Agar Cubes (Diffusion)

In this lab, we put Agar Cubes in an OH solution to test diffusion.

Here is the data we found (ratios are flipped to V:SA on the table):

The cube that diffused best was the smallest (1cmx1cm) cube.

Our group found that the smaller the size of the cube, the easier and faster it was to diffuse. We agreed that this was because of the SA:V ratio. The higher the Surface Area compared to Volume, the more efficiently the cube (or cell) will diffuse.

Cells are smaller rather than larger because if they were larger, they would be less efficient in diffusion. Diffusion is important because it is a factor in the exportation of water, oxygen and nutrients between cells. Smaller cells also diffuse quicker.

If we are comparing 3 cubes with different SA:V ratios, for example cubes, A(3:1), B(5:2) and C(4:1), C would have the best diffusion efficiency. The SA:V ratio is higher and therefore allows for easier and quicker diffusion.

Our larger organs are made of smaller cells in order to provide maximum surface area coverage. This helps gases to be exchanged efficiently. There are high SA:V ratios wherever gases are exchanged in the human body.

Certain cells, such as bacteria, are unable to grow to the size of a small fish due to the fact that the SA:V ratio decreases as the size of the cell increases, as shown by our data. Once the cell gets too large, it will be unable to diffuse efficiently and therefore would affect its ability to provide water, oxygen and nutrients.

Some advantages of being multicellular includes the diversity of cells, which allows for different functions in the organism. Each type of cell has its own function. The different functions allow each organ in the body to preform their duties, such as, in the respiratory system or digestive system. This is what makes multicellular organs complex.

Protein Synthesis

This blog post will describe the processes of Transcription and Protein Synthesis.

To begin with, let me explain the differences between mRNA and DNA.  Their names and structures are similar but there are a few important differences between the two. Even though there a multiple types of RNA with different jobs, there is only one type of DNA with one job. Our focus will be on mRNA. Firstly, you may notice that in the following photos, brown beads are used to represent the base Uracil. This base only exists in RNA in the place of the pyramidine, Thymine which, exists in DNA. mRNA also has only one back bone instead of two. This is because mRNA doesn’t have binds between the nucleotide bases and mRNA needs to be readily able to bond with another strand of RNA.

(The above photo shows the RNA backbone, represented by the red pipecleaner on the left, and the DNA “sense strand” represented by the blue pipecleaner on the right. The fuzzy peach represents mRNA polymerase)

The main purpose of RNA is to carry the information from the DNA, which can not leave the nucleus, to the outside so that proteins can be built. Even though DNA is important for the building of proteins, it is very large and can’t leave the nucleus. This is why RNA transcription is important. mRNA can leave the nucleus with ease and it can be read by the cytoplasm.

Transcription happens in 3 main steps:

1) Unwinding:

The original DNA splits into two strands with the help of the enzyme, DNA Helicase. The sense strand, which starts with the sequence TAC is the strand that mRNA will pair with as the other strand will not be understood and will not produce a protein.

2) Complimentary Base Pairing:

Now that the DNA is split and ready to pair, complimentary base pairing can begin. The enzyme known as, mRNA polymerase, represented by the fuzzy peach in the photos below, helps with this step.

(The mRNA polymerase forms H-bonds, represented by the white pipe cleaners, between the nucleotides as it moves across the ladder-like structure.)

3) Seperation from DNA

Now that the DNA transcription is complete, the mRNA must separate from the DNA, again with the help of RNA polymerase. After the mRNA has detached, the DNA sense strand bonds back with the “non-sense strand” and goes back to its original double helix shape.

The mRNA is now good to go, with the correct sequence and can leave the nucleus to build a protein.

Reflection: Transcription

This model serves a good visual guide as to how transcription happens in the cells. The beads are great for showing complimentary base pairs with the bits of white pipecleaner showing the h-bonds. However, there are a few details that are inaccurate in this model. For example, the backbones look like a long piece with phosphate wrapped around it, when in reality the backbone is made up of an alternating chain of sugar and phosphate. It would be hard to represent this with the materials given. The instructions were also a bit confusing.

Translation

The next step in building a protein is called, translation. This is where the mRNA uses the information obtained from the DNA to form a polypeptide. The three main steps in translation are as follows.

1) Initiation:

This step is where mRNA attaches itself the bottom piece of the ribosome, or the small ribosomal unit. After that, the large and small ribosomal units attach. The process truly starts when the P-Site (left on the above photo) reads the start codon (AUG, circled on the strip of paper) provided by the mRNA.

2) Elongation:

The second, and longest step in the translation process. After reading the start codon is read, the A-Site (on the right side in the above photos)  reads the next codon. The tRNA, shown in green, then brings in the anticodon for it. The anticodon has the 3 complimentary bases to match the 3 bases on the mRNA codon. The tRNA also comes with an amino acid and then attaches to the P-Site. The next one then binds to A-Site. The amino acid then releases the tRNA and starts (or continues) the chain of amino acids on the P-Site.

3) Termination:

The final step, which is exactly what it says. The process terminates once the stop codon is read. In this case, the stop codon is, UGA (other stop codons include UAA and UAG).  It is highlighted in the above photo. Since there is no anticodon or matching amino acids for the stop codon, the ribosomal unit knows that the protein is complete. It then let’s go of the tRNA and the polypeptide chain (shown in blue).

Reflection: Translation

This model was, in my opinion, clearer and easier to understand than the pipecleaner model. Although this model does not show the true form of mRNA, it does show what tRNA looks like and it is very clear which piece represents what molecule. Due to the clarity of the pieces and the instructions, it was easy for me to figure out the process and easily put together the steps. However, this model also fails to demonstrate the small ribosomal unit versus the large ribosomal unit which merge and split and the beginning of the process and end respectively. Instead it is shown as one big piece with a hole in it where the mRNA slips in.

DNA Structure and Replication

Deoxyribonucleic acid, known more commonly as DNA, is an essential building block in what makes you, you and me, me. It is made up of phosphates, sugars and nitrogen.

DNA’s form resembles a kind of twisted ladder which  consists of two antiparallel strands (antiparallel because they are each read in opposite directions) with rungs made up of the complimentary base paired nucleotides. The force that holds this ladder together is the hydrogen bonding between the strands and nucleotides. This is represented in the above photos by white pipecleaners with beads on them. The beads are paired with specific colours to represents complimentary base pairs. (Ex. Blue and yellow = Adenine and Thymine, Purple and green = Guanine and Cytosine).

The above photos show DNA and the process of DNA Replication modeled by pipecleaners and beads. When DNA replicates it is unzipped with the help of a DNA helicase, represented by the watermelon candy. The DNA strands are now separated and, with the help of DNA polymerase (blue Bigfoot) they find different strands to pair up with through complimentary base pairing. However, the polymerase can only read DNA in one direction so the DNA ligase (Red Bigfoot), reads the other side and attaches the bases in the other direction. The joining of adjacent nucleotides is now complete. The complimentary base pairing is, again, represented by the beads on the white pipecleaners (white shown represents hydrogen bonding). In the end there are two identical strands of DNA.

Reflection-

This assignment modeled DNA Structure and DNA Replication well, but there were times where our group was confused by the instructions and had to seek help from other groups.

The pipecleaners were also a little bit difficult to work with in regards to hooking and unhooking the pieces of white pipecleaners. This took a lot of time that could’ve been spent on the blog post. Aside from that, I believe the beads worked well and the candy was colourful which helped me remember what they represented and their function better.

From this project I got to apply my knowledge of DNA Structure and Replication and this helped me retain the information I learned.