DNA and Protein Synthesis

Posted on by caitlins2015

Explain the Structure of DNA

DNA or Deoxyribonucleic acid is made out of sugars (deoxyribose), phosphates, and nitrogen bases. DNA is a polymer that is made of nucleotide monomers. DNA has 2 sugar-phosphate backbones which form 2 antiparallel strands. These strands twist into a double helix shape. Between these strands or backbones we find the nucleotides: Adenine and Guanine (purines) and Cytosine and Thymine (pyrimidines). Each nucleotide has a complementary base. Adenine will always pair up or form an H-Bond with Thymine, and Guanine will always pair up with Cytosine.

Here we can see the two DNA strands. We can tell they are antiparallel due to the location of the phosphate (represented by the pink bead). DNA is read starting from the 3′ end to the 5’end. The left strand starts with phosphate at the top or so it’s the 5′ end. This means the left strand will read from the bottom up. The right strands starts with a sugar and ends with a phosphate. The right strands will be read starting from the sugar therefore it will be read downwards instead. Since these two strands are read in opposite directions, they are antiparallel.

 

In this photo we can see the complimentary base paring. Adenine (two yellow beads) is always H-bonded (shown by the white pipe cleaner rung) with Thymine (blue bead). Guanine (two purple beads) is always paired with Cytosine (green bead)

 

Here we can see that the DNA ladder has been twisted to form a double helix.

How does this activity help model the structure of DNA? What changes could we make to improve the accuracy of this model?

This model emphasizes the complimentary base pairing. The different colours help to show where the phosphate is found in the backbone and the pattern of the complimentary base pairs. We are able to see how the purines and pyrimidines bond with each other. The white pipe cleaners do a good job at representing the H-Bonds between the nucleotide bases. One change that could be made to improve the accuracy of this model is to use specific measurements. To increase accuracy we would have the measurements of our pipe cleaners as well as the spacing between the pipe cleaners and beads have similar proportions of actual DNA. This would allow us to better understand the proportions between how long a DNA strand is compared to how wide it is.

 

When does DNA replication occur?

DNA replication occurs right before cell division. Before a cell can divide, it will need its own copy of instructions or DNA to keep in its nucleus.

Name and describe the 3 steps involved in DNA replication. Why does the process occur different on the “leading” and “lagging” strands?

Step 1: Unwinding and Unzipping

The DNA helicase (represented by the Watermelon slice) unwinds the DNA from its double helix form so it starts to look like a flat ladder. The DNA helicase breaks the H-bonds between the complimentary base pairs; unzipping the DNA strand into two two separate strands.

 

Step 2: Complimentary Base Paring

DNA polymerase (represented by the Blue Bigfoot Candy) is responsible for H-Bonding new nucleotides to the original or parent strand. Due to DNA strands being antiparallel, the synthesis direction of the strands will be opposite of each other. DNA polymerase reads the sugar part of the nucleotide then the phosphate part. It starts at the sugar and will travel towards the phosphate end
In this picture we can see that the DNA polymerase has moved along the strand and H-Bonded new nucleotides to the parent strands. The left DNA polymerase started at the sugar end of the backbone and is travelling upwards towards the phosphate end. The right DNA is downwards towards the sugar end.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Step 3: Joining adjacent nucleotides

DNA ligase attaches the nucleotides to the sugar-phosphate backbone.

In step 2, we stated that during complimentary base pairing, the DNA polymerase has to follow a certain synthesis direction. It must travel away from the phosphate end and towards the sugar end. The strands are antiparallel, meaning the synthesis direction is different for each strand which results in a “leading” strand and a “lagging” strand. The nucleotides are added differently to the leading and lagging strands. The DNA polymerase on the leading strand simply follows the helicase. The lagging strand, on the other hand, goes in the opposite direction of the helicase. As the helicase unwinds and unzips more of the DNA, the polymerase of the lagging strand has to go back in order to complete the complimentary base pairing. In summary, the polymerase of the leading strand will add the nucleotide bases all in one segment. The polymerase of the lagging strand will have to complete the complementary base pairing in multiple segments. These segments will later be attached together in the 3rd step by the ligase.

At the end of the replication process, we are left with two identical DNA molecules. Each DNA molecule has one strand from the original or parent DNA and one newly created or daughter strand.

What did you do to model the complimentary base paring and joining of adjacent nucleotides steps of DNA replication. In what ways was this activity well suited to showing this process? In what ways was it inaccurate?

To model the steps of the complimentary base pairing we first separated a section of the DNA molecule. Once we had the strands partially separated, we then added the appropriate base pairs. This activity helped break down the 3 different steps and provide a better understanding of the responsibility of each enzyme. We could clearly see and understand that the helicase was in charge of unwinding the DNA from it’s double helix form and separating the strands. This activity was able to provide a basic demonstration on the difference between the lagging and leading strands as well. As we created the two diagrams for step 2, we followed the basic directions that the polymerase would’ve followed. When we were adding the complimentary bases onto the leading strand, we followed the strand in the same direction throughout the entire process. As more of the strand was separated, we continued to travel upwards. On the lagging strand, you would add nucleotides until you reached the end of the strand. Once more of the strand was separated you would  have to back up, past your initial staring place, and synthesize downwards until you met up with your original segment.

This activity is quite inaccurate in showing the actual movements of the enzymes. This activity isolates the enzymes so we don’t see how these enzymes would be working on this DNA molecule at the same time. In the activity process, we move each enzyme individually, however in real life, the enzymes would be working simultaneously. I also found this activity was inaccurate at modelling the process of the ligase enzyme. The photo is decent but the way you would manipulate your model to create that photo is not reflective of the real life process.

RNA Transcription

How is mRNA different than DNA?

mRNA is only a single strand as it only has one backbone. DNA is made of two back bones so it has two strands. DNA uses the nucleotides Adenine(yellow), Guanine(purple), Thymine(blue), and Cytosine (green) with the base pairs of Adenine/Thymine and Guanine/Cytosine. mRNA on the other hand does not contain Thymine. The nucleotide Uracil(brown) is used instead making the base pairs of RNA Adenine/Uracil and Guanine/Cytosine.

Both mRNA and DNA have sugar-phosphate backbones but the sugars used for each of them are different. Like their names indicate, DNA uses deoxyribose while RNA uses ribose. Another key difference between the two is that mRNA is able to leave the nucleus while DNA cannot. mRNA or messenger RNA serves to deliver DNA’s messages to places outside of the nucleus.

Describe the process of transcription

In the first step of transcription, the DNA unwinds and unzips.
One strand of the DNA will be used as a template to create the mRNA strand. This DNA strand is called the sense strand. The strand that is not being transcribed is called the nonsense strand. RNA polymerase is in charge of the complimentary base pairing. The RNA polymerase is responsible for the H-Bonding between the RNA nucleotides and the sense strand’s DNA nucleotides. It is also responsible for joining the nucleotides into a backbone.
Once the gene has been transcribed, the mRNA detaches from the sense strand. The two DNA strands then zip and wind back into its original form. After some modifications, the single mRNA strand will be ready to leave the nucleus to deliver the DNA’s message.

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 helped the break down the steps of RNA transcription. The activity demonstrates how the DNA behaves and how it is used as a template in the formation of mRNA. This activity was also a great way to compare the similarities and differences between the replication of DNA vs the transcription of RNA. This model only shows the gist of what happens during each step. Not all the processes and enzymes that would be used are shown. For example, the description of RNA polymerase is quite basic. The task of the polymerase is clear but how it goes about doing that is not as clear. This activity did not show how mRNA is modified in preparation of leaving the nucleus as well. This activity also inaccurately shows mRNA as being the exact same length as the DNA strand.

Protein Synthesis 

RNA Transcription 

During transcription, the RNA Polymerase transcribes DNA’s message onto the mRNA strand. We can see that as the RNA Polymerase moves along the DNA strand, the mRNA strand is created with the complimentary base pairs.
Once the RNA polymerase is finished transcribing the DNA strand,  the mRNA detaches itself and the DNA strand that was being transcribed (sense strand) and the one that wasn’t being transcribed (nonsense strand) reform together. Now  that the mRNA contains the DNA’s message, it is ready to leave the nucleus to deliver this message.

Describe the process of translation

  1. Initiation
During initiation, the ribosome holds onto the mRNA. Initiation begins at the start codon “AUG”. A codon is a sequence of three nucleotides that refer to a specific amino acid. The first codon, which is the start codon, will be read at site P.
Initiation begins when the start codon is read by the ribosome and a tRNA (transfer RNA) brings the correct amino acid to site P. AUG, the start codon, triggers tRNA to bring over the amino acid methionine. The tRNA that carries the amino acid, has an anticodon at the bottom that allows it to complimentary base pair with the mRNA.

2. Elongation

The next codon, which is in site A, is also read. the ribosome brings in another complimentary tRNA that is holding the amino acid that corresponds to the codon to site A. In this example, we can see that GGU is a codon for glycine.
Once the A and P sites are full, the amino acid from site P is moved onto the amino acid at site A. Since the tRNA at site P is no longer holding an amino acid, the tRNA releases from the mRNA and floats away.
Once the previous tRNA that was in site P has floated away, the ribosome shifts down the mRNA so that the codon that was in site A is now in site P.
Now that the third codon of the mRNA has been moved into site A, another tRNA comes in to fill the spot.
Just like before, the amino acids that were in site P, are passed onto the amino acid at site A. The ribosome shifts down so that site P is filled once more and a new codon enters site A.

3. Termination

The process of elongation will continue until a codon enters site A that does not have a corresponding tRNA. These codons are called stop codons. When a stop codon is read by the ribosome, the process of termination begins.
The stop codon causes the ribosome to release the mRNA, tRNA and the polypeptide chain. Note: pictured above is only a polypeptide chain/ a small portion of a protein.

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 great job at accurately breaking down and modeling the steps of translation. The paper cut outs were very clear and allowed for the activity to be quite hands on. This activity really helped me to understand the movements and actions that occur during elongation. The cut outs allowed me to be hands on, for example, I would physically move the tRNA or the amino acids from the different sites. One thing that was inaccurate with this model is that we showed that only one ribosome was translating this mRNA. In real life, there would be multiple ribosomes that are simultaneously going along the mRNA and making the protein.

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