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Agar Cubes Lab

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1.       n terms of maximizing diffusion, what was the most effective cube you tested?
 The 1cm^3 cube was the most efficient at maximizing diffusion.

2.       Why was size most effective at maximizing diffusion? What are the important factors that affect how materials diffuse into cells or tissues?
   The ratio of the surface area to volume was 6:1, meaning that this cube had 6 times the space to absorb the solution than needed to be coloured.

3.       If a large surface area is helpful to cells, why do cells not grow very large?
 Cells growing larger would increase the surface area, but it would also increase the volume that the surface area needs to absorb nutrients for and would thus be ineffective.

4.       You have 3 cubes, A, B and C. They have surface-volume ratios of 3:1, 5:2 and 4;1 respectively. Which of these cubes is going to be the most effective at maximizing diffusion, how do you know this?
Cube C will be the most effective at maximizing diffusion, as it has the greatest ratio of surface area to volume. It has more surface area that is able to absorb nutrients for the comparatively small volume.

5.       How does your body adapt surface area to volume ratios to help exchange gases?
 Smaller cells and organelles have evolved over time to be able to efficiently absorb and exchange gases to power themselves and the cell they belong to.

6.       Why can’t certain cells, like bacteria, get to be the size of a small fish?
Because the ratio of surface area to volume would be unsustainable and not enough nutrients would be able to be absorbed to power the cell.

7.       What are the advantages of large organisms being multicellular?
 Have many small cells better allows each to be able to function properly and to be able to exchange nutrients and gases with one another with minimal effort, as well as for nutrients to be absorbed most efficiently.

 

DNA and Protein Synthesis

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  1. Explain the structure of DNA – use the terms nucleotides, antiparallel strands, and complementary base pairings. DNA belongs to the group of molecules called nucleotides, which all contain a sugar, nitrogenous base and a phosphate group.
  2. How does this activity help model the structure of DNA? What changes could we make to improve the accuracy of this model? Be detailed and constructive. We used blue pipe cleaners with black beads to model the sugar and phosphate groups that make up the DNA backbone, as well as white pipe cleaners with coloured beads to represent the four nitrogenous bases. Each white pipe cleaner was hooked to the one across from it that held its complementary base pair; the hooks representing the hydrogen bonds. Reducing the length of the white pipe cleaner could make the model more accurate, as in reality there is nothing separating the nitrogenous bases from the backbone of the molecule.
  3. When does DNA replication occur? DNA replication occurs during mitosis. To create a clone of the cell it is dividing from, the nucleus must also contain an exact replica of the chromosomes and DNA in the previous cell and every other cell in the body for it to do its job properly.
  4. Name and describe the 3 steps involved in DNA replication. Why does this process occur differently on the ‘leading’ and ‘lagging’ strands? 1. Unwinding and ‘unzipping,’ this process is completed by the helicase, which runs down the strand of conjoined DNA and breaks the hydrogen bonds between the complementary base pairs, effectively creating two parent strands. 2. Complementary base pairing. Completed by the polymerase, it follows the helicase down the strand to pair the bases exposed on the parent strand. Because the strands are anti-parallel, the polymerases must travel in opposite directions. While one may be able to follow the helicase, the other must read chunks at a time in the opposite direction and backtrack to return to the helicase. 3. Joining of adjacent nucleotides. The ligase then follows the polymerase down the strand and joins the fragments together to create a fully formed backbone and newly replicated DNA molecule.
  5. The model today wasn’t a great fit for the process we were exploring. What did you do to model the complementary base pairing of adjacent nucleotides steps of DNA replication? In what ways was this activity well suited to showing this process? In what ways was it inaccurate? The model was able to show the general placement of each part of the process but was not able to fully replicate the bonds between the nitrogenous bases and the backbone of the molecule.
  6. How is mRNA different from DNA? Besides having their own unique nitrogenous base, (uracil and thymine) DNA and mRNA are structurally different as well. While DNA can be up to 85 million base pairs long, mRNA is usually only 1000. Also, while DNA has two backbones made from the sugar deoxyribose, mRNA only has one, made from ribose.
  7. Describe the process of transcription. DNA unwinds itself from the chromosome it was contained in and is unzipped. An RNA polymerase reads the ‘sense’ strand and pairs the bases with their complementary RNA counterparts. Once complete, the newly formed mRNA molecule breaks off of the DNA, which re-zips itself and rewinds itself back into the chromosome it came from.
  8. How did today’s activity do a good job modelling the process of transcription? In what ways was our model inaccurate. The model did a good job showing the general structure of the molecules involved in the process but again did not properly show the proportions to which everything is actually to scale.

(Picture were not able to be uploaded at this time)

What Darwin Never Knew

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Charles Darwin’s findings in South America and the Galapagos islands promted him to think of what has been called the “Greastest Idea of all time”; The theory of evolution. In South America, Darwin found the fossils of a giant sloth, which he was able to trace back to modern, smaller size sloths that were still alive. This was the evidence that put his train of thought in motion. Later, he travelled to the Galapagos islands and made many observations there, as well as collecting samples of different animals, most notably the Galapagos finches. However, Darwin did not fully complete his theory until he returned home. There, he studied his findings and was intruiged by the finches. He noted all the similarities and differences between the finches, such as their different sizes and beaks. Darwin arrived at his theory after studying embryos of different species and noted that they all started out very similar, and that the developmental process was where they began to slowly differentiate. This sparked an idea of a common ancestor. For example, a single species of finch could have journeyed to the Galapagos and, over time, have evolved into many different species. Darwin’s theory was absolutely correct, however, he had no idea how it happened.

What Darwin never knew about was DNA. A species gradually changes over time through random genetic mutations, which can give different characteristics to a member of a species. Should this mutation be beneficial to said member, chances are that they will live long enough to reproduce, and thus pass on the mutation to their offspring. Keeping a specific group of a species isolated long enough, (isolating the gene pool), will broaden the chances of a new species forming, since the two seperated groups will keep different mutations contained within their individual offspring. Given enough time, the single species could easily become two. This is how a single common ancestor could’ve, over many years, become the millions of species that we have on our planet today. In conclusion, DNA was the missing link to Darwin’s theory of evolution, the key to all life on earth.

Biology Kingdoms

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Archaebacteria

Sulfolobus islandicus

growth occurs in volcanic springs, optimally at a temperature of 80 degrees celcius with a ph of 2-3

growth occurs in volcanic springs, optimally at a temperature of 80 degrees Celsius with a ph of 2-3

Ignicoccus hospitalis

Lives in marine hydrothermal vents temperatures range up to 464 degrees Celsius

Lives in marine hydrothermal vents temperatures range up to 464 degrees Celsius

 

Eubacteria

E-coli

A bacteria found in the intestines of humans and animals, it is usually harmless except for certain strands which most commonly cause illness by ingesting uncooked beef.
A bacteria found in the intestines of humans and animals, it is usually harmless except for certain strands which most commonly cause illness by ingesting uncooked beef.

Salmonella

A bacteria most commonly found in animal produce, such as beef, poultry, eggs and milk.
A bacteria most commonly found in animal produce, such as beef, poultry, eggs and milk.

 

Protist

Amobea

A single-celled organism that uses protoplasm to hunt and move
An unicellular organism that uses protoplasm to hunt and move

Volvox globator

An organism that travels in colonies living in water. The organisms link to eachother through cytoplasm and
An organism that travels in colonies living in water. The organisms link to eachother through cytoplasm and propel the colony through the water.

Fungi

Agaricus bisporus

Also known as a Portobello mushroom, it is found in European and North American grasslands.
Also known as a Portobello mushroom, it is found in European and North American grasslands.

Lichen

A fungus that can grow in nearly any environment, from the desert to the tundra to solid rock
A fungus that can grow in nearly any environment, from the desert to the tundra to solid rock

Animalia

The common spotted cuscus

A nocturnal marsupial often found in northern Australia, it is often confused with a monkey or sloth, due to its sluggish movements.
A nocturnal marsupial often found in northern Australia, it is often confused with a monkey or sloth, due to its sluggish movements.

Grimpoteuthis

this species of 'umbrella octopus' lives at a depth of 3-4km underwater, their floppy ears protruding from their head is what earns them the nickname 'Dumbo'
this species of ‘umbrella octopus’ lives at a depth of 3-4km underwater, their floppy ears protruding from their head is what earns them the nickname ‘Dumbo’

Plants

Rafflesia arnoldii

The world's largest flower spans 3ft in diametre and pollinates by giving off an odour of rotting meat to attract flies and other bugs to pollinate when in bloom
The world’s largest flower spans 3ft in diametre and pollinates by giving off an odour of rotting meat to attract flies and other bugs to pollinate when in bloom

Baobab

The baobab
The baobab is a tree that can live to be 500 years old and can store up to 300 litres of water in it’s trunk, typically growing in Africa and Australia.

Water For Elephants: Connection

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CAPTAIN! my Captain! our fearful trip is done;
The ship has weather’d every rack, the prize we sought is won;
The port is near, the bells I hear, the people all exulting,
While follow eyes the steady keel, the vessel grim and daring:
But O heart! heart! heart!
O the bleeding drops of red,
Where on the deck my Captain lies,
Fallen cold and dead.
O Captain! my Captain! rise up and hear the bells;
Rise up–for you the flag is flung–for you the bugle trills; 10
For you bouquets and ribbon’d wreaths–for you the shores a-crowding;
For you they call, the swaying mass, their eager faces turning;
Here Captain! dear father!
This arm beneath your head;
It is some dream that on the deck,
You’ve fallen cold and dead.
My Captain does not answer, his lips are pale and still;
My father does not feel my arm, he has no pulse nor will;
The ship is anchor’d safe and sound, its voyage closed and done;
From fearful trip, the victor ship, comes in with object won; 20
Exult, O shores, and ring, O bells!
But I, with mournful tread,
Walk the deck my Captain lies,
Fallen cold and dead.

– Walt Whitman

This poem shares many similarities to the climax and falling action of the book Water for Elephants, as it represents the clean break of a long journey for Jacob and Marlena. At the end of the book Jacob and Marlena know that they are in danger and must leave the circus soon, to escape from August and Uncle Al, and the potentially fatal fate that awaits them there if they don’t. However, the night they are to make their escape, the animals are all let loose, causing a stampede in the middle of the show. In the chaos that ensues, Rosie the elephant kills August and a few days later Uncle Al is found dead. Since the people in charge of the circus are no longer able to perform their duties, the circus comes to an end as well. The circus collapsing marks the end of a long voyage for Jacob and Marlena, and it severs a clean break for them since they know that now there is no home to return to, even if they wanted to go back. Similarly, the end of the voyage in the poem leaves no other option but to continue forward. The Captain, however, has gone down with the trip, further impeding the possibility of travel, except by a different ship. I feel that this poem relates more to Marlena than Jacob, in refernce to the captain, because Marlena was August’s wife who loved him, at one point. Though they had the rockiest of relationships and she left him before he was dead, there is still an emotional attachment there, and she still mourns her husband even though she has a bright future waiting ahead of her, albeit uncertain. Similarly the sailor in the poem mourns his captain in the face of victory. With no more captain to direct the ship, the voyage ends, marking a new beginning for all aboard.

TKAM: Thematic Statements

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When one person lacks empathy towards another, the result can be prejudice.

In the novel To Kill a Mockingbird, Harper Lee explores how a lack of empathy towards other people can lead to predjudice through Jem and Scout, two young children beginning to lose their innocence and become aware of the world around them. This includes a valuable lesson taught to them in many different forms but best summed up by Atticus, their father, in chapter 3. “You never really understand a person until you consider things from his point of view(…)until you climb into his skin and walk around in it,” (Lee, page 39).
This lesson is reinforced when they have an encounter with Mrs. Dubose, the old lady who lives up the street and seemingly takes pleasure in insulting the children whenever they pass by. She has built herself a reputation of being “vicious” (page 133), as described by Scout. The children express their feelings to Atticus who tells them to pay her no mind; she’s a sick old lady. Jem has difficulty taking this to heart, however, and ends up destroying Mrs. Dubose’s camellias in a fit of anger. As punishment he is made to go read to Mrs. Dubose for two hours six days of the week. During his time there, he finds out how sick she really is and, after her death, that she was a recovering morphine addict. The children then realize where Atticus’ respect for her came from, and they discover some of their own for her and her bravery. After this, they learned a valuable lesson in seeing past people’s faults by putting themselves in others’ shoes. Was Jem able to do this before, Mrs. Dubose’s camellias might have been spared.
Another experience with Boo Radley leads to the same conclusion. Because the children, nor most anyone, has seen him outside in years, rumors have taken root in people’s minds that he is crazy and dangerous. Of course, children being as impressionable as they are, the Radley lot is avoided at all costs. However, their curiosity eventually gets the best of them and they want to find out if the rumors are true. After a few dangerous escapades and close calls, their mind becomes preoccupied by other things. But their curiosity is eventually satiated in finding out that Boo Radley has been there protecting them all along, even when they didn’t realize it. At the very end of the book, Scout puts herself in Boo Radleys shoes and sees that the most feared person in Maycomb is actually the one with the biggest heart.

Inquiry Post # 1: Caged Bird

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Can hope, when discouraged, lead to resilience?

The poem ‘Caged Bird’, by Maya Angelou, describes the situation of the imprisonned bird; and how it longs to be free like the others. This desire is expressed in it’s song, For the caged bird/sings of freedom. The bird in this poem, though trapped, does not give up hope, but instead uses the ability he has. His wings are clipped/and his feet are tied/so he opens his throat to sing. This bird in the poem, though defeated, still took the action he could against his imprisonment and made known that his hope of freedom was not gone or forgotten, but only more definite than ever. In the book ‘To kill a Mockingbird’, by Harper Lee, the black community of Maycomb County has little say in what hand they are dealt in life, and when Tom Robinson is falsley accused of the rape of a white girl, they know there is nothing they can do that will change the outcome. However, they go to the trial anyways and, with Atticus’ help, a presentable case defending Tom Robinson is made. Despite the evidence being perfectly clear, the jury has no intentions of letting him go free. The black community, though their hands and feet are tied, they show their support by their gratitude towards Atticus, and the faith and quiet determination speaks volumes about their unwavering resilience.

I chose this photo because it represents the mentality behind thhis poem, and it speaks of being restricted from having basic rights. This picture represents the author's emotions when she wrote this poem and how, finally, after so many years of opression, Maya Angelou's song is finally heard.
I chose this photo because it represents the mentality behind thhis poem, and it speaks of being restricted from having basic rights. This picture represents the author’s emotions when she wrote this poem and how, finally, after so many years of opression, Maya Angelou’s song is finally heard.

 

 

Aleutian Arc

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Aleutian Arc

The Aleutian arc is a volcanic arc that has formed due to the subduction of the pacific plate under the North american plate. As the pacific plate gets pushed further and further underneath the north american plate pressure builds up and magma is pushed through to the surface of the north american plate, forming volcanoes.

http://www.nasa.gov/multimedia/imagegallery/image_feature_589.html

Manganese Part 2

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A common compound of manganese is the ionic compound manganese dioxide. (MnO2) This has been used since ancient times when glassmakers would use it to prevent corrosion and a green tint from forming on their glass. The element manganese was discovered by this compound originally, and by the mid-18th century scientists were aware that manganese dioxide (also known as Pyrolusite) contained a new element. The first impure sample of manganese was isolated by Johan Gottlieb Gahn by reducing the oxide with carbon.

Manganese Dioxide