Unit 5 Reflection

DNA Extraction Lab

   This unit was about genetic code and how it is regulated, expressed and in rare cases mutated. In the DNA Extraction Lab I learned how to extract DNA. This involved the process of first extracting the cheek cells, then adding salt, detergent, and a catalyst pineapple juice, and finally a layer of alcohol on top to extract. In the process of this lab I learned more about the structure of DNA and how it wraps around histones inside the nucleus. In the Protein Synthesis Lab I learned how proteins where created. This involved the process of the RNA polymerase zipping down the DNA and making a strand of messenger RNA in the process. The RNA can be thought of as a temporary copy for the DNA. Then, the RNA goes out the nucleus through the pores and travels to the ribosomes where it attaches and each 3 bases on the RNA are one codon which codes for one amino acid. Once the amino acids have built up and the ribosome reads a stop codon on the RNA, the amino acids are released and fold up into a protein. Some of these concepts, where quite confusing at first because they are complicated and hard to understand. But over time I came to learn and understand the concepts of this Unit, and now I understand them very well. I want to learn more about these concepts because they are very interesting and I could learn more on this topic.

Protein Synthesis Lab

   Over this unit and over the last semester I have also grown as a student. To be a good student means that you can learn better and make connections better in the things you learn, rather than just memorizing the facts. Since finals is coming up I made a study guide for the semester. Although this was an assigned assignment I wanted to make the most of it so I would be better able to understand some of the topics that I still do not understand from this semester. Since I am a visual learner I decided to make my study guide mostly containing visuals. I think these visuals will help my studying a lot because they are not only just facts written down but they show how everything connects, which is necessary for any practical application of this knowledge in the future. Before I would just study what I had to study to get a good grade, however studying in a way that connects all the concepts would not only help me more now, but also help a lot in the future when I am learning science. Also as a student I have learned to pay attention to the details more. When our group was doing the DNA Extraction Lab we had at first put the instructions in the wrong order. But after I double checked it I found that we where supposed to layer the alcohol on last after it was shaken so that it would have a layer and not be mixed into the solution. If I had not double checked these instructions, we would not have been able to successfully extract the DNA in this lab.

Semester 1 Study Guide

Protein Synthesis Lab

   In order to make a protein, first the RNA must be made by the RNA polymerase using the DNA as blueprint. The single stranded messenger RNA then goes out of the nucleus through the pores in the nuclear membrane. The RNA then goes to the Ribosomes where it attaches and starts to create the protein. Each sequence of 3 nitrogen bases on the RNA is a codon which codes for 1 amino acid in a protein. The process of creating a protein is started by a start codon in the RNA and ended by a stop codon in the RNA. Once the RNA is finished with being read, the stop codon releases the amino acids and they fold up into a protein.

https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/ribosomes-and-protein-synthesis-110/the-protein-synthesis-machinery-449-11674/

   The mutations that have the greatest effect on changing bases are the insertion and deletion mutations. These are known as frame shift mutations and they have a great effect because they shift every base over creating a major problem and very different amino acids. The mutations that seemed to have the least effect on proteins where substitution mutations because they only changed one amino acid in the sequence. Mutations can have very different effects depending on where the mutation occurs.  If an insertion or deletion happens near the end of a sequence it might not have as great of an effect as if it where near the beginning, as long as it does not interfere with the stop codon. Even substitution mutations can have great effects if they are in a spot where they create a new codon that is greatly different then the original codon and could have major effects.

http://academic.pgcc.edu/~kroberts/Lecture/Chapter%207/mutation.html

   In step 5 I chose a mutation that would insert T after AT. The resulting amino acid sequence was Met-Stop. This created a stop codon right after the start codon making the protein very small. In this example I used an insertion, however the same result could be made by a substitution of T with the nitrogen base after AT. This shows how the location of  mutation can effect the result of a mutation. If I where to do a substitution in a different place it would likely have not had as great of an effect.

  Albinism is a genetic disorder caused by a mutation in the TYR gene. The TYR gene is the gene that produces the pigment melanin in humans. With this mutation people are not able to produce pigment in their skin and eyes. This changes the phenotype of a person to having no pigment in their skin, hair and eyes.
https://www.dnalc.org/view/15932-what-is-albinism-.html

http://slideplayer.com/slide/5699007/

DNA Extraction Lab

   In this lab we asked the question, How can DNA be separated from cheek cells in order to study it? We found that DNA could be seperated from cheek cells by first using Gatorade to extract the cheek cells. Then adding salt, detergent, and pineapple juice to go through the processes. Then we would layer a layer of alcohol on top of the solution. After we preformed the experiment I found that the DNA from the cheek cell floated up to the top of the alcohol layer in my sample. This DNA was a tangled strands of most likely many strands of DNA. This experiment worked because the salt facilitated precipitation by shielding the ends of the negative phosphates, allowing them to move closer together.  Then the soap emulsifyed the protiens and lipids in the cell, this disrupted the polarity in the cell membrance causing the cell to release all of it's contents. The pineapple juice acting as a Catabolic protease then further broke down histones which are proteins that DNA wraps around. The alcohol which is nonpolar then caused the DNA to precipitate where the solution touches the alcohol.

   Our data contradicts the expected results because not everyone had a good sample of DNA that precipitated to the top of the alcohol even though I did get a good sample. This happened even when people did the procedure correctly. The most likely cause of this is because not everyone swabbed their mouth enough to get a large enough sample of the cheek cells. However I did swab a bit excessively, so I had a good sample. We could help eliminate these errors by having everyone swab excessively as I had done, the sample may look a bit disgusting, but that is because it if filled with cheek cells which are absolutely necessary for the extraction process. We could also use a stronger solution to extract the cheek cells than Gatorade, however it might not taste as well.

   This lab was done to demonstrate how to extract DNA from human cheek cells. From this lab I learned the process of DNA extraction, which helps me understand the concept of how DNA condenses for mitosis and when geneticists condence DNA to study it. Based on my experience I now know how to condense and extract DNA from cheek cells.

Unit 4 Reflection

   In my most recent lab, The Coin Sex Lab, I tested the outcome of inheritance for gender, bipolarity, colorblindness, and a dihybrid cross for eye color and hair color. The monohybrid cross for gender was based on the outcome of XX-XY, which using the punnet square you can predict that 50% will be female and 50% will be male. The colorblind portion of this test was X-linked, while the bipolarity portion was autosomal. In the dihybrid test, I flipped coins to represent the alleles of a gene where each side of the coin was a certain allele. This represents the 50-50 probability of a certain allele resulting in the recombination. In the dihybrid cross, when when two double heterozygous dihybrids where crossed, the actual results where quite different than the expected results. The expected results said that there would be 9 brown haired brown eyed, 3 brown haired blue eyed, 3 blond haired brown eyed, and 1 blond haired blue eyed. But in the actual results there where 11 brown haired brown eyed, 0 brown hair blue eyed, 4 blond hair brown eyed, and 1 blond hair blue eyed. In this experiment blue eyes, and blond hair where homozygous recessive. This difference in numbers is because the expected results are the most probable results, this however does not mean the actual results are always going to follow this. The actual traits are random, however certain combinations have a higher probability than others. This means that probability is only limited to how likely a combination is going to happen, not what is going to be the exact result.  This understanding relates to life because it can be used to predict the phenotypes of children with parents who have certain traits.

Meiosis

   This unit was about sex, including the topics of inheritance, mitosis, meiosis, and asexual vs. sexual reproduction. My most recent project which is used to explain how the probability of genetic inheritance and randomness work together, and that the probability of an offspring's traits can be known but not completely predicted. Punnet squares can be used to know the probability of both monohybrid and dihybrid crosses. Mitosis is how cells reproduce by cloning themselves, and Meiosis is the process in which a cell divides into two gametes, each with half of it's genetic code that might be used to create a new organism. Asexual reproduction is when an organism basically clones itself, creating a new organism with the same genetic code. Sexual reproduction is when an organism combines half of it's genetic code with half of another's code to create a new organism. Both of these have costs and benefits, see my blog post about this for more information. Most of this content was easy to learn, however I did not immediately understand dihybrid crosses, now I understand them.

X-linked Inheritance

   From this experience I learned the many concepts of reproduction and how they all work together. I learned how to do dihybrid punnet squares, which was new to me because all I had done before was monohybrid punnet squares.  Also I learned about the process of meiosis, which I had not known about before. X-linked recessive genes like colorblindness are interesting because they will express themselves in males more often because they only need 1 chromosome to be recessive, because there is only 1 X chromosome in males. While doing the Genetics Infographic I reviewed content I had learned earlier in the unit, and previewed content I would learn later in the unit. This was useful to help understand the topics myself and to help other people understand the topic. I want to learn more about polyhybrid crosses since I did not fully understand this concept. Besides that, all the content was easy to learn and I know much more about genetics now than I did in the beginning of the unit.

Image citations can be found at the bottom of the Genetics Infographic.

Genetics Infographic

For higher quality go here:

https://www.easel.ly/infographic/nruhup

Sexual vs Asexual Reproduction

   Sexual reproduction has some benefits and some negative parts to it.  "An asexual female who appears in a population should have twice as many offspring as her sexual counterpart." (215).  This shows that asexual reproduction is much more efficient then sexual reproduction because it can do twice as much.  "After a brief and glorious flowering, asexuals vanish.  Which has led scientists to conclude that exclusive asexuality is an evolutionary dead end" (216).  This shows that without the mixing of genes organisms will become extinct very fast.  "'We have several ways. We pick up DNA that's loose in the environment.  We gather DNA from passing viruses.  We even plunder the genes of dead bacteria- the cognoscenti call it necrophilia.'" (217) This is an example of a asexual organism that plunders genes from other organisms to survive, E. coli.  "'Would be extremely different from each other.  Each will have accumulated different mutations.'"(222).  This quote shows how asexual organisms still create genetically different organisms through mutations.

Unit 3 Relection

   This unit was about cells and the many concepts related to them.  Early in the unit we learned about macromolecules.  These include proteins, lipids, carbohydrates, and nucleic acids.  They are the building blocks for all cells.  We learned where each macromolecule is in a cell by doing the macromolecule lab, in which we tested the different parts of an egg for the different macromolecules found in cells.  Later we learned about the membrane and how molecules diffuse through it.  This is done by the processes of osmosis, passive diffusion, facilitated diffusion, and active transport.  We learned more about this process in the egg diffusion lab in which we placed an egg in syrup and an egg in water and the egg in syrup lost it's water and shriveled up.  After that we learned how proteins are made in the different organelles of the cell and how they are transported outside of the cell.  In the tour of a cell vodcast we learned about all the organelles and their functions.  We later applied this knowledge to the microscopic organism lab where we identified the different organelles inside cells.  And in the end we learned about the process of photosynthesis and cellular respiration.  This unit went well and there where no major setbacks.  The content was easy to learn, and I had no trouble understanding the concepts that where taught in this unit.  I also did not have any problem working in the collaborative environment.

    From these experiences I learned what cells are made of and the processes that they do.  I learned that cells are made from the macromolecules lipids, proteins, carbohydrates, and nucleic acids and certain macromolecules are used to make certain parts of the cells.  I also learned how the macromolecules are produced in a cell.  The process of diffusion through cell membranes is interesting because it can take place in the many different ways of passive diffusion, facilitated diffusion, osmosis, and active transport.  Then most recently the concepts of photosynthesis and cellular respiration.  I would like to learn more about the cytoskeleton of a cell, we covered this topic very briefly and I believe that more could be done about this to reach a better understanding of this topic.  Also the process of mitosis I would like to learn more about and how one cell and divide into 2. 

Amoeba from the microscopic organism lab:

Results of the Egg Macromolecules Lab:

Results of the Egg Diffusion Lab:

Microscopic Organism Lab

Power: 400
This cell is unique because it has many mitochondria.
I observe the purple nucleus in the corners of the cells.
These cells are Eukaryotic and Heterotrophic.

Power: 400
This side it unique because it shows the vein of a plant and how molecules are transported to cells.
I observe that the cells have cell walls that are easy to see and the organelles are mostly transparent.
These cells are Eukaryotic and Autotrophic.

Power: 100
These cells are unique because the chloroplasts are lined up in a spiral line.
I observe that the cells in this algae form long chains.
These cells are Eukaryotic and Autotrophic.

Power: 400
These cells are unique from the other cells before this because they are significantly smaller.
I observe that these cells come in many different shapes and sizes.
These cells are Prokaryotic and Autotrophic.

Power: 400
This cell is unique because it makes energy from the sun but has no chloroplasts.  This is because they are the ancient chloroplasts that chloroplasts today evolved from.
I observe that these cells are in rings.
These cells are Prokaryotic and Autotrophic.

Power: 400
This cell is unique because it is both autotrophic and heterotrophic at the same time.
I see that the cell has a nucleus, flagellum, and also Chloroplasts.
This cell is Eukaryotic, Autotrophic, and Heterotrophic.

Power: 400
This cell is unique because they all have many different colors.
This cell is relatively large and have visible organelles and pseudopods.
This cell is Eukaryotic and Heterotrophic.

   In this lab we observed the prepared slides of these organisms under microscopes and recorded what we saw in the slides.  Then I took pictures of the slides and labeled them (the ones above).  This helped us understand the structure of the cells, both how they are arranged in muscle and leaf tissue, and how the organelles are inside the cell.

Cell Parts I was able to identify:

• Muscle cell: nucleus, muscle fiber, striations
• Ligustrum: chloroplasts, nucleus, cell wall, epidermis cell, vein
• Spirogyra: cell wall, chloroplasts, cytoplasm, nucleus
• Bacteria Cells: coccus, bacillus, spirilum, 
• Cynobacteria: rings of cynobacteria
• Euglena: nucleus, chloroplast, flagellum
• Amoeba: nucleus, cell membrane, pseudopods, mitochondria

Autotrophs have chloroplasts, or in the case of cynobacteria, are their own chloroplast.  They produce their own energy from light and store it as glucose.  Heterotrophs consume other organisms to acquire energy, they consume these other organisms by swallowing them in the cell membrane and then breaking down their nutrients with the lysosomes.  They usually have a flagellum or pseudopods to move around faster. Eukaryotes are more advanced cells that have their DNA stored inside a nucleus.  They have organells and they make up all the plants and animals that we know, as well as many types of single cellular organisms too. Prokaryotes are more primitive cells that are much older in origin but still most common.  Bacteria and Cynobacteria are prokaryotes.  They do not have a nucleus that stores the DNA and they do not have organelles, but they do have DNA which is in their cytoplasm.

Egg Diffusion Lab

   In this lab, we placed one egg in sugar (corn syrup), and another egg in deionized water for 48 hours.  The eggs had both been in vinegar for 48 hours to dissolve the egg shell, and had sat in water for a week prior to the experiment. 

   When we took the observations we found that the mass and circumference of the egg sample in sugar had decreased.  This had happened because the egg in the sugar solution was hypertonic, so it lost water to try to make an equal concentrations on both sides of the membrane.  The solvent of water diffused through the membrane to the lower concentration of water in the corn syrup.  The solute sugar had molecules to big to be moved through the membrane by passive diffusion so it stayed outside of the egg.  

   A cell's internal environment changes when its external environment changes because many molecules passively diffuse and the internal environment tries to mirror the external environment to reach equilibrium.  

   This lab demonstrates the concept of passive diffusion in which solvents on the side of the membrane with high concentration, will move through to the side of the membrane with low concentration to try to reach equilibrium in the concentration of the solutions.  This process does not require any energy.  

   Vegetables are sprinkled with water in markets to keep the solvent water the same concentration in the plant, preventing the plant from drying out and wilting.  plants along roadsides that are salted will become hypotonic and will gain too much water when the plant try's to reach equilibrium in the concentration of the salt and water inside the plant. 

   Based on this experiment I would want to learn more about how solutes effect multi-cellular organisms.  This could be done by seeing how salt or sugar would effect plants when they are watered a solution that has a solute inside it.

Group Data:

Class Data:

Egg Macromolecules Lab

   In different parts of the egg there are different types of macromolecules.  When the egg membrane was tested it was found that on a scale of 0-10 there where 10 proteins and 3 lipids.  This shows that the egg membrane contains proteins and lipids.  Since we know the molecular structure of the membrane, we can infer that the proteins in the membrane are transport proteins that allow molecules in or out of the cell.  The lipids in the membrane are the main structure of the membrane and the main composition of the egg membrane.  The egg white contains proteins and lipids too.  On the test they both scored a 6 on a scale of 0-10.  The proteins in the egg white are most likely enzymes to protect the egg from invasive growths.  The lipids in the egg white are to give the chicken nutrition inside the egg.  The egg yolk contains many proteins and a small amount of lipids.  For proteins it scored an 8, and lipids scored a 1 on the test.  The egg yolk is a basic structure for the chicken to grow and contains mostly proteins to grow.

   While our hypothesis supported our data our data might have been effected by a few factors.  One of these factors is that the original data was the qualitative color of the sample, quantified by scaling it from 0-10 based on the person's opinion, so there is still no exact number for it.  Also the observations where taken by 4 different people so the opinions would vary from person to person.  And lastly, the data was taken from only one set of data, and not the average of a large set of data which would be more accurate.   Due to these errors, in future experiments we could also have all the observations taken by one person.  Or we could take more sets of data to produce a more accurate result.  However with the time limitations of a class period this might not be realistic in a class setting.

   I would however, recommend a color key similar to the color key on ph tests, but for the different solutions we are using to test the egg.  This would help make our data more quantitative and accurate, so that each particular color has a designated number.  This lab was done to demonstrate which macromolecules where found in each particular part of the egg.  This understanding can be applied to which parts of the cell contain each macromolecule, since the egg is a very large cell.  From this lab I learned where each marcomolecule is inside a cell which helps me understand macromolecules and their uses in the different parts of the cell.  Based on my experience from this lab, I can understand what each particular macromolecule is used for, and I know how to use some of the solutions that we used to test for macromolecules.

The macromolecules that I tested for in lipids:

The macromolecules my group members tested for in proteins, polysaccharides, and monosaccharides:

Unit 2 Reflection

   This unit was about basic chemistry, macro molecules, and enzymes.  In the chemistry for biologists vodcast we learned about the elements and the different types of bonding, the properties of water and why water is important, and the ph scale.  From this vodcast I learned how the hydrogen atoms in water molecules are charged so that they attach to things which was interesting.
   Macro molecules was about Lipids, nucleic acids, proteins, and the different types of carbohydrates and sugars.  To apply what we learned to an experiment we did the sweetness lab in which we tasted the different kinds of sugars that we had learned about during the lesson and rated them on how sweet they where to find which ones where sweetest.  I concluded that the monosaccharides where the sweetest carbohydrates, followed by disacchurides, and polysaccharides where the least sweet tasting.  In this lab I learned about a few sugars that I had not known about before.
   The enzyme vodcast explained the properties of a special kind of protein called an enzyme that helps make chemical reactions happen much faster.  To find the optimal conditions in which enzymes operate most effectively we did two labs.  The first lab was a digital enzyme lab in which we tested how ph and the amount of substrate, and found that the test tubes with neutral ph, and larger amounts of substrate created more product.  Then we did the cheese lab in which we tested the optimal conditions for making cheese by testing the ph, temperature, and curdling agent.  The class concluded that the most effective curdling agent was chymosin, and an acidic ph, and high temperature was best for producing cheese.  This lab not only taught me about enzymes but also how cheese is made.
   This unit was interesting and filled with information that answered all my questions, because of this I have no unanswered questions.  The unit was easy to understand so I understand the concepts that where covered.  I want to learn more about enzymes and macro molecules in the future.

Sweetness Lab

  In this experiment I found that monosaccharaides are very sweet, disaccharides are sort of sweet and polysaccharides are not sweet at all.  Fructose that scored a 190, Glucose that scored a 50, and Galactose that scored a 20, where all monosaccharides that scored decently high on this test.  Maltose a 10, and lactose a 0 where both disaccharides that scored low on this test.  Sucrose, however is an outlier from my claim, a disaccharide that scored a 100 on the taste test.  The polysaccharides Cellulose and Starch scored a 0 on the sweetness test, supporting my claim.

  An organism or cell might digest the sugars differently based on their structure.  A monosaccharide would most likely quickly digest because it only has one ring.  Disaccharides might take a bit longer to digest because they have 2 rings.  And polysaccharides would most likely take the most time to be digested by the organism or cell but the bonds it has would in all release more energy than the others.

  Not all the testers would give the same rating for each sugar because of some variations.  The person testing the sugar is taking qualitative data and then quantifying it which can always create some variation since it is mostly based on comparison to the other sugars.  There is no exact number for each of the sugars when it is only based on a person's qualitative evidence.  The sugar that was tasted prior to the sugar tasted could have effected the taste if the prior flavor was still lingering.  Also some people have a better sense of taste and can taste the sugars more strongly than others.

  Humans taste sweetness through the taste buds on the side of the tongue farther back.  The side of the tongue that tastes the sugars could effect how much a person tastes the sweetness of the sugar. Monosaccaraides taste sweet because for survival people prefer the sugars that they can digest quickly and get a quick burst of energy, rather then taking the time to digest a polysaccharide.

Biology Characteristics Collage

Jean Lab

  In this experiment we bleached denim jean squares in different concentration solutions of bleach and water. In the results we found out that the squares in the higher concentrations of bleach became a brighter color, however the fabric in the jean squares that where bleached in high concentration also weakened.  The question of this lab was, What concentration of bleach can make the color lightest without visible damage to the fabric.  The answer to this would be the jean squares in the 100% bleach concentration. Although if you felt the fabric you would feel that the fabric was a bit thinner than it had been before there was no damage that was visible from the outside.
   Our data contradicts the expected results because the 100% bleach solution from the store was not literally 100% bleach, it was a solution this would have made the 100% bleach solution sample not as heavily damaged as it would have been in pure bleach.  Also, our data was unexpected because one of the 25% bleach solution sample was accidentally doused in water right after it was soaked in the bleach, this would effect our results because that sample did not have as much time to let the bleach soak in for 9 minutes as the rest of the samples had.  Our data might have also resulted differently than might happen because we also soaked 3 of the jean samples at a time because we where low on time, this might have caused some of the samples to not get enough bleach for each one, that might have caused the samples to not be as light of a color and as weak of a fabric.  Next time we should take more time for the lab and do the procedure exactly as it says.  We should also make sure that all of us know what we are doing so accidents in the lab don't happen.
This lab was done to demonstrate the lab process, so we know how to do labs in the future.  From this lab I learned how to do a lab which helps me understand the lab taking process.  Based on my experience from this lab I will know how to effectively take scientific labs in the future.