Translation

 Background knowledge

• The complete mRNA leave the nucleus and goes into the  cytoplasm
• polypeptide= many proteins
• The goal of translation is to create proteins

Act I
Initiation:



tRNA forms a complex with the with the ribosomal sub units
 this complex then binds with mRNA at the 5' cap and scans the mRNA

transfer RNA brings amino acids that correspond to the codons on mRNA
tRNA recognizes these codons by the anticodon loop attached to it
The starter codon is AUG which corresponds with the amino acid Methionine , the anticodon loop for it is UAC

Elongation
The polypeptide becomes longer one amino acid at a time
The first tRNA carrying the starter amino acid AUG goes to the P site
when the next tRNA brings the amino acid the previous tRNA goes to the E site

Termination
The codons UCC, UCA, UCG, UCU have no corresponding tRNA sequence so this process stops
Now the termination proteins release the ribosome from the mRNA, the polypeptide chain is released

Transcription

ACT I

• Transcription factors attach to the TATA box also known as the promoter
• The sequences before the TATA box are known as upstream, after the TATA box is known as downstream

• Transcription factors that bind to the the TATA box help attract RNA polymerase 2
• Once  RNA Polymerase 2 binds to transcription factors a transcription initiation complex is created and RNA starts transcribing
• A DNA strand can be transcribed  by several RNA polymerase 2, at a time

Act II

• The double stranded DNA is separated at certain points by RNA polymerase 2 
• The strand being transcribed is the template strand ( antisense) the other strand is the coding strand( sense) 
• The  RNA polymerase 2 binds RNA nucleotides to the template base pairs
• As the RNA strands grow they trail off from each polymerase and the DNA strands reform a helix 
• The RNA strand and template strand are anti-parallel
• Genes are read 3'-5' which creates a 5'-3' RNA molecule
• In RNA there is ''U'' instead of ''T" in the base pairs e.g A=U , T=A

Act III

• The terminator signals the end of transcription, it is the sequence AAUAAA
• At the end of the pre-mRNA molecule that was just synthesized a G cap is added to then of 5' and a Poly(A) tail is added at the end of the 3' 
• Introns (junk sequences that must be removed)
•  Extrons ( sequences that must be expressed) 
• The  spliceosome loops and cuts out the introns 
• It is composed of proteins and  snRNP
•  Every snRNPs has  a small nuclear RNA molecule/ snRNA
• The spliceosome also joins the exons, to create a mRNA molecule
• A messenger RNA has now been synthesized from the DNA strands

DNA Replication: Initiation,Elongation,Termination

Act I 

Initiation

Helicase splits/opens the template DNA strand at the replication fork = creation of bubble

Single-strand binding proteins stabilize the unwound parental DNA , otherwise there is a risk the strands will bond back together

A lot of tension has built up , from parts of the DNA strands being straightened. The gyrase cuts the stands to release tension

RNA primase creates RNA primers that act as a starting point for replication

The DNA polymerase III recognize the primers

Act II

Elongation 

The parental strands are replicated  in the direction of 5' to 3' 

Leading strand- Polymerase III begins adding nucleotides to the RNA primer in the direction of the opening  replication fork, it does this continuously

The lagging strand waits for enough of the replication fork to open ...... when it has opened sufficiently a DNA primer  attaches to the parental strand and polymerase III  makes a new starting point( discontinuous process)

The second strand is composed of  Okazaki fragments ( 100-200 nucleotides long) and RNA  primers 

Lagging= discontinuous, RNA primers, Okazaki fragments , polymerase III

Leading= continuous, 1 Primer, Polymerase III

The two new strands are assembled in the opposite direction

Act III

Termination 

Polymerase I removes the RNA nucelotides  one at a time, replacing them with DNA nucleotides, this process is catalyzed by DNA ligase 

Polymerase I and polymerase II( slow enzyme)  are repair mechanisms, they work to repair damage done to DNA during replication, and proofread

Catabolism & Anabolism

Catabolism

• Chemical reactions that result in the break down of complex organic molecules into simpler substances
• Releases energy that is used to start chemical reactions

Anabolism

• Simpler substances combine to become more complex
• requires energy
• build new molecules
• store energy

* Energy from catabolic reactions is used for anabolic reactions

Anabolic + catabolic=Metabolism 

Non-Cyclic

Anabolic reaction

Cyclic

Anabolic reactiom

Calvin Cycle

Anabolic reaction

Glycolosis

Catabolic reaction

Catabolic reaction

Krebs

Catabolic reaction

The Sad But True Story:Of The Passenger Pigeon

The Sad But True Story: Of The Passenger Pigeon (Ectopistes migratorius)





The passenger bird once constituted an estimated 25-40 % of America's bird population

When Europeans first discovered America there were 3-5 billion passenger pigeons

Never again will  a passenger pigeon soar through the sky... as 100 years ago they became extinct

Millions of these magnificent birds would travel in one flock.One flock traveling at sixty miles an hour would take several days to pass over a particular area.

 When they  migrated in  March and April one flock could block out the sun, making the sky dark for days.



The passenger pigeons had almost no defense mechanism, so they would travel in mass flocks as a means of protection against predators.

They would roost and feed in hardwood forests, until their natural habitat started being diminished and turned into farmland. Causing the pigeons to land on farmer's fields.

Humans started to kill passenger pigeons
- To protect their crop from being eaten
-  they were a cheap source of food , which was great for feeding slaves




The real slaughter of passenger pigeons started in the 1800's
They were :

• netted by baiting traps
• shot at nesting sites
• knocked out of  trees with long sticks
• the fumes of sulfur would case the birds to become dazed and fall out of trees

By using trains hunters could track and follow the flock giving them no rest and no time to mate and care for their young

In Michigan 50 000 pigeons were killed per day for 5 consecutive months.

In 1860 the decrease in population was noticeable, but nothing was successfully done to  protect their species

By 1890 they were considered a rare species, with only a few thousand remaining

A Glimpse of Hope

Finally the voice of conservationists was heard and a bill was passed  in Michigan,   making it illegal to net pigeons within two miles of a nesting area

However this law was hardly enforced... and the mass hunting continued

 In 1897 a ten year hunting ban on passenger pigeons began 

 It Was Too Late

 Despite conservationists efforts
 Not being able to breed and protect their blind and now defenseless young ,the population plummeted

Without a large flock the pigeons were defenseless to prey and unable to follow normal migration and mating habits

By 1914 only one of the species remained

Never again will man witness the beauty of  millions of passenger pigeons filling the sky above




Last of her species, died at 1 p.m.,
1 September 1914, age 29, in the
Cincinnati Zoological Garden.

Photosynthesis

Photosynthesis

- It was developed 450 million years ago 


Chemiosmosis:  The movement of chemicals from high to low concentrations via semi permable membranes

Oxidized = Giving away electrons
Reduced= Gaining electrons

PSI needs P700 from the sun
PSII needs to receive P680 from the sun

Chlorophyll is a green pigment found in chloroplasts









Thylakoids store molecules that absorb  energy from the sun


Light-dependent reaction
traps solar energy and uses it to generate ATP and NADPH

light- independent reaction
Assimilates carbon dioxide to produce an organic molecule that can be used to produce biologically important molecules

Hydrogen= single proton


NADP exists to carry energy around

ADP spins very fast and the protons need to slow it down to form ATP

Fetal Pig Dissection

Fetal Pig Dissection 

Below abdominal cavity

Step 1

Identifying the sex of the pig
-Finding no opening around the umbilical cord and a small opening near the anus we discovered it to be female





Step 2
 

-Cutting below the abdominal cavity to reach the organs

- Many thick layers of skin and fat protected the pig's organs making it hard to cut open


Step 3

Delicately detaching the bottom layer of  skin from organs, as to not puncture organs


Step 4



Viewing the intestines and liver




Step 5



Removing the liver

Step 6




Removing the intestines

Step 7


Removing the stomach carefully as not to rupture it
we noticed the esophageal sphincter( small opening)

Step 8




Removing the pancreas
We found it to be surprisingly thin and short




Liver, intestine, pancreas


Step 9


After removing the intestines, stomach, liver,and pancreas; we were able to locate the kidneys located near the pig's back

Step 10

cross section of the kidney

Step 11


Removal of the Ovaries




Close up


Above the Abdominal Cavity

Step 12
Removing the brain










Step 13



Removing the eye

The Story of Stuff: A critical Analysis

The Story of Stuff: A critical Analysis

1.     The message of “The Story of Stuff” is that the  production system is in in crisis. Annie explains how we as consumers need to stop buying  so much stuff if we want to save what is left of Earth’s resources . Also that in order to create the products we as consumers love; workers are being exploited.  Also chemicals are being released into the atmosphere and these chemicals that cote our products are endangering our health and the worker’s health.  I think the overall take home point for each consumer is that with every dollar they spend they can choose to support this toxic cycle or make choices that support a healthy planet.

This is a system in Crisis!

3.       Annie uses the persuasive technique of showing the viewer why what she is saying affects them directly.   For example she focuses on the harm that the production cycle has on the consumer, the factory workers, and those who lose their resources as to sway each of these categories of people that this vicious cycle has to stop.  As a consumer I was swayed when she mentioned that most synthetic chemicals have not been tested for safety.  Also when she discussed perceived obsolescence I felt betrayed by the corporations who design my products.  As a consumer I was disgusted by these facts and therefore I believe Annie’s persuasive technique of making the message personal to the audience to be highly effective.

What are we really allowing into our homes, our bodies, our atmosphere? 

5. Annie is fully on the side of the environment and strongly against corporations and hold prejudices against the government. Therefore all of the information she presents is missing half the picture and is coming from this perspective. Even if she is telling us facts the whole picture is much more complicated than her bias allows us to perceive. For example:  Yes, harming the environment is wrong but people desperately rely on the jobs she is so casually saying shouldn't exist. 

7.     I believe that the story of stuff makes convincing arguments as her points are explained thoroughly and with details.  For example Annie did not just state that chemicals that are part of the production process are very harmful, she used examples such as the chemicals put on pillows. Also she explained the whole cycle of production thoroughly which helped the viewer see the damage being down to the Earth and humans at each stage.  Based off all the evidence and explanations in the video I am convinced that recycling is not enough and serious life choices need to be made on the individual level in order for change to occur.

If  You don't make the change, who will?  

Video Worksheet: The Cove

Is Marine land as happy a place for the dolphins as it is the visitors? 

Worksheet: The Cove

1. Rich O’Barry is the main defender of dolphins in this documentary.

3. Rich O’Barry became involved in saving the dolphins after many years of training and doing shows with dolphins. His main dolphin named Cathy became depressed and committed suicide.  Through working with dolphins he knew how intelligent dolphins and came to realize that captivity is no place for them.  After years of helping to build up the commercial dolphin industry he feels responsible for helping show the world the truth about the horrors of the cove where dolphins like Cathy are captured.

5. Dolphins are part of the cetacean mammalian order.

7. Small Islands in the Caribbean are being bribed by Japan to support whaling in exchange for financial support.

9. When the dolphins are trapped in the cove representatives from aquariums and other organizations that use animals for amusement come and pick which dolphins they want. They usually want young females as they are popular with crowds.

11. The goal of the documentary is to raise awareness and reveal to the world the horrors that are happening in the cove of Taiji. The creators of the documentary hope that people who learn about these atrocities will speak up and help stop the killing of dolphins.

13. Bio magnification occurs when small fish have mercury within them from pollutants and then mass quantities of these small fish are consumed by larger fish.  This makes the mercury intake for large fish very high. The higher up in the food change the more the mercury intake.  Small fish have small quantities of mercury in them but dolphins who feed off thousands of small fish have very high mercury levels.

15. The fisherman think about the offer and the refuse because they have been told by the government that the reason for the killing the dolphins for meat is pest control. The fishermen have been told that dolphins and whales harm the Japanese fish supply making them pests.

17. A special effects team hides cameras in rocks.

19. When the deputy of Fisheries claims that the dolphins are killed instantly and humanely a crew member shows him a video. The video shows dolphins being stabbed by spears and frantically swimming around gushing blood and other ways that dolphins are slaughtered that illustrate the lack of humanity in the act.

21. A dolphin that is captured and wounded swims over nets trying to reach them but is badly wounded and does not make it to them.  The divers are deeply disturbed by seeing a creature they love so much understand that they are there to help; but not being able to help it.

The Dolphins we All Adore

The Costly Price For Show Case Dolphins

23. Going to marine land supports the fishermen who make around $ 150 000 for a show case dolphin. If these fishermen didn’t make such a large profit they would not being killing as many dolphins as the industry would be much smaller. When fishermen are selling dolphin meat they only make $600 per dolphin. Therefore the prospect of selling a dolphin for commercial reasons makes this market much bigger and draw people to the job.