Biochem L 15-16

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  1. During DNA repair how is the parent strand recognized?
    Methylated Adenine on the GATC Sequences
  2. Many melanomas at a young age point to what?
    A Problem with DNA repair
  3. What protein mediates Methyl-directed mismatch repair in E-Coli and what does it do?
    Mut protein, Repairs bulky lesions such as pyrimadine dimmers caused by UV light
  4. What fills in the gap created by the SEGMENT being removed by endonuclease during Methyl-directed mismatch repair?
    DNA polymerase fills in the gap and DNA ligase seals the gap
  5. What is the difference between nucleotide excision repair and base excision repair?
    Base excision repair removes just the problem base, not a segment of DNA.
  6. What process is used to repair bases lost to spontaneous deamination and how prevalent in spontaneous deamination in purine bases?
    Base excision repair, and about 10,000 puring bases per cell per day
  7. What is spontaneous deamination?
    Cystine loses an NH3 and becomes Uracil.
  8. What are two causes of and methods to rectify double strand DNA breaks?
    • Radiation and Free radicals
    • Non-homologous end joining (NHEI) – error prone, Homologous repair – most accurate
  9. What three diseases are the result of defects in DNA repair?
    • Xeroderma Pigmentosa
    • Ataxia Telangiectasia
    • HNPCC (Lynch Syndrome)
  10. What is wrong with people who have Xeroderma Pigmantosa?
    Cells lack the ability to remove pyrimidine dymers
  11. What is wrong with Ataxia Telangiectasia (AT) people?
    There is a problem with kinase ATM which disrupts signaling, causes ataxia, which is walking like a drunk
  12. What is wrong with people who have HNPCC (lynch Syndrome)?
    They lack the ability to repair mismatches in DNA. Since they cannot deal with mismatches, cancer is generated. About 5% of colon cancer patients have this.
  13. What are the nine types of RNA?
    • mRNA (messanger RNA) (formerly known as heterogeneous nuclear RNA) – Protein Coding
    • rRNA (ribosomal RNA) - catalytic
    • tRNA (transfer RNA) - catalytic
    • snRNA (small nuclear RNA) - catalytic
    • snoRNA (small nucleolar RNA) - catalytic
    • scaRNA (small Cajal body specific RNA) - catalytic
    • miRNA (micro RNA) - regulatory
    • siRNA (small interfering RNA) - regulatory
    • riboswitch (found more in prokaryotes) – regulatory
  14. What is the leading cause of death in infants and what does it involve?
    Spinal muscular atrophy, due to mutations in the survival of motor neurons (SMN) protein. SMN helps in snRNP biogenesis.
  15. What are four ways RNA can be modified?
    • Terminal additions
    • Base modifications
    • Trimming
    • Splicing
  16. How many genes are there in the human genome? How many proteins? How is this possible?
    30000 genes, 100000 proteins, base modification and splicing
  17. What percent of RNA in a cell is mRNA?
  18. What does monocistronic mean?
    mRNA carries information from only one gene, this is the common type of mRNA in eukaryotes
  19. what is the UTR and what does it do?
    Untranslated region of mRNA, it helps to regulate the half-life of the message
  20. What does polucistronic?
    mRNA carries information from more that one gene, This happens in prokaryotes.
  21. What are the 7 sizes of rRNA and do they correspond with prokaryotes or eukaryotes?
    • 23S, 16S, 5S – Prokaryotes
    • 28S, 18S, 5.8S, and 5S – Eukaryotes
  22. What percent of RNA in a cell is composed of rRNA?
  23. What percent of the RNA in a cell is composed of tRNA?
  24. What pairs between the tRNA and the mRNA during translation?
    The anticodon in tRNA pairs with the codon in mRNA during translation to add the appropriate amino acid
  25. What are the spliceosomal snRNAs?
    U1, U2, U4, U5, and U6
  26. What does the spliceosome do?
    Splices together exons and removes introns
  27. What is systemic lupus erythematosus?
    An autoimmune disease that involved autoimmune antibodies (Abs) to snRNPs
  28. What are snoRNAs?
    Small nucleolar ribonucleicproteins, they function as Guide RNAs that help determine where modification of rRNA takes place by base pairing
  29. What are scaRNAs?
    Small Cajal body-specific RNAs, they are guide RNAs found in the Cajal body, which is a nuclear subdomain, they guide the 2’O methyation and pseudouridylation found in snRNAs and snoRNAs
  30. What do miRNA do?
    Base pair with specific mRNA, usually the 3’UTR of the mRNA and promote mRNA degradation or reduced translation
  31. What does siRNA do?
    Used in the RISC complex to target the RNA produced by the transposon and virus, can also be used in research to knock down specific genes
  32. What is a riboswitch?
    Short sequence of RNA that can bind to small molecules and change confirmation to start or stop transcription
  33. How many RNA polymerases are in Prokaryotes and in Eukaryotes?
    • Prokaryotes – one RNA polymerase
    • Eukaryotes – three RNA polymerases
  34. Where are sigma factors found, Eukaryotes or Prokaryotes?
  35. Where are nucleosomes found, Eukaryotes or Prokaryotes?
  36. Do prokaryotes extensively modify mRNA?
    No, since translation occurs with transcription, the mRNA do not have the chance to extensively modify mRNA as eukaryotes do.
  37. RNA is complementary to the DNA ___________________ strand and identical to the _______________ strand except ___ replaces _____
    • Template (antisense)
    • Coding (sense)
    • U
    • T
  38. What do holoenzymes do?
    They are enzymes in conjunction with cofactors (sigma factors) that function to recognize promoters to aid in transcription, usually of proteins that will function in response to the stimuli that created the cofactors (such as alcohol sigma factors responding to alcohol ingestion by promoting genes that break down alcohol)
  39. What are the three phases of transcription?
    • Initiation
    • Elongation
    • Termination
  40. What does rifampin do?
    Antibiotic that binds to the beta subunit of RNA pol and inhibits initiation
  41. What is a way to inhibit initation in prokaryotes?
    The antibiotic rifampin, which binds to the beta subunit of RNA pol and inhibits initiation
  42. What is Actinomycin and how does it act?
    Anti-cancer agent that disrupts transcription by inhibiting elongation
  43. What is a way to inhibit elongation in eukaryotic cells?
    Actinomycin D is an anti-cancer agent that inhibits elongation, thus disrupting transcription
  44. What is rho dependant termination?
    Rho binds to C rich regions of RNA near the 3’ end and moves towards the 3’ end and then disrupts RNA/DNA hybrid with helicase activity
  45. What is RNA pol I?
    Eukaryotic RNA polymerase found in the nucleolus. Functions in the production of rRNA precursor that gives rise to 28S, 18S, and 5.8S rRNA
  46. What is RNA pol II?
    Eukaryotic RNA polymerase that makes heterogeneous nuclear RNA (hnRNA) – which gives rise to mRNA
  47. What is RNA pol III?
    Eukaryotic RNA polymerase that makes tRNA and 5S rRNA
  48. What does histone acetyltransferase (HAT) and histone deacetylase (HDAC) do?
    • HAT acetylates lysine on histones, causing euchromatin (loose and open DNA)
    • HDAC deacetylates lysine on histones causing heterochromatin (closed and transriptionally inactive DNA)
  49. What are the differences between cis elements and trans factors?
    • Cis elements are sequences in the DNA that promote transcription, such as the TATA box, CAAT box, GC box etc.
    • Trans factors bind to DNA to impact gene expression
  50. What are four types of trans factors?
    • Transcription factors – these bind to DNA using motifs such as leucine zippers or zinc fingers
    • Chromatin remodeling complex
    • Enhancer binding proteins
    • Mediator proteins
  51. What is alpha-amanitin and what does it do?
    It is a trans factor that comes from the death cap mushroom and inhibits RNA pol II
Card Set
Biochem L 15-16
Flashcards for L 15-16
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