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

6. What country indirectly runs the International Whaling Commission?
A: Japan

8. How do the fisherman trap the dolphins in the cove?
A: The method is called the "drive hunt". Fishing boats form a barrier that traps the dolphins between the boats and the cove. The fishermen then lower a stick-like material into the water and knock on one end of it. This produces sounds within the water that is perceived by the dolphins. This sound barrier scares the dolphins and forces them towards the cove.

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

23. If you go to Marineland are you contributing to dolphin slaughter?
A: Yes. By paying to watch dolphins, I am sending the message that I support the industry. Although my decision matters little, it is from little things that great changes are made. As long as people are ignorant of the indirect slaughter of dolphins through captivity, they will continue contributing to the industry, which goads it into expanding and thriving.

The results show that the more the subjects pinches, the harder it becomes to pinch. This is due to muscle fatigue caused by accumulation of lactic acid. I suspect anaerobic respiration will be our area of focus next.

Energy

• In a local closed system, orderliness can arise without entropy increasing. However, the energy used to maintain this order will be transferred to an unusable form, hence causing entropy to increase outside the system. 
• In chemical reactions, entropy increases when
• Solids become liquid/gas products (or liquid becomes gas products)
• x moles of reactant molecules form more than x moles of product molecules
• Complex molecules form simpler molecules
• Solutes diffuse to achieve a homogeneous mixture 

Metabolism

• Energy in a reaction

• 1) Activation energy is absorbed by the reactants to break bonds 2) Reactants enter transition state 3) As products form by bonding, energy is released
• Product is more stable (bond energy is higher) than reactants 
• Change in Heat energy is negative = Exothermic reaction; Change in heat energy is positive = Endothermic
• Free Energy (usable energy) in a reaction
• Change in Gibbs free energy is negative = Exergonic reaction [spontaneous]; Change in Gibbs free energy is positive = Endergonic reaction [not spontaneous]
• Metabolic Reactions
• ATP + ATPase --> ADP + Pi + Energy
• Energy is usually not released as heat; Instead, it is coupled with an endergonic reaction 
• Redox reaction
• Involves oxidation and reduction
• A series of redox reactants result in the final oxidizing agent (that gets reduced) being the strongest 

Enzymes

• Reduces activation energy required for a reaction
• Enzymes are inhibited by competitive inhibitors (resembling the substrate) and noncompetitive inhibitors (alters binding site by binding to another site)
• Allosteric sites
• Activators: bind to these sites to stabilize an active form of the enzyme
• Inhibitors: bind to these sites to stabilize an inactive form of the enzyme
• Feedback Inhibition: Substrate --enzyme 1--> Intermediate A --enzyme 2--> Intermediate B --enzyme 3 --> end product...............end product inhibits enzyme 1.
• If end product concentration decreases, less enzyme 1 is inhibited and more end product is produced. 

Gel Electrophoresis

• Used in vector cloning (to isolate the gene of interest), RFLP (to compare fragments), DNA Sequencing

Vector Cloning (Overview, RE)

• Required materials: pBluescript vector plasmid, Restriction Enzymes, Ligase, Bacteria
• Steps
• Cut donor DNA with restriction enzymes, find the targeted DNA fragment through gel electrophoresis 
• Remove section of pBluescript using compatible RE, attach DNA fragment into plasmid at sticky ends, Bind the 2 pieces of DNA using ligase
• Reintroduce pBluescript into the bacterial vector through transformation
• Select bacteria that contains the targeted gene
• Introduce the selected bacteria to a host 

RFLP (Restricted Fragment Length Polymorphism)

•  Steps
• Cut DNA using RE (blunt)
•  Gel electrophoresis
• Southern blotting (or hybridization) onto a autoradiogram
• Compare sequences of interest 

PCR (Polymerase Chain Reaction) 

• Materials: Taq Polymerase, DNA primers, dNTPs, PCR Machine 
• Process: heat --> Cool --> Slight heat = 1 cycle
• The required piece of DNA will be obtained after the 3rd cycle 

DNA Sequencing

• Materials: DNA Polymerase, Radioactive DNA primers, dNTPs, ddNTPs
• All lanes (A T C G) will contain strands of DNA with its complete set of nucleotides 

PCR vs Vector Cloning

• Both amplify a sequence of DNA
• Vector Cloning is concerned with the protein as the end result, while PCR is only concerned with the DNA sequence. In fact, the sequence of concern in PCR might not even code for a protein.
• PCR replicates DNA through artificial methods, while Vector Cloning replicates DNA by exploiting bacteria's natural mechanisms.

PCR vs DNA Sequencing

• PCR requires a little amount of DNA, while DNA sequencing requires a lot. 
• The central idea of both techniques exploit the process of DNA replication 

When transcribing from the student's perspective (not the RNA polymerase II), do the following:

1. Find 5'TATA3'. It will be on both coding and template strands.
2. Look 5' to 3' on each strand and find AATAA. This will be the coding strand.
3. Look for intronic sequence by focusing on one strand of the intronic sequence. Look for it by running in the same direction indicated by the intron along one strand of the DNA. Then run along the other strand.

*Remember to also transcribe AAUAA on the pre-mRNA, but not to include the TATA box

In the following relationships, = indicate the same, while # indicates complementary:
Anticodon (in order of translation, ie.5' to 3' on mRNA) # 5'mRNA3' = 5'coding strand3' # 3'template strand5'
Hence Anticodon (in order of 5'mRNA3') = 3'template strand5'

Replication (1 and 2)
1. New DNA can only elongate from 5' to 3'. This means DNA polymerase III will move in the 3' to 5' direction with respect to the old DNA strand.
2. The leading and lagging strands are not the same on both replications forks in a replication bubble.
3. Sequence of Enzymes/Other Proteins
    Initiation - Helicase, Single Stranded Binding Proteins, Gyrase, Primase
    Elongation - DNA Polymerase III
    Termination - DNA Polymerase I, Ligase


Transcription (TFs (extra) and Spliceosomes)
4. In eukaryotes, RNA Polymerase II does not recognize the TATA box by itself. Transcription factors have to first bind to the TATA box and signal to RNA Poly. II.
5. Although the TATA box is read from 5' to 3', RNA Polymerase moves along the template (antisense) strand in the 3' to 5' direction. This causes an RNA molecule to elongate from 5' to 3'. This also means that the coding (sense) strand should be copied (by students, not RNA Poly II) from the 5' to 3' direction.
6. Transcription stops when RNA Poly II polymerizes an AAUAA sequence on the transcribed mRNA. This is equivalent to a TTATT sequence on the template strand or AATAA on the coding strand.
7. Sequence of Events
    Initiation - 5'TATA3' box, Transcription Factors, RNA Polymerase II
    Elongation - RNA Polymerase II (mRNA has U instead of T)
    Termination - AAUAA on mRNA
8. pre-RNA is modified by adding a 5' G cap and a 3' poly A tail to stabilize it. Introns are then cut out by spliceosomes (containing snRNP which contains snRNA and proteins), leaving the exons.

Translation (http://moodle.ayjscience.ca/mod/url/view.php?id=340&redirect=1)
9. mRNA is read 5' to 3' (which is also 5' to 3' on the coding strand). It is read codon by codon (3 by 3) starting from the codon AUG (ATG on coding strand), which codes for methyanine, until a stop codon is reached.
10. Prokaryotes have 30s and 50s ribosomal subunits; Eukaryotes have 40s and 60s subunits.
11. Translocation occurs when the ribosome shifts the tRNA from one site to the next. Because mRNA is bonded to tRNA at its anticodon, it also shifts along with it. This causes the mRNA molecule to move towards the 5' direction while the ribosome translocates towards the 3' direction.
12. There are 61 amino acid coding codons, but only 45 anti-codons. This is possible because of 3rd position wobble.
13. Sequence of Events
      Initiation - 5'AUG3', small and large ribosomal subunits, tRNA bound to methyanine
      Elongation - tRNA
      Termination - Stop codon

Extra: Control of Gene Expression: http://www.mcgrawhill.ca/school/applets/abbio/ch18/controlgene_control_of_.swf

The presentation on "Deaf by Design" made me realize that an entire culture exists within the Deaf community. Before, my limited knowledge of the deaf caused me to categorize them as part of an encompassing "handicapped" community, along with the blind and physically impaired. The article, however, changed that view. It also made me realize that other handicapped individuals are also part of a larger community with its own culture.

The presentation itself was quite interesting, mainly because of Mr Chung's delivery style. However, I would have employed more creative techniques to engage the class instead of the classic lecture/class discussion paradigm.