Exam 3 Questions and Review

Possible Questions for Exam 3

Compare/Contrast of Transcription Replication

  • Similarities
    • Polymerase: complementary strand synthesis
      • moves in 3' to 5' direction
      • new strand synthesized in 5' to 3' direction
    • Sequence of nucleotide bases as genetic code
    • Occurs in the nucleus (in eukaryotic cells)

Differences

  • DNA polymerase vs. RNA polymerase
  • DNA replication: leading strand and lagging strand
    • Creation of Okazaki fragments
  • Transcription: "leading strand" only (5' to 3')
  • Replication: polymerase and ligase necessary
    • 2 full copies made
  • Transcription: 1 full copy with one partial complementary copy

Explain why during DNA replication that it is necessary for Okazaki fragments to be made:
DNA polymerase is only capable of moving in the 3' to 5' direction on the template DNA strand (chemically, the OH on the 3' end is necessary to begin replication. The 3' OH comes from the primer used to initiate replication). Because DNA is complementary and antiparallel, there are two strands moving in opposite directions. DNA is tightly coiled on itself, so it is impossible for the DNA to simply fully unzip itself to allow polymerase to easily move in the 3' to 5' direction (according to the template strand). A replication bubble is made around the area being actively replicated. This bubble contains both strands of DNA, one moving in the 5' to 3' direction, and the complementary strand moving in the 3' to 5' direction. Once the DNA in the replication bubble has been replicated, the replication bubble can move. If the bubble moves in one direction, it follows the flow of 3' to 5' replication (according to the template strand) and the synthesis of the new strand can be continued. The other direction, however, does not have the 3' OH on the newly synthesized fragment of DNA. necessary to continue replication. In the new replication bubble, one strand is continually synthesized, and the other strand must recruit a primer to initiate synthesis of a new section of DNA. The fragmented pieces of DNA from the strand that does not follow the natural flow of the polymerase are called Okazaki fragments. After replication is completed, primers made of RNA are removed from the newly synthesized strand of DNA. The chunks that are missing (from where the primers used to be, especially between okazaki fragments) are then filled in and strung together by DNA ligase. The result of DNA replication is two full copies of DNA. This discussion is assuming a visualization of ONLY one way directional replication. Because DNA replication is BIDIRECTIONAL, it is important to note that the replication bubble moves in either direction of the ORI site. This effectively creates 2 replication bubbles, 2 leading strands and 2 lagging strands. Therefore, each strand of DNA will contain Okazaki fragments that need to be patched by DNA ligase.

Diagram! Draw a diagram of DNA replication at the SECOND replication bubble. Things to label: primer, direction of DNA strand, polymerase, Okazaki fragments, leading strand, lagging strand, direction of newly synthesized strand, direction of primer and DNA helicase. Star the items that are either identical or highly conserved between replication and transcription

DNA replication is semi-conservative; the Meselson-Stahl experiment showed this. Explain what is meant by the term semi-conservative and explain how the Meselson-Stahl experiment showed that DNA was semi-conservative

It can be argued that mutations are evolutionary advantages, but it can also be argued that mutations are detrimental. Of the following, which choices support that mutations are evolutionarily advantageous?
1. Mutations occur randomly
2. Mutations lead to a higher genetic variation within a population that can lead to protection against disease
3. Mutations lead to a higher genetic variation within a population that can lead to more highly adapted individuals to a specific environment
4. Mutations are caused by physical changes in the organisms environment and therefore create an organism more highly adapted to its environment
5. Mutations in somatic cells are passed to future generations through sexual reproduction
6. When a mutation occurs in the first base of a codon, it will change the amino acid coded for by the codon

The following situation is entirely made up, no known proteins or diseases are mentioned John, Paul and George are full brothers. As such, one would expect them to share some characteristics, but George is different than his brothers. While John and Paul enjoy eating licorice, George cannot. Licorice contains the proteins licoracious, which can be fatal if not broken down by the enzyme licoraciousase. This complex enzyme is composed of a LONG STRING of amino acids, where >99.9% of the amino acids are necessary for the enzyme to function. When comparing the genome of John and Paul to their brother George, which of the following mutations most likely occurred to George's genome when replication of the licoraciousase enzyme gene before George was actually George
1. Silent
2. Synonomous
3. Missense
4. Nonsense
5. Frameshift

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