DNA Replication

Initiation:
- Helicase unwinds double helix and breaks the hydrogen bonds
- Single strand bonding pairs keep the DNA separated and stabilized
- Gyrase relives tension between the two strands of DNA by cutting them
- RNA Primase signals polymerase II by putting primers to begin replication

Elongation:
- DNA opens up as replication forks
- DNA polymerase II adds nucleotide to 3' end
- 2 strands: lagging/leading
- Leading strand: RNA primes starts replication and DNA polymerase III replicates 5 to 3 towards the opening
- Lagging strand replicates the 5 to 3 template strand so it is replicating 3 to 5. Since DNA polymerase III only replicates 5 to 3 in segments okazaki fragments. RNA primes starts each segment with primer and DNA polymerase III continues until the end of the segment.

Termination:
- DNA Ligase joins okazaki fragments together
- DNA polymerase I proofreads the bases then replaces the RNA with DNA
- The two DNA molecules separate

DNA Translation

Initiation:
- Initiator factors assemble small tRNA initiator and mRNA
-mRNA is transferred to the ribosome on the endoplasmic reticulum once it is moved out of the nucleus
- Ribosomes are made up of two units: large and small subunits
- Large subunits join together to form an active ribosome
- The large subunit contains three sites: E, P, and A
- P site has tRNA with polypeptides attached to it, A site has tRNA with amino acid to be added to the polypeptide, and E site has uncharged tRNA with no amino acid attached
- tRNA moves in the A site and reads the mRNA sequence in threes (codon) starting with AUG as the first codon

Elongation:
- Polypeptides become longer, one amino acid at a time
- tRNA contains anticodon that binds with these codons
- Each tRNA carries a peptide that when binded with the codon, it moves to the P site and picks up all of the other peptides from the previous tRNA in the P site. The previous tRNA moves to the E site and exits the ribosome.
- This creates a chain of peptides called polypeptide
- There are 64 combination of 3 pairs for base sequences but only 20 amino acids. This is due to the wobble effect making every amino acid responsible for 2-3 different base sequences and  decreasing the chance of mutation

Termination:
- Stop codon on mRNA is reached
- There are 3 base sequences that signal a stop codon for the polypeptide chain
- tRNA that carry the anticodons move into the A site and are the last tRNA to move in before translation stops
- Once translation stops, the ribosome breaks up and everything attached to it breaks off with the end result of a polypeptide chain and later on protein

DNA Transcription

Initiation:
- Transcription machine is assembled
- Transcription Factors spot out the promoter (TATA box)  and termination (AAUAA) region on either strand and begin copying the base sequences to make pre-mRNA.
- For each gene only one strand of double strand DNA is transcribed
- The strand being used to make the pre-mRNA is called the template (antisense) strand and the other strand is the coding (sense) strand
- RNA polymerase II crates an initiation complex
- DNA unwinds and RNA polymerase II starts transcription

Elongation:
- The coding strand and the RNA strand are very similar with Thymine being replaced with Uracil
- Nucleotides are added to the 3' end (OH)
- The m-RNA strand stars from the promoter and copies until the AAUAA
- The pre-mRNA is anti-parallel with the template strand and transcribes downstream

Termination:
- Once the RNA polymerase reaches the AAUAA sequence, transcription stops
- Pre-mRNA cuts off and  the DNA strands get winded back together
- Pre-mRNA is then guarded by a G-Cap on the 5' side and Poly-A-Tail on the 3' side due to enzymes in the cytoplasm that try to break down the mRNA
-Pre-mRNA contains useless sequence parts called introns that are not needed. They are taken out of the mRNA by spliceosome and the eons are connected.

Metabolism Process: Catabolism vs Anabolism

Catabolism: The set of metabolic pathways that breaks down molecules into smaller units to release energy. 

Krebs Cycle - Acetyl CoA produces ATP, NADH, and FADH.

Glycolysis - Where glucose is broken down into pyruvate molecules, ATP and NADH are produced.

ETC (Electron Transport Chain) transports electrons when they undergo chemiosmosis, as a result ATP is produced. 

Anabolism: It is a metabolic process that uses energy from the sun or ATP to synthesize a large molecule from smaller molecules.

Calvin Cycle - Where carbon fixation takes place and it uses ATP/NADPH to form G3P.

Cyclic - The Cyclic process uses P700 from the sun to produce to form ATP.

Non Cyclic - The Non-Cyclic process uses P680 and P700 from the sun to form ATP and NADPH.

Metabolism: The sum of all chemical reactions that occur in the cell (anabolic/catabolic processes)

ROM Trip

On friday we had the chance to go to the ROM Museum and University Of Toronto for two lectures. We saw some interesting animals mostly ranging from 76 million years ago to present. Also, we had a tour guide in ROM which I think really changed my perspective towards the museum and the different things presented to us. The tour guide gave us some background stories about some of the interesting animals, and I found the "Passenger Pigeons" the most interesting to talk about.

These Passenger Pigeons caught my attention the most because of their exctinction due to recent human activities. The Passenger Pigeons were once one of the most abundant birds in North America and they come from the French word passager which means to"pass by". The tour guide gave us some general information about these pigeons and finally went into details. She said that there was once 3 to 5 billion of these pigeons in America alone. She also added, the exctinction of these birds were due to habitat loss which led to a mass deforestation. They were also commercialized as a cheap food for the slave in the 19th century. There were some attempts to save these birds by breeding the surviving captive pigeons were not successful. The passenger pigeon needs a large number of optimum breeding conditions. It was not possible to reestablish the species with a few captive birds and eventually, small captive flocks weakened and died. The last Passenger Pigeon was "Martha" which was named after Martha Washington. She died at the end of Zoological Garden and was donated to Smithsonian Institution where her body was mounted for display. After we heard the story of these pigeons I personally felt depressed because it changed the way I thought about nature in general and what humans to our nature and habitat. In my opinion this story should be shared around to raise awareness about the extinction of different animals around the world due to the human activities.

Leaf Photosynthesis

What happens inside a leaf (10 key points)

1. This procedure starts with an oxygen molecule and two hydrogen molecules. The bonding between them is called covalent bond.
2. When an element loses an electron it's called oxidization
3. When an element gains an electron it's called reduction
4. PSI and PSII need to be activated, therefore they need the sunlight to get oxidized
5. The NADP becomes oxidized and it needs 1 hydrogen molecule to become NADPH
6. Photolysis is when an electron comes from a hydrogen molecule
7. The adenine in this process binds with two phosphorus molecules and becomes ADP which is adenine phosphate 
8. The job of the ADP is too spin so the hydrogen molecules can leave the leaf and filter out since they create an acetic environment which is not suitable for the leaf
9. When the hydrogen goes through, it slows down the spinning of ADP
10. There is also a third phosphate in this process which comes in and joins the diphosphate to become a source of energy in the form of ATP

Pig Dissection

Day 1 - Reproductive System/Abdominal Cavity

We had the opportunity to dissect a pig this week along with four other group members. As we studied the different systems and organs in our body we can see how different animals have the same body structure and organ system as we do. To start, we collected the material/tools needed: gloves, goggles, scissors, pins, and scalpel.

First we analyzed the different parts of the pig too see the basic structure from the outside. We saw that our pig was a female from the urogenital papilla found near the anus. Following the handout we got, we started cutting the pig along the stomach and around the umbilical cord to open up the abdominal cavity.

In this picture you can see the umbilical vein. In order to get underneath the organs we had to cut it.

 After getting to the organs we can see the liver which covers a major part of this system visually. In this picture you can see the small and large intestine, stomach, and one of the kidneys are visible. Also, the pancreas is under the stomach and the structure along the stomach is spleen.

Abdominal Activity

The Liver

Pancreas, Stomach, Small and Large intestines, and Spleen

The Kidney 

As we opened the stomach and went further we found black particles in fluids. 

Then we removed the uterus and in the picture the urinary sac is between the pinkish tubes, and behind that are the ovaries.

Day 2 - Thoracic Cavity/Head

Basically, on the second day we moved up to the thoracic cavity and finally the head. We were able to see the lungs, heart, thyroid glands, the brain, and the lens. The first organ we saw was the heart which was surrounded by various of veins, arteries, and the aorta. In these pictures you can see the circulatory system:

Ribcage surrounding the Heart

Lungs and the Heart

Our next task was to isolate the thyroid glands. As we moved further up it was harder to see these glands because it was covered with fats which were the same colour. The thyroid gland is there for growth and development of the pig. There were also the parathyroid glands which were located on the thyroid gland, but we were not able to clearly identify and isolate them. 

The next step was to isolate the brain and (brainstem as a bonus). This was a hard to part to get through because we had to be really cautious of what we were doing. The cartilage wasn't fully developed yet, therefore we had to cut it so that it didn't damage the brain. Although we were able to see the brainstem in the end, we couldn't successfully isolate it with the brain. In the following pictures it shows this process:

The last step of this lab was to isolate the eye. The eye is located near the brain and it is one of the most developed organs in the system. We could see a small yellow lens which was in a shape of sphere/circle.