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BIO 123 Chapters 10-12 Lecture Notes

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by: Amber Logan

BIO 123 Chapters 10-12 Lecture Notes BIOL 123

Marketplace > University of New Mexico > Biology > BIOL 123 > BIO 123 Chapters 10 12 Lecture Notes
Amber Logan
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Lecture notes for BIO 123 Chapters 10 (DNA, Its Structure and Replication), 11 (The Regulation of Gene Expression), and 12 (GMOs and Climate Change). Also includes the Big Picture concepts from pr...
Biology for Health Related Sciences and Non-Majors
Dr. Dorothy C. Scholl
Study Guide
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This 10 page Study Guide was uploaded by Amber Logan on Saturday December 5, 2015. The Study Guide belongs to BIOL 123 at University of New Mexico taught by Dr. Dorothy C. Scholl in Fall 2015. Since its upload, it has received 337 views. For similar materials see Biology for Health Related Sciences and Non-Majors in Biology at University of New Mexico.


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Date Created: 12/05/15
Chapters  10 -­12  Lecture  Notes   DNA,  Its  Structure  and  Replication;;  Th e  Regulation  of  Gene   Expression;;  GMOs  and  Climate  Change     (10.1)  The  Discovery  of  DNA  as  Molecule  of  Heredity     •   Early  1900s  –  we  knew  that  proteins  and  DNA  were  the  major  components  of  chromosomes,   but  didn’t  know  if  the  genetic  material  contained  in  genes  was  protein  or  DNA   •   1952  –  discovered  that  genetic  material  is  DNA   o   found  through  experimentation  w/  bacteria   •   Watson  &  Crick  –  credited  w/  the  discovery  of  the  structure  of  DNA   o   Rosalind  Franklin  –  had  a  huge  role  w/  her  research  in  X-­ray  crystallography,  but  was   not  given  credit     (10.2)  The  Structure  of  DNA  and  RNA     •   DNA  =  deoxyribonucleic  acid   o   Monomer  =  nucleotides  (deoxyribonucleotides)   §   All  nucleotides  have:  (see  Image  1)   1)   5-­carbon  sugar   2)   phosphate  functional  group   3)   variable  nitrogenous  base   o   purines  =  double-­ringed  bases  –  adenine  (A)  and  guanine  (G)   o   pyrimidines  =  single-­ringed  bases  –  thymine  (T)  and  cytosine  (C)   §   NOTE:  You  can  remember  this  by  noticing  that  pyrimidine,   thymine,  and  cytosine  all  have  a  “y”  in  them   o   purines  always  bond  to  pyrimidines  by  hydrogen  bonds  –  A  always   bonds  to  T  w/  2  hydrogen  bonds,  G  always  bonds  to  C  w/  3   hydrogen  bonds   §   We  can  tell  that  an  A-­T  rich  region  is  the  beginning  of  a   protein-­coding  gene  because  A’s  and  T’s  are  easier  to  break   apart  than  G’s  and  C’s   §   Chargaff’s  Rule  =  says  that  there  is  always  a  1:1  ratio  of   purines  to  pyrimidines   o   Polymer  =  nucleic  acids   §   Double-­stranded  helical  structure  –  held  together  by  hydrogen  bonds  between   complimentary  nitrogenous  bases   §   Backbone  is  formed  by  dehydration  synthesis  reactions  between  the  sugar  and   the  phosphate  (=  phosphodiester  bonds)   §   DNA  is  antiparallel  –  each  strand  has  a  3’  and  a  5’  end,  and  they  always  run   opposite  of  one  another   •   i.e.:  3’  -­-­-­-­-­-­-­-­-­-­-­-­-­-­-­  5’                5’  -­-­-­-­-­-­-­-­-­-­-­-­-­-­-­  3’           Image  1   Image  2     •   RNA  =  ribonucleic  acid   o   Monomer  =  ribonucleotides   o   3  main  differences  between  RNA  and  DNA:   §   RNA  contains  ribose,  DNA  contains  deoxyribose  sugar   §   RNA  uses  uracil,  DNA  uses  thymine   §   RNA  is  single-­stranded   §   NOTE:  To  remember  this,  think  “R  U  Single?”  where  “R”  stands  for  ribose  sugar,   “U”  stands  for  uracil,  and  “single”  is  referring  to  its  being  single-­stranded  J   o   RNA  is  not  antiparallel  –  it  doesn’t  have  a  second  strand  to  be  antiparallel  to     (10.3)  DNA  Replication     •   Only  occurs  when  a  cell  needs  to  divide   o   Every  time  a  cell  divides,  you  have  to  copy  ~  6  billion  base  pairs!   o   Cells  in  G 0do  not  replicate  their  DNA  but  they  do  still  carry  out  transcription  and   translation  in  order  to  build  proteins   •   DNA  replication  is  semi-­conservative  (=  when  a  cell  divides,  the  2  resulting  daughter  cells   have  1  strand  from  the  original/parental  DNA  and  1  strand  of  the  new/copied  DNA)     •   Key  enzymes  involved  in  DNA  replication:  (see  Image  3)   o   Helicase  –  unwinds  the  double-­helix  structure  of  DNA   o   Topoisomerase  –  binds  to  newly  unwound  strands  of  DNA  and  keeps  them  from   winding  up  again   o   Single-­stranded  binding  proteins  (SSBPs)  –  spacer  molecules  that  hold  the   replication  fork/bubble  apart   o   DNA  polymerase  –  builds  new  strand  of  DNA  by  putting  in  complimentary  bases     §   Is  a  proofreader  –  finds  mistakes  in  nitrogenous  base  sequence  and  fixes  it   •   DNA  repair   o   3  steps  in  DNA  repair:   1)   Recognition  –  DNA  polymerase  recognizes  mistake   2)   Removal  –  DNA  polymerase  enzymatically  digests  wrong   base   3)   Replacement  –  DNA  polymerase  replaces  w/  correct  base   o   Viral  vector  =  DNA  vaccine  where  you  attach  the  correct  gene  to  a   harmless  virus  so  that  the  virus  can  “infect”  cells  w/  the  correct  DNA   •   These  mistakes  can  be  caused  by  mutations  from  carcinogens  (e.g.:  UV   light,  gases,  chemicals,  etc.)   o   UV  rays  disable  genes  by  causing  thymine-­to-­thymine  bonds  (=   thymine  dimers)   §   XP  gene  –  repairs  DNA  by  breaking  thymine  dimers   §   The  effect  of  UV  light  has  a  cumulative  effect  –  visible   damage  in  adult  skin  could  have  begun  developing  decades   prior   o   Ligase  –  hooks/ligates  okazaki  fragments  (=  fragments  of  replicated  DNA  on  the   lagging  strand)  together   •   Steps  in  DNA  replication:   1)   Helicase  unwinds  DNA   2)   DNA  polymerase  binds  to  unwound  strands  and  builds  new  strand   §   This  can  only  occur  in  1  direction   3)   Ligase  puts  fragments  of  lagging  strand  and  new  strands  of  DNA  together   •   The  3’  -­-­-­-­-­  5’  strand  produces  the  leading  strand,  while  the  5’  -­-­-­-­-­  3’  strand  produces  the   lagging  strand       Image  3     (10.4)  Gene  Expression  (Transcription,  Translation,  and  the  Genetic  Code)     •   Gene  expression  =  the  process  where  information  stored  in  DNA  is  used  to  make  a  product   (usually  a  protein)   o   Flow  of  information  in  a  cell:  DNA    RNA    protein  (structural,  antibodies,  enzymes,   etc.)   o   Cells  are  highly  specialized  (in  what  genes  are  being  expressed)   §   This  specialization  is  based  on  chemicals  signals  that  cells  receive  in  utero   §   Gene  expression  changes  as  you  develop  –  this  is  why  we  don’t  look  like  we  did   when  we  were  babies   •   Transcription  and  translation  are  the  2  major  steps  in  protein  synthesis       Transcription     •   Transcription  =  when  a  protein-­coding  sequence  on  DNA  is  copied  to  an  mRNA   o   Takes  place  inside  the  nucleus   o   Gene  =  sequence  of  DNA  that  is  transcribed  into  RNA   §   3  types  of  RNA   1)   messenger  RNA  (mRNA)  –  copies  DNA  and  leaves  nucleus   2)   transfer  RNA  (tRNA)  –  brings  amino  acids  to  ribosome   3)   ribosomal  RNA  (rRNA)  –  structural  component  of  ribosome   o   RNA  polymerase  =  key  enzyme  involved  in  transcription;;  the  DNA  polymerase  of   transcription   §   Transcription  begins  when  RNA  polymerase  binds  to  promoter  region  and  stops   when  it  reaches  the  terminator  region   •   Transcription  can  occur  in  either  direction,  unlike  DNA  replication,  which   can  only  occur  in  1  direction   o   Codon  =  unique  sequence  of  3  bases  (64  total)   §   Start  codon  –  AUG  (methionine)   §   Stop  codons  –  UAA,  UAG,  and  UGA   §   The  first  and  second  letters  are  the  most  important  –  the  third  is  considered   “wobbly”   o   Intervening  sequences  =  extra  bases  in  the  middle  of  a  protein-­coding  sequence   §   Introns  =  intervening  sequences  –  are  removed  from  strand   §   Exons  =  code  for  making  a  protein  –  are  stuck  together  by  ligase  (=  RNA   splicing)  once  introns  are  removed         Image  4     Translation     •   Translation  =  when  the  language  of  a  nucleotide  is  translated  into  the  language  of  amino   acids   •   Occurs  in  the  ribosome   •   Involves  ribosome,  mRNA,  and  tRNA   o   mRNA  brings  protein-­coding  sequence  from  nucleus   o   tRNA  brings  amino  acids  to  the  ribosome  from  the  cytoplasm  based  off  of  its  anticodon   sequence  (=  complimentary  base  sequence  to  mRNA  that  lets  the  tRNA  bind  to  the   correct  amino  acid;;  1  3  base-­sequence  per  tRNA)   •   Begins  when  mRNA  binds  to  a  ribosome  and  tRNA  binds  to  start  codon  on  mRNA   o   There  are  3  binding  spots  in  a  ribosome  for  mRNA  à  3  tRNAs  can  bind  at  1  time   o   tRNA  moves  through  ribosome  like  a  factory  line,  adding  amino  acids  to  the  polypeptide   1  at  a  time   •   Once  end  codon  is  reached,  the  amino  acid  chain  is  released  and  travels  to  the  Golgi   Apparatus  where  it  is  packaged  and  sent  off     Structure  of  an  Amino  Acid         Image  5         Image  6   The  Genetic  Code     •   The  genetic  code  is…   o   Not  ambiguous  –  there  are  20  amino  acids  coded  for  by  64  codons   o   Redundant  –  multiple  codon  sequences  code  for  the  same  amino  acid   o   Virtually  universal  –  used  by  all  living  things  on  Earth   §   This  is  a  key  piece  of  evidence  of  evolution     (10.5)  Mutations,  Gene  Duplications,  and  Chromosomal  Rearrangements:      The  Ultimate  Source  of  Variation     •   Mutation  =  any  change  in  base  sequence   •   Types  of  mutations:   o   Point  mutations  =  when  a  single  base  is  altered   §   e.g.:  substitutions  (=  when  1  base  is  substituted  for  another)         Image  7     o   Frameshift  =  when  the  sequence  of  amino  acids  is  altered   §   e.g.:  insertions  (=  when  base(s)  is/are  inserted  into  a  sequence  in  the  wrong   position)  and  deletions  (=  when  base(s)  is/are  deleted  from  a  gene  sequence)   §   results  in  reading  the  codon  sequence  in  the  wrong  order   §   usually  stops  protein  synthesis/translation  before  it  is  completed         Image  8     o   Silent  mutations  –  cause  no  change  in  structure  of  protein   §   Usually  occur  when  the  3  base  of  a  codon  is  mutated  (because  the  3  base  is   rd “wobbly”)   •   Some  mutations  can  be  beneficial  –  over  time,  these  can  be  selected  for  and  cause  evolution   in  a  population         (11.1)  Prokaryotes  Use  Operons  to  Regulate  Gene  Expression     Prokaryotic  DNA   vs.   Eukaryotic  DNA     •   Bacteria  have  a  single  circular  chromosome   •   All  genetic  material  is  in  the  nucleus   •   Has  very  little  noncoding  DNA  à  is  much   •   Has  a  lot  of  noncoding  DNA  (junk   more  efficient  at  transcription  and  translation   DNA,  switches,  etc.)   o   Genome  is  organized  by  function   o   Spacer  DNA  =  coding   •   During  gene  replication,  bacterial  DNA   sequences  between  protein-­ doesn’t  have  to  wrap  around  histones  for   coding  genes   organization   o   Transposons  =  sequences  that   •   Gene  expression  –  bacteria  can  reorganize   move  from  1  position  on  a   gene  expression  to  adapt  to  environment   chromosome  to  another  –  may   o   Operon  =  sequence  of  DNA  that   disrupt  gene’s  function   includes  groups  of  genes  to  make   o   Regulatory  DNA  =  control  gene   different  proteins  plus  their  control   expression   sequences   o   Structural  DNA  =  have  an   §   Control  sequences  -­  gene   architectural  function  (e.g.:   centromere)   promoters  (=  regions  of  DNA   that  are  on/off  switches  for   •   During  gene  replication,  genes  wrap   transcription)   around  histones   §   Allows  bacteria  to  turn  gene   •   Gene  expression  –  we  can  change   expression  on/off  very  quickly   which  genes  are  expressed  through  a   and  do  transcription  and   series  of  internal  and  external   translation  simultaneously   (environmental)  cues   o   Transcription  factor  =   regulatory  proteins  that  interact   w/  the  environment  and   regulatory  DNA  to  control  gene   expression   •   Have  housekeeping  genes  (–  play   essential  role  in  flow  of  information  in  a   cell)   o   These  genes  are  highly   conserved  (=  don’t  change   much  over  time)       Image  9     (12)  Bonus  Question  Topics     •   GMO  =  genetically  modified  organism   o   Transgenic  organism  =  one  that  has  had  the  genes  of  1  organism  inserted  into  it   •   Climate  change  =  changes  in  the  average  weather  for  a  region  over  time   o   Earth’s  climate  has  been  getting  warmer   o   Greenhouse  effect  =  the  trapping  of  the  sun's  warmth  in  a  planet's  lower  atmosphere   due  to  the  greater  transparency  of  the  atmosphere  to  visible  radiation  from  the  sun         Image  9     Big  Picture  Concepts  from  Previous  Chapters     •   Biology  =  the  study  of  life   o   Cell  theory:   §   All  cells  come  from  preexisting,  living  cells   §   All  cells  have  DNA  as  molecule  of  heredity   §   All  living  things  are  composed  of  1+  cells  –  what  does  it  mean  to  be  alive?   o   All  cells  have…   §   Plasma  membrane   §   Ribosomes   §   Enzymes   o   Emergent  properties  of  life  –  idea  that  the  cell  is  the  basic  unit  of  life   •   Scientific  method  –  how  to  do  science   1)   Observation   2)   Hypothesis   §   Null  hypothesis  =  “of  no  effect;;”  the  independent  variable  will  not  have  an  effect   §   Alternative  hypothesis  =  the  independent  variable  will  have  an  effect   3)   Experimentation   §   Independent  variable  =  the  thing  you  manipulate;;  given  to  the  experimental   group   §   Dependent  variable  =  the  thing  you  measure/your  results   §   Experimental  group  =  receives  the  independent  variable   §   Control  group  =  does  not  receive  the  independent  variable   4)   Data  collection/analysis   §   Biostatistics  –  a  p-­value  ≤  0.05  indicates  statistical  significance   5)   Conclusion   •   Evolution  by  natural  selection   o   Natural  selection  =  theory  that  individuals  who  are  best  adapted  to  their  environment   will  be  more  likely  to  survive  and  reproduce   §   Key  to  survival  of  healthy  genes   o   Bacteria  and  antibiotic  resistance         Picture  Credit:   Image  1:­microscopic/dna1.htm   Image  2:   Image  3:­link-­topoisomerase-­interrupting-­drugs-­to-­autism/   Image  4:­are-­exons-­and-­introns-­what-­is-­the-­difference-­between-­          them   Image  5:­are-­amino-­acids-­definition-­structure-­quiz.html   Image  6:  My  personal  lecture  notes   Image  7:   Image  8:  Dr.  Scholl’s  Chapter  10  &  11  PowerPoint   Image  9:­gas/  


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