The Flow of Genetic Information

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The Flow of Genetic Information
2012-11-14 18:27:08
Molecular Biology

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  1.                                                               i.      __ have instructions for making proteins
    1.      Nucleic acids and proteins contain information written in __
    2.      Transcription and translation
    • Genes
    • two different chemical languages
  2.                                                               i.      Transcription
    1.      Synthesis of __using __
    2.      Transcribed= __
    3.      DNA is __for RNA
    4.      Synthesis ofwhich RNA
    • RNA
    • DNA
    • rewritten
    • template
    •  ANY RNA
  3.                                                               i.      Translation
    1.      Synthesis of a __using the information in the mRNA
    2.      Cell translates nucleotide sequence into__of polypeptide
    3.      Occurs in __
    • polypeptide
    •  amino acid sequence
    • ribosomes
  4.                                                                                      i.      Both occur in all organisms
                                                                ii.      Basic mechanics for bacteria and eukaryotes
    1.      Bacteria don’t have __; so, their DNA is not separated by __ from __and the other protein-synthesizing equipment
    a.      Allows __of mRNA to begin while __still going
  5. nuclei
    • nuclear membranes
    • ribosomes
    • translation
    • transcription
  6. 1.      Eukaryotes have __ that separates two process
    a.      __in nucleus
    b.      __in cytoplasm
    c.       However, before this occurs, they are __
    d.      Transcription produces __ and further __yields __
    e.       The initial RNA transcript from any gene is called a __
    • nuclear envelope
    • Transcription
    • Translation
    • modified
    • pre-mRNA
    • processing
    • finished mRNA
    • primary transcript
  7. 1.      Genes program __ via genetic messages in the form of mRNA
    a.     __
    b.      Some RNA can act as __for __, but still this is the central dogma
    • protein synthesis
    •  CENTRAL DOGMA (DNA-->RNA-->Protein)
    • templates
    • DNA synthesis
  8. Genetic codon is written in __.
  9. Discovery of codons: How did they determine that they were triplets?
    • 1.      Single yields only four amino acids
    • 2.      Two-nucleotide sequence= 16
    • 3.      Triplets of nucleotide basis can form all amino acids
    • a.      There can be 64
  10. a.      __: the genetic instructions for a polypeptide chain are written in the DNA as a series of __, three-nucleotide words, which are then transcribed into complementary series of non-overlapping three-nucleotide words in mRNA and translated into __
    • Triplet code
    • nonoverlapping
    • amino acids
  11.                                                               i.      For each gene, only one DNA strand acts as template= __
    1.      For any given gene, the __ is used as the template every time the gene is transcribed
                                                                ii.      Like DNA, RNA is synthesized in __direction and is __to template strand
    • template strand
    • same strand
    • antiparallel
    • complementary
  12.                                                               i.      mRNA nucleotide triplets are called __, written in __ direction
    1.      __= DNA nucleotide triplets along nontemplate strand and are complmentary to template strand and identical to mRNA except for thymine and uracil
    • codons
    • 5’-->
    • 3’
    • codon
  13. 1.      __
    a.      The sequence of codons along an mRNA molecule is decoded into a sequence of amino acids making up a polypeptide chain
  14. 1.      Each codon specifies what?

    a.      Because codons are nucleotide triplets, the number of nucleotides making up a genetic message ust be __times the number of amino acids
                                                                                                                                          i.      Ex: 300 nucleotidesà polypeptide with __amino acids
    • which amino acid will be incorporated
    • three
    • 100
  15.                                                               i.      First codon decoded in 1961 by __
    1.      Synthesized artificial mRNA by linking identical RNA nucleotides containing uracil as their base
    a.      UUU: poly-U added to test-tube
                                                                                                                                          i.      UUUàpolypeptide
    Marshall Nirenberg
  16. 1.      Three codons don’t designate amino acids; they are “__”, marking the end of __
    2.      __signals beginning of translation and adds __
    a.      Polypeptide chains start with __
    • stop codons
    • translation
    • AUG
    • methionine
    • methionine
  17.                                                               i.      There is a __, but no __
    1.      Several codons may specify one amino acid, but no codon ever specifies another amino acid other than their own
    a.      Usually the redundant amino acids differ in the __nucleotide base of the codon
                                                                ii.      Must be read in correct__—correct groupings
    1.      Must be read from __to __
    • redundancy
    • ambiguity
    • third
    •  reading frame
    • left
    • right
  18. a.      __pries two strands of DNA apart and joins together RNA nucleotides complementary to the DNA template strand, elongating the __
                                                                  i.      Only in __ direction
                                                                ii.      Unlike DNA pol, they can __
    b.      DNA sequence where RNA pol attaches and begins transcription= __
                                                                  i.      In bacteria,__ end
    • RNA
    • RNA polynucleotide
    • 5à3
    • start a chain from scratch and don’t need a primer
    • promoter
    •  terminator signals
  19. a.      Direction of transcription= __and other direction as __
    b.      Stretch of DNA transcribed into RNA is __  
    c.       Bacteria
                                                                  i.      Single type of __ that synthesizes several RNAs
    d.      Eukaryotes
                                                                  i.      At least __types
    1.     __used in mRNA synthesis
    • downstream
    • upstream
    • transcription unit
    • RNA pol
    • three
    •  RNA pol II
  20. a.      Synthesis
                                                                  i.      Initiation
    1.      __includes start point and extends several nucleotide pairs __from start point
    a.     __ binds in pecise location and orientation on promoter, determining where __begins and which DNA is template strand
    b.      Bacteria have RNA pol that specifically recognizes and binds to __
    c.       Eukaryotes require proteins called __ to mediate the binding of __ and initatio transcription
                                                                                                                                          i.      After __ bind, then __binds
                                                                                                                                        ii.      This complex is called __
    1.      __ is crucial __
    • Promoter
    • upstream
    •  RNA pol
    • transcription
    • promoter
    • transcription factors
    • RNA polymerase
    • transcription factors
    • RNA pol II
    • transcription initiation complex
    • TATA box
    • promoter DNA sequence
  21.                                                               i.      Elongation
    1.      RNA pol moves along adding nucleotides and untwisting helix
    a.      When done, pulls away
                                                                                                                                          i.      __nucleotides per sec in euk
    2.      Single gene can be transcribed simultaneously by several __
    • 40
    • polymerases
  22.                                                               i.      Termination
    1.      Bacteria:
    a.      __functions as signal, causing __to detach from DNA and release transcript, which requires__
    2.      Euk:
    a.     __transcribes __in __
                                                                                                                                          i.      At about __ nucleotides downstream from signal, proteins cut pre-mRNA free
    • Terminator
    • polymerase
    •  no further modification
    •  RNA pol II
    • polyadenylation signal
    • pre-mRNA
    • 10-35
  23. I.                   mRNA Processing
    a.      both ends of primary transcript are altered
    b.      certain interior sections are__and remaining parts __together
    c.       Alteration at ends      
                                                                  i.      explain
    •  cut out
    • spliced
    • 5’ end receives 5’ cap, a modified form of G ucleotide added onto 5’ end after transcription of first 20-40 nucleotides
    • 3’ end receives poly-A-tail
  24. Functions of modification at ends
    •                                                               i.      Functions
    • 1.      Facilitate export form nucleus
    • 2.      Protect form degradation by hydrolytic enzymes
    • 3.      Help ribosomes attach to 5’ end of mRNA
  25.                                                               i.     
    __are parts of mRNA not
  26. a.      RNA splicing
                                                                  i.      Due to long __stretches of nucleotides, regions that aren’t translated are __
    1.      Usually interspersed in __

    2.      Non-coding segments: __
    3.      __: expressed into amino acid sequences
    • noncoding
    • cut out
    • pre-mRNA
    • introns
    • Exons
  27.                                                               i.      Although introns and exons transcribed, modified mRNA does not have introns; they’re cut out and exons j oined. How?
    • 1.      Signal for splicing at end of intron
    • a.      Small nuclear ribonucleoproteins recognize splice sites and join to form spliceosome, which interacts with certain sites along intron, releasing it, which is rapidly degraded, and joining together two exons that flanked intron
    •                                                                                                                                       i.      snRNAs catalyze process and participate in spliceosome assembly and splice site recognition
    • b.      Ribozymes
  28. a.      Ribozymes
                                                                  i.      RNAs that function as __
    1.      __RNA functions as __and catalyzes its own __
    • enzymes
    • Intron
    • ribozyme
    • excision 
  29.                                                               i.      3 properties:

    •  Due to single-stranded, they can base pair with complementary regions in same moleculeà 3D structure
    • 2.      Some bases contain functional groups that may participate in catalysis
    • 3.      Ability of RNA to hydrogen bond with other nucleic acids adds specificity to its catalytic activity
  30. a.      A single gene may encode more than one polypeptide type; it depends on which segments are treated as __during __
                                                                  i.      This is __
    1.      Proteins often have modular architecture consisting of discrete structural and functional regions called __
    a.      Different __code for different domains of protein
    • exons
    • RNA processing
    • alternative RNA splicing
    • domains
    • exons
  31. 1.      Presence of __facilitates evolution of new and potentially beneficial proteins as a result of __
    a.      __ increase probability of crossing over between __of alleles of gene
                                                                                                                                          i.      Could lead to new proteins with novel combinations of functions
    • introns
    • exon shuffling
    • Introns
    • exons
  32. I.                   __
    a.      Series of codons along mRNAà translated by tRNA, which transfers amino acids from pool to growing polypeptide
    b.      __
    • Translation
    • tRNA
  33. a.      tRNA
                                                                  i.      not all identical; translates particular __
    1.      contains __, which base pairs with complementary codon on mRNA
                                                                ii.      structure:
    1.      single RNA strand that is __nucleotides long
    a.      because of presence of complementary stretches of nucleotide bases that can __ to each other, single-strand can fold back upon itself and form 3d structure
                                                                                                                                          i.      folds and twists into compact 3D structure that is roughly__-shaped
    1.      loop extending from end includes __
    2.      3’ end is attachment site for __
    • mRNA codon
    • anticodon
    • 80
    • hydrogen bond
    •  L
    • anticodon
    • amino acid
  34.                                                               i.      Accurate translation requires two instances of molecular recognition
    1.      First?
    a.     this is carried out by?
                                                                                                                                          i.      active site fits only specific combo of amino acid and tRNA
    1.      twenty different synthetases
    a.      catalyzs____
    2.      second one?
    a.      flexible base pairing between third nucleotide= __
    •  tRNA binds to mRNA codon specifying particular amino acid
    •  carried out by aminoacyl-tRNA synthetases
    • covalent attachment of amino acid to tRNA
    • aminoacyl tRNA
    • pairing of tRNA anticodon with mRNA codon
    • wobble
  35. a.      __is most abundant type of RNA
                                                                  i.      eukaryotic ribosomes larger and differ in molecular composition from bacteria
  36. a.      Ribosomes
                                                                  i.      Bindig site for mRNA
                                                                ii.      Three binding sites for tRNA
    1.      What are they?
    a.      Amino acid added to __ end and added through __bond
    • P-site: holds tRNA with growing polypeptide
    • A site holds tRNA carring next amino acid
    • E site: exit site
    • carboxyl
    • peptide
  37.                                                               i.      __is primarily responsible for catalyizing peptide bond
  38. Translation's three stages
    • initiation
    • elongation 
    • termination
  39. Initiation of Translation 
    Brings together__
    a.      Small ribosomal subunit binds to both __and specific __ with __
                                                                                                                                          i.      Binds mRNA at specific sequence upstream __       
                                                                                                                                        ii.      In euk: small subunit, with initiator tRNA already bound, binds to__of mRNA and scans downstream until reaching start codon
    2.      __
    a.      Initiation factors bring all together
    3.      __used
    4.      Initiator tRNA sits in__ site
    a.      Synthesis from __end to __end
    •  mRNA, tRNA with first amino acid, two subunits of ribosomes
    • mRNA
    • initiator tRNA
    • methionine
    • start codon, AUG
    •  5’ cap
    • Translation initiation complex
    • GTP
    •  P
    • amino
    • carboxyl
  40.                                                               i.      Elongation of Termination
    1.      Added to__ end
    a.      __ help

    •  C-terminus
    • Elongation factors
  41. Three steps of Elongation in Translation
    •                                                                                                                                       i.      codon recognition: anticodon base pairs with complementary codon in A site; GTP used
    •                                                                                                                                     ii.      Peptide bond formation: rRNA molecule catalyzes peptide bond between carboxyl end of growing chain and new amino acid; polypeptide now attached to tRNA in A site
    •                                                                                                                                   iii.      Translocation: ribosome translocates tRNA in A site to P site and tRNA in P site to A site, where it’s released; GTP used
  42.                                                               i.      Termination
    1.      Stop codon signals end by __, which binds to stop codon in__ site
    a.      Adds __ instead of amino acid, breaking bond between polypeptide and tRNA in P site, releasing it
    2.      Complex breaks apart
    • release factor
    •  A
    • water molecule
  43. a.      __
                                                                  i.      Several polypeptides can translate one mRNA simultaneously
    b.      Modification
                                                                  i.      Coil and folds due to primary structure forming 3D molecule
                                                                ii.     __required before particular job assigned
    1.      four examples of modifications
    • Polyribosomes
    •  Post-translational modifications
    • Attachment of sugars, lipids, phosphate groups, etc
    • 2.      Removal of amino acids from amino end
    • 3.      Cleaved
    • 4.      Joined together
  44. I.                   Mutations
    a.      Changes in gentic information
    b.      __: change in single nucleotide pair
                                                                  i.      In gameteà inherited
                                                                ii.      Sickle- cell replaces glumatic acid with valine 
  45. a.      Types
                                                                  i.      __: replacement of one nucleotide and partner with another pair
    1.      May have no effect due to redundancy
    a.      __mutation
    • Nucleotide-pair substitution:
    • Silent
  46. 1.      Change of amino acid
    a.      __mutation
                                                                                                                                          i.      Little effect if new amino acid has similar properties to other amino acid and may be in unimportant region
                                                                                                                                        ii.      If in crucial place, like active site, protein activity altered
  47. 1.      Substitution mutations are usually missense   altered codon still codes for an amino acid and makes sense, though not the right sense
    a.      If it changes amino acid codon into stop codon= __
                                                                                                                                          i.      Termination of translation 
    nonsense mutation
  48.                                                               i.      Insertions and Deletions
    1.      Additions or losses of nucleotide pairs in gene
    a.      Disastrous due to altering of__
                                                                                                                                          i.      __
    1.      Occur when insertion or deletion is not multiple of three
    a.      Improper grouping
    •  reading frame
    • Frameshift mutation
  49.                                                               i.      Mutagens
    1.      Mutations arise through errors in replication or recombination leading to nucleotide-pair substitutions, insertions, and deletions
    a.      If not corrected, spontaneous mutation occurs
    2.      Agents that cause mutations= __
    a.      Chemical mutagens
                                                                                                                                          i.      Nucleotide analongs are chemicals similar to normal DNA nucleotides but pair incorrectly 
  50. mutagens