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BIOL 239 – Post-Midterm Notes

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University of Waterloo
BIOL 239
Christine Dupont

BIOL  239  –  Genetics     Topic  11:  DNA  Replication     Three  possible  methods  of  DNA  replication:   • Semiconservative  replication   o One  strand  is  conserved  from  the  parental  strand,  and  the  other  is  newly   synthesized   • Conservative   o Start  with  original  molecule,  get  a  brand -­‐new,  double-­‐stranded  molecule  from  it   • Dispersive   o Parts  of  both  strands  are  being  replicated   o End  up  with  inter-­‐strand  hybrids  of  each  other     1958,  Matthew  Meselson   and  Franklin  Stahl  provided  experimental  proof  of  semiconservative   replication   • Studies  with  controlled  isotopic  composition  of  nucleotides  incorporated  into  daughter  DNA   strands   • E.  coli  grown  on   N,  then  transferred  to  medium  coN  for  two  generations   14 15 o Determined  that  more  and  more  pro portionately  of   N  diminishing   N  band   o Therefore,  semiconservative  model  is  the  method  of  DNA  replication     Initiation:  first  step  in  DNA  replication   • DnaA  protein  binds  to  four  9 -­‐bp  repeats  in  oriC   • Additional  DnaA  protein  molecules  bind  cooperatively,  forming  a  complex  with  oriC   wrapped  on  the  surface   o 3D  conformation   o AT-­‐rich  region  opens  up  because  it  has  one  less  hydrogen  bond  than  GC  regions   • DnaB  protein  (DNA  helicase)  and  DnaC  protein  join  the  initiation  complex  and   produce  a   replication  bubble   o Helicase  catalyzes  the  unwinding  of  the  parental  double  helix   o Single-­‐stranded  binding  proteins  (SSB)  coat  DNA  to  keep  strands  from  binding   back  together  via  complementary  base  pairing     Elongation:  second  step  in  DNA  replication   • DNA  polymerase  can  only  add  nucleotides  to  the  3’  OH  end  of  the  new  strands   o Synthesis  is  always  5’  à  3’   • An  RNA  primer  is  needed  to  provide  a  free  3’  OH  on  which  DNA  polymerase  can  add   nucleotides  for  synthesis   o DNA  primase  makes  the  primer   o DNA  polymerase  adds  nucleotides  based  on  the  parental  strand  template   • DNA  polymerase  III  extends  DNA  using  RNA  primers   • DNA  polymerase  I  removes  primers,  replaces  them  with  DNA   • DNA  ligase  links  adjacent  nucleotides     o Catalyzes  formation  of  phosphodiester  bond   o Seals  3’  OH  and  5’  phosphate  nicks   o Completes  lagging  strand  formation,  creating  a  full,  intact,  double -­‐stranded  piece  of   DNA   • Leading  strand:  continuous  strand  allowing  3’  extension  all  the  way  through   • Lagging  strand:  synthesis  is  not  continuous;  also  called   Okazaki  fragments     Proofreading  by  DNA  polymerase  I  and  DNA  polymerase  III  is   exonuclease  activity     The  Problem  With  Circular  Chromosomes   • Without  an  axis  of  rotation,  the  unwinding  process  would  produce  positive  supercoils  in   front  of  the  replication  forks   • Topoisomerases  make  transient  nicks  to  relieve  torsion  and  prevent  DNA  breaks   o Also  separate  intertwined  daughter  molecules  after  replication     Eukaryotes  have  large,  linear  chromosomes  so  they  must  replicate  their  entire  DNA  in  S  phase   • Initiate  DNA  replication  at  multiple  points  along  the  chromosome   o Would  take  too  long  if  each  chromosome  only  had  one  origin  of  replication   o Replication  bubbles  (replicons)  join  together  until  termini  are  reached,  quickly   replicating  DNA     The  Problem  With  Linear  Chromosomes   • Cellular  lifespan  is  linked  to  DNA  replication   • Progressive  rounds  of  replication  shorten   telomeres  at  the  ends  of  each  chromosome   o People  with  longer  telomeres  tend  to  live  longer,  healthier  lives   o Reactivating  telomerase  may  increase  the  probability  of  cancer     Telomerase  resolves  the  terminal  primer  problem  in  the  newly  synthesized,  incomplete  lagging   strand   • Binds  and  extends  3’  end   • RNA-­‐templated  DNA  synthesis   • Translocation   • Repeat  extension  and  translocation  several  times  before  releasing  telomerase   • DNA-­‐templated  DNA  synthesis     Topic  12:  The  Genetic  Code   • Each  nucleotide  triplet  is  known  as  a   codon   o Codes  for  a  single  amino  acid  that  makes  up  a  polypeptide   o Discovered  in  1961  by  Francis  Crick  and  Sydney  Benner  after  studying  the   bacteriophage  T4  rIIB  gene   • Start  codon:  AUG  (RNA)  /  ATG  (DNA)   o Translated  into  methionine   • Stop  codons:  UAA,  UAG,  UGA  (RNA)  /  TAA,  TAG,  TGA  (DNA)     Gene  Expression:  the  flow  of  genetic  information  from  DNA  to  RNA  to  protein   • Central  dogma:  DNA  à  transcription  à  RNA  à  translation  à  protein   • There  is  a  linear  relationship  between  the  nucleotide  sequence  in  a  gene  (or  mRNA   transcript)  and  the  order  of  amino  acids  in  the  polypeptide  chain  specified  by  said  gene     Reading  Frame:  the  partitioning  of  groups  of  three  nucleotides  such  that  the  sequential   interpretation  of  each  succeeding  triplet  generates  the  correct  order  of  amino  acids  in  the  resulting   polypeptide  chain   • Start  triplet  must  be  in  frame  with  the  stop  triplet     Intragenic  Suppression:  the  restriction  of  gene  function  by  one  mutation  cancelling  the  other  in  the   same  gene   • By  adding/removing  nucleotides,  you  can  change  the  function  of  the  protein  product   • If  a  gene  sustains  three  (or  multiples  of  three)  nucleotide  mutations  of  the  same  type  (ex.   insertions  OR  deletions),  the  protein  can  still  function   o Single  nucleotide  insertions  or  deletions  will  shift  the  reading  frame  and  alter  the   protein  from  that  point  on     Frameshift  Mutations:  changes  that  alter  the  grouping  of  nucleotides  into  codons   • Frameshifts  in  one  gene  do  not  affect  other  genes     Moving  from  5’  to  3’  end  of  mRNA,  each  successive  codon  is  sequentially  interpreted  into  an  amino   acid,  starting  with  the  N  (amino)  terminus  and  ending  with  the  C  (carboxy)  terminus   • RNA-­‐like  strand  =  coding/sense/+  strand   o Looks  like  mRNA  but  has  Ts  instead  of  Us   o Contains  start  and  stop  codons   • Template  strand  =  non-­‐coding/nonsense/-­‐  strand   o Complementary   o Used  to  make  mRNA     Nonsense  Codons:  also  known  as  stop  codons   • UAA,  UAG,  UGA  do  not  correspond  to  any  amino  acids   • When  they  appear  in  frame,  translation  stops  and  the  ribosome  fa lls  apart,  terminating  the   polypeptide  chain     Topic  13:  Transcription   • The  process  by  which  the  polymerization  of  ribonucleotides  guided  by  complementary  base   pairing  produces  an  RNA  transcript  of  a  gene   o Only  the  transcript  is  translated   • Nucleotides  are  added  in  the  5’  à  3’direction   • Uracil  is  incorporated  in  place  of  thymine  in  RNA     RNA  Polymerase:  enzyme  that  catalyzes  transcription   • DNA-­‐dependent  RNA  polymerase   • Uses  DNA  as  template  to  make  RNA     Promoters:  DNA  sequences  near  the  beginnings  of  genes  that  sig nal  to  RNA  polymerase  where  to   begin  transcription     Terminators:  sequences  in  RNA  products  that  tell  RNA  polymerase  where  to  stop     Note:  promoters  and  terminators  are  NOT  start/stop  codons     Steps  in  Translation  –  E.  coli   • Initiation  of  transcription   o Sigma  factor  recognizes  promoter  sequence  and  brings  RNA  polymerase  to  it   o RNA  polymerase  core  enzyme  has  synthesis  capacity  and  doesn’t  need  a  primer   • Elongation   o No  SSBs,  so  the  DNA  helix  reforms  and  displaces  the  RNA  transcript   • Two  methods  for  transcription  termi nation   o Rho-­‐dependent:  rho  protein  recognizes  sequences  of  terminators  and  binds  to   them;  RNA  polymerase  hits  it  and  stops  transcription   o Rho-­‐independent:  sequence-­‐mediated  within  the  gene;  no  protein  involved     Termination:  final  step  in  transcription   • End  of  terminator  region  has  sequences  that  can  base  pair  with  each  other   o Area  of  weak  hydrogen  bonding  (rich  in  As)   • Stem  and  loop  structure  forms,  destabilizing  the  polymerase   o mRNA  released     In  eukaryotes,  transcription  and  translation  are  spatially  and  tempora lly  separated   • Transcription  occurs  in  the  nucleus   • Translation  occurs  in  the  rough  endoplasmic  reticulum     Post-­‐translational  modifications  solve  the  issue  of  getting  the  transcripts  into  the  cytoplasm  in   eukaryotes   • Addition  of  methylated  cap  at  5’  end  protects  from  nuclease  degradation   o G3P  added  by  methyl  transferases  in  reverse  orientation   o Critical  for  efficient  translation  of  mRNA   o In  prokaryotes,  the  5’  end  of  the  transcript  has  a  triphosphate,  rather  than  a   methylated  cap   • Addition  of  100-­‐200  adenosines  to  the  3’  end  (poly-­‐A-­‐tail)   ’ o Ribonuclease  cleaves  primary  transcript  to  form  a  new  3  sequence   o Poly-­‐A-­‐polymerase  adds  As  to  this  new  3 ’  end     o Stabilizes  mRNA,  prevents  degradation,  aids  in  efficiency  of  translation   • Cap  and  tail  are  recognized  by  initiation  fac tors,  which  bring  them  together  and  circularize   the  mRNA   o Ribosome  recognizes  this  in  translation     RNA  Splicing:  removal  of  introns   • Exons:  sequences  found  in  both  a  gene’s  DNA  and  in  the  mature  mRNA   o Coding  sequences  for  the  protein  product   o Exons  are  expressed   • Introns:  sequences  found  in  a  gene’s  DNA  but  not  in  the  mature  mRNA   o Removed  from  primary  transcript   o Introns  are  intervening  sequences   • Splicing  is  usually  carried  out  by  a  complex  known  as  a   spliceosome   o Some  RNA  transcripts  are  self -­‐splicing   • Not  all  eukaryotic  genes  contain  introns,  so  they  don’t  all  do  splicing     Why  are  introns  present?   • Allow  for  alternative  splicing   • In  some  cases,  splicing  may  occur  between  splice  donor  site  of  one  intron  and  the  acceptor   site  of  another  intron  downstream   o Produces  different  mature  mRNA  molecules  that  may  encode  related  proteins  with   different,  though  partially  overlapping,  amino  acid  sequences   o Similar  but  slightly  different  functions  within  the  cell     Trans-­‐Splicing:  a  form  of  alternative  splicing  in  which  an  exon  from  on e  transcript  can  be  joined  to   an  exon  from  a  different  transcript   • Dealing  with  two  different  genes  that  may  be  from  different  chromosomes     Topic  14:  Translation   • The  process  by  which  the  genetic  code  carried  by  mRNA  directs  the  synthesis  of  proteins   from  amino  acids   • Requires  mRNA,  tRNA  with  attached  amino  acid,  ribosomes  to  assemble  polypeptide     Transfer  RNAs  (tRNAs)   • Short,  single-­‐stranded  RNA  molecules   • Have  their  own  genes,  but  don’t  make  proteins   • tRNAs  carry  modified  bases  produced  by  chemical  alterations   of  A,  U,  G,  C  nucleotides   • Each  tRNA  carries  one  particular  amino  acid   o At  the  other  end  is  an   anticodon:  a  series  of  three  bases  that  recognize  and  bind  in  a   complementary  fashion  to  codons  on  open  reading  frames   o  Amino  acid  binds  to  3’  end     Aminoacyl  tRNA  Synthetases:  catalyze  the  attachment  of  a  tRNA  to  its  conjugate  amino  acid   • Charges  tRNA  with  a  particular  amino  acid,  making  a  covalent  bond  with  the  3’  O H  of  the   tRNA   • Base  pairing  between  an  mRNA  codon  and  a  tRNA  anticodon  determine  where  an  amino  acid   becomes  incorporated  into  a  growing  polypeptide   o Codons  and  anticodons  are  always  read  in  the  5’   à  3’  direction     Wobble  Rule:  some  tRNAs  recognize  more  than  one  codon  for  the  amino  acid  they  carry   • Genetic  code  is  degenerate   o 64  possibilities,  20  amino  acids   • Reads  the  first  two  base  pairs  of  the  codon   o Third  base  doesn’t  have  to  be  an  exact  complement     Ribosomes:  complex  structures  composed  of  protein  and  RNA  that  are  the  site  of  protein  synthesis   • Size  differs  between  prokaryotes  and  eukaryotes   o Prokaryotic  small  subunit  carries  16S  rRNA   o Eukaryotic  small  subunit  carries  18S  rRNA   • Reads  mRNA  from  5’  à  3’   o Brings  in  charged  tRNA,  joins  amino  acid  to  another  amino  acid  via  peptide  bond,   shifts,  releases  it  into  first  site;  another  comes  in     E.  coli  Translation:  Initiation  Phase   • Shine-­‐Dalgarno  Sequence  (AGGAGG)  is  specifically  recognized  by  complementary   sequences  in  the  16S  rRNA  of  the  30S  subunit   o 6-­‐10  base  pairs  downstream  from  the  start   o Highly  conserved   o Small  subunit  directed  to  start  codon  by  upstream  Shine -­‐Dalgarno  sequence   • The  presence  of  a  nearby  downstream  AUG  codon  signals  the  initiation  of  translation  by  the   addition  of  a  tRNA  carrying  formylmethionine   o Large  50S  subunit  binds  so  that    is  placed  in  the  P  site  of  the  ribosome     E.  coli  Translation:  Elongation  Phase   • Elongation  factors  escort  the  next  tRNA  into  the  A  site  of  the  ribosome   • Peptidyl  transferase  catalyzes  the  formation  of  a  peptide  bond  between  the  C  terminus  of   formylmethionine  and  the  N  terminus  of  the  second  amino  acid   o Causes  release  of  amino  ac id  (Fmet)  from  its  tRNA  in  the  P  site   o Ribosome  moves  (5’  à  3’)   o Free  tRNA  moves  to  E  site   • A  site  now  available  for  incoming  charged  tRNA   • Free  tRNA  in  E  site  released   • Process  repeats   • Several  ribosomes  can  work  on  one  messenger   o As  soon  as  one  Shine-­‐Dalgarno  sequence  is  free,  another  can  move  in     E.  coli  Translation:  Termination  Phase   • Stop  codon  encountered   o No  associated  tRNA   • Release  factor  recognizes  stop  codon,  moves  into  A  site   • Polypeptide  released  from  C  terminal  tRNA   • mRNA,  tRNA,  ribosomal  subunits  all  diss ociate  from  each  other     Eukaryotic  Translation:  Initiation  Phase     • No  Shine-­‐Dalgarno  sequence   • 40S  ribosome  subunit  recognizes  and  binds  to  5’  methylated  cap   o Scans  along  mRNA  until  it  finds  initiation  of  translation  sequence  (start  codon)   • Initiator  tRNA  carries  Met  not  Fmet   • Rest  of  translation  is  similar  to  that  of  prokaryotes     Polyribosome:  a  complex  of  several  ribosomes  translating  from  the  same  mRNA     Post-­‐Translational  Processing:  modifications  that  occur  to  the  protein  after  translation   • Cleavage  may  remove  an  amino  acid  or  split  a  polyprotein  into  several  smaller  polypeptides   o 80-­‐90%  get  Met  removed  in  E.  coli  since  most  proteins  don’t  start  with  it   o Viruses  typically  cleave  a  large  translation  product  into  multiple  smaller   polypeptides   • Addition  of  chemical  constituents  may  modify  a  polypeptide  after  translation   o ex.  phosphorylation     How  do  mutations  affect  the  products  of  gene  expression?   • Silent  Mutation:  a  mutation  in  the  third  position  of  a  codon   o Due  to  wobble  rule,  the  same  amino  acid  is  produced   • Missense  Mutation:  a  mutation  in  the  first  position  of  a  codon   o New  amino  acid  formed  may  impact  protein  product   • Nonsense  Mutation:  stop  codon  where  there  should  be  a  reading  codon   o Premature  truncation  of  translation   o Protein  is  shorter  than  it  should  be,  possibly  al tering  function   • Frameshift  Mutation:  everything  that  follows  is  altered   o Usually  more  detrimental  at  start  of  gene   o Can’t  definitively  say  it  will  affect  protein   • Intron  mutation:  removed,  inconsequential   • Altered  promoter  sequence  can  either  prevent  or  increa se  transcription/translation   • Altered  spliceosome  sequences  could  abolish  getting  rid  of  the  intron   o Frameshift  error,  inadvertent  stop  codons  may  result   • Mutation  in  transcription  termination   o Poly-­‐A-­‐tail  may  not  be  added,  degrading  the  protein  once  it  enters  the  cytosol  and   preventing  translation  from  occurring     Topic  15:  Gene  Regulation  in  Prokaryotes     Role  of  RNA  Polymerase  in  Transcription   • Recognition  of  the  promoter   • Directed  by  the  sigma  factor   o Recognizes  -­‐10  region  (TATA  box)  and  -­‐35  region   • Transcription  starts  at  +1  nucleotide   • Without  these  regions,  transcription  would  not  occur     1950s,  Jacques  Monad  and  François  Jacob  studied  E.  coli  lactose-­‐utilization  mutants   • Negative  regulation   • lacZ  encodes  ß-­‐galactosidase,  which  breaks  down  lactose  into  glucose  and  galactose   • lacY  encodes  permease,  which  transports  lactose  into  the  cell   • lacA  encodes  transacetylase,  which  adds  an  acetyl  group  to  allolactose   o Can  abolish  lacA  and  still  have  lactose  metabolism   • lac  genes  are  transcribed  together   o When  lacZ  is  repressed  or  induced,  the  same  effect  is  observed  for   lacA  and  lacY   • The  three  genes  are  transcribed  as  part  of  the  same   polycistronic  mRNA   o One  mRNA  with  two  or  more  transcribed  genes  on  it   o Gives  relatively  equal  amounts  of  protein  products  that  are  translated     1961,  operon  theory  of  gene  regulation  was  published   • Operon:  a  unit  of  DNA  composed  of  specific  genes,  plus  a  promoter  and  an  operator,  which   act  in  unison  to  regulate  the  response  of  the  structural  genes  to  environmental  changes   • Promoter:  makes  transcript   • Operator:  controls  whether  or  not  it  will  be  transcribed     Evidence  for  a  lac  Repressor  Protein   • Operator  is  concentration  dependent   o Always  made  at  very  low  levels   o Upregulated  when  lactose  comes  in   • Mutations  in  lacI  result  in  mutants  that  synthesize  ß -­‐galactosidase  and  lac  permease  even  in   the  absence  of  lactose   o Constitutive  mutants:  result  in  protein  synthesis  irrespective  of  environmental   conditions   • Hypothesized  that  lacI  encodes  a  negative  regulator  or  repressor  that  binds  near  the   promoter  of  the  lactose  utilizat ion  genes  at  the  operator  site   o Binds  to  two  21bp  conserved  sequences  in  DNA  of   lac  operon   § DNA-­‐binding  domain  and  inducer -­‐binding  domain   o Most  of  this  monomer  is  used  to  bind  allolactose,  changing  the  conformation  of  the   repressor  so  that  DNA-­‐binding  domains  cannot  bind  DNA   § Allolactose  removes  repressor  from  operator  so  polymerase  can  bind  and   translation  can  occur   o Negative  regulation:  repressor  shuts  things  off   § Positive  regulation  would  involve  DNA  turning  things  on     Operator  Mutants   • In  lacI  cells,  constitutive  expression  occurs  because  there  is  no  repressor   • O :  constitutive  operator   o Repressor  can’t  recognize  and  bind  to  operator   o lac  enzymes  synthesized  constitutively     The  Diptheria  toxin  is  controlled  in  a  similar  manner   • In  the  presence  of  high  iron  concentrations,  the  repressor  binds  the  toxin  so  that  it  isn’t   produced   o Iron  is  rarely  around  in  a  free  form  though;  is  complexed  with  protein   • In  the  presence  of  low  iron  concentrations,  the  toxin  is  expressed   o Toxin  ribosylates  eukaryotic  eEF -­‐2,  which  becomes  inactivated  and  stops  the   transfer  of  growing  polypeptide  chains  from  the  A  to  P  site  of  the  ribosome   o Translation  stops,  so  the  cell  starves  and  iron  is  released     Topic  16:  Gene  Regulation  in  Eukaryotes     Eukaryotes  generally  do  not  organize  genes  into  operons  like  prokaryotes  do     In  eukaryotes,  3  RNA  polymerases  transcribe  different  sets  of  genes   • E.  coli  only  has  one  RNA  polymerase   • RNA  polymerase  II  transcribes  structural  genes  that  produce  proteins   • RNA  polymerases  I  and  III  recognize  promoters  from  tRNA  and  r RNA     Cis-­‐acting  regulatory  regions  are  recognized  by  RNA  polymerase  II   • Core  promoter:  always  very  close  to  the  gene’s  coding  region   o Includes  initiation  site  where  transcription  begins   (+1  of  translation)   • TATA  box:  consists  of  ~7  nucleotides  located  at  the   -­‐30  position   • CAAT  box:  ~-­‐75-­‐100   • GC  boxes   • Enhancer:  regulatory  site  that  can  be  located  far  away  from  the  promoter  (>10  000  bp)  or   can  be  quite  close   o Enhances  transcription   o Some  genes  have  multiple  enhancer  sequences     Basal  Factors:  required  for  binding  to  the  promoter  to  maintain  a  basal  level  of  transcription   • Low-­‐level  transcription  occurs  with  only  basal  factors  bound  to  the  DNA     TATA  Box  Binding  Protein  (TBP) :  essential  to  initiation  of  transcription  from  all  class  II  genes  with   a  TATA  box   • Analogous  to  sigma  factor  in  E.  coli   • Comes  in  first,  binds  to  TATA  box     TBP-­‐Associated  Factors  (TAFs) :  join  initiation  complex  after  TBP  binds  to  TATA  box     Transcriptional  Activators :  bind  to  enhancer  sequence  and  can  increase  transcription  100 -­‐fold  or   more  above  the  ba sal  level   • 2  important  structural  domains:  DNA -­‐binding  domain,  transcriptional-­‐activation  domain   • Activators:  proteins  that  bind  to  enhancers  and  increase  the  transcription  rate   • Repressors:  bind  to  silencers  and  slow  transcription   • Silencers:  bind  repressor,  stopping  enhancement  and  returning  it  to  basal  transcription   levels   o Concentration-­‐dependent   • Coactivators:  “adapter”  molecules  that  integrate  signals  from  activators  and  repressors   • Basal  transcription  factors:    position  RNA  polymerase  at  the  start  of  the  co ding  region     Most  eukaryotic  activators  must  form   dimers  to  function   • Homomers:  multimeric  proteins  composed  of  identical  subunits   o 2  subunits:  homodimers   • Heteromers:  multimeric  proteins  composed  of  non-­‐identical  subunits   o 2  subunits:  heterodimers   • Leucine  Zipper:  DNA  binding  domain  recognizes  a  specific  sequence   o Dimerization  domain  interacts  with  basal  factors  to  increase  transcription     Steroids  work  at  the  level  of  coactivation  of  transcription  factors   • Bind  to  activators  that  are  produced  all  the  time   • Impart  reversible  allosteric  effects   o Transcription  factor  undergoes  a  conformational  change,  binds  to  enhancer  element   o Transcription  rate  of  target  gene  increases   • Enhancer  element:  glucocorticoid  response  element   • Activator  protein:  glucocorticoid  receptor     Transcriptional  Repressors:  diminish  transcriptional  activity   • May  bind  to  enhancer  element  to  prevent  enhancement  (competitive)   • May  bind  to  other  specific  DNA -­‐encoded  sequences  (silencers)  to  diminish  transcription   • Competition  for  binding  between  repressor  and  activator  proteins   o Repressor  binds  DNA  directly   • Quenching:  repressor  binds  directly  to  activator   o May  block  the  DNA -­‐binding  region  so  that  only  basal  transcription  levels  can  occur   o May  block  the  activation  domain  so  that  the  enhancer  and  activator  can’t  inte ract   with  basal  factors   o Doesn’t  directly  bind  to  DNA     Methylation  patterns  of  DNA  and  histone  proteins  affect  transcription   • DNA  (weakly  negative  charge)  wraps  around  histones  (positive  charge)   o Affecting  the  charge  affects  wrapping   • Acetyl  groups  added  to  hi stone  tails  to  reduce  electrical  attraction  of  negative  DNA  to   positive  lysine  in  tails   o Reduces  positive  charge,  making  it  easier  to  unwrap  DNA  from  histone  and  expose   the  gene     Epigenetics:  chemical  modifications  of  the  genetic  code   • Associated  with  methylation  of  CpG  dinucleotides  in  highly  condensed  heterochromatin   o Heterochromatin:  regions  of  chromatids  that  are  tightly  wrapped  up  in  a   nucleosome   • Highly  methylated  DNA  gets  silenced  since  it  isn’t  available  for  unwrapping   • ex.  silenced  X  chromosome  in  Barr   body   Genomic  Imprinting  and  Epigenetic  Effects   • Methylation  of  CpG  dinucleotides  in  DNA  frequently  inhibit  transcription   • Methylation  patterns  can  be  inherited  from  mother  or  father   o Variable  expression/incomplete  penetrance   • Diet  can  also  change  methylation  p atterns,  and  these  patterns  can  be  inherited  by  other  cells   or  offspring   • End  up  with  different  phenotypes  despite  having  identical  sequences     Topic  17:  Restriction  Enzymes  &  Cloning     Restriction  Enzymes:  endonucleases  that  exist  naturally  in  prokaryotes
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