Mol Bio Mid Review part 2

  1. Chromosomes of eukaryotes are __
    long linear DNA molecules plus their associated proteins
  2. Chromosomes of most of __ are circular.
    • -prokaryotes, genetic materials of some viruses, DNA of mitochondria, and plasmids
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  3. A circular DNA can be generated by __
    covalently joining both ends of a DNA molecule (covalently closed circular DNA (cccDNA)

    Circular DNA is in topological constrict (cannot very freely rotate)
  4. number of turns of one strand around the other strand
    twist number (Tw)

    • one twist per ~10 base (positive number)
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  5. number of turns of the double strand around itself
    • writhe number (Wr)
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  6. causes supercoil (writhe)
    • opening the 2 strands
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  7. If there is no writhe, the cccDNA is called __
    relaxed (LK0 = Tw + O)
  8. If LK = Tw - Wr
    • LK < LK0
    • Supercoil is negative
  9. If LK = Tw + Wr
    • LK > LK0
    • Supercoil is positive
  10. DNA can be long or short, which changes the LK value, thus to normalize the LK, the __ is calculated
    super helical density (σ)

    • σ = ΔLK / LK
    • ΔLK (Linking difference) = LK - LK°
  11. The supercoil can be resolved by making a temporary break in__ bond(s) of one or both DNA strand(s). This is done usually by __ enzymes.
    phosphodiester; topoisomerase

    • After the release of the supercoil (decreasing LK) the phosphodiester bond is restored.
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  12. __ introduce a break in one strand’s phosphodiester bond (a nick) and pass the second strand through the generated gap. The two ends of thebroken strand are then re-aligned.
    • Type I topoisomerases
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  13. __ break both strands of the double helix, creating a “gate” through which a second segment of the double helix is passed. Requires the use of ATP
    • Type II topoisomerases
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  14. Bacteria also have the enzyme __ which is a type of topoisomerase. Instead of relaxing the DNA, it induces negative supercoil which is favorable for DNA replication and transcription.
  15. DNA topoisomers
    circular DNA of the same size but different linking number (LK)
  16. Relaxed circular DNA moves __ in gel electrophoresis than linear DNA. Supercoiled DNA moves __.
    slower; faster (as it is more compact)

    • The more supercoiled, the faster it moves
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  17. Because of 2' OH, RNA double helices are closer to the structure of __
    • A-DNA (wide & shallow minor grooves & narrow deep major grooves)
    • This structure is not well suited for sequence specific recognition of RNA
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  18. The sequence recognition of double helix RNA is achieved by relaying on the structure of __
    • hairpin loops, bulges, & distortions of non-canonical base pairs (e.g. tRNA)
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  19. __ side chains act as acids or bases which tend to be __ under physiological conditions. Side chains form __ bonds and are often involved in chemical reactions.
    • Hydrophilic;
    • fully charged (+ or -);
    • ionic

    This refers to polar charged amino acids
  20. neutral (uncharged) polar amino acids
    • Hydrophilic side chains allow them to participate in chemical reactions, form H-bonds, and associate with water.
    • post-translational modifications: phosphorylation of OH- groups
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  21. Nonpolar amino acids have __ side chains that consist almost entirely of __ atoms.
    hydrophobic; C & H

    • These amino acids tend to form the inner core of soluble proteins, buried away from the aqueous medium. They play an important role in membranes by associating with the lipid bilayer.
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  22. Except __, all amino acids have 4 different groups attached to carbon alpha. This gives them the chirality.
    glycine (R group is H)
  23. Amino acids in regular proteins are __ amino acids.
    • L
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    Image Upload 14
  24. primary structure of proteins
    Image Upload 15

    sequence of amino acid residues in the polypeptide chain
  25. secondary structure of proteins
    • regular local structures with repeated hydrogen bonds in the backbone
    • alpha helix (collagen) & beta sheet (spider silk)
  26. alpha helix
    • right handed helix
    • hydrogen bonds between the backbone carbonyl (C=O) of one residue & backbone (N) of the amide
    • 4 amino acid residues down the chain
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  27. tertiary structure
    • folded structure of an entire polypeptide
    • side chain dependent packing of the secondary elements and some other elements between them such as a loop or a turn made of amino acid residues
    • can fold into different shapes: fibrous: elongated, often structure roles. globular: compact, often enzymes
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  28. In eukaryotes, most protein breakdown involves __
    ubiquitin and the proteasome
  29. Ubiquitin is involved in __
    • energy-dependent proteolysis reactions
    • There are enzymes that attach ubiquitin molecules, single or in chains, to lysine amino acids in other proteins that are targeted for breakdown.
  30. Ubiquitination of a protein depends on the presence or absence of __
    amino acid motifs that act as degredation-susceptibility signals and the specific enzymes doing ubiquitination
  31. A protein must be __ before in can enter the proteasome. After entering the proteasome, __
    unfolded; the ubiquitinated proteins are degraded in it

    • This unfolding probably occurs through an energy-dependent process
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  32. Part of the protein penetrates into the major and minor grooves of the DNA in order to __
    recognize and achieve direct readout of the sequence (sequence specific binding proteins)

    This is usually accompanied by more general interactions with the surface of the DNA molecule, which may simply stabilize the DNA-protein complex.
  33. examples of specific DNA-binding motifs
    • helix–turn–helix (HTH) motif
    • zinc finger motif
    • Leucine zippers

    (more detail on Structure of proteins part 2, not sure if more info is needed since they're not on the review slide)
Card Set
Mol Bio Mid Review part 2
Week 6