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BIOL 1030 Exam 1 Study Guide

by: Emma Cox

BIOL 1030 Exam 1 Study Guide BIOL 1030 - 002

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Emma Cox
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This is a comprehensive study guide of materials for Exam 1. It includes detailed notes from chapters 26, 27, 28, and 29 in our textbook.
Organismal Biology
Debbie R. Folkerts
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This 14 page Study Guide was uploaded by Emma Cox on Tuesday February 2, 2016. The Study Guide belongs to BIOL 1030 - 002 at Auburn University taught by Debbie R. Folkerts in Summer 2015. Since its upload, it has received 401 views. For similar materials see Organismal Biology in Biology at Auburn University.


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Date Created: 02/02/16
Bio  Chapter  26   Sunday,  January  31,  2016   8:55  PM   Chapter  26:  Phylogeny  and  the  Tree  of  Life   Investigating  the  Tree  of  Life   •   Phylogeny  -­‐-­‐  the  evolutionary  history  of  a  species  or  group  of  species   •   Systematics  -­‐-­‐  a  discipline  focused  on  classifying  organisms  and  determining  their  evolutionary   relationships       26.1  Phylogenies  show  evolutionary  relationships   •   Taxonomy  -­‐-­‐  how  organisms  are  named  and  classified   Binomial  Nomenclature   •   Developed  by  Carolus  Linnaeus   •   Binomial  -­‐-­‐  two  part,  Latin,  scientific  name  of  an  organism   o   Composed  of  Genus  +  specific  epithet   Hierarchical  Classification     • From  smaller  to  larger:     Genera  -­‐-­‐  families  -­‐-­‐  orders  -­‐-­‐  classes  -­‐-­‐  phyla  -­‐-­‐  kingdoms  -­‐-­‐  domains   •   Taxon  -­‐-­‐  the  named  taxonomic  unit  at  any  level  of  the  hierarchy   Linking  Classification  and  Phylogeny   •   Phylogenetic  tree  -­‐-­‐  branching  diagram  that  represents  the  evolutionary  history  of  an  organism   •   A  phylogenetic  tree  represents  a  HYPOTHESIS  about  evolutionary  relationships   •   Branch  points  -­‐-­‐  divergence  of  two  evolutionary  lineages  from  a  common  ancestor   •   Sister  taxa  -­‐-­‐  groups  of  organisms  that  share  an  immediate  common  ancestor  and  are  each  others   closest  relatives   •   Rooted  phylogenetic  tree  -­‐-­‐  a  branch  point  within  the  tree  represents  the  most  recent  common   ancestor  of  all  the  taxa  in  the  tree     • Basal  taxon  -­‐-­‐  lineage  that  diverges  early  in  the  history  of  a  group  and  lies  on  a  branch  that   originates  near  the  common  ancestor   •   Polytomy  -­‐-­‐  branch  point  from  which  more  than  two  descendant  groups  emerge   What  We  Can  and  Cannot  Learn  From  Phylogenetic  Trees   •   Trees  show  patterns  of  descent,  not  phenotypic  similarity   •   The  sequence  of  branching  in  a  tree  does  not  necessarily  indicate  the  a ctual  ages  of  the  particular   species   •   We  should  not  assume  that  a  taxon  on  a  phylogenetic  tree  evolved  from  the  taxon  next  to  it   Applying  Phylogenies   •   Identifying  closely  related  organisms  allows  us  to  establish  a  "reservoir"  of  beneficial  alleles  that   can  be  transferred  to  cultivated  organisms  by  cross -­‐breeding  or  genetic  engineering   •   Infer  species  identities  by  analyzing  the  relatedness  of  DNA  sequences  from  different  organisms       26.2  Phylogenies  are  inferred  from  morphological  and  molecular  data   Morphological  and  Molecular  Homologies   •   Phenotypic  and  genetic  similarities  due  to  shared  ancestry  =  homologies   •   Organisms  that  share  very  similar  morphologies  or  similar  DNA  sequences  are  likely  to  be  closely   related   Sorting  Homology  from  Analogy   •   Analogy  -­‐-­‐  similarity  between  organisms  due  to  convergent  evolution   •   Convergent  evolution  is  when  similar  environmental  pressures  and  natural  selection  produce   similar  adaptations  in  organisms  from  different  evolutionary  lineages   •   Homoplasies  -­‐-­‐  analogous  structures  that  arise  independently   •   The  more  elements  that  are  similar  in  two  complex  structures,  the  more  likely  it  is  that  they   evolved  from  a  common  ancestor   Evaluating  Molecular  Homologies   •   If  species  are  closely  related,  their  DNA  sequences  probably  differ  at  o nly  one  or  a  few  sites       26.3  Shared  characters  are  used  to  construct  phylogenetic  trees   Cladistics   •   Cladistics  -­‐-­‐  common  ancestry  is  the  primary  criterion  used  to  classify  organisms   •   Clades  -­‐-­‐  groups  of  species  that  include  an  ancestral  species  and  all  of  i ts  descendants   •   Monophyletic  -­‐-­‐  consists  of  an  ancestral  species  and  all  of  its  descendants   •   Paraphyletic  -­‐-­‐  consists  of  ancestral  species  and  some,  but  not  all,  of  its  descendants   •   Polyphyletic  -­‐-­‐  includes  distantly  related  species  but  does  not  include  the  m ost  recent  common   ancestor   Shared  Ancestral  and  Shared  Derived  Characters   •   Shared  ancestral  character  -­‐-­‐  a  character  that  originated  in  an  ancestor  of  the  taxon   •   Shared  derived  character  -­‐-­‐  an  evolutionary  novelty  unique  to  a  particular  clade   Inferring  Phylogenies  Using  Derived  Characters     • Outgroup  -­‐-­‐  a  species  or  group  of  species  from  an  evolutionary  lineage  that  is  known  to  have   diverged  before  the  lineage  that  includes  the  species  we  are  studying   o   A  suitable  one  can  be  determined  based  on  evidence  from   morphology,  paleontology,   embryonic  development,  and  gene  sequences   •   Ingroup  -­‐-­‐  the  species  we  are  studying   •   Derived  characters  can  be  determined  by  comparing  members  of  the  ingroup  with  each  other  and   with  the  outgroup   Phylogenetic  Trees  with  Proportional  Branch  Lengths     • Branch  lengths  can  be  drawn  to  represent  the  numbers  of  changes  that  have  taken  place  in  a   particular  DNA  sequence  in  that  lineage   •   Branch  lengths  can  be  proportional  to  time   Maximum  Parsimony  and  Maximum  Likelihood   •   Can  never  be  sure  of  the   most  accurate  tree  for  a  large  data  set   •   Maximum  parsimony  -­‐-­‐  we  should  first  investigate  the  simplest  explanation  that  is  consistent  with   the  facts;  minimalist  approach   •   Maximum  likelihood  -­‐-­‐  identifies  the  tree  most  likely  to  have  produced  a  given  set  of  D NA  data,   based  on  certain  probability  rules  about  how  DNA  sequences  change  over  time   •   When  a  large  amount  of  data  is  accurate,  these  two  methods  yield  similar  trees   Phylogenetic  Trees  as  Hypotheses   •   Phylogenetic  bracketing  allows  us  to  predict  that  features   shared  by  two  groups  of  closely  related   organisms  are  present  in  their  common  ancestor  and  all  of  its  descendants  unless  independent   data  indicate  otherwise       26.4  An  organism's  evolutionary  history  is  documented  in  its  genome   •   DNA  sequences  show  phylogenet ic  relationships  that  cannot  be  determined  by  nonmolecular   methods   Gene  Duplications  and  Gene  Families   •   Gene  families  -­‐-­‐  groups  of  related  genes  within  an  organism's  genome   •   Gene  duplication  increases  the  number  of  genes  in  the  genome,  providing  more   opportunities  for   further  evolutionary  changes   •   Orthologous  genes  -­‐-­‐  homology  is  the  result  of  a  speciation  event  and  hence  occurs  between   genes  found  in  different  species   •   Paralogous  genes  -­‐-­‐  homology  results  from  gene  duplication   -­‐-­‐  multiple  copies  of  thes e  genes   have  diverged  from  one  another  within  a  species;  more  than  one  copy  in  the  genome   Genome  Evolution   •   Lineages  that  diverged  long  ago  often  share  many  orthologous  genes     •   The  number  of  genes  a  species  has  doesn't  seem  to  increase  through  duplication  at  the  same  rate   as  perceived  phenotypic  complexity       26.5  Molecular  clocks  help  track  evolutionary  time   Molecular  Clocks     • Molecular  clock  -­‐-­‐  an  approach  for  measuring  the  absolute  time  of  evolutionary  change  based  on   the  observation  that  some  genes  and  other  regions  of  genomes  appear  to  evolve  at  constant  rates   o   For  orthologous  genes:  assume  number  of  nucleotide  substitutions  proportional  to  the  time   that  has  elapsed  since  the  genes  branched  from  their  common  ancestor   o   For  paralogous  genes:  assume  number  of  sub stitutions  proportional  to  the  time  since  the   ancestral  gene  was  duplicated   •   Not  always  accurate  because:   o   Some  portions  of  genome  have  evolved  in  irregular  bursts   o   Same  gene  may  evolve  at  different  rates  in  different  groups  of  organisms   o   The  rate  of  the  clock  may  vary  greatly  from  one  gene  to  another   Differences  in  Clock  Speed   •   If  the  mutated  gene  is  one  critical  for  survival,  the  mutation  will  be  unfavorable  and  gene  changes   will  occur  slowly.  If  the  mutated  gene  is  not  critical  fewer  mutations  will  be  harmful  and  changes   will  occur  more  quickly   Potential  Problems  with  Molecular  Clocks   •   Natural  selection  changes  direction  which  can  lead  to  averaging  out  of  changes,  allowing  this  to  be   an  approximate  marker  of  elapsed  time   •   Estimates  can  be  wrong  because  of  the   assumption  that  clocks  have  been  constant  for  long   periods  of  time   •   By  studying  genes  of  multiple  taxa,  outliers  may  average  out   Applying  a  Molecular  Clock:  Dating  the  Origin  of  HIV   •   HIV  -­‐  1M  first  spread  to  humans  around  1910       26.6  Our  understanding  of  the  tree  of  life  continues  to  change  based  on  new  data   From  Two  Kingdoms  to  Three  Domains   •   3  Domains:  Bacteria,  Eukarya,  and  Archaea   The  Important  Role  of  Horizontal  Gene  Transfer   •   Comparisons  of  complete  genomes  from  the  three  domains  show  that  there  have  been   substantial  movements  of  genes  between  organisms  in  the  different  domains   •   Horizontal  gene  transfer  -­‐-­‐  genes  are  transferred  from  one  genome  to  another  through   mechanisms  such  as  exchange  of  transposable  elements  and  plasmid,  viral  infection,  and  perhaps   fusion  of  organisms       Bio  Chapter  27   Monday,  February  1,  2016   12:27  AM   Chapter  27:  Bacteria  and  Archaea   Masters  of  Adaptation   •   Prokaryotes  are  the  most  abundant  organisms  on  earth   -­‐-­‐  can  adapt  to  a  broad  range  of  habitats       27.1  Structural  and  functional  adaptations  contribute  to  prokaryotic  success   •   Most  prokaryotes  are  unicellular,  typically  very  small   Cell-­‐Surface  Structures   •   Cell  wall  maintains  shape,  protects  cell,  prevents  from  bursting  in  hypotonic  environment   •   Cell  wall  contains  peptidoglycan  -­‐-­‐  polymer  composed  of  modified  sugars  cross -­‐linked  by  short   polypeptides   •   Archaeal  cell  walls  contain  a  variety  of  polysaccharides  and  proteins  but  lack  peptidoglycan   •   Gram  stain  -­‐-­‐  categorize  bacterial  species  according  to  differences  in  cell  wall  composition   o   Gram  positive  -­‐-­‐  simpler  cell  walls  with  large  amount  of  peptidoglycan   o   Gram  negative  -­‐-­‐  less  peptidoglycan  and  structurally  more  complex,  outer  membrane   contain  lipopolysaccharides   •   In  medicine,  gram  negative  more  resistant  than  gram  positive  due  to  outer  membr ane   •   Antibiotics  like  penicillin  inhibit  the  peptidoglycan  cross -­‐linking  resulting  in  a  nonfunctional  cell   wall   •   Capsule  -­‐-­‐  sticky  layer  of  polysaccharide/protein  surrounding  cell  wall  that  enables  prokaryotes  to   adhere  to  their  substrate  or  to  other  individ uals  in  a  colony   •   Endospore  -­‐-­‐  copy  of  original  cells  chromosome  surrounded  by  a  tough,  multilayered  structure;   very  durable;  can  remain  dormant  but  viable  for  centuries   •   Fimbriae  -­‐-­‐  hairlike  appendages  that  allow  prokaryotes  to  stick  to  their  substrate  or  o ne  another;   shorter  and  more  numerous  than  pili   •   Pili  -­‐-­‐  appendages  that  pull  two  cells  together  prior  to  DNA  transfer  from  one  cell  to  the  other   Motility   •   Taxis  -­‐-­‐  directed  movement  toward  or  away  from  a  stimulus  (chemotaxis:  response  to  chemical,   phototaxis:  light)   •   Moving  toward  stimulus  is  positive  taxis,  moving  away  is  negative   •   Flagella  =  most  common  form  of  movement;  flagella  of  the  domains  made  up  of  different  proteins   =  analogous  structures   Evolutionary  Origins  of  Bacterial  Flagella   •   Only  half  of  the  proteins  that  comprise  the  motor,  hook,  and  filament  of  flagella  are  necessary.   This  suggests  that  the  bacterial  flagellum  evolved  as  other  proteins  were  added  to  an  ancestral   secretory  system   o   Exaptation  -­‐-­‐  the  process  in  which  existing  structures  t ake  on  new  functions  through  descent   with  modification   Internal  Organization  of  DNA   •   Less  DNA   •   Most  lack  compartmentalization   •   One  circular  chromosome  with  fewer  proteins   •   Nucleoid  -­‐-­‐  region  of  cytoplasm  not  enclosed  by  a  membrane  that  contains  the  chromosome   •   Plasmids  -­‐-­‐  smaller  rings  of  independently  replicating  DNA  molecules,  most  carry  only  a  few  genes   Reproduction     • Binary  fission  -­‐-­‐  single  prokaryotic  cell  divides  into  2  cells   •   They  are  small,  they  reproduce  by  binary  fission,  and  they  often  have  short  genera tion  times       27.2  Rapid  reproduction,  mutation,  and  genetic  recombination  promote  genetic   diversity  in  prokaryotes   Rapid  Reproduction  and  Mutation   •   Most  genetic  variation  in  sexual  populations  results  from  the  way  existing  alleles  are  arranged  in   new  combinations  during  meiosis  and  fertilization     • New  mutations,  through  rare  on  a  per  gene  basis,  can  increase  genetic  diversity  quickly  in  a   species  with  short  generation  times  and  large  populations   Genetic  Recombination   •   Genetic  recombination   -­‐-­‐  the  combining  of  DNA  from  two  sources   •   Horizontal  gene  transfer   -­‐-­‐  transfer  of  genes  between  organisms  of  different  species   Transformation  and  Transduction   •   Transformation  -­‐-­‐  the  genotype  and  possibly  phenotype  of  a  prokaryotic  cell  are  altered  by  the   uptake  of  foreign  DNA  from  its  surroundings   •   Transduction  -­‐-­‐  phages  carry  prokaryotic  genes  from  one  host  cell  to  another   Conjugation  and  Plasmids   •   Conjugation  -­‐-­‐  DNA  is  transferred  between  two  prokaryotic  cells  (usually  of  the  same  species)  that   are  temporarily  joined   •   In  bacteria,  the  DNA  transfer  is  always  one  way   •   Pilus  of  donor  cell  attaches  to  recipient  and  retracts,  pulling  the  two  cells  together.  A  temporary   mating  bridge  structure  forms  between  the  cells  and  DNA  is  transferred   •   F  factor  -­‐-­‐  25  genes  required  for  the  produ ction  of  a  pili;  (f  for  fertility)   The  F  Factor  as  a  plasmid   + -­‐ •   F  plasmid  -­‐-­‐  cells  containing  this  (F  cells)  function  as  DNA  donors  during  conjugation.  F  are   recipients.  Condition  is  transferrable   The  F  factor  in  the  chromosome   •   A  cell  with  F  factor  built  in to  its  chromosome  is  and  Hfr  cell   •   Hfr  cells  act  as  donor  during  conjugation  with  an  F  cell.  DNA  enters  the  cell  and  homologous   -­‐ regions  of  the  Hfr  and  F  chromosome  may  align  =  segments  of  DNA  are  exchanged  and  recipient   becomes  recombinant   R  Plasmids  and  Antibiotic  Resistance   •   R-­‐plasmids  -­‐-­‐  carry  "resistance  genes"  which  code  for  enzymes  that  specifically  destroy  or   otherwise  hinder  the  effectiveness  of  certain  antibiotics       27.3  Diverse  nutritional  and  metabolic  adaptations  have  evolved  in  prokaryotes   •   Phototrophs  obtain  energy  from  light   •   Chemotrophs  obtain  energy  from  chemicals   •   Autotrophs  need  only  a  carbon  source   •   Heterotrophs  require  at  least  one  organic  nutrient  to  make  other  organic  compounds   The  Role  of  Oxygen  in  Metabolism   •   Obligate  aerobes  -­‐-­‐  must  use  oxygen  for  cellular  respiration  and  cannot  grow  without  it   •   Obligate  anaerobes  -­‐-­‐  are  poisoned  by  oxygen;  some  live  exclusively  by  fermentation,  others  use   anaerobic  respiration   •   Anaerobic  respiration  -­‐-­‐  extract  chemical  energy  using  substances  other  than  oxygen   •   Facultative  anaerobes  -­‐-­‐  use  oxygen  if  it  is  present  but  can  also  carry  out  fermentation  or   anaerobic  respiration  in  an  anaerobic  environment   Nitrogen  Metabolism   •   Nitrogen  is  essential  for  produ ction  of  amino  acids  and  nucleic  acids  in  all  organisms   •   Nitrogen  fixation  -­‐-­‐  conversion  of  atmospheric  nitrogen  to  ammonia   •   Nitrogen  fixing  prokaryotes  can  increase  the  nitrogen  available  to  plants   Metabolic  Cooperation   •   Oxygen  inactivates  the  enzymes  involv ed  in  nitrogen  fixation  so  one  cell  cannot  do  both  at  the   same  time   •   Heterocysts  -­‐-­‐  cells  that  carry  out  only  nitrogen  fixation;  surrounded  by  a  thick  cell  wall  that   prevents  the  entry  of  oxygen     • Biofilms  -­‐-­‐  surface-­‐coating  colonies.  Cells  in  biofilms  secrete  signaling  molecules  that  recruit   nearby  cells,  causing  the  colonies  to  grow  and  produce  polysaccharides  and  proteins  that  stick  the   cells  to  the  substrate       27.4  Prokaryotes  have  radiated  into  a  diverse  set  of  lineages   An  Overview  of  Prokaryotic  Diversity   •   Metagenomics  -­‐-­‐  obtaining  genetic  genomes  from  environmental  samples   •   Due  to  horizontal  gene  transfer,  significant  portions  of  the  genomes  of  many  prokaryotes  are   mosaics  of  genes  imported  from  other  s pecies   Bacteria   •   Includes  every  major  mode  of  nutrition  and  metabolism   Archaea   •   Extremophiles  -­‐-­‐  live  in  extreme  conditions   •   Extreme  halophiles  -­‐-­‐  live  in  highly  salty  environments     • Extreme  thermophiles  -­‐-­‐  thrive  in  very  hot  environments   •   Methanogens  -­‐-­‐  archaea  that  release  methane  as  a  by-­‐product  of  their  unique  ways  of  obtaining   energy       27.5  Prokaryotes  play  crucial  roles  in  the  biosphere   Chemical  Recycling   •   Decomposers  -­‐-­‐  breakdown  dead  organisms  as  well  as  waste  products  and  thereby  unlock   supplies  of  carbon,  nitrogen,  and  other  elements   •   Prokaryotes  can  convert  some  molecules  to  forms  that  can  be  taken  up  by  other  organisms   Ecological  Interactions   •   Symbiosis  -­‐-­‐  an  ecological  relationship  in  which  two  species  live  in  close  contact  with  each  other   •   Host  -­‐-­‐  the  larger  organism  in  a  symbiotic  relationship   •   Symbiont-­‐-­‐  the  smaller  organism  in  a  symbiotic  relationship   •   Mutualism  -­‐-­‐  interaction  in  which  both  species  benefit   •   Commensalism  -­‐-­‐  one  species  benefits  while  the  other  is  neither  harmed  nor  benefitted   •   Parasitism  -­‐-­‐  ecological  relationship  in  which  a  parasite  eats  the  cell  contents,  tissues,  or  body   fluids  of  its  host   •   Pathogens  -­‐-­‐  parasites  that  cause  disease       27.6  Prokaryotes  have  both  beneficial  and  harmful  impacts  of  humans   Mutualistic  Bacteria   •   Bacteria  aid  human  digestion  and  immunity   Pathogenic  Bacteria   •   Exotoxins  -­‐-­‐  proteins  secreted  by  certain  bacteria  and  other  organisms   •   Endotoxins  -­‐-­‐  lipopolysaccharide  components  of  the  outer  membrane  of  gram -­‐negative  bacteria;   released  only  when  the  bacteria  die  and  their  cell  walls  break  down     Bio  Chapter  28   Monday,  February  1,  2016   12:29  AM   Chapter  28:  Protists   Living  Small   •   Protists  -­‐-­‐  mostly  unicellular  eukaryotes       28.1  Most  eukaryotes  a  single-­‐celled  organisms   •   Eukaryotes  have  membrane  bound  organelles   •   Eukaryotes  have  a  well  developed   cytoskeleton  that  provides  structural  support,  enabling  cells  to   have  asymmetrical  form,  change  shape  as  the  feed,  move,  or  grow   Structural  and  Functional  Diversity  in  Protists   •   Most  protists  are  unicellular  but  some  are  colonial  and  multicellular   •   Cellular  functions  carried  out  by  subcellular  organelles   •   Heterotrophs,  photoautotrophs,    and  mixotrophs   •   Mixotrophs  -­‐-­‐  combine  photosynthesis  and  heterotrophic  nutrition   •   All  three  sexual  lifecycles   •   Ongoing  changes  in  our  understanding  of  phylogeny  in  protists   Endosymbiosis  in  Eukaryotic  Evolution   •   Endosymbiosis  -­‐-­‐  a  relationship  between  two  species  in  which  one  organism  lives  inside  the  cell  or   cells  of  another  organism   •   Mitochondria  arose  from  an  alpha  proteobacterium  which  was  engulfed  by  an  archaeal  cell  that   may  have  evolved  to  have  eukaryotic  features   Plastid  Evolution:  A  Closer  Look   •   Heterotrophic  eukaryote  acquired  an  additional  endosymbiont   -­‐-­‐  a  photosynthetic   cyanobacterium  -­‐-­‐  that  then  evolved  into  plastids  =  two  lineages  of  photosynthetic  protists  (algae):   red  algae  and  green  algae   •   Algae  have  a  double  membrane  with  transport  proteins   •   Secondary  endosymbiosis  -­‐-­‐  algae  were  ingested  in  the  food  vacuoles  of  heterotrophic  eukaryotes   and  became  endosymbionts  themselves       28.2  Excavates  include  protists  with  modified  mitochondria  and  protists  with   unique  flagella   •   Excavata  -­‐-­‐  based  on  morphological  studies  of  the  cytoskeleton;  some  members  have  an   "excavated"  feeding  groove  on  one  side  of  the  cell  body   o   Ex.  Diplomonads,  parabasalids,  and  euglenozoans   Diplomonads  and  Parabasalids   •   Lack  plastids   •   Highly  modified  mitochondiria   •   Most  are  anaerobic   •   Diplomonads  -­‐-­‐  have  reduced  mitochondria  called  mitosomes,  lack  functional  electron  transport   chains   o   Ex.  Giardia  intestinalis   •   Parabasalids  -­‐-­‐  have  reduced  mitochondria  called  hydrogenosomes,  anaerobic   -­‐  release  Hydrogen   as  a  by-­‐product   o   Ex.  Trichomonas  vaginalis   Euglenozoans   •   Euglenozoans  -­‐-­‐  includes  predatory  heterotrophs,  photosynthetic  autotrophs,  mixotrophs,  and   parasites;  main  feature:  a   rod  with  either  a  spiral  or  a  crystalline  structure  inside  each  of  their   flagella   Kinetoplastids   •   Kineotoplastids  -­‐-­‐  have  a  single,  large  mitochondrion  that  contains  an  organized  mass  of  DNA   called  a  kinetoplast   •   Feed  on  prokaryotes  in  freshwater,  marine,   and  moist  terrestrial  ecosystems,  species  that   parasitize  animals,  plants,  and  other  protists   o   Ex.  Trypanosoma  -­‐-­‐  sleeping  sickness   Euglenids   •   Euglenid  -­‐-­‐  has  a  pocket  at  one  end  of  the  cell  from  which  one  or  two  flagella  emerge   •   Some  are  mixotrophs,  others  e ngulf  prey  by  phagocytosis       28.3  The  "SAR"  clade  is  a  highly  diverse  group  of  protists  defined  by  DNA   similarities   •   Based  on  whole-­‐genome  DNA  sequences;  includes  stramenopiles,  alveolates,  and  rhizarians   •   Stramenopiles  and  alveolates  originated  through  seco ndary  endosymbiosis   Stramenopiles   •   Stramenopiles  -­‐-­‐  photosynthetic;  characteristic  flagellum  has  numerous  fine  hairlike  projections   paired  with  a  shorter,  smooth  flagellum   Diatoms     • Diatoms  -­‐-­‐  unicellular  algae  with  glass -­‐like  wall  made  of  silicon  dioxide  embedded  in  an  organic   matrix  that  provides  protection  from  being  crushed  by  predators   •   Very  abundant  (evidence  in   diatomaceous  earth  of  the  fossil  layer)   •   During  blooms,  experience  rapid  population  growth  due  to  ample  nutrients  being  available;  they   living  ones  sink  to  the  bottom  and  pump  carbon  to  the  ocean  floor   Golden  Algae   •   Golden  algae  -­‐-­‐  color  due  to  yellow  and  brown  carotenoids;  biflagellated  cells   •   freshwater   •   All  are  photosynthetic,  some  are  mixotrophs  that  use  phagocytosis     • Most  are  unicellular   Brown  Algae   •   Brown  algae  -­‐-­‐  largest  and  most  complex;  all  multicellular;  most  marine   •   Rootlike  holdfast  anchors  the  algae  and  stemlike   stipe,  which  supports  the  leaflike  blades   •   Adaptations  that  allow  their  main  photosynthetic  surfaces  to  be  near  the  surface  of  the  water   Alternation  of  Generations   •   Alternation  of  generations  -­‐-­‐  alternation  of  multicellular  haploid  and  diploid  forms     • Diploid  sporophyte  produces  haploid  spores  (zoospores)  that  move  by  flagella   •   Zoospores  develop  into  haploid  multicellular  gametophytes  wh ich  produce  gametes   •   Union  of  two  gametes  (fertilization)  results  in  a  diploid  zygote  which  grows  and  becomes  a   multicellular  sporophyte   •   Heteromorphic  -­‐-­‐  sporophytes  and  gametophytes  are  structurally  different   •   Isomorphic  -­‐-­‐  sporophytes  and  gametophytes  look  similar  to  each  other  although  they  differ  in   chromosome  number   Alveolates   •   Alveolates  -­‐-­‐  have  membrane  enclosed  sacs  (alveoli)  just  under  the  plasma  membrane   Dinoflagellates   •   Dinoflagellates  -­‐-­‐  cells  reinforced  by  cellulose  plates   •   Two  flagella  located  in  g rooves  in  the  cellulose  plates  make  them  spin  as  they  move   •   Some  are  purely  heterotrophic,  others  are  photosynthetic  ( phytoplankton),  or  mixotrophs   •   During  a  bloom,  create  red  tide  that  turns  the  water  red  and  produce  toxins  that  kill  fish   Apicomplexans   •   Apicomplexans  -­‐-­‐  almost  all  are  parasites  of  animals  that  spread  through  host  as  tiny,  infectious   cells  called  sporozoites     • Apex  of  cell  contains  complex  of  organelles  for  penetrating  host  tissues  and  cells   •   Not  photosynthetic  but  some  have  a  modified  plasti d   •   Complex  lifecycle  requiring  2+  hosts  (ex.   Plasmodium  -­‐-­‐  malaria)   Ciliates   •   Ciliates  -­‐-­‐  named  for  use  of  cilia  to  move  and  feed   •   Most  are  predators   •   Have  two  types  of  nuclei:  tiny  micronuclei  and  large  macronuclei   •   Conjugation  -­‐-­‐  a  sexual  process  in  which  two  individuals  exchange  haploid  micronuclei  but  do  not   reproduce  =  genetic  diversity   •   Reproduce  asexually  through  binary  fission   •   Genes  in  macronucleus  control  functions  of  cell   Rhizarians   •   Amoebas  -­‐-­‐  move  and  feed  through   pseudopodia  (extensions  that  extend  and  are  anchored,  then   cytoplasm  streams  into  it  =  movement)   Radiolarians   •   Radiolarians  -­‐-­‐  have  delicate,  symmetrical  internal  skeletons  made  of  silica   •   Mostly  marine   •   Psuedopodia  radiate  from  central  body   •   Engulfs  smaller  microorganisms  that  become  attached  to   the  pseudopodia   Forams   •   Foraminiferans  -­‐-­‐  porous  shell  called  tests  made  of  single  piece  of  organic  material  hardened  by   calcium  carbonate   •   Marine  and  freshwater   Cercozoams   •   Cercozoams  -­‐-­‐  ameboid  and  flagellated  protists  that  feed  using  threadlike  pseudopodia   •   Marine,  freshwater,  and  soil   •   Most  are  heterotrophs       28.4  red  algae  and  green  algae  are  the  closest  relatives  of  land  plants   •   Archaeplastida  -­‐-­‐  monophyletic  group  including  red  algae,  green  algae,  and  land  plants.     o   Descended  from  ancient  protist  that  engul fed  cyanobacterium   Red  Algae   •   Red  algae  -­‐-­‐  red  due  to  photosynthetic  pigment  phycoerythrin   •   Most  are  multicellular   •   Sexual  reproduction  -­‐-­‐  commonly  have  alternation  of  generations   •   Don’t  have  flagellated  gametes   -­‐-­‐  water  currents  bring  gametes  together   Green  Algae   •   Green  algae  -­‐-­‐  chloroplasts  very  similar  to  plants'   •   Divided  into  two  groups   -­‐-­‐  charophytes  and  chlorophytes   •   Charophytes  most  closely  related  to  land  plants   •   Chlorophytes  -­‐-­‐  larger  size  and  greater  complexity  because   o   Formation  of  colonies   o   Formation  of  true  multicellular  bodies  by  cell  division  and  differentiation   o   Repeated  division  of  nuclei  with  no  cytoplasmic  vision       28.5  Unikonts  include  protists  that  are  closely  related  to  fungi  and  animals   •   Unikonta  -­‐-­‐  includes  animals,  fungi,  and  some  protists   Amoebozoans   •   Amoebozoans  -­‐-­‐  includes  many  species  of  amoeba  that  have  lobe  or  tube  shaped  pseudopodia   rather  than  threadlike  pseudopodia   Slime  Molds   •   Produce  fruiting  bodies  that  aid  in  spore  dispersal   •   Plasmodial  slime  molds   o   Brightly  olored   o   Form  a  mass  called  plasmodium     o   Unicellular  mass  of  cytoplasm  that  is  undivided  by  plasma  membranes  and  contains  many   nuclei  -­‐-­‐  "supercell"  due  to  mitosis  not  followed  by  cytokinesis   o   Plasmodium  extends  pseudopodia  to  engulf  food  particles  by  phagocytosis   -­‐-­‐  if  habitat  dries   up  it  differentiates  into  fruiting  bodies  for  sexual  reproduction   •   Cellular  slime  molds   o   When  food  is  depleted  cells  aggregate  but  remain  separated  by  their  plasma  membranes   -­‐-­‐   form  an  asexual  fruiting  body   o   Cells  forming  stalk  dry  up  but  spores  cells  at  top  sur vive  -­‐-­‐  some  cells  have  mutated  so  they   never  go  to  the  stalk  but  the  stalk  cells  wont  reproduce  with  them   Tubulinids   •   Lobe  or  tube  shaped  pseuodopodia   •   Unicellular   •   Most  are  heterotrophs   Entamoebas   •   Parasites   •   E.  histolytica  is  only  pathogenic  one  -­‐-­‐  causes  dysentery   Opisthokonts   •   Opisthokonts  -­‐-­‐  animals,  fungi,  and  several  groups  of  protists       28.6  Protists  play  key  roles  in  ecological  communities   •   Most  are  aquatic   Symbiotic  Protists   •   Dinoflagellates  are  food  providing  symbiontic  partners  of  coral  polyps  which   build  coral  reefs   •   Protists  in  gut  of  termites  that  allow  them  to  digest  wood   Photosynthetic  Protists   •   Producers  -­‐-­‐  organisms  that  use  energy  from  light  (or  inorganic  chemicals)  to  convert  carbon   dioxide  to  organic  compounds       Bio  Chapter  29   Monday,  February  1,  2016   12:29  AM   Chapter  29:  Plant  Diversity  I:  How  Plants  Colonized  Land   The  Greening  of  Earth   •   Plants  supply  oxygen  and  food  to  terrestrial  animals  and  create  habitats  for  organisms  by   stabilizing  the  soil       29.1  Land  plants  evolved  from  green  algae   Morphological  and  Molecular  Evidence   •   Plants  are  multicellular,  eukaryotic,  photosynthetic  autotrophs   •   Plants  have  cell  wall  made  of  cellulose   •   Have  chloroplasts  with  chlorophyll  a  and  b   •   Similar  to  charophytes   o   Rings  of  cellulose-­‐synthesizing  proteins  in  the  plasma  membrane   o   Structure  of  flagellated  sperm   o   Formation  of  a  phragmoplast   (a  group  of  microtubules  between  daughter  nuclei  of  dividing   cells)   Adaptations  Enabling  the  Move  to  Land   •   Sporopollenin  -­‐-­‐  layer  of  durable  polymer  in  charophytes  that  prevents  exposed  zygotes  from   drying  out   o   Allow  plants  to  grow  out  of  water   Derived  Traits  of  Plants   •   Alternation  of  generations   •   Multicellular,  dependent  embryos   •   Walled  spores  produced  in   sporangia  (produces  the  spores)   •   Multicellular  gametangia  (where  gametes  are  produced)   •   Apical  Meristems  (produces  cells  that  protect  the  plant)   •   Cuticle  -­‐-­‐  covering  of  wax  and  other  polymers  that  acts  as  waterproofing  to  prevent  excess  water   loss  and  protecting  against  microbial  attack     • Stomata  -­‐-­‐  pores  that  allow  the  exchange  of  carbon  dioxide  and  oxygen  between  the  outside  air   and  the  plant   The  Origin  and  Diversification  of  Plants   •   Vascular  tissue  -­‐-­‐  cells  joining  into  tubes  that  transport  water  and  nutrients  throughout  the  plant  =   vascular  plants   •   Nonvascular  plants  often  informally  called  bryophytes     •   Lycophytes  -­‐-­‐  club  mosses  and  their  realtives;  seedless  vascular   •   Monilophytes    -­‐-­‐  ferns  and  their  relatives;  seedless  vascular   •   Grade  -­‐-­‐  group  of  organisms  that  share  key  biological  features;  don’t  necessarily  share  the  same   ancestry   •   Seed  -­‐-­‐  embryo  packaged  with  a  supply  of  nutrients  inside  a  protective  coat   •   Gymnosperms  -­‐-­‐  "naked  seed"  plants;  seeds  are  not  enclosed  in  chambers;  conifers   •   Angiosperms  -­‐-­‐  all  flowering  plants;  seeds  develop  inside  chambers  that  originate  within  flowers       29.2  Mosses  and  other  nonvascular  plants  have  life  cycles  dominated  by   gametophytes   •   Liverworts  -­‐-­‐  phylum  Hepatophyta   •   Mosses  -­‐-­‐  phylum  Bryophyta   •   Hornwarts  -­‐-­‐  phylum  Anthocerophyta   •   Earliest  lineages  to  have  diverged  from  the  common  ancestor  of  land  plants   Bryophyte  Gametophytes   •   Haploid  gametophytes  are  the  dominant  stage  of  the  life  cycle   •   Protonema  -­‐-­‐  mass  of  green,  branched,  once -­‐cell-­‐thick  filaments     • Protonema  produces  buds  which  has  an  apical  meristem  that  generates   gametophores  (gamete   producing  structure)   •   A  protonema  +  a  gametophore  =   the  body  of  a  moss  gametophyte   •   Rhizoids  -­‐-­‐  long,  tubular  single  cells  (liverworts  and  hornworts)  or  filaments  of  cells  (mosses)  that   anchor  the  gametophytes   •   Gametangia  -­‐-­‐  formed  by  gametophytes;  produces  gametes  and  is  covered  with  protective  tissue   o   Archegonium  -­‐-­‐  produce  one  egg   o   Antheridium  -­‐-­‐  produce  one  sperm   •   Bryophyte  sperm  need  water  to  get  to  the  egg  =  most  live  in  moist  environment   •   Many  bryophytes  can  increase  the  number  of  individuals  in  a  local  area  through  various  methods   of  asexual  reproduction   Bryophyte  Sporophytes   •   Cells  contain  plastids  that  are  green  and  photosynthetic   •   Cannot  live  independently   -­‐-­‐  attached  to  and  dependent  on  gametophyte  for  sugars,  amino  acids,   minerals,  and  water     • Smallest  of  all  plant  sporophytes   •   Consist  of  a  foot,  a  seta,  a nd  a  sporangium   o   Foot  -­‐-­‐  embedded  in  the  archegonium,  absorbs  nutrients  from  the  gametophytes   o   Seta  -­‐-­‐  stalk,  conducts  these  materials  to  the  sporangium   o   Sporangium/Capsule  -­‐-­‐  uses  materials  to  produce  spores  by  meiosis   •   Peristome  -­‐-­‐  ring  of  interlocking  tooth-­‐like  structure  found  on  the  upper  part  of  the  capsule.  Open   under  dry  conditions,  close  under  moist.  Allow  spores  to  be  gradually  discharged  into  the  wind   •   Moss  and  hornwort  sporophytes  larger  and  more  complex  than  liverwort   The  Ecological  and  Economic  Importance  of  Mosses     • Help  retain  nitrogen  in  bare  sandy  soil   •   Harbor  nitrogen  fixing  cyanobacteria  increasing  nitrogen  availability   •   absorb  damaging  levels  of  UV  in  deserts  or  higher  altitudes   •   Peat  -­‐-­‐  partially  decayed  organic  material   o   Can  be  used  as  fuel   o   Can  preserve  corpses   o   Carbon  reservoirs  stabilize  atmospheric  CO  concent2ations       29.3  Ferns  and  other  seedless  vascular  plants  were  the  first  plants  to  grow  tall   Origins  and  Traits  of  Vascular  Plants   •   Branched  sporophytes  not   dependent  on  gametophytes  for  nutrition   •   Main  traits  that  characterize  living  vascular  plants:  life  cycles  with  dominant  sporophytes,   transport  in  vascular  tissues  called  Xylem  and  phloem,  and  well -­‐developed  roots  and  leaves,   including  spore-­‐bearing  leaves  called  sporophylls   Life  Cycles  with  Dominant  Sporophytes   •   Sporophytes  are  larger  and  more  complex  than  gametophytes   Transport  in  Xylem  and  Phloem   •   Xylem:  conducts  most  of  the  water  and  minerals   •   Tracheids  -­‐-­‐  tube  shaped  cells  in  the  xylem  that  carry  water  and  minerals  up  from  the  roots   •   Lignin  -­‐-­‐  polymer  that  strenthens  the  cell  walls  of  water -­‐conducting  cells  in  vascular  plants   •   Phloem  -­‐-­‐  tissue  that  has  cells  arranged  into  tubes  that  distribute  sugars,  amino  acids,  and  other   organic  products   •   Lignin  helped  plants  grow  taller   •   Taller  plants  outcompete  shorter  one  for  sunlight  and  their  spores  disperse  farther   Evolution  of  Roots   •   Roots  -­‐-­‐  organs  that  absorb  water  and  nutrient  from  the  soil  &  anchor  vascular  plants   •   May  have  evolved  from  lower  portion  of  the  stem   Evolution  of  Leaves   •   Leaves  -­‐-­‐  increase  the  surface  area  of  the  plant  body  and  are  the  primary  photosynthetic  organ  of   vascular  plants   o   Microphylls  -­‐-­‐  small  spine-­‐shaped  leaves  supported  by  a  single  strand  of  vascular  tissure;   lycophytes  only   o   Megaphylss  -­‐-­‐  leaves  with  highly  branched  vascular  system   Sporophylls  and  Spore  Variations   •   Sporophylls  -­‐-­‐  modified  leaves  that  bear  sporangia   •   Sori  -­‐-­‐  clusters  of  sporangia  produced  by  fern  sporophylls   •   Strobili  -­‐-­‐  groups  of  sporophylls  forming  a  cone-­‐like  structure  in  many  lycophytes  and  most   gymnosperms     • Homosporous  -­‐-­‐  one  type  of  sporangium  that  produces  one  type  of  spore  that  typically  grows  into   a  bisexual  gametophyte;  most  seedless  vascular  plant  species   •   Heterosporous  -­‐-­‐  has  two  types  of  sporangia  and  produces  two  kinds  of  spores   •   Megaspores  -­‐-­‐  develop  into  female  gametophytes;  produced  by  megasporangia  on   megasporophylls     •   Microspores  -­‐-­‐  develop  into  male  gametophytes   Classification  of  Seedless  Vascular  Plants   Phylum  Lycophyta:  Club  Mosses,  Spike  Mosses,  and  Quillworts   •   Most  ancient  group  of  vascular  plants   Phylum  Monilophyta:  Ferns,  Horsetails,  and  Whisk  Ferns  and  Relatives   •   Most  widespread  seedless,  vascular  plants   •   Megaphyll  leaves  and  roots  that  can  branch  at  various  points     • Equisetum  =  horsetails;  found  in  marshy  places  and  along  streams   •   Psilotum  and  Tmesipteris  =  whiskferns;  only  vascular  plants  lacking  true  roots   The  Significance  of  Seedless  Vascular  Plants   •   Contributed  to  large  reduction  in  carbon  dioxide  levels  during  the  carbonifero us  period   •   Seedless  vascular  plants  forming  the  first  forests  eventually  became  coal          


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