DNA and Protein Synthesis:

 

 

 

 

 

 

 

 

 

Explain the structure of DNA- use the terms nucleotides, antiparallel strands and complimentary base pairing

• • DNA, or deoxyribonucleic acid, itself is a polymer (macromolecule) made up of monomer nucleotides (including a phosphate group, 5-carbon sugar (deoxyribose), and a nitrogenous base). DNA is made up of two backbones with bases that stick between the two backbones. The
    

    *DNA molecule in it’s complete double helix shape*

    backbone that makes up DNA is made from sugars (deoxyribose), and phosphates. The nucleotide bases face into “ladders”, with the rungs formed by hydrogen bonds in between the base pairings. Complimentary base pairing refers to the pairings that happen in between the nucleotide bases (adenine, thymine, guanine, cytosine): the idea that nucleotide bases will always pair with the same partner. Nucleotide bases can be either a purine (double-ringed structure) or a pyramid (single-ringed structure) and one specific purine will always bind to one specific pyrimidine: Adenine will always bind to thymine, and guanine will always bind to cytosine. DNA is made up of two antiparallel (read in opposite directions) strands that are complimentary to each other: meaning they can give the same message.

• How does this activity help model the structure of DNA?What changes could we make to improve the accuracy of this model? Be detailed and constructive.
  • Making models of DNA allows a student to study not only the overall structure of a DNA strand and molecule, but practice the process through which DNA is constructed, as well as receive a more hands-on knowledge of the topic at hand. The blue pipe cleaners were able to represent the backbones of a DNA molecule, the coloured beads represent the nucleotide bases (and the idea of complimentary base pairing), while the small white pipe cleaners capture the idea of hydrogen bonds that occur between complimentary bases. One change that could possibly be made to improve the accuracy of the project and model, would be the size of white pipe cleaners that acted as h-bonds. Clearly replicating the ratio within DNA molecules would be difficult,  however ensuring the white pipe cleaners were even in size would have ensured our double helix molecule was more accurate in shape (the different-sized h-bonds made it difficult to twist the molecule into the double helix). H-bonding in general is always much more complicated than simply two strands hooking together (as the model shows), and the overall spacing, size and proportions of the model are off as well. 

• When does DNA replication occur?
  • DNA replication will occur directly prior to cell division as it is necessary for the cell to properly divide: DNA replication works as a semi-conservative process where the replicated strands will all contain one “old/original” strand and then have one “new/replicated” strand to create a full new DNA in a double helix.
• Name and describe the 3 steps involved in DNA replication. Why does the process occur differently
  

  *Unwinding step*

  on the leading and lagging strands?

  • Unwinding: the step where the helix will unwind, and the DNA helicase will start to cause the two strands to unwind and “unzip”, as the H-bonds in-between base-pairs “breaks”
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    *Complimentary Base Pairing step*

    Complimentary base pairing: the step where the nucleotides (that are always present within the nucleotides) move into place and start to form h-bonds with a “partner” on strand- this process is facilitated by DNA polymerase.

  • Joining: the final step where the nucleotides on new strands form covalent bonds, binding together side by side with the
    

    *Joining step*

    sugar-phosphate backbone. The DNA ligase enzyme is responsible for this process : which results in the re-shaping and forming of the new DNA as a complete replica of the original DNA strand. The leading is bound continuously as the DNA unzips, but the lagging strand is bound in fragments as DNA “unzips” and DNA ligase glues fragments (Okazaki fragments)

 

 

• The model today wasn’t a great fit for the process we are exploring. What did you do to model the complimentary base pairing and joining of adjacent nucleotides steps in DNA replication? In what ways was this activity well suited to showing this process? In what ways was it inaccurate?
  • We were able to model the complimentary base pairing and the joining of the adjacent nucleotide steps of DNA replication by using two new pieces (strands) of blue pipe cleaners (in addition to our other DNA molecule) (representing the sugar phosphate backbones) that had complimentary pairs of bases to the original DNA strands which became “hydrogen-bonded” together to demonstrate the process through which “unzipped”-strands came together with a new strand to form a replicated (but new) DNA molecule. We completed this process by “using” the DNA “polymerase” and the DNA “ligase” to complete this process. This activity was well-suited to showing the process as it clearly displayed the method through which the molecule unzips (by the polymerase), as well as how one molecules develops into two separate, and complete copies due to this unwinding and unzipping process. One way that the process was ill-suited to demonstration of this process was the way it showed hydrogen bonding (as hooks, and etc.), as well as the development/changing of the sugar phosphate background (how new ones form in real DNA replication, how they are bonded, etc.). The overall process and model was well-suited to demonstrating the DNA replication process, however the finer details (including the complexity, method the DNA polymerase and ligase enzymes are “used”, and the details surrounding the sugar-phosphate backbones) were lost with the basic pipe-cleaner model.