The Cove

1. Ric O'Barry
3. He became very involved because he was a dolphin trainer and saw a dolphin commit suicide.
5. Cetacean
7. Because they're receiving financial support from Japan.
9. They're pierced with spears and bleed to death.
11. To uncover what was happening in the cove and revealing it to everyone.
13. It happens when pollutants are introduced into an ecosystem. The consumers consume the plants that have been effected by pollutants. This will effect the food chain,
15. Because they say it's their tradition and they're told by the government that dolphins are eating all the other fish.
17. The cameras were disguised as rocks.
19. Showed him a cruel slaughter of dolphins on his phone.
21. They see a dolphin with lots of wounds swimming towards them escaping from the cove. The dolphin however died of the wounds.
23. Yes, because Marineland needs dolphins. The dolphins come from Taiji. Some of the dolphins are chosen and the ones not chosen will be killed by the fishers.

Photosynthesis and Cellular Respiration

Photosynthesis:

• photosynthesis transfers electrons from water to energy-poor carbon dioxide molecules, forming energy rich sugar molecules
• This electron transfer is an example of an oxidation-reduction process: the water is oxidized (loses electrons) and the CO₂ is reduced (gains electrons)
• Photosynthesis, the process by which green plants and certain other organisms transform light  energy into chemical energy . During photosynthesis in green plants, light energy  is captured and used to convert  water, Carbon dioxide  and minerals into oxygen and energy-rich organic compound
• In PSII, ( 680nm)  the electrons are removed from water molecules to create oxygen and protons. These protons are then directed through Photosystem I (PSI) to create carbohydrates from carbon dioxide

Cellular Respiration:

• Starting with 6 carbon sugar, glycolysis produces two 3 -carbon pyruvate molecules
• glycolysis does not require oxygen
• All the reactions in glycolysis occurs in the Cytoplasm, each step is catalyzed by a specific enzyme
• Krebs cycle begins after the two molecules of the three carbon sugar produced in glycolysis are converted to acetyl CoA
• ETC (electron transport chain) requires oxygen directly

Fetal Pig Dissection

  

  

We had the pig dissection during class on April 27 and 28. The pig's organs are labeled as followed:

The brain is a major part of the nervous system. It's responsible for controlling and coordinating the body.












The lens refracts incoming light in the eye.

 The heart supplies blood to the organs of the body.

 The lungs give blood oxygen from the air and take away carbon dioxide.

 The liver aids digestion by producing bile which converts glucose to fat.

 The kidneys are behind the liver and the other organs. They filter blood and remove unwanted waste while absorbing important nutrients.

The stomach is connected to the small intestine and it's the location where food is held to be broken down.

Nervous System

-consists of CNS (Central Nervous System) and PNS (Peripheral Nervous System)
-CNS includes the brain and the spinal cord while the PNS includes everything else
-2 main types of cells: neurons and glial cells
-glial cells support the neurons, nourish, remove waste, defend against infection
-glial cells also provide supporting framework for nervous system tissue
-neurons are the basic structural and functional unit of the system
-neurons conduct electrochemical signals and are organized into tissues called nerves
-all neurons share 4 common features: dendrites, a cell body, an axon, branching ends
-dendrites: -short, branching terminals
                  - receive nerve impulses from other neurons or sensory receptors
                  - relay the impulse to the cell body
-cell body: - contains nucleus
                  - site of cell's metabolic reactions
                  - processes input from dendrites
-axon:        - conducts impulses away from cell body and to terminal ends
-branching ends: -release chemical signals into the space between it and the receptors or dendrites of neighbouring cells

Gene Cloning Methods Comparison:

PCR:

-can amplify any piece of DNA without using cells like Sanger
-Heat is used to denature DNA
-Errors of PCR limits the number of good copies that can be made when large amount of gene are needed.
-DNA is incubated in a test tube with special DNA polymerase (Taq pol)
-DNA template, dNTP, primers (2 known sequence), and taq pol
-has repetitive steps of heating and then cooling DNA
-used in RFLP

Vector Cloning:
-Apply gene of interest into plasmid to bacterial cell
-DNA ligase glue cut sequence of DNA together
-Direct manipulation of genes for practical purposes
-gel electrophoresis and RFLP used to contain gene of interest 
-uses RE, vector DNA, and bacterial cells
-Takes longer than the other methods

Sanger DNA sequencing:
-can amplify any piece of DNA without using cells like PCR
-DNA template, dNTP, primers (1 known sequence), polymerase, and ddNTP
-the first letter of the new sequence is missing
-used to sequence DNA

All:
-all need DNA template 
-all produce new copies of DNA
-all manipulate DNA

DNA Translation

Initiation:

• For protein synthesis to begin, Initiation Factors assemble the small ribosomal sub-unit, mRNA, initiator tRNA, and large ribosomal sub-unit
• Small ribosomal sub-unit attaches to the mRNA near the start codon (AUG)
• Initiator tRNA (UAC) binds to the codon
• a large ribosomal sub-unit joins to form the active ribosome
• The 3 binding sites are A (Amino acid), P (Peptide), E (Exit)

Elongation:

• Protein synthesis occurs
• Polypeptide becomes longer
• when the initiator tRNA is bound to the ribosome, the A site is occupied by the tRNA
• Anti-codon base pairs with the second mRNA codon , ribosome can link the second amino acid together 
• Peptide bond forms between the first and second amino acids
• resulting dipeptide is attached to the tRNA at A site
• the mRNA moves along by one codon and enters the P site
• tRNA carrying the next amino acid enters the A site
• the polypeptide chain is transferred to the amino acids in the A site
• mRNA moves along by one codon and the tRNA which no longer carries an amino acid exits from the E site

Termination:

• the phase begins when a stop codon is reached on the mRNA
• the polypeptide and the components of translation are separated (KA-BOOM)
• A release factor (protein) cuts the polypeptide from the last tRNA
• the polypeptide will then fold into a 3D shape which is ready to perform its cellular activities 

DNA Transcription

Initiation: 

Initiation complex:
-Transcription factors recognize and locate the TATA box
-TATA box is the promoter region

• RNA polymerase II unwinds and opens a section of the double helix
• RNA polymerase II binds to the promoter region 
• RNA transcription begins in the coding strand of DNA with RNA polymerase II

Elongation:

• RNA pol II synthesizes a strand of mRNA (complimentary to template strand)
• "T"is replaced with "U" in the mRNA strand
• RNA pol II works in the direction of 5' to 3'
• mRNA is anti parallel with the DNA Template strand (Antisense), and is similar to the DNA Coding strand (Sense)
• transcription goes from upstream (promoter) to downstream (terminator)

Termination:

• Transcription stops and RNA pol II detaches from the DNA strand when it reaches the "AAA UAA" signal
• pre-mRNA becomes RNA by the addition of a G-cap to the 5' end and the addition of a 3'poly-A tail to the 3' end
• Intron sections of the mRNA are cut out by the spliceosome and the Exons are joined together 
• Spliceosome are assembled from snRNP which are proteins that contain snRNA who recognize the Intron segements

Quote of the Day #1

"Science and everyday life cannot and should not be separated." -Rosalind Franklin

The 3 Acts of DNA Replication

Initiation:

• Helicase unwinds and separates DNA (at the point of origin)
• Binding proteins bind to keep the DNA strands apart and unwound
• Gyrase enzyme cuts the DNA to release the tension
• Primase makes an RNA primer which the DNA polymerase III uses to begin replicating the new strands

Elongation:

• Polymerase III adds nucleotides to the 3' of the new strand
• DNA's anti parallel structure results in the new strands growing in opposite directions
• Leading vs Lagging strands:
•  the leading strand replicates continuously
•  the lagging strand replicates discontinuously
•  RNA primase synthesis RNA primer
•  Polymerase III extends the strand by adding new nucleotides to the 3' end
•  a new DNA fragment is generated from the end of each primer
•  the DNA fragments are called Okazaki fragments
•  Polymerase I removes RNA primer and fills the gap by extending the neighbouring DNA
•  Okazaki fragments are joined by DNA Ligase

Termination:

• Newly formed strands rewind
• Replication machine dismantles as the new DNA molecules separate from each other and the DNA replication is complete