DNA Replication

1.DNA is comprised of nucleotides which are made of deoxyribose (sugar), phosphate, and a nitrogen-containing base.  In our model, deoxyribose is a green pentagon, phosphate is a teal circle, and the bases are hexagons or polygons.  The deoxyribose and phosphate part of the nucleotide form the backbone of the DNA and the bases connect the two backbones.  There are two groups of bases, each containing two types of bases: purines, which include Adenine (baby blue polygon) and Guanine (Robin’s egg blue polygon), and Pyrimidines, which include Thymine (yellow hexagon) and Cytosine (beige hexagon).

When two strands of DNA connect at the bases using hydrogen bonds, they take part in complementary base pairing. This means that one purine and one pyrimidine bond to each other, either Adenine and Thymine or Guanine and Cytosine.  These bases are complementary to each other so they will always bond with each other.  When the strands connect, they are antiparallel.  This means that one strand is read “forward” (3’ to 5’) and the other is going the other way (5’ to 3’).  Antiparallel strands are clearly shown in our model.  The left strand has 3’ at the bottom and 5’ at the top, meaning it is read forward and the right strand is the opposite.  Our model shows all of the parts of the DNA segment.

2. DNA replication occurs when it is time to make more DNA, before cell division.

3. There are three steps in DNA replication.  Unwinding, Complimentary base pairing, and Joining.  Unwinding is the first step where the DNA helix shape unwinds and the two antiparallel strands of DNA unzip by breaking the H-bonds

between the complimentary paired bases.  This step is facilitated by an enzyme called DNA Helicase, represented by scissors in our model, and prepares the DNA to be replicated.  This is demonstrated in two pictures from our model that have scissors to represent DNA Helicase.  The first picture shows the middle of Unwinding and the second picture shows the result.

The next step is Complimentary base pairing which is only possible now that the two original DNA strands are separated.

For this step, DNA Polymerase (a yellow circle attached to a triangle in our model)

 

has nucleotides attach to the original, now separated, strands of DNA.  The bases from the new nucleotides pair with their complementary base from the original strand and hydrogen bond.  They arrange themselves in antiparallel strands.  This step creates two ladders of DNA, each with an original strand and a new strand in a semiconservative fashion.

The last step of DNA replication is Joining.  In this step, the nucleotides from the new strand on the new DNA ladder covalently bond to their adjacent neighbours.  DNA ligase (a yellow heart in our model) “glues” fragments of nucleotides and repairs any damages.  The last two steps happen differently for the Leading strand and the Lagging strand.  The Leading strand is the strand that is from 3’ to 5’ and the Lagging strand is from 5’ to 3’.  DNA polymerase can only read and bond a strand in a “forward” direction (starting at 3’) so it can continuously read and bond the Leading strand.  It is more complicated for the DNA polymerase to read and bond the Lagging strand.  As the DNA helicase unzips the DNA strands, the polymerase has to jump to the front and work backwards, resulting in small segments that are skipped while the polymerase jumps to the front.  These small segments are called Okazaki fragments, in which the DNA ligase then glues.

 

4. To model the complementary base pairing step and the joining of adjacent nucleotides step,

we used a yellow shape that looked like a circle with a triangle attached. This was what we used to model DNA polymerase.  We used a yellow heart to model DNA ligase.  We showed that as it went, the DNA nucleotides formed Hydrogen bonds between the bases and Covalent bonds between adjacent Deoxyribose sugars and Phosphate. To demonstrate the Lagging strand, we showed a section that had not yet been bonded with sections of bonded nucleotides on either side.

This activity was well suited to show DNA replication because we were able to show the key steps from DNA replication and move the pieces around.  It was inaccurate because we were unable to show the double helix shape DNA has.

RNA Transcription

5. mRNA is different from DNA in 3 key ways.  They have different structures, sugars, and one base.  Structurally, DNA is very long while mRNA is short. DNA also has two strands which make a double helix shape while mRNA only has one strand.  They also vary in the sugar that makes up each nucleotide.  DNA is partially made of Deoxyribose sugar while mRNA is made of Ribose sugar.  The last difference between mRNA and DNA is that DNA has pyrimidine Thymine as one of its bases while mRNA has Uracil.

6. The first step for transcription, like replication, is one part of a DNA spiral, a gene, unwinds and unzips.  This allows all of the future steps to happen.   After the unwinding and unzipping of a gene, RNA bases Hydrogen-bond to their complementary DNA bases, on one strand; however, as discussed previously, RNA does not have Thymine.

Instead, RNA has Uracil (yellow hexagon with hashtag on our model) so DNA Adenine bases have to bond to RNA Uracil bases, instead of Thymine.  Now the RNA nucleotides attached to the newly bonded bases covalently bond to their adjacent neighbours.  All three of the previous steps have been similar to DNA replication, with a few differences but the future step is not.

The next step is where the RNA strand detaches from the DNA strand, breaking the Hydrogen-bonds between complementary paired bases.  After the new RNA strand has detached, the DNA reverts to its double helix shape by zipping and winding back up.

 

 

7. Today’s activity did a good job of modelling RNA transcription because we were able to show the major steps and ideas.  We were able to move, attach, and detach any nucleotides and strands which helped my learning.  It was inaccurate in one major way.  Since we were unable to show the double helix shape of DNA, it was hard to show the unwinding and rewinding of the first and last steps for transcription.  Our strands were also really short, so we were unable to show just one section of the helix unwinding and unzipping to expose a gene, we had to do it for the whole strand.

RNA Translation

I was absent from this class

8. While DNA replication and RNA transcription had a few similarities, RNA translation does not.  RNA translation happens after RNA transcription, and it is where RNA messages from the DNA strand get turned into proteins.  The first step of translation is initiation.  Initiation is where mRNA (long string of white paper in our model) attaches to the small subunit of a ribosome and then two ribosome subunits bind together (red shape in our model).  This is the setup for the rest of Translation to take place.  The next step is elongation, which is a longer stage than initiation.

Before we continue, we need to know some vocabulary.  A codon is three consecutive mRNA bases that code for an amino acid. An anticodon is the tRNA code that is complementary to a codon, (adenine binds with uracil and cytosine with guanine).  During elongation, the ribosome holds on to the mRNA that is attached and allows the

complementary tRNA (green shape in our model) to attach to the mRNA’s binding sites, anticodons and codons bind together.

 

A tRNA binds to the P site on a ribosome and another to the A site.

This allows the amino acid (blue square in our model) to let go of the tRNA and then it binds to an adjacent amino acid. Now that a tRNA does not have an amino acid attached to it, the empty tRNA leaves the ribosome allowing the ribosome to move down the mRNA.  This causes the tRNA that was at the A site to move to the P site and a new tRNA to bind to the mRNA codon at the A site.

 

The last stage is termination.  This does not happen until during the elongation stage, an mRNA reads a stop codon.  A stop codon is a codon without a complementary anticodon that prevents any new amino acids from being added to the chain.  When no new amino acids are being added to the chain, the ribosome can dissociate back into its two subunits, releasing the polypeptide.  This is the end of the translation process.
9. We were able to demonstrate the key ideas and steps with our model.  We were able to show the mRNA being read, the ribosome with the two binding sites (A and P), the two tRNA bonded to the ribosome, and the amino acids.  We were unable to show multiple ribosomes reading the mRNA at the same time or the two ribosome subunits joining and disassociating at the beginning and end of the process, respectfully.