Mol Bio Midterm Review part 1

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  1. Central Dogma
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    • by Francis Crick
  2. Describe the results of the experiment with the virulent bacteria/avirulent bacteria.
    It was found that when heat-killed virulent bacteria was mixed in with avirulent bacteria, the mouse dies. This is due to the thick capsule gene being passed on from the virulent to the avirulent bacteria.
  3. The conversion of living harmless bacteria into the virulent bacteria is called __

    Transforming Principle = genetic material

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  4. Describe how pure DNA isolation was further proof of DNA being the genetic material.
    • When pure DNA from a pathogenic (S) cell was isolated and added to a nonpathogenic (R) cell, this produced a pathogenic (S) cell after recombination and cell division.
    • CapS = gene responsible for generation of a capsule, giving a smooth appearance

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  5. How was the semiconservative scheme discovered to be the correct one for DNA replication? (Meselson-Stahl experiment)
    Bacteria grown in 15N > 14N & harvested the cells after 1 & 2 generations. DNA was isolated and density gradient centrifugation was performed. After transfer to the regular media, there was only 1 band of DNA after 1 generation indicating a 15N-14N hybrid. There were 2 bands (15N-14N & 14N-14N) after 2 generations. These results indicate DNA replication is semiconservative.

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  6. enzymes that perform transcription
    • RNA polymerases 
    • (transcribe RNA from DNA)
  7. RNA polymerase needs a presence of __
    DNA & nucleotides ATP, UTP, GTP, CTP
  8. __ is used as a template for transcription
    1 strand of DNA

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  9. The Pulse Chase assay shows __
    that RNA is synthesized in the nucleus & then localized in the cytoplasm.
  10. genome
    the entire genetic complement of a living organism that contains the biological info needed to construct & maintain a living example of that organism

    • made of DNA in most organisms
    • made of RNA in some viruses
  11. nucleoside vs nucleotide
    • nucleoside = base + sugar
    • nucleotide = base + sugar + phosphate (1 or 2 or 3)
  12. Nucleotides are linked by __ bonds connecting the __
    • phosphodiester;
    • 3' of the sugar of one nucleotide to the 5' of the next nucleotide's sugar

    There is a polarity in the structure of each strand, starting at 5' phosphate & ending with the 3'-OH on the other end.

    In one strand of DNA, nucleotides can be arranged in any order (any nucleotide can follow the same or any other nucleotide)
  13. Major & minor grooves refer to __
    the angles of glycosidic bonds.

    One one side of each glycosidic bond the less open angle is ~120 degrees (minor) & on the other side of it, it is ~240 degrees (major)
  14. __ grooves are more important for interaction of proteins with DNA, because __
    • Major;
    • they are wider so there is more room for interaction
  15. Considering the chemical groups of base pairs in major grooves, there are possibilities
    of additional hydrogen bonds (donor & acceptor & hydrophobic bonds (Vander Waals) between DNA & other molecules (proteins)
  16. B-form
    • the average conformation of the double helix seen in physiological conditions
    • right handed
    • Depending on the sequence of DNA, may change to some extent affecting the major & minor grooves

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  17. A-form
    • double helix conformation that sometimes occur in DNA protein interactions
    • more similar to RNA if it makes a double strand structure
    • right handed
    • wider helical diameter than B-form so more # of bases per complete turn
    • lower rise per base pair, so shorter distance per complete turn

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  18. denaturation
    • separation of the strands of DNA from each other
    • can happen by breaking hydrogen bonds by high temp or high pH
  19. hybridization or annealing
    • The 2 strands can be reattached if the temp or pH are brought down.
    • This reattachment is by restoration of hydrogen bonds.
    • For hybridization to occur, both strands should be complementary.
  20. UV absorption is __ in double stranded DNA than 2 separate single strands of DNA (denatured) due to __. Increasing temperature will cause a __
    • less (40%);
    • the stack of bases in double stranded DNA that makes them unavailable to UV;
    • rapid increase in absorption

    Thus it is possible to determine the melting point of DNA (Tm)

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  21. factors affecting the melting temp of DNA
    • size of DNA (number of bases) - short DNA fragments have lower melting points
    • GC content - Higher GC = more hydrogen bonds = higher melting point. Also in base pair stacks, G:C has more interaction with adjacent base pairs.
    • Ionic strengths - Higher salt concentration = higher melting point. High levels of positively charged ions surround the negatively charged phosphates in DNA backbone, therefore it is easier for both strands to not repel each other.
  22. shape of eukaryotic chromosomes
    long & linear (DNA molecules + their associated proteins)
  23. shape of prokaryotic chromosomes

    (also genetic material of some viruses & DNA of mitochondria)
  24. plasmids
    independent circular DNA mostly found in bacteria, but not considered to be part of their genome
  25. number of turns of one strand around the other strand, one twist per ~10 base (positive number)
    twist number (Tw)

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  26. the number of turns of the double strand around itself
    writhe number (Wr)

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  27. __ causes supercoil (writhe) __ supercoil increases the torsion. __ decreases the torsion.
    • Opening the 2 strands;
    • Postive;
    • Negative
  28. Tw + Wr =
    linking number (LK)

    If there is no writhe, the cccDNA (covalently closed circular DNA) is called relaxed. (Lk0 = Tw + 0)
  29. The supercoil is negative when __ & positive when __
    • LK = Tw - Wr > LK < LK0;
    • LK = Tw + Wr > LK > LK0
  30. DNA can be long or short, which changes the LK value, thus to normalize the LK, the __ is calculated.
    super helical density (σ) is calculated

    σ = ΔLK/LK0
  31. The supercoil can be resolved by making a temporary break in __ bonds of one or both strands of DNA. This is usually done by __ enzymes. After releasing the supercoil, which __ LK, the bond is restored.
    • phosphodiester;
    • topoisomerase;
    • decreases
  32. topoisomerase I
    introduces a break in one strand's phosphodiester bond (a nick) & passes the 2nd strand through the generated gap. The 2 ends of the broken strand are realigned.
  33. topoisomerase II
    breaks both strands of the double helix, creating a "gate" through which a 2nd segment of the double helix is passed.

    Unlike topoisomerase I, this requires the use of ATP.
  34. Bacteria also have the enzyme __ which is a type of topoisomerase. Instead of relaxing the DNA, it __
    • gyrase;
    • induces negative supercoil which is favorable for DNA replication & transcription
  35. electrophoretic mobility of DNA topoisomers
    DNA topoisomers: circular DNA of the same size but different LK

    Relaxed circular DNA moves slower in gel electrophoresis than linear DNA. Supercoiled DNA moves faster as it is more compact. The more supercoiled, the faster it moves.

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  36. Because of __, RNA double helices are closer to the structure of __. In this conformation, the __ groove is more accessible to proteins.
    • 2'OH;
    • A-DNA (wide shallow minor grooves & narrow deep major grooves);
    • minor

    Since the minor groove doesn't have much chemical info, it is not well suited for sequence specific recognition of RNA.
  37. The sequence recognition of RNA is achieved by __
    relaying on the structure of hairpins, loops, bulges, & distortions of non-canonical base pairs (e.g. tRNA)
Card Set:
Mol Bio Midterm Review part 1
2017-10-23 22:23:07

DNA, genetic material, RNA, supercoil, topoisomerase
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