Gene Expression S1M1

  1. Extracting information from DNA is called
    Gene expression
  2. Transcription
    • Reading the DNA and making some type of RNA
    • The first half of gene expression
  3. How long is the amino acid code made by the rRNA
  4. If uracil is found in DNA what happens
    Enzymes remove them quickly
  5. What is one treatment for cancer related to Thymine and Uracil
    A drug replaces the Thymine with Uracil and therefore is marked to die
  6. How is RNA different from DNA
    • It is smaller
    • Contains ribose instead of deoxyribose
    • Contains uracil instead of thymine
    • Most RNAs are single stranded
  7. What is another class of RNA's that functions in splicing
    Small nuclear RNA's called snRNA
  8. What does RNA Polymerase I do
    It makes pre rRNA in the Nucleolus
  9. What does RNA polymerase II do
    It makes mRNA precursur in the nucleoplasm, and snRNA
  10. What does RNA Polymerase III do
    It makes tRNA, rRNA, as well as snRNA. But is only active in about 10% of the cells
  11. What inhibits the Pol I, II, and III
    Alpha amanitin (very small amounts needed)
  12. What is the most important component of the ribosomes
  13. RNA in ribosomes of Eukaryotes consists of
    • 28S (large subunit)
    • 18S (small subunit)
    • 5.8S (large subunit)
    • 5S (large subunit)
  14. The major human rRNA species are synthesized by cleavage from a common 13 kb transcription unit which is part of a 40 kb tandemly repeated unit that occurs 80 times on each of which chromosomes tips
    13,14,15, 21 and 22
  15. Transcription Unit 13kb is clipped down by
    RNases to smaller units
  16. How are most of the rRNA's synthesized in the cell
    The larger rRNAs are synthesized as a unit by RNA pol I and then processed
  17. What poisons have terrorists used to kill people
    Ricin (Residue from castor oil)
  18. What does Ricin do to the ribosome
    It removes one adenine from the 28S rRNA
  19. How does Ricin alter ribosomes
    The Ricin A is an enzyme that binds and depurinates a specific adenine of the 28S rRNA
  20. Ricin interferes with the ability of the eukaryotic ribosome to interact with eEF1 and eEF2. How does it do this?
    By depurinating an adenine in the 28S rRNA thereby inactivating the large 60s ribosomal subunit.
  21. What are the smallest of the 3 major RNA's
  22. Every tRNA has what attached to the 3' end
    CCA, The A (adenosine) is where amino acids are attached
  23. How many codons are there
    64 (61 code for amino acids)
  24. RNA's contain Thymine, How is it possible if RNA polymerase do not incorporate thymine when making RNA
    The U or C that is incorporated by RNA pol is post-transcriptionally changed to a T
  25. What are some of the modifications that occur in the tRNA pre-transcriptionally
    • Some of the nucleotides are removed
    • Some of the nucleotides are modified
    • CCA is added to the 3' end of all tRNA's
  26. What would happen to the dihydrouridine if it were available during the transcription of tRNA genes
    It would be ignored because you only incorporate A, C, G, and U when making a tRNA, all others will be ignored
  27. MIDD is a mutation in what mitochondrial DNA- encoded gene having what effect
    • tRNA(leu,uur)
    • Damages Complex 1 in Ox Phos therefore making less ATP
  28. What RNA group causes Maternally Inherited Diabetes and Deafness (MIDD)
    • tRNA
    • The disease causes hearing loss, Diabetes, and Cardiomyopathy.
    • This is caused by the change in just one base, often it happens in the mitochondria
  29. What is MELAS and how is it caused
    • Mitochondrial Encephalopathy, Lactic Acidosis, Stroke-Like Episodes
    • This is caused by the change in just one tRNA base, often it happens in the mitochondria
  30. DNA in the mitochondria doesn't do what as readily as that in the nucleus
    Get repaired
  31. A mutated tRNAleu reduces the amount of what made in the mitochondria
    Complex I which affects the amount of ATP made
  32. Topoisomerase is used for both
    DNA replication and RNA transcription
  33. The base sequence of the strand of DNA used as the template for transcription has the base sequence GATCTAC. What is the base sequence of the RNA product? (All sequences are written according to standard convention.)
  34. Unlike DNA polymerases, RNA polymerases
    Can initiate synthesis of their polynucleotide product
  35. The growth of RNA proceeds
  36. A coding strand is written
    5'-3' the coding strand contains the coding genes
  37. What is the coding strand
    This is the strand that is above the template strand that contains the exact nucleotides as end product of the transcription differing only by the T's being replaced by U's
  38. Nucleotides are always added to what end
    The 3' prime end
  39. What are the Eukaryotic promoters
    CAAT box and TATA (Hogness) box
  40. Promoters most of the time will be where
    Usually up stream
  41. What is a promoter
    A gene where the proteins bind to direct the RNA polymerase II to start making RNA
  42. What is an Enhancer
    They bind to activators that stimulate the transcription factors to make the RNA polymerase more active. They are a sequence of DNA that binds to the portein.
  43. Genes that are considered housekeeping genes that are consistently being made are considered
    Constitutive (essential)
  44. Genes that are needed at lower levels are limited how
    Their promoters are usually weak
  45. What are regulated genes
    They are genes expressed at different levels under specific conditions
  46. What is LCR (Locus control region)
    Opens up the chromatin to be coded whereas without it they cannot. Used often to regulate periods in life for a gene to be expressed
  47. Enhancers, and many silencers, can be found
    • They can be found 5’ of a coding region, 3’ of a coding region, and in the introns of a gene
    • The point is that they are recognized easily no matter their orientation
  48. What keeps the globin genes off in non-erythrocytes
    They lack (LCR's) Locus control regions that are only expressed in erythrocytes
  49. Exons vs Entrons
    Exons code for proteins, Entrons don't
  50. The pre-mRNA is processed in what 3 ways
    • 5' cap is added
    • Splicing out of Introns
    • The addition of a poly A tail
  51. C terminal domain (CTD)
    Required to modify mRNA, It coordinates the processing events of capping, splicing and polyadenylation (poly A tail)
  52. The N terminus is located where on the protein when it is being made
    On the beginning of the protein, the C terminus is on the end
  53. Whats the significance of the 5' cap
    Are unique in eukaryotic mRNA
  54. What coordinates transcription with pre-mRNA processing
    The C-terminal domain of RNA pol II
  55. The 5' end of an Intron you have a --, in the middle an -, and at the 3' an --
    • (5' to 3') GU, A, AG
    • If any are mutated the gene won't be spliced out
  56. Splicing of Eukaryotes is carried out by
    A combination of snRNA's and proteins called spliceosomes
  57. The splicing of introns in mRNA precursors is carried out by
  58. What is the function of th 5' cap
    Essential unit for the ribosome to bind to the 5’ end of the mRNA.
  59. A geneticist introduces the genes for a super-spliceosome into the human germline that is able to remove every intron without fail. In which way would people with this genetic innovation differ from the rest of the species?
    They would produce fewer unique proteins
  60. The 5' cap and the 3' poly-A tail are added in the production of mature eukaryotic mRNA. The 5' cap and the 3' poly-A tail have which respective functions?
    Translation initiation and transcript stability
  61. Gene expression involves what two processes
    • Transcription – reading the DNA to make RNA
    • Translation – reading the mRNA to make protein
  62. A specific codon ALWAYS codes for the
    Same amino acid
  63. The four Characteristics of the Genetic Code are
    • Specificity- Always codes for one amino acid
    • Universality- Every organism uses the genetic code
    • Redundancy- An amino acid may have more then one code for it
    • Nonoverlapping and commaless- the code is read from a fixed starting point, taken three at a time. Nothing tells the ribosome where a codon starts or stops.
  64. No signal exists in the genetic code to
    Indicate the end of one codon and the beginning of another
  65. A mutation that changes one of the nucleotides in a gene’s coding region are one of three senerios
    • 1. Not change the amino acid for which the codon is coding (silent mutations)
    • 2. Change the amino acid for which the codon is coding (missense mutations).
    • 3. Change the codon to a stop codon (nonsense mutations)
  66. Frame-shift mutations can happen by
    The addition or subtraction of any nucleotides, and will create a protein that is usually “nonsensical” or “nonsensical and truncated”.
  67. Frame-shift mutations have what end effect
    The amino acid sequence beyond the frame shift is always altered
  68. Aminoacyl-tRNA synthetases is
    Needed to attach amino acids to tRNAs and are very accurate in hooking the correct amino acid to the correct tRNA
  69. ATP and GTP roles in translation
    ATP is needed to hook up tRNAs and amino acids; GTP is needed to translate the mRNA
  70. How many high energy phosphate-bond equivalents are needed for activating amino acids for protein synthesis
    2, ATP and GTP
  71. The anticodon base pairs in what fashion on the tRNA
    Complementary fashion with the codon in the mRNA during translation
  72. The ribosomes of the prokaryotes and eukaryotes are different how
    • Eukaryotic ribosomes
    • –Are 80S in size
  73. Some of the tRNAs can recognize more than one codon how, what is this called
    • Non-traditional base pairing between the 1st codon on the tRNA and 3rd on the mRNA
    • Wobble position
  74. eIF4 initiation factors bind to what having what effect
    5’ cap (cap binding proteins – CBPs) also known as an translation initiator factor
  75. Alternative splicing is the reason we can
    • Make so many proteins with so few genes, 74% of the genes do this
    • This is selective splicing essentially
  76. Polyadenylation is
    The addition of a poly(A) tail to an RNA molecule
  77. Transcription is terminated in Eukaryotes by
    Rat1 Race, this follows the transcription and once it catches up it, it terminates transcription
  78. AUG
    Start Codon
  79. With what mRNA codon would the tRNA 5' UAC 3' be able to form a codon-anticodon base pairing interaction?
    5' GUA 3'
  80. Which base, when it occurs in the wobble position in tRNA, can bind to three different bases (A, U and C)?
  81. Formation of the peptide bond during protein synthesis does not require
    ATP or GTP
  82. Peptide bond formation is catalyzed by
    The large subunit rRNA
  83. Cycloheximide inhibits the peptidyl transferase reaction in eukaryotes. It does so by binding to
    The 60S ribosomal subunit
  84. Most mRNA are translated by more than one ribosome at a time and are called
  85. Translation is terminated by a release factor (RF) and what stop codons
    UGA, UAG, or UAA codons
  86. Ferritin is
    A cytosolic iron binding protein expressed when iron is abundant in the cell. Transferrin is its receptor
  87. Interferon in response to pathogens being in the system allow
    communication between cells to trigger the protective defenses of the immune system that eradicate pathogens or tumors.
  88. What is the target of the polio protease
  89. Which post-translational modification is most frequently used to rapidly alter protein function
  90. Diphtheria toxin is produced by the gram positive bacilli effects what in translation
    eEF2 making it so tRNA cannot move to the P site
  91. Ribonuclease (Rnase)
    is a type of nuclease that catalyzes the degradation of RNA into smaller components
  92. Poly A Binding Proteins (PBP)
    Activate translation
Card Set
Gene Expression S1M1