Letter to a Biology Student

Dear Biology Student, 

     My name is Monica Stratakos, and I took biology as a freshman when I was fourteen. Last year, I went to Redwood Middle School. This year, I took Health/Drivers Ed first semester in Mr. Lugo's class. Second semester I took World Geo with Mr. Dwyer. I also took Algebra 2 Honors with Mrs. Troxell. I took Spanish 2 with Mrs. Voorhees, and I had Mr. Rector for English. I missed a lot of school for second semester due to out of state national tournaments, so I still had a lot of missing assignments at the end of the school year. Outside of school, I play a lot of tennis. On the first day, I did not expect to have anything to do besides get the syllabus for each class.

     Mr. Orre expects you to be on time with your notebook out, and working on your "do now." A usual class day consists of reviewing the previous night's vodcast with your group, and then do a lab that relates to the vodcast. It is expected that you have your notebook everyday and you are ready to work when the second bell rings. For labs, we usually review the lab as a class, then do the lab and a write-up on blogger. The write-ups are usually fifty points. Homework usually takes fifteen minutes for the vodcast and CFU. If you put him on 2.0 speed, it usually takes a shorter amount of time. Most vodcasts are between ten and twenty minutes long. I do not remember taking any quizzes in this class. Tests are always multiple choice. At the end of the second semester, my average test grade was an 80. The notebook consistes of the table of contents, vodcasts, and DO NOW's. My blog ( http://monicabio9.blogspot.com/ ) consisted of all the labs and unit reflections from first and second semester.  My favorite blog was the pGLO lab ( http://monicabio9.blogspot.com/2017/01/pglo-lab.html ). I really liked this lab because the bacteria glowed a green-white color, and I took some really nice photos. Over the course of the year, I got more responsible with my homework. I did 75% of homework first semester, and second semester I did 90%. 

     Mr. Orre hates phones out in class, and talking when he is talking. To earn a good grade on assignments, be sure to fill in all the required parts. Homework is very important in this class because it is almost the same percent of your grade as tests. To get the most out of Mr. Orre's class, actually watch his vodcasts the day before and do the CFU. I think I should have studied a little earlier for tests. I always studied the night before, but I know I could have done better. Also, when I was absent, I was more than five vodcasts behind. I should have done them before I got to class because I had no idea what was happening in class.
     Overall, I had a very fun time in this class. I liked most of the labs except the pig dissection. Next year, I am taking Chemistry Honors because I think I will have a fun time in that class. Good luck this school year!!!

From,
Monica Stratakos

Pig Dissection

The purpose of this Pig Dissection was to understand the body structure. This unit was about homeostasis, the digestive system, the circulatory system, the respiratory system, the nervous system, the endocrine system, and the immune system. After cutting open the pig, my group and I identified the specific parts of our pig. We also cut the heart open to identify the four parts of the heart, which I learned in the circulatory and respiratory system vodcast. Oxygen-poor blood enters the right atrium from the body through the superior and inferior vena cava. From the right atrium, it then goes to the right ventricle through the tricuspid valve. Then, it goes to the lungs through the pulmonary valve to the pulmonary artery. Oxygen rich blood from the lungs enters the left atrium and goes through the left ventricle and leaves to the body through the aorta. My favorite part of the dissection was before the pig was cut open because I got a little bit dizzy when i saw the pig get cut open. I think this dissection was a valuable experience because it proves that I will not be a doctor when i grow up because I can not handle blood or cut open organs.

Here is our youtube video:

20 time individual reflection

Our 20 time project was about pollution. We gathered information to see how many people knew that pollution was hurting our Earth. At first, we tried to raise money by selling boba at our school. We planned to put stickers about pollution on the drinks, and donate the money to a pollution fund. We could not do this because we had to be part of a club to sell anything at our school. Instead, we made posters and a survey. We placed the posters around San Jose. Over 150 people took the survey from across the country and Hong Kong. I had many friends from Texas, New York, Florida, and many parts of Southern California take the quiz and a lot of them had no idea how bad our Earth was doing. I asked a lot of people from tennis to take the survey and most had no idea how much the world was being polluted. 52% of the people surveyed were a little concerned about global warming. 69% of the 150 surveyed said they wanted to help save the Earth. About 3/4 of the people knew that the living condition of the environment would be worse for the coming generation. 84% believed that the global temperature had risen from the 1800s. If I could do this project again, Vivienne and I would definitely set up a clean up to raise more awareness. After learning about pollution, I cut down on how much trash my family and I produce, trying to use less plastic and recycle more. I have learned that batteries are actually recyclable. Before this project, I put used batteries in the garbage.

Vivienne and I will continue this project by raising more awareness and possibly scheduling a clean up.

Unit 9 Reflection

http://bit.ly/2r1bqcm

This picture shows the diffferent levels of taxonomy.
The levels get smaller near the bottom because it is
more specific towards one species

http://bit.ly/2r82L4r

This shows the historyof the Earth in a 24-hour time period

Unit 9 was called "What on Earth Evolved". I learned about the different levels of taxonomy. The taxonomic levels are (from most inclusive to least inclusive): domain, kingdom, phylum, class, order, family, genus, species. The three domains are: bacteria, archaea, and eukarya. Protists, fungi, plants, and animals belong to the domain eukarya. The kingdom protista are diverse, unicellular or mulitcellular, plants or animals. Some examples of protists are:  slime molds, red algae, paramecium, and amoeba. The kingdom fungi consists of heterotrophic decomposers that can be unicellular or multicellular. They can bee found in all habitats on Earth (ex. mushrooms, yeasts, molds, and lichens). Non-vascular, vascular seedless pants, and seed plants make up the plantae kingdom. Mosses, ferns, lilies, and oak all belong to the plantae kingdom. The kingdom animalia consists of multicelluular consumers and heterotrophs. Some examples are: sponges, jellyfish, earthworms, sea stars, fish, amphibians, reptiles, birds, and mammals.


My previous post was the "Geologic Timeline Reflection"( http://monicabio9.blogspot.com/2017/04/geologic-timeline-reflection.html ). This post explained that the Earth is 4.543 billion years old. Many animals existed before humans. Humans have only been on the Earth for 200,000 years. Animals like the tiktaalik lived 375 million years ago. Dinosaurs lived between 230 and 65 million years ago. Humans are just a small fraction of life.

I am still a little confused about why scientists some scientist like to clump species together, while others like to have subspecies. I think it would be a lot easier if there were no subspecies because it gets very confusing.

I think I did pretty well on my What on Earth Evolved presentation. Mine was about the tiktaalik, which was one of the first land animals. I think I could have made my speech a little bit longer, but other than that, everything ran smoothly. This was a really good assignment to practice my public speaking. In the future, I think I will elaborate more on my slides and not read directly off the slides.


Here is my What on Earth Evolved Presentation:

Geologic Timeline Reflection

The Cambrian Explosion is a sudden appearance in the fossil record of complex animals that had mineralized skeletal remains. This is considered to be the most important evolutionary event in the history of life on Earth. 96% of species became extinct after the Permian mass extinction. There were at least two or more phases of extinction over the span of millions of years. This was the the insect population's one and only mass extinction. This tragic event may have been caused by an asteroid impact or a drop in oxygen levels. 65 million years ago, the dinosaurs died in Cretaceous mass extinction. This mass extinction may have been caused by flood basalt eruptions affecting the world's climate, and a drastic fall in sea level.

The Earth is approximately 4.543 billion years old. The Silurian Extinction happened 439 million years ago. Dinosaurs lived between 230 and 65 million years ago in the Mesozoic Era. This was millions of years before the first homo sapien appeared. Modern humans evolved 200,000 years ago. Compared to the Earth, humans are a relatively new species. If the timeline of Earth was based off a one year calendar with the Big Bang occurring on January 1, humans have only been around for about five minutes. I was surprised that we have impacted the world so much in the five minutes that humans have been on the Earth.

The last 200,000 years have been mainly dominated by humans. In the past 50 years, humans have burned tons and tons of fossil fuels. The human society has also dumped massive amounts of trash into landfills and oceans. With all the technologies we have created to change the Earth for the better, we have dumped so much waste that the Earth might never recover.

My question is "How do scientists know what happened in every mass extinction?"

Earth life in 24 hours

Unit 8 Reflection

This unit was about constant change. Variation is any difference in traits within a population such as height or eye color. Variation exists because of crossing over, meiosis, mutations, and sex. Artificial selection occurs when humans select traits from a population's variation that they want, and only mate individuals with those traits. Darwin discovered that evolution is caused by natural selection. He came p with for observations and two conclusions explaining how populations can change or evolve over time because of natural selection. A gene is a section of DNA that gives instructions for a trait. An allele is different variations of a gene that give different variations of that trait. Genetic variation is stored in the gene pool, and these gene pools can change over time. Allele frequency is how common an allele is in a population. Evolution acts on a population, as natural selection acts on an individual. A species is a group of individuals that can reproduce and have fertile offspring. Speciation is the rise of two or more species from one existing species. Embryology is the similar stages of embryo development that suggest common ancestry. Gene flow is moving alleles from one population to another. Natural selection selects for traits advantageous for survival. The 4 eras are: Precambrian Era, Paleozic Era, Mesozoic Era, and Cenozoic Era.

This is a picture of my graph from the Hunger Games
 Lab. It shows the gene flow in the population.

This is an image of gene flow. It shows how
the alleles move from one population to another.

I want to learn more about the rate of evolution because it is very slow for some populations and not for others. I would like to know how to increase the rate of evolution because some species have a very slow rate of evolution. Since my reflection on Unit 7 ( https://monicabio9.blogspot.com/2017/03/unit-7-reflection.html ) I have tried to focus more on not being so passive agressive. I have tired to consider both sides of the argument and not be mad about which was the argument went. 

Hunger Games Final Analysis

1. I was not here for the Hunger Games Lab, but I was able to get data from a team member. In this lab, students tried to survive and reproduce. This simulates evolution. 
2. Pinchers were the best at capturing food because they could use their thumb and index finger.
3. The population did evolve. In the beginning, the "A" allele had a frequency of 52%, and the "a" allele had a frequency of 48%. At the end of the lab, the "A" allele had a frequency of 23%, and the "a" allele had a frequency of 77%.
4. The placement of the food and the amount needed to survive was random. The genotype was also random because it was based off of a coin flip. The way that a person picked up food was nonrandom. This could have effected the population because there were no favored genotypes. 
5. If there was less food, the results would be different because there would be more of a fight for survival with the same amount of people and less food. This would lead to less people surviving. On the other hand, if there was more food, people wouldn't have to fight for survival as much, and therefore more people would survive. If there is a fire, there would be less acorns for a population of squirrels to eat, which would lead to the survival of the fittest.
6. The results would be different if there was not incomplete dominance. Without incomplete dominance, there would be no knucklers which would lead to more stumpys.
7. Natural selection is the process of weeding out phenotypes in a population that don't help individuals survive which leads to populations evolving overtime. Evolution is the process by which a population improves its gene pool. Evolution is caused by natural selection.
8. The stumpys were the best at strategizing. They reproduced only with each other, which made their population bounce back.
9. In evolution, the population evolves. Natural selection acts on the pheontype because it acts on the traits.
10. How quickly does evolution occur?

Unit 7 Reflection

Unit 7 was about the study of ecology. Ecology is the study of interactions between organisms and their environment. A habitat is a place that includes all aspects of an area where an organism lives including biotic and abiotic factors. Biotic factors are living things. The root word "bio" means living. Abiotic factors are non-living things. The levels of organization are: organism, population, community, ecosystem, and biome/biosphere. Producers provide energy for other organisms in an ecosystem, while consumers get their energy from eating living or once-living resources. A food chain shows how each organism gets its energy.

This is a picture of a food web. There are more primary producers than tertiary
consumers because the higher up the food web, the more scarce the organism is.

This is a picture of a food chain. It is not as complicated as a food web.

 Primary producers are  the source of all energy in an ecosystem. The 10% rule states that with the amount of energy produced at each level, only 10% is passed on to the next level. The other 90% is lost as waste. An energy pyramid shows how energy is transferred from producers up the food chain to top level consumers. Population ecology is the study of populations in relation to the environment. Succession is the sequence of community and ecosystem changes after a disturbance. Primary succession occurs where succession begins with no soil to start with. Secondary succession begins in an area where soil remains after a disturbance. Biodiversity is the total number of species in an ecosystem. Genetic diversity is all the different genes within a population and between different populations. Species diversity is the variety of species in an ecosystem and throughout the biosphere. Ecosystem diversity is the different types of ecosystems throughout the planet. Biodiversity is threatened due to habitat loss, introduced species, over exploitation, and change in climate.

I really enjoyed watching the movie "Bag It" in class. There were many interesting facts about plastic and how much gets wasted annually. Before watching this video, I never really thought about plastic and the effect it had on other organisms. After watching the movie I went home and looked up more interesting facts about the Great Pacific Garbage Patch. This patch is located between Hawaii and Japan. Since the plastic is not biodegradable, it breaks down into smaller pieces called mircoplastics. It is said that 70% of the garbage is below the water, so no one knows how much trash is really in the Great Pacific Garbage Patch.

Our biology conservation project was about the Artic Tundra. I really liked working in a group to complete this project because it was fun to learn about this cold and dry place with others. We were able to finish our project before the break so we had no time pressure to submit it on time. We had a bit of trouble getting the audio to work with our video, but other than that, our project had no other major problems. I learned that there are many endangered species in the Artic Tundra including: polar bears, arctic foxes and beluga whales. Our group collaborated well through facebook messenger. Here is a link to our video: https://drive.google.com/file/d/0B0rHk8eio-sFaDlVNXY2NEhoTUU/view?usp=sharing

My dominant conflict style was passive aggressive. I like to indirectly resist the demands of others. If i get in an argument, I usually let the other person win. After letting the other person choose what the want to do, I usually hold a grudge and make sure that the other person knows. I can be more assertive by trying not to hold a grudge and just let the argument go.

Unit 6 Reflection

     This unit was about was about biotechnology and its purpose. Biotechnology is the study of living things in order to benefit mankind. The four applications of biotechnology are industrial/environmental (converting sugars into acids through the process of fermentation), medical/pharmaceutical (putting in a healthy copy of a gene into cells of a defective gene through gene therapy), agricultural (genetic modified organisms or GMO), and diagnostic (searching for genes or DNA segments indicating risk for diseases through the process of genetic testing).

     The polymerase chain reaction, also known as PCR, is a procedure used to amplify a specific DNA region. Gel electrophoresis uses electricity to separate DNA fragments based on size. Sequencing is a process that determines the exact order of a given DNA strand.
     Recombinate DNA Technology (rDNA) inserts DNA of one organism into DNA of another organism. This process is often described as genetic engineering. 
     Bioethics is the study of decision making as it applies to moral decisions that have to be made because of advances in biology, medicine, or technology.       I really enjoyed this unit because it was very hands on and had a lot of interesting labs. My favorite lab was the pGLO lab because the result was really interesting. 

This is a picture of the container that had LB, AMP, and ARA.

This is a picture of the gel electrophoresis lab with the gels loaded.

     I learned that when arabanose sugar is added to the bacteria E.coli, the bacteria glows green under UV light. The arabonose sugar is the trigger that makes the bacteria glow. The glowing florescent protein (GFP) is extracted from jellyfish.
     I really struggled to understand the last vodcast, the pGLO prelab vodcast. I was not really sure what the outcome of each of the plates were when i was watching the vodcast. After re-watching the vodcast, and doing the lab, I was able to understand the effects of arabanose sugar and its function.
     I wonder about the many jobs in the biotech world. I think some day in the near future, the world will be very advanced in biotech and become too advanced.

My new years goals were:

• Smart Goal #1:

I will start studying at least 5 days before every test I take, and take notes when I am studying. To make sure I achieve this goal, I will set reminders on my phone. Since I like to procrastinate a lot I will have to pretend that the test is the next day so I can actually study.

• Smart Goal #2:

I will try my best in everything I do, and during lectures in class I will actively listen and make sure that I ask questions when I don't understand something. While I am actively listening, I will take notes and review the topics that I learned in class while completing my homework.

     So far, I have achieved smart goal 1 and 2. I have been taking notes while i was studying, and I completed my textbooks early in the unit. Also, I have been paying attention in class and participating. I think that I set good and reasonable goals that will challenge me to do my best throughout this semester.

pGLO Lab

Plate	Number of Colonies	Color of colonies under room light	Color of colonies under   UV light
- pGLO LB	0	none	none
- pGLO LB/amp	none	none	none
+ pGLO LB/amp	2	white/clear	white/clear
+ pGLO LB/amp/ara	At least 4	white/clear	bright green

          2. The two new traits that the transformed bacteria have are: the ability to glow under UV light and ampicillin resistance.

          3.  I think there were millions of bacteria in the 100 uL of bacteria that was spread on each plate because bacteria are very small in size, many bacteria could be found in a little amount of E.coli.

          4. The rold of arabinose in the plates was to activate the gene that makes the bacteria glow green when UV light is present.

         5.  a)GFP can be used to dye cancer cells and shbow images of them

              b) GFP can show if the bacteria took a new gene properly

              c) GFP can show if someone had a drug overdose

         

         6. Genetic engineering can be used to create genetically modified crops. Corn, papaya, cotton, and soy are all at a high risk for being genetically modified. Crops are genetically modified to increase the resistance against a disease in a crop.

Candy Electrophoresis Lab

1. The reference blue dye was way behind and the actual blue dye from the candy. All the reference dye fell off because during the experiment, our class went to an assembly. We did not come back from the assembly in time. I did not see any dyes that were a different color than any of the reference bands.  There were no dyes that moved in the wrong direction.

2. The "fast green FCF" looked like the Blue 1 that I examined in the lab. They had similar chemical compositions, and their structures also looked very alike. The "citrus red 2" looks very similar to the Red 40 that I used in the lab. Although these dyes did not have the same composition, their structures were still similar.

3. I think that dog food manufactures such as Beneful and Snausages Breakfast Bites have food dyes in their product becuase dogs prefer more colorful food. If the food did not have a good taste, but it was colored like a dog treat, I think a dog would get tricked by the color of the food and still eat it.

4. I think that an artificial food color would be preferable to a natural food color because artificial food colors have more sugar, and therefore taste better than a natural food color.

5. The two factors that control the distance the colored dye solutions migrate are the charge of the dye and the length. If the DNA segment is longer, then it will travel slower. If the DNA segment is shorter, it will travel quicker.

6. Electricity is the force that helps the dyes move through the gel. Once the dyes are put in the gel, I turned on the electrical force.

7. The gel causes the molecules to separate by size because it takes the longer DNA more time to go through the gel. The shorter DNA has an easier time getting through the gel because it has to go through small sections of the gel.

8. The DNA of molecules with molecular weights of 600, 1000, 2000, and 5000 daltons would separate from lightest to heaviest. This means that the DNA with the molecular weight of 600 would go through the gel first, followed by the 1000 and 2000 weights. The 5000 weight would finish last because it weighs the most, making it the slowest.

New Year Goals

• Smart Goal #1:

I will start studying at least 5 days before every test I take, and take notes when I am studying. To make sure I achieve this goal, I will set reminders on my phone. Since I like to procrastinate a lot I will have to pretend that the test is the next day so I can actually study.

• Smart Goal #2:

I will try my best in everything I do, and during lectures in class I will actively listen and make sure that I ask questions when I don't understand something. While I am actively listening, I will take notes and review the topics that I learned in class while completing my homework.

Unit 5 Reflection

Unit 5 was about genetic code, DNA replication, making proteins, mutations, and gene expression and regulation. DNA is a double helix made up of two strands twisted around each other like a twisted ladder. DNA is made up of nucleotides. Nucleotides are made up of 3 parts: a nitrogen base (A, T, C, G), a phosphate group, and a sugar (deoxyribose). Phosphate and sugar make up the sides of the ladder and the bases are the steps. DNA is anti-parallel. This means that each nucleotide covalently bonds with another. Nitrogen bases come in two types: double rings called purines(adenine and guanine), and single rings called pyrimidines (thymine and cytosine). Adenine always pairs with thymine, and Cytosine always pairs with guanine. Code is a system of words or symbols that are substituted for other words.

Semi-conservable replication is the process of creating two identical strands of DNA from one original strand. Two strands end up with half of the original strand. First, enzyme unzips DNA by breaking down hydrogen bonds that hold nitrogen bases together. Then, DNA polymerase add matching nucleotides to each strand. The result is two identical strands of DNA molecules that form are identical to the original DNA molecule.

The central dogma of biology is that information flows from DNA to RNA to proteins. Proteins make up out traits (phenotypes). RNA is single-stranded, has a ribose,contains uracil, and is a temporary copy of DNA. RNA delivers a copy to the ribosomes, and the ribosome uses this RNA copy to make proteins. Transcription is a process in the nucleus where RNA polymerase reads and copies the DNA code (gene) for a protein as mRNA. In the process of transcription, DNA unzips, RNA polymerase matches spare nucleotides to make an RNA strand,and mRNA is produced and leaves the nucleus for the cytoplasm. Translation is a process that takes place in the cytoplasm. First mRNA arrives at the ribosome. Then, the ribosome reads mRNA three bases at a time and transcribes the DNA language into amino acids. Each three-base sequence is known as a codon. Each codon codes for one amino acid.

A mutation is a change in DNA code (genes.) The effect can be none and sometimes it can be fatal. Mutagen is anything that causes a mutation. Mutations can happen naturally too. Point mutations are a change in one or two base pairs. These types of mutations are very small and common. A substitution is a change in which one nucleotide is substituted for another. The two types of frameshift mutations are insertion and deletion. Insertion is a mutation where one extra base pair is put in code. Deletion is a mutation in which one base pair is left out of the code. Inversion is a mutation where DNA breaks off and bonds in reverse order. Translocation is the part of a chromosome that breaks off and bonds with another. Mutations cause changes in DNA which cause changes in life. Proteins are essential to life.

This is a picture of an RNA strand being translated to an amino acid.

Gene expression is the process of a gene being used to produce a gene product or phenotype. Gene regulation is a mechanism used by cells to increase or decrease the expression of a gene. Every cell in your body has the same DNA but not all cells look the same. Cells look different because each type of cell expresses or turns on genes specific to those cells. Environment can affect how and when genes are expressed. Gene regulation is the process where cells do not want to waste energy or overexpress genes so they have many steps that are used to control gene expression. A promoter is the location on DNA where RNA polymerase attaches. An operon is a series of genes used to control the expression of a single gene. The operator is a “switch” or segment of DNA at the start of a gene that prevents or allows RNA polymerase from attaching and reading the gene. Eukaryotic regulation is much more complicated than bacterial regulation. EXons are EXpressed and introns are sequences that are cut out. Histones are proteins that allow DNA to coil. Nucleosomes are DNA that is wrapped twice around like a histone. Genes whose promoters are wrapped up in nucleosomes are not expressed. Different enzymes are involved in breaking histones free or binding them up to control gene expression. This is passed to future cells during development.
I really liked learning about making proteins and DNA. I had a difficult time on the protein synthesis lab because I did not understand how to convert a DNA strand to an RNA strand. After going back and watching the vodcast, I understood how to convert DNA to RNA. I also struggled in understanding the last vodcast. The vodcast was about gene expression and requlation. I didn't know the different parts of the operon. After doing the do now in class, I had a better visual understanding of an operon.

This is a picture from the protein synthesis lab that was difficult.

Protein Synthesis Lab

   
    There are many steps required to make a protein. First, RNA polymerase reads and copies the DNA code or gene for a protein as an mRNA copy through the process of transcription. Transcription happens in the nucleus. In the process of transcription, DNA unzips. Then, RNA polymerase matches spare nucleotides to make an RNA strand. mRNA is produced and leaves the nucleus for the cytoplasm. After transcription happens, the mRNA arrives at the ribosome. In the process of translation, the ribosome reads RNA three bases at a time and translates DNA language into protein language. Each three-base sequence is called a codon. Each codon codes for one amino acid.

A mutation is a change in DNA code. An insertion is a mutation in which an extra base pair is put in code. A deletion is a mutation where a base pair is left out of the code. The mutation substitution happens when one nucleotide is substituted for another. In my opinion, substitution affected the protein the least because it only changed one nucleotide. A deletion affected the protein the most when it was added in the beginning because it changed every nucleotide after it was added. It does matter where the mutation occurs when it is a deletion or insertion because all the code after the added or deleted nucleotide is affected.

   

 In step 7, I chose to do a deletion. I think that a deletion affects the DNA code the most. It does matter where the mutation occurs. I put my deletion in the beginning, so all my code was affected.

http://bit.ly/2hnDHVv
This is a picture of a child with Progeria.
Mutations can have a big impact on a person's life. They can create genetic disorders. Progeria causes accelerated aging. Most children who have progeria die at the age of 13. Their death is causes by a stroke or heart attack. Progeria is caused by a mutation that is located on the LMNA gene which is a protein. This protein gives support to the cell nucleus. 

   

Human DNA Extraction Lab

In this lab, we asked the question how can DNA be separated from cheek cells in order to study it? We found that it is possible to separate DNA from cheek cells. My hypothesis stated that if DNA can be seoarated fromm cheek cells, then DNA would be visible after precipitation. First, we swished Gatorade in our mouth for 30 seconds. Then, we added enzymes to speed up the process. The enzymes that were added were: salt and dishwasher soap to the solution. Since the DNA was still insoluble, we added rubbing alcohol to the solution. When we added the rubbing alcohol, the DNA percipitated from the Gatorade. In this lab, the rubbing alcohol was a protease because it catalyzed the splitting of the interior peptide bonds in a protein. The DNA rising from the gatorade was a catabolic process, which gave rise to substances of decreasing complexity. I could see the DNA after the DNA was percipitated. This data supports our claim because we could extract DNA from cheek cells, and I predicted that the DNA would be visible after precipitation.
     While our hypothesis was supported by our data, because there was no procedure in this lab, there could have been errors. In the beginning of the lab, we were given a piece of paper with the procedure. However, this paper did not have the steps of the lab in the right order. We had a tough time putting the procedure in order, and we had a big discussion at our table about which step was first. Another error was that someone at our table poured too much Gatorade into my cup. Because of this, I had a hard time swishing all the Gatorade in my mouth. If I had less Gatorade, I probably could have gotten more cheek cells. Due to these errors, I would recommend having an accurate procedure.
     This lab was done to demonstrate DNA replication and extraction. From this lab, I learned that DNA can be extracted from cheek cells, which helps me understand the concept of DNA extraction. Based on my experience from this lab, I now know how complicated DNA is and I was able to see what my DNA looks like.

Coin Sex Lab and Unit 4 Reflection

     In the coin sex lab, we flipped coins to show the probability of the phenotype of an offspring. The coins demonstrated the probability of a child inheriting their parents' genes. In the dihybrid cross, two individuals were both double heterozygous. The dominant alleles were brown hair (B) and brown eyes (E). The recessive alleles were blonde hair (b) and blue eyes (e). Meiosis is the process of making gametes in testes or ovaries. There were two different possibilities for meiosis. By completing the Punnett Square, I found that the expected outcome was 9 offspring with brown hair and brown eyes, 3 offspring with brown hair and blue eyes, 3 offspring with blonde hair and brown eyes, and 1 offspring with blonde hair and blue eyes. After flipping the coins and collecting my data, I found that Punnett Square is an accurate representation in predicting the phenotype of an offspring. I got 9 offspring with brown hair and brown eyes, 3 offspring with brown hair and blue eyes, 3 offspring with blonde hair and brown eyes, and 1 offspring with blonde hair and blue eyes when flipping the coins.
     The autosomal dominance lab determined the probability of having a bipolar offspring if one parent is heterozygous for the trait and the other parent is homozygous and does not have the trait. The Punnett Square was a monohybrid of Bb x bb, where B is the bipolar allele and b is the normal allele. I predicted that 50% of the offspring would have the bipolar disorder. After flipping the coins and collecting the data, I came to the conclusion that 4 offspring had bipolar disorder, and 6 were normal. Although the Punnett Square was not a completely accurate representation of my results, the Punnett Square was pretty close to accurate.
     In the X-Linked Recessive part of the lab, the female was a carrier of colorblindness, and the male had normal color vision. The Punnett Square was a monohybrid of X^B X^b by X^B Y. Through  recombination, the alleles from each parent combined. One offspring was colorblind, and the other nine offspring were normal. When using probability to predict an offspring's traits, a person cannot assume what traits an offspring can have. Instead, they can predict the likelihood of a trait being dominant.

    This unit was about the cell cycle, asexual vs. sexual reproduction, meiosis, Punnett Squares, Mendel's Sex Laws, and genetic exceptions and complications. The cell cycle has three steps: interphase, mitosis, and cytokinesis. In interphase, DNA is copied. Mitosis is the process in which DNA and organelles are split up. Cells divide into two cells during cytokinesis. 
     Asexual reproduction requires one parent. The offspring is genetically identical. Asexual reproduction is easy, takes a short amount of time, does not need a mate, and can make a lot of offspring. Asexual reproduction has no genetic variation, is not resistant to change. The offspring of asexual reproduction are more likely to go extinct if their environment changes. Sexual reproduction requires two parents, and each parent contributes half of offspring's DNA through sperm or egg. Sexual reproduction creates genetic variation, and new traits arise in the population. The costs of sexual reproduction requires a lot of time.
     Sex is determined by a pair of sex chromosomes. Homologus chromosomes are chromosomes that come in pairs, in which one there is one copy from each parent. Sex cells are called gametes. Males produce sperm, while females produce egg. Haploid cells are sex cells that have half of the chromosomes. All body cells are diploid, meaning that cells have two copies of every chromosome. Asexual reproduction always produces diploid cells. 
     Meiosis is the process of making gametes in testes or ovaries. There are four stages in meiosis, but the cell divides twice, meaning that a cell goes through the four stages two times. The four stages are: prophase, metaphase, anaphase, and telophase. The process of meiosis 1 splits homologus chromosomes. Meiosis 2 splits sister chromatids. 
     A trait is a characteristic. A gene is a piece of DNA that gives an organism its trait. Gregor Mendel experimented with pea plants and mated peas to observe their traits. He discovered that traits are determined by two copies of a gene. Some versions of a gene are dominant over the others. A genotype is the alleles that an organism has. A phenotype is the physical trait that results due to an organism's traits. Individuals that have the same two alleles are called homozygous. Individuals with two different alleles are heterozygous. 
    The Law of Segregation, a principle introduced by Mendel, states that the gene pairs of a trait separate where gametes are formed because of meiosis. The Law of Independent Assortment states that gene pairs separate independently, or randomly, from each other during meiosis. The Punnett Square predicts possible genotypes of gametes. 
     Autosomal inheritance is the process in which an organism inherits the gene responsible for a trait from all the 22 autosomes. X-Linked inheritance is when an organism inherits the gene responsible for a trait from the x-chromosome. 
     Incomplete dominance happens when neither allele is dominant nor completely recessive. Both alleles will both be completely expressed in codominance. In other words, codominance has both phenotypes. Codominant alleles are neither dominant nor recessive. 
     Because chromosomes have many genes, the closer they are together, the more likely they are to be inherited together through gene linkage. In epistasis, one gene alters the phenotype of another gene. Multifunctional disorders are disorders where an environment affects genetics. Most humans are polygenic because they have two or more genes to determine their phenotype. 

     http://bit.ly/2fvBp72

     This unit was very fun because I really liked learning about Punnett Squares and how they can determine the probability of an offspring having a specific genotype. I struggled to understand the difference between meiosis and mitosis so I did some extra research. I understood how some versions of alleles could be dominant over others, but I had a difficult time figuring out how codominance works. In my opinion, the infographic helped me get a better understanding of the main concepts from this unit. I definitely feel that I am a better student than I was yesterday because I have expanded my knowledge in biology. I would like to know more about the works that Mendel did to influence the world of biology today.  

Picture of my infographic: https://magic.piktochart.com/output/17955851-genetics

Sexual vs. Asexual Benifits

Is sexual reproduction important?

     Sexual reproduction is necessary for life. "[Sex] prevents parasites from becoming too well adapted to their hosts" (Judson 228). Sexual reproductions remove harmful mutations from the population. Sexual reproduction has a slower production rate. "Sex is an advantage because it breaks up gene combinations" (Judson 229).
     Asexual reproduction does not require fertilization, but there is very little variation, which can cause extinction. "...mammals clone once in a while, when an embryo splits early in development" (Judson 215).
     Some animals reproduce sexually and asexually. "Armadillos... engage in both sexual and asexual reproduction"(Judson 229).
     I learned that many species reproduce in different ways. Some reproduce more than others, and some reproduce sexually, while others reproduce asexually. I understood the text and all my questions were answered in the text.

Unit 3 Reflection

     Unit 3 was about cells and their functions. Macromolecules serve as the building blocks for life because they make up different parts of the cell and they all serve different purposes. The cell theory states that all things are composed of cells, a cell is the basic unit of life, and new cells generate from existing cells. Prokaryotic cells have no nucleus, while eukaryotic cells have a nucleus.

     Membranes and their unique characteristics are so essential for life because they all have different functions that are necessary for life. The nuclear membrane holds DNA in the nucleus and allows RNA to leave through the pores. The lysosome holds enzymes for recycling proteins. The endoplasmic reticulum (ER) holds proteins as they are finished off and holds lipids as they are made. The vesicles export molecules in and out of the cell. The golgi apparatus packages and releases finished proteins, lipids, and hormones. The membranes in chloroplasts and mitochondria creates carbohydrates through the process of photosynthesis, and breaks down carbohydrates through the process of cellular respiration. The cell membrane holds all cell contents inside and protects from the outside environment. The cell membrane also controls the passage of molecules inside.

       Semipermeable membranes allow some molecules to cross the membrane, while others can not. Passive transports require no effort or energy. Active transports use energy to bring rare but highly needed molecules into the cell. Diffusion is the movement of small molecules from high to low concentration through the lipid bilayer. Proteins that make it possible for large molecules to pass through the membrane through the process of facilitated diffusion. Osmosis is the diffusion of water across selectively permeable membrane. An isotonic solution is when the solute concentration is the same outside and inside the cell. A hypertonic solution is a solute concentration that is greater than that inside the cell. A hypotonic solution is a solute concentration that is less than that inside the cell.
     Cells specialize in making proteins. Mitosis is the process in which one cell reproduces by dividing into two cells. Photosynthesis converts light into chemical energy. A cell creates energy by creating ATP  from glucose to power the cell. The endosymbiotic theory explains how a large cell ingested bacteria and became part of it.
     Photosynthesis is the process in which plants produce glucose and oxygen using sunlight and carbon dioxide. Light dependent reactions occur in the thylakoids of grana. Light independent reactions occur in the stroma.
     Cellular respiration is the process of breaking down glucose into energy. It has 3 stages: glycolysis, krebs cycle, and the electron transport chain. Glycolysis produces two ATP for every one glucose molecule. The Krebs Cycle coverts molecules from glycolysis into two ATP, CO2, Nadh, and FADH2. The electron transport chain uses oxygen, NADH, Fadh2, and converts ATP into ADP. This last stage produces 32 ATP.
     The process of photosynthesis and the process of cellular respiration undo each other. Photosynthesis occurs in the chloroplasts in autotrophs, while cellular respiration occurs in the mitochondria in autotrophs and heterotrophs.
     Overalll, I really enjoyed this unit. I liked learning about photosynthesis and cellular respiration. I had a tough time remembering the function of each organelle in a  cell. I had a fun time looking at cells under a microscope, and I realized how complicated a single cell can be. 

Photosynthesis Virtual Labs

Lab 1: Glencoe Photosynthesis Lab

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 the color in the visible spectrum is blue or red, then the plant will grow bigger.

If the color in the visible spectrum is green, then the plant will grow the smallest.

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 tested my hypothesis by planting spinach in all the different lights for 30 days. Then I did the same for the radish and lettuce.In my experiment, the controlled variable was the type of plant. The variable that I changed to compare the growth was the color of the light.

Results:

Filter Color	Spinach Avg. Height (cm)	Radish Avg. Height (cm)	Lettuce Avg. Height (cm)
Red	18	12	12
Orange	16	7	5
Green	3	2	3
Blue	18	15	12
Violet	15	11	7

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 data supported my hypothesis. I predicted that the blue light and the red light would show the most plant growth and that green light would show the least amount of plant growth. I found that spinach grew best under the red light and the blue light. The radishes showed the second most amount of plant growth under red and blue light. The lettuce showed the least amount of plant growth under red and blue light compared to the spinach and the radish.

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

I conclude that blue light causes the most plant growth in the visible spectrum.

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

I would expect a normal rate of growth under white light because white light is an average of all light lengths.