Translation

When mRNA is sent out to the cytoplasm, it enters a Ribosome, which has tRNA Transmission RNA). They are used to create proteins which are coded for on the mRNA.

Each mRNA strand codes for one protein. Proteins are long chains of polypeptides.

• Codons are sets of three nucleotides found on the mRNA sequence. Each one codes for a specific polypeptide.
• AntiCodons are sets of three nucleotides found on the tRNA. Each AntiCodon is complimentary to one Codon.

The mRNA passes through the ribosome. When it finds the correct tRNA sequence which is complimentary to the specific codon, the appropriate polypeptide is added to a chain. The tRNA is then replaced by another and the mRNA moves forward one codon. In this way, proteins are synthesized for use in the cell.

• Each codon codes for a specific polypeptide.
• The mRNA is read in the 5' to 3' direction.
• There is one start codon, UAG, which prompts the polypeptide chain to begin. There are several stop codons, which prompt the proteins to detach from the tRNA.

DNA Transcription

Transcription is the process through which a DNA strand is copied to mRNA (Messenger RNA), where it will be used to synthesize proteins (long strands of polypeptides). The mRNA is sent out into the cytoplasm of the cell, where it will be translated by Ribosomes.

Stage 1: Initiation

• Polymerase II starts reading the template DNA strand 3' to 5'. The template DNA strand is also called the 'antisense' strand. The opposite strand is called the 'coding' or 'sense' strand because it has (almost) the same nucleotides as the RNA sequence will have.
• The DNA is unwound as the Polymerase II is reading it.
• Once the 'TATA' box is found, proteins mark its location as the start position. This sequence (TATA) is also referred to as the 'promoter' sequence

Stage 2: Elongation

• Polymerase II codes the RNA sequence complimentary to the template strand in the 5' to 3' direction. The sequence is almost identical to the coding strand, which is alos complimentary to the template strand.
• RNA doesn't have a T (Thymine) nucleotide, it uses U (Uracil) instead.
• The RNA Polymerase copies the coding strand and replaces the T nucleotides with U.
• The 5' end of the mRNA strand is called 'upstream' and the 3' downstream, so the RNA is replicated upstream to downstream.

Stage 3: Termination

• When the termination sequence is encountered, the RNA is completed. (Terminator sequence is "AAAUAAA")
• Introns are sections of the DNA that don't have a purpose in coding for genes, and these are removed from the mRNA by proteins called spliceosomes, in a process called 'RNA splicing'. The parts that remain, which code for proteins, are called exons.
• To protect the mRNA from the harsh conditions outside the nucleus, a modified 'G' nucleotide is added to the 5' end and a 'Poly-A Tail' is added to the 3' end. The Poly-A Tail consists of a long strand of A nucleotides.

DNA Replication

1. Initiation

• Helicase unwinds the DNA and starts separating the strands.
• Single-Strand Binding proteins hold the strands in place and prevent them from coming back together
• Gryase cuts the DNA into smaller parts to prevent the tension from building up
• Primase place RNA Primers to signal Polymerase III to start making the replicated strand.

2. Elongation

• Polymerase III creates the replicated strand in the 5' to 3' direction.
  • The leading strand is done continuously (it is being unzipped in the 3' to 5' direction so the new strand can be created in the 5' to 3' direction without any breaks
  • The 'lagging' strand needs to be replicated in the opposite direction so it is done in sections called Okazaki Fragments.
• RNA Primase starts off each Okazaki Fragment and Polymerase III follows. Each Okazaki Fragment is approximately 100-200 nucleotides long

3. Termination

• Polymerase I 'proofreads' the replicated strand and corrects any errors. It also removes the RNA Primers and replaces them with Deoxyribonucleotides.
• Ligase forms Phosphodiester bonds between the Okazaki Fragments to hold them together.

Photosynthesis and Cellular Respiration Activity

In class we did a group activity, in which each group had to make a three-dimensional representation of one process of cellular respiration or photosynthesis. Our group was responsible for the non-cyclic electron transport chain in photosynthesis, which is pictured last. Following are all the models:

The ROM (and the Gairdner Symposium)

This Halloween, our class had the privilege of attending the Gairdner Symposium at the University of Toronto, where we were given speeches by recipients of the award about their lives with science. However, as interesting as that was, this blog post is about the tour of the ROM we had the opportunity to partake in following the presentation. We were led by a very knowledgeable and interesting tour guide who did a very good job explaining each exhibit and its significance. One in particular which stuck in my mind was one about the Arctic Fox and its main food source, the lemmings.

At first glance, the case shows what seems to be an unsurprising or relatively insignificant - An Arctic Fox with a minuscule lemming limply dangling from its jaw. "Okay," you might think, "What's so special about that?"

At least, that's what I thought when I looked at the display case before our tour guide started explaining the special, albeit delicate predator-prey relationship the Arctic Fox shares with the lemming. The entire basis of population dynamics is that populations of all species are interconnected in some way, and a slight fluctuation in one can affect the other in sometimes unpredictable ways. It's pretty difficult to demonstrate this idea better than the Arctic Fox.

Lemmings have what's known as a "boom and bust" population cycle - their population size fluctuates immensely. They have been known to go from exorbitant population sizes to near extinction in the span of a few generations. In fact, people have speculated that they might even commit suicide to give their species a better chance at survival (but this idea was faulty in many aspects).

Instead, what controls their population size is the carrying capacity - the maximum number of individuals that can survive in the given space with the given amount of resources. When population sizes start getting our of control, food and space becomes scarce, disease rates ramp up, and predators become more abundant due to an increase in the amount of available food - this is where the Arctic Fox comes in. Over time, the sizes of both the populations have been observed to have a strong correlation with each other. When the lemmings go through a "boom" phase, or have large numbers, the Arctic foxes will also have large litter sizes that year, and vice-versa for when the lemmings go through a "bust."

This is just a small aspect of population dynamics, but does a very good job in demonstrating how different species are interconnected in complicated, yet delicate ways. The main idea that the guide wanted us to walk away with after that presentation was that scientists have to consider every single aspect of a species' life before they can take any sort of action (like a conservation effort). This can often be difficult because of all the possible factors that can be present and have an effect in their lives.

Overall, the ROM was a positive experience which I took away a lot from. We covered a lot of different topics throughout the tour, including parasitic flowers smelling like rotten meat¹, how humans drove the most abundant bird species to complete extinction², fish that explode when caught³, and of course, dinosaur skeletons.

¹ Rafflesia
² Passenger Pigeon
³ Deep sea fish (like the angler fish)

10 Points on Photosynthesis

• Photosynthesis converts light energy (carried by photons) into ATP, which is a molecule which can store energy in a form that is usable by the plant.
• Chloroplasts are transparent organelles which contain grana, which are stacks of thylakoids which in turn contain a green pigment called chlorophyll. This is where photosynthesis takes place.
• Chlorophyll absorbs all wavelengths of light except for green (and yellow), which they reflect to our eyes.
• An electron transfer chain is used to synthesize ATP
• Oxidation occurs when electrons are lost. Reduction occurs when electrons are gained.
• PS2 (Photosystem 2) is simulated by light of wavelength 680 nm and takes two electrons from a water molecule, breaking the covalent bond which holds it together. Oxygen and H2 are separated.
• The electrons travel through the transport chain using oxidation and reduction reactions. It goes from PS2 to PQ to B6F. B6F pumps hydrogen ions into the chloroplast when it gets the electron, and then passes it on to PC.
• The next link in the chain is PS1 (Photosystem 1). It gets simulated by light of wavelength 700 nm and is then reduced. The electron then goes to Fd (ferrodoxin) and FNR.
• NADP is the end of the chain, and a positive hydrogen ion (proton) neutralizes it.
• ATP is formed by ATP synthase. It spins ADP around. (when this combines to one phosphate it becomes ATP). The hydrogen ions 'slow' the spinning down and the last phosphate attaches to the combination and becomes ATP.

Fetal Pig Dissection

Day 1 — Abdominal Cavity & reproductive system

This week, we had the opportunity to perform a fetal pig dissection. I, along with my group members (Benn, Amriya, Amir and Jianan), performed the dissection on a pig fetus to see the various organs and organ systems as they appeared in real life. We began the lab by gathering all the required materials; including scissors, pins, a scalpel, latex gloves, and goggles.

Our pig was female because of the urogenital papilla near the anus. We started by going through the lower body; the first day of the two-day lab would be devoted to exploring the abdominal cavity. Following our handout, we first made an incision along the stomach, followed by an incision laterally across it and around the umbilical cord to expose the abdominal cavity.

The umbilical vein was visible at this point, and we had to cut it to get to the organs underneath.

The umbilical vein is the elastic-looking cord ending at the liver.

The first organ we encountered was the liver. The umbilical vein led to the liver. It was a large structure which surrounded the stomach and parts of the small intestine.

After removing the liver, most of the other parts of the cavity were visible. The stomach is visible in the following pictures, as well as the large & small intestine and one of the kidneys. The structure running along the stomach is the spleen, where blood cells mature. The pancreas is right under the stomach.

Inside the abdominal cavity	The liver
Stomach, small & large intestines, spleen  and pancreas	Kidney (Located at the back and to the sides - we left the other one inside).

The stomach wasn’t empty. Inside were small dark objects inside a fluid. [below, left]

The uterus was then removed. The urinary bladder is the sac in between the two reddish tubes. The ovaries are located behind it. [above, right]

Day 2 — Thoracic cavity and head

On the second day of the dissection, we moved up to the thoracic cavity. Inside we were able to locate the heart, lungs, and thyroid glands. The heart was the first organ we encountered, surrounded by the aorta and various other veins and arteries. This is the center of the circulatory system, so there were larger blood vessels (to hold a larger amount of blood from the rest of the body) and the heart was very muscular, to be able to pump blood non-stop all around the body.

Heart, surrounded by ribcage and lungs

Heart with lungs

Moving further up the chest and into the neck area, we were able to isolate the thyroid gland. We found it near the esophagus and the various muscles and blood vessels which were going to the head. The thyroid gland is responsible for controlling the growth of the pig, and would have released the growth hormones necessary for the development of the pig. The parathyroid glands are supposed to be located on the thyroid gland, but we were unable to isolate them.

Thyroid gland

Our next step was to proceed to the head; isolating the brain (and hopefully, the brainstem). We had to exercise extra caution during this part because we had to cut through cartilage (the bone hadn’t developer yet) in the skull, all while trying not to damage the brain. Below are a few pictures of this process. In the end, while we could see the brainstem, we weren’t able to extract it along with the brain. 

The last part of our process was isolating the eye. Located close to the brain, this is one of the most developed organs we had examined so far. Inside, we could see a small yellowish sphere — which was the lens.