Hunger Games Lab

1) In this lab, we simulated natural selection by having different individuals with different traits compete to survive. The food was corks, and the variation was how we picked up the food. Stumpys, with the phenotype AA, picked up food between their wrists. Pinchers, with the phenotype aa, picked it up between their thumb and index finger. Knucklers, with the phenotype Aa, picked up food between the second knuckles of their index and middle fingers. An individual needed certain amounts of food to survive after each trial. Because of this, the populations kept changing.
2) The knucklers were the best at capturing food, and this is shown because their populations were mostly the highest. The individuals with this trait were able to pick up more food between their knuckles and could quickly collect and store the food.
3) The population did evolve because the allele frequencies of A and a kept changing throughout the lab. The frequency of the A allele changed from 0.50 at the first trial to 0.38 at the last. The a allele's frequency changed from 0.50 to 0.62. Evolution is changes in allele frequency over time, so evolution occurred.
4) The placement of the food was random and was an example of genetic drift. Depending on who was nearest to the food, they were able to collect the most food. Also, people cheating, not conforming to the trait that they were supposed to have, was random. Different people did this throughout the trials, and that affected the results. What was not random was the starting populations, when each trait had an equal population size. Also, the type of food and and the traits that individuals had weren't random.
5) If the food were bigger, it would probably be harder for knucklers to pick it up between their knuckles and the pinchers would have an advantage, and the stumpys could also. If the food were smaller, the stumpys could have a hard time picking it up, while the pinchers and knucklers could pick up more food at once.
6) If there was not incomplete dominance, then the intermediate species would have a different trait, and it would not be knucklers. This would affect allele frequency because these individuals would probably have more, or less, success than that of the knucklers.
7) Natural selection is the driving force behind evolution. Changes occur in a population naturally because of the enivroment or ecosystem an organism is in. Some species will have an advantage, while others will not. The frequency of the helpful trait will increase, while the other will decrease.
8) Some people tried to put much food as they could into their pockets and that way, they were able to store and collect more food than others. Also, people did cheat, and that helped them survive until the next trial. Some individuals probably would have died if they had completely followed the rules. Overall, these factors just helped more people survive, with the knucklers maintaining the highest population.
9) In evolution, populations, not individuals, evolve. When an organism is born, they are stuck with the genes their parents gave them. Only when they reproduce does the population evolve, because of a change in allele frequency. Natural selection acts on phenotypes, not genotypes. Depending on the traits an organism has, natural selection, based on whether the traits are helpful or not, either makes the population have that trait or decrease in individuals with that trait.
10) How would the addition of another trait affect the population's evolution?

Unit 7 Reflection

     This unit was about ecology and conservation biology. Ecology is the study of interactions between different organisms and their environment. Some big ideas of ecology are homeostasis and interdependence. The levels of organization of ecology are organisms, population, communities, ecosystems, biomes (an area of the world that contains many ecosystems), and the biosphere (Earth). We also learned about food chains and webs, and the differences between them. If one organism declines in an ecosystem, then, a domino effect is sent throughout the food web, and other populations could decrease. Next, we learned about the energy in ecosystems, which can be shown through biomass pyramids, pyramids of numbers, and energy pyramids. Only 10% of the energy at one trophic level (primary producers, primary consumers, secondary consumers, tertiary consumers, and quaternary consumers) is passed to the level, so there is less energy to go around as you go up the energy pyramid. That is why it is important to have many primary producers who transfer all of the energy to the next levels. Another part of ecology is population ecology, the study of populations in relation to the environment. Many different factors, like deaths or immigration, affect the rise and decrease of populations. Exponential growth is the doubling of a population over time. Logistic growth is when the rate of growth slows down as the carrying capacity is reached. A carrying capacity is the maximum point at which an environment support a population. The human population has been exponentially growing for some time now, and after more time, it is expected that it will reach its carrying capacity. At carrying capacity, the population will decline and rise again or level off (number of births will equal the amount of deaths).

https://upload.wikimedia.org/wikipedia/en/3/3a/Human_population_growth_from_1800_to_2000.png

     There are also different cycles that help to keep an ecosystem healthy. Ecological succession occurs with a sequence of community and ecosystem changes after a disturbance (ex. fire in Yellowstone causes the ecosystem to grow). Primary succession is when everything in a ecosystem has been harmed/disturbed, while secondary succession happens when part of an area is still intact. The water cycle includes evaporation and precipitation, while the carbon cycle involves cellular respiration. The nitrogen cycle can be the conversion of nitrogen gas into nitrates for plants or the breaking down of nitrogen from waste (into nitrates) from waste or dead organisms. Phosphorous makes up ATP, DNA, and lipids, and it is deposited by water and made available to plants. Decomposers and producers are critical to life. High biodiversity is important for ecosystems to be considered healthy because organisms are resistant to changes. Populations with producers & decomposers/tertiary & quaternery concumers are features of a healthy ecosystem. Four causes of species loss are climate change, overexploitation (harvesting organisms too fast/much so populations cannot rebound), introduced/exotic species, and habitat loss. There are five ways to conserve/protect ecosystems: identify and protect (biodiversity) hot spots, conservation (protect what we still have), smart planning (some solutions to help ecosystems (ex. movement corridors)), restoration (ex. jumpstart succession), and sustainable development (development that meets the needs of people today without limiting the ability of future generations). Finally, there are small things that each person can do to help, and if everyone does something small, there will be a big effect.

http://study.com/cimages/multimages/16/Landbridge.png

     I want to learn more about the different ways people are trying to conserve ecosystems through sustainable development or smart planning. The movement corridor and green roof are interesting ideas. I do not have any unanswered questions. I wonder about how people can raise awareness for the enviromental issues the earth is facing. Also, I wonder how we can all consume less and not run of resources. The Conservation Biologist project was a good project because I got to learn more about a place in the U.S. (the Great Plains) and the threats facing it. I thought my group worked well together, and everyone took part and did their work. Also, I got to practice explaining about a topic (in the video) besides just listening, and when you explain something to someone else, you learn it better yourself. I felt that our group could have recorded our video earlier because we went one day extra on our schedule to finish the presentation. Overall, our group did a good job on the project and created a educational video. My dominant conflict style is aggressiveness, with assertiveness the second, then passiveness, then finally passive-aggressiveness. I feel that in some situations, I could be aggressive or passive. I don't ask for help a lot, so that can improve my assertiveness. I don't think I am passive-aggressive often, but sometimes I can be. I think that whether I am aggressive or passive depends on where I am or who I am with, but I should try to be assertive most of the time. I could voice my ideas more, think about what I say before I say it, and say what I think is the right thing to do.

Unit 6 Reflection

     This unit focused mostly on biotechnology and the ethics attached to it. Biotechnology itself is the study or manipulation of living things in order to benefit mankind. Examples of it include biofuels, CSI work, and fermentation. Also, genetically modified organisms, or GMOs, are created using biotech. Ethics are also discussed when talking about different biotechnological possibilites, and the specific name for that is bioethics. Bioethics is the study of decision-making as it applies to moral decisions that have to be made because of advances in biology, medicine, or technology. A few examples of bioethical questions are: Should humeans be cloned to be organ donors?; Should drug companies be allowed to patent genes? and Should we use stem cells from embryos in order to treat diseases of living people? We also learned about recombinant DNA. Recombinant DNA is DNA that has been made by inserting the DNA of one organism into the DNA of another. It is created using restriction enzymes and ligase. The enzymes look for a specific sequence in DNA. From there, a new DNA strand can be formed by attaching a new strand to the sticky ends of the old one, using the enzyme called ligase. This DNA can also be used in bacteria. When plasmids and recombinant DNA are mixed and put in bacteria, the bacteria can grow a specific protein which can be extracted and used. Finally, there was a vodcast about the pGLO lab, which included a review of gel electrophoresis. It involves a plasmid called pGLO, ampicillin, and arabinose. It will be explained more later in this reflection.

https://upload.wikimedia.org/wikipedia/commons/d/de/Biotech-firm-application.png

     My strengths were almost the same they always are. I did all the vodcasts and other assignments and turned them on time. I paid attention in class and during labs, while also doing parts of the lab. I also believe that I have my topic for my 20 time project. A weakness I have is probably procrastinating because sometimes I do the vodcasts the day before they are due. Also, I left the textbooks until near the due date. I also think that I can have better lab skills because during the pGLO lab, I reused a pipette when the procedure said to get a new one after each time you use it.

   Successful transformation of E. coli with pGLO plasmid! #biology #gofalconpower pic.twitter.com/a0lgGzVul2

— Mr. Orre's Class (@OrreBiology) January 27, 2017

     The 3 labs we did were the electrophoresis virtual lab, the candy electrophoresis lab, and the pGLO lab. The virtual lab was going through the steps of electrophoresis and using it on DNA (all virtually). First, you extract DNA and then load it into a gel. At one end is a negative charge and at the other end is a positive charge. DNA will move towards the positive charge because it is negatively charged. If a strand is long, it will move slower and therefore, faster, and smaller strands will move quicker therefore longer. Then, you can measure the length of the DNA in bp (base pairs). The candy electrophoresis lab was actually electrophoresing different dyes of different candies to see how long each of their DNA strands are. The pGLO lab was using bacterial transformation. Using a plasmid called pGLO (some with DNA and some with no DNA), we had to combine the plasmid with arabinose, ampicillin, and GFP (glowing fluorescent protein). Then, we had to freeze and heat shock the bacteria so that it would pick up the plasmid. On three different plates, we tried to grow the bacteria. If it picked up the plasmid, the bacteria grew. Adding arabinose caused one of the bacteria to glow (an expected result). As always, I got better at doing the labs and following the procedure while also reinforcing the concepts that I had learned in the vodcasts, like gel electrophoresis and bacterial transformation.

https://upload.wikimedia.org/wikipedia/commons/thumb/6/60/Gel_electrophoresis_2.jpg/320px-Gel_electrophoresis_2.jpg 

      I have no questions that I want to have answered. I want to learn more about genetically modified organisms. Also, bioethics is interesting to discuss because there can be so many different views on one topic or question, and it is always important to hear everyone's ideas to make an informed decision for yourself. My SMART goals were to study in different ways for tests and participate more in class. I think that I have partly acheived my second goal because I have talked more in small dicussion groups, like the Biotech World Cafe. I have not made progress on the first goal. So, my next steps are to raise my hand more during class and make some changes to my studying technique.

pGLO Lab

pGLO Observations , Data Recording & Analysis

1.

Obtain your team plates.  Observe your set of  “+pGLO” plates under room light and with UV light.  Record numbers of colonies and color of colonies. Fill in the table below. Plate Number of Colonies Color of colonies under room light Color of colonies under   UV light - pGLO LB 0 Light Gray Dark Gray - pGLO LB/amp None None None + pGLO LB/amp 6 Light Gray Dark Gray + pGLO LB/amp/ara 7 White Green

2.	What two new traits do your transformed bacteria have?
	The transformed bacteria now glows (because of the GFP) and is resistant to ampicilin.
3.	Estimate how many bacteria were in the 100 uL of bacteria that you spread on each plate. Explain your logic.
	There are over a million bacteria in one colony. I predict that about ten colonies are in a hundred microliters (uL). Therefore, there would be about ten or eleven million bacteria in one hundred microliters.
4.	What is the role of arabinose in the plates?
	The arabinose provides a way to control the expression of the glowing fluorescent protein (GFP) gene. If it is present, the GFP will cause to the bacteria to glow. If it isn't, then that won't happen.
5.	List and briefly explain three current uses for GFP (green fluorescent protein) in research or applied science.
	- Fluorescence microscopy GFP is used with fluorescence microscopes, microscopes that use fluorescence to study properties of substances. GFP has advanced and redefined this field and will cause some substances studied to fluoresce. - Macro-photography Certain biological processes, like the spread of virus infections, can be followed using labeling. This labeling is done with GFP. Epifluourescent camera attachments are now used instead of UV light. - Transgenic Animals Some animals have been genetically engineered to glow using GFP. These animals can help scientists study certain things, like human diseases, and were also marketed as pets.
6.	Give an example of another application of genetic engineering.

Bacteria can modified to make certain proteins that can obtained and used. For

example, insulin and spider silk, which are difficult to get naturally, can be made

by genetically engineered bacteria.

Candy Electrophoresis Lab

In this lab we electrophoresed four reference dyes and four candies: red Mike and Ike's, purple Skittles, green M&Ms, and orange Reeses. The blue reference dye didn't match any of the candies' or references' length. Every dye had only one color band. Also, none of the dyes moved towards the cathode. The purple and red candy had a different dye color. The red and purple areas were also larger than those of the reference dyes. These dyes are probably just variations of the red reference dye. The dyes Citrus red 2 and Fast green FCF would migrate similarly to the dyes in this lab because they have similar structures to the reference dyes.

             

              

Dog food manufacturers may put artifical food colors in dog food to make it look more appealing to buy. Also, people will buy the food if it looks good and has color. Additionally, it could taste good for dogs. Foods I eat that would probably have artificial dyes are chips, candy (like M&Ms), macaroni and cheese, and soda (not too often). Artificial food colors can be preferable to companies rather than natural food dyes because it could be less expensive, taste better, and look appealing to eat. The length of the DNA fragment and the molecules in the dye control what distance the dye migrates. Electricity is the force that helps to move the dyes through the gel. Positive and negative charges at each end of the gel causes the molecules to separate by size. The smaller the DNA fragment, the longer/faster the fragment goes toward the positive charge (because DNA has a negative charge). The opposite happens for large fragments. DNA molecules of the lengths 600, 1000, 2000, 5000 daltons would separate like this: The 5000 wouldn't go far and would be closest to the cathode. The 600 would go the farthest distance. The 1000 would be second and the 2000 would be third, closer to the 5000-length molecule.

SMART Goals

     One goal that I have for this semester is to study better for tests. I will find a way to study that helps me remember the material I learn from each unit. I can try different studying methods, such as using Quizlet, answering questions from Relate and Reviews and Do Nows, taking the CFUs again, and re-watching parts of vodcasts. For each unit, I can try each or multiple techniques. By the end of the semester, I hope to study in a way that helps and benefits me, so that I can use this method or one like it for another class.
     Another goal that I will try to accomplish is participating more in classes. Participation is important, and it helps you to speak better and for longer amounts of time. I can start by raising my hand a few times. As the semester goes on, I want to share my answers or ideas more often, but not all the time. Also, I can be more involved when doing things in class like projects or labs. This could help me overall have a better experience in class and gain more knowledge.

Unit 5 Reflection

     This unit focused on four main concepts: DNA replication, protein synthesis, mutations, and gene expression/regulation. DNA has to be replicated identically because all cells have the same DNA. It has to unzip and fill in the bases missing in the base pairs. This is done by the DNA Polymerase, and now there are two identical strands of DNA. Protein synthesis is the process of making a protein. RNA is heavily involved in this process. The synthesis starts with transcription. DNA is unzipped again and this time, the RNA Polymerase copies the gene to mRNA (messengerRNA). Thymine is replaced with uracil, and after this is over, the mRNA goes to a ribosome. Now, translation can begin. The ribosome, or rRNA, reads the mRNA three bases at a time. These three bases are called a codon. One codon translates to one amino acid, and the animo acids formed are chained together by the ribosome. The chain folds and becomes a protein. This whole process can also be referred to as "walking the dogma". Mutations can be harmful or helpful to organisms and there are different types. Point mutations only affect one or two bases at a time. Substitution switches one base for another. Framshift mutations, like insertion and deletion, can add or subtract one or two bases in a sequence. Also, inversion and translocation involves DNA or chromosomes breaking and bonding with itself or other chromosomes. Finally, gene expression is the process of DNA being used to produce a phenotype. Gene expression has to be regulated, otherwise, ears would grow from your stomach, or eyes could grow on the top of your head. In prokaryotes, a operon, with a promoter, operator, and other parts, is used to regulate the expression of genes. Eukaryotic regulation uses proteins (called transcription factors) to control transcription. After that, the DNA is separated into exons, used DNA, and introns, unused DNA. DNA can wrap around proteins called histones to form nucleosomes.

https://c2.staticflickr.com/8/7447/9488926466_9116099def_z.jpg

https://upload.wikimedia.org/wikipedia/commons/0/0c/Lac-operon.jpeg

     My strengths were completing the vodcasts on time and basically understanding the concepts by the time I got to class. During class, I was able to completely understand the concepts with Do Nows, recapping the vodcast, and labs. I think that I can do better on labs and not make mistakes I can avoid. During the DNA extraction lab, for example, I was not able to extract DNA, probably because of an error I had made during the process. Also, I should do my textbook notes early and not procrastinate on them until the last minute.
     I am a better student than I was before because I have gotten better at managing the class over time. I can now follow along with the vodcast and pause less often. It is now easier for me to write Relate and Reviews, and I realize that they help a lot, especially now studying for the final. I believe that I am a good student because I do my work, understand the concepts taught to me, and be efficient and thorough with my work. I took the VARK questionnaire, and it said that I have a multimodal learning preference, and I wasn't sure what to do with that result. In conclusion, I am getting through the class, but I can always get better than I am now.