Archive of ‘Grade 12’ category

AP12 – Agar Cube Lab –

What exactly is cell diffusion?

What do elephants, humans, plants and insects all have in common? Cell diffusion! Diffusion is the exchange of materials entering or exiting across the cell membrane, where dissolved molecules move from areas of high concentration to low concentration. As cells grow larger, their surface area to volume ratio decreases. This means that while the cell (it’s volume) grows larger, its surface area does not increase to the same degree. This can make taking in nutrients, transporting electrons, and the elimination of waste, much more difficult to accomplish.

However, in eukaryotic cells (such as those in plants and animals), they are large, so they contain membrane-bound organelles to provide additional surface areas to allow for adequate transportation within the cell, such as:

  • The endoplasmic reticulum
  • The plasma membrane
  • Cristae of the mitochondria.

How can this be demonstrated with agar cubes?

[reference table]

The same result can be seen in our agar cubes. Initially, I had the hypothesis that the NaOH would diffuse into every cube fully, but at a faster rate than it had actually occurred. However, the NaOH that the cubes were submerged in, had to reach into each of the cube’s volumes quickly. In the time-lapse below, you are able to see that the NaOH will diffuse into each size of cube at the same rate, however with the given time period of ten minutes, the cube with the greatest reached proportion was the smallest (1cm3) cube. In the time that it took the NaOH to reach the center of the smallest cube, it was only able to reach 42.1% of the largest cube (3cm3). This means, that in order to maximize diffusion, the cube’s surface area to volume ratio must not be too small (for example: in the 3cm3 cube), otherwise diffusion will not be able to occur at fast enough rates to reach the entire volume of the cube.

The NaOH will dissolve through the outer surface of the cube, and then into the cube’s volume. As the NaOH was able to completely diffuse into the centre of the smallest cube, this renders it as well adapted to exchange substances with its environment through diffusion. If you exchanged NaOH with oxygen or nutrients, the process would be the same for a cell. However, while time, cell size, and the surface area to volume ratio were the only variables in our experiment, there are several other factors that can affect how materials diffuse into cells or tissues, such as: concentration, temperature, the type of material being diffused, and cell polarity (differences of shape, structure, and function in a cell).

As you could see with the agar cubes, when large cubes, unlike small cubes, are poorly adapted to exchange substances within its environment, as they are unable to reach its centre in a timely manner, due to the low surface area to volume ratio.

This could be seen by the pink NaOH only reaching 42.1% of the largest (3cm3) cube. It is the same result in cells, as oxygen won’t be able to reach its centre, and waste will not be able to exit through diffusion, ultimately causing a large portion to suffocate. Thus, if a cell grows to be too large, then the diffusion will not be able to compensate for the much larger volume to small surface area, meaning that cells will not grow to be too large. For example: if a cubes surface area increased by a factor of four, the volume would then increase by a factor of eight.

Knowing what we now know, if you were given the choice between three cubes with a surface area to volume ratio of: 3:1, 5:2, and 4:1, which would you choose based on maximized diffusion?

It would be the 4:1 cube! This is because, it has the highest ratio, just like the smallest (1cm3) cube in our experiment, which had a ratio of 6:1. Remember: the highest ratio means that the surface area of the cube / cell is going to be the closest in size to its volume, meaning that it can maximize diffusion and be properly adapted to its environment.

Now, you’re probably wondering how diffusion is used in humans or animals, since we are talking about cells, after all. In human exchange of gases, for example, there must first be enough surface area for the cell in order it to diffuse with its organelles, and the volume of the cell. In order to achieve more surface area, our bodies are use a few different techniques such as: dividing our cells so they become smaller, and also shape cells into longer thinner forms, instead of being round, and fat to further reduce cells volume, while simultaneously creating a larger surface area.

Cell division is the reason that cells cannot grow to be very big. One of its purposes is for the survival of the cell, to allow the cell to be able to continue its intake and disposal of waste, without having its volume becoming too big for its surface area. Its other functions include:

  • Reproduction of an entire unicellular organism
  • Growth and repair of tissues in multicellular animals
  • Production of gametes for reproduction in multicellular animals

The cell is then able to exchange gases (by both entering and exiting it) without taking as long as it would have needed to, as the surface area to volume ratio is now larger. However, it is not only humans who strive to lower this ratio. Another example would be the size of ears that elephants have.

Much like humans, elephants also constantly maintain a high body temperature, however if this temperature grows too high, it can cause a reduction in enzymes function (due to a denaturing of the enzymes, which could lead to death). So, much like our largest agate cube (3cm3), elephants also have a relatively small surface area compared to their overall volume (a low surface area to volume ratio), which means that they will not diffuse heat out of their bodies well. So, elephants adapted to their large size (volume), by creating a large additional surface area (their ears, a tissue), to allow for better heat diffusion.

What is a multicellular organism?

While most cells are not able to grow past a certain size (due to cell division), some are still able to grow to a larger extent than others. So, in order to compensate for this large cell size, some organisms are multicellular. A multicellular organism differs from a unicellular organism, as it requires multiple cells to properly function, whereas a unicellular organism is able to conduct all required functions through only itself. Examples of a multicellular organisms are human beings, plants, animals, birds and insects.

Each of these multicellular organisms are composed of different cells joining together. These cells know when to join together, because once a singular cell becomes too large to be properly adapted to its environment, multiple cells will begin to join together. Eventually, the joined cells will begin communicating with each other and their genes will decide themselves when cell division should occur, rather than the environment leading this process. This growth brings multiple advantages to the organism. Firstly, it better protects your insides from the outside. It also allows for pieces of the joined cell to die, because they can be easily replaced, which ultimately allows you to live longer. It also allows different cells in the group, to begin to take on different roles (such as the outside cells using their flagella to move, while the inner one’s digest food).

AP12 – Pipecleaner DNA –

The structure of DNA:

DNA (deoxyribonucleic acid) is found in the nucleus of eukaryotes and the cytosol of prokaryotes, and is made up of a chain of repeating subunits (of monomers), called nucleotides. In each nucleotide, there are three main parts: a phosphate group, a sugar, and a nitrogenous base.


These phosphate groups are what make the DNA (nucleic acid) an acid. Attached to the phosphate groups, are a cycle / ring structured molecule, which is a five-carbon sugar. These alternating phosphate and sugar groups along the sides of DNA are its backbone. While these backbones seem to run parallel to each other, one is in fact the pointing in a different direction (upside down – the left strand is 5’ (prime) to 3’, and the right strand is 3’ to 5’, all on the five-carbon sugars) than the other, thus causing it to be antiparallel. [as shown below]

The five-carbon sugar which would be a Ribose sugar in RNA, becomes a Deoxyribose sugar in DNA, as it contains a hydrogen atom instead of a hydroxyl atom on its two-prime carbon (deoxyribo). The final part of the DNA structure, are the nitrogenous bases. Nitrogenous bases are classified into two different groups: purines and pyrimidines. The two-ringed bases are purines, whereas the one-ringed bases are pyrimidines. Within purines and pyrimidines are four different types of bases. In purines there is adenine, and guanine. In pyrimidines there is thymine, and cytosine. Adenine will always bond with thymine, and guanine with cytosine. This is referred to as complementary base pairing. As pyrimidine will always bond with a purine, it causes DNA to form a spiral / helix, and due to DNA being double stranded, its structure is therefore referred to as double helix.


How modeling DNA structure out of pipecleaners can be helpful:

For me, this activity helped to break down both the structure of DNA and the processes that occur to achieve this structure. The steps in which DNA functions became more clear, however I found that it could have been more useful to use two different colored bonded pipe cleaners to represent the two strands of DNA, instead of beads to represent the 5-carbon sugars. If we could have possibly used blue and orange pipe cleaner pieces connected together to form a DNA strand, then I would have found more clarity in what the beads were supposed to represent. Contrarily, I found that the use of beads as complimentary bases to improve my understanding of how their pairing works greatly, and I am now able to better remember what purines and pyrimidines pair together, and their differences as bases.

When does DNA replication occur?

DNA replication occurs during the synthesis phase of interphase and the mitotic phase of a eukaryotic cell. Interphase is a part of the cell cycle, which will cause DNA will go through three stages of change: first gap (G1), synthesis (S), and second gap (G2). Both the G1 and G2 phase together are recognized as interphase. During the G1 phase, the cell will physically grow larger, copy its organelles, and create molecular building blocks. Next, during the S phase, the cell will synthesize a copy of the DNA in its nucleus, while also duplicating the centrosome (helps separate DNA during mitotic phase). Following this process is the G2 phase, which causes the cell to further grow, creates proteins as well as organelles. Once this phase ends, the mitotic phase will occur. Here, the cell will divide the copied DNA and cytoplasm, thus creating two new cells. Within the mitotic phase, there are two existing processes: mitosis and cytokinesis. Four different stages exist within mitosis: prophase, metaphase, anaphase, and telophase. After both processes have taken place, then the DNA replication will have finished, and is dependent to the cell it is replicating, as to when the next daughter cell will be created.


The steps of DNA replication:

Some of the key components to DNA replication are enzymes, helicase, DNA polymerase, primase, ligase Enzymes are able to speed up reactions as well as build up or break down the items that they act upon.

Beginning at the origin, Helicase is able to “unzip” / unwind the two strands of DNA, by breaking the hydrogen bonds that attach the nitrogenous bases (adenine, thymine, cytosine, guanine). While this process occurs, single stranded binding proteins (SSB proteins) will bind to the separated DNA strands in order to prevent them from coming back together. During this process, topoisomerase will also control the DNA to prevent it from supercoiling (over winding of the DNA). DNA polymerase is then able to replicate DNA molecules in order to build the new strand of DNA, however it is unable to work without a primer. This primer (made up of RNA) is created by primase, which directs DNA polymerase to the point where it should begin to work on both strands of the DNA.

Why the steps of DNA replication occur differently in leading and lagging strands?

DNA polymerase will build the new strand of DNA in the 5’ to 3’ direction, and as DNA strands are antiparallel (left is 3’ to 5’, and right is 5’ to 3’), DNA polymerase will build the left 3’ to 5’ strand smoothly moving forward, while building on the 5’ to 3’ strand will force it to move from right to left, thus having to jump to the newest un-winded right (5’) section, and causing primers to continually be placed at the newest starting point, in order to continue building the DNA.

These two strands are categorized as leading (3’ to 5’), and lagging (5’ to 3’). After DNA polymerase has occurred in lagging strands, it will result in fragmentation between each 3’ 5’ section where it had to jump to the newest un-winded point. These are known as Okazaki fragments. As the primase primers are made up of RNA, ligase is then used to “glue” the gaps between Okazaki fragments, using nucleic bases to seal them. This entire process results in two identical DNA molecules, both being composed of old and new synthesized strands, which can be referred to as a semi-conservative process.

How replicating DNA with pipecleaners could be helpful:

With this activity, to represent complimentary base pairing along with the joining of adjacent nucleotides, I used a DNA strand, and un-winded the H-bonds that bonded the nucleic base acids, and demonstrated the both the helicase and DNA polymerase through drawing around the strand of DNA. This process was accurate in the steps that take place throughout the process of DNA replication, however it was not visually demonstrative in the process.

I found it hard to demonstrate the leading and lagging strands being copied (including the fragments that are created throughout this process on the lagging strand, along with demonstrating the primase that will seal them). While I also found it difficult to properly show the helicase breaking the seal, I think that drawing it going through the DNA strand helped to clarify the process further.

Pre-Calc 12 – Core Competency Reflection –

Core Competency Reflection:
How had this unit impacted your creative and critical thinking and communication skills?

This past unit has had a constructive impact on both my creative and critical skills in both my thinking and communicating. Throughout the unit, I encountered many obstacles and challenges, and was forced through this to put my critical and creative thinking into action. When confronted by a challenge, I would first begin by breaking down the question that was troubling me, to a simpler form. If that did not work, I would then refer to previously taken notes. However, if neither of these options worked, it was then that I would communicate my confusion to a pier, or teacher. This would usually result in an explanation to my question, although it would sometimes require a deeper exploration into the subject as well as some creativity in solving the problem from both parties. While math itself teaches one the different functions of numbers, and the laws that go with them, it also teaches life skills such as problem-solving, critical thinking, and communication, which was ultimately demonstrated to me throughout the past unit.