The Purpose (Protein)- Translation

Act I: Initiation:
The large and small ribososomal subunits binds to the 5' cap of a mRNA molecule and scans it until it reaches the AUG start codon (which corresponds to the amino acid methionine). Then the 1st aminoacyl-tRNA(the indicator methionine-tRNA) binds to the start codon in the P site.
Act II: Elongation:
1. Another tRNA with  an anticodon and amino acid that corresponds with the codon (a threesome of bases on the mRNA) in the A site enters the ribosome. Next the animo acid (Met),  from the tRNA in the P site froms a peptide bond with the amino acid on the tRNA in the A site.
The Wobble effect is when even if the third base of a codon is different, it still codes for the same amino acid, thus reducing the chance of mutation.
2. During translocation, the ribosome moves to the next codon while the 2 tRNA remain bound to their codons, leaving a vacant A site, and the empty tRNA in the E site (where tRNA is released).
Steps 1&2 are repeated for each codon.
Act II: Termination:
When the A site arrives at a stop codon (UAA, UAG, or UGA), a protein release factor binds instead of a tRNA. The polypeptide chain is released from the tRNA, because there is no amino acid in the A site. The ribosomal units separate and the tRNA and the release factor are also freed.

Transcription (Synthesis of RNA)

Act I: Initiation:
(In eukaryotes):
1.Transcription factors recognize and bind to the promoter, "TATA" Box.
2.RNA polymerase II binds to the transcription factors and creates a Transcription Initiation Complex.
(In prokaryotes):
1. RNA polymerase II bind directly to the promoter region.
Act II: Elongation:
RNA polymerase untwists the double helix DNA, separates strands, then synthesises RNA as it base-pairs along the template in a 5'-> 3' direction.
The distinction between DNA and RNA synthesis? Instead of T pairing with A, it is U. And instead of new stand forming a bond with the template, it trails off from the polymeraseas RNA is single-stranded.
Act III: Termination:

(In eukaryotes):

RNA polymerase for hundreds of A nucleotides after the terminator, "AAUAA".
To protect the new RNA sequence from the hydrolytic enzymes in the cytoplasm, a G-cap is added to the 5' end, and a Poly A Tail, the collection of adenine nucleotides, at the 3' end.
But that's not all, RNA splicing is also needed to remove the introns (non-coding segments that also help in protecting the mRNA transcript) admist the exons, which actually codes for the amino acids(our next step with the mRNA). This splicing is accomplished by a spliceosome, with is formed by snRNPs (made up of protein and snRNA) and other proteins combining with the pre-mRNA. SnRNA base-pairs with the nucleotides at the end of the intron, and then the transcript is cut to release the intron, and the exons are spliced together.
(In prokaryotes):
Polymerase stops transcription at the end of the terminator, and the RNA and DNA are released.

The Replication of Old Man DNA

Note: Cast

Act I: Initiation:
Once upon a time, there was a DNA that felt that it was time to replicate. He was very old so he enlisted the help of the younger generation.
First, a replication fork is to be formed to separate the strands. This is done by Helicase. He untwistes a section of DNA, then he pulls apart the strands easily because of the weak hydrogen bonds. But he realized that he could not hold the strand apart by himself, so he called upon his buddy, Single-strand binding proteins, who specializes in this job.
While this was happening Old man DNA complained that other parts of his structure became too tight. So Gyrase comes in to release the tension.
Then finally, the synthesis of the daughter strands can begin.
Act II: Elongation:
Since the DNA has been split into 2 strands and each runs anti-parallel to each other. And the new daughter strand is to be synthesised in a 5'-> 3' direction. The 2 daughter strands needs to be formed, each one in the opposite direction of the Old man DNA stand, or template. And depending on whether it is forming towards the fork or away, it is a different process.
Leading strand (towards the fork):
First, RNA primase builds a small RNA segment called RNA primer. Then DNA polymerase III adds nucleotides to the RNA primer continuously.
Things are not so easy for the Lagging strand (away from the direction of fork opening):
The daughter strand is synthesized discontinuously, in sections, where it also starts with a RNA primase, RNA primer, and DNA polymerase III. This is called an Okazaki fragment.
But that's not all, when the Okazaki fragment runs into the RNA primer of another Okazaki fragment in front of it, in comes DNA polymerase I to replace the RNA neucleotides with DNA.
Act III: Termination:
And finally DNA ligase, AKA the Glue man, who's been called in by the youngsters and waiting while this is all taking place, can join the Okazaki fragments. As well Polymerase I & DNA Polymerase II proofreads and repair errors.

Metabolism: Anabolism/Catabolism

In order to visualize Metabolism (biochemical reactions that occur in living organisms),we made 3D posters to model the reactions that takes place.

Anabolism (photosynthesis)- synthesizing molecules from smaller components in order to store energy, requires energy in the process. (Photons ---> Glucose)

Noncyclic Photophosphorylation (light-dependent):
- P680 absorbs a photon, the excited electron goes to b6-f complex, then to P700 where electrons get excited by photons, then they are used by NADP reductase to reduce NADP+
- Oxygen and NADPH are formed
- can produce ATP

Cyclic Photophosphorylation (light-dependent):
- electron in P700 is excited by a photon, instead of being used to reduce NADP+ like in noncyclic photophosphorylation, electrons from Fd is passed to b6-f complex and back to P700
- no NADPH or oxygen is formed
- can produce more ATP the little NADP is available.






Calvin Cycle (light-independent):
- rubisco fixs CO2 and RuBP (5C) to become 2 PGA (3C)---> 2BPG (3C)---> 2 G3P (3C)
- some G3P are used to make glucose, others recycled (G3Px2---> 1 glucose)
- uses ATP and NADPH













Catabolism (celluar respiration)- breaking down complex molecules into smaller units, releasing energy in the process. (Glucose ---> ATP)

Glycolysis:
- Glucose---> Glucose 6-phosphate---> Fructose 6-phosphate---> Fructose 1,6-phosphate ---> Dihydroxyacetone/G3P---> 2 BPG---> 3PG---> 2PG---> 2 PEP---> 2 pyruvate
- 2 ATP consumes, 4 ATP produced, 2 H2O produced













Kreb's Cycle:
- OXAL (4C)+Acetyl-CoA (2C)---> CIT(6C)---> ISO (6C)---> alphaKG (5C)---> Succinyl-CoA (4C)---> SUC (4C)---> FUM (4C)---> MAL (4C)---> OXAL (4C)
- produces 2 ATP, 6 NADH, 2 FADH2













Electron Transport Chain:
- 2H+---> 1 ATP
- NADH passes 2 electrons to NADH dehydrogenase---> bc1 complex---> Cytochrome oxidase complex => 6 H+
1 NADP---> 3 ATP, 24 ATP (2 NADP from glycolysis behaves like FADH2)
- FADH2 passes 2 electrons to bc1 complex---> Cytochrome oxidase complex => 4 H+
1 FADH2---> 2ATP, 8 ATP





Sources:

• Nordqvist, Christian. "What Is Metabolism? How Do Anabolism and Catabolism Affect Body Weight?" Medical News Today. MediLexicon International, 26 Sept. 2014. Web. 10 Nov. 2014.
• Carter-Edwards, Trent. Biology 12. Toronto: McGraw-Hill Ryerson, 2011. Print.

U of T and ROM Halloween Trip

U of T Auditorium:

The 2 speakers, who won the Gairdner award, spoke about their experiences in the field of science. They had very different speaking styles.
The 1st speaker spoke to the audience about his experieces in science and gave advices. One of the advices is to don't be afraid to be wrong and experiment, by telling his story of making the wrong hypothesis, but still help millions with his conclusion. He also encouraged students to get involved with arts and literature.  He also used a funny approach which really engaged the audience.
The 2nd speaker used slides as an visual aid for her speech. She talked about experiences in the lab, but she also spoke about the topic of her research more, so sometimes it seemed more like a chromosome lesson. Her story also mentioned the advice of taking constructive criticism.
Overall, the speehes were inspirational, and there were many things to take away from it.

ROM:


The Largest Cast Dinosaur model in Canada

The ultimate message of the Rom tour was that in order to protect endangered species, we need to learn about them, like where they live, their habits, what they eat, and their predators.

Over the course of about 8 interesting exhibits, the story of the Passenger Pigeons  was the one that truck me the most. It was a case that marked the 100 aniversary of the extinction of Passenger Pigeons. This showed that even a species with a population of billions was be terminated with the activities of mankind in the course of only 1 decade. And the moral was to protect the species that are endangered now and not to give to the theory of "it will never go extinct because of the shear number", because it was seen in this example. And to conserve species so that the next generations can be able to experience what we have.

Passenger Pigeons; 100 Years of Silence

Leaf Pigmentation: Chemiosmosis Notes

Chemiosmosis- Hydrogen ions moving from high to low concentration through a membrane.

 

1) PSII removes electron bond from H2O (photolysis) after being stimulated by sunlight, breaking up O and H2.

2) Losing electrons means being oxidized, gaining is being reduced.

3) PQ  takes the electrons from PSII, then b6f is reduced and allows Hydrogen to move out to the thylakoid lumen.

4) PC reduces from b6f, then PSI is activated by sunlight and is reduced as well.

5) Electron then pass through Fd , FNR then NADP.

6) The bond between the two hydrogen atoms separate and one bonds to NADP to form NADPH.

7) A takes 2 phosphates to form ADP, and spins with ATP synthase.

8) Hydrogen moves through and slows the ATP synthase and ADP down, breaking off ADP and allows 1 phosphate to attach to ADP, forming ATP.

9) ATP synthase help move Hydogen ions.
10) PSII consists of proteins.

Note: Highlighted phrases refer to the movement of Hydrogen ions.

Fetal Pig Dissection lab

In this lab, we looked at the body systems in a pig, specifically, the endocrine, reproductive, and nervous system.

The pig that we had was small compared to the others', the same size as the metal tray, about 17cm. We concluded that it was a female, because there was a genital papilla and a urogenital opening. The pig had 4 toes on each leg. 

(Top) The liver was the largest organ in the body, but comparable with the intestine, located beneath the diaphram. (Middle) The stomach was filled with a brown fluid. (Bottom) The pancreas was withing the intestines.

(Top) Small intestine and large intestine was below the liver. (Bottom) A part of the liver.

The heart was surrounded by the lungs. The aorta, vena cavas, and pulmonary veins and arteries were clearly visible.

(Top) The kidneys were accidentally cut in half, but in doing so, we could see the nephrons in the kidney bean-shaped kidney. It was located behind the intestines. (Bottom) Ovaries, also kidney-shaped, had what appears to be thin fallopian tubes attached. It was located below the large intestine and the bladder.

The Brain was mushy when we cut open the hard skull. It is suspected the this is because it had not fully developed yet.                                               It is believed that only one group had their pig brain intact.===>

The eyeball was about .5 cm, and had a film on the outside.

Through the dissection activity, we learned most about the locations and appearence of the organs in the systems we learned in class, in a body similiar to a human's.

 

"The Story of Stuff": A critical Analysis

1. The overall message to the audience is about the process of product production to consumption, and that buying thing has a lot of negative effects to the environment, to workers, and to your own health.
3. The persuasive techniques that Annie use include animation, sound effects and voice-over. She also kept the audience's attention by presenting interesting facts.
5. The bias that annie have is she focused only on the negative things that the process of product consumption has, but did not talk about the corporation's point of view and the effect it has on the economy.
7. I think the vidoe makes a convincing argument, because it gave mind-bogling facts, and talks about things that are important to me, like the toxins in breastmilk, and doing better for the environment.

"The Cove" Worksheet Answers

1. The main defender of dolphins was Ric O'Barry.
3. He was so involved with saving dophines because he was a dolphin trainer and witnessed the suicide of a dolphin.
5. Dolphins are cetacean mammals.
7. Islands in the Caribbean support whaling because allegedly, Japan is supporting them financially.
9. Once the dolphins are trapped, they are pierced with spears by fishermen, and bleed to death.
11. The purpose of this documentary is to inform audiences about the gruesome japanese fishing practices, and the dangers of eating dolphin meat.
13. Biomagnification happens when the concentration of toxic substance increases higher up the food chain.
15. The fisherman refuse to stop hunting dolphins because they say it's in their tradtion, and the government told them that the dolphins are eating all the fish.
17. The crew disguised the cameras as rocks.
19. When the deputy claimed that the dolphins were killed instantaneously, a crew member showed him the secretly obtained footage of the cruel slaughter of dolphins on a phone.
21. When they first saw the cove, the two divers witnessed a struggling bleeding dolphin taking its last breathes.
23. If I go to Marineland, I would be contributing to dolphin slaughter, because I would be giving the message to whoever is in charge of buying dolphins, that I want to see dolphin entertainment.

Macaroni Mark-recapture

In this lab, Group 5 examined the Mark-recapture Sampling Technique used to estimate population size.

In our Second trial, 100 pastas were "captured" from a baggie.

They were each marked with the design that included 3 circles.

The 100 marked pastas were then "released" back into the baggie, then mixed together.

Now, 100 pastas are randomly selected, and the number of marked pastas is recorded at 14.

The population size is then calculated using the formula: # of pastas captured & marked/population size= # of marked pastas recaptured/total # of pastas recaptured

Using the formula, we found that the estimated population size was 714. We had also counted the total number of pastas that were in the baggie, which was 615.

We used the same procedures in our 1st trial, however we marked 40 pastas and recaptured 45 in total, and found 1 that was marked. That estimated population size worked out to be 1800, way off from the actual count.

Analysis:

1. To compare the size of the population using the Mark-recapture method vs the true size, we calculated the margin of error using the formula: % error= (Theoretical size- Exprimental size)/Theoretical size.

We found that the margin of error for the 2nd trial was 16%, while it was 104% with the average of both the 1st and 2nd trials. Therefore we ruled the 1st trial as an outlier. We suspect that the reason that the 1st trial was so far off was because we did not mark that many pastas compare to total amount of pasta, and also it may not have been mixed well before we recaptured.

Overall, the estimate and the true size were pretty close, a difference of 99, and it was a little less tedious to use the Mark-recapture method.

2. a) There are many problems that could affect the accuracy of our estimate, including not having marking enough individuals relative to the total population size, which we did, where we got many unmarked pastas compared to marked. Other problems may be incomplete mixing, and the probability of recapturing a completely evenly distributed sample.

b) Ecologists using the Mark-recapture method with animal popuations may encounter problems like animals migrating, the tags falling off, capturing and tagging enough individuals, and naturals disasters that may kill mass populations.

3. To get more accurate data, we could conduct more trials and combine the information, capture and mark more pastas, and finally mix the baggie more throughoutly.