DNA Damage, repair, Transcription (2)

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pctran90
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DNA Damage, repair, Transcription (2)
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2013-06-15 23:17:04
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UNC MED Biochemistry DNA Damage repair Transcription
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June 13 UNC MED Biochemistry DNA Damage, repair, Transcription
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  1. abasic site
    a location in DNA that has neither a purine nor a pyrimidine base, either spontaneously or due to DNA damage
  2. apoptosis
    a form of cell death which removes cells that have accumulated more damage than can be repaired.
  3. base excision repair
    • Corrects base mis-match.
    • Involves recognition and replacement of single base alterations, primarily resulting from spontaneous damage.
  4. checkpoint
    a point in G1 (before S) and G2 (before M) wherein the cell responds to DNA damage by either blocking the normal progression to S or M, giving the cell time to repair the DNA damage or by apoptosis
  5. cis-acting/trans-acting
    • 1)The DNA sequences involved in expression of a gene. elements do not move in the cell and they affect only DNA molecules in which they are contained; similarly, mutation of this sequence affects expression of only the gene containing that element.
    • 2)The proteins that bind to cis. are free to diffuse through the cell and can affect multiple, unlinked targets; mutation of this affects all of the genes with which that factor interacts.
  6. closed/open complex
    • 1)Transcription begins when the σ subunit binds a promoter sequence in conjunction with RNA polymerase. This initial DNA-RNA polymerase complex is called this.
    • 2)polymerase unwinds about 14 base pairs of the DNA to form the open complex, at which point the polymerase pairs the first nucleotide with the base at the start site.
  7. consensus sequence
    An idealized sequence representing the bases occurring with highest frequency at each position in a functional nucleic acid site, e.g., a site to which a protein binds.
  8. deamination
    The spontaneous loss of an amine group (NH2) from a base changes a standard base to a non-standard base.
  9. depurination/depyrimidation
    • both are spontaneous DNA damage.
    • 1) more frequent, loss of a purine.
    • 2)loss of a pyrimidine
  10. DNA adduct
    Many chemicals form covalent bonds, with the bases, causing replication block or mis-incorporation. This cause blocks in DNA replication or lead to mis-incorporation of nucleotides
  11. DNA ligase
    a polymerase that seals a nick/fill gap left by cleavage and excision of a a single nucleotide gap
  12. DNA-binding domain/activation domain
    The transcription factors that bind enhancer sequences usually contains two different regions, a DNA binding domain that binds to a specific DNA sequence and an activation domain that interacts with other proteins that promote recruitment of TFIID and RNA polymerase II.
  13. enhancer
    increase the frequency of transcription
  14. exonucleases
    "proofread" removes the incorrect nucleotide at the end of the chain and allows the polymerase a second chance to add the correct nucleotide.
  15. glycosylase
    specific for each base recognizes and removes the damaged base.
  16. mismatch pair
    causes Hereditary nonpolyposis colorectal cancer: high risk of predominantly colon cancer, but also cancers of many other organs.
  17. mRNA
    Encode information to synthesize proteins. Sequences of bacterial mRNAs exactly same as their gene sequences. Sequences of eukaryotic mRNAs initially exactly same as gene sequence, but later altered. Most exist at <100 molecules/cell. Some encoding abundant proteins exist at >1000 molecules/cell.
  18. mutation
    a permanent change in DNA sequence, from a single base pair to a large chromosomal alteration. Accumulation of such alterations causes cancer and many other diseases.
  19. nucleotide excision repair
    Removes base with adduct. the primary means to repair UV photoproducts. It can also repair many types of base damage not recognized by a specific glycosylase.
  20. promoter
    The element in the DNA that determines the start site of transcription. Is usually a short DNA sequence located 5’ of the start site.
  21. pyrimidine dimer
    Absorption of UV light by two adjacent pyrimidines (T-T, T-C, C-C, etc.) can result in the bases becoming covalently joined to form __. cause distortions in the DNA helical structure, because the 1.6 Å long covalent bonds joining the bases are shorter than the normal 3.4 Å spacing between bases in DNA. This distortion prevents the dimer from base pairing with the opposite strand and will cause a block in DNA replication.
  22. reactive oxygen species
    Oxidation damage to DNA is caused by ionizing radiation (gamma rays, X-rays) or normal oxidative metabolism. Damage is caused by formation of free radicals, usually from water, which generates OH molecules with an unpaired electron (hydroxyl radical). Hydroxyl radicals cleave the deoxyribose sugar or the phosphate backbone, leaving a strand break, or they modify a base, resulting in a replication block or mis-incorporation during replication. The best studied oxidatively damaged base is 8-oxoguanine (8-oxoG). DNA polymerases misread oxoG as T and insert A instead of C.
  23. repressor
    interfere with the complete assembly of a transcription complex on the promoter, usually by binding to sites that overlap the binding sites for initiation factors.
  24. TATA box
    Many of the RNA polymerase II promoters have this sequence. Is similar to the -10 region of bacterial promoters, and the A+T rich nature of both sequences is probably important for the initial separation of the DNA strands.
  25. tautomer
    Are alternate forms of the bases in which a proton shifts position. T and G are normally in keto form, but rarely and transiently exist as enol tautomers. A and C are normally in amino form, but transiently exist as imino tautomers.
  26. transcription factor
    Enhancer and repressor sequence are binding sites for trans-acting proteins known collectively as this..
  27. tRNA
    small (70-80 nucleotides) carriers of amino acids for protein synthesis. All cells contain >100 different tRNAs (but there are only 20 amino acids in proteins) which together comprise ~5% of total cellular RNA.
  28. rRNA
    The ribosome is a huge RNA-protein complex that “translates” mRNA sequences into protein sequences. rRNA molecules comprise >60% of ribosome mass. rRNAs carry out the activities of the ribosome. 3 rRNAs of different size and sequence in bacteria. 4 rRNAs of different size and sequence in eukaryotes.

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