Gene Expression: The Flow of Information from DNA to RNA to Protein II

  1. Transcription is the process by which the polymerization of __________ guided by complementary base pairing produces an RNA transcript of a gene
  2. State and explain the three steps of transcription in bacterial cells
    Image Upload 2
    Image Upload 4
    Image Upload 6
    • Initiation
    • Elongation
    • Termination (extrinsic vs intrinsic)
    • (pg 265-6)
  3. In the transcription process, the enzyme ____ _______ catalyzes transcription. DNA sequences near the beginning of genes, called _______, signal RNA polymerase where to begin transcription. Most bacterial gene promoters have almost ______ nucleotide sequences in each of two short regions. These are the sites at which RNA polymerase makes particularly _____ contact with the promoters
    Image Upload 8
    • RNA polymerase
    • promoters
    • identical 
    • strong
  4. RNA polymerase adds nucleotides to the growing RNA polymer in the _______ direction. The chemical mechanism of this nucleotide adding reaction is similar to the formation of _________ bonds between nucleotides during DNA replication with one exception (which is?)
    • 5' to 3' direction
    • phosphodiester bonds
    • Transcription uses ribonucleotide triphosphates (ATP, CTP, GTP, and UTP) instead of deoxyribonucleotide triphosphates.
  5. _________ of the high-energy bonds in each ribonucleotide triphosphate provides the energy needed for elongation
  6. Seqeunces in the RNA products, known as ________, tell RNA polymerase where to stop transcription
  7. A eukaryotic ___ _____ ___ transcribes genes that encode proteins. The fig illustrates the general structure of the DNA regions of euk. genes that allow ___ ______ ___ to initiate transcription
    • RNA polymerase II
    • RNA polymerase II (pol II)
  8. A key difference with prok is that sequences called _______ that can be thousands of base pairs away from the promoters are often also required for the efficient transcription of euk genes
  9. The AIDS virus uses an exceptional form of transcription, known as _______ _________, to construct a double strand of DNA from an RNA template
    reverse transcription
  10. The result of transcription is a single strand of RNA known as a ______ ___________. In prokaryotic organisims, the RNA produced by transcription is the actual _____ that guides protein synthesis
    • primary transcript
    • mRNA
  11. In euk organisms, by contrast, most primary transcripts undergo _____ _______ in the nucleus before they migrate to the cytoplasm to direct synthesis. This processing has played a fundamental role in the evolution of ________ organisms
    • RNA processing 
    • complex
  12. Some RNA processing in eukaryotes modifies only the 5' or 3' ends of the _______ _______, leaving the info content of the rest of the mRNA untouched
    primary transcript
  13. Why is the content of the mature mRNA  related but not identical to the complete set of DNA nucleotide pairs in the original gene?
    Other processing deletes blocks of info from the middle of the primary transcript
  14. The nucleotide at the 5' end of a euk mRNA is a G in ________ orientation from the rest of the molecule; it is connected through a ___________ linkage to the first nucleotide in the primary transcript
    • reverse
    • triphosphate
  15. The backward G is not ________ from DNA. Instead, a special ______ enzyme adds it to the primary transcript after __________ of the trasncript's first few nucleotides
    • transcribed
    • capping enzyme
    • polymerization
  16. Enyzmes known as ______ ________ then add methyl (-CH3) groups to the backward G and to one or more of the succeeding nucleotides in the RNA, forming a so called ________ _____
    Image Upload 10
    • methyl transferases
    • methylated cap
  17. The gene for collagen (an abundant ______ in connective tissue) has two introns. By contrast, the dystrophin gene has more than 80 introns; the mean intron lenght is 35 kb, but one intron is an amazing _____ kb long
    • protein
    • 400 kb long
  18. The introns range from ____ bp to over ____ kb. Exons in contrast, vary in size from about ___ bp to a few kilobases
    • 50 bp 
    • 100 kb
    • 50 bp
  19. The greater size variation seen in introns compared to exons reflects which 2 facts:
    • introns do not encode polypeptides 
    • introns do not appear in mature mRNA

    As a result, fewer restrictions exist on the sizes and base sequences of introns
  20. Mature mRNAs must contain all of the ______ that are translated into amino acid, including the ______ and ______ codons
    • codons
    • initiation and termination
  21. In addition, mature mRNAs have sequences at their 5' and 3' ends that are not translated, but still play important roles in regulating the efficiency of translation. They are called  __________ regions, and are located just after the _________ _____ and just before the _______ _______, respectively 
    Image Upload 12
    • 5' and 3' untranslated regions (UTRs)
    • methylated cap 
    • poly-A tail
  22. Besides the cap and tail themselves, all of the sequences in a mature mRNA, including all of the codons and both UTRs, must be ________ from the gene's exons
  23. Introns can interrupt a gene at any location, even between the _______ making up a single codon. In such a case, the three nucleotides of the codon are present in two different (but ________) exons
    • nucleotides
    • successive
  24. How do cells make a mature mRNA from a gene whose coding sequences are interrupted by introns?
    The answer is that cells first make a primary transcript containing all of a gene's introns and exons, and then they remove the introns from the primary transcript by RNA splicing
  25. RNA splicing
    the process that deletes introns and joins together successive exons to form a mature mRNA consisting only of exons
  26. Why must a gene have one more exon than it does introns?
    Because the first and last exons of the primary transcript become the 5' and 3' ends of the mRNA, while all the intervening introns are spliced out
  27. To construct the mature mRNA, splicing must be remarkably ________. For example, if an intron lies within a codon, splicing must _______ the intron and _________ the codon without disrupting the _______ _______ of the mRNA
    • precise
    • remove 
    • reconstitute 
    • reading frame
  28. Three types of short sequences within the primary transcript (purpose?)
    • splice donors, splice acceptors, and branch sites
    • To help ensure the specificity of splicing
  29. These sites make it possible to sever the the connections between an ______ and the _____ that precede and follow it, and then to join the formerly distant _______
    • intron and exon
    • exons
  30. The mechanism for the two sequential cuts in the primary transcript (4-story)
    Image Upload 14
    Image Upload 16
    • The first cut is at the splice-donor site, at the 5' end of the intron
    • After this first cut, the new 5' end of the intron attaches, via a novel 2'-5' phosphodiester bond, to an A at the branch site located within the intron, forming a lartiat structure
    • The second cut is at the splice-acceptor site, at the 3' end of the intron; this cut removes the intron 
    • The discarded intron is degraded, and the precise splicing of adjacent exons completes the process of intron removal
  31. Splicing normally requires a complicated intranuclear machine called the ________, which ensures that all of the splicing reactions take place in concert
  32. The spliceosome consists of four subunits known as ______ ______ ___________. Each of which contains one or two ______ ______ ________ 100 - 300 nucleotides long, associated with proteins in a discrete particle
    • small nuclear ribonucleoproteins or snRNPs
    • small nuclear RNAs (snRNAs)
  33. Certain snRNAs can _____ _____ with the splice donor and splice acceptor sequences in the ________ _________, so these snRNAs are particularly important in bringing together the two exons that flank an intron
    • base pair
    • primary transcript
  34. Given the complexities of spliceosome structure, it is remarkable that a few primary transcripts can splice them selves without the aid of spliceosome or any additional factor. These rare primary transcripts function as _________ (define)
    ribozymes: RNA molecules that can act as enzymes and catalyze a specific biochemical reaction
  35. Sometimes RNA splicing joins together the _____ ______ and ______ _______ at the opposite ends of an intron, resulting in ______ of the intron and _______ of the two successive and now adjacent exons
    • splice donor and splice acceptor
    • removal 
    • fusion
  36. Alternative splicing produces different ______ molecules that may encode related ______ with different, though partially overlapping, ____ _____ sequences and functions
    • mRNA
    • proteins
    • amino acids
  37. In effect then, alternative splicing can tailor the nucleotide sequence of a primary transcript to produce more than one kind of _________. _______ ______ largely explains how the 25,000 genes in the human genome can encode the hundreds of thousands of different _________ estimated to exist in human cells
    • polypeptide
    • Alternative splicing
    • proteins
  38. Translation takes place on _______ that coordinate the movements of _______ ______ carrying specific amino acids with the genetic instructions of an mRNA
    • ribosomes 
    • transfer RNAs
  39. No obvious chemical _______ or ______ exists between the nucleotide triplets of mRNA codons and the amino acids they specify. Rather, transfer RNAs (tRNAs) serve as _______ molecules that mediate the transfer of info from ______ _____ to _____
    • similarity or affinity
    • adapter
    • nucleic acids 
    • protein
  40. Transfer RNAs are _____, _____-stranded RNA molecules 74-95 nucleotides in length.
    • short
    • single-stranded
  41. Several of the nucleotides in tRNAs contain _______ bases produced by chemical alterations of the principal A, G, C, and U nucleotides. Each tRNA carries one particular ______ _____, and all cells must have at least one _______ for each of the common 20 amino acids specified by the genetic code. The name of a tRNA reflects the _____ _____ it carries
    • modified 
    • amino acids
    • tRNA 
    • amino acid
  42. The three levels of the structure of tRNAs
    Image Upload 18
    • The nucleotide sequence of a tRNA constitutes the primary structure 
    • Short complementary regions within a tRNA's single strand can form base pairs with each other to create a characteristic cloverleaf shape; this is the tRNA's secondary structure
    • Folding in three-dimensional space creates a tertiary structure that looks like a compact letter L
  43. At the bottom end of the L, the tRNA carries an _________ (define)
    Image Upload 20
    anticodon: three nucleotides complementary to an mRNA codon specifying the amino acid carried by the tRNA
  44. The anticodon _____ forms base pairs with other regions of the tRNA, it is ______ available for base pairing with its complementary mRNA codon
    • never
    • always
  45. As with other complementary base sequences, during pairing at the ribosome, the strands of anticodon and codon run ________ to each other.
    • antiparallel
    • *If for example, the anticodon is 3' CCU 5', the complementary mRNA codon is 5' GGA 3', specifying the amino acid glycine
  46. At the other end of the L, where the 5' and 3' ends of the tRNA strand are found, enzymes known as ___________-_______ _________ connect the tRNA to the amino acid that corresponds to the anticodon
    Image Upload 22
    aminoacyl-tRNA synthetases
  47. These aminoacyl-tRNA synthetases are extraordinarily specific (explain)
    They recognize unique features of a particular tRNA including the anticodon, while also recognizing the corresponding amino acid
  48. Aminoacyl-tRNA synthetases are, the only molecules that read the languages of both _____ _____ and ______. Thus they are the actual molecular ________
    • nucleic acid and proteins
    • translators
  49. Normally, one ________-____ ________ exists for each of the the 20 common amino acids. Each _______ functions with only one amino acid, but the enzyme may recognize several different ______ specific for that amino acid
    • aminoacyl-tRNA synthetase
    • synthetase
    • tRNAs
  50. The figure illustrates the _____-step process that establishes the ______ bond between an amino acid and the 3' end of its corresponding tRNA
    Image Upload 24
    • two step 
    • covalent
  51. A tRNA covalently coupled to its amino acid is called a ______ _______. The bond between the amino acid and tRNA contains substantial energy that is later used to drive _______ bond formation
    • charged tRNA 
    • peptide bond
  52. While attachment of the appropriate amino acid charges a tRNA, the amino acid itself does not play a _______ role in determining where it becomes incorporated in a growing polypeptide chain. Instead, the specific interaction between a ______ _______ and an _____ _______ make the decision
    • siginificant
    • tRNA's anticodon
    • mRNA's codon
  53. Although at least one kind of tRNA exists for each of the 20 common amino acids, cells do not necessarily carry tRNAs with anticodons that are  ___________ to all of the 61 possible codon triplets in the genetic code. E. coli, for example, makes 79 different tRNAs containing 42 different anticodons. Although several of the 79 tRNAs in this collection obviously have the same anticodon, 61-42=19 of the 61 potential ________ are not represented
    • complementary
    • anticodons
  54. Thus 19 mRNA codons will not find a _________ anticodon in the E. coli collection of tRNAs.
  55. How can an organism construct proper polypeptides if some of the codons in its mRNAs cannot locate tRNAs with complementary anticodons?
    • The answer is that some tRNAs can recognize more than one codon for the amino acid with which they are charged
    • That is, the anticodons of these tRNAs can interact with more than one codon for the same amino acid, in keeping with the degenerate nature of the genetic code
  56. Francis Crick spelled out some rules of base pairing between codons and anticodons. He reasoned that the 3' nucleotide in many codons adds ______ to the specificity of the codon. For example, 5' GGU 3', 5' GGC 3' all encode glycine.
  57. It does not matter whether the ____ nucleotide in the codon is U, C, A or G as long as the first two letters are GG (for glycine). The same is true for other amino acids encoded by four different codons, such as vaine (GU)
  58. For amino acids specified by two different codons, the first two bases of the codon are, once again, ________ the same, while the third base must be either one of the two ________  or one of the two __________
    • always 
    • purines (A or G)
    • pyrimidines (U or C)
  59. Thus, 5' CAA 3' and 5' CAG 3' are both codons for glutamine and 5' CAU 3' and 5' CAC 3' are both codons for histidine. If pu stands for either purine and Py stands for either pyrimidine then CAPu represents the codon for ______ and CAPy represents the codons for ________
    • glutamine 
    • histidine
  60. The 5' nucleotide of a tRNA's anticodon can often pair with more than one kind of nucleotide in the _____ position of an mRNA's codon. Remember, after base pairing the bases in the anticodon run ________ to the bases in the codon.
    • 3'
    • antiparallel
  61. A single tRNA charged with a particular amino acid can thus recognize _______ or even _____ of the codons for that amino acid. This flexibility in base pairing between the 3' nucleotide in the codon and the 5' nucleotide in the anticodon is known as _______
    • several 
    • all
    • wobble
    • Image Upload 26
  62. The combination of normal base pairing at the first two positions of a codon with wobble at the _______ position clarifies why multiple codons for a single amino acid usually start with the same two letters
  63. An important aspect of wobble is the chemical modification of certain bases at the 5' end of the anticodon (the _______ position). An A in the ______ position of a tRNA is always modified to _________, and a U in the wobble position is always modified in one of ______ possible ways.
    • wobble 
    • wobble
    • inosine (I)
    • three
    • Image Upload 28
    • Image Upload 30
  64. By contrast, G in the anticodon wobble position is always ________, while modification of C occurs only in the tRNAs of some ________ species. Wobble bases are modified by specific enzymes that act on the tRNA after it has been synthesized by ________
    • unmodified
    • bacterial 
    • transcription
  65. The wobble rules delimit the anticodon sequences and the wobble base modifications that are consistent with the genetic code. For example, methionine (Met) specified by one codon (AUG). Give a detailed explanation of the result
    Image Upload 32
    Met-specific tRNAs must either have a C at the 5'end of their anticodns (5' CAU 3'), or a U that is modified to xm5U, because these are the only only nucleotides at the position that can base pair only with the G at the 3' end of the Met codon
  66. Ribosomes facilitate polypeptide synthesis in various ways. (5) State them
    pg 276
  67. In E. coli, ribosomes consist of ______ different ribosomal RNAs and _____ different ribosomal proteins. These components associate to form two different ribosomal subunits called the _____ subunits and the _____ subunits (with S designating a coefficient of ________ related to the _____ and ______ of the subunit). Which is smaller?
    • three
    • 52
    • 30S
    • 50S
    • sedimentation 
    • size and shape
    • the 30S is smaller
  68. Before translation begins, the two subunits exist as _______ entities in the cytoplasm. Soon after the start of translation, they come together to reconstitute a complete _________. In euks. they have ____ components than their prok counterparts but they still consist of _____ dissociable subunits
    • separate
    • ribosome
    • more
    • two
    • Image Upload 34
  69. The small 30S subunit is the part of the ribosome that initially binds to _____. The larger 50S subunit contributes an enzyme known as ______ _______, which catalyzes formation of the peptide bonds joining adjacent amino acids
    • mRNA
    • peptidyl transferases
  70. Label
    Image Upload 36
    Image Upload 38
  71. Both the small and the large subunits contribute to the three distinct tRNA binding areas knwon as the ________ site , the ________ site and the ______ site.
    • aminoacyl (or A) site
    • peptidyl (or P) 
    • exit (or E) site
  72. Finally, other regions of the ribosome distributed over the _____ subunits serve as points of contact for some of the additional proteins that play roles in translation
  73. Fig 8.24
    Other colors: 
    Image Upload 40
    • Green: tRNA in the A site
    • Red: tRNA in the P site
    • Lavender: ribosomal proteins
    • Other colors: ribosomal RNAs (rRNA)
    • *pg 277
  74. As was the case for transcription, translation consists of three phases (3)
    • Initiation: phase that sets the stage for polypetide synthesis
    • Elongation: amino acids are added to a growing polypeptide
    • Termination: phase that brings polypeptide synthesis to a halt and enables the ribosome to release a completed chain of amino acids
  75. Explain the biochemical basis of colinearity, that is the correspondence between the 5' to 3' direction in the mRNA and the N-terminus to C-terminus direction in the resulting polypeptide (5-story)
    pg 277
  76. Translation story
    pg 278-279
  77. Shine-Dalgarno box
    Kozak sequence
    • Shine-Dalgarno box: a sequence of six nucleotides in mRNA that is one of two elements comprising a ribosome binding site (the other element is the initiation codon)
    • Kozak sequence: Kozak consensus orKozak sequence is a sequence which occurs on eukaryotic mRNA and has the consensus (gcc)gccRccAUGG. The Kozak consensus sequence plays a major role in the initiation of the translation process.
  78. Polyribosome
    structure formed by the simultaneous translation of a single mRNA molecule by multiple ribosomes
  79. Protein structure is not irrevocably fixed at the completion of _________. Several different processes may subsequently modify a polypeptide's structure. Cleavage may remove amino acids, such as the N-terminal fMet, from a polypeptide, or it may generate several ________ polypeptides from one ______ product of translation
    • translation 
    • smaller
    • larger
    • Image Upload 42
  80. The larger polypeptide made before it is cleaved into smaller polypeptides is often called a _________. Also some proteins are synthesized in inactive forms called ______ that are activated by enzymatic cleavage that removes an ________ _______
    • polyprotein
    • zymogens 
    • N-terminal prosegment
  81. Two reasons why posttransational modifications can be very important.
    Name the most important mod
    • The biochemical function of many enzymes depends directly on the addition (or sometimes removal) of phosphate groups
    • Posttranslational modifications may alter the way a protein folds, its ability to interact with other proteins, its stability, its activity or its location in the cell
    • Image Upload 44
Card Set
Gene Expression: The Flow of Information from DNA to RNA to Protein II
Ch 8.2-