Unit 7 Reflection

In this unit, we learned about Ecology, the study of interactions between organisms and their environment, and its' basics: the idea of Homeostasis/Equilibrium, which is that like the body environments are healthiest when they're in balance, and the idea of Interdependence, when all living things are dependent on each other, and abiotic(nonliving) factors for survival. In a ecosystem, there are habitats and their niches, which includes all factors that species need to survive, stay healthy, and reproduce. We also went through the different Levels of Organization on Earth: Organism,  an individual living thing, Population, group of the same species that live in 1 area, Community, group of different species that live together in 1 area, Ecoystem, includes all abiotic and biotic factors, and the Biome/Biosphere, which is a large are of the world that's made of several ecosystems. In this world, animals, called Consumers aka Heterotrophs, compete with each other for food/energy(except for Producers/Autotrophs), Food Chains and Food Webs show this. Food Chains show how each organisms gets its energy; in the chain, the arrow points to the one getting energy. There are different levels in a Food Chain, called Trophic levels, that are based on what something eats. The 5 Trophic levels are (from lowest to highest): Primary Producer, Primary Consumer, Secondary Consumer, Tertiary Consumer, and Quaternary Consumer. There are not only different level Consumers, there are also different type of Consumers: Herbivores(plant eaters), Carnivores(meat eaters), Omnivore(everything eaters), and Detritivore/Decomposers (dead/decaying eaters). In comparison to Food Chains, Food Webs are more accurate and most of the animals in Food Webs eat more than 1 thing. Relating to Ecosystem Energy, we also learned about the transfer of Energy. We learned the Unit of Energy: Biomass, which is a method of measuring energy and is the total dry mass (weight) of organisms in a given area. Biomass is measured in calories (or Joules) and it's without water because water has no energy. The energy is stored in bands of cellulose; as consumers eat, they transform energy, passing on only 10% to the next level. Very little stays in the organism, 90% is lost as waste (such as heat). Energy being transformed is shown through Energy Pyramids. There is also the Population Pyramid which shows the effect of the 10% Rule: If only 10% of energy is passed on, less and less energy is available for top level consumers. This results in having fewer consumers and smaller populations at higher levels. Coming from the Population Pyramid, Population Ecology, the study of population relation to the environment, was also went through. It includes density, the # of individuals per unit area/volume, and dispersion, the pattern of spacing through individuals within bounds boundaries of population. There are also certain factors that affect population, including immigration, influence of new individuals from other areas, and emigration, which is movement leaving. Births and Deaths are also large factors that affect the population. There's also Exponential Growth, when there's lots of growth over a short time, which is something we humans are going through. In Ecosystem recycling, there is Succession, three types: Ecological succession, the sequence  of community and ecosystem changes after a disturbance, Primary succession, when succession begins with no soil to start with, and Secondary succession, which begins in an area where soil remains after a disturbance. In Succession, there's an order: it begins with Pioneer species to Intermediate species than finally to the Climax community. In an Ecosystem, the producers are critical, but they're also limited by the amount of nutrients they have. No nutrients mean no energy produced. And if there's no producers, then there's no carbon energy for life. Alongside with producers, decomposers are also critical. The four nutrients are Water, Carbon, Nitrogen, Phosphorous and without their cycles there wouldn't be any in the atmosphere. There's also the health of an Ecosystem, which includes it's loss (endangered/threatened species, mass extinctions, etc.) , it's gains (emigration, introduced/exotic species, etc),  and over exploitation and change in climate. Last and not least, we also learned how we could help the planet be better, by identifying the problem(s), solving/reducing the problem(s), and spreading awareness to everyone.

I don't think I have any unanswered questions but I would like to learn more about the different types of succession and I would like to see more examples regarding them. I wonder when our planet will become a disastrous place that we can no longer survive in and how it became to be that (if it was because of us).

The Conservation Biologist Project actually went better than I thought it was going to go. A lot of things went well: all my team members cooperated, we each completed our parts in time, and we each tried to help each other out as much as possible. There were barely, if not any, arguing and I think the collaboration went really well. I sincerely think that we all did a good job and nothing really went badly, except for some technical issues at the end. I didn't really learn anything, I think the main reason why the collaboration was so good was because we each were willing to put in as much effort as we can in this project. Through the self assessment test, I found out that my dominant conflict style is aggressiveness. When people are rude or sarcastic toward me, I tend to do it back. I also consider myself pretty heated since little things can easily aggravate me. I'm also super short-tempered and snappy when I'm under stress. In order to be more assertive, I need to be more direct and stop letting things I disagree with pass and let my voice be heard.

Unit 6 Reflection

In this unit, something we learned about was Biotechnology, the study and manipulation of livings things in order to benefit mankind, and how it applies to our lives. We learned that it was a large field that usually focuses on understanding of DNA, proteins, and inheritance. With these understandings, were its' 4 applications: Industrial and Environmental Biotechnology (ex: fermentation for food/beverages, biofuels, etc.), Agriculture Biotechnology (ex: Breeding of plants/animals, transgenic organisms, aquaculture), Medical/ Pharmaceutical Biotechnology (ex: medicines from plants. fungi. animals, etc.), and Diagnostic Research Biotechnology (ex: DNA identification for crime scenes and the compare and contrast of DNA for organisms). When learning about these applications and how they take place in my life I realized that they are constantly a part of my life, whether it's the medicine I take from plants or the GMO fruits that I eat. With Biotechnology comes Bioethics, the study of decision-making as it applies to moral decisions that have to be made due to advances in biology (such as biotechnology), medicine, and technology. We learned about the factors involved in making a bioethical decision: our moral (a conviction position, having to do with weather something is considered right or wrong) and our values ( what we see as important or moral; everyone's values are DIFFERENT). There are also steps to making a bioethical decision: how before deciding anything in Biotechnology you should identify the problem, think out the pros and cons, and so on so forth. Really, it's a lot like making a normal important decision. Another kind of technology we learned about was Recombinant DNA technology, rDNA, which is the insertion of DNA of one organism into the DNA of another. This is often described as genetic engineering. There are certain tools needed in order for this process to happen: the gene of interest, restriction enzymes (they cut the DNA if they read the specific sequence), plasmids, which contains the replication gene that tells the plasmid to be copied and has antibiotic resistance,  and ligase, the enzyme that finishes it all off by reattaching the base pairs. We also got familiar with the technologies of Biotechnology: Polymerase Chain Reaction (PCR), a procedure that yields millions of copies of a sequence of DNA, Gel Electrophoresis, using electricity to separate DNA fragments of known lengths, and Sequencing, the determination of the exact sequence, or order, of a given DNA strand using DNA polymerase, primers, extra bases, and florescent dyes. The last essential understanding to this unit was Bacterial Transformation, the process by which bacterial cells take up naked DNA molecules, and how we can use green fluorescent protein to identify the number of bacterial colonies, due to its' glowing under a UV light because of the arabonose that activates the gene. 

I'm proud to say that in this unit, for the most part, I understood what was going on and the concepts. Because of the emphasis we put on Gel Electrophoresis, I feel as if I have a true understanding for it and believe that it could be one of my strongest strengths in this unit. Another one of my strengths was Bioethics, since for that you only really needed logic to understand it, and Biotechnology and it's applications since I realized how much of a part it plays in my life. I also really understood rDNA and the restriction enzymes because of the lab we did in class, it really demonstrated the process and I feel pretty comfortable with the concept. Along with my strengths were my weaknesses. I had a hard time understanding the connection of Bacterial Transformation and pGLO. I don't fully understand how they relate and I don't really understand what happened in the pGLO lab. I also don't really understand what sequencing is and why it's an essential understanding in this unit since I feel as if we didn't really go over it since we mostly focused on Gel Electrophoresis. 

The labs that we did in this unit were the "Thinking Like a Biotechnican" lab http://lkbiologyblog.blogspot.com/2016/01/thinking-like-biotechnician.html , in which we made models of recombinant DNA,

the Candy Electrophoresis lab http://lkbiologyblog.blogspot.com/2016/01/candy-electrophoresis-lab.html , in which we got familiar with the process of Gel Electrophoresis, and the pGLO lab http://lkbiologyblog.blogspot.com/2016/01/pglo-lab.html , in which we transformed bacteria. From this, I've developed a deeper understanding about rDNA and its' tools and the process of Gel Electrophoresis, 

I would like to learn more about my unanswered questions: sequencing, since I can barely grasp what it is and I feel like we didn't go over it a lot, and Bacterial Transformation and it's connection to what we did in the pGLO lab. I wonder what these concepts are and I wonder if they are important in our lives and if so then how.

My goal to get a better grade in Biology this semester is slowly moving along. I think I've been making improvements and I'm very proud of them. So far I've been turning all my assignments in in time, except for the one previous virtual lab, and I've been really understanding how what's talked about in the vodcasts relate to what we do in the labs, other then the pGLO lab. Even though I'm slowly getting better, I still have a lot of things to work on. I haven't started reading ahead in the textbook and I'm still procrastinating a lot, even though I'm better at not procrastinating than before now. Procrastination has always been a bad habit for me so it's very hard to break now. My next steps regarding this goal will be to keep on turning assignments in in time, to continue observing the connection of the vodcasts and the labs, to start reading ahead in the textbook, and to fight the urge to procrastinate even harder. My second goal, to have a better sleep schedule, has been a complete wreck. My sleeping schedule right now is all over the place due to the fact that I still procrastinate too much, which leads to me staying up late at night or even pulling an all nighter, and that I take long naps during the day after school and only wake up at 9 PM or later. For this goal, my next steps will be to definitely stop procrastinating so much, that it leads to restless nights, and to stop taking such long naps after school. 

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 carpet Yellowish Tan Greenish Blue - pGLO LB/amp none + pGLO LB/amp 164 Yellowish Tan Greenish Blue + pGLO LB/amp/ara 59 Yellowish Tan Greenish Blue

2.	What two new traits do your transformed bacteria have?
	Two new traits my transformed bacteria have are ampicillin resistance and arabinose.
3.	Estimate how many bacteria were in the 100 uL of bacteria that you spread on each plate. Explain your logic.
	There were probably only one or two colonies of bacteria in the 100 uL of bacteria that was spread on each plate because when we got the bacteria with the lobe we only got a tiny amount of it.
4.	What is the role of arabinose in the plates?
	The role of arabinose in the plates was to activate the gene so that it could glow.
5.	List and briefly explain three current uses for GFP (green fluorescent protein) in research or applied science.
	In cellular biology, GFP has been used as: Reporter Gene (a gene that researchers attach to a regulatory sequence of another gene of interest in bacteria cell culture, animals or plants) Cell Maker Fusion Tag (a protein or a peptide located either on the C- or N- terminal of the target protein)
6.	Give an example of another application of genetic engineering.

Genetic engineering is also used in agriculture to create genetically-modified crops or genetically-modified organisms.

Candy Electrophoresis Lab

1) When analyzing the results of my gel, none of my experimental samples contained dyes that did not match the four reference dyes. There were no dye bands that were a different size than any of the reference bands, no dyes that were a complete different color than any of the reference bands, no more than one color band, and no dyes that were moving in the “wrong” direction. Both of the blue samples matched with the blue reference dye as moving the slowest, meaning they're also the longest strands. The yellow, orange, and red reference samples and dyes all traveled the same length in the gel. 2) Out of the four structures of the dyes pictured (Carminic acid, Betanin (beetroot red), Fast green FCF, and Citrus red 2), the dyes that would migrate similarly to the dyes I examined in this lab would be Citrus red 2 for the red, yellow, orange dyes and Betanin for the blue dye. Citrus red 2 would migrate similarly to the red, yellow, orange dyes because all their structures are alike, short, which means that they would all travel quickly. Betanin would migrate similarly to the blue dye because both their structures are alike, long(est), which would make them move slowly. 3) Dog food manufacturers put artificial food colors in dog food in order to make it look more appealing and "better" (tastier, healthier) to the the owners of the dog that are buying the food. 5) Two factors that control the distance the colored dye solutions migrate are the length (longer = travel more slowly; shorter = travel faster) and charge of the dyes. 6) The force that helps move the dyes through the gel is electricity. 7) The component of the electrophoresis system that causes the molecules to separate by size are the gel lanes and the electric current that runs through the gel because it's what causes how fast short structured dyes move and how slow long structured dyes move. 8) DNA molecules with molecular weights of 600, 1000, 2000, and 5000 Daltons would separate in this order: The DNA molecule weighing 600 would be the first one ahead (furthest from the wells), since it weights the least thus would be quickest, the 1000 Dalton DNA molecule would follow behind, which would also have the 2000 Dalton DNA molecule behind it, and lastly would be the 5000 Dalton DNA molecule (closest to the wells), since it weights the heaviest and thus would be the slowest.

Thinking Like a Biotechnician

Recombinant DNA, the process of the insertion of one organism's DNA into the DNA of another, requires a transformation. Restriction enzymes, bacterial enzymes that are major tools of recombinant DNA technology, recognizes a specific nucleotide sequence in DNA molecules, and cuts the backbones of the molecules at that sequence. In this experiment, the restriction enzyme I used was Eco RI because it made cuts close to the insulin gene, on both sides, and it could cut the plasmid and cell DNA. In this experiment, I chose a restriction enzyme that cut the plasmid in only one place but if it had cut the plasmid in two different places than the result would not be not just one fragment of DNA, but two fragments of DNA. After the restriction enzyme does its work, there then is a set of double-stranded DNA fragment with "sticky ends", single stranded ends. The bases of these single stranded ends easily form base pairs with the complementary bases on other DNA molecules. Therefore, these ends can be used to join DNA pieces that are from different sources. Using plasmids, small circular pieces of DNA found in bacteria, the recombinant DNA molecules can be made to replicate and function genetically within a cell. Small DNA fragments are inserted into the plasmids, then introduced into bacterial cells. As the bacteria reproduces, so do the recombinant plasmids, resulting a bacterial colony in which the foreign gene has been cloned. The antibiotic I would use in my petri dishes to see if bacteria have taken in my plasmid is kanamycin because it's the one that the plasmid had resistance to, which would help me identify the bacteria that had taken in my plasmid because the bacteria that hadn't would all be killed off. Anitbiotics that I wouldn't use would be tetracycline and ampicillin because the plasmid didn't have resistance to it, which wouldn't help me identify the bacteria that had taken in my plasmid because there would be none since all of them had been killed off. This technology could be important in everyday life because it lets us insert new genes into already there genes, which could be programmed to benefit us by making organisms/plants better or (more) beneficial to us. Some real life examples of this technology being used are pest resistant crops, vaccines, and transgenic animals.

New Year's Goals

My first goal for this semester is to get a better grade than the grade I got for Biology last semester. My plan to achieve this goal is to study earlier, procrastinate less, read ahead in the textbook, finish all the lab conclusions in time, and pay more attention to how the labs we do in class and what we learn from the vodcasts relate. My second goal for this semester is to have a better sleep schedule. My plan to achieve this goal is to not take long naps during the day, not procrastinate on homework and studying so that I don't have to sleep too late or pull an all nighter, and to try to sleep at a certain time every night so that my body gets used to it and it'll be easier for me to fall asleep.

Unit 5 Reflection

One of the essential understandings of Unit 5 was our Genetic Code: DNA = Deoxyribonucleic acid, its' Double Helix structure, the 3 parts of Nucleotides, how its' antiparallel, how the backbones run in opposite 5' to 3" directions from each other, the Nitrogen Bases and its' two types (Double rings: purines, Single rings: pyrimidines), the Base Pair Rules ("A" goes with "T", "G" goes with "C"), and its' function, which is a place of information for proteins. Another essential understanding was about how DNA is a copy machine: Semi-conservative Replication, which is the process of creating two identical strands of DNA from one strand, each resulting strand ending up with half of the original strand. "Walking the Dogma" was also a essential understanding in Unit 5. We learned about the structural differences between DNA and RNA, the functions of RNA (serves as temporary copy of a gene, delivers the copy to the ribosomes, and ribosomes using RNA to make proteins), Transcription (process where RNA Polymerase reads and copies the DNA code for a protein as mRNA copy) and Translation, which results in a protein. We also learned about Mutations, changes in the DNA code, Mutagon, anything that causes a mutation, point mutations, a change in 1 or 2 base pairs of DNA, when it's less and more harmful, the two type of point mutations, substitution and frameshift mutation, gene expression (process of a gene being used to produce a gene product or phenotype), and gene regulation (mechanism used by cells to increase or decrease the expression of a gene).

In this unit, my strengths were the Base Pair Rules and Transcription and Translation. I also believe that mutations were another strength of mine. For me, these topics were easy to understand and very interesting, I enjoyed going through the process of learning about these topics. I guess it was easy for me to understand them because I found them interesting, which made me eager to learn about them. I was very surprised by the fact that in this unit, I had few weaknesses. I still don't fully understand the whole antiparallel direction that our DNA goes in and memorizing the structural differences between DNA and RNA will definitely be hard for me. From these experiences, I didn't learn any new skills but I did learn a lot more about us human beings and what goes on inside us so yes I do believe that I'm a better student today than yesterday. I would like to learn more about our brain and how our emotions work. I don't have any unanswered questions about the topic that we've done but I really would like to learn about us mentally. I tend to wonder about what goes on inside our bodies that make us feel the certain emotions we feel and I think it would be interesting to learn about that. Last unit I took the Vark Questionnaire and since visual learning was supposedly one of my strong points, I decided to search up pictures that show the process of Transcription and Translation, since at first I was a bit confused about the processes. Once I had studied the drawings, the processes became a lot more clear and understandable for me, to the point where it became one of my strengths in this unit. I would say it went pretty well and that in the next unit, I'll definitely be doing more of that.