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BIS 010: EVeryday Biology Week 2 Notes

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by: AlexandraRita Notetaker

BIS 010: EVeryday Biology Week 2 Notes BIS 010 021

Marketplace > University of California - Davis > Biology > BIS 010 021 > BIS 010 EVeryday Biology Week 2 Notes
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Week 2 notes that cover lecture from Tuesday and Thursday. Each new Set of notes will be uploaded on thursday. A study guide will be posted before exams.
General Biology
Class Notes
BIS 010, Biology, Everyday Biology, popular, upload, good notes, Davis, UC Davis, Bio
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"Yes YES!! Thank you for these. I'm such a bad notetaker :/ will definitely be looking forward to these"
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This 22 page Class Notes was uploaded by AlexandraRita Notetaker on Thursday April 7, 2016. The Class Notes belongs to BIS 010 021 at University of California - Davis taught by Debello in Spring 2016. Since its upload, it has received 200 views. For similar materials see General Biology in Biology at University of California - Davis.


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Date Created: 04/07/16
Everyday  Biology   th Day  3  (April  5 )  Everyday  Chemistry   Emergence   •  Complicated  behaviors  and  patterns  can  often  emerge  from  simple   underlying  rules   •  Separation,  alignment,  cohesion   •   Life  as  an  emergent  property  -­‐  a  collection  (not  one  or  two)  of  specific   non-­‐living  things   -­‐Life  has  certain  features   •  Complicated  behaviors  and  patterns  can  often  emerge  from  simple   underlying  rules   •  Biological  systems:  cells  -­‐  brain  -­‐  behavior     •  At  the  molecular  level  -­‐  polymers   -­‐  Behavior  of  molecules  based  on  the  rules  of  chemistry     Polymerization  is  central  to  biology     -­‐Harnessing  chemistry  to  efficiently  “evolve”     -­‐Covelant  and  Hydrogen  Bonds   -­‐Polymerization:  individual  molecules  assemble  into  long  chains   •   harnessing  chemistry  to  efficiently  “evolve”   •   Nucleotides  à  DNA,  RNA  4  monomer  types   •   Monomer  +Monomer  à  Polymer   •    Amino  acids  à  polypeptide/protein  20  monomer  types   A  few  types  of  monomers  generate  a  tremendous   diversity  of   polymers.     Building  Blocks  of  “life”             The  Atoms  and  Molecules  of  Life         All  life  forms  on  earth  are  carbon-­‐   based  (organic)  -­‐  the  "backbone"  of   biology     •  Carbon  forms  the  backbone  of  most   key  molecules  of  life  •  Water  (H2O)   accounts  for  most  of  the  Oxygen   2     Why  Carbon?   •   Two  qualities  of  carbon:  small  size  (radius)  and  unique  electron   configuration  (molecular  glue)   •   Molecular  glue:  valence  of  4  –  can  make  up  to  four  bonds   -­‐H,  O,  N,  S  AND  itself,  C,  to  make  “carbon  backbon es’   •   Small  size:  carbon  radius  small               3     Chemistry  of  Life:  Atoms   Electronegativity  -­‐attract     electrons  Number  of  valence   electrons   i t   A   -­‐Carbon  is  small   -­‐Carbon  like  to  make  4  bonds   -­‐Valence  electrons  are  the  glue  that  can  hold  molecules  together  =reactivity.   Atoms  prefer  to  have  the  valence  or  outer  shell  comprised  of  8   electrons.     Levels  of  Organization   Atoms  à  Molocules    Polymerization  (carbon  Mol)   How  are  molecules  formed  and  how  do  they  interact?   •   Covalent  bonds:  hold  atoms  together  within  molecules  -­‐  sharing  of   electrons  -­‐  very  strong  glue   4   •   Ionic:  donating/accepting  electrons  to  become  an  ion,  easily  formed   between  valence  1  and  7  atoms  such  as  Na+  Cl-­‐   •   Hydrogen  bonds  -­‐  where  hydrogen  forms  bonds  simultaneously  with   two  other  atoms.   -­‐Facilitates  interaction  between  molecules  with  unlike  atoms  which  have   partial  charges  due  to  their  respective  differences  in  electronegativity.     Why  Water?   •   The  best  solvent  -­‐  it  dissolves  things  really  well     •   Large  liquid  range   •   It  has  capillary  action  -­‐  adhesive   •   High  heat  capacity:  absorbs  heat     -­‐it  protects  us     •   Water  can  form  an  acid  and  a  base   -­‐involved  in  acid/base  chemistry  in  life   Drives  the  formation  of  larger  structures  essential  for  life:  proteins  and  lipid   membranes     The  Essential  Water     -­‐Charge  distribution  of  water   •   The  electronegative  oxygen  atom  pulls  electron  density  away  from   hydrogen.   •   The  oxygen  carries  a  partial  negative  and  the  hydrogen  atoms  carry   partial  positive  charges.   -­‐Water  has  a  permanent  dipole  -­‐  water  is  “polar”       5       Liquid  water   •   Each  water  molecule  is  held  within  a  dynamic  framework  of  0 -­‐4   hydrogen  bonds  depending  on  the  location  of  water  i.e.,  air  interface.   •   The  mutual  attraction  between  water  molecules  is  called  "cohesion."     Polar  Vs.  NonPolar  and  Water  Solubility   Polar   •   Water  is  polar   •   Oxygen  tends  to  create  polar  molecules   •   Sugars  are  polar  and  water  soluble  or  hydrophilic     Nonpolar   •   Methane  is  nonpolar   •   Carbon  and  hydrogen  tend  to  create  nonpolar  molecules   •   Grease  is  nonpolar  and  not  water  soluble  or  hydrophobic       The  Hydrophobic  Effect   •   The  observed  tendency  of  nonpolar  substances  to  aggregate  in  aqueous   solution  and  exclude  water  molecules.   •   Non  polar  substances  disrupt  hydrogen  bonds  B/T  water   •   Charles  Tanford  “The  Hydrophobic  Effect:  Formation  of  Micelles  and   Biological  Membranes”  Science  1978     •   The  hydrophobic  effect  drives  self-­‐  organization  of  membranes  and   protein  folding  -­‐  proteins  have  evolved  to  contain  hydrophobic  “cores”.     6       Higher  Order  Life  Molecules   •   DNA   -­‐Phosphates  Links   -­‐Base  gives  Identity   -­‐Cellulose  (sugar)  Backbone   •   Protein   -­‐Amino  groups   -­‐Amino  Acids  joined  by  peptide  group   -­‐Peptide  bonded  backbone     A  few  types  of  monomers  generate  a  tremendous  diversity  of  polymers   -­‐There  are  more  than  10^10  different  possible  DNA  sequences  of  length  17.   -­‐DNA  Polymerase  copies  each  strand  of  DNA  double  helix     Biological  Membranes     Atoms  à  Molocules  à   Polymerization  (lipids)   •   Membranes:  Impearable   to  water  and  boundaries   that  define  compartments •   Membranes  separate  the   inside  of  a  cell  from  the   outside   •   Membranes  define   specialized  compartments  within  a  cell   7       The  RNA  hypothesis:   •   RNA  as  the  original  spontaneous  polymer  that  could  replicate  chemically   •   fatty  acids  which  could  assemble  to  create  a  compartment  that  can  grow   and  divide  and  facilitate  RNA  replication   •   Current  DNA-­‐RNA-­‐protein-­‐lipid-­‐based  life  evolved  from  self  replicating   RNA  molecule  or  RNA-­‐like  molecule  plus  lipid  based  system.     •   RNA  can  store  information  (like  DNA)  AND  catalyze  (like  protein)  all  of   the  chemical  reactions  required  for  life.   •   RNA  is  needed  to  make  proteins  (ribosome)  and  catalyzes  peptide  bond   formation.     •   Many  essential  cofactors  in  cell  (ATP,  NADH,  acetyl -­‐CoA)  are  structurally   related  to  RNA     •   Deoxyribonucleotides  (DNA)  are  made  from  ribonucleotides,  which   makes  RNA.       Microbes   •   Bacteria   •   Archaea   •   Eukaryotes     -­‐Some  earliest  evidence  of  life  are  microfossils  interpreted  to  be  bacteria   based  primarily  on  size/shape   -­‐Relationships  among  species  are  deduced  from  shared  characteristics,   including  sequences  of  DNA     8       Common  ancestry  around  1843   •   Common  ancestor  gives  rise  to  2  independent  lineages   •   Natural  groups,  or  “clades”,  share  certain  properties  (one  invention)   •   Pattern  of  change  (tree  topology  or  pattern)   •   Rate  of  change  (branch  length)   •          Length  of  line  proportional  to  amount  of  change  (varia ble)   •   Phylogenetic  trees  are  representations  of  evolutionary  relationships     Homology   “The  same  organ  in  different  animals  under  a  variety  of  form  and  function” ’   •   Because  all  life  shares  a  common  ancestry  -­‐  so  should  the  “parts”  of  life
   •   Homology  is  similarity  due  to  common  descent   •   Analogy  is  due  to  adaptation  to  the  same  environmental  condition   (convergence)   •  “Levels”  of  homology’     Steps  in  Assessing  Homology   1.  Classify  features   2.  Classify  similar  in  similar  positions  (e.g.structures)    3.  Link  features  to  tree  of  evolutionary  relationships           9       Relationships  among  species  are  deduced  from  shared  characteristics,   including  sequences  of  DNA   Heredity  -­‐  genetics  -­‐  genes  (the  code)   End  of  Notes  Day  3                                             10     Day  4  (April  7 )  Origin  of  life-­‐  Viral  Life   Diversity  in  microbes   •   is  reflected  in  the  way  that  they:   -­‐  obtain  energy  and  nutrients     -­‐  respond  to  environment   -­‐  regulate  genes   -­‐  survive  adverse  conditions   ...  not  as  in  shape  (morphology)   “natural”  groups  of  organisms  (or  genes)                   Branches  can  rotate  around  nodes  Nodes  are  can  rotate  360°    -­‐  like  a  mobile             11     Microbes   •   Carl  Woese  used  rRNA  genes  to  determine  “natural”  or  evolutionary   relationships  among  microbes     Requirements  of  a  gene  “proxy”  for  an  organismal   phylogeny   •   The  Ribosome  (70S-­‐80S)   •   Ribosomes  are  present  in  all  cellular  life   •   Homologous:  similar  in  position,  structure,  and  evolutionary  origin  but   not  necessarily  in  function.   •   ribosomes  are  the  cell’s  protein  factory  and  are  composed  of  proteins   and  RNA   •   ribosomal  RNA  (rRNA)  =  RNA  component  of  the  ribosome   •   some  regions  of  rRNA  is  variable  and  some  regions  are  not  as  variable     Multiple  sequence  alignment:   •   taxa  in  rows   •   homologous  positions  in  columns   •   use  “gaps”  or  “indels”  to  bring  homologous   •   positions  in  alignment   12     The  “Big  Tree”   •   All  cellular  life  is   related  (one   origin) •   Last  universal   common   ancestor  (LUCA)   •   Three  domains   of  life,  not  two:   Bacteria,   Archaea,   Eukarya   •   Most  life  is   microbial  (still)   •   Natural   taxonomy:   based  on   evolutionary   relatedness  i.e,   allows   phylogeny  to  be   predictive   à  Related  organisms  (or  related  genes)  should  have  similar  properties  (not   that  we  always  know  “which”  properties  those  are)     •   How  do  you  get  bigger?  Energy  canyon....   •   Archaea  +  bacteria  overcome  the  “energy”  canyon   Two  groups  of  bacteria  are  related  to  eukaryotic  organelles  (mitochondria   and  chloroplast)   13     Domain  of  Life  (1977)   •   Kuhnian  paradigm  shift  (scientific  revolution)   •   Lack  of  understanding  of  archaeal  biology     •   Much  research  was  on  Archaea  in  Germany     •   Genomes  and  new  microbes  have  helped  Ongoing  “prokaryote”  debate     Risk   •   Risk  is  the  likelihood  of  X  happening     Calculating  Risk   •   Relative  Risk:  is  the  ratio  of  the  probability  of  an  event  occurring  (for   example,  developing  a  disease,  being  injured)  in  an  exposed  group  to  the   probability  of  the  event  occurring  in  a  comparison,  non -­‐exposed  group.   •   Increased  Risk:  Probability  that  the  risk  of  a  given  situation  will  go  up.         Example  of  Calculating  Risk     •   24  Ebola  infections/2014   •   33  people/year  die  by  lightening   Fraction:  24  people/year  out  how  many?  316,000,000   •   1/13.1  million  people  Frequency  of  X:  7.6  x  10-­‐8     •   7.6  x  10-­‐8  x  100  =  0.0000076%   14       Calculating  Risk       Discovery  Of  Viruses   •   1880s  Tobacco  Mosaic  Virus  (Beijerinck/Ivanovski)   •   He  took  sap  of  sick  plants  and  injected  into  healthy  ones     •  It  grew  bacteria  from  sap  -­‐  not  infectious   •   He  then  added  it  to  contagious  fluid:   •   He  used  alcohol  and  boiled  it   •   let  it  dry  on  paper   •   still  infectious     Martinus  Beijerinck   •   Filtered  sap  from  sick  tobacco  plants  took  juice  and  then  infected   tobacco   -fluid  caused  disease  =  contagious  living  fluid  =  virus   15     Later  Discoveries   à  95%  protein  but  also  DNA  and  maybe  sometimes  RNA   à  protein  shells  holding  a  just  few  genes     Relative  Size  of  Viruses   General  Characteristics  of  Viruses   •   Need  cells  to  replicate   •   Contain  a  single  type  of  nucleic  acid,   •   Either  DNA  or  RNA  (not  both)   •   Single-­‐  or  double-­‐stranded   •   Contain  a  protein  coat  that  surrounds  the  nucleic  acid  Some  are  enclosed   by  an  envelope   •   Some  viruses  have  spikes   •   Viruses  infect  all  forms  of  cellular  life:  But  viruses  infect  specific  types  of   cells  in  one  host   16     Viral  Structures     •   Nucleic  acid   -­‐DNA  or  RNA  (>2  genes  <  )  Capsid •   Capsomeres  (units  of  capsid)   •   Envelope:  made  of  lipids  obtained  from   the  host  Spikes   •   Virion:  a  complete  infectious  particle   •   Nucleocapsid:  nucleic  acid  plus  capsid     Are  Viruses  Alive?   •   Viruses  have  genetic  material  (DNA,  RNA,  protein)   •   They  can  replicate  (but  require  a  host)   •   They  exchange  genetic  information  with  living  things  don’t  make  their   own  energy   •   “borrowed”  life?  emergent  property  of  non-­‐living  things   •   Radiolab:  Shrink  (Mimivirus)   •   They  self  Assemble     Flu  (influenza)   •   every  year  5-­‐10%  of  adults  and  20-­‐30%  of  children  get  the  flu  250,000-­‐ 500,000  die  of  flu  every  year   •   infects  lining  of  airways  and  paves  ways  for  other  infections  flu  comes   from  birds  (also  hosts)   •   flu  virus  can  mutate,  then  adapt  to  human  hosts   •   sometimes  cells  have  >  1  kind  of  virus,  and  viruses  can  combine  and   swap  genes   17       BIOSYNTHESIS:  RNA  Viruses   •   Host  cells  do  not  possess  RNA-­‐dependent  polymerases.   •   These  enzymes  are  required  to  make  viral  mRNA  and  replicate  genomes.   •   Viruses  do  have  RNA-­‐dependent  polymerases   •   RNA  viruses  are  classified  using  a  (+)  or  (–)  strand  designation  for  their   genomes   •   Double-­‐stranded  RNA  viruses  contain  one  (+)  strand  and  one  (–)  strand.   Single-­‐stranded  RNA  viruses  are  either:   -­‐(+)  single-­‐stranded     -­‐(–)  single-­‐stranded     Why  do  viruses  have  specificity  for  certain  cells?   •   Viruses  enter  cells  after  binding  to  highly  specific  cell  surface  proteins   •   Viruses  must  be  able  to  replicate  in  their  host  cells  and  escape  from   them   Why  can  some  viruses  infect  multiple  hosts?   •   Viruses  enter  cells   after  binding  to   highly  specific  cell   surface  protiens   •   Other  species  have   homologs  of  these   key  proteins       18     BIOSYNTHESIS: Double-­‐stranded  DNA  Viruses   •   Double-­‐stranded  DNA  viruses  use  the  same  mechanisms  as  the  host  cell   for  biosynthesis.   •   One  strand  of  viral  DNA  is  transcribed  into  mRNA.  It  uses  either  the  host   cell  or  viral  RNA  polymerase.   •               How  does  a  virus  cause  cancer?   •   Viruses  need  to  use  the  host  cell  machinery  to  replicate.   •   This  extra  activity  can  cause  increased  cell  division   •   HPV  can  boost  the  activity  of  the  host  cell’s  machinery  that  copies  DNA.   •   Increased  cell  division  combined  with  additional  mutations  leads  to   cancer     BIOSYNTHESIS:  (+)  Single-­‐stranded  RNA  Viruses   •   The  (+)  strand  is  already  mRNA.   -­‐It  can  be  directly  translated  into  viral  proteins.   •   Genome  replication  has  2  steps:   •   The  (+)  strand  is  copied   into  (–)  template   •   The  template  is  used  to   make  more  (+)  strands. 19     Why  do  we  have  “receptors”  for  viruses?   •   HIV  uses  cell  surface  proteins  called   •   CD4  and  CCR5  as  “receptors”   •   People  with   mutations  in  CCR5  are   resistant  to  HIV   •   CCR5  has  a  “normal”   function.  It  detects   chemical  signals  to   help  recruit  immune   cells  to  sites  of   infection   •   CD4  and  CCR5  are  present  on  the  surface  of  certain  immune  cells   •   HIV  has  co-­‐opted  this  protein  to  be  a  virus  receptor Why  do  we  have  “receptors”  for  viruses?   •   HIV  uses  cell  surface  proteins  called  CD4  and  CCR5  as  “receptors”   •   People  with  mutations  in  CCR5  are  resistant  to  HIV   •   CCR5  has  a  “normal”  function.  It  detects  chemical  signals  to  help  recruit   immune  cells  to  sites  of  infection   •   CD4  and  CCR5  are  present  on  the  surface  of  certain  immune  cells   •   HIV  has  co-­‐opted  this  protein  to  be  a  virus  receptor     Viruses  Mediate  Evolution   •   Endogenous  Retroviruses   •   retroviruses  -­‐  insert  genetic  material  into  host  DNA   •   "endogenous”  =  from  within  riddled  with  copying  mistakes   20   •   remain  a  silent,  hobbled  passenger  in  the  genome   •   viral  genomes  become  part  of  host  genome  many  remain  dormant  and   are  not  pathogenic     We  are  actually  part  virus:   •   the  human  genome  about  100,000  copies  of  dead  viruses  in  our  genome   =  8%  of  our  total  DNA   •   one  virus  carries  a  protein  called  syncytin  expressed  in  the  placenta   •   in  all  placental  mammals,  syncytin  is  key  for  drawing  nutrients  into  the   embryo’s  bloodstream     Giant  Viruses   •   First  discovered  in  1999  as  pathogens  of  algae  They  often  infect  amoeba   •   Size  of  particles  can  be  ~200  nm  (violates  the  size  paradigm)   •   Family:  nucleocytoplasmic  large  DNA  virus  (NCLDV)  Genomes  can  be  as   big  as  those  of  some  bacteria   •   They  can  even  be  parasitized  by  other  viruses  (e.g.  the  virophage   Sputnik)   •   Mimivirus  was  originally  mistaken  for  a  bacterium,  because  of  its  size   and  it  was  identified  during  investigation  of  a  pneumonia  outbreak   associated  with  a  water  cooling  tower  in  the  U.K.               21     Where  did  this  giant  virus  come  from?   •   Originate  from  simple  virus  -­‐  acquire  genes  from  hosts.   •   But,  very  few  genes  have  homology  to  host  genes  (<10%)   •   Reductive  evolution:  a  cellular  form  of  life  reduced  its  essential  genes   -­‐ parasite   •   But,  no  obvious  homology  with  any  of  the  major  domains  of  life.   •   Pre-­‐date  cellular  life  -­‐  some  gave  rise  to  cells  others  stayed  as  giant  virus     End  of  Notes  Day  4  Week  2   22  


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