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BIOS 206 Course Notes and Unit 3 Study Guide

by: Plambam31

BIOS 206 Course Notes and Unit 3 Study Guide Bios 206

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This bundle includes important material from all different portions of the course - from Unit 1 all the way to Unit 3. This includes notes on Mitosis and Meiosis and their stages, different centrom...
Dr. Christensen
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This 14 page Bundle was uploaded by Plambam31 on Wednesday August 17, 2016. The Bundle belongs to Bios 206 at University of Nebraska Lincoln taught by Dr. Christensen in Spring 2016. Since its upload, it has received 53 views.


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Date Created: 08/17/16
 BIOS  206  -­‐  General  Genetics  –  Dr.  Christensen     Unit  3  Mid-­‐Term  Study  Guide       Chapter  9     Heteroplasmy  =  when  one  or  more  organelles  have  a  mutation,  but  are  in  a  population  of   mostly  normal  organelles,  so  the  mutant  phenotype  is  not  revealed.  This  is  because  the  normal   organelles  perform  the  wild-­‐type  function.     Chapter  16     Inducible  System  =  Enzymes  produced  only  when  specific  chemical  substrates  are  present  (lac   operon  -­‐>  always  off  (unless  lactose  turns  it  on).     Repressible  system  =  Enzymes  always  produced  unless  turned  off  by  repressor  (Trp  operon  -­‐>   always  on  (unless  tryptofan  turns  it  off).     Constitutive  Enzymes  =  Enzymes  produced  continuously.     Negative  Control  =  expression  occurs  unless  it  is  shut  off  by  some  regulator  molecule       -­‐  Tryptofan  =  negative  control  for  the  trp  operon  (turns  off  transcription)     -­‐  Glucose  =  negative  control  for  the  lac  operon     -­‐Repressor  molecule  from  lacI  gene  is  a  negative  control  for  lac  operon     Positive  Control  =  Transcription  occurs  only  if  a  regulator  molecule  directly  stimulates  RNA   production       -­‐Lactose  is  positive  control  for  the  lac  operon     -­‐cAMP-­‐CAP  complex  in  lac  operon  performs  positive  control.     Cis-­‐acting  element  =  regulatory  region  on  the  same  strand  as  the  genes  it  regulates  (site  for   trans-­‐acting  elements  to  bind)     Trans-­‐acting  element  =  Molecule  that  control  transcription  by  binding  to  cis-­‐acting  sites.     LacZ  =  structural  gene  coding  for  B-­‐galactosidase  (converts  lactose  to  glucose  and  galactose)     LacY  =  structural  gene  coding  for  permease  (allows  lactose  to  enter  the  cell)     LacA  =  structural  gene  coding  for  transacetylase  (possibly  removes  toxic  byproducts  of  lactose   digestion)     Operator  region  =  cis-­‐acting  regulator  region  that’s  adjacent  to  structural  genes.     Repressor  Gene  (lacI)  =  produces  a  trans-­‐acting  product  that  binds  to  the  operator  (represses)       CAP  (catabolite-­‐activating  protein)  =  When  glucose  is  absent,  CAP  forms  a  complex  with  cyclic   adenosine  monophosphate  (cAMP)  and  binds  to  CAP-­‐binding  site.  This  acts  as  a  positive  control   by  allowing  RNA  polymerase  to  bind  to  the  promoter  and  thus  causing  transcription  to  occur.     -­‐  When  glucose  is  present,  cAMP  levels  decrease,  and  CAP-­‐cAMP  complex  doesn’t  form,  and   transcription  diminishes.     Promoter  =  This  is  where  RNA  polymerase  binds     Chapter  17     DNA  of  Eukaryotes:     -­‐Greater  amount  than  prokaryotic  cells.       -­‐Eukaryotic  DNA  is  associated  with  histones  and  other  proteins  to  form  highly  compact   chromatin  structures  within  a  nucleus     -­‐mRNA  must  be  spliced,  capped,  and  polyadenylated  prior  to  transport  from  the  nucleus     Histone  Acetylation  =  catalyzed  by  HATs  and  is  causes  an  increase  in  transcription  by  opening   up  chromatin  structure,  turning  it  into  euchromatin  (Histones  can  also  be  modified  by   methylation  and  phosphorylation).     Histone  Deacetylation  =  catalyzed  by  HDACs  and  causes  a  decrease  in  transcription  by  closing   chromatin  structure,  turning  it  into  heterochromatin.     DNA  Methylation  =  Occurs  most  often  in  the  cytosine  of  CpG  islands  and  causes  a  decrease  in   gene  expression.     Cis-­‐acting  sequence  =  located  on  the  same  chromosome  as  the  gene  it  regulates       -­‐Promoters   -­‐Enhancers   -­‐Silencers     Promoters  =  sequences  that  serve  as  recognition  sites  for  transcription  machinery.  Include:     -­‐Initiator  (Inr)   -­‐TATA  box   -­‐BRE   -­‐Downstream  Promoter  Element  (DPE)   -­‐Motif  Ten  Element  (MTE)   -­‐CAAT  and  GC  boxes  =  proximal  promoter  elements  upstream  of  TATA  and  BRE,  enhancing  basal   transcription     Enhancers  =  Cis-­‐acting  sites  that  up-­‐regulate  transcription  (Can  be  within,  on  either  side,  or   some  distance  from  the  gene)     Silencers  =  Cis-­‐acting  sites  that  down-­‐regulate  transcription.     Transcription  Factors  =  Transcription  regulatory  proteins  that  target  cis-­‐acting  regulatory  sites   and  bind  to  them,  either  increasing  or  decreasing  transcription.     -­‐Activators  =  increase  transcription     -­‐Repressors  =  decrease  transcription     Two  Functional  Domains  of  Transcription  Factors:     1.  DNA  Binding  Domain  –  Binds  to  specific  DNA  sequence     Types  of  DNA  binding  domains:   -­‐Basic  Leucine  Zipper   -­‐Zinc  finger   -­‐Helix-­‐turn-­‐Helix     2.  Trans-­‐Activating  Domain  –  Activates  or  represses  transcription  by  binding  to  other   transcription  factors  or  RNA  polymerase.     GAL  System  in  Yeast:     -­‐Inducible  system:  presence  or  absence  of  galactose  regulates  transcription  of  structural  genes   (GAL1,  GAL2,  GAL7,  and  GAL10)     -­‐Positive  Control:  Gal4p  is  necessary  for  transcription  to  occur     -­‐The  4  structural  genes  digest  galactose     -­‐3  regulatory  genes:  GAL4,  GAL80,  and  GAL3  –  regulate  transcription  of  structural  genes     -­‐Absence  of  galactose  =  Gal4p  is  bound  to  UAS  along  with  Gal80p  –  No  Transcription     -­‐Presence  of  galactose  =  Gal3p  (inducer)  binds  to  Gal80p,  so  Gal4p  trans-­‐activating  domain   becomes  exposed  –  Transcription  Occurs     UAS  =  upstream  activating  sequence.  Acts  as  an  enhancer.  They  are  constitutively  open  (free  of   nucleosomes)/  DNase  hypersensitive  (not  naturally  cut  by  DNase.  It’s  a  lab  technique  done  in   vitro)     Alternative  Splicing  –  Number  of  proteins  a  cell  can  make  (  its  proteome)  is  greater  than  the   number  of  genes  in  its  genome.       -­‐2/3  of  human  genes  undergo  this   -­‐Humans  produce  hundreds  of  thousands  of  different  proteins  from  just  20,000  genes     Sex  Lethal  (Sxl)  =  Switch  in  Drosophila  that  selects  the  pathway  of  sexual  development  in  a   female-­‐specific  fashion     siRNA  and  miRNA  -­‐  repress  mRNA  translation  and  trigger  mRNA  degradation     EPIGENETICS     Epigenetic  Trait  –  mitotically  or  meiotically  inherited  phenotype  that  results  from  a  change  in   gene  expression  without  changing  DNA  sequences.     Epigenome  –  genome  including  DNA  sequence  AND  all  epigenetic  traits     Epigenetic  code:   -­‐regulates  processes   -­‐explains  phenotypic  variation     Consists  of:   -­‐DNA  Methylation   -­‐Histone  Modification  –  alters  structure  of  chromatin  (open  or  close  structure)     X  chromosomes  of  females  being  changed  into  Barr  Bodies  =  example  of  epigenetics   (methylation)     Imprinted  Genes  =  show  expression  of  only  the  maternal  allele  or  paternal  allele     -­‐Hypermethylation  and  Hypomethylation  are  properties  of  cancers.           Chapter  20     Recombinant  DNA  =  DNA  created  by  joining  together  pieces  of  DNA  from  different  sources.     Steps:     1.  Cut  DNA  w/restriction  enzymes   2.  Ligate  DNA  to  a  plasmid  vector     3.  Insert  plasmid  into  host  cell   4.  Allow  it  to  replicate     5.  Collect  DNA  from  host  cell     Restriction  Enzyme  =  An  enzyme  that  recognizes  a  specific  DNA  sequence  and  cuts  the   phosphodiester  bonds  at  that  site,  forming  “sticky”  ends  (DNA  fragments  with  single-­‐stranded,   cohesive  overhanging  ends)  or  blunt  ends  (DNA  fragments  with  double-­‐stranded  ends)     -­‐Restriction  sites  are  usually  palindromic:  (5’  ATGCAT  3’)                              (3’  TACGTA  5’)     -­‐Restriction  sites  are  palindromic  to  ensure  that  both  strands  get  cut  and  so  the  DNA  sequence   being  inserted  to  the  vector  can  be  ligated  due  to  complimentary  palindromic  ends.     Vectors  =  DNA  molecules  that  can  replicate  cloned  DNA  fragments  in  a  host  cell.     -­‐Must  be  able  to  replicate  independently  (origin  of  replication)   -­‐Should  have  several  restriction  sites  to  allow  insertion  of  DNA   -­‐Must  have  selectable  marker  such  as  antibiotic  resistance     Types  of  Vectors:     Plasmid  =  Double  stranded  DNA  molecule  that  replicates  autonomously  in  bacterial  cells     Bacteriophage  Vectors  =  Lambda  vectors  –rarely  used  anymore     Cosmids  =  Combination  of  plasmids  and  phages.        –carry  up  to  50  kb  of  inserted  DNA   -­‐Have  advantage  of  being  delivered  efficiently  by  phage,  and  then  once  inside,  it  replicates  as  a   plasmid   -­‐Not  used  much  anymore     BAC  =  Bacterial  Artificial  Chromosome     -­‐Carry  up  to  300  kb  of  inserted  DNA   E.  coli  is  used  as  a  prokaryotic  host  cell  when  working  with  plasmids     Yeast  is  used  as  a  eukaryotic  host  cell  for  DNA  cloning  and  expression  of  eukaryotic  genes     Genomic  Library  –  contains  at  least  one  copy  of  all  the  DNA  in  the  genome       cDNA  Library  –  contains  complimentary  DNA  copies  of  the  mRNA  in  a  cell     Prepared  by:     -­‐isolating  mRNA  from  cells   -­‐Using  reverse  transcriptase  to  synthesize  complimentary  DNA     -­‐Cloning  the  cDNA  molecules  into  a  vector     -­‐cDNA  represents  the  genes  being  expressed  in  cells  at  the  time  the  library  was  made       Probe  =  Any  DNA  or  RNA  sequence  that  is  complimentary  to  the  target  gene  of  the  sequence  to   be  identified     -­‐Probes  are  used  to  screen  a  library  to  recover  clones  of  a  specific  gene     PCR  (Polymerase  Chain  Reaction)  =  Amplifies/makes  copies  of  a  target  DNA  sequence  without   host  cells     Advantages:   -­‐requires  small  amount  of  input  DNA   -­‐specificity  is  controlled  by  the  primer  sequence   -­‐Creates  billions  of  copies  very  quickly     Disadvantages:   -­‐very  susceptible  to  contamination   -­‐information  about  the  sequence  must  be  known  to  design  primers   -­‐error  prone   -­‐cannot  amplify  long  segments  of  DNA     Southern  Blot  (name  of  person)  =  allows  identification  of  one  DNA  fragment  in  a  complete   genome     -­‐specificity  is  due  to  a  probe     2  steps:   -­‐separation  of  DNA  fragments  by  size   -­‐identification  of  fragment  of  interest  by  hybridization     northern  blot  –  Uses  RNA  on  the  gel  –  separated  by  size     Chapter  21     DNA  Sequencing  –  Process  of  determining  the  order  of  nucleotides  (A,T,G,C)  within  a  DNA   molecule     Sanger  DNA  Sequencing  –  Chain  termination  sequencing       -­‐adds  deoxynucleotides,  but  then  adds  di-­‐deoxynucleotides  (No  OH  group)  to  end  the  chain   with  fluorescent  tags  which  allows  for  automatic  detection  of  the  DNA  sequence.     Clone-­‐by-­‐Clone  Sequencing  –  Slowest  method.  Expensive.  Not  used  much  anymore.     -­‐Cut  DNA  with  restriction  enzymes   -­‐Clone  fragment  into  BAC  or  YAC       Whole  Genome  Shotgun  (WGS)  –  Faster  more  efficient  method.  Uses  Contigs  (contiguous   fragments)  =  overlapping  fragments  that  collectively  form  a  DNA  molecule     -­‐Cut  DNA  with  different  restriction  enzymes   -­‐Overlap  sequenced  fragments  using  computer   -­‐Fragments  aligned  based  on  identical  DNA  sequences     Next  Gen  Sequencing  (High  throughput)  –  best  type  of  sequencing  –computer  automated     Genomics  =  study  of  genomes  (complete  set  of  DNA  in  a  single  cell  of  an  organism)     Structural  Genomics  =  focuses  on  analyzing  nucleotide  sequences  to  identify  genes  and   regulatory  elements     Bioinformatics  =  Use  of  computer  hardware  to  organize,  share,  and  analyze  data  related  to   gene  expression  and  protein  structure  and  function.     Open  Reading  Frames  (ORF)  =  Sequences  that  do  not  include  a  stop  codon  –  may  represent  a   protein  coding  gene     Functional  Genomics  =  Attempt  to  identify  functions  of  genes     Homologous  genes  =  genes  that  are  thought  to  have  descended  from  a  common  ancestor   Orthologs  =  homologous  genes  from  different  species     Paralogs  =  homologous  genes  from  the  same  species     The  Human  Genome  Project  (HGP)       -­‐Less  than  2%  of  the  genome  codes  for  proteins     -­‐There  are  only  about  25,000  protein  coding  genes  (alternative  splicing)     J.  Craig  Venter     -­‐Sequenced  own  genome   -­‐First  diploid  sequence  of  a  human     Single  Nucleotide  Polymorphisms  (SNP)     -­‐Are  alleles   -­‐Often  have  no  phenotype   -­‐Are  single  base  changes   -­‐Variation  between  different  humans  is  a  polymorphism     Comparative  Genomics  =  Compares  the  genomes  of  different  organisms  to  answer  questions   about  genetics.     -­‐Humans  share  large  numbers  of  genes  with  other  species.  98%  with  chimpanzees.  75%  of   genes  are  shared  with  dogs.     -­‐Comparative  genomics  identifies  members  of  Multigene  Families  including  nonfunctional   pseudogenes.     -­‐Group  of  related  multigene  families  is  a  superfamily     Metagenomics  =  study  of  genomes  of  entire  communities  of  organisms     -­‐allows  analysis  of  genomes  of  all  organisms  in  an  environmental  sample.  –Bacteria  in  lakes,  etc.     Transcriptomics  =  Global  analysis  of  gene  expression.  Involves  RNA     Proteomics  =  Study  of  proteomes  (complete  sets  of  proteins  encoded  by  a  cells  genome)     Systems  Biology  =  Takes  holistic  approach  and  incorporates  data  from  genomics,   transcriptomics,  and  proteomics  to  analyze  interactions.  This  is  the  interactome  


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