Sunday, November 30, 2014

DNA Transcription

Initiation:

  • Transcription Factors locate promoter region (TATA box) 
  • TF binds with promoter 
  • Pol 2 begins to transcribe by reading TF
  • DNA begin to unwind and become more stable
  • Transcription takes place on complementary strand
Elongation:
  • 5' to 3' direction 
  • anti-parallel from template (antisense)
  • similar to coding (sense) 
  • T (thymine) is replaced by U (uracil) 
  • Goes from upstream to down stream
Termination:
  • Stops when it reaches AAAAUAAA

DNA replication Story

Act 1: Initiation 
There once was a DNA that felt lonely, so he wanted to replicate itself, so he called the replication company for help.  The replication company sent out helicase, who's job is to help unwind the DNA, which is a really simple task, because of the weak hydrogen bonds, this results in two strands (the initiation point where the splitting starts is known as the replication fork).  Helicase's assistant, single-strand-binding protein has a very important job, they are to help stabilize the newly unwound single strands.  The process was too painful for the DNA, but fortunately helicase had brought in his other co-worker Gyrase to ease his pain.
Act 2: Elongation 
Now DNA is split into two strands, each running anti-parallel to each other.  One strand is oriented in the 5' to 3' direction, while the other strand is oriented in the 3' to 5' strand. DNA polymerase attaches new nucleotides to the 3' end of the 5' to 3' strand (leading strand). Okazaki Fragments generate during the synthesis of the lagging strand of the 3' to 5' strand.
Act 3: Termination
Later, the Okazaki Fragments are joined together by DNA ligase, and POL 1 comes along to do a quality check of what happened (proofreading).

Sunday, November 9, 2014

Relationships between Catabolism, Anabolism and Metabolism

Time to bring everything together :)
AnabolismThe phase of metabolism in which simple substances are synthesized into the complex materials of living tissue.

 Cyclic Cycle










Non-Cyclic Cycle










Calvin Cycle

CatabolismThe metabolic breakdown of complex molecules into simpler ones, often resulting in a release of energy. 


Glycolysis 


















Kreb Cycle


















Electron Transport Chain
Metablisimthe chemical processes that occur within a living organism in order to maintain life.
Anabolism + Catabolism = Metabolism


Saturday, November 1, 2014

Bio Trip to Downtown

Yesterday was our biology trip to U of T and to the ROM.  It wasn't easy getting to school by 8:00 AM, but at least most of us were able to get some more sleep on the bus.  The lectures that were presented were very interesting to hear, and motivated some of us in one way or another into choosing what we want to go into or do with our lives.  But I felt that the auditorium wasn't placed in the best location, because we were able to hear the subway pass by below us.  After the lecture we were let to roam downtown to find lunch and then head back to the ROM by 1, which meant that we had more than an hour to find food, and when I say food I meant McDonald's.
I've been to the ROM so many times as a kid, but I never really had a person take us around the ROM, it was mostly a "go as you please" type of thing where we basically just walked around the ROM aimlessly, although there was this one time I went to the ROM with my Latin class and was able to touch some of the artifacts and had a mini lesson from a teacher that worked there.
The lady that was giving us our lesson was really nice, and she knew everything there was to know about the animals in the display.  She seems like a person who was really passionate about her work, and looked like she really enjoyed doing what she did.  She gave us a variety of lessons; she gave us a lesson about the mistletoe bird, and how the seed of the mistletoe causes the bird to poop 25 minutes after eating it and causes their poop to be stuck on their tails causing the bird to rub it against a tree, the flower that looked like a pokemon which creates a stench that smells like rotting meat and is the colour of dead meat that will attract bugs like flies, the story about lemmings and how their population is inconsistent and that one year there can be a huge population of them and then the next they would be on the brink of extinction, and a story about the corals and how they are so sensitive to change that the plant species that live on them will leave and cause the coral to be "bleached".
Since we only need to write about one story that she had told us I will be talking about the story about the passenger pigeons.

Passenger pigeons were pigeons that enjoyed staying in big flocks, and when I say big I mean real big, as in they have the ability to cover the sun and rain bird poop, making it seem like the world's ending I guess.  One of the reasons that they fly in such big numbers is because it is safe to be in great numbers since they don't have any protective mechanisms that will help them since they're just pigeons.
Since Passenger birds was abundant back then, having a population of over 3.5 billion, humans decided to kill them for food, since I guess they thought pigeon meat taste good, and also to make sure they don't eat all their crops, although according to our teacher the pigeon's poop will become very beneficial for next year's crop.  You can shoot up at the sky with a gun and you are 100% guaranteed to be able to get at least one pigeon.  Another method that the humans did was pluck out the eyes of a passenger pigeon and then tie it on a tree to make to fly in distress.  Many birds that see this will want to fly towards the poor bird and try to save it since they are social birds, but end up being clubbed to death.  There was a record that over 4000 pigeons were killed a day for a few months which ended up killing a lot of the population.  Since these pigeons are social birds they start to die off when their population starts decreasing.  Because of the decrease of population, the birds did not breed often, resulting in another factor that had caused their population to decrease even more.  The last passenger pigeon was a female at the Cincinnati Zoo (1914).  It really saddens me that humans are the cause of the extinction of animals.  Without this tour, I wouldn't have learned about passenger pigeons.     

Monday, October 20, 2014

Taking a deeper look into Photosynthesis (10 points)


  1. Two hydrogen bond with one oxygen to form water 
  2. LEO: Lose Electron Oxidation
  3. GER: Gain Electron Reduction
  4. PS2 and PS1 must have light to stimulate it so that it can gain electrons
  5. Photalysis is when an electron from a water molecule is being taken away
  6. PQ takes the electrons away from PS2 and becomes PQH2
  7. b6f then takes the electrons which then forms a bridge with PQH2 to allow hydrogen atoms to enter
  8. PC then take's b6f's electrons but then is later on taken away by PS1 when it is stimulated by sunlight
  9. FD then takes away the electrons then FNR.  NADP breaks up the sister bonds, splitting them into two, only taking one and leaving the other
  10. STP synthase is when the spinning is slowed down for the hydrogen to be released 

Pig Dissection Blog

Last week I did the second dissection ever, and hopefully my last.  This Dissection was to be helpful in enriching us about the systems (nervous, endocrine and urinary).  I personally did not enjoy doing the dissection (strange how I am able to watch Hannibal, but not be able to handle a dissection), but being able to see it in three dimensional form and not just on a flat piece of paper, made me have a better understanding of how each system worked.

Day 1: Dissection of lower body

Here we are trying to see if our fetal pig is a boy or girl, but we were not able to; we would need to see if there are ovaries in the fetal pig or not

Let the dissection begin:

We then start taking out it's organs

Small intestine
Kidneys
 Spleen
 We accidentally burst the stomach

Bottom half complete 
Day 2: Dissection of upper body

Cutting through thoracic cavity
Time to take out everything from the top half

Here we have the heart
Lungs
Here we are trying to take out the brain as carefully as possible.
well that didn't go as well as expected
Time to go dissect the eye

Here's the lens the other group's fetal pig


All in all the dissection was alright.  I actually had enough guts to cut open the skull which was a pretty okay experience that I do not ever want to do again.




 

Sunday, September 21, 2014

The Story of Stuff: A Critical Analysis (Even Numbers)

2.  I believe that the audience that Annie Leonard is trying to reach is the consumers of USA, and the world.

4.  I think that Annie uses the format of a 20 minute video rather than another format like a report, web blog, or poster is because formats such as a report and poster does not get the attention of an audience.  She makes her video into this format (with pictures, and her standing there stating the facts) so that it can be easily understood (children are able to understand it and possibly people who's first language is not English).

6.  I think that the business people would disagree with what Annie has to say, because what she is saying is causing them to lose business, since most of their costumers would be informed about what is happening, and the business tactics that they are using.  What she is saying may cause the business people to raise the price of their products, because they would have to make their products in a safe environment where their employees are paid fairly and will be working in safe conditions where it would not affect their health.  Also they would have to find a solution that would reduce the amount of garbage that is being produced, and to make their product more efficient where it's main purpose is not to be broken after a few months of usage or to be replaced frequently.

8.  I don't really think this video has affected the way I think about consumption, because I already know about everything that the video is talking about.   There is no way that the cheap products that we are buying off the shelves of Walmart and other stores is coming from a place that pays their employees fairly.  I already know that the products that we are buying are producing a lot of garbage from first hand experience, so I tend to buy things of higher quality, and try to buy products that aren't made in China, or any other Asian countries that don't make a safe environment for their employees.  I'm one of those people that don't go with the trend, so when I buy electronics I would buy something that would last me a long time.                      

Monday, September 8, 2014

Video Worksheet: The Cover (Even numbers)

2. The dolphin slaughter takes place in Taiji, Japan, they are the biggest exporters of live dolphins that are used in marine shows, and dolphin meat that are sold in fish markets.

4. Ric 'o' Barry was a former dolphin trainer, he helped capture and train five wild dolphins who played the role "flipper" in a TV series.  The TV series was a big hit, and had made dolphins more popular, and loved by the general public, and had resulted in marine parks having dolphins as one of their attractions.  One of the dolphins "committed suicide," by closing her blowhole voluntarily in order to suffocate, and died in Ric's arms.  The death of this dolphin had made Ric realize that dolphins aren't meant to be living in captivity, they were meant to run free into the wild, where there is no limits to how far they swim.  Ric, later on got sent to jail, because he tried to free the remaining dolphins that were kept in captivity back into the wild.  After he finished his time in jail, he had decided to change people's minds, he wanted to inform people of what was happening to the dolphins.

6. The country that indirectly runs the International Whaling Commission is Japan.  Japan would pay some small countries that were having difficulties financially and pay them money so that they do not go against them in the IWC conferences.

8. Fishermen would make noises by hitting a hammer against a pole.  Since dolphins are very sensitive to sound, they would run away from the sound that was made by the sailors.  The dolphins would then swim towards the lagoon/cove, and then the next day, people would go to the lagoon and look for bottled nose dolphin females to send to different parts of the world, and then kill the rest for the meat.    

10. Around 23, 000 dolphins are killed in the secret cove a year.

12.  The toxic substance that is found in dolphin meat and any other oceanic animal is mercury.

14.  Japanese people eat meat, because there is still some nutrients in the dolphin meat.  Also some fish stores in Japan sold dolphin meat labeled as whale meat.

16. Fish is severely declining because around 7/10 people rely on fish for protein, so there is an increase in demand of fish, which makes many fisherman over fish the fish.

18. Dolphin meat is sold as whale meat in fish markets, but the government chooses to not interfere.

20. The main character went through the conference with a big screen attached to him, that showed the hidden camera footage's of what happens in the secret cove.

22. Whaling was banned in 1986.

Friday, September 5, 2014

Mark-Recapture Sampling

Materials Used:

  • 1 bag of uncooked pasta
  • Sharpie markers

Methods:

Trial #1
1. Capturing of the pasta population 



2. Marking the captured population
Number of pasta caught and marked in first sample: 40




3. Releasing of marked and captured pasta population, and mixed with general population




  4. Taking another sample with eyes closed and recording how much was in the sample and how many of them were marked
Number of pasta caught in second try: 52
Number of marked pasta caught: 4



5.  Estimate of population calculations:
M/N = m/n, where M is the number of pasta caught and marked in first sample, N is total population, m is number of marked pasta caught in second sample, and n is the number of second sample

40/N = 4/52
40 = 4/52 x N
40 x 52/4 = N
There for N = 520

Trial #2:

1. Capture of the pasta population
Number of pasta caught: 90


2. Marking population 



4. Capturing pasta for the second time with eyes closed
Number of pasta caught: 28
Number of marked pasta recaptured: 5


5. Estimate of population size for trial #2
M/N = m/n, where M is the number of pasta caught and marked in first sample, N is total population, m is number of marked pasta caught in second sample, and n is the number of second sample

90/N = 5/28
90 = 5/28 x N
90 x 28/5 = N
There for N = 504

Trial #3:

1. Capture of pasta population
Number of pasta caught: 33


 2. Marking the captured population


3. Releasing the marked pasta back to the general population and randomly mixing it



4. Randomly capturing pasta with eyes closed, and recording how much was captured and how many marked pasta were recaptured
Number of captured pasta: 50
Number of marked pasta: 2


5. Estimate of population calculations:
M/N = m/n, where M is the number of pasta caught and marked in first sample, N is total population, m is number of marked pasta caught in second sample, and n is the number of second sample
33/N = 2/50
33 = 2/50 x N
33 x 50/2 = N
There for N = 825

% error = (theoretical - experimental) / theoretical
= (543 - 616) / 543
=13.4%

Analysis:

  1. Out of the three trials, the first trial was the closets, with an estimate of 520.  
  2. The problems that might affect the accuracy of my estimate may have been the number of pasta that we took out of the bag the first time and the number of pasta that we took out the second time to see how many pastas we recaptured.
    Problems that ecologists studying animal populations encounter may be that the animals may have been smarter than they have anticipated, and that the animal that they have marked may have had figured a way to remove the mark that had been put on them.  An example of this is that dolphins help one another to remove the marker that was put on them, or they rub it against something that would have been able to help them get rid of it.  
  3. An improvement that my group could have is that we could have captured around the same amount that we captured the first time, because during the first capture we would take a big hand full, but then when it was the second try, we took a small hand full, so it was inconsistent. Also it would more accurate if we were to do more trials, so that the % error would be less.