are changed in a mutation, it affects the RNA, which can either have no effect on the protein, or completely change it, depending on whether the mutation is a substitution, deletion, or insertion. Substitutions substitute one base for another. This type of mutation has very little affect on the protein, if any. It can only change one amino acid, or it may not change it at all, which is called a silent mutation. insertions and deletions have the greatest affect, because they change both the amino acid they are inserted on, and the rest of the DNA sequence. These mutations are most dangerous near the beginning of the gene, because they will affect more codons.

An example of a mutation. The plant produces different colored flowers.

In this lab, we chose a mutation to use on a DNA sequence. I chose to delete the first base, which had a huge affect, as it changed every following codon, causing the protein to have completely different amino acids, and the stop codon to appear early and end the protein before it should have. The effect would have been less if I did this in a later spot in the DNA, because less codons would have been affected.

The protein used to be:

MET-TYR-LYS-HIS-VAL-ILE-ASN-CYS-ILE

After my mutation, it changed to:

CYS-THR-ASX-MET

Mutations could affect my life because they can happen during mitosis, which means that one can occur at any time. An example of a mutation is Progeria, which causes accelerated aging. People with this disease often die from age related diseases at around age 13, such as heart attacks and strokes.

DNA Extraction Lab

In this lab, we asked how we could extract DNA from cheek cells. We found that removing the cheek cells by scratching the inside of our mouths with Gatorade, which homogenized the cells, which means that the Gatorade and cheek cells formed a colloid, and then mixing the Gatorade with salt, soap, and enzymes in pineapple juice, which  lysed the solution, meaning that the cell membrane and nuclear membrane breaks down. We then put a layer of alcohol which caused the DNA to turn in a precipitate. This worked, because after the process, we were able to see small strings and chunks in the alcohol, which was the DNA, meaning that our process worked.

One error I made was not getting enough cheek cells. When swishing the Gatorade in my mouth, I mistimed how long I was supposed to have the Gatorade in my mouth, so I gathered fewer cheek cells than others. I could fix this error in the future by using a stopwatch. Another error I may have made was using too much Gatorade, so when we poured the Gatorade with the cheek cells into the test tube, I may have poured less cells and more Gatorade, resulting in less DNA. I could fix this error by more carefully measuring any liquids.

The purpose of this lab was to show how every cell in the body has DNA in it, even if they don't use all parts of the DNA. From what I learned in this lab, I could collect cells and use them for other purposes, or collect DNA of other organisms.

Unit 4 Reflection

Unit 4 was about the cell cycle, genetics, and reproduction, and specifically about sexual reproduction.

The cell cycle is the process that divides a cell into two genetically identical cells. The first step is Interphase, which is where a cell spends most of its time. It grow, and duplicates its DNA. Next is Prophase, where the nuclear membrane dissolves and chromosomes form. After that is Metaphase, where the chromosomes line up in the center of the cell. Then, in Anaphase, the sister chromatids are pulled apart into opposite sides of the cell. Then is Telophase, where the nuclear membrane reforms, and the cells start separating. In Cytokinesis, the cells are fully split apart and the organelles duplicate.

Sexual reproduction is the combination of two cells, sperm and egg, from two different organisms to create an organism that is genetically different from the two parents. Some examples of sexual reproduction include broadcast spawning, paired spawning, spores, seeds, and copulation. Asexual reproduction is a single parent creating a genetic clone of itself. Some examples of asexual reproduction are binary fission, regeneration, and budding. Sexual and asexual reproduction both have costs and benefits. Some costs of sexual reproduction are that it takes lots of time and energy, it exposes you to STDs and parasites, not all get to reproduce, and it creates some bad genetic combinations. But its benefits are that it creates new genetic combs which create resistance to change, and it creates competition which results in only the best reproducing. The benefits of asexual reproduction are that it is fast and easy, doesn't require a mate, and you can create a lot of offspring quickly. But the costs are that it creates no genetic variation, which makes it more likely for the species to go extinct.

At this point while summarizing, I had to return to my notes, so this is a reminder to myself to study this part. Chromosomes are DNA that come in a pair, one from each parent. The types of chromosomes are autosomal and sex chromosomes. Sex chromosomes determine the gender of the child. XX is female, and XY is male. Sometimes, there are variations where someone can have extra chromosomes, such as XXY, which results in infertility, and XYY and XXX, which both let the organism have a fairly normal life. Autosomal chromosomes are all the other ones. Chromosomes come in homologous pairs, each coming from a different parent. A cell will a full set of chromosomes is a diploid cell.All cells that make up your body are diploid. Cells with half the number of chromosomes are haploids. Sex cells, or gametes, are haploids. Gametes are produced in a process called meiosis, which is similar to mitosis in the way that it splits apart to create new cells. But in meiosis, 4 cells are created, and they are genetically different haploids gametes. Meiosis happens in 2 phases, each which splits up the cells, meiosis 1 and meiosis 2. Meiosis 1 splits the homologous chromosome pairs apart, and meiosis 2 splits the sister chromatids. During prophase of meiosis 1, the homologous chromosomes cross over to exchange chunks of DNA. This is what makes them genetically different, and leads to many different genetic combinations.

Leaving my notes, the next SEX-ion (I'm so punny) was on how sex and traits are related. In sex, two gametes join to create a new organism. Gregor Mendel crossed different plants in order to find out how their traits were inherited. The first generation of one of the crosses was with purebred purple and purebred white flowers. The offspring had only purple flowers. After they self fertilized and reproduced, there was a 1:3 ration of white to purple. Mendel discovered that some genes, or pieces of DNA responsible for traits, were dominant, and some were recessive. Genes come in pairs, called alleles. If an organism has a dominant allele, then the organism will get that trait, no matter what the other allele is. But if the organism has 2 recessive alleles, then they will get the recessive trait. In the flowers, purple was dominant, and white was recessive. You can predict the probability of getting a certain phenotype, or physical trait, if you know the genotype, or genes, of the parents. When an organism has 2 of the same allele, it is called homozygous, but if it has 2 different alleles, it is heterozygous.

In sex, you can use a diagram called a punnet square to predict the probability of a phenotype if you know the genotype of the parents. In Meiosis, when crossing over occurs, a copy of an allele could go to any of the four haploid cells. So if an organism had the genotype Aa (capital is dominant, lowercase is recessive) they two of the four possible gametes would have the A gene, and the other two would have the a gene. Punnet squares show the results of crossing all the possible gametes for a given number of genes.

	A	a
A	AA	Aa
a	Aa	aa

In this punnet square, two heterozygotes were crossed, and the probabilty of having a homozygous recessive child is 1/4, because there is only one combination that would result in that.

Returning to my notes again marks another section I should review. You are stuck with whatever genes you get. Some autosomal dominant traits you can get are bipolar disorder, widow's peak, and the ability to curl your tongue. Some autosomal recessive traits include albinism, cystic fibrosis, and sickle cell anemia. Traits can also be X-linked. One X-linked dominant trait is Coffin Lowry Syndrome, which is a physical and mental handicap. Some X-linked recessive traits include colorblindness, and hemophilia.

Once again leaving my notes, the next section is on genetic complications. Genes are not all dominant and recessive. Some traits have incomplete dominance, which means that the two phenotypes from each gene combine to create a new phenotype in heterozygous genotypes. Codominance is when both traits in a heterozygous genotype are expressed completely at the same time. Gene linkage is when two genes are close together on a chromosomes, which makes it more likely for them to be inherited together. Epistasis is when a master gene controls other genes. Multifactorial disorders are when the environment influences how genes affect the phenotype of an organism. And polygenetics is when several genes control a single trait.

The final section is more on punnet squares and the different types of crosses. Monohybrid crosses are crosses where only one gene is crossed. They are done in a 2x2 punnet square. Dihybrid crosses are when 2 genes are being crossed. They are done in a 4x4 punnet square. And finally, test crosses are for finding the genotype for a trait of in an organism with an unknown genotype. To do this, you would cross them with a homozygous recessive organism. If the offspring all have the recessive trait, then the unknown is homozygous recessive. If some have the recessive trait and some have the dominant trait, then the unknown is heterozygous. If all the offspring have the dominant trait, then the unknown is homozygous dominant.

Based off of my experience writing this, I will spend more time studying the different traits found in humans and how chromosomes change in Meiosis.

Coin Sex Lab

In this lab, we flipped coins to simulate the randomness of alleles crossing over and recombination in sex. The coins represented the two copies of a gene, and flipping them simulated the randomness of which gene the gamete would get in meiosis, also known as the law of independent assortment. The results we got for simulating getting a male or female were the same as the expected result, 1/2 probability either way, because the females are homozygous, and don't get to determine the gender, while males are heterozygous, so they determine the gender with the one Y chromosome they have which has a 50% chance of being inherited. We then we simulated a monohybrid cross where we tested the probability of inheritance for an autosomal gene that causes bipolar disorder. Bipolar disorder is caused by a dominant gene, and we crossed a homozygous recessive person with a heterozygous person. We predicted that 50% of the children would have bipolar disorder, but we were wrong when our simulation resulted in 8 normal children and 2 children with bipolar disorder. This shows that the probability of getting a trait is not the same as the ratio of people with the trait, because getting a certain allele is completely random, so it doesn't necessarily follow the probability. The third trait that we tested was colorblindness, an X-linked recessive trait. Males are more likely to inherit X-linked traits because they only have one X chromosome. We crossed a heterozygous female and a male with normal vision. We predicted that 25% of the children will be colorblind males. We found that 3 out of 10 were colorblind males, which is about 25%. Our final cross was a dihybrid cross where we tested hair and eye color. We predicted that there was a 1 out of 16 chance of getting a double homozygous child from 2 double heterozygous parents. Our prediction was correct, and we got that result. All these crosses show how you can predict the probability of having a certain child, but you can't predict what the child will be.

Genetics Infographic

https://magic.piktochart.com/output/9061358-reproduction-infograph

This is the link the the full size image, which is actually legible.

Unit 3 Reflection

In Unit 3, we studied the different types and parts of cells, and their functions, and we focused specifically on cellular respiration and photosynthesis.

The different types of cells are eukaryotes and prokaryotes. Prokaryotes are cells that don't have a nucleus or most organelles. Some examples of prokaryotes include bacteria. Eukaryotes are cells with most organelles, including a nucleus. It is theorized that mitochondria and chloroplasts are prokaryotic cells that continued to live after being eaten by a eukaryotic cell.

Membranes of cells are made of 2 layers of lipids. Different membranes include in nuclear membrane, which holds the DNA in the nucleus. The lysosome digests old organelles that don't work any more, or old cells that don't work. There are 2 types of Endoplasmic Reticulum (ER), rough ER, which has ribisomes on the surface, and it helps finish making proteins. Smooth ER has no ribisomes on the surface, and detoxifies drugs. Vesicles take things out of cells. the Golgi Apparatus packages finished proteins, lipids, and hormones. Chloroplasts go through the process of photosynthesis to make glucose, and mitochondria break down glucose to create ATP for energy. And the cell membrane holds everything in the cell, and selects what enters and leaves. Other organelles are the nucleolus, which is the center of the nucleus, which starts ribisome production. In the nucleus, DNA is stored. Vacuoles store things sch as water, salts, proteins, and carbs, but not all cells have vacuoles.

Cellular Respiration and Photosynthesis were the most complicated processes we learned about, so we learned a simpler and less detailed version of both processes. Even so, they are both still somewhat difficult to understand.

A Simple Diagram of  Chloroplast

Photosynthesis occurs in the chloroplasts of cells that contain them. It consists of 2 parts, light dependent reactions, and light independent reactions. The light dependent reactions start with energy from light going through the electron transport chain inside the thykaloid. In this process, ATP and NADPH, an electron carrier, are produced. The ATP is produced when H+ ions from water go into the thykaloid, and escape through the ATP Synthase molecules, which spin to turn ADP into ATP. Then, the ATP, NADHP, and CO2 go through the Calvin Cycle in the stroma to create glucose. After going through the cycle 6 times, 1 glucose molecule is created.

Cellular respiration is the opposite of Photosynthesis. Instead of energy water, and CO2 being used to create glucose and oxygen, glucose and oxygen are used to create CO2, water, and ATP (energy). Cellular respiration goes through 3 steps. The first step is glycolysis, which takes place in the cytoplasm. It turns glucose into 2 ATP molecules, and creates Pyruvic acid, which goes to the next step, the Krebs cycle. The Krebs cycle converts the Pyruvic acid into 2 ATP, CO2, and electron carrying molecules called NADH and FADH2. Then, those electron carrying molecules and oxygen go to the electron transport chain, which uses all of those molecules to convert ADP into ATP, and creates 32 ATP, making a total of 36 for all of cellular respiration.

A much more detailed diagram of Cellular Respiration

Overall, this unit contained lots of information regarding the different organelles of eukaryotes, and focused a lot on photosynthesis and cellular respiration, the most complex topics of the unit. My only remaining questions are how prokaryotes function, since they have no organelles or nucleus.

Photosynthesis Virtual Labs

Photosynthesis Virtual Labs.

Lab 1: Glencoe Photosynthesis Lab

http://www.glencoe.com/sites/common_assets/science/virtual_labs/LS12/LS12.html

Analysis Questions

1. Make a hypothesis about which color in the visible spectrum causes the most plant growth and which color in the visible spectrum causes the least plant growth?

If chlorophyll is green, and reflects green light, then a plant exposed only to green light will not grow as well as a plant exposed to another color of light

If violet light has the shortest wavelength of all visible light, which has the most energy, then a plant exposed to violet light will grow better than a plant exposed to other colors of light.

2. How did you test your hypothesis? Which variables did you control in your experiment and which variable did you change in order to compare your growth results?

I grew both violet and green light exposed plants and compared them both to plants growing under red light as a control, and then compared the other colors of light to red.

Results:

Filter Color	Spinach Avg. Height (cm)	Raddish Avg. Height (cm)	Lettuce Avg. Height (cm)
Red			11 ⅔
Orange			6
Green			3 ⅓
Blue			12
Violet			8 ⅔

3. Analyze the results of your experiment. Did your data support your hypothesis? Explain. If you conducted tests with more than one type of seed, explain any differences or similarities you found among types of seeds.

My hypothesis was partially supported by my data. As I predicted, plants growing under green light grew the shortest of all the plants, but violet light didn’t cause the plants to grow the most. Instead, blue caused the most plant growth.

4. What conclusions can you draw about which color in the visible spectrum causes the most plant growth?

When grown under blue light, a plant will grow taller than if it was grown under a different color of light.

5. Given that white light contains all colors of the spectrum, what growth results would you expect under white light?

I would expect similar growth, because white light contains blue light, which caused the most plant growth.

Site 2: Photolab

http://www.kscience.co.uk/animations/photolab.swf

This simulation allows you to manipulate many variables. You already observed how light colors will affect the growth of a plant, in this simulation you can directly measure the rate of photosynthesis by counting the number of bubbles of oxygen that are released.

There are 3 other potential variables you could test with this simulation: amount of carbon dioxide, light intensity, and temperature.

Choose one variable and design and experiment that would test how this factor affects the rate of photosynthesis. Remember, that when designing an experiment, you need to keep all variables constant except the one you are testing. Collect data and write a lab report of your findings that includes:

• Question
• Hypothesis
• Experimental parameters (in other words, what is the dependent variable, independent variable, and control?)
• Data table
• Conclusion (Just 1st and 3rd paragraphs since there's no way to make errors in a virtual lab)

*Type this document on a word processor or in Google Docs and submit via Canvas.

In this lab we asked how temperature affected the rate of photosynthesis in plants. My hypothesis was that a plant subjected to higher temperatures would photosynthesize at a faster rate than a plant subjected to lower temperatures. To test this in the virtual lab, I set white light intensity and amount of Carbon Dioxide to the maximum allowed, and counted the amount of bubbles per minute at different temperatures, because without Carbon Dioxide and Light, photosynthesis would not occur.  My data showed that 25 degrees (C)  was the optimal temperature for photosynthesis because the most oxygen was produced at that temperature. This is probably because the enzymes in plants work best at that temperature, and anything lower or higher will begin to denature them.

This lab was done to demonstrate the effect on external conditions on internal functions such as photosynthesis. From this lab I learned how the rate of photosynthesis can be easily measured by counting the amount of oxygen bubbles, which helps me understand the reactants and products, such as oxygen, of photosynthesis and what happens to them. Based on my experience from this, I could choose optimal conditions for growing plants in a controlled environment.

Temperature Vs. Rate of Photosynthesis

Temperature (C)	Bubbles/Minute
10	24
25	66
40	54

Egg Diffusion Lab

In this lab, we took two eggs, dissolved the shells in vinegar, and then put one egg in deionized water, and the other one in sugar water. Before putting them in, we measured their masses and circumference around the middle of the egg the short way. We left the eggs in their solutions, and after 48 hours, we removed them and remeasured the circumference and mass of each. Based on the class averages, the eggs put in deionized water grew in both mass and circumference, and the egg that was put in the sugar water shrunk significantly in both mass and circumference. This happened due to the process of diffusion. Diffusion is when molecules enter a cell through the cell membrane. The water went through osmosis, which is a type of passive diffusion which uses no energy. Usually in diffusion, molecules move from an area of high concentration to low concentration. But in osmosis, the solvent of a solution goes from an area of low concentration to high concentration. In solutions, the solute can't pass through the membrane, but the solvent, such as water, can, so it will move to an area of high solute concentration, which will have a lower solvent concentration. Solutions with more solute than inside the cell are hypertonic, such as the sugar water. When the egg was placed in the sugar water, there was more solute outside the cell than inside, so water left the egg to where there was more solute, which decreased the mass by an average of -51.7% and decreased the circumference by an average of -23.67%. This is a good example of how a cell reacts to the outside environment. When we put the egg in the vinegar, the acidity dissolved the eggshell, but also some of the vinegar was absorbed by the cell through diffusion. Then when we put the egg in the water, some of the vinegar left the egg, which explains some of the groups that reported a decrease in mass and circumference. When it was put in the sugar, both the vinegar and the water left the egg through diffusion. Diffusion is important to cells, because they need to get things like water and oxygen to function, which enter through diffusion. Diffusion is a process that you can see daily. In markets, vegetables are sprinkled with water so they don't go limp, because the water diffuses into the vegetables' cells. When salt is used to melt ice on roads, the plants lose water because of diffusion as well. The high concentration of salt in the solution around them cause water to leave the plant cells, which is another example of osmosis. Based on this experiment, I would like to test it on living cells, because this process makes me think of how skin cells wrinkle when in water, which makes me wonder if diffusion is taking places with skin cells.

Deionized Water
Group #	1	2	3	4	5	6	7	Average
% Change in Mass		-0.54%	-1.47%	10.50%	0.74%	-4.20%	-5.10%	0.18%
% Change in Circumference		-2.89%	0%	21%	0%	-12.90%	-4%	0.20%

Sugar Water
Group #	1	2	3	4	5	6	7	Average
% Change in Mass		-49.72%	-55.00%	-52.00%	-49.60%	-52.40%	-56.70%	-51.70%
% Change in Circumference		-23.68%	-28%	-21%	-29%	-26.50%	-38%	-23.67%

Egg Macromolecules Lab Conclusion

In this lab, we asked which macromolecules, monosaccharides, polysaccharides, proteins, and lipids, if any, are found in the yolk, white, and membrane of an egg. We found that the egg yolk contained monosaccharides, the egg white contained monosaccharides, polysaccharides, proteins, and lipids, and the egg membrane contained monosaccharides, polysaccharides, and lipids. We tested for monosaccharides using benedicts solution, a solution that turns from blue to either green or orange in the presence of monosaccharides. When tested with the benedicts solution, the egg membrane turned dark blue, the egg yolk turned green-blue, and the egg white turned a different shade of blue, indicating monosaccharides in all 3. When testing for polysaccharides, iodine, which turns from brown to black in the presence of polysaccharides, was used to test for them. The iodine caused the egg membrane to turn dark brown, and the egg white to turn orange/light brown, which indicated polysaccharides in the egg membrane, and very few polysaccharides in the egg white. A mixture of Sodium Hydroxide (NaOH) and Copper Sulfate (CuSO₄) was used to test for proteins because when mixed with proteins, it turns from blue to purple. When mixed with all parts of the egg, only the egg white changed to a darker blue, which indicated proteins. Finally, we tested for lipids. For lipids, we used the chemical Sudan III, which changes from red to orange in the presence of lipids. Using that, the egg membrane and egg white turned orange, indicating lipids in both. The reason we found monosaccharides, polysaccharides, and lipids in the egg white was because they are used for energy by the developing organism. Proteins were found there because the organism can break them down and make its own proteins. The egg membrane had polysaccharides because they are used to communicate with other cells, and lipids were found because the membrane is made of phospholipids. Monosaccharides should not have been found, and were probably due to an experimental error. The yolk contained monosaccharides for energy.

Our data was unexpected due to various errors we made. When data from other identical experiments run in the class was compared, many people found macromolecules in parts of the egg that other groups didn't. In the egg membrane, we should have found proteins in addition to all of the other molecules we found because proteins are used during active transport in the egg membrane. In the egg yolk, we should have found polysaccharides for energy, lipids for the membrane around the yolk, and proteins for the developing organism. These errors were most likely caused by the color the egg yolk affecting the color of the chemical that was supposed to reveal the macromolecules. To fix this, less of the egg and more of the chemical should be used to test so the chemical reaction is more visible. Another error was in the lipid test. It was difficult to distinguish between the red that the chemical started as, and the orange it turned into because they are similar colors. To fix this, we could, again, use more of the chemical and less of the egg parts.

This lab was done to demonstrate where macromolecules are found in cells, and why there are there. From this lab I learned the purpose of different macromolecules, which helps me understand how cells carry out actions such as developing proteins and converting energy. Based on my experience from this lab, I can more accurately judge the effect of obvious errors in experiments, and have a better understanding on how cells work.

20 Questions Without Answers

After reading the article, "The 20 big questions in science," I was most interested in the question, about time travel. It interests me because scientist actually have a hypothesis for time travel, when I had always heard that time travel was impossible. Their hypothesis involves them using spaceships and wormholes.

The following are my big 20 questions.
1. Do all people seem the same colors the same way? (Ex: Is my red the same as your blue?)
2. What happens when you die?
3. Is there a limit to how big the universe can get?
4. What was there before the big bang?
5. What is the smallest thing that makes up other things? (Ex: What are protons made of? What are those things made of? Etc.)
6. Why does your voice sound different in a recording?
7. What is the fourth dimension?
8. Why did humans evolve to be the dominant species on the Earth, and not another species, or why not multiple species?
9. How would the Grandfather Paradox affect the world if time travel was possible?
10. Why can nothing go faster than the speed of light?
11. What would happen if electrons didn't repel each other, and we could actually touch things?
12. Is there anything completely random? (Ex: If watched closely enough, and all surrounding conditions are known, then a dice toss could be predicted.)
13. Do animals other than humans have feelings?
14. Is there a maximum limit to how hot something can get?
15. What will happen to something when it reaches 0 kelvin?
16. How much is the Earth worth in the US Dollar, ignoring supply and demand, just counting resources, location, and size?
17. How many protons can an atom have?
18. Could the Banach-Tarski Paradox ever be applied to anything in the real world?
19. At what point during evolution is a species defined as a different species than its predecessors?
20. Is there anything other than matter and energy in the universe?

Identifying Questions and Hypotheses

           Scientists in the University of Pittsburgh grew human heart tissue out of human stem cells that contracted in a petri dish. They used induced pluripotent stem cells (iPS) from human skin cells. iPS cells can be made to become any cell in the body. After being placed on a non-living "scaffold" of mouse heart cells. It developed into a heart muscle, and after 20 days of blood supply, it began contracting. The experiment was done to help repair damaged cells in the human body. They hypothesized that iPS cells would work just as well as stem cells from an embryo. Previous knowledge they had was how stem cells work from human embryos.

http://news.discovery.com/tech/biotechnology/stem-cells-grow-beating-heart-130814.htm

Unit 2 Reflection

Unit 2 was titled miniature biology. It was about atoms, water, and the four macro-molecules, lipids, nucleic acid, proteins, and carbohydrates, with extra focus on a type of protein called an enzyme.

Atoms are the smallest unit of matter that can't be divided into smaller pieces. Atoms are made of protons, which have a positive charge, and neutrons, which have a neutral charge, in the nucleus, and electrons, which have a negative charge, circling around the nucleus. The number of protons and electrons are always the same in an atom. The number of neutrons can change, but the element will still have the same chemical properties and be called an isotope. Elements are pure substances made of only one type of atom. Atoms can bond together in several ways. 3 of the bonds are ionic, covalent, and hydrogen. Ionic bonds are when one atom gives an electron to another atom, creating a positive ion (the atom that gave the electron) and a negative ion (the atom that received the electron) which are attracted together. Covalent bonds are when 2 atoms share electrons. The electrons circle around both atoms, but tend to stay more towards the atom with more protons because it has a more positive charge, which attracts the negative electrons. This causes an molecule to be polar, where one part is more negatively charged, and another part of the molecule is more positively charged. An example of this is water, where the oxygen is more negatively charged, and the hydrogen atoms are more positively charged. In water, hydrogen bonds can form where two oppositely charged part of polar molecules have a weak attraction towards each other. When atoms react, they bond to form a new substance which has completely different chemical properties than the original atoms that it came from.

Water, as previously mentioned, is a polar molecule, with a negative oxygen atom, and two positive hydrogen atoms. This makes water cohesive, which causes it to hydrogen bond to itself and stick together, which causes water to bead up in dew. It is also adhesive, which makes it hydrogen bond to other surfaces, like a meniscus on a graduated cylinder. When both adhesion and cohesion are combined in a small enough area, it causes capillary action, which can make water flow up against the pull of gravity. Water is known as the universal solvent, because it can dissolve many things. Substances that dissolve things are called solvents, and the things that are dissolved are called solutes. Everything has a pH, which is its level of acidity. If something has a pH of 7, it is neutral. If it is above 7 to a maximum of 14, it is basic. If it is below seven to a minimum of 1, it is acidic. Acids are sour, corrosive to metal, and have more positive H+ (hydrogen) ions than negative OH- (hydroxide) ions. Bases are bitter, and have more OH- ions than H+ ions. When if either an acid or a base is combine with the opposite, it becomes less basic or less acidic.

The four macro molecules are lipids, proteins, nucleic acid, and carbohydrates. All macro-molecules are made of carbon, which has the ability to bond with itself. Carbohydrates are made up of one or more rings of carbon, hydrogen, and carbon. They are used to store energy in animals, and make up the structure of plants. When a carbohydrate is made of only one ring, it is a monosaccharide, like fructose. When it is made of 2 or more rings, it is a disaccharide, like lactose. When it is made of 3 or more rings, it is a polysaccharide, like starch. Monosaccharides and polysaccharides taste sweet, and polysaccharides don't. Proteins are made of a combination of 20 total amino acids. They have several levels of structure. First in the primary structure, which is the amino acids bonding together. Multiple amino acids bonded together are polypeptides. The next level is the Secondary structure. The bonded amino acids hydrogen bond together to form a helix. Next is the Tertiary structure, where the amino acid bonds cause folding. Then the last level is the Quaternary Structure, where multiple tertiary structures bond to make a large protein.

Cheese Lab Conclusion

In this lab we asked what the optimal conditions and curdling agents for making cheese are. Out hypothesis was supported when we found that Chymosin in a hot, acidic, environment was the fastest. We tested Chymosin, Rennin, and buttermilk curdling agents in milk, as well as plain milk as a control, in basic, acidic, neutral, hot, cold, and warm environments separately. The buttermilk and plain milk did not curdle the milk at all. Neither Chymosin nor Rennin curdled the milk in cold or basic temperatures, but curdled it in all other conditions. With an acid, both curdled the milk in about 5 minutes, but when tested in a neutral environment, Rennin curdled the milk in 10 minutes and the Chymosin took 15 minutes. When tested warm environment, they both curdled in about 15 minutes. In the hot environment, it took 5 minutes for the Chymosin to curdle the milk and 10 minutes for the Rennin to curdle it. They both performed equally well in an acidic environment and a warm environment, but the Chymosin performed better in the hot environment, and the Rennin performed better in the neutral pH environment. Because hot, acidic, environments appear to be most favorable for curdling milk, the Chymosin performed better due to its faster time in the hot environment.

Although out hypothesis was supported, there may have been errors. We only checked for curdling every 5 minutes, so some curdling agents may have caused curdling earlier than others, but no one checked it then, leading to imprecise data. Another factor that may have caused error was having the different curdling agents being tested in the hot environment in one place. While checking for curdling, I accidentally checked a different curdling agent once, which led to confusion and basing the data off of a different independent variable. To fix theses errors, we could check the curdling agents more often, perhaps once every minute, and more label the samples with group names in addition to what factor they are testing.

This lab was done to demonstrate the effect of different pH and temperature on enzymes. From this lab I learned that some enzymes perform more effectively with different substrates in different conditions, which helps me understand what causes enzymes to denature and what causes them to work more efficiently. Based on my experience from this lab, I could more easily find optimal conditions for enzymes to speed up other reactions that may have a high activation energy or take a long time to perform naturally.

Curdling Agent	Chymosin	Rennin	Buttermilk	Milk (Control)
Acid	5	5
Base
pH Control	15	10
Cold
Hot	5	10
Temp Control	15	15