Protein Synthesis Lab

In order to make a protein, the first step is having the DNA sequence read and transcribed into RNA. RNA polymers read and copy the DNA code for a protein as an mRNA copy. Base pairing rules apply, but U replaces T. The next step is translation. MRNA arrives at the ribosome, which reads mRNA three bases at a time, or reads the codons, and translate DNA language (A,G,C,U) into protein language (amino acids)
 
https://upload.wikimedia.org/wikipedia/commons/thumb/3/38/Protein_primary_structure.svg/2000px-Protein_primary_structure.svg.png

Deletion and insertion seemed to be the most changing forms of mutation. Substitution effected the protein code the least. Where the mutation occurs does matter for all the forms of mutation. The earlier the code, the most damage deletion and insertion do. Substitution just need to change an essential nucleotide to make any sort of difference.

https://upload.wikimedia.org/wikipedia/commons/5/50/Mutation_par_substitution.png

I chose the insertion mutation because it seemed to have changed the amino acids the most. Insertion did change the amino acids almost as much as deletion did, and it definitely changed more than substitution. Since I inserted a new nucleotide in the very beginning, it had the biggest effect on the sequence, showing how important where the mutation occurs is.

https://upload.wikimedia.org/wikipedia/commons/thumb/6/6d/RNA-codons-aminoacids.svg/2000px-RNA-codons-aminoacids.svg.png

Mutations could greatly affect my life. They could constrict me from doing many things and functioning properly, or they could be minor and not have to big of an effect on my life. For example, huntington disease is an inherited mutation in which nerve cells in the brain break down over time. Huntington's disease is an autosomal dominant gene. There is a 50% of children inheriting the gene.

http://hdsa.org/wp-content/themes/hdsa/images/img_HD2.png

Unit 5 Reflection

This unit was focused on DNA and replication of it. Themes and essential understandings were centered on what mutations are (a change in the DNA codes) and how they were caused (substitution and framshift mutations). They were also centered around transcription (the process where RNA polymers read and copy the DNA code for a protein as mRNA copy) and translation  of DNA.
Gene expression, which is the process of a gene being used to produce a gene product, and gene regulation, a mechanism used by cells to increase or decrease the expression of a gene, were my strengths because they made a lot of sense to me and I could picture these very well. It was hard remembering the what exons, sequences that are "expresses," and introns, sequences that are cut out, are because they sound very similar. Also, not getting promoter, the location on DNA where RNA polymerase attaches, operon, a series of genes used to control the expression of a single gene, and operator, a "switch" or segment of DNA at the start of a gene that prevents or allows RNA polymerase from attatching and reading the gene, mixed up is pretty difficult. The pictures below help me imagine them so I can remember them more easily.
Because I learned a lot more about the interworkings of DNA, I understand chromosomes, cells, and organisms a lot more now, and going back and reviewing those topics will be a lot easier.
I want to learn more about how mutation pushes evolution further and faster.


https://upload.wikimedia.org/wikipedia/commons/0/07/Gene.png

https://upload.wikimedia.org/wikipedia/commons/thumb/2/22/Lac_Operon.svg/2000px-Lac_Operon.svg.png

DNA Extraction Lab

In this lab, we asked ourselves, "how can DNA be separated from cheek cells in order to study it?" We were able to find DNA from cheek cells by first breaking down the cell membranes and nuclear material of the cheek cell sample. We did this by homogenizing the cell tissue with polar liquid. We then facilitated the precipitation by shielding the negative phosphate ends of the DNA by adding salt. We then added soap to lyse the cell membranes and to emulsify the proteins and lipids of the cell. To further break down cell membranes and other nuclear material, catabolic proteases were added. We saw the DNA floating around in the test tubes, showing that the process had worked to find DNA. One error was that we put in a couple more drops of pineapple juice, or our catabolic proteases. This could have hurt our data because the cell membrane AND the DNA could have both been broken down. Another error was that we might have put in too much salt because the direction called for "a pinch of salt", which is not an exact measurement, leaving lots of room for error. This could have affected our data because the solution could have been over facilitated, allowing the negative phosphates of the DNA too close together. Being more careful would solve the first problem, and more specific instructions would have solved the second one. The purpose of this lab was to grasp a better understanding of DNA and its surroundings. This lab relates to where DNA is in the cell, which is something we learned in class. This lab would come in handy when looking for genetic disorders or for curious parents to see what a new child might possibly look like.




https://ge.unl.edu/journey-of-a-gene/knowledge/flash-cards/

Unit 4 Reflection

In this unit, I learned about reproduction. I mainly learned about how certain cells reproduce in cycles such as mitosis and meiosis, and how to find the probability of new organisms. Punnett squares and gene inheritance, like recessive, codominant, dominant, and X and Y chromosome rules, were the easiest to remember because I had already learned about them in seventh grade. Remembering all the steps in mitosis and meiosis and their difference is a lot harder because there is a lot more new and tricky information to remember. I did not learn any new information from doing the inforgraphic because the information that I used in it was from the vodcasts, but doing the inforgraphic did reinforce all the information and helped me remember it a lot easier. Also, the pictures helped me see the information a lot better and help me remember a lot more of it. I am a better student today than I was before because I now know I learn and remember science a lot better when I can picture it and clearly see it in my head, which the infographic helped me to do. I want to learn more about DNA.

My preferred learning style is being hands on. I kind of already knew that, but I was surprised on how much more I was kinesthetic than everything else. To take in information, I should use all my senses, hands-on approaches to learning, and trial and error exercises. To study, I should put real life examples into my work and put pictures to illustrate an idea. To perform well on a test, I should role play the exam.

Coin Lab Relate and Review

In this lab, we explored genetics possibilities for a possible child between two students. Coins served as a model for the genetic concept of randomness, or the law of independent assortment. The coins also showed recombination, which is the rearrangement of genetic material, especially by crossing over in chromosomes or by the artificial joining of segments of DNA from different organisms. Recombination often occurs during meiosis. We first found the probability of getting certain alleles for different genes. Monohybrid crosses were a lot simpler to predict, especially if they were homozygous, because they did not rely on other factors, like diyhybrid crosses. In our autosomal experiment, were we crossed two double heterozygous alleles, we predicted that the the ratio of phenotypes would be 9:3:3:1. I claimed that the results would be very similar to what we predicted, but not the exact same because of the randomness of the experiment. Our results had the ratio 10:2:3:1, which supports my claim because it is very similar to what we predicted but slightly different due to the randomness of the experiment. In our X-linked inheritance experiment about colorblindness, we had similar results. There are some limitations while relying on probability. Probability can say what is possible, but it can not say what will happen in actuality. Also, sometimes there are too many possible combinations for punnet squares and/or other probability tools to be useful, such as predicting all the major alleles that will show up in a child. Lastly, like in this experiment, when a dominant allele showed up, we assumed it was heterozygous, but we did not know for sure, leaving out punnet squares and probability open to error. In real life, this could help me predict whether or not I have some genetic diseases or disorders. This would be helpful so I can detect them ahead of time and get treated a lot faster and better. Also, I were to have a child, it would help me to find ways to avoid having them inherit genetic diseases or disorders, or it would help me predict what my child would look like.

Genetics Infograph

LINK TO FULL SIZED INFOGRAPHIC:

https://magic.piktochart.com/output/9217449-biology-infographic-copy-d

Unit Three Reflection

This unit was about organelles in the cell and what they do. This unit was also about how photosynthesis and cellular respiration works. I remembered how photosynthesis works the best because I had learned a lot about it before. I was okay at remembering cellular respiration, for I had also learned about it before, but not as much as photosynthesis and not as in depth as I learned about it now. Remembering what each organelle does was probably the hardest to remember because even though I learned a lot about them before, there are just so many of them that do so much that it's hard to hold on to all that information.
I learned a lot about how cells work, and how plants, animals, and even I function. It was also interesting experimenting on the egg, using it as a substitute for a cell, and really seeing up close how cells work.
I want to learn more about other systems that organelles make up, like the digestive system. But for the test I will use flashcards are rewrite what I had learn to reinforce the information in my mind.

Egg Diffusion Lab

 In this lab, we put one egg in sugar water and another in normal water, which was the control. We then waited a couple of days to see what would happen. 

 When there was a high concentration of sugar water, outside the egg, or when there was a hypertonic solution, water left the egg through the egg membrane through the process of passive diffusion. Because water left the egg, the egg's mass and circumference shrunk. Water was the solvent and the sugar was the solute. In my group's experiment, our mass decreased by 52% and our circumference decreased by 20.6%.

A cell's internal and external environment changes often through diffusion. It changes to achieve equilibrium. Vinegar made the egg gain water, water made the egg grow even more, while sugar made the egg shrink.

 This lab shows how cells react to hypertonic and hypotonic solutions that it is in. For example, when there is a low concentration of sugar water, or in our case just water, the cell and the egg reacts by taking in that water and expanding to reach equilibrium. This is one of the things I learned in class.

 Vegetables are sprinkled with water so they will absorb it due to diffusion and keep it fresh. The plants along the roadside would release water due to the high concentration of salt to achieve equilibrium.

I would want to test limp celery and other vegetables in water to see if it would grow. This would be helpful because sometimes I have vegetables for too long and they start to go limp.

Egg Macromolecules Lab

In this egg lab we asked the question, "Can macromolecules be identified in an egg cell?"
In the egg membrane, we identified macromolecule that could be found. One of the macromolecules we found was protein. We know there was protein because the egg membrane turned light purple. We also learned in class that proteins are in cell membranes because they let things in and out of the cell. This evidence supports the claim that a macromolecule could be identified because we identified protein when the membrane turned light purple, and because of the information we learned in class.
In an egg white, we also identified a macromolecule. We found lipids. We know there were lipids because the egg white turned to a bright orange. In class, we learned lipids are in the cytoplasm, or egg white, of the cell, because lipids hold a lot of energy and are also in mitochondria, which are also in the cytoplasm, or egg white, of the cell. This evidence supports our claim because we identified lipids when the egg white turned bright orange, and because of the information we learned in class.
In the egg yolk, we identified monosaccharides. We know there were monosaccharides because the egg yolk turned from blue to green. We also learned in class that monosaccharides are in the cell nucleus, or egg yolk, because the chain of monosaccharides allows the nucleus to receive energy and get rid of waste. This evidence supports our claim because we identified monosaccharides in the egg yolk when the yolk turned from blue to green, and because of the information we learned in class.
One possible error we had was that when we were putting the egg yolk in a beaker, we accidentally put some egg white in there with it. This could have effected our data because when we were testing the egg yolk for certain macromolecules, we could have found certain macromolecules that are only in the egg white and thought it was in the egg yolk, too.
A second possible error we made was not cleaning the cell membrane. When we tested it, the membrane still had egg white on it. This could have effected our data because when we were testing the egg membrane for certain macromolecules, we could have found certain macromolecules that are only in the egg white and thought it was in the egg membrane, too. Two possible fixes for these problems are to be more careful while pouring the egg yolk into a beaker, and to clean the egg membrane.
The purpose of this lab was to find which macromolecules were in which parts of the cell. This relates to what we learned in class because we learned a lot about what macromolecule was in each part of the cell. This information could be used in other ways that finding out what macromolecules were in the egg. We could use this data to find out what other macromolecules are in other foods we ate, how much of the macromolecule is in the food, and to create a better diet.

Inquiry Hour Blog Post 1.2: Generating questions

One of the questions I am most interested in is, "What makes us human?" This is an interesting question because many animals have similar traits as humans, yet they do not not create and destroy things nearly as much as we do. A possible hypothesis to help answer this question is "If the mastery of fire makes us human, then teaching another animal to make fire will help it to advance to human levels of intellect."
Here is a list of twenty questions that I am interested in:

1. Why is the sky blue?
2. Why do we see colors?
3. Why do boomerangs come back?
4. Why don't spiders stick to their webs? 
5. Why are flamingos pink?
6. What happens when you faint?
7. Why do bruises change colors?
8. Why do people go bald?
9. Why do men grow facial hair?
10. Why do things fade in the sun?
11. Why does black heat up in the sun faster?
12. How do glasses work?
13. How do contacts work?
14. Why do things look darker when they are wet?
15. How does hair know when to stop growing?
16. Why does your stomach make noises?
17. Why do I have to use a number 2 pencil?
18. Why am I upside-down when I look in a spoon?
19. Do plants get cancer?
20. Why are we ticklish?

Unit 2 Reflection

This unit was about an introduction to chemistry for biologists. We learned a lot about the anatomy of an atom, learning about the positiveness of protons and how electrons circled around the atom's nucleus, able to be shared or taken from other atoms and/or elements. Things like this was the easiest for me to learn about, mainly because I had already learned and memorized their functions and structure in eighth grade. I also knew a little about macromolecules, such as carbohydrates, lipids, nucleic acid, and proteins, but I did not know nearly as many details as what was taught in class. We learned about how carbs can join together to form rings. Monosaccharides have one rings, disaccharides have two rings, and polysaccharides have three or more.
Lipids make up cell membranes and are used to make hormones and for energy storage. Lipids break bonds between carbon and hydrogen to get energy when glucose is running low.
Proteins are large molecules made of smaller molecules called amino acids. There are two types of proteins. Structural proteins are the building blocks of bodies. Some examples of structural proteins are hemoglobin, which carries oxygen in blood, muscle proteins, which make up muscles, and collagen, which is the most abundant protein in your body. It is in skin, tendons, cartilage, bone, and more.
Enzymes are the other type proteins. Enzymes make chemical reactions happen; they break molecules apart or pule molecules together.
I want to learn more about disease in the body, how it is treated, and what happens when it is not.

Cheese Lab Conclusion

In this lab, we asked the question, “What are the optimal conditions and curdling agents for making cheese?” We found chymosin and rennin the best curdling agents. Our evidence for this is that we found that 0.25 mL of lemon juice in chymosin and rennin in hot water were the best curdling agents. These three agents curdled the fastest, for they curdled in five minutes.

One error that we had is that we could not watch the test tubes all the time; we only checked in on them every five minutes. This could effect our data because some of the agents might have curdled faster than five minutes, but we will not know because we only saw the amount of curdling after five minutes. A second possible error could be that we did not have the perfect amount of lemon juice in the test tube. This could effect our data because it would change the speed that the substance in the tube curdled.To improve these errors, we could check the test tubes more often and get more precise droppers.

The purpose of this lab was to understand enzymes more and how they affected the curdling process. In the lab, I learned more about denaturing enzymes, which is also something I learned in class. Learning how enzymes can be sped up or denatured could come in handy in preserving food and understanding why we use refrigerators.

Class Data
Curling Agent	Chymosin	Rennin	Buttermilk	Milk (control)
Acid	5	5
Base
Cold
Hot	5	10
Temp Control	15	15
pH Control	15	10

Sweetness Labs

The question provided in this lab was, "how does the structure of a carbohydrate affect its taste (sweetness)?" We found that monosaccharides were the sweetest, disaccharides were the second sweetest, and polysaccharides were the least sweet. On average, the sweetness level of monosaccharides was 95, while disaccharides was 66, and polysaccharides was 9. This evidence shows the levels of sweetness and which saccharides are the sweetest.

Carbohydrate structure affects how cells use them. More rings in a structure would hold more sugar and energy, and less rings would hold less sugar. There are three reasons why the sugars would taste different for different people. First of all, some people have more papillae, meaning they are more sensitive to tasting certain things. Also, some people have certain genes, probably arising from evolutionary pressure in different parts of the world, which detect bitter tastes more highly. Lastly, the nose is also involved in tasting. Because our noses detect smells slightly differently and some of us could not have smelt the sugar before we tasted it, the sugar could taste different to different people.
People having different amounts of papillae is the number one reason why we would think certain things are sweeter or more bitter than other people.

Identifying Questions and Hypotheses

The experiment I found was asked if increasing daily coffee consumption reduced type 2 diabetes risk. The hypothesis was similar to if people who increased the amount of coffee they drank by more than one cup over a four year period had a lower risk for type 2 diabetes, then increasing coffee intake helps reduce type 2 diabetes risk. Previous studies had shown that higher coffee consumption was associated with lower type 2 diabetes. At the end of the experiment, they found this was a true statement, for those people had an 11% lower risk for getting type 2 diabetes.

Original Study: http://www.hsph.harvard.edu/news/press-releases/increasing-daily-coffee-intake-may-reduce-type-2-diabetes-risk/

Biology Collage

Jean Lab