Unit 5 Reflection

      In this unit we learned about genes and mutations. DNA is the code of life. It is made with a double helix which is two strands twisted around each other. It is made up of nucleotides which is made of a nitrogen base, phosphate group, and a sugar. The nitrogen bases wither come in double rings called purines such as adenine and guanine or single rings called pyrimidines such as thymine and cytosine. Semi-conservative replication is the process of creating two identical strands of DNA from one strand. the two strands end up with half of the original strand. The first step is unzipping, where the enzyme unzips DNA by breaking hydrogen bonds that hold nitrogen bases together. Then DNA polymerase adds matching nucleotides to each strand. The central dogma of biology is DNA to RNA which is transcription, then RNA to proten which is translation, and finally, protein to organism which is the phenotype. Transcription is the process where RNA polymerase reads and copies the DNA code for a protein as mRNA copy. The three steps of transcription are first DNA unzips, then RNA polymerase matches spare nucleotides to make an RNA strand, and finally, messenger RNA is produced and leaves the nucleus for the cytoplasm. Then in translation, mRNA arrives at the ribosome which reads the mRNA three bases at a time and translates DNA language to protein language.Each base sequence is known as a codon and each codon codes for one amino acid. The result is a long chain of amino acids which twists, folds, and combines with other chains and becomes a protein.
      We also learned about mutations, which is a change in the DNA code. Point mutations are a change in one or two base pairs of DNA. This is very small and common. The two main types are substitution and frameshift mutation.
     The most difficult part of this unit was about gene expression and regulation. Gene expression is the process of a gene ceing used to produce a gene product or phenotype. Gene regulation is mechanism used by cells to increase or decrease the expression of a gene. Every cell in our body has the same DNA but not all cells look the same. Cells look different because each type of cell expresses genes specific to those cells. Cells don't want to waste energy so thy have a variety of steps to control gene expression. There is a promoter, location on DNA where RNA polymerase attaches. The 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 of allows RNA polymerase from attaching and reading the gene. An example would be the lac operon, where bacteria uses lactase to break down lactose.

Protein Synthesis Lab

     To produce protein, first is transcription. RNA polymerase matches reads and copies the DNA code for a protein as a messenger RNA copy. Then in translation, the messenger arrives at the ribosome. Then, the ribosome reads the mRNa three bases at a time and translates DNA language into protein language. The result is a protein! 

      Substitution seemed to have the least effect on the proteins since the protein ended up not changing at all. Deletion seemed to have the greatest effect. The protein became a lot shorter than it was originally, which meant a lot of information was left out. It does matter where the mutation occurs. If it was at the end, the results might have been different and only a small portion would've been left out. 

      I chose to do deletion again but in a different position because it seemed to change the protein the most. I took out one part from the very beginning, and it didn't change much from the first deletion. I feel like if I deleted a portion from the end instead, the results would have been different.

     Mutations affect our life since it could happen to any one of us. Mutations are the reasons for why cancer and other diseases happen. One disease that is caused my mutations is phenylketonuria. Without treatment it causes intellectual disabilities. 

DNA extraction lab

The question was How can DNA be separated from cheek cells in order to study it. In this lab we had a procedure and tried to group them according to the three basic steps: homogenization, lysis, and precipitation. We swished Gatorade around in our mouth and spit it back out. The Gatorade homogenized it. The Gatorade and saliva mixture didn't mix and the DNA precipitated because the Gatorade was polar and the alcohol was non polar. One possible error we made was when we put the alcohol in. If we didn't carefully add in the alcohol, then the two solution could have mixed and we wouldn't have been able to see the DNA. To improve this I would recommend people to carefully pour in the alcohol. Another possible error was that we didn't swish around the Gatorade in our mouth enough. This wouldn't have gotten enough DNA in the solution which would've affected how it formed later.


 

Unit 4 Reflection

This unit was about the cell cycle, genetics, The cell cycle is a series of steps that take place when a cell duplicates or reproduces. Three reasons for the cell cycle is reproduction, growth and development, and cell and tissue repair. There are two types of reproduction, sexual and asexual. In asexual reproduction , there is only one parent. All the offspring are genetically identical. Some benefits of asexual reproduction is that it's easy, takes a short amount of time, you don't need a mate, and can make lots of offspring. The cost is that there is no genetic variation and is will make it more likely to go extinct if a new pathogen attacks them or their environment changes. The benefits of sexual reproduction is that it creates genetic variation, can allow the parents to raise the young to ensure survival, and create competition for mates, ensuring the best pass on their genes. The cost is that it requires lots of energy and time. It exposes you to parasites and STDs. It could create genetic combinations that are bad. We also learned that all body cells are diploid and all gametes are haploid. In meiosis, there are four stages just like mitosis, but in meiosis it divides twice. Homozygous is having two of the same allele while heterozygous is having two different alleles. The law of segregation states that the gene pairs for a trait separate when gametes are formed. The law of independent assortment states that the gene pairs separate randomly from each other during meiosis. Autosomal inheritance is when an organism inherits or gets the gene responsible for a trait from all the other 22 chromosomes which are called autosomes. X-linked inheritance is when an organism inherits, or gets, the gene responsible for a trait from the x chromosome. The most difficult thing to understand in this unit is probably crosses. A dihybrid cross is comparing two genes at the same time and the phenotypic ration is 9:3:3:1.
My preferred learning style is kinesthetic and these results were expected. I will still try to study in different ways but copying down diagrams would probably be helpful to me for studying.

Coin Sex Lab

In this lab, we flipped coins to simulate the randomness of alleles. The coins were the genes and the sides were like the different alleles. This simulated the process of meiosis and the recombination of these genes. This showed how random it is. There is a very low chance of getting homozygous genotypes in dihybrid crosses. You can see what the probability of something is, but you'll never know what you will actually get. The coin flipping was also gene segregation and the results after flipping was the recombination. In part two we tested autosomal dominance, the ones on the 22 chromosomes. In part 3 we did an experiment on x-linked recessive traits, which in this experiment we used the allele for colorblindness. X-linked inheritance is the trait you get from the x chromosome. Monohybrid was the ones we did using only one gene. We also found the different probabilities for either heterozygous or homozygous phenotypes. For the first experiment, the females were homozygous x. Males were heterozygous. Our last experiment was dihybrid, and tested for the different colors of hair and eyes. It was wither brown or blonde hair and brown or blue eyes. This experiment showed that neither trait affected the other and it was possible to get lots of different combinations. This relates to our life because it shows what the probability is of getting certain traits for our offspring.

Genetics Infographic

Link to a bigger image:  https://magic.piktochart.com/output/8996330-genetics

Unit 3 Reflection

In this unit we learned about the cell theory, activation energy, membranes, osmosis and diffusion, what a cell does, photosynthesis, and cellular respiration, The most challenging thing about this unit is cellular respiration. There are three steps to cellular respiration. The first step to it is glycoolysis which occurs in the cytoplasm. 2 ATP molecules are produced for one glucose molecule in this step. The second step is the Krebs cycle which converts molecules from glycolysis into 2 ATP, carbon dioxide, and electron carrying molecules. The final step is the electron transport chain which occurs within the inner membrane of mitochondria. It uses oxygen, NADH, and FADH2 to convert ADP into ATP. 32 ATP is produced in this step. This whole process produces a total of 36 ATP, 6 carbon dioxide, and 6 water. Cellular respiration is the process of cells braking down glucose into energy. Photosynthesis is where plants produce glucose and oxygen using sunlight and carbon dioxide. Autotrophs carry out photosynthesis and can be macroscopic or microscopic. They can be multicellular of unicellular. Mesophyll cells are a collection of cells containing chloroplasts. A chloroplast is an organelle containing stroma and grana. Stroma is the space inside chloroplasts and grana is a stack of thylakoids. Thylakoids are membranes that contain chlorophyll. A light dependent reaction occurs in thylakoids of grana. Light is absorbed and energy is transferred between molecules by the electron transport chain. It produces NADPH and ATP. Water is split which releases oxygen and pumping H+ ions into the thylakoid membrane. ATP synthase uses H+ movement to produce ATP. ATP synthase facilitates diffusioin of H+ from high to low concentration. As H+ moves from thylakoid to stroma, ATP is produced. In a light independent reaction, it produces sugar from carbon dioxide using ATP and NADPH from light reactions. The calvin cycle rotates 6 times to produce 1 glucose molecule. I learned a lot from this unit but there is still a lot to learn about biology. I learned a lot about cellular respiration and how photosynthesis works.

Egg Diffusion Lab

Our question was how and why does a cell's internal environment change, as it's external environment changes? We two eggs in vinegar and let it sit for two days. We then washed off the vinegar and put it in water instead. Adding the vinegar go ride of the egg membrane which exposed the rest of the egg. We then put one egg in water and another egg in sugar water. 

When we put the sugar concentration increased, the egg shrank. It shrank because there was a high concentration of sugar and a low concentration of sugar so the water in the egg diffused outside instead. For the one in water, in grew because there was more solute inside than outside so the solvent went inside the egg and the egg grew. This was a hypertonic diffusion. 

A cell's internal environment changes as the external environment changes because of diffusion. There was a low concentration of sugar in the deonized water so there was actually more solute in the egg than in the solvent. The one with sugar water was hypertonic because there was a higher concentration of sugar in the solvent, causing the egg to shrink. So the water diffused from inside the egg to the outside. These were all examples of passive diffusion.

 This lab demonstrates the biological principle of diffusion. It shows how diffusion works within cells.

Fresh vegetables are sprinkled with water at markets to keep them fresh. It is the make sure the vegetables don't lose too much water and dry up. Roads are salted to melt ice because it requires an even lower temperature to freeze ice so putting salt on the ice will help melt it. Too much salt can dehydrate plants. Salt absorbs moisture in water. 

If you were to create a new experiment you would want to test how different concentrations effect cells.  

Cure for Cancer?

One of the big questions of science is "Will there ever be a cure for cancer?" The current hypothesis is that if cancer is a living thing, then there will never be a cure for cancer. We can prevent and treat it, but there is no definite cure for cancer. The longer we live the more likely something will go wrong. Cancer has been around since dinosaurs and it is still here.

20 Big Questions:
1. Will there ever be an end to learning?
2. Why are there different skin colors?
3. What is the meaning of life?
4. Why is the sky blue?
5. Why don't we have a tail?
6. Will there ever be an end to sickness?
7. Why is grass green?
8. Why don't plants grow faster?
9. Is it possible to never get sick?
10. How did people know about sugar?
11. Who was the first to start baking?
12. Why are some people smarter than others?
13. Why do we have hair?
14. How do computers work?
15. Who invented mechanical pencils?
16. Why are all our tastes different?
17. Is it possible to make a new color?
18. Who invented the first shoes?
19. Who invented glasses?
20. Who invented hair ties?

Egg Macromolecules Lab Conclusion

The question for this egg macromolecules lab is "Can macromolecules be identified in an egg cell?" Macromolecules can be identified in egg cells. Polysaccharides can be found in the egg membrane. For egg white a tiny bit of protein can be found. Monosacccharides can be found in egg yolks. For polysaccharides we did a test using iodine. The color should change from brown to black if a polysaccharide was present. In the egg membrane it turned dark brown and and its quantitative amount was 7. For monosaccharides we used benedicts solution which would have turned green or orange if there was a monosaccharide present. It was present in the egg yolk with a quantitative amount of 6. Lastly, in egg white, proteins were found. Although there was an error in protein because we didn't mix properly, there was a slight sign of protein. We used sodium hydroxide and copper sulfate to test for proteins. It should have turned from blue to purple. One big error we made was the testing for proteins. Almost none of them were positive. This was because we didn't mix the sodium hydroxide and copper sulfate enough. Another possible error we made was measuring. We might not have measured properly which would be another reason why it didn't test positive for some of the other macromolecules. To improve this experiment, it would be better to mix the sodium hydroxide and copper sulfate a bit better. Another thing would be to measure more accurately. The purpose of this lab was to find which macromolecules go in which part of the cell. This relates to us learning about macromolecules and cells in class. This can be applied for future studies on biology. We now know what macromolecules go in what part of a cell.

Identifying Questions and Hypotheses

In this article NASA says that there are signs of water on Mars. The question is "Is it possible for there to be life on Mars?" The hypothesis is If there is water on Mars, then it is possible for there to be life on Mars. Scientists say that there are definite signs of liquid water on present day Mars. If there is water, there is life. This study can help build on the possibility of contemporary life on Mars. I knew that scientists were talking about people living on Mars before. I never knew that there was water on Mars.

http://www.nytimes.com/2015/09/29/science/space/mars-life-liquid-water.html?_r=0

Unit 2 Reflection

      This unit was about the chemistry of life.The first section was about atoms. It talked about protons, neutrons, and electrons.Subatomic particles that make up atoms are protons, neutrons, and electrons. A chemical element is a pure substance that consist entirely of one type of atom. Atoms of the same element that differ in the number of neutrons are isotopes. Because they have the same number of electrons, all isotopes of an element have the same chemical properties. A chemical compound is a substance formed by the chemical combination of two or more elements in definite proportions. An ionic bond is formed when one or more electrons are transferred from one atom to another. A covalent bond forms when electrons are shared between atoms. The molecule is the smallest unit of most compounds.Van der Waals forces are when molecules are close together and a slight attraction develops between the oppositely charged regions of nearby molecules.
      The second section was about the properties of water. It also talked about valence electrons and why carbon was so versatile. Carbon is very versatile because it was four valence electrons. It can bond with different elements easily. Water is polar because there is an uneven distribution of electrons between the oxygen and hydrogen atoms. Cohesion is an attraction between molecules of the same substance. Adhesion is an attraction between molecules of different substances. A mixture is a material composed of two or more elements of compounds that are physically mixed together but not chemically combines. All components of a solution are evenly distributed throughout the solution. A solute is the substance that is dissolved. A solvent is the substance in which the solute dissolves. The mixture of water and non dissolved material is called suspension. Buffers are weak acids or bases that can react with strong acids or bases to prevent sharp, sudden changes in pH.
      It also talked about carbohydrates, lipids, proteins, and Nucleic acids. Proteins are made up of amino acids. It also talked about what an acid and base were. The topics about proteins was the most confusing. I feel like I pretty much understand everything about atoms, but not macromolecules. Different enzymes work better in different conditions of pH and temperature.Smaller units called monomers, join together to form polymers. Carbohydrates are compounds made up of carbon, hydrogen, and oxygen atoms, usually a ratio of 1:2:1. Living things use carbohydrates as their main source of energy. Plants and some animals also use carbohydrates for structural purposes. Lipids are made mostly of carbon and hydrogen atoms. Lipids can be used to store energy Some lipids are important parts of biological membranes and waterproof coverings.

Cheese Lab Conclusion

Time to Curdle (minutes)
Curdling Agent:	chymosin	rennin	buttermilk	milk (control)
Acid	5	5
Base
Cold
Hot	5	10
Temp control	15	15
pH control	15	10

In this lab we asked the question, what are the optimal conditions and curdling agents for making cheese? We found that hot and acidic conditions with chymosin were the best for curdling cheese. The time in acids was only 5 minutes for both chymosin and rennin. Buttermilk and milk both didn’t curdle within 15 minutes. In hot environments for chymosin it only took 5 minutes to curdle as well and 10 for rennin. Since rennin comes from a calfs stomach, warmer and more acidic environments are better for curdling. This data supports our claim because acidic and hot temperatures made the cheese curdle the fastest.

While our hypothesis that warmer and more acidic conditions with chymosin with make cheese curdle faster, there could have been errors due to how the lab was set. We checked to see if it curdled every five minutes, but the acid ones might have curdled even faster than 5 minutes. This would have affected the data. It might have shown that chymosin was faster than rennin.  Another data we might have made is when we were measuring how much curdling agents to put into the milk. The medicine droppers had air bubbles in them and it was hard to measure them exactly. Because of that, each test tube had different amounts of curdling agent. Due to these errors, in future experiments I would recommend for us to be more careful and check ever two minutes rather than five.

This lab was done to demonstrate chemical reactions. From this lab I learned that different conditions would affect the results which helps me understand the concept of chemical reactions. Based on my experience from this lab, I know that warmer and more acidic environments would help cheese curdle faster.     

Sweetness Lab

      The question was how does the structure of a carbohydrate affect its taste. Monosaccharides were all sweet. Glucose, fructose, and galactose were all very sweet, there degree of sweetness are all over 100. Disaccharides such as maltose and lactose, were less sweet in the 50s-70s range. Except for sucrose, they all werent that sweet. Polysaccharides were pretty much tasteless. Starch and cellulose are all in the 20s and lower.  Fructose is found in fruits and honey so it was expected that it would be sweet. Sucrose is basically table sugar so it was pretty sweet as well.
      Monosaccharides  are major fuel for cellular work. Disaccharides are a nutritional source for monosaccharides. Polysaccharides can be used for storage or as building materials for the cell or the whole orgamism.
      The rating for the sweetness might be different for different people because everyone has different taste buds. One person might find something super sweet while the other finds it normal. Tasters could rank the same samples differently because every ones taste buds are different.

                  

Characteristics of Life

Jean lab

In the Jean lab, we asked the question “What concentration of bleach is best to fade the color out of new denim material in 10 minutes without visible damage to the fabric”. In our data table we used the numbers 0-10 to describe the color removal and fabric damage where 0 is no change and 10 is a big change. The 0% bleach was 0 for all of them which means it had no change in color or fabric damage. The 12.5% it was a 1.6 for color removal and an average of 1 for fabric damage. There was almost no change at all in this one. In the 25% bleach it was an average of 2.3 for color removal and 1.2 for fabric damage. There was very little change. For the 50% one, it was an average of 5.3 for color removal and 3.3 for fabric damage. You could tell that it was faded and there was very little fabric damage. In the 100% it was an average of 8.6 for color removal and 5 for fabric damage. This one was very faded, it had yellow tints as well. There was a little visible damage and the fabric was thinned out. We found that the 50% bleach was the best. We knew before that bleach fades out the color or takes out the stains in fabrics. It is to be used with white clothes. This data supports our claim because there a significant change in color faded and not a lot of damage in fabric.

A possible error that we might have made is not measuring very accurately. We might have measured too little or too much bleach which would have made a change in the results. While our hypothesis was supported by our data, there could have been errors due to not measuring accurately. One error we made is only washing out the jean squares once when we were supposed to wash them out twice. This might have affected the color of the jean squares. Another possible error that could have been made is that we took the jean squares one by one rather than all at the same time which could have made some of the jean squares more soaked in the bleach than the others. Due to these errors, in future experiments I would recommend taking more time for measuring rather than trying to finish the experiment quickly, wash the jean squares twice, and to take out the squares all at the same time and separate them on the paper towel.

This lab was done to demonstrate which concentration of bleach would be best to fade out the color in new denim material in 10 minutes without visible damage to the fabric. This lab could be improved by having more solution in the petri dishes. I felt that some of the jean squares did not really soak in the solution because there was too little solution. Another thing that might have improved this lab is using pipettes for measuring. It was really hard to measure accurately just by pouring it in.This lab is important to learning about the scientific method and how the concentration of bleach is like. From this lab I learned that 50% bleach would be best to fade out jeans which helps me understand the concept of bleaching. I also learned about the steps and procedures of the scientific method because of this lab. Based on my experience from this lab, when I dye jeans I will use a 50% concentration.

Concentration (% bleach)	Average color removal	Average fabric damage
100	8.6	5
50	5.3	3.3
25	2.3	1.3
12.5	1.6	1
0	0	0