Unit 5 Reflection

         In unit 5, we learned about Walking the Dogma. It includes learning about our genetic code, DNA, the central dogma of biology, mutations, and gene expression and regulation. We did some labs to explain more about DNA.

       We learned about our genetic code. We learned about the structure of our code which includes a double helix which is two strands twisted around each other and is made of nucleotides. Nucleotides are made up of three parts, an anitrogen base, a phosphate group and a sugar. In our genetic code, our DNA is antiparallel which is when each nucleotide bonds with another nucleotide. Also our code is made of nitrogen bases that includes purines and pyrimidines. We learned about our DNA. It includes semi conservative DNA replication. It includes many steps that includes unzipping and zipping. The result of this is getting 2 identical strands. We learned that the base pair rules are A=U, C=G, T=A.
       We learned about RNA and DNA and its structural differences like being single stranded, having rbose and containing uracil. The function of RNA is that it serves as a temporary copy of a gene , delivers the copy to the ribosomes, and ribosomes would use the copy to make proteins. We learned about transcription and translation. Transcription is a process where RNA polymerase reads and copies DNA code for the messenger RNA. Translation is when the messenger RNA arrives at the ribosome and is read 3 bases at a time and turned into protein. The result of this is that a long chain of amino acids are made and chains of amino acids twist, folds and combines with other chains. We learned about the types of mutations . It includes point mutation where a change in one or two base paris of DNA, very small and are very common. It also includes frameshift mutation, Substitution , insertion and deletion. Frameshift mutation is a mutation that includes insertion and deletion. Insertion is when an extra base pair is added to the code. Deletion is when a base pair is left out of the code.
       Lastly, we learned about gene expression and regulation.  We learned that gene regulation is cells that don't want to waste energy or over express genes and have a variety of steps used to control the expression of a single gene. We learned about eukaryotic regulation. It's more complex that bacterial regulation and proteins will bind before a gene and are required for the gene to be expressed.

Protein Synthesis Lab Conclusion

1. To make a protein, a section of DNA is copied by an enzyme to create messenger RNA. The messenger RNA leaves the nucleus and travels to the cytoplasm. The messenger RNA then bonds with a ribosome. The ribosomes reads a codon and determines the amino acid that corresponds with the sequence and is determined by the codon that is read by the ribosome. They are bonded together and when the messenger RNA is done translated, it is folded up to become a protein.


https://upload.wikimedia.org/wikipedia/commons/thumb/3/38/Protein_primary_structure.svg/2000px-Protein_primary_structure.svg.png


2. The mutation that had the most effect to the protein is frameshift mutation because it involves insertion and deletion that has a great effect to the amino acids. When the DNA inserted another base, the amino acids changed into different amino acids. When the DNA deleted a base, the amino acids started twice. The weakest mutation is substitution because it only substitutes a base for another and does not effect the amino acids much as most of the proteins still were the same from the original amino acid sequence.


https://upload.wikimedia.org/wikipedia/commons/b/b1/Point_Mutation.jpg


3. In step 7, I chose insertion because it's a harmful mutation. Insertion is more effective to the amino acids than deletion and substitution because more amino acids turn into different amino acids than deletion and substitution. It matters where the mutation occurs because has to occur between the codons.

https://upload.wikimedia.org/wikipedia/commons/0/06/Insertion-genetics.png

4. Mutations can affect our life by causing proteins to not work properly and can cause disorders in the body.
Conditional Mutations:
A type of mutation that affects the phenotype by temperature.


http://www.nature.com/scitable/content/5140/10[1].1038_ncb437-f2_full.jpg

DNA Extraction Lab

In this lab, our question was how can DNA be separated from cheek cells in order to study it? Our result was alcohol, a non polar mixture and DNA, a polar mixture separated into layers and the DNA precipitated to the interphase of the mixture and DNA went to the alcohol layer. During this experiment, we used our teeth to scratch our cheek cells and got a bit of Gatorade and swished it in our mouth for 30 seconds which is an example of homogenization. We then added salt, pineapple juice, a catabolic proteases, and detergent to lyse the cell membranes. We then added alcohol tocreate 2 layers. The DNA then rose to the alcohol layer and could be picked up with a transfer pipette. This supports the claim by showing that DNA can be separated by nonpolar and polar liquids.

Even though the results we got from the lab was the right result, there was some errors that occurred during this experiment. One error is this lab was the time. In this lab, we did not count exactly 5 minutes before checking the Gatorade mixture. This affected how some of the DNA did not wrap around. Another error was the amount of Gatorade added to the test tube.  We may have added too much in the test tube which affected how much alcohol we added.  We may not have added enough for more DNA to precipitate to the surface. In order for these errors to not occur, we should be more careful and follow instructions better.

In conclusion, the purpose of this lab was to determine how to extract your own DNA. This lab relates to what we learned about DNA. We learned that it can be found in the nucleus and organisms and what is in the DNA. This can be applied to other concepts relating to observing DNA in human and living organisms with your own eyes and learning how to remove DNA from humans and living organisms to make observations.

Unit 4 Reflection

This unit was about Sex in Genetics. We learned about the cell cycle and its reasons which includes Reproduction, Growth and Development, and Cell tissue and repair. The steps of the cell cycle is Interphase, mitosis and cytokinesis. In interphase, cell grows, copies itself and prepares for division. In mitosis, it consists of prophase, metaphase, anaphase, and telophase. In prophase, DNA becomes visible. In metaphase, chromosomes line up at the equator. In anaphase, spindle fibers pull the chromosomes apart and in telophase, new nuclear membranes form and spindle fibers disappear. In cytokinesis, the cells split into two identical cells, the rest of organelles are divided and the cell membranes pinch apart. We learned about the reason why sex is great because of asexual and sexual reproduction and its cost and benefits. Sex can create sex cells which can create offspring. Sex chromosomes can create sex and can be determined by autosomes. It also includes Meiosis which is the process of making gametes. The steps of meiosis is the same as mitosis but but meiosis divides twice. There is Meiosis I and Meiosis II and Meiosis I splits homologous chromosomes and Meiosis II splits sister chromatids. It also involves crossing over.

We learned about Mendel's laws which are the law of segregation and the law of independent assortment. The law of segregation states that gene pairs for a trait separate when gametes are formed and the law of independent assortment is when gene pairs separate independently.  We learned about his discoveries of sex by crossing purebred purple and white together. That when he discovered that traits are determined by two copies of a gene. He later realized that sex is great because he could predict the phenotype of an offspring if he knew the genotype of the parents. We learned about calculating the chances of a certain offspring by using punnett squares.

Lastly, we learned about the different types of crosses. The types of crosses we learned was the monohybrid cross, the dihybrid cross, and the test cross. The monohybrid cross crosses homozygous dominant with homozygous recessive, dihybrid cross crosses double homozygous dominant with double homozygous recessive and test cross crosses unknown individuals with known homozygous recessive individuals. We also made an infographic about genetics and it helped me learn more about it.

In this unit, I learned a lot about genetics and sex. I never knew that sex was so useful in life and I though it was something that was inappropriate to talk about. This unit helped me build up on more genetics that I had learned in 7th grade. From the infographic, I learned more about the background of genetics and how to make infographics.

https://upload.wikimedia.org/wikipedia/commons/thumb/8/8b/Independent_assortment_%26_segregation.svg/2000px-Independent_assortment_%26_segregation.svg.png

https://upload.wikimedia.org/wikipedia/commons/d/d3/Gregor_Mendel.png

Coin Sex Lab Relate and Review

In this lab, we flipped some coins to determine the traits that a child could have by probability. We tested for sex of offspring that included getting heterozygous and homozygous combinations, autosomal dominance, x linked recessive to find x linked inheritance, and dihybrid crosses to find possibilities for traits that can be made from each genotype. The coins served as a model for genetics by the way it was demonstrated. The coins are the Genes and the coin flipping in the air is meiosis or gene segregation to create alleles. Meiosis from the coin flip created recombinations of crosses of genes to create phenotypes. In the dihybrid cross simulation, the expected results for this simulation was that out of 16 individuals, 4 individuals would have brown hair, brown eyes, 4 individuals would have brown hair blue eyes, 4 individuals would have blonde hair, brown eyes, and 4 individual would have blonde hair. As a result, 12 people would have brown hair, brown eyes, 2 people have brown hair, blue eyes, 1 will have blonde hair, brown eyes and 1 will have blonde hair, blue eyes. These results reflect on how probability can be affected. The results that can be obtained using probability is that probability is mostly not accurate comparing to results that should be expected to get. The limits of using probability for predicting our offspring's traits is that we would not know what kind of possibilities to expect when genotypes cross to form phenotypes. It also would affect our knowledge of punnett squares and how they are used for predicting offsprings. This helps me understand how sex works when it comes to predicting offsprings and traits. With this knowledge, I can use it to tell what kind of person I am. I can figure out what kind of traits I would have right now and tell what kind of offspring I got these traits from.

Genetic Infographic

https://magic.piktochart.com/editor/piktochart/8998168

Unit 3 reflection

Unit 3 Reflection

         In this unit, we learned about cells, photosynthesis and cellular respiration. In cells, we learned about the discovery of the cell that led to the cell theory, prokaryotes and eukaryotes, cell boundaries, and the diversity of cellular life. The discovery of the cell began by Robert Hooke using an compound microscope to look at a thin slice of cork and called the chambers in it cells. Later on, Anton Van Leeuwenhoek used a single lens microscope to look at pond water and other living things. He noticed that organisms were everywhere. In 1838, German botanist Matthias Schleiden concluded that all plants are made of cells and in 1839, German biologist Theodore Schwann concluded that all animals are made of cells. In 1855, German physician Rudolf Virchow concluded that new cells could be produced only from existing cells. This led to the cell theory that states, all living things are made of cells, cells are the basic units of structure and function in all living things and new cells come from existing cells.

        Prokaryotes and Eukaryotes are two types of cells. Prokaryotes have genetic material that a nucleus contains and are smaller than a eukaryotes. They do not contain a nucleus but they carry out every activity associated with living things. Bacteria are prokaryotes. Eukaryotes are cells that have a nucleus. They are larger than prokaryotes and have their genetic material separated from the rest of the cell. They are very specialized as they contain lots of structures and internal membranes. They can be unicellular or multicellular organisms. The structure of eukaryotes are made of many organelles. It's divided into two major parts, the nucleus and the cytoplasm.  The cytoplasm is the portion of cells outside the nucleus and the nucleus is the brain of the cells as it helps make instructions for making proteins and other important molecules. There are two types of eukaryotes, plant and animal cells. Plant cells contain a vacuole, lysosomes, chloroplasts, cell membrane, cell wall, golgi apparatus, mitochondria, rough er, nucleus, nucleolus, ribosomes, smooth er, nucleus, nucleolus, ad nuclear envelope. Ribosomes are small particles of RNA and protein. Endoplasmic Reticulum is the site where lipid components of the cell membrane are assembled and exports proteins and other materials. The difference between smooth er and rough er is rough er has ribosomes on the outside and smooth er doesn't. Golgi apparatus helps modify, sort, and package proteins and other materials from the er for storage or secretion. Lysosomes are small organelles filled with enzymes that help break down lipids, carbohydrates, and proteins into small molecules. They also break down old organelles. Vacuoles are storage sacs that store water, salts, protein and carbohydrates. Mitochondria are organelles that convert chemical energy into energy that cells can use. Chloroplasts are organelles that capture the energy from sunlight to convert it into chemical energy to do photosynthesis. An animal cell contains nucleolus, nucleus, nuclear envelope, rough er, golgi apparatus, ribosomes, cell membrane, mitochondria, smooth er and centrioles. Nuclear envelopes are composed of two membranes and is filled with holes on the outside to let material move in and out of the nucleus. Nucleolus is the inside of the nucleus and the centrioles are organelles that involve in making spindles of fiber in cell division. 

        In cell boundaries, cell membranes and cell walls let specific molecules to go in and out of the cell by many forms of processes. The processes are diffusion, and osmosis. They're are many forms of diffusion like facilitated diffusion. Facilitated diffusion helps the diffusion of glucose across the membrane. Diffusion is a process when particles tend to move from high concentration to low concentration. Osmosis is the diffusion of water though a selective permeable membrane. They are involved in three types of solutions, isotonic, hypertonic, and hypotonic. Isotonic is neutral as solutes stays in the cell, hypertonic has a higher solute concentration as water goes out of the cell and hypotonic has a lower solute concentration as water goes into the cell. Active transport is involved in diffusion. They move cells in the opposite direction by concentration difference. There are four processes that involve movement in the cell membrane. Endocytosis takes material into the cell by pockets of the cell membrane, phagocytosis eats cells by surrounding particles, pinocytosis takes up liquid, and exocytosis release material from the cell. The diversity of cell life is by the levels of organization of cells, tissues, organs, and organ systems. 

        Photosynthesis and cellular respiration are processes that require glucose. Photosynthesis is made by producing glucose and oxygen using CO2 and sunlight. Cellular respiration helps break down glucose into energy. Photosynthesis occurs in chloroplasts and thylakoids and cellular respiration occurs in mitochondria and mitochondrion. They are both made by cycles. 

         This unit was a unit that was very interesting to me. I learned a lot in this unit and did many labs to relate to this unit. So far, this is one of my favorite units because of the topics and I learned a lot from it.

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 dark or light colors attract green plants, then they will grow a lot.

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 using a green color for one side and an orange color for the other. My control variable was the light as the color remained the same for the whole simulation. The variable that was changed was

Results:

Filter Color	Spinach Avg. Height (cm)	Raddish Avg. Height (cm)	Lettuce Avg. Height (cm)
Red	18.33cm	13cm	11cm
Orange	14.66cm	8cm	6.5cm
Green	2.33cm	1.5cm	3.33cm
Blue	19.33cm	14cm	12.33cm
Violet	16.33cm	10cm	8.33cm

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.

The data supported the hypothesis. If more than one type of seed was tested, the sizes of each type of plant would be different in growth and would be the same by the color of the plant.

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

Blue color to the plants was most effective in growth than the other colors while green was the least effective as the plants grew the least.

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

I would expect great results in terms of growth. It would average at least 20 centimeters for the spinach, 16cm for the radish and 14 cm for the lettuce

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.

The question of this experiment is what is the best way of making photosynthesis the fastest? My hypothesis is that if white light is effective for growing plants, then it will be effective for photosynthesis. My Hypothesis was correct. In this experiment, I tested for the white, orange, green, and blue light

For each light, the higher the intensity was, the amount of bubbles that appear increased. The most effective light was the white light as more bubbles appeared more ever time the intensity was increased. The worst one was the green light as bubbles appeared the least on each intensity. This shows that colors like white are more effective because it attracts with plants well when doing photosynthesis and green is the least effective of all because it reflects off plant colors. The control variable was the temperature of the water. The independent variable was the intensity of the light against the water. The dependent variable was the result of the each tested intensity for each color of light.

This lab was about learning about how to create photosynthesis the fastest way. There were many possibilities of doing this like increasing sunlight by using a light source. This lab can be used in other experiment dealing with photosynthesis. This lab was a good experience on learning to create photosynthesis the fastest way.

Light Intensity Data Table (Time:30 seconds)

Light Intensity	White(Times bubbled in 30 seconds)	Blue(Times bubbled in 30 seconds)	Green (Times bubbled in 30 seconds)	Orange (Times bubbled in 30 seconds)
5	8	7	2	6
10	15	15	5	11
15	20	18	7	16
20	24	21	8	19
25	27	23	9	21
30	29	26	9	23
35	30	27	10	24
40	31	29	9	27
45	33	30	10	29
50	34	31	10	30

Egg Diffusion Lab

In this lab, we took 2 eggs and put one in deionized water and one in sugar water in separate cups and let it sit in a cool place to see changes in shape and size in each egg.
When the sugar concentration increased in the cup, the mass and circumference of the egg decreased. This was caused by the sugar water which is a hypertonic solution, a solute solution that has greater concentration than inside the cell and as a result, the cell loses water. The egg mass and circumference was originally weighed 88.91 grams and the length was 16 centimeters. At the end, the egg was 13 centimeters and weighed 41.99 grams. The egg mass and circumference was lost by diffusion. This change in mass and circumference also changed by high concentration of the inside of the egg when it was put in the sugar water and the molecules did not have much space to move around as it lost mass and circumference, there was a change in low concentration as molecules had more space to move around. The membrane in the egg also shrunk as a result of low concentration.
A cell's internal environment changes by the places the egg was put in. It was put in many solutions like vinegar, water, and in sugar water. This resulted in the change of the egg as it decreased when it was put in the sugar water because it's a hypertonic solution.
This lab demonstrated how a hypertonic solution is involved in a change of size in an object like an egg. The egg became smaller and smaller as the egg was left in the sugar water for long periods of time.
This lab is related to many things in the real world. One thing it is related to is fresh water sprinkled in vegetable. Fresh water is sprayed on vegetables to keep them fresh and keeping them in good shape. This is related to the lab by the egg as it broke apart when it was put into the sugar water. Another thing this lab is related to is roads that need salt to melt roads. This is needed so cars can drive on it safer. Salting to the plants damages the plants. This happens because of the salt on the plant cells causes the cells from the cell's cytoplasm to move out of the cell by osmosis.
An experiment that can use this experiment to make another experiment is how your hands shrivel up by putting it in water for long periods of time. Based on this experiment, this experiment would want to test the amount of time that the fingertips of the hand will shrivel up in cold water.

Egg Cell Macromolecule Lab

Egg Cell Macromolecule Lab Conclusion

           Our question in this lab was can macromolecules be identified in an egg cell. We found out that macromolecules can be found in an egg yolk, egg membrane, and egg white. We tested them for four macromolecules, monosaccharides, polysaccharides, lipids, and proteins. We tested each of them for the egg membrane, egg yolk, and egg white and rated in each them for the quantitative amount for each macromolecule. The egg yolk was tested positive for the proteins and lipids. For the protein, it turned purple and we rated it a 1 out of 10. For the lipids, it turned orange and we rated the quantitative amount a 9 out of 10. For the egg membrane, it tested positive for the polysaccharides, protein, monosaccharides and lipids. It turned dark brown for the polysaccharides and we rated the quantitative amount a 8 out of 10. For the proteins, it turned purple and we rated the quantitative amount a 8 out of 10. For the monosaccharides, it turned purple and rated it a 5 out of 10. For the lipids, it turned pink and rated it a 1 out of 10. For the egg white, it tested positive for the monosaccharides and proteins. For the monosaccharides, it turned into green and orange and rated it a 2 out of 10. For the proteins, it turned purple and rated it 4 out 10. This evidence shows that macromolecules can be found in an egg.
          There were many errors in this lab that had affected our results. One error was the way we judged the colors of each test. For example, the color of the macromolecule in the egg white for the monosaccharide test was multicolored and we judged it as a green and orange when there was more colors like yellow and blue. This had affected our results by saying that it had macromolecules when it didn't have any. Another error was how we might have accidentally mixed many things in one test tube like adding egg membrane and yolk together. This affected our result by the color shown after we let it sit it another solution and in warm water. Also, the results would not be accurate for whether the macromolecule was present or not. To avoid these errors from happening, we should have used different spoons for different parts of the egg to put in the test tube and being more aware of the colors in each test tube.
           The purpose of this lab was to know how to identify monosaccharides from an egg membrane, yolk and white. This lab was related to what we learned about the 4 macromolecules. We learned that they are found in many types of food that are made and sold especially eggs. This lab can be applied to other situations relating to looking at other food containing macromolecules.

Inquiry Hour Blog 1.1

Identifying Questions And Hypotheses

http://www.sciencedaily.com/releases/2015/09/150924124045.htm

Question: Can new methods that make longer streams of plasma with greater longevity lead to powered lightning rods?

Hypothesis: If a powerful laser beam shoots in the air and ionized the molecules, then it can channel a potentially damaging lightning bolt. 

Prior knowledge of hypothesis: If Benjamin Franklin invented the lightning rod to protect people from lightning strikes, then lasers could replace metal poles.

Inquiry Hour Blog Post 1.2: 20 big questions.

Inquiry Hour Blog Post: 20 Big Questions

I liked the question, will we ever cure cancer. I like this question because many people in the world are suffering from many varieties of cancer that can be life threatening. The hypothesis for this question is if more than 3.7 million people get cancer every year and survive, then other people who are suffering from cancer may survive. 

20 questions:

1.Will the world ever end?

Maybe, if Earth remains the same

2. Will extinct animals come back to life?

No, if animals are extinct, they cannot be made again.

3. Can everyone get a robot?

Maybe, if we are intelligent enough to crack intelligence and apply it to a robot. Robots must be affordable for families to buy. 

4. When will a successful time machine be invented?

When Einstein's theory can be applied to more theories relating to it and successfully turning back the clock.

5. Can college tuition be a lot cheaper?
When a petition for cheaper tuition is signed by many people and given to the president to sign.

6. When can we get the faster computers?
In a while till quantum computing and new material that makes computers faster are invented. They are then applied to computers to get sold.
7. When will everyone have food to eat including the homeless?
When we get enough water to grow more food and build more farms and plantations for food to grow.
8.When can we become immortal?
We may not ever become immortal. We can live for a long time, but that will happen by treating yourself well.
9. How can we avoid bad bacteria going into our bodies?
By using antibiotics right and inventing another type of medicine that can go well with antibiotics and helps avoid bad bacteria.
10. When will prime numbers be no longer used?
They will always be used in math in everyday life to solve math problems. So the answer is no.
11. When will the drought end?
The drought may end in a long time unless we start getting constant heavy rain that will last about a year or less.
12. What is so good about blogger?
It helps us make our own blog and to show others your accomplishments you've done. It stores writing that is valuable to them to show to others.
13.What would happen if we had no trees?
We would not have photosynthesis and have no air to breathe into. Also, our air would be polluted and we would not live a long time.
14. What would happen if we had no animals?
We would have no meat in our stomachs and would be not be very muscular.
15. How do we make man made elements?
 By using different types of materials to make unique looking elements.
16. Can we live in other planets other than Earth?
We could live in mars because the weather is similar to Earth, but will be hard to live in because Mars is empty.
17. Who created the universe?
Steven Hawking. He accepted god's role to the universe but argued that god didn't create the universe.
18. Who invented the elements?
Many scientists each created elements which was later put together by Dmitri Mentaleev
19. Where is the best place to obtain water for plants?
Water can be obtained everywhere you go and can be used to drink or water plants. There's isn't a specific place to find water to use in everyday life.
20. Why does animals want to attack humans?
They want to have their own space, fear, food, anger and protect their young from humans.