Genomics #1 Gene Structure

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  1. What are the protein-coding regions of DNA/RNA called?
  2. Define Pseudogene:
    a duplicate gene that has been mutated and is no longer functional
  3. Coding regions only account for ______% of the entire human genome.
  4. Define Intergenic and how much of the human genome is considered intergenic?
    • genes that do not code for anything (genome-wide-repeats),
    • 62%
  5. What are the (3) non-coding regions in between exons called?
    • 1) Gene-associated regions (introns, regulatory sequences, promoters, enhancers, etc.),
    • 2) Pseudogenes � copies of genes that are no longer functional,
    • 3) Gene fragments
  6. Name the four DNA-Binding Domains:
    • helix turn helix,
    • zinc finger,
    • leucine zipper,
    • helix loop helix
  7. DNA-Binding domains make many different types of bonds. Name the two categories of bonds with the specific type(s) of bonds:
    • 1) Permanent- covalent,
    • 2) Reversible- hydrogen bonds, hydrophobic interactions, and van der Waals forces
  8. T/F: A common feature of DNA-Binding Domains is they bind to specific DNA sequences with high affinity (but have a low affinity for other DNA).
  9. Helix- Turn-Helix contains (2)___________ connected by a fixed angle turn.
    alpha helixes (dimer)
  10. What part of a Helix- Turn-Helix binds to the DNA and what is the name of the specific binding location on the DNA?
    • the most C-terminal,
    • the recognition Helix (the major groove of the DNA)
  11. T/F: Centromeres and heterochromotin are non coding sequences.
  12. rDNA is DNA that codes for_________.
  13. Besides being on chromosomes, where do we find DNA?
  14. What are the 3 types of DNA coding regions?
    • Gene coding regions,
    • Protein coding regions
    • Intergenic regions
  15. Transcription factors bind to __________ to recruit polymerase to initiate transcription.
    the promoter region
  16. The _________ region binds addition factors to promote transcription.
    enhaner region
  17. Helix-Loop-Helix contains a dimeric__________ instead of the ___________ found in Helix-Turn-Helix.
    • Loop,
    • Turn
  18. Zinc Finger motifs connect _________structuress to one another through ________or ______and _______ interactions.
    • secondary structures,
    • through 4 cys or (2 cys and 2 his)
  19. T/F: Minimal Zinc-Finger motifs attached to a protein increases its affinity of the protein for the DNA.
    False: Multiple increase the affinity
  20. What are the two regions of the Leucine Zipper binding protein? Which binds to a number of hydrophobic interactions to hold the 2 alpha helices together?
    • DNA bindig region and the Zipper region,
    • Zipper region
  21. T/F: The DNA must be unwound in order for the binding of a binding protein.
    False: Multiple increase the affinity
  22. How can a binding protein bind to an wound dsDNA strand?
    In the major groove there are atoms of nucleotides that are not used in the binding of the two strands that can be used by the binding protein.
  23. What is a common AA sequence in the 5' end that marks the splice site in the DNA sequence?
  24. The 3' splice site of a DNA sequence contains a stretch of __________ followed by a N(any nucleotide) and ending with______.
    • poly-pyrimidine chain
    • CAG
  25. T/F: The most common intron are known as GU-AG intron because it begins with GU and ends with AG. Less common are the AU-AC introns.
  26. T/F: The order of a conserved 3' splice site (from 3' to5') starts with a "AG" then a "N" then a poly-pyrimidine then upstream is an Adenine.
  27. How many snRNPs are in a Spliceosome? Name them:
    (5), U1, U2, U4, U5, and U6
  28. When proteins form complexes directly with snRNAs, they form____________.
    snRNPs (small nuclear ribonucleoprotein particles).
  29. What is a snRNA? What is a snRNP?
    • small nuclear RNAs (typically ~100-300 nucleotides long),
    • Complexes formed by snRNA with other proteins in a spliceosome
  30. The binding ability of U1 to the 5' splice site is because?
    It has complimentary snRNAs to the 5' that help it to localize
  31. After the U1 binds the 5', ________ binds to the 3' splice site.
    U2AF (auxiliary factor)
  32. After the U1 binds the 5' and U2AF binds to the 3' splice site. The following _____ binds and then ______ will bind with conserved A in the intron. Then _______ and _______ are free to diffuse away.
    • SF1,
    • U2,
    • SF1 and U2AF
  33. Which (2) snRNPs of the spliceosome pull together the various ends of the intron? Which recruits additional (3)________ namely _____ , ______, and _______. Now the hydroxyl attack happens.
    • U1 and U2,
    • additional snRNPs, U4, U5, and U6
  34. What happens in a splicing reaction (3 steps)?
    The conserved A is covalently attached to the G at the beginning of the intron (5')end. One end of the RNA is cut leaving a lasso (loop) structure on the end of the mRNA. Then another hydroxyl attack where the exon attacks 3' splice site, cutting the intron free and attaching the two ends of the exons together.
  35. T/F: In GU-AG introns, splicing takes place by hydroxyl attacks that bind the end of one exon to the beginning of another exon.
    True, at least in the GU-AG introns,
  36. In the human genome, what % of genes have 0 introns?
  37. If mRNA is not linear, how can splicing in the correct location be done?
    • 1) in 3D structures, the outside sites are available to splice first,
    • 2) proteins and other factors
  38. What is the role of an Exonic Splicing Enhancer(ESE) in splicing?
    promote the inclusion of a particular exon in the mRNA
  39. What is the role of an Exonic Splicing Silencer(ESS) in splicing?
    promote the exclusion of a particular exon in the mRNA
  40. What is the role of an Intronic Splicing Enhancer (ISE) in splicing?
    promote the inclusion of a particular intron in the mRNA
  41. What is the role of an Intronic Splicing Silencer(ISS) in splicing?
    promote the exclusion of a particular intron in the mRNA
  42. What are Antisense Oligonucleotides?
    short pieces of ssDNA or ssRNA that are complimentary and designed for certain sequences in the mRNA to alter transcription.
  43. What are some possiblities that Antisense Oligonucleotides can alter transcription?
    • bind to the 5' end inhibiting transcription,
    • bind/ inhibit inclusion,
    • exclusion of introns or exons
    • (almost any binding protein alteration)
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Genomics #1 Gene Structure

questions from genomics gene structure
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