Chapter 6

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Chapter 6
2010-10-20 00:20:23
Cellular Molecular Biology

Gene to Protein
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  1. True/false: Genes can be expressed with different efficiences.
    True. A gene can be expressed more compared to another gene. The gene with more expression will have greater amounts of proteins then the less expressed gene.
  2. How do uracil and thymine differentiate?
    Thymine has a methyl group where Uracil has a single H group.
  3. How does DNA and RNA differ in structure?
    on the 2' carbon, RNA has a hydroxl group where as in DNA the 2' has a Hydrogen.
  4. RNA is mainly single stranded and will not form any other structure.
    False. Yes, RNA is mainly single stranded but RNA can fold into other specific structures. Complimentary regions allow RNA to fold in 3D shapes. Can form conventional base-pairing (forming rungs) as well as form non-conventional base-pairing interactions (folds interacting with folds)
  5. RNA can unwind the DNA helix.
    True. RNA polymerase can unwind the DNA at the active site exposing the template strand in prokaryotes. However, in eukaryotes RNA polymerase can not unwind double-stranded DNA, TFIIH has a helicase subunit.
  6. RNA uses incoming nucleotides called ____ _____.
    ribonucleoside triphophates.
  7. What is a transcriptional unit?
    A sequence of DNA that is transcribed.
  8. How many genes will a transcript code for in eukaryotes?
    1 gene. In contrast, prokaryotes will code for a series of neighbouring genes.
  9. How many genes will a transcript code for in prokaryotes?
    A transcript will code for a series of neighbouring genes. In contrast, eukaryote transcripts will code for only one gene.
  10. In bacteria, what signals for initiation of transcription?
    the binding of the sigma factor to the RNA polymerase to form a RNA polymerase halo complex.
  11. In bacterial transcription, what signals elongation?
    When the sigma factor dissociates from the RNA polymerase.
  12. In baterial transcription, what is the process of termination?
    DNA contains ter sequences that code for complimentary regions in the transcript that will cause a loop formation. Then following a set of UUUUUU destabilizes RNA polymerases hold on DNA and causes the polymerase to fall off.
  13. Two important characteristics of ter sequences?
    • 1) sequences of DNA codes for self-complimentary regions of RNA to form a RNA loop
    • 2) series of U-nucleotides in RNA make the dissociation easier.
  14. In the bacterial promoter, what is found at the -10 sequence?
    At the -35 sequence?
    • The TATAA box (-10)
    • -35 = TTGACA
  15. How long is the bacterial promoter?
    ~60 base pairs long. (from -40 to +20)
  16. RNA is synthesized in the ___ to ___ direction.
    5' to 3' direction. Therefore, RNA polymerase moves in the 3' to 5' direction.
  17. What is the start site for transcription?
    +1 AGTC
  18. Eukaryotic transcription differs by the use of 3 RNA polymerases. Name them.
    RNA polymerase I,II, and III
  19. RNA polymerase _ transcribes the 45s precursor rRNA which is made into subunits : ___,___,___. they code for what kind of genes?
    • I
    • 5.8s, 18s, and 28s; codes for rRNA genes
  20. This polymerase transcribes all-protein coding genes, snoRNA, miRNA, siRNA and most snRNA genes.
    Polymerase II
  21. RNA polymerase III codes for what type of genes?
    tRNA genes, 5s rRNA genes, sRNA genes and genes for other small RNAs
  22. Mitochondrial RNA polymerase is similar to ______ RNA polymerase which are both similar to _____ RNA polymerase.
    chloroplast and bacterial
  23. Not all RNA polymerases are composed of subunits.
    False. All RNA polymerase are composed of subunits.
  24. Transcription in eukaryotes cells the involvement of proteins call ____ _____ ____
    general transcription factors
  25. The are 3 groups of GTF's what are they?
    TFI,TFII,TFIII. Each roman numeral represents its association with the corresponding RNA polymerase. TFI with RNA polymerase I, TFII with RNA polymerase II ect.
  26. There are _ TFIIs
  27. In eukaryotes, RNA polymerase __ transcribes most genes.
  28. TFIID has __ major subunits. Name them. (found in eukaryotes)
    2; TBD ( - 30 TATA Binding Protein) and TAF subunits
  29. TFIIH has _ subunits. Its role it to...
    9 subunits; unwinds DNA at transcriptional start point.
  30. Which Transcription factor has helicase as a subunit? What kind of cell is it found in?
    TFIIH. found in eukaryotic cells.
  31. how far is the TATTA box from the transcriptional start point in eukaryotic cells?
    25 nucleotides away.
  32. the 5' methyl cap is added during the ____ phase
    elongation. It require capping factors associated with the tail of RNA polymerase
  33. The 5' methyl cap and associated proteins (CBC) function to;
    • help the RNA to be properly processed and exported (5' cap first)
    • play important roles in the translation of mRNA
  34. Human genes have an average of _ exons and _ introns
    • 9 exons
    • 8 introns
  35. (Most/some)_____ hnRNAs can be spliced in a variety of ways by _____________
    • MOST
    • alternative RNA splicing
  36. Alternative splicing produces __ which produces___
    • produces slightly differnt mRNAs
    • produces slightly differnt proteins from the same gene
  37. When does RNA splicing occur?
    during the elongation phase
  38. RNA splicing occurs at ____ _____ located at the ______ of introns and exons
    • consensus (nucleotide) sequences
    • junctions
  39. 3 important consensus sequences invloved in RNA splicing..
    • 5' splice junction located at 5' end of intron; typically longer to branch point
    • 3' splice junction located at 3' end of intron;typicall shorter to branch point
    • branch point "A nucleotide"
  40. the branch point site in an intron forms?
    the base of excised lariat
  41. Name the snRNAs involved in splicing
    U1, U2, U4, U5, and U6. U3 has not role in splicing hnRNA (rRNA)
  42. snRNA leaves the nucleus to combine with ____ and returns to the nucleus as a ____
    • protein binding complex
    • snRNP
  43. The U1 snRNP forms base pairs with the ___ splice junction and the BBP(_____)
    • 5'
    • branch-point binding protein
  44. The U2 snRNP _____ BBP and U2AF and forms ____ pairs with the ___ ____ consensus sequence
    • displaces
    • base pairs
    • branch-point
  45. What snRNPs come into the scence as a triplet?
    U4/U6 and U5. U4 and U6 are held together tightly via base-pair interactions.
  46. The triplet snRNP complex acts to?
    position the pre-mRNA properly for the first phosphoryl-transferase reaction
  47. RNA-RNA rearangments occur that break apart __/__ and allow __ to displace U1 at the 5' splice junction to form an active site for the second ____ ____ which completes the splice
    • U4/U6
    • U6
    • phosphoryl-transferase reaction
  48. pre-mRNA is another word for ___
  49. ____ is a formed snRNP complex. Utilizes branch point "_" to cut the hnRNA at the __ splice site
    • spliceosome
    • A
    • 5'
  50. the 5' cut (RNA splicing) becomes covelently linked to ____ forming a loop called a ____
    • A (branch-point site)
    • lariat
  51. exons (post splicing) are _____ linked. The excised ____ RNA will be degraded/recycled in the ____ and the snRNPs will be degraded/recycled
    • covalently
    • intron
    • degraded
    • nucleus
    • recycled
  52. ____ proteins associated with the tail of RNA polymerase are also required in addition to snRNPs
  53. True/false: Introns are only removed via snRNPs
    False: Introns may be removed without these aids by special splicing proteins associated with the tail of RNA polymerase
  54. Self-splicing introns. Group I utilizes ___ ___ _ nucleotide to initiate the splicing process.
    Group II utilizes an "_" nucleotide that is apart of the intron itself.
    • Group I- free-floating G
    • Group II- A nucleotide
  55. introns are degraded by ___
  56. Describe the last event of hnRNA modification
    Addition of a poly-A tail to the 3' end which is specified by consensus nucleotide sequences
  57. termination is signaled by RNA nucleotide sequence ______, of which 10-30 nucleotides upstream cleavage occurs after DNA polymerase has transcribed exposing a ___ group. The DNA polymerase continues to transcribe, transcribing ter sequences rich in __ or __. This has loose ___ for the polymerase and it falls off.
    • AAUAAA
    • -OH
    • GU or U-rich
    • affinity
  58. this enzyme adds the 3' poly-A tail
    poly-A polymerase
  59. ____ and ___ proteins recognize the RNA sequence AAUAAA (poly- A site) and bind to it leaving the RNA polymerase ___.
    • CPSF and CstF
    • tail
  60. Poly-A polymerase (PAP) adds _ A at a time
  61. Unlike RNA polymerase, this enzyme in mRNA 3' processing DOES NOT require a template
    poly-A polymerase (PAP)
  62. The poly-A tail is about ____ A's long.
  63. The 5' cap is added after or before the poly-A tail
    before. After cleavage of the RNA after poly-A tail has been added, the RNA polymerase II continues to transcribe. This new RNA lacks a 5' cap and is degraded by 5'-3' exonuclease
  64. mRNA are ____ exported. A mature mRNA is ready and signaled by a variet of ___
    • selectively
    • proteins
  65. ______ complexes are bound to the introns to help identify them for destruction by ___
    • hnRNP
    • exosomes
  66. mRNA is exported out the nucleus through a ___ ____ ____ with the ___ end going first
    • nuclear pore complex
    • 5' cap
  67. True/false: Many mRNA proteins dissociate before and after exiting the nucleus
  68. a protein call _____ nids to the mRNA to signal for export from the nucleus
    nuclear export receptor
  69. In eukaryotes, a exported mRNA will form a ____ shape due to protein interactions
    circular shape. Inititation factors bind
  70. the most abundant non-coding RNAs are _____
    rRNAs. Important components of ribosomes.
  71. Eukaryotic rRNAs are synthesized via RNA polymerase _
  72. RNA polymerase ___ transcribes hnRNA
  73. in Eukaryotes, RNA polymerase _ transcribes the important ___ precursor ____
    • I
    • 45s precursor rRNA from the 45s rRNA genes
  74. Human cells have ~ ___ copies of rRNA genes distibuted in groups on 5 different haploid (therefore, on _ chromosomes in diploid cells)chromosomes; name them
    • 200
    • 10
    • chromosome 13,14,15,21,22
  75. 45s Precursor rRNA is a ____ RNA transcript synthesized by RNA polymerase __
    • primary
    • I
    • *RNA polymerase II transcribes hnRNA
  76. 45s precursor rRNA is degraded in _ rRNA molecules; __,__ and __
    • 3
    • 5.8s, 18s, and 28s.
    • *5s rRNA is made elsewhere
  77. 45s precursor rRNA goes through ___ ___ having degraded regions of the nucleotide sequence
    chemical modification
  78. 2 types of 45s precursor modifications
    • Uridiene is converted to pseudouridine
    • 2'-oxygen of RNA is mthylated
  79. What enzymes are responsible for modifications of precursor rRNA? Where do the modifications occur?
    snoRNP complexes. snoRNAs determine sites of modification by base-pairing to complimentary sequences on the precursor rRNA. The snoRNAs are bound to proteins, the complex is a snoRNP. They contain the enzyme to modify the rRNA.

    occurs in the nucleolus
  80. 5s rRNA is produced by which enzyme?
    RNA polymerase III
  81. As prophase proceeds, the nucleolus ____ and no ___ precursor is made. The ___ precursor becomes active in euchromatin
    • disintergrates
    • 45s
    • 45s
  82. ____ ____ consists of __ loops thats project into the nucleolus. They organize info like formation of the nucleolus
    • nucleolar organizers
    • 10
  83. telomerase is made in/out of the nucleus
    synthesized in the nucleus
  84. An immature large RNA subunit and a immature small RNA subunit are exported to the ____ for final assembly. The assembled ribosome consists of the ___ subunit and the smaller ____ subunit
    • cytoplasm
    • 60s
    • 40s
  85. the number of possible codons is _x_x_ = 64. but there are only _ types of amino acids. Therefore, the genetic code is ____
    • 4x4x4
    • 20 amino acids
    • redundant
  86. The start codon is ___
  87. the 3' end of tRNA is common to all tRNAs. The common sequence is ___
  88. the __ end on tRNA is covalently linked to an amino acid
  89. the shape of a tRNA resembles a ___
  90. the tRNA precursor is synthsized by RNA polymerase ___
    III. Also synthesizes 5s rRNA
  91. tRNA goes through _ significant alterations
  92. The alterations of tRNA include;
    • 1) 5' end - removal of leader sequence
    • 2) 3' end - replacement of 2 nucleotides by CCA
    • 3) chemical modifications of some bases
    • 4) excisions of an intron
    • 5) change in conformation
  93. ___ ____ attach the correct amino acods to the appropriate tRNAs
    amino-acyl tRNA synthesases
  94. a _ step process links an amino acid to a tRNA
  95. Step 1 of linking an amino acid to a tRNA invloves the amino acid reacting with ___ to produce a ____ amino acid releasing __
    • ATP
    • adenylated (ribose sugar + adenine)
    • relases 2pi
  96. Step 2 of linking an amino acid to a tRNA involves the _____ amino acid reacting with ____ to produce an ______ tRNA and releases AMP
    • adenylated
    • tRNA
    • aminoacyl
  97. Like DNA polymerase tRNA is a ____ ____ enzyme due to its editing site
  98. tRNA synthesase has 2 catalytic sites called the ____ site and the ____ site
    • synthesizing site - binds amino acid to tRNA
    • editing site- checks correctness. Incorrect will be removed
  99. In eukaryotes the TATA box is located at the ___ region and is recognized by the ___ protein
    • -30
    • TBP (TATA binding protein)
  100. The GTF (Eukaryotes) ____ recognized the transcription start point
    • TFIID
    • TBP subunit recognizes TATA
  101. TFIIE has the function to ____
    attract and regulate TFIIH. Has 2 subunits
  102. the tRNA precursor is a (functional/non-functional)_______ molecule
    functional. Goes through 5 alterations
  103. A growing amino acid chain grows from the ___ to the ___ end
    amino end to the carboxyl end
  104. A tRNA that has contributed its amino acid and has already dissociated is termed ____ tRNA
    deacylated tRNA
  105. To form a peptide bond (incoming tRNA) ____ end reacts with the ____ end of the growing chain
    amino (NH2) reacts with the carboxyl end (-O-C=O) to produce O=C-NH
  106. The prokaryotic ribosome is named ____ and consists of 2 subunits ___ and ____; .The eukaryotic enzyme is called ___ and consists of 2 subunits ___ and ____
    • 70s; composed of 50s and 30s subunits
    • 80s; composed of 60s and 40s subunits
  107. the prokaryotic 70s ribosome adds ____ amino acids per second. the eukaryotic 80s ribosome adds __ amino acids per second.
    • 20
    • 2
  108. ____ proteins play important roles in all 3 phases of translation
    cytosolic proteins (Initiation factors, elongation factors and termination factors)
  109. The elongation phase of translation involves ___ steps
  110. formation of a peptide bond is catalyzed by _____ (this enzyme is the ____ rRNA molecule acting as the ____ in the large RSU)
    • peptidyl transferase
    • larger rRNA
    • ribozyme
  111. _____ of the large RSU changes the relative position of the tRNAs. Shifts in the 5' to 3' direction
  112. _____ of the small RSU for a distance of _ nucleotides
    • translocation
    • 3 (a codon length)
  113. During elongation, translation factors hydrolyze ___ to provide energy
  114. In prokaryotic translation ___ causes step 4 ( translocation of the small RSU)
  115. the ____ phase established the correct reading frame for translation
  116. In bacteria, a special initiator _____ carries _______
    • tRNA
    • formylmethionine
  117. the original methionine is removed by _____
    methionine aminopeptidase
  118. the initiator tRNA starts translation by binding to the ___ site of the ribosome
    P-site. Carries eIF2 and GTP
  119. Initiator tRNA moves along the RNA in the __ to __ direction searching for the first ___
    • 5' to 3'
    • AUG
    • *hydrolyzes ATP to move
    • this event sets the correct reading frame for translation
  120. In bacterial translation, no 5' cap is present. Each bacterial mRNA has a _________ located several nucleotides upstream from a ______. This is called a ____
    • ribosome-binding site
    • start codon AUG
    • shine-Delgarno sequence
  121. Bacterial mRNAs are usually ______. While Eukaryotic mRNAs are typically _____
    • polycistronic
    • monocistronic
  122. Binding of the ___ factor to the _ site signals termination. Breaks the last peptide bond via ___
    • RF
    • A-site
    • hydrolysis
    • Note: stop codons are UAA UAG
  123. In bacteria trancription and translation are ___
  124. A ____ is a eukaryotic mRNA that is translated simutaneously by many ____
    • polyribosome
    • ribosomes
  125. This ____ inhibitor blocks binding of aminoacyl-tRNA to the A-site of the ribosome. Another inhibitor _____ blocks mRNA synthesis by binding preferentially to RNA polymerase II
    • tetracycline (about 1/2 antibiotics work by interfering with bacterial ribosomes)
    • alpha- amanitin
  126. In translation, some proteins begin folding during ____
  127. Proteins with hydrophobic regions may ___ out of solution and form ____. Proper folding involved proteins called ___
    • precipitate
    • aggregates
    • molecular chaperones - 2 families
  128. In eukaryotes there are 2 major families of molecular chaperones the ____ family and the ___family known as ____
    • hsp70
    • hsp60 = chaperonins
  129. The ____ enzyme digests incompletely folded proteins. The proteins are tagged with ______ chain and are digested into ____ ____
    • proteasome
    • polyubiquitin chain
    • short peptides
  130. A protein that is to be ubiquitied will give off a _____ signal for the _____ ligase to add ubiquiton to. The activation of the signal involves a ____ ____ in normal proteins.
    • degradation
    • ubiquiton
    • exposed hydrophobic region
  131. There are __ destabilizing amino acids at the amino end
  132. The only kind of proteins resistant to proteases
    protein aggregates
  133. the most important step in regulation of gene expression
    initiation of transcription