Unit 5 Reflection

Unit 5 was all  about DNA, RNA, and their functions. DNA is a double helix structure that has nucleotides that code for proteins. The nitrogen bases are Adenine, Thymine, Guanine, and cytosine. A and T pair up while G and C pair up.

When RNA needs to be made, an enzyme called RNA polymerase unzips the DNA and pairs a nucleotide with each strand of DNA. In RNA, the base Thymine is replaced with Uracil (U). This single stranded mRNA breaks off and travels through the cytoplasm to a ribosome. In the ribosome, the RNA is read three base pairs at a time. Each three bases codes for a codon and each codon represents an amino acid. The amino acids keep adding on to the polypeptide until a stop codon is reached.

A mutation is a change in the genome. Mutations can either be harmful, give benefits, or have no affect at all. A point mutation is a mutation that changes on or two bases. A substitution is swapping one base out for another. A frameshift mutation is a deletion or insertion of a base and changes every codon that comes after the mutation.

Another concept is gene regulation and expression. In any given cell, only a fraction of the DNA is used to express a phenotype. In prokaryotic cells, a repressor is attached to the operator that prevents the RNA polymerase from reading the DNA, but the repressor detaches when lactose is present allowing the gene to be expressed. However, this process is much more complex in human cells.

This unit was not to difficult, as I found the process of making a protein and mutations fairly straightforward. The concept of gene regulation was difficult to understand and it was very complex. This unit helped me understand the last two units better, as they were also about genetics. Making the study guide helped me learn, because if forced me to answer questions and told me what I knew and did not know. This unit has helped me grow as a student, because it made me have to try harder to learn things I did not understand. A question I have about this unit is how the mRNA travels through the cytoplasm to the ribosome without getting lost.

https://commons.wikimedia.org/wiki/File:0323_DNA_Replication.jpg

Protein Synthesis

The creation of a protein is a several step process. It starts with an enzyme unzipping the DNA. Another enzyme then goes along the DNA and reads the sequence and puts a the matching base pair with each base. Instead of matching A with T, it replaces the T with a U. The completed RNA then detaches from the DNA and travels to a ribosome. The mRNA is read and every 3 bases represents a codon. Each codon represents an amino acid. The ribosome goes down the line and reads every codon until it reaches a stop codon. The amino acids then break off and the protein is complete.


Mutations can either change a gene dramatically or not at all. A simple substitution in the DNA either causes one or two codons to change or sometimes, none at all. A frameshift mutation such as an insertion or deletion can cause big changes and change every codon after it. A frameshift mutation at the beginning of a sequence would cause more damage than at the end, because a frameshift causes every codon after it to change. If it occurred at the end, only a few would change.

When I chose the mutation I would like to do on a DNA strand, I chose an insertion. I chose this because it would allow me to stop the translation right after it started. It caused the most change out of all mutations because it didn't allow for any amino acids to be coded for except the start codon. It mattered where th mutation occurred, because it occurred right after the start codon. If it had been towards the end, the amino acids that came before would have still been coded for.

Having a mutation could result in several things. A mutation could result in death, a disease, or nothing at all. We all have many proteins in our body that carry out essential functions such as carrying oxygen in the blood. An alteration to one of these important proteins could have some major consequences. For example, Parkinson disease in often caused by a mutation in one of several genes. It causes loss of control of muscles. Some mutations can guarantee that an individual will develop Parkinson, and another mutation increases an individuals risk of getting the disease.


Works Cited:

Eisen, Jonathan. “Fact Sheet: DNA-RNA-Protein.” MicroBEnet: the Microbiology of the Built Environment Network., Alfred P. Sloan Foundation, 29 Oct. 2013, www.microbe.net/simple-guides/fact-sheet-dna-rna-protein/. 

“What Kinds of Gene Mutations Are Possible? - Genetics Home Reference.” U.S. National Library of Medicine, National Institutes of Health, 6 Dec. 2016, ghr.nlm.nih.gov/primer/mutationsanddisorders/possiblemutations.

“Animal Genetics.” Print Page, web2.mendelu.cz/af_291_projekty2/vseo/print.php?page=315&typ=html.

http://web2.mendelu.cz/af_291_projekty2/vseo/print.php?page=315&typ=html

“National Institutes of Health.” National Institutes of Health, U.S. Department of Health and Human Services, 21 July 216ADAD, www.niehs.nih.gov/health/topics/conditions/parkinson/.

DNA Extraction Lab

In this lab we asked the question, can DNA be separated from cheek cells and if so at what point will you be able to see the DNA. We predicted that it would be possible and the DNA would be visible after the stage where alcohol was added. We found that it is possible to separate the DNA in a process of homogenization, lysis, and precipitation. After the alcohol was added to the solution, the DNA was clearly visible, floating above the solution in the alcohol. This would make sense, because the alcohol is a polar substance and DNA is nonpolar, so the polar substance should draw out the DNA, which is exactly what happened in our experiment.

While our hypothesis was supported by our data, there could have been errors due to mistakes in the procedure and inaccurate measurements. When making our procedure, we placed one of the steps incorrectly, so after pouring in the alcohol and extracting the DNA we had to shake the vile ruining our extracted  DNA. Also, when measuring things like soap and enzyme into the solution, everyone had a different idea of how much to add, resulting in members of the group having different solutions. This could have caused people to have different results, skewing the data. In the future these errors could be avoided if the procedure is given to students and one student does all the measuring to keep it consistent. 

This lab was done to demonstrate how molecules interact with one another and how DNA can be extracted from organisms. This helps me understand the concepts of polar and non-polar and to understand DNA and how it works and interacts with other substances. Based on my experience with this lab, I can apply my knowledge of DNA to other labs and I now know how to create a proper lab procedure from several different parts.

Unit 4 Reflection

The coin sex lab was a lab done to demonstrate Mendel's sex laws like the law of independent assortment and segregation. Probability states that in a dihybrid cross, the ratio of phenotypes should be 9:3:3:1. In our experiment, we got a phenotypical ratio of 7:4:4:1. Although this is not exactly what the prediction is, it is close enough to the expected.
Although using genetics you can predict some traits of offspring it is not 100% reliable. When predicting traits, you are predicting the chance of having a trait. For example, by looking at the genotypes of parents, you can predict that the baby has a 50% chance of being colorblind, but you cannot be totally sure. This relates to life, because by knowing your genotype you can predict what traits your offspring may have.

Unit 4 was called "Why is sex so great?" It was about how two a sperm and egg produce a genetically different offspring. Some topics that we learned about were asexual vs sexual reproduction, chromosomes, sex cells, haploid vs diploid, meiosis and mitosis, Mendel's sex laws, genes and alleles (dominant/recessive) punnett squares, autosomal and X-linked inheritance, incomplete dominance, codominance, gene linkage, epistasis, and multifactorial disorders. 

Some things I found difficult to understand were meiosis and mitosis. Some things I understood well were punnett squares and inheritance. 

I want to learn more about is how mitosis and meiosis works.

I learned a lot about genetics and inheritance and more study techniques. I learned from the infographic that visuals help the learning process. I wasa better student in this unit because I managed my time efficiently and stayed on top of all of my vodcasts and notes.


The Vark questionnaire showed that I was more of a kinesthetic and visual learner than an aural and read/write learner. I was not surprised with my results because I remember more of visual information and learn a lot better from labs. To help me study for upcoming tests, I can draw pictures and study those to help me retain the information.

My results: Visual-9, Aural-4, Read/Write-3, and Kinesthetic-12

Genetics Infographic

Is Sex Important?

Some advantages of sexual reproduction are that genes vary between generations. Also, changing genes can get rid of harmful mutations that the parents may have accumulated in their genes according to Muller's theory. When their are offspring that have many harmful mutations, those mutations will not be passed on and will end there. A disadvantage to sexual reproduction, as claimed by Dr. Tatiana is that there is competition between males and that qualities that attract a mate may not be the same qualities needed to survive.

An advantage to asexual reproduction is that to keep the population the same, each female needs to have one offspring, as supposed to two in sexual reproduction. Also, asexual organisms have been living on earth the longest according to Miss Philodina. A disadvantage to asexual reproduction is the susceptibility to diseases. The red queen theory points out that if one asexual organism is susceptible to a certain disease, than the entire population can be wiped out by a single disease.

Something I would like to know is why some species reproduce asexually and others sexually.

Unit 3 Reflection

This unit was all about cells and their functions. The unit started just by familiarizing ourselves with the cells parts and how it works. Once we had an understanding of the cells parts, concepts like osmosis and diffusion were introduced. Having an understanding of that led to learning about photosynthesis and cellular respiration. I did not fully understand the material presented at the beginning, but working as a group on things like labs really helped me understand the content. I was able to finish the homework on time which gave me an advantage during class, but I did miss a vodcast causing me to be behind the next class.

Some major concepts I learned in this unit that may be helpful were diffusion, photosynthesis, and cellular respiration. These things will be useful to know in future science classes. I also learned that finishing the homework on time or early gave me a huge advantage and that missing or putting off homework made it harder for myself.

I want to learn more about the process of photosynthesis. It was a little confusing so I will re-watch the vodcast on it and re-read the textbook on it. I will do this to be prepared for the test. I may also watch some other vodcasts on things I had trouble with and study my textbook notes to be prepared.

Microscopic Organism Lab

Muscle cell: Nucleus, Striations

Ligustrum: Epidermis Cell, Veins, chloroplasts

Spirogyra: Cytoplasm, chloroplast, cell wall

Bacteria: Bacillus, Coccus, Spirilum

Cyanobacteria: Single cells

Euglena: Nucleus, Chloroplasts

Amoeba: Nucleus, Cell membrane, Pseudopods

The autotrophs we observed had cell walls. They also had chloroplast which made them green. The heterotrophs on the other hand did not have cell walls, making them have less structure and different colors. In the eukaryotes, I could identify different parts of the cell and organelles. Prokaryotes, however, do not have organelles and were much simpler than the eukaryotes. 

Photosynthesis Virtual Lab

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 plants are exposed to different colors of light, than the plant exposed to red or blue light will have the most growth, while the plant exposed to green light will grow the least.

2. How did you test your hypothesis? Which variables did you control in your experiment and which variable did you change in order to compare your growth results?

I tested the hypothesis by exposing the plants to each color of light for 30 days. A variable I controled was the type of plant. I changed the color of light in each test.

Results:

Filter Color	Spinach Avg. Height (cm)	Radish Avg. Height (cm)	Lettuce Avg. Height (cm)
Red	18.3	12.6	11
Orange	14.6	8	6
Green	2	1.3	3
Blue	19.3	14	12
Violet	16.3	10.1	8

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 did support my hypothesis. The plants exposed to red or blue light consistently grew the tallest and the green light plants grew the least in each of the tests. The order of best light to worst light was consistent through all of the plants.  

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

I can conclude that the colors blue, red, and violet point to more plant growth, while colors like green lead to poor plant growth.

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

White light would produce a height that is the average of these tests.

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)

In this lab we attempted to answer the question of how does temperature affect photosynthesis in plants. I found that the higher the temperature, the less photosynthesis that occurred. I know this because at 10°C there were the most bubbles indicating photosynthesis was occurring and the more the temperature was increased, the fewer bubbles appeared. Scientific studies show that temperature affects the light independent reaction in photosynthesis. This supports are data in saying that photosynthesis slowed down.

This lab was done to demonstrate how temperature affects the rate of photosynthesis. A major concept learned from this is how photosynthesis works and how certain factors can affect how efficiently it works. Based on my experience from this lab, I know know better on how photosynthesis works which could help me on future labs.

Data:

Water Temperature (C)                                            Bubbles per 5 seconds

10	6
25	5
40	2

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

Amoeba

Power: 400x
This aboeba is unique because it uses its cell membrane to devour other cells. I observed that the aboeba came in many sizes, shapes, and colors. This cell is eukaryotic, because it has organelles and is a heterotroph because it eats other organism to get its energy.

Euglena

(The flagellum is not visible in this picture)
Power: 400x
Euglena cells are unique because they can be both autotrophic and heterotrophic. I observed that it is very green, which means that it has lots of chloroplasts. It is a eukaryote because it has a nucleus and organelles but is not classified as a autotroph or heterotroph.

Cyanobacteria

Power: 400x
This cell is unique because it consists of many cells together. I noticed that they often form chains of cells. Cyanobacteria are prokaryotes like other bacteria. These cells are autotrophic, because they carry out photosynthesis.

Bacteria Cells

Power: 400x
These bacteria cells are unique because they come in several shapes and sizes. Something I observed is that the bacteria cells are extremely small compared to the other cells. The bacteria are prokaryotic because they do not have any organelles or a nucleus. They are heterotrophs because they don't make their energy, but instead get energy from other organisms.

Spirogyra

Power: 400x
This cell is unique because most of the cell is taken up by the central vacuole, pushing all of the organelles to the outside. I noticed that the cell is very long and skinny. This cell is a eukaryote, because you can see organelles like the nucleus and chloroplasts. It is autotrophic because it has chloroplasts and makes its own energy through photosynthesis.

Ligustrum Plant Cells

Power: 400x
This organism is unique because in this view you can see several different types of cells. I observed that the inner cells that do the photosynthesis are greener because they contain more chloroplasts than the outer epidermis cells. These cells are eukaryotes, because they have nuclei and organelles like mitochondria and chloroplast. These cells are also autotrophs, because they make their own energy using photosynthesis.

Skeletal Muscle Tissue

The power used on the microscope to take this photo was 400x.
This cell is unique because unlike many other cells it has multiple nuclei in each cell. I observed that each cell is very long and tube-like. This muscle cell is eukaryotic because it has a nucleus and organelles. It is heterotrophic because it gets its energy from other organisms.

Egg Diffusion Lab

Looking at the class data, the mass and circumference of the egg increased when placed in the deionized water and decreased when placed the sugar water. The change occurred because of the solution's attempt at balancing the concentration of macromolecules in and out of the egg. The egg contains large amounts of solute compared to the deionized water solvent. Water than diffused into the egg to make the concentrations of solute equal, causing the egg to enlarge. When placed in the sugar water there was a higher concentration of solute outside of the egg, so the solvent, water, diffused out of the egg to balance out the concentration. The result was a deflated looking egg with a lowered mass and circumference.


A cells interior environment can change as its exterior environment changes. This could be to maintain homeostasis, or internal conditions of an organism. When the cell was put in vinegar first, and then water, and then either deionized water or sugar water. This caused the egg to diffuse water many times, either in or out of the cell.

This lab was all about the scientific principle of diffusion and osmosis. Diffusion is a cell letting molecules in and out of the membrane. It demonstrates this by showing how water can move in and out of a cell when the environments between them vary.

Fresh vegetables are sprinkled with water so they will absorb that water making it more juicy and to preserve freshness. Roads are salted to melt ice, but causes plants on roadsides to dry up. They dry up because their is a higher concentration of salt outside the plant, so it will loose water to try and balance out that concentration.

Another experiment that could be made based off this experiment and what we learned, could be an experiment about molecules diffusing across a cell membrane. The previous experiment was about how water diffuses across the membrane, so this experiment will teach us about how molecules diffuse.

Egg Cell Macromolecules Lab

In this lab we asked the question of what macromolecules would be present in different parts of a egg cell. We tested for the macromolecules, protein, monosaccharide carbohydrates, polysaccharide carbohydrates and lipids.

The presence of lipids was tested on an egg membrane and were found to be abundant. The data showed the abundance of lipids because when the membrane was exposed to chemicals, the chemical had an immense color change. This would make sense because the cell membrane is mostly made of lipids.

In the protein test, proteins were found to be prominent in the egg white of the egg cell. When exposed to the chemical that identifies protein presence, the chemical changed color rapidly, indicating that many proteins were present in the egg white. This is logical because the cytoplasm/egg white of a cell is made of proteins to be used as structure, and a food source.

When the egg yolk was tested for macromolecules, the most common macromolecules were monosaccharides. When tested with the chemical the chemical changed from blue to orange, signifying that large amounts of monosaccharide sugars were found in that portion of the egg. It would make sense that sugar would be found in the yolk, because the yolk is where the embryo develops and the sugars provide energy and food.

All but one of the evidences supported our claims. We claimed that proteins would be the most common in egg whites and that lipids would be found in the membrane, but did not hypothesis that the yolk would contain lots of monosaccharides.


While our data largely supported or hypothesis, some errors may have taken place in the procedure. It is possible that some of the transfer pipettes and spoons could have been mixed with different substances while carrying out the procedure. Also, a different person judged each test, possibly skewing results with differing opinions of scaling the color change. These could have caused the data to be invalid, because of inconsistency. To reduce possible errors in future experiments, we can try to be careful of mixing substances and have one person to be the judge of all the chemicals so the data will be consistent.

This lab was preformed to demonstrate where the macromolecules we studied are found in a cell and to deeper the understanding of how they work and what they do. In class we learned about the different types of macromolecules and what they do, and this lab showed how they were present in a cell and why they were in different parts of the cell. This lab taught me how I should carry out a procedure in a lab, because this lab was very messy and that could have been fixed by being more careful. Also, we took to long on the lab and the cleanup process took to long. In the future I will be more focused on doing labs as quickly and efficiently as possible.

Unit 2 Reflection

Unit 2 was largely about different types of macromolecules and how they are essential for life. The main types are carbohydrates, lipids, nucleic acids and proteins. Each serve a different functions necessary for life to exist. Carbohydrates are a macromolocule made of rings of glucose, used primarily for energy and sometimes for structure. We learned about carbohydrates and their structure in the sweetness lab. Lipids are another macromolecule that makes up oils, waxes, and fats. It is made of a charged head and a fatty acid tail. Organisms use lipids for energy storage and cell structure. Nucleic acids are polymers made up of nucleotides. Nucleic acids make up DNA and RNA. Without these, life could not exist. Proteins are made of amino acids, and make up muscles, hair, bones, and parts of cells. Proteins also make up enzymes. Enzymes are a type of biological catalyst that speeds up chemical reactions inside the body by lowering activation energy. We learned about enzymes and how they were affected by factors such as pH and temperature in the virtual enzyme lab and in the cheese lab.

Another important thing we learned was how molecules interacted with each other through bonds and such. The reason water molecules can bond with each other is because of polarity.  This means that water has an unequal charge, meaning that one side of the molecule in positively charged while the other side in negatively charged. This allows water to be attracted to itself, a force called cohesion, as well as many other molecules in adhesion. 

Something that was hard for me to understand solely through the vodcasts and  chapter notes were the enzymes and how they worked. Doing the labs in class helped me understand them and how they worked. I think I also benefited from the collaborative setting, because if I was unsure or did not understand something, the people in my group could help me.

Something that I learned from this unit is how to have better lab procedure. Especially in the cheese lab, many people, including our group, did not follow the specific instructions and the outcome was a messy lab that may have not yielded accurate results. Now we know to follow directions better to have a lab that is easier and more productive. I was also able to handle the class and homework better in this unit by learning how to manage my time better and get things done more efficiently. 

Some things I would like to learn more about are enzyme structure, and more about how they work. I found the experiments we did with enzymes interesting and relevant. They exist in everyday items and are present in our own bodies and have a huge effect. 

Sweet lab

Generally speaking, monosaccharides and disaccharides are usually sweeter than polysaccharides. All of the monosaccharides and disaccharides were rated significantly sweeter than both the polysaccharides. Both of the polysaccharides were given very low sweetness ratings by all members of the group, while most of the monosaccharides and disaccharides were given fairly high sweetness ratings, proving that monosaccharides and disaccharides are sweeter than polysaccharides.

The shape of carbohydrates may affect the way organisms use them. For example, carbs with either one or two rings of glucose may be primarily used for energy because they are simple and easy to break down. Polysaccharides, or carbs with three or more rings may be used for structural support in addition to energy.

All the testers in this lab did not give each carbohydrate the same sweetness rating. This may be because everyone is different and people may have different opinions. Some people also have differing taste buds, some being more sensitive to sweetness than others People from different places evolved to taste things differently. This is another reason why tasters may have ranked the samples differently. Our brains detect sweetness in the first place by using the taste detecting cells and taste transmitters in out tongues and brains.  

Biology Collage

Jean Lab

In this lab, we answered the question, what is the best concentration of bleach to fade the color of new jeans with the least fabric damage. We found that 100% bleach gave the best color removal with relatively little fabric damage. There was an average of 8.5 color removal and an average damage of just 3.6. Just looking at the jeans squares, the color removal was immediately noticeable and extreme, while the damage was nearly unnoticeable. This data supports our claim that 100% bleach is the most effective, because it had more than twice the color removal as some of the other data samples. This would make sense, because bleach has color removing power, so the more bleach the more color removal. 

While our hypothesis is supported by the data, there could have been errors due to the fact that the jeans samples we used in the test were not consistent. For one specific test, we sometimes used up to three different jeans samples, making hard to judge the effectiveness of the color removal and the compare the damage. This made the data inconsistent and possibly inaccurate. Also, our timing was not always completely accurate, often being off by a few seconds. This may have affected the results by making the tests inconsistent. In future labs, this would be an easy fix. To fix, just make sure you use fabric all from the same jeans and keep everything that is not the independent variable consistent. 

This lab was done to demonstrate how bleach can affect the color of jeans and to teach us proper lab procedures. The procedure can be adjusted to give more accurate results by stating that all jeans used in the same test have to be the same and by giving students more time to complete the lab. The procedure used in this lab followed the scientific method and the procedures for labs we learned in the vodcasts. By doing this lab, I expanded my knowledge of lab procedures and was able to practice carrying out a real lab. This will help me in every lab going forward, because lab procedure is a skill used for any science lab.

Works Cited