March | 2019 | Chiyoung's Blog

Hypothesis

Smaller the cube is, faster it is diffuse as it has smaller surface area.

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

The 1cm cube was the most effective one.

Why was that size most effective at maximizing diffusion? What are the important factors that affect how materials diffuse into cells or tissues?

The smaller the size, higher the SA: V ratio. Due to small surface area, it has less surface to cover. Therefore, could have many materials pass through in and out of the “cell” by diffusion.
Some important factors might be time, size, and possibly temperature.

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

Cells would not grow bigger as it would be difficult to transport nutrients to the center and would take longer to regenerate. However, smaller the size, the faster it would be to travel and take lesser time overall.

You have three cubes A, B, and C. They have surface to 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?

C has the highest surface area to volume ratio. This means that for every cubic unit of cytoplasm, there are more cell membrane than in cubes A and B. This allows for more materials to be able to enter the cytoplasm through diffusion. Therefore, cube C will be most effective at maximizing diffusion.

How does your body adapt surface area to volume ratios to help exchange gases

Our body adapts the ratio for Alveoli, an air-filled sac inside our lungs. They need a large surface area to volume ratio to allow gas exchange to occur more rapidly in our body.

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

Bacteria are single-celled organisms. As seen in the lab, cells prefer to have a lower volume, so being the size of a fish would not help the functions of the cell. A cell needs to stay small for diffusion of materials.

What are the advantage of large organisms being multi-cellular?

The advantages are that protein can enter into cells directly, rather then needing the assistance of materials to diffuse into the center of a bigger cell.

Transcription

How is mRNA different than DNA?

The function of mRNA is slightly different than DNA – mRNA copies the information needed to build a protein, which is located on one gene of DNA. mRNA then transfers to the cytoplasm where the protein is built. mRNA is also shorter than DNA and mRNA has one strand while DNA has two

Describe the process of transcription.

Transcription is the process of bringing instructions to build a protein from DNA in the nucleus to ribosomes in the cytoplasm. This is done by messenger RNA (mRNA). In the nucleus, the DNA unzips itself at the location of the gene that needs to be read. This is called the sense strand of the gene and is shown by the blue pipecleaner strand. The mRNA then builds a copy using complimentary base pairs of the strand, which is the red pipecleaner strand in the photo. Blue Thymine beads also change to brown Uracil beads on the mRNA strand. This is all facilitated by the RNA polymerase, or the fuzzy peach in the photo. It separates itself from the DNA when the gene copy is made and the RNA transfers out of the nucleus and into the cytoplasm. The mRNA is then read by ribosomes in the cytoplasm to build the protein in the translation step.

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

Today’s activity did a good job modelling RNA transcription because we had a different color bead to represent Uracil from Thymine, a different colored pipecleaner for the RNA strand, and the pipecleaners make it easy to separate the nitrogen bases bonds. One way our model was inaccurate was that since our DNA strand was very short, the mRNA made a copy of the whole DNA, calling the whole strand a “gene”. This is possible, but a gene is usually just a section of DNA. In the body, the DNA only unwinds in that specific area, the mRNA makes a copy of the gene, and then the DNA reforms whole again. As well, RNA strands are usually shorter than DNA strands, but in this activity, they were the same size.

Translations Describe the process of translation: initiation, elongation, termination.

The process of translation is in three steps. The first is initiation. In this step, the ribosome looks for the start codon “AUG” on the mRNA. When it finds this codon, the two ribosome subunits (red paper shape in photo) bind together and start reading the mRNA with AUG in the P site. The second step is elongation. The ribosome brings in tRNA (green paper in photos) with the anticodon that matches codons on the mRNA. The tRNA is also holding the matching amino acid to the codon. The amino acids are the blue papers in the photo. When tRNA binds to the “P” site, another tRNA binds to the codon in the “A” site. When both spots are full, the amino acid detaches from the tRNA on the “P” site and attaches itself to the amino acid on the “A” site. The tRNA in the P site then detaches itself from the ribosome, and the ribosome then moves so that the tRNA in the A site is now in the P site. A new tRNA attaches itself to the new exposed codon in the A site, and the process continues. The last step is termination. The elongation cycle ends when the ribosome reads a “STOP” codon. This is a codon that has no matching tRNA amino acid. No amino acid is added to the chain, so the polypeptide is released, and the ribosome detaches from the mRNA.

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

Today’s activity did a good job modelling the process of translation because the paper made it easy to visualize the process. Because the paper is easy to move, you can model the elongation steps in a very similar way to how it’s done in the body. The matching up codons to anticodons and amino acids was also very easy with these models. One way that the model was inaccurate was that the RNA was missing the phosphate – sugar strand. It only showed the bases. As well, the ribosome was one piece when we started, but the ribosome should be in two subunits and then join during initiation. The shapes of the amino acids on the paper were also not accurate to how they look. They are much more randomly shaped than the paper shows.