Unit 5 Reflection

The theme of Unit 5 was DNA and how it affects our daily lives. It went over concepts such as what DNA is, how it is replicated, how DNA is used to create proteins, as well as how genes are regulated and expressed in cells. The main understanding of this unit was to understand how DNA affects and controls our whole lives. This unit taught us how to look at the big picture of DNA and not simply what it is, but how it in fact affects our whole bodies and how are genes are expressed to create organisms. My main strength in this unit was my understanding of how DNA is used to create. Through the process of protein synthesis, in which the DNA is transcribed to RNA and then translated to proteins, DNA is changed into proteins which act as the phenotype and expression of genes. The enzyme RNA polymerase reads the DNA split strand and changes the base thymine with uracil, create a single RNA strand. The ribosome then reads the RNA strand and reads it one codon at time (pairs of 3 bases which code for a specific acid) and creates the protein. The protein synthesis lab gave a visual representation of the process which helped me to understand it and allowed me to experiment with mutations and how they affect genes. One concept I had a hard time understanding was how genes are regulated and expressed due to the complexity of the concept and how it is intertwined with protein synthesis. The diagram during the Lac opperon do now gave me a greater explanation because it provided a properly labeled visual diagram which incorporated all the vocab from this concept. My notes during the vodcast were sub par which really hurt my understanding.

https://en.wikipedia.org/wiki/Protein_biosynthesis#/media/File:Ribosome_mRNA_translation_en.svg

I learned that it is important to look into the deeper meaning of things and their effect rather then just taking them for face value. This was seen with DNA, as I learned about the actual effects of DNA rather than just accepting that there is something called DNA. I also learned that you should be willing to ask for help, as I asked my brother to help me with the concept of protein synthesis since he has taken biology before and is a biochemistry major.

http://biosocialmethods.isr.umich.edu/wp-content/uploads/2014/09/central-dogma-enhanced.png

From the Vark questionnaire I learned that I am mainly a visual and reading/writing learner, which is why I have started to learn more by using notes and drawing diagrams which give me a visual representation of certain concepts. I wonder how organisms were first able to create protein and other molecules when they first evolved since they had to first create certain organelles with out these processes. I feel that I am a better student today since I truly understand DNA and how it effects organisms, rather than in 7th grade biology where I new what DNA was but what is was and how it was different than RNA.

Protein Synthesis Lab Analysis

-       The process of protein synthesis changes DNA into RNA, and then into proteins. The steps of this include transcription and translation. During transcription, RNA polymerase binds to the DNA and separates the DNA strands. RNA polymerase then uses one strand of DNA to as a template and attaches the corresponding nucleotide to create the strand of RNA. The base thymine is switched with the base uracil. The new RNA strand then travels from the nucleus to the ribosome. In translation, the ribosome reads the codons (pairs of 3 bases) to create a specific amino acid, which is then attached to a long string to create a protein.

     Changes in the base pairs of DNA molecules can have a major effect depending on the type of mutation that occurs and where in the DNA sequence it occurs. The 2 types of mutations are point mutations and frameshift mutations. Point mutations can be harmless and may only change one codon, though the amino acid coded is still the same. Frameshift mutations can drastically alter the DNA sequence and change the proteins created. The insertion and deletion of bases change all of the codons after the change and greatly affects which amino acids the codons code for due to them all being changed. A frameshift mutations earlier in the sequence is the most harmful as it has the most codons to change.

    

    The mutation that we chose for our was a deletion of a base near the beginning of the sequence. We chose this mutation since it was a frameshift mutation and we believed that it would cause the most damage. Compared to other mutations, this one changed the most base codons and changed the most amino acids, creating different ones and getting rid of the stop codon. It matters where the mutation occurs because earlier mutations change all the ones behind them and have a greater effect.

    One real life mutation that occurs in human organisms is sickle cell anemia, which is the result of point mutation in one of the nucleotides for the protein of hemoglobin. The mutation causes the red blood cells to distort and form clots, greatly endangering the body.

Human DNA Extraction Lab Conclusion

In this lab we asked the question of "how can DNA be separated from cheek cells in order to study it?" We found that you can separate DNA from cheek cells through the steps of homogenization, lysis, and precipitation, which is where the DNA first becomes visible. Our claim was correct since we used this process to extract DNA, and the DNA came out in creamy white clumps once the alcohol was added on top of the solution, which acted to draw out the precipitate (DNA). Our qualitative data supports our claim since the DNA is supposed to float to the top since it is nonpolar and the alcohol is polar, so it floats the top (precipitation) . The protocol for extracting DNA that we followed properly worked, which allowed us to extract the DNA.

While our hypothesis was supported by our data, there could have been errors due to an incorrect ordering of the lab procedure and improper measurements of liquids and enzymes added to the solution. In the lab, we were required to properly order the steps of the lab according to the steps of DNA protocol. We decided to put soap into the solution before salt, which incorrectly follows the procedure since soap is added to lyse the cell membrane and emulsify the lipids, while salt is used to facilitate precipitation of the DNA, and since lysis comes before precipitation, so our ordering was wrong. This could have had a major effect, as the DNA may have not been properly extracted and we may have not gained enough of the DNA. Improper measurements of solutions could have effected the data since unequal measurements could have changed the solution and the way it effected the DNA. Due to there errors, in future experiments I would recommend that the protocol be given to us beforehand so that everyone follows the same procedure, but is is impossible get rid of the improper measurements due to the chance of human error.

This lab was done to demonstrate how DNA can be extracted from cells and how to create a procedure for labs based off given information. From this lab I learned the three basic steps of DNA extraction (homogenization, lysis, and precipitation), which helps me understand the concepts of how DNA is extracted and how different solutions interact with the molecules within DNA. Based on my experience from this lab, I can apply my knowledge to different labs involving DNA and now know how to create a lab procedure by identifying different given parts and putting them in order.

Unit 4 Reflection

Unit 4 was about sex. It went into the details of the sex cycle, genetics, and how genes affect our daily lives. The essential understandings were how do genes affect our physical traits and why is sex great. Through the genetics infographic, we learned about genetics and the different types of genetic inheritance. The coin sex lab gave a great explanation of how genetics work and how to use probability to predict different types of crosses, such as autosomal, x-linked, monohybrid, and dyhybrid crosses. The vodcast on meiosis gave a basic understanding of how meiosis and mitosis are different and the different steps of meiosis. I hard a hard time at first of understanding Mendel's 2 laws and how chromosomes split, but I understood better once I had a visual representation from the diagram and the passing on my genes mini lab. I easily picked up on the different types of genetic crosses and the different abnormalities that can occur since we learned the basics of them in 7th grade biology.
After taking the VARK questionnaire, my results were 7 Visual, 2 Aural, 6 Reading Writing, and 9 Kinesthetic. The results were what I expected because I generally learn either by watching someone or through using logic (not in the test) and examples. Currently I read over the notes and redo the CFU's to test myself, and answer the vodcasts my self to truly test weather I can understand the content. I can use more visual techniques such as notecards and color-coding concepts in order to properly absorb them while continuing my same studying ways. This will play to my learning styles as reading/writing but also the visual and kinesthetic aspects.

Genetics Infographic

Here is the link to the published version of this infographic (larger version):

Why is Sex Great Infographic

Coin Sex Lab Analysis

In this lab, we asked the question of "how is probability used to predict what our offspring will be?" We flipped coins marked with different alleles of genes to simulate Mendel's laws of segregation and assortment and model dihybrid crosses, x -linked inheritance, autosomal dominance crosses, and the sex of offspring. Coins served as a good model for genes because there was a 50% chance of getting either gene, which showed the two laws and used probability to find actual ample sized results. During meiosis, the chromosomes split, which is represented by the flipping of the coin, showing the random probability of having either allele. Through recombination, the genes are combined and we can find the genotype and phenotype of an organism. This results in many pairings, some homozygous and some heterozygous. The phenotypic ratio for dihybrid double heterozygous crosses is 1:3:3:9, with 9 being the phenotype both dominant, the 3's as 1 recessive and 1 dominant, and the 1 being both recessive. Our actual results through the flipping of coins garnered the result of 3:1:2:10. The differences in the results of the data is due to the representation of the Law of Independent Assortment and the random probability of getting any phenotype, though some have higher chances due to dominant and recessive alleles. The limit of probability comes from the randomness of gene separation and the ability for genes to mutate and cross with each other, which creates new, unaccounted alleles. These changes cannot be predicted by punnet squares and probability. This understanding of the probability of crosses can help predict what genes and traits my children will have in the future and what unknown traits I may have right now,

Photosynthesis Virtual Labs Analysis

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 red, blue and violet are best used by plants, then plants will grow best under these colors.

If green and yellow provide the least energy for plants, then plants will grow worse under these conditions.

 

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 used the light and plant growth virtual lab and measured the average heights of the plants under the different conditions. In this lab, there was no control lab to compare to, and the independent variable was the color of the light used.

Results:

Filter Color	Spinach Avg. Height (cm)	Radish Avg. Height (cm)	Lettuce Avg. Height (cm)
Red	18
Orange	14
Green	2
Blue	19
Violet	16

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 our hypothesis as the colors which we predicted would grow plants better had higher average heights and the colors which we predicted would do worse had lower height averages.

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

Colors closer to the end of the visible color spectrum provide more energy and help plants grow better than visible light closer to the middle of the spectrum.

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

I would expect plants under white light to grow the best and have the highest average height because white light contains all the colors in the spectrum and thus has the combined energy of all of them.

Site 2: Photolab

• Question: Does the amount of carbon dioxide present during photosynthesis affect the rate of photosynthesis?
• Hypothesis: If photosynthesis uses carbon dioxide to create glucose, and to gain more of a product you need more of the reactants, then an increase in carbon dioxide levels will increase the rate of photosynthesis.
• Experimental Parameters:
• Dependant Variable: The amount of oxygen released.

• Independent Variable: Level of carbon dioxide in the water.
• Control: Water with a low level of carbon dioxide.
• Constant:
• Temperature: 10
• Light Intensity: 20%
• Data Table

Amount of Oxygen Released
Time:		15s	30s
Levels of Carbon Dioxide	High	4	8
	Low	3	6

Conclusion

In this lab we asked the question, does the amount of carbon dioxide present during photosynthesis affect the rate of photosynthesis? We found that the amount of carbon affects the rate of photosynthesis. For every 15s in the virtual lab, when there was a low amount of carbon dioxide, only 3 bubbles rose, while the high amount of carbon dioxide caused 4 bubbles. The bubbles are a product of photosynthesis as the oxygen is released and causes a bubble to rise to the top. Also, to create a faster rate of reactions and more products in science, you need a higher amount of reactants, which is why a higher amount of carbon dioxide causes a faster reaction and more product. This data supports our claim because it shows how a higher amount of carbon dioxide increases the reaction and shows the differences caused by varying amounts.

This lab was done to demonstrate the effects of external parameters on the rate of photosynthesis. From this lab I learned how different external environmental changes affect the rate of photosynthesis, which helps me understand the concept of photosynthesis and how an increase in reactants increases the rate and product from a reaction. Based on my experience from this lab, I now know how to design a functional experiment and how to change variables to answer questions.

Unit 3 Reflection

       Unit 3 of biology was about the characteristics/structure of cells and how they function and create energy. The themes of this unit were how cells create energy, the different kinds of cells, the functions of cell organelles, and diffusion. Learning about osmosis and diffusion was easy because they are based of the principles of high and low concentration and how molecules move from low to high concentration. The vodcast on osmosis and diffusion helped to explain this, as it clearly showed how water diffuses to compensate for the size of other molecules. the egg diffusion lab clearly showed how osmosis works in real life conditions and gave a hands on experience into cellular biology. The vodcast on the different parts of the cell was interesting because it was done by someone else, and it gave a broader understanding of the functions of the different organelles. The microscope lab experiment helped to identify the different parts in cell and was very fun, though finding many of the organelles proved challenging. On the other hand, learning about photosynthesis and cellular respiration was harder than expected. Even though the vodcasts on these topics were very in depth, the complexity of the topics was much harder to remember. The text book notes gave an even deeper insight on the process that occurs in both, but the lack of background knowledge I had on both hurt me, as I didn't truly understand the reactions occurring in the cell. I still don't understand how exactly the cell converts light into energy, and weather the ATP is molecule or from of energy. This unit helped become a better student by forcing me to study and learn more about concepts I didn't understand. I previous years, I picked up and remembered lessons very quickly, so this unit was a change because I had to actually study on the topics of cellular respiration and photosynthesis. Some questions I have include: Is ATP and actual molecule or an invisible energy?; why do certain light waves have less energy than others?; If cells can still create energy without oxygen, how long can the body survive without oxygen?

Egg Diffusion Lab Analysis

          In this lab, we observed the quantitative change to the mass and circumferences that occurred when eggs were placed in different solutions. The eggs were first placed in vinegar to dissolve the shell and then were placed in deionized water. Next, were collected data on the mass, circumference, and qualitative features of the two eggs. One of the eggs was placed in deionized water again, while the other was placed in corn syrup. The egg in the water grew in size, while the egg in syrup shrink in size and became translucent.

          On average, the mass and circumference of the egg in the increased sugar concentration decrease by -51.7% and -23.67% respectively. The cause of the change was the high concentration of sugar outside the cell caused the water to diffuse to the sugar, causing the egg to shrink. Molecules move from areas of high concentration to areas of low concentration in order to create equilibrium, but sugar molecules are to large to diffuse through the semi-permeable membrane, so the smaller water molecules will move to the sugar through passive diffusion to compensate for the sugars immobility. The effect of this is seen in our data.

          A cells internal environmental condition changes based on its external environment because needs to properly compensate with the changes in order to survive. This can happen from the movement of water from areas of low solute concentration to areas of high solute concentration.  

          This lab demonstrates the principal of diffusion by showing a real life example of how diffusion occurs and the effects of it on cells.

          Fresh vegetables are sprinkled water because the water diffuses into the cells sue to a low solute concentration outside the cell, thus keeping the vegetables from becoming limp. The salt accumulated alongside roads can cause the vegetable cells to become hyper tonic because there is larger concentration of solute outside the cell, causing water to diffuse from the cell towards the cell.

          Based on this experiment I would want to test the effects of salt water on the human body and what it does to it. This relates to the previous experiment as it to deals with diffusion, but this experiment would go more in depth into the biological effects of shrinking cells on the human body.  

Egg Cell Macromolecules Lab Analysis

In this lab we asked the question "can macromolecules be identified in an egg cell?" We found that each part of the egg cell contained different macromolecules through a series of tests. To test for the different macromolecules, each part of the egg was placed in a solution that contained solvents that reacted with the macromolecules.

The egg membrane tested positive for lipids, polysaccharides, and monosaccharides. The polysaccharide turned black from the iodine test, and the lipids turned orange from the Sudan III solution, while the monosaccharides turned blue from the Benedicts solution test. These tests show that the egg membranes tested positive for these different macromolecules as the colors observed changed from the presence of the macromolecules. This is because the cell membrane is made of phospholipids and carbohydrates are found on the outside of membranes for communication.

The egg white tested positive for all of the macromolecules we tested for. he polysaccharide turned black from the iodine test, the lipids turned orange from the Sudan III solution, and the proteins turned purple from the sodium hydroxide copper sulfate solution, while the monosaccharides turned blue from the Benedicts solution test. These tests show that the egg membranes tested positive for these different macromolecules as the colors observed changed from the presence of the macromolecules. This is because the egg white is used as energy storage for the nucleus, so  carbohydrates and lipids a re stored there. It also contains proteins for proper growth, development, and protection (enzymes for immunity).

The egg yolk tested positive for polysaccharides and monosaccharides. The polysaccharide turned black from the iodine test, and the monosaccharides turned blue from the Benedicts solution test. These tests show that the egg membranes tested positive for these different macromolecules as the colors observed changed from the presence of the macromolecules. This is because the egg cell nucleus is made of carbohydrates for energy and structure and contains an inner membrane that uses them for communication. In addition, the egg yolk should have tested positive for proteins and lipids as proteins make up the nucleus of the cell and the lipids are used to store energy for development.

        While our hypotheses were supported by our data, there could have been possible errors due to human error and difference data collection. The human error came in many forms, such as problems in measuring liquids for the different macromolecule tests and accidental mixing of the solution. These errors may have impacted the data, as improper liquid measurements lead to inexact solution levels, so the egg cell parts may have been exposed to an improper levels of solution, which would change the qualitative color change. Accidental mixings of the solutions may have diluted the color into the egg cell parts, thus changing the color outcome. Another error was the difference in data collection and observation. Because the data was qualitative, it was subjective to opinion, and people interpreted the changes in color differently, so the data may have been slightly altered. Due to these errors, in future experiments I would recommend being more accurate when measuring items, which may be impossible to cease, and creating a more quantitative way of measuring the qualitative data.

         This lab was done to demonstrate what parts of cells the where macromolecules are found in cell. From this lab I learned what macromolecules are found in the different parts of cells and what they are used for, which helps me understand the concept of cells and their different organelles. Based on my experience from this lab, I now know what cells are made of, which will provide context and background information for other parts cellular anatomy.

Questions on My Mind

         After reading the article "20 Big Questions In Science", the question that I am most interested in is "what is consciousness." I am interested in this question because I wonder about what causes our brain to have thoughts and speak with itself. How does ones consciousness develop? Currently, one hypothesis is that different regions of the brain connect with each other and consciousness is there way of communicating with each other.

My 20 Big Questions:

1. What caused the big bang?
2. What happens when multiverses collide?
3. What causes gravity?
4. How is light created?
5. Is it possible to live for ever?
6. Is there an end to the universe?
7. How can time slow down?
8. Are there other living organisms in the universe?
9. Can humans live for ever?
10. What factors cause evolution to occur in species?
11. Can an organism be recreated?
12. Can humans travel at the speed of light?
13. What is inside a blackhole?
14. How do humans dream?
15. What are atoms made of?
16. How is pure energy created?
17. Do any people in the world share the same iris?
18. Why are flamingos pink?
19. What causes siamese twins to be born?
20. Are mosquitos contributing members of the ecosystem?

Identifying Questions and Hypotheses

          The study I found is called the Stanford Marshmellow Experiment, and it was a study done in the late 1960's on the delayed gratification in children, when it develops, and what conditions it develops in.. They found that children used many methods, such as closing their eyes, hurting themselves or thinking of dark thoughts that would allow them to wait. It the test, children were told that either they could have one marshmallow now, or two in fifteen minutes. In follow up experiments, they noticed that children who were able to delay there gratification tended to have better life outcomes, such as higher SAT scores and healthier BMI's.

          The original question asked when does the control of delayed gratification develop in children. The hypothesis of the experiment was if different socioeconomic backgrounds, ethnicity's and age effect the way that children think, then delayed gratification will develop in children later in life and those who come from better economic backgrounds. This hypothesis was based on the prior knowledge of a similar test done in Trinidad in which different ethnicity's effected the results and children from poor backgrounds were more likely to gain the immediate reward rather then wait and fear losing the reward.

https://en.wikipedia.org/wiki/Stanford_marshmallow_experiment

http://theness.com/neurologicablog/index.php/the-marshmallow-test/

Unit 2 Reflection

       Unit 2 of biology was about the chemistry of life and chemistry is used to create the cells and other parts of living organisms. The theme of this unit were how chemistry is used to create matter and in turn biology. This included sub units about the the different carbon compounds, the properties of water, enzymes and chemical reactions. Learning about the different carbon compounds and enzymes were easy because the fundamental chemistry of them is based of off carbon connections and in the case of enzymes, proteins. the The macro molecule vodcasts clearly showed how different structures of carbon can create different molecules with different purposes. This included carbohydrates, lipids, proteins, and nucleic acid. The sweetness lab showed the difference between complex and simple carbohydrates and difference in taste between them.  In the messing with enzymes vodcast, it clearly explained the factors that effects enzymes and how they can be denatured. The experiment we did on cheese curdling was a very fun way to learn about how different environmental conditions can effect enzymes and to further our understanding of them. On the other hand, I had a hard time with the properties of water, in particularly polarity and how it allows water to easily combine with itself and other molecules. I still don't fully understand the meaning of polarity and weather other molecules not known as water can be polar. Despite doing the vodcast, it would have been nice to do an experiment on it to gain a further understanding on it. The properties that make water wet were easy to understand and I learned what they are, but polarity and how it effects water still confuse me. I learned from this unit how chemical reactions take place and how different conditions can effect what happens. This can help in the future with biology because chemical reactions and chemistry itself is very important in biology and chemical reactions happen at a microscopic level in cells to allow the body to properly function. One thing I want to learn more about besides polarity are ions. Despite knowing that hydrogen ions effect the pH level of compounds and molecules, I don't fully understand what an ion is and how it can make a compound a acid or a base. are there any molecules besides water that are neutral on the pH scale. I also want to know more about activation energy and how chemical reactions are able to absorb energy. How do they collect and harness the energy to create more chemical reactions? How is energy created from the breaking of chemical bonds? Are bonds created from matter or are they just a chemical attraction holding them together. These are some of the questions I have and things I wonder about. 

Cheese Lab Analysis

In this lab we asked the question of “what are the optimal conditions and curdling agents for making cheese.” We found that the optimal conditions for making cheese are a hot temperature and an acidic pH level, while the best curdling agents were chymosin and rennin. In the lab, curdling agents that were placed in acid took an average of 5 minutes, while curdling agents placed in bases did not curdle. Likewise, curdling agents placed under a hot temperature took very little time (5 and 10 minutes) while curdling agents placed under a cold temperature did not curdle. In both situations, curdling agents with controls for their temperatures and pH levels took longer time to curdle than the acid and hot temperature. The best curdling agents for making cheese were chymosin and rennin based off the process of elimination, as they were the only curdling agents that curdled. Rennin took less time with an average pH (10 versus 15 minutes) while chymosin was better in with hot temperatures (5 versus 10 minutes). Cheese is created with the enzyme rennin, which is found in the stomach of baby calves and is kept in a warm, acidic environment for it to survive. This data supports our claim because it shows that chymosin and renin are the best curdling agents since they are the only ones that curdled, and that the best environment is a hot and acidic one because they had the fastest times and are the environment in which renin is naturally found.

While our hypothesis was supported by our data, there could have been possible errors due to human error and inconsistencies due to the timings of when we observed the test tubes. The human error came in many forms, such as problems in measuring liquids for the different enzyme solutions and inconsistent control temperatures. These errors may have impacted the data, as improper liquid measurements lead to inexact solution levels, so the solutions may have been exposed to varying levels of enzymes and acid/base. Differences in armpit temperatures (which were used as a control) may have caused certain solutions to curdle slower are faster than they would have under ideal conditions. Another cause was the length in time between checking on solutions. Experimenters were to check every 5 minutes for curdling ,which left a gap in time in which the solutions may have curdled, causing imperfect data. Due to these errors, in future experiments I would recommend decreasing the time between observations to create more accurate data and to properly measure solutions, which may not be possible due to there always being human error.

This lab was done to show the effects of temperature and pH level on enzymes and to find the best curdling agent for cheese. From this lab I learned how temperature and pH level affect enzymes, which helps me understand the concept of enzymes and activation energy, which can be decreased by a higher temperature and allow the enzyme to work more effectively under the right circumstances. Based on my experience from this lab, I now know the best conditions for enzymes to function in and can create the best conditioned environment for future experiments with enzymes.

Time to Curdle (minutes)
Curdling Agent:	Chymosin	Renin	Buttermilk	Milk (Control)
Acid	5	5
Base
pH Control	15	10
Cold
Hot	5	10
Temp Control	15	15