07 - Nucleic Acid Structure & Function

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07 - Nucleic Acid Structure & Function
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2014-08-22 20:16:10
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nucleic acid structure function
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Nucleic Acid Structure & Function
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  1. Purine nucleobases
    Adenine and guanine
  2. Pyrimidine nucleobases
    Uracil, cytosine, and thymine
  3. What will the complete hydrolysis of nucleic acids yield?
    The individual components; nucleobases, pentose sugar, and phosphate
  4. How many H-bonds are between G&C and between A&T/U?
    There are three hydrogen bonds between G&C and two hydrogen bonds between A&T/U
  5. What stabilizes the double helix?
    Combination of hydrophobic forces and van der Waals interactions; H-bonds between bases from opposite strands
  6. What is hybridization?
    It is a technique based on the association of complementary strands; based on the capacity of complementary strands to anneal in which one of the strands is labeled with radiotracer or a fluorescence marker
  7. How many forms of DNA are there and what are they called?
    B DNA, A DNA, and Z DNA; B DNA is the physiological form we think of in regards to DNA, it has is right handed and there is one helical turn ~ every 10 bps
  8. What is the difference between negative and positive supercoiling?
    • Negative twists in the opposite direction of the double-helix, and unwinds DNA; positive twists in the same direction as the double helix and
    • overwinds DNA
  9. What type of DNA can undergo supercoiling?
    Only covalently closed circular DNA or ends-constrained linear DNA can undergo supercoiling
  10. Negative supercoiling of bacterial DNA
    Gyrase negatively supercoils bacterial DNA; results in transient double stranded breaks; supercoiling is ATP-dependent and it aids in DNA packing, replication, and transcription; this mechanism is the target of anti-bacterial drugs (ciprofloxacin and novobiocin)
  11. What are the two epigenetic modifications which alter chromatin structure?
    Methylation of C residues in –CpG- and histone modification
  12. What does methylation of –CpG- lead to?
    Generally leads to chromatin compaction and gene silencing; methylation of Cs in CpG islands results in long-term silencing of a gene; inactive X csome and other imprinted genes are heavily methylated
  13. What are CpG islands?
    Regions of DNA with a high density of CpG dimers; these are found in the regulatory regions of most human genes
  14. What does histone modification lead to?
    This is a post translational modification of histone tails, and the result of this modification depends on which histone is modified; acetylation generally leads to open chromatin structure and activation of genes
  15. How are histones acetylated and deacyetylated?
    A gene activator recruits histone acetyltransferase to acetulate a histone; a gene repressor recruits histone deacetylase to deactylates the histone
  16. Structure of RNA
    Mostly single stranded, but the strands to loop back to form intra-strand base-pairing (this defines the structure of RNA); where the RNA loops back and is paired, the strands are anti-parallel
  17. Transfer RNA (tRNA)
    75-85 bases long; contain bases like pseudouridin and ribothymidine; there is one tRNA for every AA; serves as an adaptor molecule during protein synthesis; forms a two dimensional “clover leaf” structure; it is compacted to a highly folded L-shaped conformation; one end of the L has an anticodon loop with the other end having an AA binding site attached to the 2’C or 3’C of the sugar; the 3’ end has the sequence CCA
  18. Aminoacyl-tRNA
    AN AA attached to a tRNA molecule
  19. What rRNA sizes are found in prokaryotes?
    23S (catalyzes the peptide bond formation), 16S (helps identify the first codon during translation), and 5S
  20. What rRNA sizes are found in eukaryotes?
    28S, 18S, 5.8S, and 5S
  21. Does rRNA base bair?
    Yes, it has considerable intra-strand base pairing
  22. Messenger RNA (mRNA)
    Least abundant, with a short half-life, this RNA has very little intra-strand base pairing; its primary sequence encodes proteins; it has a 5’ cap (7-methylguanosine triphosphate) and a poly(A) tail at the 3’ end; prokaryotic mRNA does not have a cap and tail
  23. What additional functional RNAs are found in eukaryotes?
    hnRNA, snRNA, scRNA, lncRNA, miRNA, and siRNA
  24. hnRNA
    mRNA precursors; has 5’cap and poly A tail
  25. snRNA
    There are 90; several hundred nucleotides long; U-rich, involved in the maturation of pre-mRNA
  26. scRNA
    Associated with proteins involved in the recognition of signal peptides on proteins
  27. lncRNA
    Over 200 bases; some are capped, polyA tailed, spliced; Xist silences one of the X csomes
  28. miRNA
    • Single stranded; 19-25 nucleotides long; may target up to hundreds of
    • mRNAs; non-coding, purely for regulatory purposes important for post-transcriptional gene silencing, affects a wide variety of cellular functions; role in cancer, viral infections, and wound healing; inhibits
    • translation of mRNA
  29. siRNA
    Double stranded; 21-22 nt; knock down specific genes; regulates the gene that expresses it; cleaves mRNA; acts as gene-silencing guardians in plants and animals that do not have antibody or cell-mediated immunity
  30. Transition temperature Tm
    Temperature at which 50% of the helix is denatured
  31. Hyperchromic shift
    • An increase in absorbace at 260 nm, associated with denaturation; this
    • is the wavelength at which nucleobases absorb light

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