Unit 10 Reflection

Unit 10, the final unit of the year, was about physiology. We learned about the different organs and organ systems in the body, including the digestive system, circulatory and respiratory systems, immune system, lymph system, endocrine system, and nervous system.

The digestive system is responsible for breaking down food and absorbing the vitamins, minerals, fats, proteins, and carbohydrates. In the mouth, food is broken into smaller pieces, and the digestion of carbohydrates begins. Then food is swallowed, and is moved to the stomach in a process called peristalsis. While people usually think of the stomach when thinking of digestion, most of the digestion occurs in the first part of the small intestine called the duodenum. The small intestine is also where absorption occurs. The intestines are covered in small structures called villi, which absorb nutrients. The lining of the small intestine is folded to increase surface area and maximize the amount of villi. The villi are covered in microvilli, which also absorb nutrients. The large intestine absorbs water and gets rid of solid waste. Your digestive system is full of bacteria, which help to digest food and ferment indigestible food.

The duodenum

The nervous system is what sends signals all over your body. The two different parts of the nervous system are the central nervous system (CNS) and peripheral nervous system (PNS). The central nervous system is made of your brain and spine, and the peripheral nervous system is made of the nerves that spread throughout your body. There are four different parts of the brain. The cerebrum controls thoughts, movement, and emotion. The deincephalon works with the endocrine system and sends information to the cerebrum. The cerebellum  controls subconscious thoughts, determines body position, and calculates force of muscle movements. The spinal cord receives impulses from sensory neurons and sends signals to motor neurons. Neurons are specialized cells for sending and receiving signals. Sensory neurons carry signals from sensory organs like eyes, ears, and nose. Internuerons carry information from sensory neurons to motor neurons. Motor neurons send signals from the CNS to muscles and glands.

The endocrine system is like the nervous system, because it is used to send signals to other parts of the body, but the endocrine system does it more slowly and has longer lasting signals. Different glands in the body release hormones into the bloodstream, which cause changes to certain cells in the body. Some of the important glands are the hypothalamus gland, which links the pituitary gland and the nervous system. The pituitary gland controls the other glands. The thyroid gland absorbs iodine and regulates growth. On the thyroid gland are the parathyroids, which regulate calcium levels. The adrenal gland releases epinephrine, which controls the "fight or flight" response. The pancreas releases both insulin and glucagon to control blood sugar levels.

The circulatory and respiratory systems work together to bring oxygen to all the cells in the body so that they can perform cellular respiration and create energy in the form of ATP for the body. The diaphragm is the muscle that causes the lungs to expand and contract, which controls breathing. The oxygen inhaled diffuses into the bloodstream at the alveoli, and carbon dioxide also diffuses out of the bloodstream to be exhaled. Oxygenated blood flows through arteries, and when it is low in oxygen it flows through veins. Blood flows through the body, and then returns to the heart through two veins, the superior and inferior vena cava. Blood goes from the right atrium to the right ventricle, and then goes through the pulmonary artery to the lungs where it gets oxygen. The blood comes back in the pulmonary vein to the left atrium, then it goes to the left ventricle, and leaves for the rest of the body in the aorta.

The alveoli, where oxygen and carbon dioxide diffuse in and out of the capillaries

The next system we learned about is the immune system. The immune system has two methods to fight off pathogens, innate immunity and adaptive immunity. Innate immunity is a general defense that doesn't target any specific pathogen. The first part of this defense is the skin on the outside of out body, mucous membranes, and the acidity of certain parts of out bodies. After that come the internal defenses, such as phagocytes, which eat pathogens. Another type of cell is the natural killer cell. They kill pathogens or infected cells. After these defenses is the adaptive immunity. T and B cells are created with different antigens on them. If a certain antigen matches and kills the pathogen, copies of that cell are created to prevent getting infected by the same pathogen twice.

The final system we learned about is the lymph system, and inflammatory response. The lymph system collects waste and blood from tissues all over the body. The lymph nodes also create white blood cells when you get sick. The inflammatory response is how a body responds to pathogens, and is part of the innate immunity. The different types of inflammation are acute inflammation, which occurs at a single spot where a pathogen is, and systemic inflammation, which occurs throughout the whole body. In the small intestine, if things other than digested food get through the intestinal wall, it can cause systemic inflammation. Chronic systemic inflammation is when the body is constantly doing systemic inflammation, and makes it harder for the immune system to do its job.

Overall, this unit was easy to understand, and probably one of my favorites. If at all, I'll spend most of my time reviewing the lymph and endocrine systems. Other than that, I understand all the organs we learned about.

I'm sorry to disappoint the two people who actually read this blog, but this is going to be my final post, because the school year is about to come to a close. If this is your first time reading this blog, check out my best work here and here. I'm glad I got the chance to share my work with anyone who had to learn the same stuff, or who was just interested in it, and I hope enjoyed reading it.

20 Time Final Post

Well, 20% of my time in biology has come and gone, and a few days ago, we did this presentation you see here (I'm on the left). We encountered many difficulties, such as calculating radiation. Our final product was meant to be an infograph, but we ran short on time and didn't finish. If you want to see the unfinished infograph, check here. The fact that it is unfinished isn't important, what's important was what we accomplished. Overall, I believe we did very well on our presentation. We were both nervous, and stuttered a bit, but with the little rehearsal we got, we did a lot better than I thought we would. Our preparation was limited because we were unable to get together before the presentation. This was a great project that gave us an opportunity to learn what we wanted, and I just wish we had more time to work on it. If you want to see what my partner said about this project, check out his post here.

Unit 9 Reflection

Unit 9 was about taxonomy, and focused on the different domains and kingdoms, and some important phyla, mostly in the domain Eukarya.

Taxonomy is naming and classifying organisms. Organisms are named Genus species, with the first word capitalized and the second lowercase. The different levels of taxonomy (from largest to smallest) are domain, kingdom, phylum, class, order, family, genus, then species. The three major domains are Archaea, Bacteria, and Eukarya. The different kingdoms in the domain Eukarya are Protista, Fungi, Plantae, and Animalia.

Bacteria are prokaryotic unicellular organisms that come in rods, cones, and spirals. The cell walls contain peptidoglycan, which can be detected in a gram stain. Bacteria have flagella which help them move. Chemoheterotrophs take in organic molecules. Photoautotrophs do photosynthesis. Chemoautotrophs use energy from chemical reactions for energy. Obligate Aerobes need oxygen to survive. Obligate Anaerobes can't survive with oxygen. Facultative Anaerobes can survive with and without oxygen.

Fungi, which aren't plants, are multi-cellular, except for yeasts. Hyphae are long strands of fungi, and mycellium are underground hyphae. Sac fungi have a reproductive sac. Yeast fungi are single celled sac fungi. Club fungi have club shaped bodies. They can reproduce sexually, asexually, or both.

An example of Club Fungi

Plants first grew at the edge of water, and eventually were able to grow away from water. Some plants have a vascular system, meaning they can move resources throughout them. Some plant phyla include Bryophyta, which are non vascular, seedless plants, like moss. Pterophyta are seedless, vascular plants. Gymnosperms use cones to reproduce. Cycads look like palm trees, Ginkgo have only one remaining species, and conifers are the most common plant. Angiosperms are flowering plants, and produce seeds in fruit. An angiosperm can be a monocot, meaning it has a single seed leaf, or dicot, meaning it has a double seed leaf.

Invertebrates in the animal kingdom don't have vertebrates. Sponges, which are invertebrates, are the most primitive animals. Some phyla of invertebrates are Cnidarians, which have stinging cells, and two body forms, which are the Medusa and the Polyp. The classes of Cnidarians are Scyphozoans, Anthozoans, Hydrozoans, and Cubozoans. The phylum of Flatworms contains parasitic organisms with an incomplete digestive system. Molluska have a complete digestive tract, and either radula for feeding, a mantle, or a ctenidia, which is a respiratory system. Annelida are worms that have a segmented body, such as earthworms, marine worms, and leeches. Arthropods are some of the most diverse animals. They have an exoskeleton, jointed apendeges, segmented body pars, sensory organs, and an open circulatory system. Crustacea have two body sections, antennae, an exoskeleton, and a carapace, which is a hard outer shell. Echinoderms have an internal skeleton, a complete digestive system, and some can regenerate limbs. They also have a water vascular system, which uses water pressure to move.

Example of an Annelid

Vertebrates, or chordates, unlike invertebrates, do have backbones. There are seven classes of vertebrates. Agnatha were the first vertebrates, and the two remaining groups are lampreys and hagfish. Chondricthyes have cartilage skeletons, have jaws, and must move to breathe. Osteichtyes are have bone skeletons, and also have jaws. An important type of fish is the lobe finned fish. This fish evolved into all tetrapods. You can learn more about this fish in the presentation I did in my class. Amphibians are tetrapods that live both on land and in water. They also go through metamorphosis, such as tadpoles turning into frogs. Reptiles are ectotherms, which means that their body temperature is determined by the environment. Class aves, which are birds, have hollow bones. Finally, class mammalia are large brained endotherms, which means their temperature isn't controlled by the environment. They have hair mammary glands, and sensitive ears.

Overall, this is probably the hardest unit so far, just because of the massive amount of content covered in it. I will continue to study, and hopefully be able to remember every phylum.

My Inner Fish

We just finished watching the series, "Your Inner Fish." The series discussed the different features of modern mammals that came from fish and reptiles, and how the benefited us, such as hair, skin, bone structure, and hearing. There were many fossils that showed how certain features transitioned from reptile or fish to mammals, and there are some species that still show some of these transitions alive today. Like we learned in class, natural selection chooses the best traits to be passed down, and possibly create a new species. Two of the most important questions we were asked were, "Why are mass extinctions important?" and, "Why is the series called 'Your Inner Fish'?" Mass extinctions are extremely important. They cause many species to go extinct, which allows the surviving species to take their place, and allows new organisms to evolve. Without them, we wouldn't be here today. The name of the series may not seem as important, but it explains a lot. Because we have all evolved from fish, this helps to reveal that we have many similar traits with fish, but because of evolution and natural selection, we have become a whole new species.

Diagrams of different embryos showing how some of the similarities  between humans and fish

SQUIDS!!!

In the group of invertebrates, there is a certain phylum called the molluska, which is one of the phyla we are learning about in class. This phylum contains squids, including the largest squid, and also the largest invertebrate, is the colossal squid, also called Mesonychoteuthis hamiltoni. They are 12 to 14 meters in length, and can weigh up to 750 Kilograms. They also have the largest known eyes of any animal, being around 30 to 40 centimeters in diameter. They eat large fish and other small squids with their beaks, which are the largest of any squid, but Antarctic toothfish are a large part of their diet. They only need to eat about 30 grams per day, and have hooks on their tentacles. Colossal squids are a large part of the sperm whales' diet, making up 77% of their consumed biomass. They live about 1000 meters deep in the antarctic area.

http://marinebio.org/species.asp?id=247
https://en.wikipedia.org/wiki/Colossal_squid

Geological Timeline Reflection

We recently did a project where we created a timeline that represented the events that happened in Earth's history. This timeline went from the Hadean era to the present.

There were many important events over Earth's history, but some are more important than others. The three most important events are the creation of life, the mass extinctions, and the evolution of humans. It is rather self explanatory why the creation of life is important, because it led to every living thing on Earth. Life was created sometime during the Precambrian era, where the oldest prokaryotic fossils were found. It isn't known how life was created, but there are various theories and hypotheses, such as that the first amino acids came on a meteorite. Without life being created, the Earth would be a barren rock like some of the other planets. Like the creation of life, mass extinctions completely changed the Earth. They killed off lots of species, and caused new species to become dominant. In the Cretaceous period, half of plants and animals were killed off from a meteor. Humans may not have become the dominant species if this didn't happen. Humans have changed the Earth dramatically in the short time we have been here, which makes the evolution of our species one of the most important events in Earth's history. We have increased global temperatures, destroyed ecosystems, and are the cause of the next mass extinction. Without humans, none of this would have happened, and the planet would be in a lot better shape.

When we learned how long the Earth had existed, I had trouble picturing how long of a time it actually was. Most of the time on Earth was spent without life on it, and humans have been around for an extremely short time compared to the rest of Earth's history. What surprised me is how long Earth really has been around, about 4.6 billion years. This is a third of the universe's 13.7 billion year old existence. I found it interesting that the Earth was that old compared to the universe.

A diagram showing the events in Earth's history

As mentioned previously, humans have greatly impacted the Earth in the short time we have been here. We are causing the 6th mass extinction. We need to stop harming the planet, because even in the short time we have been here, we have drastically changed the Earth. For more detail on the issues facing the planet, check here. We have quickly become the dominant species on our planet, and have started changing other species to benefit us. We have bred animals to create different breeds, and we have genetically modified species to do many different things, like plants that are resistant to insects. A certain type of bacteria evolved to decompose plastic created by human activity. Despite the minuscule time we have been on the planet, we have changed a lot.

The only remaining questions that I have are ones that can't be answered. How was life created on Earth? If it came from a meteor, how was that life created? Someday, these questions may be answered, but we can only hypothesize until then.

Hunger Games Lab

In this lab we simulated different phenotypes of a population competing for food. The different phenotypes were "stumpy," "knuckler," and "pincher." The stumpy phenotypes could only pick up food with its wrists, the knuckler could only pick up food with the knuckles of its first and second fingers, and the pincher could only pick up food with it's thumb and first finger. It simulated natural selection, because traits that didn't allow the individual to collect more food died out.

The pincher phenotype was the best at picking up food. It was able to collect the most food with each grab, and was able to store it somewhere the quickest. The stumpy phenotype was unable to collect food well, and took a long time to store it. The knuckler phenotype was in the middle, not as slow as stumpy but not as fast as pincher.

We asked the question, "Do populations evolve?" We determined that the population did evolve. Evolution is defined as the change of allele frequency over time. The alleles we measured are the allele for how the individual can collect food. All alleles started off at about the same amount, but after one "year," the "a" allele frequency decreased dramatically, because all the stumpy phenotypes died. The allele frequency went from 48% A allele and 52% a allele to 31% A allele and 69% A allele. This was a change in allele frequency, so the population evolved. The allele frequency continued to change, so the population continued to evolve.

Allele Frequency Over 7 Years

In this lab, like in nature, some things were random, while others were not. The placement of food was random, sometimes spread evenly, sometimes in piles, and once all in the same spot. This made the survival random and linked to whether you were close to the food. Another random aspect was offspring. The alleles selected from offspring were a 50-50 chance. At the same time, offspring weren't random. You could choose your mate and possibly guarantee a certain phenotype, which increased the frequency of that allele.

The results of this lab would have been very different if the food was a different size. Making the food smaller would have made it a lot harder for the already struggling stumpy phenotype, and would have helped both knuckler and pincher phenotypes. Making the food larger would have helped the stumpy and pincher phenotypes, but would have immensely harmed the knuckler phenotype, causing a disruptive selection pattern.

If there was no incomplete dominance, meaning the knuckler phenotype wouldn't exist, then there would eventually be no more stumpy phenotype, and that means no more A allele. After one year, there was no more stumpy phenotype, and if there was no incomplete dominance, then any individual with the A allele would be a stumpy, and then die.

Natural selection lets the best phenotypes survive, and makes them more common, which changes the allele frequency. Because the allele frequency is what determines if a species evolves, that means natural selection causes evolution.

There were many different strategies to increase survival and reproduction. One was to go where there was the least competition, so no one would steal food. Another was to have easy storage for food, like the hood of a hoodie sweater. Another strategy was cheating and not using the phenotype they had. Because everyone had access to at least one of these strategies, it meant that whoever had an advantage no one else had would survive, and the pinchers had that advantage. In nature, the species with the best phenotype will win, but the strategies don't get passed down unless they are genetic. This means that if someone is very aggressive in food collection, their offspring might not be.

In evolution, populations evolve, not individuals, because individuals can't change their genotype. Natural selection acts on the phenotype of an individual, deciding whether it will survive or not. This is because the phenotype is the physical thing that helps or harms the organism, not the genotype.

Bird Beak Lab Conclusion

In this lab, we simulated different types of bird beaks with tweezers, binder clips, spoons, and scissors, and attempted to collect food, which we represented with rubber bands, toothpicks, paper clips, and macaroni, and the amount we collected determined how many offspring we had each year. The first simulation was normal, but then we had an environmental change to make collecting food different. Out environmental change was that we only had 10 seconds to collect food.
We verified that the individuals with the better traits would have more offspring. The tweezer beak was able to collect the most food, and therefore had the most offspring, 22 compared to 8 offspring from the spoon beak, 11 from the binder clip beak, and 15 from the scissor beak. This also verifies our second claim, which is that populations begin to look more like the "winners," or the most successful genotype. At the beginning, we were the only four birds, so tweezer beaked birds made up 25% of the population, or 1 out of 4. After several years, and several offspring, there were 22 out of 56 total offspring, making 39% of the population tweezer beaks, which is more than any other type of beak. This happened because the tweezer beak was able to collect food more effectively than the other beak phenotypes, so had the most offspring. The other birds had less offspring, so the tweezer beak made up more of the population.

After testing Darwin's conclusions, we asked what would happen if a disease affected the species. To simulate them having less energy, we reduced the time to collect food to 10 seconds. We found that with less time, all phenotypes produced less offspring, but tweezers and scissors produced the most. This is because the disease affected everyone equally, so all phenotypes collected less food.

While we tried to make this lab accurate, we did have some errors. We had different people collecting food with the different beaks at the same time. This means that someone may have been better at collecting food than someone else, making the data lean towards whoever was best at collecting, not necessarily what beak was best at collecting. We could have solved this by rotating beaks and having each person try out each beak. Another error we had was that the scissors were slightly magnetic. This made the collection of paper clips slightly easier, and some of the contact between the tweezers made them very slightly magnetic, but that made no difference because the attraction was so weak. This error could have been prevented by testing all metal "beaks" against each other to see if they were magnetic.

This lab was done to demonstrate how evolution can take place over a short period of time. From this lab I learned how Darwin's conclusions affect species with different phenotypes, which helps me understand the process of natural selection. Based on my experience from this lab, I could artificially select certain traits from a population to make a specific type of organism.

Unit 7 Reflection

Unit 7 was about different ecosystems and the threats facing them. It was also about how populations and ecosystems change over time.

There are several levels of organization in the environment. The biosphere is the entire Earth, and all the ecosystems in it. Biomes are large sections of the Earth made of ecosystems. Ecosystems are the biotic and abiotic factors that work together. Communities are collections of populations. A populations is several organisms of the same species. And an organism is a single living thing. Organisms have different habitats and niches. A habitat is where an organism lives, and a niche is what it needs to survive.

Organisms are sorted into food webs, which can be simplified into food webs. They both show how energy is transferred in an ecosystem. The levels of organization are the primary producer, which is eaten by the primary consumer, eaten by secondary consumers, eaten by tertiary consumer, and eaten by quaternary consumers. If an organism is removed, then all organisms above it on the food chain will decrease in populations. If the top consumer is removed, then it will be an alternating effect of organisms decreasing and increasing. When an organism is eaten, about 10% of the energy is transferred. Energy is measured in biomass, or the amount of dry mass in an organism. Because of this, populations are smaller at higher levels on the food chain.

Populations grow and shrink because of births, deaths, immigration, and emigration. There are two types of growth in populations, exponential growth, were a population grows above the carrying capacity, and logistic growth, where it grow until the carrying capacity. Some populations depend other populations for food, so grow and shrink with them. The human population is growing rapidly, and the carrying capacity is estimated to be around 10 to 15 billion.

After a big disturbance, ecosystems can still continue in succession. Primary succession is when there is no soil for life to start in, and secondary succession is when there is soil for life to start in. The order of succession is pioneer species, which are the first species after a disturbance, intermediate species, which come after pioneer species, and then the climax community, which is when there are many different populations.

Pioneer species in primary succession, probably after a volcano eruption.

There are several different nutrient cycles that are necessary for life. The water cycle involves water evaporating, precipitating, and being used by organisms. The carbon cycle involves carbon being absorbed from the atmosphere by plants, and then animals breathe CO2 back into the air. The nitrogen cycle involves bacteria converting nitrogen gas into nitrates, which are used by plants. Some bacteria break down nitrogen from dead organisms. And some bacteria break down nitrates into nitrogen gas. The phosphorous cycle involves the fungus Mycorrhizae making phosphorous available to its host from the soil.

A diagram explaining the water cycle

Many ecosystems are being threatened due to an increase in extinctions. We may be in a 6th mass extinction. Many plants contain substances that can be used in prescriptions, so if they go extinct, we won't be able to get them. Many organisms help sustain human life, like bacteria decomposing things, and plants converting CO2 to Oxygen. The causes of these extinctions are farming, development, introduced species, over exploitation, and climate change. There are things we can do to help protect the environment. We can identify and protect hot spots, or areas with high biodiversity, conserve all natural habitats we still have, plan smart to make it easier for species to move, like using movement corridors, restore areas by beginning succession, and build in a way where we take up as little natural habitat as possible.

Each group in our class did a project on a threatened ecosystem, and our group chose the Arctic, facing many problems, such as climate change and companies that want to drill oil there. Possibilities of oil spills increase with planned tourism, and over fishing might also become an issue. This project went very well, and was somewhat fun to make, because we didn't have many restrictions on what to do. You can find our presentation here: https://www.youtube.com/watch?v=0nbgHaA6szk.

Overall, I understood unit 7 very well, and learned how grave the problems facing the planet really are. The sections I need to review are the nutrient cycles and the different phases of succession, because I looked at my notes when writing those parts.

Unit 6 Reflection

Unit 6 was about biotech and its various applications. It involves changing the living world by manipulating the DNA of living organisms. There are four applications of biotech, industrial, agricultural, diagnostic, and medical.

Some biotech practices are controversial, and that brings up some people's bioethics, which is what they feel is wrong and right in the biotech field. If faced with ha bioethical question, one should consider the pros and cons of each side, and try to come up with another solution if they can.

One type of biotech is recombinant DNA, which is DNA that has been altered. To do this, you need the gene that you want to insert, a restriction enzyme to cut the gene out of the DNA, and to cut the plasmid once, which is another thing you need, and you need ligase, which reattaches the genes. Recombinant DNA can be used to make large amounts of a protein like insulin. First you put the gene of interest into the organism, get a plasmid, digest the DNA, then add ligase to reattach them, mix the recombinant plasmid with the bacteria, grow the bacteria on a plate with the antibiotic it is naturally resistant to, and then extract and purify the protein, according to my notes.

Some other technologies of biotech are polymerase chain reaction, gel electrophoresis, and DNA sequencing. Polymerase chain reactions are used to make lots of copies of DNA. To do this, you need a strand of DNA that you want to duplicate, and you must denature it with heat, then add primers above and below the region of interest, and then you use DNA polymerase to extend the primers, according to my notes. Gel electrophoresis is used to identify the approximate length of strands of DNA. DNA is put into wells at the end of a gel, and a current is run through it, and the DNA is drawn towards the positive charge. Known DNA strands are used as a template to measure the length. Sequencing is determining the sequence of DNA. Special bases with dyes attached are used do replicate the DNA strand one base at a time. Then a computer analyzes it to find the order of the base pairs.

The set-up for gel electrophoresis

We did a lab on recombinant DNA in E. Coli bacteria, which you can find here: http://markbiologyblog.blogspot.com/2016/01/pglo-lab.html
to summarize what we did, we added modified plasmids to E. Coli bacteria that made them glow green when in contact with arabanose sugar, and let the multiply.

Mice modified to glow due to the pGLO gene. It is sometimes used as an indicator to make sure that a gene was taken in by an organism.

pGLO Lab

In this lab, we inserted modified DNA into E.Coli bacteria, which put the DNA into the plasmid, to make them resistant to the antibiotic ampicillin and glow green under UV light. Each plate started out with 100 micro liters of bacteria, which is about 90 bacteria per plate, because each one is about 2 micrometers long. The bacteria multiplied, resulting in many more. One of the plates contained arabinose, which attached to the promoter on the DNA and allowed the protein green fluorescent protein to be made. There are various uses of GFP. It can be used as an indicator for other transformed organisms by attaching it to the gene you are trying to insert into an organism. It is also used to study the growth of cancer in mice, as well as other diseases, such as blindness is dogs. GFP is also used to track fruit fly sperm to see how sex cells maximize their chances of fertility. There are many other ways to genetically modify organisms, such as making crops resistant to herbicides and parasites.

Plate	# of Colonies	Color: Room Light	Color: UV Light
-pGLO LB	carpeted	gray	gray
-pGLO LB/amp	0	nothing	nothing
+pGLO LB/amp	104	gray	gray
+pGLO LB/amp/ara	64 + partial carpet	gray	neon green

Upper Left: no pGLO gene with LB (helps bacteria grow).
Upper Right: no pGLO gene with ampicillin and LB.
Bottom Left: pGLO gene with ampicillin, LB, and arabinose sugar
Bottom Right: pGLO gene with ampicillin and LB

The transformed E. Coli glowing under a UV light.

Candy Electrophoresis Lab

In this lab, we ran dyes from different candies through the process of electrophoresis. The bands of our dyes were fairly normal, all dyes moving in the correct direction. Some bands left a trail behind them, the orange one on the far right leaving a blue trail. One dye that might move like this is fast green FCF, because many parts of it are negatively charged, like these dyes. Some dog foods and treats. contain dyes. I think this is because in nature, some colors symbolize something can be poisonous, like brightly colored animals, so the food is colored in a way that it won't be seen as poisonous. Artificial food colors could be preferred over natural food colors because natural food colors may affect the taste of what is being dyed, while artificial dyes can be engineered to have little to no flavor. There is also no foods that are naturally blue, even blueberries, which are a dark purple. Some dyes migrated farther than others, which is caused by the size of the molecule, and the strength of the charge. Smaller molecules, like the yellow gel, move faster, and also more strongly charged molecules are more attracted to the positive charge coming from the current, which is what makes the dye molecules move at all. The larger molecules move more slowly through the dye, such as the two blue colored dyes in the gel. The process of electrophoresis is commonly used to separate different lengths of DNA. If a DNA molecule had a weight of 600 daltons, it would go a lot farther than a DNA strand with a weight of 1,000 daltons, because it is a bigger molecule. If it had 2,000 daltons it would go even slower, and if it had 5,000 daltons, all the other molecules would move much farther.

Recombinant DNA Lab Summary

In this lab, we simulated creating recombinant DNA. Recombinant DNA is DNA from one organism that is inserted into the DNA of another organism. DNA is usually inserted into the plasmid of a bacteria. To do this, you need to gene you want to insert, the bacteria, and the antibiotic it is resistant to, a restriction enzyme, and the enzyme ligase. The restriction enzyme you need has to be an enzyme that matches the restriction site. We used the enzyme Hpa II, because it cut the plasmid once, and it cut the insulin gene above and below the gene as close to the gene as possible. It should only cut the plasmid once, because if it cut it twice, then the plasmid would turn into 2 separate pieces of DNA. When the DNA is cut, it will create sticky ends which can attach to the sticky ends of the other piece of DNA.

Sticky Ends on a sequence of DNA.

The enzyme ligase attaches the sticky ends of the gene to the sticky ends of the plasmid to make the plasmid a circle again. After you re-insert the new plasmid into the bacteria, you put it in a petri dish with the antibiotic it is resistant to, in our simulation, out bacteria was resistant to the antibiotic tetracycline. This ensures that the only bacteria  in the dish is the one that you put the recombinant DNA into. The bacteria will multiply, and all the bacteria will have the gene and create insulin. This is how insulin is created for people with diabetes. Recombinant DNA has also been used to make certain fish glow, and is a part of many other parts of our lives, such as being in many foods we eat. Many crops are resistant to herbicides and insects, which comes from recombinant DNA. Scientists have recently found a way to create self healing materials from jellyfish DNA.

Goals For 2016

This year, I will write better relate and reviews for vodcasts and chapter notes. To do this, I will go back to older vodcasts and see what I left out of the relate and reviews that is important. Then I will write all important information in the R&R, while leaving out the less important details, making them more informative and concise. I will know I have completed this when I can study for a test using only R&Rs and understand everything I need to know.

I will also make better food from leftovers in my kitchen. Whenever I make lunch, it usually involves me taking random things out of the refrigerator and putting them into a sandwich. I will start making more creative and tasty things from the leftovers without having to prepare anything apart from using the microwave. I will do this by trying new things that and choosing different methods of making them into a meal that isn't just a pile of food. I will know my goal is complete when I no longer get stumped of what to have for lunch when looking in the refrigerator.