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Midterm2_2022

  1. An enzyme in eukaryotes that makes rRNA
    RNA Pol I
  2. A conserved structural domain in core nucleosomal proteins
    Histone fold
  3. A molecular consequence of minor DNA damage going unfixed in dividing cells
    Mutation
  4. An enzyme in prokaryotes that reverts Holliday junctions to two separate DNA duplexes
    RuvC
  5. A class II general transcription factor that recognizes a majority of known eukaryotic core promoter elements
    TFIID
  6. A chemical used in nucleotide conversion in the study of cytosine methylation in eukaryotic DNA
    Sodium bisulfite
  7. A gene in diploid (and higher-ploidy) eukaryotes that is expressed exclusively from the maternal or paternal chromosome
    Imprinted gene
  8. A non-chemical mutagen that triggers large chromosomal deletions and inversions
    Ionizing radiation
  9. A non-chemical mutagen that triggers large chromosomal deletions and inversions
    Ionizing Radiation
  10. A core subunit of RNA polymerase in bacteria that can bind DNA in a sequence-specific manner
    alpha subunit
  11. A generic name of a DNA polymerase in any species that inserts random nucleotides across from a damaged chunk of DNA
    Translesion synthesis polymerase
  12. The predominant base conformation/orientation in a dNTP
    anti
  13. An RNA polymerase in eukaryotes that transcribes from promoters located inside of the transcribed region of a gene
    RNA Pol III
  14. A dimeric protein in E. coli that makes lactose operons sensitive to the presence of glucose in the cell
    Catabolic activator protein (CAP)
  15. A site in damaged DNA that lacks a nitrogenous base
    abasic site
  16. A generic name for protein complexes that alter the structure of chromatin
    Chromatin remodeling complex
  17. A natural Lac-operon inducer in E. coli
    Allolactose
  18. A man-made Lac-operon inducer in E.coli
    IPTG
  19. An enzyme that phosphorylates and restarts paused RNA Polymerase II and elongation factors in eukaryotes
    p-TEFb
  20. An alternative form of histone 2A found at sites of dsDNA breaks
    γ-H2Ax
  21. A core-promoter binding protein in eukaryotes that interacts with the minor groove of DNA
    TBP
  22. DNA repair proteins in eukaryotes that help recruit the NER machinery upon RNA Polymerase II encountering DNA damage during transcription
    CSA & CSB
  23. A generic name for a proximal promoter element in yeast that binds gene-specific transcription factor(s)
    UAS
  24. A recessive mutation in the Lac opereon in E. coli that makes cells unable to uptake lactose
    LacY(-)
  25. A distal orientation-independent promoter element in eukaryotes that represses transcription
    Silencer
  26. A protein that assists in transcription termination of some bacterial transcripts
    Rho
  27. A version of RNA Polymerase II with a non-phosphorylated C-terminal domain of the Rpb1 subunit in eukaryotes
    RNAPIIa
  28. A composite eukaryotic protein complex that remains at the core promoter after RNA polymerase II clears the promoter
    Scaffold complex
  29. A dsDNA break repair mechanism in all domains of life that does not rely on sequence similarity
    • NHEJ
    • (Non homologous end joining)
  30. A domain in many gene-specific transcription factors in eukaryotes that restores the positive charge on histone proteins
    HDAC
  31. A DNA repair protein that fixes abnormal DNA methylation by inducing oxidative demethylation
    AlkB
  32. A subunit shared between specific class I, II and III general transcription factors in eukaryotes
    TBP
  33. A DNA repair protein in bacteria that binds to hemimethylated DNA sites
    MutH
  34. A generic name of a protein that regulates transcription but lacks a DNA binding domain
    Co-regulator
  35. A generic name of an enzyme in all domains of life that recognizes a limited set of non-helix-distorting types of DNA lesions (e.g., oxidative deamination of individual nucleotides) and cleaves off damaged bases
    DNA glycosylase
  36. A single-subunit general transcription factor in eukaryotes
    TFIIB
  37. [Short answer] Why do different genetic DNA repair disorders occur at different frequencies in humans (e.g., Lynch syndrome affects 1 in 300 people, but trichothiodystrophy occurs in 1 individual out of 1 million people)? List two likely reasons.
    - Some types of DNA damage can be fixed by more than one DNA repair pathway, so mutations in some pathways may not manifest themselves as genetic disorders.


    - Different DNA repair pathways vary in the number and length of genes encoding the DNA repair proteins, with the probability of a mutation occurring being greater in a larger genetic space.

    - Some activities of DNA repair machineries are encoded by two or more redundant genes, so mutations in some genes may be phenotypically masked (and not cause a genetic disorder) due to functional compensation by the remaining paralogs.
  38. [short answer] Why does homology-directed DNA repair **not** typically occur in the G0/G1 phase of the cell cycle?
    Homology-directed DNA repair requires homologous DNA to serve as a repair template, whereas in G1/G0 chromosomal DNA has not yet replicated, so no sister chromatid is available to be used as a template.
  39. What types of DNA damage does the base excision repair (BER) machinery fix?
    Modified/damaged (e.g., deaminated, methylated, or oxidized) bases that do not result in major helix distortions (BER does NOT work on mismatched bases that lead to helix distortions!)
  40. What BER enzyme is responsible for DNA damage recognition?
    DNA glycosylase
  41. Give one example of a protein that can carry out direct reversal of DNA damage (A) and state the type of damage it can fix (B)
    A Photolyase

    B Pyrimidine dimers triggered by UV exposure
Author
saucyocelot
ID
363190
Card Set
Midterm2_2022
Description
vocab
Updated

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