Human DNA Extraction Lab Conclusion

   In this lab, we asked the question, "How can DNA be separated from cheek cells in order to study it?" We found that the separation of DNA occurs in three simple steps: homogenization, lysis, and precipitation. It is necessary to first break down the cell membrane and nuclear material by homogenizing, or to making similar in function, the cell tissue with a polar(covalent bond's electron's shared unequally) liquid. During the homogenization steps, the outer layer of the polar DNA cells broke down in the polar Gatorade. We created a mixture of Gatorade and saliva(polar) and then we added cold alcohol (nonpolar, where covalent bond's electrons are shared evenly). The combonation of the polar and nonpolar solutions created a precipate or separated substance. After collecting some information we learned that the sodium chloride(salt) added to the solution assists the separation by blocking negative phosphate ends of the DNA, enabling them to travel closer together. Soap is then added to the solution to lyse, or destroy the cells and release the opened DNA. Then catobolic proteases, a group of enzymes(catalysts, or substances used to speed up chemical reactions) used to break down protiens called histones(structural proteins of chromosomes), are mixed in the form of pineapple juice. Then, 95% isopropanol alcohol, with a different density than the mixture, is layered above it in a test tube. Because the DNA is polar and the alcohol is nonpolar, DNA is separated from the solution.
   While our hypothesis was supported by our data, there could have been errors due to the fact that our table group was challenged to number the procedure on our own. This could be improved by practicing these important skills beforehand rather than suddenly in the face of a new lab. Another possible error could have been the non-specific amount of gatorade being used in the mixture to collect the DNA. This problem can be solved by simply using measuring cups, or labeling the disposable paper cups with measurements for accuracy. These errors would have skewed the results greatly if brought to an extreme, but luckily our group seemed to handle the lab pretty well.
   This experiment tested our basic lab skills as well as our ability to apply collected information. This lab was done to demonstrate the complex process of achieving a precipitate, by using the basic knowledge we have learned from recent as well as previous vodcasts. From this lab, I not only learned a lot of new vocabulary, but how it relates to the concepts we have been studying in class. This extra background helps me put everything together to make a lot more sense, aiding me in understanding these major concepts. Based on my experience from this lab, I feel like I can especially apply the critical thinking skills I've been introduced to in future experiments.

Unit 4 Reflection

   In class, we recently did the "Coin Sex Lab" where we experimented with probabilty and predictability while applying scientific concepts we learned throughout the unit. In this lab, we collected information and defined many terms. Coins served as a model for our genetics concept when we covered them with tape and labelled them with different genotypes. We created punnet sqaures for each cross of phenotypes, and predicted possible outcomes. We then flipped them silmultaneuosly, stimulating sex, and testing probability. Then we recorded the genotypes and phenotypes as well as calculating the ratios. Lastly, we analyzed our results by comparing our results to our predictions, and relating parts of the lab to scientific concepts learned in class. We did multiple crosses;  In our dyhybrid cross stimulation, we tested two individuals and their double heterozygous phenotypes. We assessed the possible gametes based off the cross, as well as calculating a phenotypic ratio in our dyhybrid punnett square. We expected to have two homozygous children, based off of our punnet square calculations. The experiment resulted in zero homozygous children, which was not surprising considering the fact that homozygous individuals are less common. This shows that no matter what the probability may be there is no way to predict anything with complete certainty. The limit of using probability to predict offsprings' traits would be if parents were too dependent on the predictions. There is never a 100% chance of something happening, let alone an equal probability. For example, you could have two children, both girls, although the probability would be a 50/50 chance. In the dyhybrid cross, zero out of the 16 children were double homozygous for the two genes. Understanding this concept relates to the key concept of the broad differences between predicability and probability.
   This unit's essential understanding revolved around the basic principals of genetics, and how they tie in to the more complex areas of study. We focused mainly on the processes of mitosis and meiosis, forms of cell division, as well as comparing them and their widespread roles. We looked at genetics at a larger scale as well in the forms of reproduction, both sexual and asexual and the different types. We learned about how DNA is passed from generation to generation and how individuals either have the same 2 alleles(homozygous) or different 2 alleles(heterozygous). The basic vocabulary of genes, alleles, dominance, recessive, genotypes and phenotypes were explained as well as as Mendel's laws of segregation and independent assortment where gene pairs separate from each other when gametes are formed, or randomly during meiosis. Besides being introduced to the basic rules and reasons for making punnet squares, we were able to gradually apply them as we learned more concepts. We talked about X-linked and autosomal inheritance, and how dominant and recessive traits were to be portrayed in a punnet square, as well as understanding how the location of where a gene is inherited has an important role in genetic disorders. Codominance, where both alleles are completely expressed, as well as incomplete dominance where neither allele is completely dominant or recessive.  Gene linkage, epistasis, mulitifactorial disorders, and polygenetics were also summarized. Lastly, crosses were discussed. The different types of crosses that occur between parents during reproduction can determine the genotype and phenotype of the offspring by looking at certain ratios and relating the cross to all the other topics of this unit, like we assessed in the "Coin Sex Lab."
   Towards the end of the unit, the subjects we were studying began to get more complex, and as I forgot most of the foundation I had built earlier in the unit, I struggled to recall some of the most important information. My lack for review was a major setback, but after a lot I feel a lot more confident about knowing enough for the test.  The skills I was able to use during the lab helped everything make a lot more sense as it all came together. The infographic I created was an amazing help as for reviewing because I felt as if I got my ideas across efficiently. This made my infographic a  great, simple, studying tool to use early on in the studying process. I recently found out that my preferred learning style is multimodal which means that I can learn material presented in all different ways, but I have to go out of my way to study material in all these different forms. My modes of learning vary, but it takes some time to tap into the best way for me to learn in a certain subject. These results sound correct, because I have always been weary trying to find just one learning style. As for studying strategies, I know now that I need to give myself more time to study in different ways.
https://www.brightstorm.com/science/biology/mendelian-genetics/codominance-incomplete-dominance/

http://rannazbioblog.blogspot.com/2016/11/blog-post_21.html


Works cited for image: 

   The Cell Cycle. Digital image. Wikimedia. N.p., n.d. Web. 28 Nov. 2016. <https://upload.wikimedia.org/wikipedia/commons/thumb/2/2f/Animal_cell_cycle-en.svg/2000px-Animal_cell_cycle-en.svg.png>.

Genetics Infographic-Bachelors of Science in Genetics

Is Sexual Reproduction Important?

   In Olivia Judson's national bestseller, Dr Tatiana's Sex Advice to All Creation, chapter one described the advantages and disadvantages of asexual reproduction. Judson describes the different types of organisms and how they reproduce. An interesting point she mentioned was that mammals actually clone(reproduce without sex) as well, in the form of twins. She talks about how cloning is more efficient in maintaining a good demographic for population growth. Miss Philodina Roseola , the bdelloid rutifer, descending from aseuxual reproducing creatures that evolved, and have lived for over 85 million years without miosis. Another species mentioned was the E. Coli bacterium, and for bacteria, who reproduce asexually, sex is just a way to aquire extra genes. For strictly asexual organisms, genetic developments are hard to create and adapt to. Genetic mutations are generally neutral and have little effect, but when there is an effect, small changes are likely to harm the organism. Judson concluded that harmful mutations are sometimes the reasons why most asexuals go extinct.There is now way to measure mutation rates at the moment, but if the rates are low the mutations would not be the reason after all. She says that mammals are the only ones where the asexual reproduction of adults are unknown. Shuffling genes can help us evade parasites and reduce the impact of harmful mutations, where sex really enables us to survive.

Unit 3 Reflection

   This unit was about different types of cells and their functions, as well as looking at the cell at both a microscopic and global level. We learned about the two different types of cells, eukaryotes(with a nucleus) and prokaryotes(without a nucleus). We learned about the roles and functions about different organelles in the cell.We also talked about protists, plant cells, and animal cells, as well as their similarities and differences.
    My strengths were mostly based on learning the different types of organelles, although I struggled to retain the information about their individual functions. We also learned about the unique characteristics of membranes, and how they are semi-permiable (bouncers), as well as the methods of transport(passive, active, and (facilitated) diffusion).
  An important part of the unit was about diffusion, passive movement across a concentration gradient to reach equilibrium, with multiple molecules moving across the membrane. Osmosis is diffusion across a semipermeable membrane, where the cell shrinks if the solvent is lost and the cell grows if the solvent is gained.
   Water balance was also discussed, focusing mainly on tonicity, the ability of a surrounding solute to cause a cell to gain/lose water through hypertonicity and hypotonicity. Also, cell evolution was discussed as well as the principals of endocytosis(material is taken into pockets/in-folds), exocytosis(material is released from vacuole from fusion with membrane) , phagocytosis(cell eating, packages food in vacuole), and pinocytosis(takes in liquid, pinches off cell).
  Light waves were also talked about in the vodcast, as well as the visible light spectrum. We learned that we recognize colors by interpreting the color that is reflected and not absorbed. Also how shorter wavelengths have higher energy and longer wave lengths have lower energy, and colors like red, violet, and blue(with short wavelengths and high energy) are best for growing plants under light, while colors like yellow and green(long wavelengths with low energy) are not optimal conditions for maximized plant growth.
  Most of
   Lastly, cellular respiration and photosynthesis were discussed. Photosynthesis occurs in the chloroplasts of autotrophs, while cellular respiration occurs in the mitochondrion of autotrophs and heterotrophs.The products of photosynthesis are the same as the reactants of cellular respiration(and vice versa), the only difference is that the chemical energy converted in photosynthesis is light energy and in cellular respiration heat energy is used from ATP. Photosynthesis occurs when light is absorbed in the chloroplasts, then the Calvin Cycle rotates 6 times in the thylakoid to produce one glucose molecule.
   I knew a lot about the basics of photosynthesis, and I vaguely understood cellular respiration up until this point. Once I saw them compared side by side, everything made sense and all the pieces seemed to fit together. I understood the concept much better, but it still took some effort to really learn to little details that were also very important.
   In cellular respiration(AKA aerobic respiration because it requires oxygen), Glycolysis in the cytoplasm begins the cycle to create 2 ATP, then the Krebs Cycle(AKA Citric Acid Cycle) creates another two and uses oxygen to produce energy carrying  molecules(NADH and FADH2) and carbon dioxide. Then the electron transport chain, which is located in the inner membrane of the mitochondria creates 32 ATP. After cellular respiration, where glucose and oxygen are put in, 36 ATP, 6 carbon dioxide molecules and 6 water molecules are produced.
   Overall, I think I was able to remember the outline of the events in this unit, while having a hard time recalling the details, but I think doing the CFU's really helped reinforce that practice and repetition for studying. A lot of big topics were covered, but now I feel like I have a really good foundation and understanding for what to expect later on. We observed things from different angles which I really think helped me broaden my understanding of the lessons, as it appealed to all different learning styles.

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 the most energy is absorbed by the color blue, and the least energy is absorbed by the color green, then the color green causes the least plant growth and the color blue causes the most plant growth.

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?

We tested our hypothesis by placing the different plants side by side, growing half with red light and half with green light. The variables controlled were the type of plants, the brightness of light, and the days of growth. We changed the color of the light to compare our growth results.

Results:

Filter Color	Spinach Avg. Height (cm)	Radish Avg. Height (cm)	Lettuce Avg. Height (cm)
Red	18	14	12
Orange	14	8	6
Green	2	2	3
Blue	19	14	13
Violet	16	11	9

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.

 Our data supported our hypothesis, because it shows that the average height of all the plants are greater under blue light, and lower under green light. The blue lighted plants grew the most, and the green lighted plants grew the least. This is because the color green is reflected by plants, because it contains chlorophyll, a green colored pigment. Generally the lettuce seeds grew to be the shortest, regardless of the color, and the spinach grew the most, while the radish was in between.

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

  According to our data, we can conclude that the color blue causes the most plant growth. Their wavelengths cause them to be best absorbed by plants, increasing plant growth.

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

  Under white light, there would be a balance of the colors, making it a neutral under the spectrum, giving medium growth results.

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, constants, and control?)
• Data table
• Conclusion (Just 1st and 3rd paragraphs since there's no way to make errors in a virtual lab)

*Type your question, hypothesis, etc. below.  When done, submit this document via Canvas.  You may also copy and paste it into your blog.

Question: How does light intensity affect the rate of photosynthesis?

Hypothesis: If white light contains all of the colors of the visible light spectrum, then a plant grown under a light of higher intensity will grow at a faster rate under photosynthesis.

Experimental Parameters:

-Dependent variable: rate of photosynthesis

-Independent variable: light intensity

-Control: neutral light intensity (25)

-Constants: the plants, the amount of carbon dioxide(50% of bottle) , the time (45 seconds), the color of light(white), and temperature (10°)

Data Table: Rate of Photosynthesis

Light Intensity	15	25	35	50
# of oxygen bubbles	9	14	16	18

Conclusion:   In this lab we asked the question, “How does light intensity affect the rate of photosynthesis?” We found that a higher intensity of light produced more oxygen, speeding up the rate of photosynthesis. Our data shows the green plant produced more oxygen under a higher intensity of white light, than a lower intensity of white light. At a light intensity of 15, 9 oxygen bubbles appeared throughout the 45 seconds. At a light intensity of 25, 14 oxygen bubbles were produced during that time. At a light intensity of 35, 16 oxygen bubbles appeared.  At a light intensity of 50, 18 oxygen bubbles appeared during the 45 second test. Based on what we learned in the vodcasts, light is one of the 3 main elements necessary in carrying out the oxygen producing process of photosynthesis. With a higher intensity of light absorbed by the plant, the plant is therefore able to produce more oxygen through photosynthesis. This data supports our claim because it shows how with a greater light intensity, a plant will be able to create more oxygen by absorbing more light.

This lab was done to demonstrate how the quantity of a reactant, like light intensity, can affect the quantity of the remaining products of photosynthesis, like oxygen. From this lab, I learned about the key factors needed to carry out photosynthesis, and how they can affect the products, helping me understand the concept of the chemical formula of photosynthesis. Based on my experience from this lab, I could apply what I learned to another situation where I am growing a plant, because I now know what the optimal conditions are, regarding temperature, light intensity, and color.

Microscopic Organism Lab

Amoeba
Power: x400
Eukaryotic, Heterotrophic
This cell is unique because it has psuedopods that find the food to consume, and digest it by performing phagocytosis. Its cell membrane looks think like jelly.

Euglena
Power: x400
Eukaryotic, Autotrophic
This cell is unique because it could be both heterotrophic and autotrophic, and it is neither a plant or an animal. It has a flagellum that looks like a string.

Bacteria Cells:General Shapes
Power: x400
Prokaryotic, Autotrophic
This cell is unique because there are 3 main shapes(labelled above). Bacteria cells have no organelles and for this reason, considerably smaller than most cells.

Plant: Lingustrum
Power: x400
Eukaryotic, Autotrophic
This cell is unique because it is made up of 50 different species, as it is a genus of plants. The cross section shown above is green with chloroplasts, and has an apparent vein.

Cyanobacteria (Blue green Algae)
Power: x400
Prokaryotic, Autotrophic
This cell is unique because it is a prokaryotic autotroph, because it is a photosynthetic bacteria. There are no chloroplasts found in the cell.

Animal Cell: Skeletal Muscle Tissue
Power: x400
Eukaryotic, Heterotrophic
This cell is unique because it is multinucleate. There are also pink and purple colored muscle fiber, composed of bands called stritations. 

Plant Cell: Spirogyra
Power: x400
Eukaryotic, Autotrophic
This cell is unique because it is  long and skinny with a cell wall made of carbohydrates(cellulose and pectin). Although the central vacoule takes up most of the space, there is a nucleus in the center of the cell, and chlorplasts line the outer edge after they are pushed out by the vacoule.

Summary:
   In this lab, we observed and identified the different parts of microscopic cells. In the muscle cell we found the nucleus, muscle fibers and stritations. In the lingustrum we found the chloroplasts, epidermis cell, and the vein. In the spirogyra we found the cell wall, the chloroplast, and cytoplasm. In the bacteria, we were able to identify the coccus, bacillus, and spirillum. In the cyanobacteria, we found one single cell. The euglena had a nucleus, chloroplasts, and flagellum. The amoeba contained a nucleus, cell membrane, and psuedopods. The autotrophs, or producers were mostly plant and bacteria cells, some with chloroplasts that made them green. The heterotrophs were consumer cells and contained nuclei. The eukaryotes all had a nucleus, and they contained many different cells and organelles, while the prokaryotes had no nuclei, and contained no organelles.