# Diffusion in Agar Cubes

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

In terms of maximizing diffusion, the 1 cm cube was the most effective. All three cubes soaked in the sodium hydroxide solution for ten minutes, but the 2 and 3 cm cubes did not change colour on the inside as the solution had not diffused in yet.

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

That size was most effective at maximizing diffusion because it had the largest surface area to volume ratio. This, along with concentration, mass, membrane thickness, pressure, temperature, are important factors that affect how materials diffuse into cells or tissues.

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

Although a large surface area is helpful to cells, they do not grow to be very large because small cells are more efficient at diffusion. When a cell grows, its surface area to volume ratio decreases. There is comparatively less cell membrane for the substances to diffuse through resulting in the centre of the cell not receiving the substances that it needs. Diffusion is less efficient, and cell processes slow down.

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

Cube C is going to be the most effective at maximizing diffusion because it has the largest surface area to volume ratio.

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

Your body adapts surface area to volume ratios to help exchange gases by cell division, slowing down metabolism, having long and thin cells rather than round and fat cells, (nerve cells), and having folds in the cell membrane (microvilli of intestinal epithelial cells).

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

Certain cells, like bacteria, cannot get to be the size of a small fish because when they get too large, they must divide.

What are the advantages of large organisms being multicellular?

The advantages of large organisms being multicellular are overcoming the problems of small cell sizes. Each cell has a large surface area to volume ratio, and they have also evolved features such as gas exchange organs (lungs) and a circulatory system (blood) to speed up and aid the movement of materials in and out of the organism.

# Protein Synthesis

Transcription:

Messenger ribonucleic acid (mRNA) is different than DNA because its nucleotides contain ribose sugar instead of deoxyribose sugar. The nitrogenous base uracil replaces thymine found in DNA. mRNA is single-stranded and does not form a double helix in the same manner as DNA.

Transcription is the making of an RNA molecule that is complementary to a portion of DNA. This occurs in the nucleus of a cell. The enzyme RNA polymerase causes a segment of the DNA double helix to unwind and “unzip”.

RNA polymerase unzips the unwinded DNA molecule

Complementary RNA nucleotides from an RNA nucleotide pool in the nucleus pair with the DNA nucleotides of one strand.

Complementary RNA nucleotides pair with the DNA nucleotides of one strand

RNA polymerase joins the RNA nucleotides.

RNA polymerase joins the RNA nucleotides

An mRNA molecule results. It has a sequence of codons—three bases—that is complementary to the DNA triplet code.

A DNA molecule and its complementary mRNA molecule

Following transcription, the mRNA molecule passes out of the nucleus and enters the cytoplasm.

Today’s activity did a good job of modelling the process of RNA transcription by modelling many of the structural differences between DNA and mRNA. It used different coloured beads to differentiate between thymine and uracil, and modelled how mRNA has a single backbone. It also modelled how RNA polymerase works in RNA transcription. Our model was inaccurate in the way that the DNA molecule and the mRNA molecule are the same size. A DNA molecule is much larger than an mRNA molecule. In RNA transcription, only a portion of DNA is used to make an mRNA molecule. In the model, the entire DNA molecule is used.

Translation:

Translation is the use of an mRNA molecule to sequence the amino acids of a polypeptide. This takes place in the cytoplasm of a eukaryotic cell.

Initiation:

A small ribosomal subunit attaches to the mRNA strand in the vicinity of the start codon (AUG).

A ribosomal subunit attaches to the mRNA

The initiator (first) tRNA pairs with this codon. Then a large ribosomal subunit joins to the small subunit.

The initiator tRNA pairs with the start codon

Elongation:

The polypeptide lengthens one amino acid at a time. A ribosome is large enough to accommodate two tRNA molecules: the incoming molecule and the outgoing molecule.

A ribosome accommodates two tRNA molecules

The incoming tRNA molecule receives the peptide from the outgoing tRNA molecule.

The incoming tRNA molecule receives the peptide

The ribosome then moves laterally so that the next mRNA codon is available to receive an incoming tRNA molecule.

The ribosome moves laterally

Termination:

Termination of synthesis occurs at a stop codon on the mRNA strand.

Termination occurs at the stop codon

The polypeptide is enzymatically cleaved from the last tRNA molecule. The ribosome dissociates into its two subunits and falls off the mRNA.

A terminated polypeptide

Today’s activity did a good job of modelling the process of translation by modelling the differences between mRNA, rRNA, and tRNA molecules and their functions. It modelled how the ribosome moves along the mRNA molecule, accommodating two tRNA molecules at a time, and how a polypeptide forms. Our model was inaccurate in the way that it modelled the ribosome as one unit instead of two subunits, skipping a step in translation.

# DNA Structure and Replication

DNA Structure:

Deoxyribonucleic acid (DNA) is a polynucleotide. Each nucleotide has a phosphate group, a deoxyribose sugar, and a nitrogenous base. Adenine and guanine are double-ringed purine bases. Cytosine and thymine are single-ringed pyrimidine bases. DNA has two “backbones” made up of alternating phosphate and sugar (represented by white pipe-cleaners) molecules. The nitrogenous bases are bonded to the sugar molecules. They can be in any order.

DNA strand

The two DNA strands are held together by hydrogen bonding between the nitrogenous bases. A purine always bonds to a pyrimidine; adenine pairs with thymine, forming two hydrogen bonds, and cytosine pairs with guanine, forming three hydrogen bonds. This is called complimentary base pairing. The strands run antiparallel to one another, with the 3’ end of one strand opposite the 5’ end of the other.

DNA molecule

The DNA molecule twists in the form of a double helix.

DNA double helix

This activity helps model the structure of DNA by using different coloured beads and pipe-cleaners to represent phosphate groups, deoxyribose sugars, and nitrogenous bases. It uses different numbers of beads to represent whether a nitrogenous base is a purine or a pyrimidine, and models how adenine always pairs with thymine and cytosine always pairs with guanine. It also models the DNA molecule in its double helix form. To improve the accuracy of this model, we could use more white pipe-cleaners to model how adenine and thymine form two hydrogen bonds versus how cytosine and guanine form three hydrogen bonds.

DNA Replication:

DNA replication occurs before cell division. During the replication process, exact copies of DNA are produced.

Unwinding and unzipping:

The enzyme DNA helicase causes the double helix to unwind and “unzip,” breaking the hydrogen bonds between the nitrogenous bases.

DNA helicase unzips the unwinded DNA molecule

Complimentary base pairing:

Each strand serves as a template for the formation of a complementary strand. New complementary nucleotides—always present in the nucleus—fit into place by the process of complementary base pairing. This is carried out by the enzyme DNA polymerase. It can only “read” DNA from the 3’ end to the 5’ end. One backbone—the leading strand—gets complimentary nucleotides added from the top down, and the other—the lagging strand—gets them added in fragments from the bottom up.

DNA polymerase fits complementary nucleotides

Joining:

The nucleotides on the new strand form covalent bonds. The enzyme DNA ligase “glues” the fragments of the forming backbones to one another.

DNA ligase glues the fragments together

There are now two DNA molecules identical to one another and to the original molecule. DNA replication is semiconservative because each new DNA molecule has one old strand and one new strand.

Two identical DNA molecules

This model was not a great fit for the process we were exploring. To model the complimentary base pairing, we covered most of the new backbone with a sheet of paper, only revealing the first few complimentary nucleotides. To model the joining of adjacent nucleotides, we used blue play-doh to represent DNA ligase gluing the fragments together. This activity was well suited to showing this process because it modelled how the three enzymes work in DNA replication. It was inaccurate in the way that it did not model how the complimentary nucleotides on the lagging strand are added in fragments.