Translation: The Three-act Play

Initiation

Act 1: Initiation

• The mRNA comes to the cytoplasm, with a starting condon, which is  AUG, on it.
• A small ribosomal subunit binds with mRNA.
• A tRNA (transfer RNA) carrying a specific amino acid, Met, at one end and having a specific nucleotide triplet, anticodon UAC, at the other end comes to bind with the starting codon.
• Initiation factors brings the large ribosomal subunit to mRNA, placing the tRNA in the P site.

Elongation

Act 2: Elongation

• Another tRNA carrying amino acid recognizes its corresponding condon at the A site.
• An RNA molecule catalyzes the formation of a peptide bond between the polypeptide in the P site withe the new amino acid in the A site.
• The polypeptide chain is transferred to the tRNA at the A site. 
• The ribosome moves the tRNA with the attached poplypeptide form the A site to the P site. This process need energy provided by GTP.
• The first tRNA enters the E site, and as the third tRNA attaches to the A site, it exits the E site to the cytoplasm to pick another amino acid.
• The process keeps going on.

Termination

Act 3: Termination

• When one of the three stop condons(UAG, UAA and UGA) reaches the A site, a release factor cut the bond between the polypeptide chain and its tRNA at the P site.
• Polypeptide, which is known as protein, is released.
• Translation complex disassembles.

Transcription: The Three-act Play

Overview
(from http://www.mun.ca/biology/desmid/brian/BIOL2060/BIOL2060-21/CB21.html)

ACT 1: Initiation

• Transcription factors recognize the promotor, TATA box, in the template strand of DNA, and bind to it.
• The template strand is also called antisense; the other strand, coding strand, is also called the sense.
• RNA polymerase II binds to transcription factors to form a transcription initiation complex, transcription begins.

ACT 2: Elongation

• RNA polymerase II unwinds the double helix.
• RNA polymerase II adds the complimentary nucleotides to the 3' end of the growing strand.
• When adding the complimentary nucleotides to the RNA transcript, every thymine is replaced by uracil.
• As RNA polymerase II moves forward, the double helix behind re-forms, and the newly transcribed RNA molecule, RNA transcript, peels away.
• Many RNA polymerase II can work on a single DNA simultaneously.

ACT 3: Termination

• When RNA polymerase II transcribes a terminator, AAUAAA, transcription stops.
• The pre-mRNA is cut, and RNA polymerase II is released from the DNA.
• In eukaryotic cells, before the mRNA enter the cytoplasm, enzymes work on modifying them.
• G-cap (modified guanine) is added to the 5' end of pre-mRNA.
• PolyA-tail is added to the 3' end of pre-mRNA.
• Pre-mRNA combines with snRNPs and other proteins to form a spliceosome.
• The snRNA in the snRNPs base pair with nucleotides at the ends of the noncoding segments on the pre-mRNA, introns.
• Introns are excised from the pre-mRNA, then, the coding regions, exons, are spliced together in the spliceosome.
• The snRNA acts as a ribozyme, and the RNA acts as an enzyme.
• The spliceosome comes apart, releasing mRNA.

DNA Replication: The Three-act Play

Overview
(from http://www.teacherweb.com/CA/NogalesHighSchool/mespinoza/h4.aspx)

ACT 1: Initiation

• Single-strand binding proteins enter to stabilize the template strands, keeping them apart during replication.
• Helicases unwind the template DNA strands. They keep working at the replication fork to continuously open up the bubbles. 
• To release the tension, as the bubbles opening up, gyrases cut the DNA, afterwards, put it back.

ACT 2: Elongation

• RNA primase enzymes begin the process by building a small complementary RNA segment called RNA primers to the origin of the strand, therefore, DNA polymerase III can add DNA nucleotides to the RNA primer. 
• Nucleotides on the daughter strand can only elongate in 5' to 3' direction. This strand is called leading strand.
• On the opposite strand, which is called lagging strand, DNA polymerase III is moving away from the replication fork.
• On lagging strand, okazaki fragments are formed with series of RNA primers and short DNA fragments added by DNA polymerase III.

ACT 3: Termination

• DNA polymerase I enter. They remove the RNA nucleotides at the primers with DNA nucleotides.
• DNA ligase catalyzes the reaction of  forming bonds between short DNA strands on the lagging strand.
• DNA polymerase I proofread the daughter DNA.

Photosynthesis and Cellular Respiration

On Friday's class we were divided into groups to present the processes of photosynthesis and cellular respiration by creating some 3D models on chart papers.

Photosynthesis
Here is what happens during photosynthesis.

Cyclic Light Dependent Reaction

Non-cyclic Light Dependent Reaction

Calvin Cycle

From photosynthesis, glucose is synthesized and energy is stored. This kind of reactions are called anabolism.

Cellular Respiration

Glycolysis

Crebs Cycle

Electron Transportation Chain

The above shows the reactions which break down the glucose and release the energy. This kind of reactions is called catabolism.

To sum up, these two kinds of reactions, which is anabolism and catabolism, combine and form the overall metabolic processes in organisms.

A Story from ROM

On Friday, we went to the Royal Ontario Museum(ROM) for a field trip in the afternoon, after the lectures in the morning by two great and price-winning biologists in U of T.

Here is one of the stories I heard and found significant in ROM.

Passenger Pigeons

The three birds in the picture above cannot be seen flying in the sky any more. They are pigeons, but they are called passenger pigeons and are extinct.

The passenger pigeon was once the most abundant bird in North America. They are migratory and gregarious birds. People  used to see them flying with enormous amount of companions during migrating seasons. There is a record of people in Ontario seeing about 3 billion of passenger pigeons passing in the sky in spring, and they were described to "darken the sun", causing a lot of panic within folks.

Passenger pigeons live and can only live in large groups with at least thousands of companions. This is because they cannot protect themselves from the enemies. Therefore, in order to survive the predation, they hide in flocks to reduce the chance of being attacked.

There are two main factors contributing to the extinction of passenger pigeons, but they are all caused by humans. 

The first factor was over hunting. Because there were once billions of them flying by, people can't avoid noticing the appearance of an excellent source of food. They are always in large groups, so people can easily find them and either capture or kill them. It is on the record that the amount of hunting passenger pigeons in one specific forest was 5 thousand a day, and it kept going in the same way everyday within 5 months. Because they can only survive in large groups, once the great reduction of population occurs, the rest of them will die rapidly.

The second factor contributing to extinction was reduction of woods which they nested. During that time(around the beginning of the 20th century), a mass of forests was cut down  by people to become the farmlands. This is terrible because the passenger pigeons therefore lose both their shelter and food source(although they fertilize the land, no one wants pigeons to eat all his corps). 

The two factors worked together, and only in the 1914, the last passenger pigeon known died in a zoo. This is a sad and warning story to human------ a species once had an enormous amount of population can die out within a few years. Now that the fact is dreadful, only few people known about this story. This probably makes the story even sadder. 

Ten points from ETC

Above is the diagram illustrating how ETC(electron transport chain) works.

And below is my ten points concluded from the lecture(role playing).

1. PSⅡ and PSⅠ both need to absorb light in order to excite the electron, which is gained from water, and transport it.
2. The pathway of electron throughout the process is water -----> PSⅡ-----> PQ-----> b6f-----> PSⅠ-----> Fd------> FNR------> NADP
3. Two hydrogen ions was released when the water break down outside the  PSⅡ. Hydrogen ions also enter PQ to form PQH2. To form the neutral NADPH, hydrogen ion enters to play the role to balance the electron. Large amount of hydrogen ions go through the ATP synthase to slow down its spinning motion in order to form ATP.
4. The process of breaking down molecules by light is called photolysis.
5. Gaining electron of a molecule is called oxidation; losing electron of a molecule is called reduction.
6. Chemiosmosis is the movement of chemicals from high concentration to low concentration through a  selectively permeable membrane. The process of releasing ATP is chemiosmosis.
7. The one help to make ATP is called ATP synthase.
8. It is important that the oxygen leave the water molecule at the beginning, because it will come back again.
9. ETC happens in thylakoid lumen.
10. When the spinning motion of ATP synthase slows down by hygogen, a phosphate come to take away the ADP which has two phosphate atoms in it and from ATP which has three phosphate atoms in it.

Pig Dissection

We did a dissection on fetal pigs on Wednesday and Thursday. Here is a record of what we did and what we found out in the lab.

Wednesday was our first day to dissect the pig. Honestly speaking, it was my first time to dissect an animal, and it was even more interesting than I imagined. As an non-experienced dissector, I felt lucky and glad to learn the anatomy and gain both the knowledge and practical experience at the same time.

Our group got the smallest pig, but it wasn't lack of anything. Here is the overview of our result in the first day.

After we got our pig, the first thing to do was to examine its gender. Because there was a urogenital opening at the lower body, we believed it was a female, which was proved by the two ovaries we found.

ovary

After cutting the lower body open, we first isolated the liver in the middle.

liver

Then we got the small and large intestine, spleen and stomach.

small and large intestine

stomach

spleen

We isolated the two kidneys from deeper at the two sides of top of the intestine. They were cut both cut into half accidentally, and we saw the difference between medulla and cortex.

kidney

On the second day, Thursday, we began to dissect the upper body , including the brain, of the same pig.

When we open the upper body, we saw the heart was surrounded by the two lungs at back.

heart

lungs(shaped like to embrace the heart)

Then we got to work on the brain. To get the brain out, we needed first to open the very hard skull which had the job to protect the brain inside. We tried to cut from the top middle side of the skull carefully, but it was difficult to control the intensity to ensure the skull can be widely opened and the brain was not injured at the same time.

At last, we just got the mushy brain like this(probably because our pig is immature).

brain

There is the brain from the group which successfully got the one.

what the brain should look like

Finally, we also get one eyeball out. It was a tiny round ball in front of the brain.

This experience of dissection is fun, unique and also informative for me. By dissecting the body of fetal pig, I practically see what the organs look like and where they are. I think this is more meaningful because the organs in pig are quite similar to human.

The Story of Stuff: A Critical Analysis

2.What audience do you believe Annie Leonard is trying to reach?
I think Annie is trying to reach common people or consumers, especially in developed countries like the US.

4.Why do you think Annie Uses the format of a 20-minute video rather than another format, such as report, web blog, or poster?
I think the reason why she uses the 20-minute video is this format is interesting, approachable, and informative at the same time. Nowadays, many people may not have the interest and time to read a word report or a long poster so a video attracts more people. And the images in the video vividly give people the idea of what Annie is trying to illustrate.

6.Who might disagree with Annie's message? Why do you think they would disagree?
I think the economists and some people from the government might disagree with Annie's message because the rapid consumption does contribute to the growth of global economy and therefore help to  stabilize the world's political situation. People can't live on the level of living quality right now they have without a developed economy and safe political environment. And some scientists may doubt the possibility of the cycle of the whole system she proposed in the end of the video for various scientific reasons, such as some chemical changes are irreversible.

8.Has The Story of Stuff affected the way you think about consumption? If so, how?
The story of stuff makes realize I need to choose to consume the goods that could last longer. Before I may think people are free to buy any fashionable products they want and throw away the rest. After watching the video, I agree that buying "design- to- dump" products is helping some business man earning money on the cost of our planet.

Video Worksheet: The Cove

2.Where is the dolphin slaughter taking place(city and country)
In the documentary, the slaughter is taken place in Taiji, Japan.

4.What is the turning point in his life that makes him completely change and "turn his Porsches in for this crusade"?
When he was working for the  popular American TV show Flippers, the dolphin Cathy, who played Flipper most of the time, died in his arms, making him realize that this kind of animal should not suffer this stress any more.

6.What country indirectly runs the International Whaling Commission?
The IWC is indirectly ran by Japan.

8.How do the fishermen trap the dolphins in the cove?
The fishermen gather together to hunt for dolphins in the ocean, then they surround them and push them to the cove, where they can drop the nets and trap the dolphins.

10.How many dolphins are killed at this secret cove a year?
23000 dolphins are killed a year.

12.What toxic substance is found in dolphin meat?
The toxic substance is mercury.

14.Dolphin meat has 2000 ppm of mercury in it while the recommended amount is no more than 0.4 ppm. Why do many Japanese people eat then?
They are unaware of the danger they are taking and they do this under the permission of the government.

16.The number of fish is severely declining. What is the cause?
The large consumption of fish makes people over-hunting fish.

18.What is the form of propaganda they plan to use to "sell" dolphin meat to people?
They provide the compulsory lunch which includes dolphin meat to children,

20.The main character goes to the IWC and does what at the end(even though he is banned from their meetings)?
He showed the video taken secretly about the inhumane scene of fishermen in Taiji slaughtering dolphins in the cove.

22.When was whaling banned?
In 1986.

Dry Lab: Mark-Recapture Sampling

On Friday we did a dry lab, and here is what we have done and some analysis.

The purpose of this lab is using mark-recapture method to estimate the population of the pasta in a bag just to model how wildlife researchers did when they estimated the size of population in surveyed area.

Here is the materials we used. A package of macaroni and some colorful markers.

The first step of this lab was to "capture " a sample of population from the bag.

For calculation, we also recorded the number of this sample of population(M), which is 31.

Then we used the marker to mark the captured population.

For the first trial, we chose purple.

Making sure our way of marking is recognizable.（We colored the whole thing.）

After that, we released the captured population(M) back to the bag, and kept shaking it until they were randomly mixed with the general population.

Then, we took a second random sample of pasta(n) and recorded how many of them were marked(m). The data n and m were also written down for calculation which was 4 and 76.

Finally, we were able to calculate the estimated population size of the general population(N) using out recorded data M, m and n.

Here is the details of our calculation.

We used the formula of mark-recapture method.

number of individuals caught & marked in first sample(M) 

                           total population size(N)

 =   number of marked individuals recaptured(m)

total number in second sample(n)

To get the value of N, the formula can be transformed as 

N=(Mn)/m

Due to our data recorded, the calculation would be 

N=(31*76)/4

N=589

After this, we did another 2 trials in the same way, and got the N value of 1334 and 413.

Analysis

1.Compare your estimate of the size of the pasta population with the true size. How close were you?

We counted the real number of the general population as the theoretical value.The formula is shown:

theoretical value - experimental value  *100%  

               theoretical value

={721-[(589+1334+413)/3]}/721

=8%

100%-8%=92%

Therefore we have 92% of accuracy.

2.a) What problems do you think might affect the accuracy of your estimate?

The problems may include the unevenness of mixing pastas, so there would be a large chance that having more or less marked pasta in the second sample population than it should have due to the ratio.So 3 trials may not provide the number fairly enough.  Another problem is our group might have dropped some of pasta when grabbing the sample population so it can affect the accuracy of data collected, but this one is the problem that can be avoided.

b)This activity was not completely valid in that the population was non-mobile.What problems might ecologists studying animal populations encounter?

When it comes to the real animal world, the way of marking can be a problem because the animals are able to move under their own wills and try to wash the color or take away other marks. The variables in natural environment are relatively harder to control. For example, there can be natural disasters and diseases. Besides, there will be a problem of mixing if the type of animal is non-mobile because the sample population will basically remain as a population and tend not to mix with the general population.

3.How might you improve your sampling design?

To improve the sampling design, I will add more trials to provide more data in order to minimize the problem of unevenness. The size of the second captured population should be larger to offset the contingency of re-capture.( And the markers should be more suitable for coloring on pasta and more washable on hands.)