Video Worksheet: The Cove [ODD]

1. Ric O' Bary is the main "defender" in the documentary.
3. He was a dolphin trainer and witnessed the suicide of a dolphin.
5. Dolphins are in the Cetacean mammalian order.
7. Islands in the Caribbean allegedly support whaling because they are receiving financial support from Japan.
9. Once the dolphins are trapped, they are pierced with spears - bleeding to death.
11. The purpose of the documentary is to expose the gruesome Japanese fishing practices and the dangers of eating dolphin meat.
13. Biomagnification happens when the concentration of toxic substances increases higher up the food chain.
15. The fishermen refuse to stop because they believe that it is in their tradition, and that the government claims that dolphins are eating up all the fish.
17. The crew disguise the cameras as rocks and put them in less noticeable places.
19. When the deputy claimed that the dolphins were killed instantaneously, a crew member showed him on his phone a cruel slaughter of dolphins.
21. When they first saw the cove, the divers witnessed a struggling bleeding dolphin taking its final breaths.
23. By going to Marineland, I would be contributing to the profits of this business, which motivates it to continue and to grow. 

Photosynthesis vs Cellular Respiration

Photosynthesis: 

                             light

6CO2 + 6H2O --------------------> C6H12O6 + 6O2

                        chloroplast

Cellular Respiration:

C6H12O6 + 6O2 --------------------> 6CO2 + 6H2O + 36ATP

Differences: 

Similarities: 

- essentially the same reaction but reverse

- both involve in the exchange of gases (carbon dioxide, oxygen)
- both involve the movement of electrons through electron transport chain
- ATP is a key molecule in both
- ATP is produced through ATP synthase
- both take place in an organelle thought to be ingested (double membranes of mitochondria and chloroplasts)
- both have alternative pathways; photosynthesis (cyclic, C4, CAM) and respiration (fermentation) 

Light Dependent vs Light-Independent Reactions

The light independent reaction occurs in the stroma of the chloroplast, and the light dependent reaction occurs in the thylakoid of the chloroplast. In the light dependent reaction (the two photosystems), products from there are transported to the light independent reaction. In the light dependent reaction, photolysis splits two water molecules, and the H+ remains on the side, ready to be moved on to Photosystem I from II via the electron transport chain. Oxygen is released during Photosystem II. ATP synthase binds ADP and P together as the hydrogen atoms travel with the ATP synthase. In Photosystem I, NADP+ accepts and carries two pairs of hydrogen atoms, and while doing so, becomes NADPH. ATP and NADPH goes to the Calvin Cycle (light independent). In the Calvin Cycle, NADPH and ATP is taken in, and NADP+ and ADP is released to the light dependent reactions. Carbon dioxide is taken in, and glucose is released in the light independent reaction.

Light - Dependent:
makes NADPH
uses electron transport chain
needs sunlight

Light - Independent:
makes sugar
forms stored energy
uses calvin cycle
occurs in the dark

BOTH:
occurs in the chloroplast

Dissection: Fetal Pig

       A dissection was done in class to physically view the anatomy of the pig and to gain a better understanding of the organs in each focused system.

Before and After 

The sex of our pig is MALE because testis were present.

Brain - Controls almost everything that happens internally

Eye - (Lens and Cornea) Vision and optic nerves to transmit images to brain

Thyroid - Regulates metabolism and produces T3 and T4

Trachea and Larynx - The trachea allows for air passage while the larynx manipulates volume and pitch 

Heart - Propels blood throughout the body

Diaphragm - Below the lungs, a thin muscle (almost like a membrane) separates the chest cavity from the abdomen and allows for the expansion of the lungs when we breathe

Liver - Located below the diaphragm, the liver produces proteins for blood plasma, and is glycogen storage

Gallbladder - On the underside of the liver, the gallbladder produces, stores, and transports the bile to the duodenum after eating

Pancreas - In the upper abdomen behind the stomach, the pancreas produces enzymes that aid the in break down of left over food in the the stomach and produces insulin to regulate blood sugar levels

Spleen - Touching the pancreas, the spleen recycles old red blood cells and stores platelets and white blood cells

Small Intestine - 90% of the digestion and absorption of food occurs

Large Intestine - Absorption of water takes place

Stomach - Chemical (acids, enzymes, pepsin) and physical breakdown of food
We actually noticed a bit of some greenish black substance inside the stomach. We believe it to be amniotic fluid.

Kidney - Filters waste products from blood and is excreted as urine

Note: Neurons

The Structure of a Neuron
- have specialized cell structures that enable them to transmit nerve impulses
- four common features amongst neurons:

• Dendrites:
  - short branching terminals that receive nerve impulses from other neurons or sensory receptors, and relay the impulse to the cell body
  - numerous and highly branched (increases surface area available to receive information
• Cell Body:
  - processes input from dendrites
  - contains the nucleus and is the site of the cell's metabolic reactions
  - if the input is big enough, the cell body relays it to the axon in which it conducts the impulse away from the cell body to receptors or dendrites of neighboring cells (by releasing a chemical signal)
• Axon:
  - conducts the impulse away from the cell body
  - terminal end of axon branches into many fibers
  - sends chemical signals to the receptors or dendrites of neighboring cells to communicate with nearby neurons, glands, and muscles
  - some axons are enclosed in myelin sheath which gives it a shiny white appearance (myelin sheath: fatty, insulating layer composed of Shwann cells, protects myelinated axons and speeds up the rate of nerve impulse transmission)
• Branching Ends

Classifying Neurons

- three main types of neurons (sensory neurons, integration neurons, motor neurons) form the basic impulse transmission pathway of the entire nervous system

• Sensory Input:
  - sensory receptors receive stimuli and form a nerve impulse
  - transmit impulses from the sensory receptors to the central nervous system (brain and spinal cord)
• Integration:
  - process and integrate incoming sensory information, and relay outgoing motor information
  - found within the central nervous system
  - link between the sensory and motor neurons
• Motor Output:
  - transmit information from the central nervous system to effectors (muscles, glands, organs that respond to impulses from motor neurons)

The Reflex Arc

- reflexes: involuntary responses to certain stimuli
- reflex arc: simple connections of neurons that explain reflective behavior
- reflex arcs and withdrawal reflexes usually involve only three neurons to transmit messages (rapid)
- moves directly to and from the brain or spinal cord before the brain centres involved with the voluntary control have time to process the sensory information (don't feel the pain immediately but very shortly after when your brain processes it)

Biotech Techniques

Vector Cloning:
- natural DNA replication
- restriction sites
- incomplete digestion: not all sites are cut (no money no time)
- complete digestion: all sites are cut (have money have time)
- restriction enzymes cut covalent phosphodiester bonds of both strand
- DNA fusions can be name permanent by DNA ligase (seals strand by catalyzing formation of phosphodiester bonds)
- restriction enzymes need sticky ends
- fragment placed into plasmid of bacterial cell (transformation)
- 

PCR (Polymerase Chain Reaction):
- need DNA template, dNTP (dATP, dCTP, dGTP, dTTP), primers (need TWO known sequence), Taq polymerase (heat resistant)
- don't need primase, helicase, gyrase, ligase, and ssbps because it uses heat instead

Sanger's Method of Sequencing:
- need: DNA template, dNTP (dATP, dCTP, dGTP, dTTP), primers (need ONE known sequence), polymerase
- don't need primase, helicase, gyrase, ligase, and ssbps because it doesn't use heat
- need ddNTP (dideoxy NTP, two no oxygens), signals the stop of elongation since there is no oxygen for anything to attach on
Sequencing:
- the whole strand is a possibility
- strand can we cut on any letter depending on the ddNTP

Vector Cloning and PCR:
- used to replicate specific gene of interest

PCR and Sanger's Sequencing:
- need parental/ template strand
- artificial DNA replication

Vector Cloning, PCR, Sanger's Sequencing:
- DNA replicated and made in mass production

DNA Translation

* all definitions used are from McGraw-Hill Ryerson Biology 12 Textbook (Section 5.2)
APA citation: Braun, D., & Price, G. (2002). The Structure and Function of DNA. In Biology 12 (pp. 222-224). Whitby, Ont.: McGraw-Hill Ryerson.

Part 1:Initiation
1. mRNA: RNA that contains the genetic information of a gene and carries it to the protein synthesis machinery. It provides the information that determines the amino acid sequence of the protein.*
2. 5' AUG 3'
3. Ribosome
--> large subunit
--> small subunit

Part II: Elongation
4. tRNA (anticodons): reads codons, an RNA molecule that links the codons on mRNA to the corresponding amino acid for protein synthesis*
5. Codons: sequences of three nucleotide bases that specifies a particular amino acid or a stop codon*
6. Amino Acids
7. 3 sites
--> A (entrance): carries the tRNA carrying the growing polypetide chain
--> P (prision): carries the tRNA with the next amino acid
--> E (exit): tRNAs are discharged and leave the ribosome 
8. Peptide Bond: formed between the polypeptide in the P site with the new amino acid in the A site
--> separates the tRNA at the P site from the growing polypeptide chain and transfers the chain (now one amino acid longer) to the tRNA at the A site

Part III: Termination
9. Stop Codons: UAA, UAG, UGA
10. Everything disassociates.

How to transcribe a DNA sequence: 
1. Locate the TATA box
2. Identify the Coding Strand (similar to RNA) (5' TATA ------>3' AATAA)
3. Look for Terminator (AAUAA)
--> TTATT on Template Strand
--> AATAA on Coding Strand
4. Find introns
5. Find Start Codon and group the bases into 3s
6. Stop when a Stop Codon is approached.
7. Do not write "stop" when translating the sequence to amino acid sequence