Answers to The Cove

1. Who is the main "defender" of dolphins in the documentary?
Rick O'Berry, a former dolphin trainer turned activist to save dolphins.


2. Where is the dolphin slaughter taking place?
Taiji, Japan


6. Which country indirectly runs the IWC?
Japan


9. Once these dolphins are trapped what happens to some of them first?
Some of them are selected to be shipped to all parts of the world as show dolphins. Those who do not make it are then killed for meat. 


12. What toxic substance is found in dolphin meat?
Mercury

Warning: Sharks!

From an early age, Nemo and has taught me that sharks are the ultimate villain to be feared of. They are blood-thirsty, hostile, and just plain nasty. This mindset alone is the cause to my initial indifference to such a dramatic misfortune for the sharks. Why would people want to protect such a fearful creature? However, I am not cold blooded. I simply wasn't educated. Sharkwater is a documentary with a powerful message that I've never pondered upon. I've never viewed shark fin soup more than a mere luxury dish in the Chinese culture. Of course, nobody told me anything, nor did I have enough curiosity to find out more. Finally, I get my fair share of knowledge on sharks. First, the sheer number scares me. More than 10000 sharks are killed each hour! Doesn't matter what creature it is, that's still some massive killing right there. Maybe it wouldn't have triggered my attention too much if it wasn't for that sharks aren't as bad as we thought they were. In reality, they contribute to our environment and ecosystem by preying on fishes that eat plankton, an organism that consumes carbon dioxide and in turn, releases oxygen. Obviously, we can't have all the plankton eaten, right?

Anyway, the whole shark massacre is ridiculously unnecessary. The industry catches all these sharks, take off their fins and other "useful" parts, then disregard the rest of the body back into the ocean. What's the point of shark fin soup? Nothing. It's simply a part of an outdated tradition. They serve absolutely no valid purpose, not even for taste. It's just used to texturize an ordinary soup, and bam! You've got yourself a "luxurious" bowl of "holy" soup that you can serve on important ceremonies.

I don't blame anyone for being ignorant, because I was too. We just need to get the words out there, so more people can understand the severity of this unfortunate happening. People need to be educated, that's all. I'm glad movies such as Sharkwater exists, so the world can see the other side of the story. Maybe next time, Steven Spielberg can make a sequel to Jaws, called Hands.

Clothes-pin Activity

Notes on Metabolism

• Metabolism - sum of all anabolic (building complex substances from simpler subunits) and catabolic (breaking down of complex substances) processes in a cell or organism.

Laws of Thermodynamics:

1. The total amount of energy in the universe is constant. Energy cannot be created nor destroyed but only converted from one form into another. 
2. The entropy (measure of randomness or disorder in energy or in a collection of objects) of the universe increases with any change that occurs. 

Entropy increases when:

• solid reactants become liquid or gaseous products
• liquid reactants become gaseous products
• fewer moles of reactant molecules form a greater # of moles of product molecules
• complex molecules react to form simpler molecules
• difusion

• Gibbs Free energy: energy that can do useful work; mostly stored in ATP in living cells
• In order to break bonds between the reactants, activation energy must be reached.
• Exergonic reaction: spontaneous; decrease in Gibbs free energy
• Endergonic reaction: not spontaneous; increase in Gibbs free energy
• Anabolic reactions create order out of chaos in a local area of the universe at the expense of creating a greater amount of disorder in the universe as a whole. 

Redox reaction: combination of oxidation (atom loses electrons) and reduction (atom gains electrons), often occurring in a chain reaction.

Reducing agent provides electrons and oxidizing agent takes electrons. 

• Allosteric sites are receptor sites:

Activator: stabilizes the active form of the enzyme

Inhibitor: stabilizes the inactive form of the enzyme

*Textbook p.58-77

Important for Biotech Test!

Vector Cloning

1. The same restriction enzymes are used to cut desired gene and plasmid at a specific location.

2. The ends are "sticky", as they are single strands that combine together and glued by ligase, forming phosphodiester bonds.

3. Complete digestion means there are enough REs to cut at every restriction sites; Incomplete digestion means not enough to fully cut at all the sites

4. pBluescript is an engineered plasmid with multiple pre-arranged enzyme cut sites.




PCR (Polymerase Chain Reaction)

5. Materials: taq polymerase (heat resistant), single-stranded DNA primer, nucleotides and ligase

6. Heating denatures DNA; cooling allows primers to base pair to their complementary strands; taq polymerase attach at each priming site and synthesize a new DNA strand.

7. The targeted fragment is produced ONLY after third cycle, then is exponentially grown.

Gel Electrophoresis

8. Shorter DNA fragments move down the gel to the positively charged anode (since DNA is negatively charged), and larger DNA fragments remain at the top.

RFLP (Restriction Fragment Length Polymorphism)


9. DNA fragments are cut by COMPLETE digestion by multiple REs, then undergo gel electrophoresis.

DNA Sequencing


10. DIdeoxyribo-nucleotides incompletely digest the DNA fragments, terminating the sequence at each individual nucleotide (ddATP will incompletely digest at every adenine sequence).

PCR vs. DNA Sequencing

Similarities 

- Both PCR and DNA Sequencing start in the the test tubes!
- DNA polymerization is involved in both processes.

Differences

PCR 

- DNA denatures at high temperature (around 94-96 C)
- Special DNA polymerase that can withstand heat called taq polymerase is used
- Primers are used to initiate elongation

DNA Sequencing

- Dideoxyribo-nucleotides are used, which terminates the sequence since they have no OH group to bind a proceeding nucleotide.
- Only a very small amount of ddNTP is used so that incomplete "digestion" occurs, thus each possible termination site (complementary nucleotide to the ddNTP) is shown

PCR vs. Vector Cloning

Similarities

- The goal of PCR and vector cloning is to isolate a fragment DNA containing desired gene to be produced in large quantities.

- The target DNA fragment in both PCR and vector cloning grow at an exponential rate; very fast and efficient.

Differences

PCR

- Amplifies fragments of DNA without using cells.

- DNA fragments are denatured at high temperature, then it is cooled down to allow DNA primers to attach to complementary strands, finally it is heated up again for replication. 

- a special polymerase is used: taq polymerase, which elongates the DNA fragments at high temperature (around 72 C) 

Vector Cloning

- Restriction enzymes are used to cut original gene and plasmid at a specific location (using the same RE for both), containing stick end so they can be combined together and glued using ligase. 

- Bacteria are used as host cells because they contain plasmid that can easily be removed and replaced, and they can multiply at an exponential rate.

- Bacteria must be selected before being grown in culture to ensure the plasmid contains the selected gene. 

FYI: Important points for Genetics Test

DNA STRUCTURE


1. Adenine and thymine are connected by double hydrogen bonds, and guanine and cytosine are connected by triple hydrogen bonds. Adenine and Guanine are called purines; thymine and cytosine are called pyramidines.

2. DNA grows from 5' - 3'!


DNA REPLICATION

3. To replicate, the double helix of the DNA is unwound and separated to expose two template strands for the new nucleotides to attach to. The result is two identical daughter strands.

4. In replication, the leading strand (3' - 5' into the fork) continuously elongates, whereas the lagging strand (5' - 3') has to be elongated in short fragments called the okazaki fragments.

DNA TRANSCRIPTION


5. DNA transcription starts 5'TATA3' (promotor) and ends at AAUAA (terminator) on the coding strand, using the RNA Polymerase II.

6. Noncoding segments in the pre-mRNA called introns are spliced out by spliceosomes which contain snRNP and snRNA. The coding segments, extrons, are then translated into amino acid sequences.

7. The 5' end is capped with 5' cap (guanine) and the 3' end is capped with poly A tail (adenine) for protection.


DNA TRANSLATION


8. tRNA carries amino acids to the ribosome to be attached to the growing polypeptide chain.

9. Translation always starts with 5'AUG3' (Met) and ends at either UAA, UAG, or UGA.


10. tRNA reads mRNA 3 base pairs at a time (codon), but ONLY after 5'AUG3' is located.

Reflection: Deaf by Design

What's your favourite pass-time? Perhaps listening to music, chatting with your BFFs over the phone, or simply relaxing by the beach and listen to the beautiful sound of the ocean waves? For many of the things we enjoy in life, we hardly ever give it a second thought - we just take it for granted. But imagine how it would be like if it were taken away from us, and suddenly we couldn't hear anything. Everything's like a silent movie playing over and over again, except to everyone else, it's not. You feel like an outcast, a weakling, disabled. You feel devastated, yet helpless.

However, did you know that some deaf people actually enjoy being deaf? They wouldn't want to hear, even if they could. And even more shockingly, they would wish for a child that also cannot hear, even to the extreme of aborting a hearing child! Yes, I understand that as a parent, they want their child to be more like them, but don't you think that's such a selfish thought? Don't they want their child to experience the world they had never been able to? Do they really want to make their child suffer like how they did? When I watched the parents in the documentary Sound and Fury who refused to let their deaf child receive cochlear implant as she wished, I was outraged. How can they do that to their child? She obviously desired to hear, to experience the many faces of the world. But yet, her parents were so close minded, so selfish. Their defence? They wouldn't know how to educate her if she weren't deaf. Well, it's not like she doesn't know how to sign, nor will she ever forget. She will simply get the best of both worlds. They can still communicate fine with her, so I don't see what's wrong with being able to hear AND sign at the same time.

That's not even the most extreme case. There are actually deaf parents who expressed that they would abort a hearing child because they want to conceive a deaf one. To be honest, I don't even think it's really ethical for hearing parents to abort a deaf child. Maybe I'm the ignorant one here, maybe I'm the one being close minded here. I don't understand the Deaf, and I'll never be able to, unless I become deaf. I don't see being deaf as a lifestyle, as they see it, but I see it as a disability. I see it as a disability that refrains them from fully enjoying life; a barricade for career and marriage. It's too difficult for me to completely understand their point of view, but I do know one thing - if I were to have a deaf child, I would want the best for them (in my opinion), and let them get cochlear implant.

Aww, look how happy she is with her cochlear implant!