The Cove - Video Questions

2. Shown in this film, dolphin slaughtering is taking place in Taiji, Japan.

8. Fishermen trap the dolphins in the cove by creating noise underwater, taking advantage of dolphins' sensitive hearing by confusing them with the loud noises.  The dolphins are driven to the shore of the cove this way.

19. In response to the Deputy of Fisheries claims, one of the crew members had to deputy listen to a sound recording of the dolphins being slaughtered with their prolonging cries.
"If it was killed any other way, is it cruel?" (- when the deputy claimed that the dolphins were killed humanely)

21. When they first saw the cove, the two divers who were part of the crew saw dolphins swimming over nets, trying to escape towards the two at shore.  Sadly, the dolphin never made it as it died with blood trailing behind it in the water.

23. Going to Marineland, in a way, contributes to the dolphin slaughtering because most likely, the dolphins might have come from Taiji to be trained or anywhere else where dolphins are being trapped.  If they are not selected to live in a life of captivity, they will be killed.  By watching the dolphins at Marineland, we are giving them money to tell them that it's okay for them to trap dolphins away from their natural habitats.  With this money, we are simply fueling the industry that does this to dolphins.  It then becomes an indication to the industry to continue with what they are doing because there is a economical gain to be made from this.  This will keep the industry running until we stop watching dolphins and other animals do tricks in captivity.

Sea Kraits, Yellow Goatfish and White Trevally

The Sea Kraits

Sea kraits:

• genus: Laticauda
• species: colubrina
• highly venomous, but rarely bites
• up to 120 cm long
• alternating blue/yellow and black stripes
• return to land to mate
• lay eggs
• need to drink fresh water

Yellow goatfish:

• genus: Mulloidichthys
• species: martinicus
• "whiskers" from chin to search for food through sediments
• up to 39 cm long
• hunts in schools in the day, alone at night

White trevally:

• genus: Pseudocaranx
• species: dentex
• up to 1 m long
• yellow fins
• used in sushi

Sharkwater

What comes in mind when one hears the word "shark"?  For me, it would signal the beginning of the Jaws theme song.  You know, that low toned two-note repeats over and over again.  And then, in the danger of the music, I find myself thinking of the shark from the movie "Finding Nemo".  "Fish are friends, not food."  I think that is exactly what sharks are like.  If you don't bother them, they won't harm you in any way.  In fact, they are very misunderstood creatures.
During the documentary film "Sharkwater" that we watched in class (but I sadly missed out on), there was a black and white film teaching viewers how to protect themselves against shark attacks.  Although the PSA (if I may call it that) dealt with a serious matter.  I cannot help but laugh at their suggestions.  The advise that stood out most for me was to beat the water and make noise.  That got me thinking: "Wouldn't that just attract unnecessary attention?"  You began floating in the middle of the ocean peacefully and then you make yourself an easy target.  Why can we not treat sharks as any other fish?  Beautiful, graceful and harmless until you agitate it.
As for the matter of the shark fins ban.  I am glad they had enforced it.  Sharks do not deserve to be killed just for their fins, which is only 4% of their body weight.  Nothing should ever be killed unless there is a use for it and unless it is known that the impact would not be great.

Cellular Respiration Activity

Analysis:

1.  Proceeding through each trial, my strength decreased.
2. By the end of my trials, my fingers felt numb and my wrist had hurt for a period of time.
3. Warming up my hand and fingers might cause me to get more squeezes.
4. My non-dominant hand had less squeezes.  This might be because I don't use my left hand as much over my right and therefore it lacks strength.
5. There was energy spent by the muscles squeezing the clothespin.  During rest, the energy used will be replenished.

1.3 An Intro to Metabolism & 1.4 Enzymes

energy = ability to do work

catabolic reactions: breakdown of complex substances (ex)

anabolic reactions: synthesis of complex substances from smaller units (end)

metabolism = catabolic + anabolic

Potential energy is stored energy; Kinetic energy is used

work = transfer of energy

First Law of Thermodynamics: Energy can neither by created or destroyed, but converted

Energy is absorbed when bonds break

Energy is released when bonds are formed

entropy = measure of randomness/disorder ∆S ∝ disorder

free energy = energy that can do useful work

∆S ∝ 1/free energy

Second Law of Thermodynamics/Law of Entropy: disorder of the universe increases with any change

dead cell = when all its reversible reactions have reached equilibrium (blood/buffer?)

phosphorylation = attaching phosphate group to an organic molecule (synthesis of ADP + Pᵢ --> ATP)

OIL = oxidation is losing

RIG = reduction is gaining

enzymes = protein catalysts

lowers activation energy

substrate = substance catalyzed by an enzyme

active site = location where the substrate binds to

substrate + active site = enzyme-substrate complex

cofactors: Zn²⁺; Mn²⁺

coenzymes: NAD⁺ NADP⁺

competitive inhibitors = similar to substrate; blocks substrates to bind to active site

noncompetitive inhibitors = attaches to another site on enzyme --> changes shape of active sites

allosteric sites = receptor sites to inhibit/promote an enzyme's activity

activator = promotes (stabilizes active form)

allosteric inhibitor = inhibits (stabilizes inactive form)

feedback inhibition = substances catalyzed later on can be used as inhibitors

Biotech Test

That's right!  Here's another one...

Vector Cloning:

1. Isolate gene of interest
2. Cut using restriction enzymes (2 cut sites)
3. Take plasmid from bacteria
4. Cut using the SAME restriction enzymes (1 cut site)
5. Put gene of interest into plasmid using the sticky ends, glued together by ligase
6. RECOMBINANT DNA/ TRANSFORMATION
7. Culture
8. "Infect"

How to isolate the gene of interest: gel electrophoresis

Fragments get cut at various lengths.  Moves from NEGATIVE --> POSITIVE

Complete digestion: all fragments cut at restriction site

Incomplete digestion: all possible fragments are cut

VECTOR CLONING EXPRESSES THE GENE

Agarose Gel Electrophoresis Video

PCR WILL NOT

Polymerase Chain Reaction:

1. Denature DNA, break hydrogen bonds
2. DNA primers, dNTPs & Taq polymerase
3. Repeat

Replication is EXPONENTIAL after the THIRD CYCLE

Restriction Fragment Length Polymorphism

R -restriction enzymes

F- complete digestion

L -PCR

P- patterns (comparison)

DNA Sequencing (Sanger Method)

1. Denature DNA, break hydrogen bonds
2. DNA primers, dNTPs, ddNTPs & Taq polymerase
3. ddNTPs stop replication
4. PCR
5. Complementary sequence read from bottom to top

http://www.dnalc.org/resources/animations/sangerseq.html

Biotech, the things that they can do

Genetics Test

Time to apply what I've learned the last month (sigh... its only been 4 weeks of school?!!?).  I never like this part of learning... time restraints to solve questions.  Panic level just went up...

So, genetics.  Everything began somewhere, so let's start with the history:

1928: Griffith --> proteins do NOT carry traits

1952: Hershey and Chase --> DNA is the genetic material. Proteins are NOT the hereditary material

pyramidine - single ringed: cytosine, thymine

purine - double ringed: adenine, guanine

adenine = thymine

guanine ≡ cytosine

nucleotide = phosphate backbone, sugar, base

 

(difference of an OH group on carbon 2)

Bond types:

• glycosyl: sugar + nitrogenous base (CN) - intramolecular
• hydrogen bond: complementary nitrogenous bases; between nucleotides - intermolecular
• phosphodiester: sugar + phosphate (POC) - intramolecular

DNA replication is semi-conservative

1. helicase: unwinds DNA at replication fork
2. single-strand binding proteins (ssbps): attach to unpaired strands until replication begins
3. gyrase: enzyme that releases tension of unwinding but cutting the DNA strands and putting them back together again
4. primase: makes RNA primers --> signals elongation to
5. DNA polymerase III: elongates new DNA strands
6. DNA polymerase I: proofreads + converts RNA primers into DNA
7. ligase: joins gaps between Okazaki fragments (on lagging strand only)

DNA elongates ONLY in the 5' --> 3' direction

Template strand read 3' --> 5', creating a 5' --> 3' RNA strand

1. 5' TATA 3' box
2. transcription factors --> signals transcription to
3. RNA polymerase II: transcribes (don't want to stay in Toronto, but should go to University. Or else suffer getting disowned...) until
4. AATAA in the coding strand
5. 5'G cap
6. poly(A) tail
7. spliceosomes = snRNPs + snRNA: splice pre-RNA --> RNA
8. introns are OUT, exons are IN

This is pre-RNA/mRNA:

This is tRNA:

It is NOT from DNA. It floats.

RNA read in threes beginning at AUG --> Met

1. 5' AUG 3'
2. 40S ribosomal unit + 60S ribosomal unit = 80S ribosomal unit
3. P (Met), new tRNA at A, animo acid attaches to the one at A-->P-->E
4. stop codons (UAA, UGA, UAG)

Point mutation: change of ONE base pair of a gene

• base-pair substitution:
• silent mutation: no effect
• missense mutation: change amino acid
• nonsense mutation: stop codon
• frameshift mutation:
• insertion
• deletion
• inversion

(And now I have made my 10 points worth)

Deaf by Design

The first presentation of the year was given by Mr. Chung to show us what a Level 3 would look like.  If what he did was only a Level 3, then *sigh* we are going to have to work so much harder...
The presentation was on an article called Deaf by Design and was featured in Nature in 2004.  It introduced the situation of two couples with children opposite of what they wanted or expected (hearing couple with a deaf child and deaf couple with a hearing child) and a term called "deaf culture".  The controversial question behind the article was if a hearing fetus of a deaf couple should be aborted simply because it will be able to hear, or vice versa?
To me, when I was reading the article, I found the "deaf culture" to be very interesting.  It felt like it was a very unique group to be in.  While watching the video that was shown during the presentation, it was fascinating to watch all those hands and fingers dancing around, talking in a language that only certain people can use.  The video preserved the silence that they were in and there was a sense of calm in them not using their mouths but their hands.
Along with my fascination, I was enraged over the fact that expecting parents in the article would consider aborting their child due to something as small as being able to hear or not.  In my opinion, abortions should only be allowed if there are severe complications to the fetus.  I understand that deaf parents would be afraid of having a hearing child because it would mean that their child will be able to experience a side of the world that they never got a chance to.  Since they never experienced it, they fear that they might not be able to help their child and that will make their child drift further and further away from them.  However, if they teach the child and expose him/her to both hearing and non-hearing worlds, the child would get the best of both. They can live in the two societies and bridge the way for their parents to see the other side of the world.  The world is limitless, and losing one of the senses should not be a limiting factor.

BLAST FROM THE PAST: SBI3U

trait: a specific characteristic/feature represented by an organism

allele: a different form of the same trait

dominant: the form of a trait that always appear when an individual has an allele for it (BB or Bb)

recessive: the form of a trait that only appears when an individual has two (2) alleles for it (bb)

homozygous: an organism that has two (2) identical alleles of a gene (PP or pp)

heterozygous: an organism that has two (2) different alleles of a gene (Pp)

genotype: the combination of alleles for any given trait; the organism's entire genetic make-up   -----------------TRANSLATION----------------->

phenotype: the physical and physiological traits of an organism

Example: (respectively)

genotype: YY (homozygous dominant), Yy (heterozygous), yy (homozygous recessive)

phenotype: yellow seed, yellow seed [heterozygous: dominant is expressed], green seed

Parental (P) generation → First Filial (F₁) generation → Second Filial (F₂) generation

Punnett square: (a grid used to illustrate all possible genotypes of offsprings from genetic crosses)

test cross: a cross between a parent of unknown genotype and another of homozygous recessive genotype

Mendel's Law of Segregation: when gametes are formed, each must contain one allele from the two (2) of the parents

EXAMPLE: parent: Bb  possible gametes: B or b

Mendel's Law of Independent Assortment: if two (2) or more alleles are considered at the same time, the alleles have no influence over the separation of the others [disproven by linkage genes]

Law of Random Assortment: there is no telling in which gamete alleles will be in

incomplete dominance: first allele + second allele → new third allele (when heterozygous)

EXAMPLE: snapdragons (red + white → pink)

codominance: mix of first and second allele

EXAMPLE: roan horses/cows

multiple allelism: more than two (2) different alleles exist

EXAMPLE: blood types (A, B, O)

sex-linkage: alleles found only in the X chromosome has dominance over the Y chromosome

EXAMPLE: hemophilia

Cell → Nucleus → Chromosome → Chromatin → Gene → DNA→ Nucleotides ⤀ sugar, phosphate, nitrogenous bases

anti-parallel: 5-3 (other side) 3-5

Semi-conservative replication reduces the chance of genetic error because one strand of the original DNA is used as a template for the new, corresponding strand.