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Browsing monthly archives: March 2019

Diffusion in Agar Cubes

Diffusion in Agar Cubes

Data Table:

Cubes in water:

Cubes turned pink:

1. In terms of maximizing diffusion, what was the most effective size cube that you tested?

The smallest size cube, which for us was 6.4 cubic centimetres in volume. This is because the smaller the cube the more efficient it’s diffusion is.

2. Why was that size most effecting at maximizing diffusion? What are the important factors that affect how materials diffuse into tissues and cells? 

The smaller the cube, the more membrane in proportion to the rest of the cube – therefore expanding the ratio of diffused area to non-diffused are.  The cubes are representative of cells, which require a larger membranes so that materials can diffuse in and out of the cell/tissue at a more efficient pace.

3. If a large surface area is helpful to cells, why do cells not grow to be very large?

Cells that are large are not as efficient at diffusion materials, they lack a large membrane in comparison to the rest of the cell. Larger cells must divide to create two smaller cells which each have a high SA:V ratio – therefore allowing the cell to have the best efficiency. Large cells restrict the organisms size – they must divide in order to keep a high SA:V ratio – when cells are growing their volume increases faster then their surface area causing the ratio to increase in the wrong direction.

4. You have three cubes A, B and C. They have surface to volume rations of 3:1, 5:2, and 4:1 respectively. Which of these cubes is going to be the most effective at maximum diffusion, how do you know this?

Cube C – Cube C has the highest SA:V ratio, the higher the SA:V ratio the more efficient it’s diffusion and the smaller it is.

5. How does your body adapt surface area-to-volume ratios to help exchange gases?

As an animal, we are multicellular organisms. Allowing larger cells to divide to form smaller cells with a high surface are-to volume ratio which provides us with the capacity to have adequate gas exchanges. If the ratio decreases it also reduces the rate of gas exchange.

Lungs speed up to provide a more efficient way for materials to diffuse. They do this with the help of alveolus – tiny air sacs on the lungs.

6. Why can’t certain cells like bacteria, get to be the size of a small fish?

Bacteria is a unicellular organism. When there is a unicellular organism it limits it’s size because the cell needs to stay small in order to maximize diffusion efficiency. If the cell grows to be to large, the surface area increases way slower then the volume causing a decrease in the SA:V ratio, it must divide. Bacteria cannot have it’s cell divide because it’s a unicellular organism.

7. What are the advantages of large organisms being multicellular?

Multicellular organisms would be plants or animals.

  • There are unique features: Gas exchange organs, Circulatory.
  • There is no problems with organism size, they can grow much bigger the unicellular organisms – due to the fact that they can have multiple large cells which can divide to create more and more efficient diffusors.

 

 

Edumund Fitzgerald – Ballad

The vignette of the ballade The wreck of the Edumund Fitzgerald written by Gordon Lightfoot portrays two prominent themes; environment and loss.  On a denotative level the poem explores the theme of environment that warns the reader of the deadly winds and dramatic weather conditions that await the passengers of the Edmund Fitzgerald. The sailors are encountered with a gruesome side to nature: “When the gales of November came slashin’/When afternoon came it was freezin’ rain/In the face of a hurricane west wind” (22-24).  Lightfoot’s description helps the reader to understand the destruction that the environment of  Lake Superior had on the sailors. By painting a picture of  demolition and tragedy in our minds, it becomes easier to grab the connotative theme of loss. The poem encourages us to sympathize with the sailors who were robbed of their lives.  We are given the change to understand the mourning that the town experience: “The church bell chimed till it rang twenty-nine times/For each man on the Edmund Fitzgerald” (51-52).  How the loss of these men should be remembered and honoured in the faces of those they have left behind. At the same time both themes intertwine, the theme of the destruction of environment can be met with the theme of loss and remembrance. As the reader a strong takeaway should be the importance of better preparation before setting sail onto a lake known to be selfish with its’ dead. The season they sailed in was not supposed to be detrimental however the yielding of the sailors will help future sailors to prepare even when sailing prior to the stormy season. “Superior, they said, never gives up her dead/When the gales of November come early” (55-56).

 

 

The Lion King – Narrative Poem

The Lion King – Narrative Poem (By Ashiana Sunderji)

 

Not long ago, there lived the animals of Pride Rock 

Organized in a hierarchy, the lions always, on the top

But all was not well, in the family tree

There were some falling outs, dethroning and jealousy

The story you know, is quite a different version

The real one I’ll share, stirs up quite controversion. 

 

The reigning king of the animal kingdom,  Mufasa 

Had Rafiki the Babboon introduce, his new-born cub, Simba

All of the animals appeared to celebrate the ceremony 

Except for Mufasa’s brother Scar, who sulked at home angrily

A direct descendant of the king, Simba was now in line for the crown

But, Scar had longed to be the one to whom the kingdom bowed down. 

 

Simba is raised happy, he learns, lives and sings

He tells his uncle proudly, “I just can’t wait to be king”

Scar, full of rage thinks up a plan

Encourages Simba to venture off to the shadowy place of the land

Not listening to warnings, he leaves for his journey

He takes his friend Nala and they leave in a hurry.

 

When they reach the graveyard, they find themselves surrounded

Scar had sent Hyenas, the cubs retracted, astounded

Mufasa came to the rescue, fighting them off

He sent Nala home and took his son for a walk.

 

Simba asked his dad if they would always stay together

Mufasa smiled sadly, his son thought life was forever

He explained how he would have to die for his son to step forth 

Simba’s sudden epiphany, left him feeling all hurt

Mufasa gestured to the stars in the sky

“Son” he explained “When I’m gone let them be your guide.

 

Meanwhile, full of frustration, Scar cooked up a new plan

He led Simba to a cliff, left him there and ran

Hyenas down below ready to attack

Simba felt a push and held onto a tree branch.

 

Crack! The branch went, Simba let out a cry

Mufasa came running, pulled his son up but then slipped off the side

Clinging to the rocks, he struggled back up

His brother appeared suddenly, he thought he was in luck

Scar dug his claws right into Mufasas’ paws

“Long live the king” he sneered as he pushed him right off.

 

Simba found his fathers body lifeless and limp

Scar yelled from a top “Run far away Simba, don’t be a wimp”

Scar returned home and pronounced them both dead

“Bow down to your new king” He boastfully said.

 

Simba now traumatized, searches far and wide

With no where to go, he longs to find somewhere to hide

He meets some new animals Pumbaa and Timon

A meerkat and a warthog who don’t want him to be alone

 

They take him to their jungle and become his new family

“Hakuna Matata” they chant as if, they have not a single worry.

The qualities they showed, demonstrate leadership

They take care of him, like a father-son relationship.

 

Simba feels deep inside that something is wrong

The people at Pride Rock are not getting along

He knows that he is not the right person for the task

He looks at the stars, hoping it’s not too much to ask.

 

One day, upon searching for help,  Nala arrives

She stumbles upon Simba, to her pleasant surprise.

She explains to him the evil that Scar has instilled

And begs Simba to come home, out of his own good-will

Simba declines he does not want responsibility

He encourages  Pumbaa to seek out this opportunity.

 

Pumbaa returns home with Nala, with a plan to succeed

He yells at Scar for ruining the land with his greed

Finally, though refusing to leave, Scar admits to his faults

Pumbaa fights him hard, and leads him off a rock

And just like that Scar is now dead

He got what was coming, if only he had looked ahead.

 

Who would have thought the warthog had it in him?

He was an inborn leader, logical, strong, and driven

Taken aback, Nala looked him in the eye

“Simba was your family so it’s you who should  lead our tribe.”

 

With slight hesitation, the animals of the Pride rock accepted him

A revolution had occurred, the chief was no longer a lion’s kin

The monarchy overthrown, could have been perceived as a controversy

Along with the fact that the new leader, a warthog, was also a minority.

 

Pumbaa led the animals, he was their guiding light

Simba came home, he knew what he had done was right

From this moment on, leadership was no dynasty

It went to the most deserving animal with no more hierarchy!

Protein Synthesis

RNA Transcription Model

  1. How is mRNA different then DNA

mRNA differs from DNA in the sense that it uses the ribose sugar in lieu of deoxyribose. It is shorter then DNA which allows it to exit from the nuclear pore – something that DNA is not capable of. It has one strand instead of two, making it a single backbone. It does not have an double helix shape. mRNA substitutes the pyrimidine uracil for the pyrimidine thymine, meaning that all the Adenines on DNA are paired with Uracil on RNA.

  1. Describe the process of transcription

This whole process is essential because DNA carries the information for protein synthesis but is too large and vital to the nucleus to exit. Protein synthesis must occur in the cytoplasm of the cell where the ribosomes, or protein factories are located. mRNA is derived form the process of transcription in order to be able to exit the nuclear pores with DNA’s information and produce codons to be read by the ribosomes later in translation for the construction of proteins.

  1. Unwinding and unzipping of DNA

DNA helix shape unwinds. The unzipping of DNA only happens at the desired location of the gene for specific information. Exposing instructions to build the gene that is running low only. The whole 85 million long nucleotide strand does not unzip. The sense strand is the strand that RNA has it’s information transcribed from. The sense strand is the strand that carries the information for protein synthesis. The nonsense strand is useless in this process  as it  would spit out non readable info if transcribed, it bonds as a compliment to the sense strand on DNA. 

2. Complimentary based pairing with DNA

Hydrogen bonds are formed between the complimentary based pairs. RNA does not posses the pyrimidine thymine and instead the pyrimidine uracil is bonded to adenine. Guanine and Cytosine remain pairs. The  RNA strand (in red) is base pairing with the nitrogen bases on the sense strand (in blue). This is essential so that the information is copied precisely. 

3.The RNA polymerase Enzyme, represented by a fuzzy peach in this picture facilitates the bonding between the nearby nucleotides. There is a sugar & phosphate covalent bond. 

4. Separation from DNA

RNA is separated from DNA, and DNA re-zips and returns to it’s original double helix shape.

Its’ the messenger RNA (mRNA) that is now developed by the process of replication of the information the gene on DNA possessed. It is checked and refined to ensure that the introns (unnecessary sections) are removed as well as to ensure that it is capped at the ends. It then can exit through the nuclear pore.

  1. How did today’s activity do a good job of modelling the process of RNA transcription? In what ways was our model inaccurate.

Accuracies:

  • We modelled only one strand for RNA and two strands in a helix shape for DNA.
  • We used a red strand to distinguish ribose sugar and blue for deoxyribose sugar.
  • We used a brown bead for Uracil the pyrimidine that binds with Adenine in RNA and a Blue beed for Thymine the pyrimidine that binds with Adenine in DNA.
  • We modelled RNA polymerase using a fuzzy peach showing how it bonds the nucleotides in a row.

Inaccuracies:

  • We demonstrated the transcription on our entire model as it was only 18 nucleotides long however generally the RNA strand should open up, as we demonstrated in the unwinding and unzipping process and then the RNA strand should enter like so:

  • It’s inaccurate how the sense strand and the RNA strand were connected with no sign of the complimentary strand as the above photo shows that the RNA strand should enter inside the double bond of DNA and even thought it has unzipped the RNA strand should not completely replaced the complimentary strand, as the model showed  in step 2:

  • We did not demonstrate the process of the mRNA being refined before modelling translation down below.

Protein Synthesis Model

  1. Describe the process of translation: initiation, elongation and termination.

Prior to Translation, the process of transcription (as shown above) must occur in order for mRNA to be derived from the DNA sense strand. Here is a short summary:

  1. Initiation

The mRNA released from the nuclear pores and connected by transcription bonds with a small ribosome subunit in the cytoplasm. The small and large ribosome subunits then bond together. Ribosome starts to read the mRNA that has bonded to it and waits for the start codon AUG. mRNA start codon is AUG, codons produced by mRNA are complimented by anticodons produced by tRNA. There are 64 3 letter codons and from these 64: 20 amino acids can be formed. There are two binding sites in the ribosome, one is the P site and one is the A site.  This means that a ribosome can contain two tRNA’s at a time. The initial tRNA binds to the P site, and it contains one amino acid  Methionine the amino acid formed by the start codon AUG.

2. Elongation

Another tRNA binds in the A site:

 

The amino acid from the initial tRNA moves to bond with the amino acid in the new tRNA in the A site. The initial tRNA is released.

This opens up a space and the remaining tRNA is moved to the P site. A new tRNA binds in the A site.

 

 

The process continues as the amino acids from the tRNA In the P site are moved to the A site so that the tRNA in the P site can be released. Freeing up a space so that the tRNA in the A site can move over to the P site, making room for the a new tRNA.

 

3. Termination

A stop codon is read on the mRNA  – UAG, UGA or UAA. There is no amino acid that is produced from any of these stop codons which means that the process is terminated. A release factor binds in the A site, in lieu of a new tRNA, causing the breakage of the bond between the tRNA and the P site (the final tRNA). The subunits of the ribosome disconnect and the polypeptide chain of amino acids – the protein, is released.

  1. How did today’s activity do a good job of modelling the process of translation? In what ways was our model inaccurate.

Accuracies: 

  •  The start codon was modelled, as well as the anticodon that complimented it, as shown in the initiation process above. Methionine was accurately the first protein.
  • The two sites (A and P) were shown as well as the process of the new tRNA bind in the A site and the proteins transfer from the older tRNA in the P site with the newest protein in the A site.
  • The process of elongation was modelled nicely.

Inaccuracies:

  • We did not show the initial smaller ribosome subunit bonding with only the initial tRNA. We showed the initial tRNA bonding with the entire ribosomal unit when in the textbook it explains that the initial tRNA bonds with  only the smaller ribosomal unit and then bonding afterwards with the larger ribosomal subunit for completion of the ribosome.

  • We did not model the stop codon UAG, UGA or UAA.
  • We did not model a release factor bonding in the A site in order for the polypeptide to dissociate and get released.
  • We did not model the separation of the ribosomal subunits just as we did not model when they bind together. The separation occurs with the release of the polypeptide.
  • Finally, we could have modelled it better, by showing the release of the tRNA each time a little more clearer then simply having it disappear. We could have shown it outside the ribosomal unit.

 

 

 

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