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.

Unit 5 Reflection

Unit 5 was about protein synthesis, mutations, and how genes are regulated.

For this section, I had to look into my notes, but only to see how to spell some words so that doesn't count! Protein synthesis is how proteins are created from DNA. RNA polymerase makes a copy of the DNA, which is deoxyribose nucleic acid. DNA is made from a sugar, the deoxyribose, a phosphate group, and a nitrogen base, which can be either Adenine, Thymine, Guanine, or Cytosine. DNA has two strands, and twists into a double helix shape, with bases matching together. The bases match with each other, Cytosine with Guanine, and Adenine with Thymine. The copy is called RNA, which is very similar, except Thymine is replaced with Uracil, and it is single stranded instead of double stranded. This is messenger RNA. It goes out of the nucleus and to a ribosome, where it is read. Each codon, which is 3 bases, codes for one amino acid. An amino acid can be coded for by several different codons. Transfer RNA brings the amino acid to the ribosome to build the protein, and matching base pairs for the messenger RNA.


Mutations are changes in DNA. They can be deadly, or do nothing at all, which is called a silent mutation. One type of mutation is a point mutation, where a single base pair is changed. One type of point mutation is a substitution, where one base pair is substituted for another one. This type of mutation causes little to no damage, because some amino acids can be coded for in several ways, and if it does change the amino acid, it only changes one of them, which will have a small effect. The other type of point mutation is a frameshift mutation, where one base pair is added or removed. This has a large effect, and can completely ruin a protein because  in addition to changing the current codon, it shifts over all following codons, which can cause a completely different protein to be made, or cause no protein to be made at all. There are other mutations that aren't point mutations, such as inversions, which cause a piece of DNA to become unattached, and reattach backwards. Translocations are when DNA from one chromosomes attaches to a different chromosome. Mutations are caused by mutagens, such as UV, (checks notes for other mutagens) nuclear radiation, X-rays, and toxins(closes notebook).

Example of a mutation.

Gene regulation was probably the most complex part of the unit, so I will obviously be referring to my notes for this paragraph. All cells have DNA for all genes, but they don't express all genes at all times because cells don't want to waste energy by over expressing genes. A group of genes that work together is called an operon. A good example of gene regulation is the Lac Operon. The RNA attaches to the part of the DNA called the operator, and copies the gene from there. But, in Lac Operon, there is a repressor, which is like a road block, attached to the promoter. The repressor is removed when lactose appears, and attaches to it. Then, the gene can be read to create the enzyme lactase, which breaks down lactose for food. In eukaryotes, the process is more complex, and several proteins can bind before a gene. After RNA copies a gene, sections called introns, which don't code for anything, are cut out, leaving the exons, which are expressed.

1: RNA polymerase. 2: Repressor. 3: Operator. 4: Promoter. 5: Lactose

That's all we covered in unit 5. The only part I really need to study is gene regulation, and the spellings of thymine, adenine, guanine, and cytosine.