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BSCI 1510A - Graham and Patton Note Bundle

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by: Ivy Lee

BSCI 1510A - Graham and Patton Note Bundle BIOL 1510 A

Marketplace > Vanderbilt University > Biology > BIOL 1510 A > BSCI 1510A Graham and Patton Note Bundle
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Notes for an entire BSCI 1510A course with Professor Graham and Professor Patton. These notes were taken during the Fall 2015 semester and include detailed notes and word-for-word transcriptions of...
Biological Sciences
Graham and Patton
Biology, Engineering, biomedical engineering, Bio, bundle, Vanderbilt
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"Clutch. So clutch. Thank you sooo much Ivy!!! Thanks so much for your help! Needed it bad lol"

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This 148 page Bundle was uploaded by Ivy Lee on Thursday January 21, 2016. The Bundle belongs to BIOL 1510 A at Vanderbilt University taught by Graham and Patton in Fall 2015. Since its upload, it has received 32 views. For similar materials see Biological Sciences in Biology at Vanderbilt University.


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Clutch. So clutch. Thank you sooo much Ivy!!! Thanks so much for your help! Needed it bad lol



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Date Created: 01/21/16
BSCI  1510A   Lecture  1  –  Intro   August  26,  2015   1.   Bacteria   2.   Archaea   3.   Eukaryotes   *Common  evolutionary  history  for  all  organisms  =  most  profound  observation  in  biology     Common  features  of  living  things   •   Composed  of  cells   •   Genetic  info,  copied  and  stored  and  used  in  the  same  way   •   Similar  membrane  structures     Cell  Theory:   •   basic  structural  unit  of  life   •   cells  can  only  arise  from  other  cells   •   can  trace  back  to  4  billion  years   •   humans  are  made  of  4  trillion  cells   •   over  200  types  of  cells,  still  discovering   •   same  genetic  information  in  every  cell  even  though  they  are  different  types   •   there  are  specific  genes  that  turn  off/on  in  different  types  of  cells  (transcription)     Sperm  +  Egg   •   8  cell  embryo  is  pluripotent  à  capable  of  forming  into  any  tissue   •   can  remove  one  of  those  8  cells  and  use  for  anything   •   stem  cell   Induced  Pluripotent  Stem  Cells  (IPS)   •   take  adult  cells  and  reverse  to  pluripotent  stem  cell   •   Advantageous  when  populations  of  cells  die   •   Use  your  own  cells  =  more  success,  you  reject  other  people’s  cells       Human  Evolution:   •   Diverged  from  chips  5  million  years  ago  but  still  98%  of  genetic  identity  is  the  same   Genetic  complexity   •   25,000  genes     Membrane  Defines  the  Cell   •   Rather  weak  structure,  without  membrane  you  cannot  have  a  cell   •   Made  of  lipids  and  phospholipids   Prokaryotes   •   Simplest  of  cells   •   Humans  are  more  prokaryotic  cells  than  eukaryotic  cells   •   Have  10^14  bacterial  cells,  more  than  500  bacterial  species   Eukaryotic  cells   •   Size  20  micrometers   •   Bacterium  are  1-­‐2  micrometers   •   Internal  membrane   •   Cytoskeletal  filaments     Protozoa:   •   Innovations  of  internal  compartments   •   Single  cells  can  eat  other  cells   •   3  domains  and  6  kingdoms     Lecture  2  –  Chemistry  of  Life   th August  28 ,  2015     -­‐‑   Chemistry  of  life  is  dominated  by  C,  O,  N,  H  and  their  abilities  to  bond  to  make  larger   molecules   o   They  can  form  strong  bonds  +  diverse  molecules   -­‐‑   Ca,  Mg,  K,  Na,  Cl  exist  as  monoatomic  ions   -­‐‑   P  is  present  as 4PO  in  nucleotides,  RNA,  DNA   o   Intermediate  strength  covalent  bonds   -­‐‑   Life  evolved  in  water   -­‐‑   Water  dominates  physical  properties  of  cells   -­‐‑   Formation  of  bonds  =  release  of  energy   -­‐‑   Thermal  energy  @  body  temperature  =  ~0.6  kcal/mol   -­‐‑   85  kcal/mol  of  energy  is  needed  to  break  C—C  bond     Water   •   Bond  angles  in  water  make  it  polar  in  nature,  O  is  more  electronegative  than  H   •   Dipole  moments  indicate  charge  separation   •   Dispersion  forces  <  dipole  <  hydrogen  bonding  <  ionic  bonding   •   Each  H O 2 can  bond  with  4  other  H O 2  molecules  and  constantly  break  and  form  (fluidity)   •   No  electrons  are  shared  in  hydrogen  bonds   •   Ice  is  less  dense  than  water   •   Water  will  induce  coalescence  of  hydrophobic  compounds  to  minimize  their  surface   area   •   Surface  Tension:  elastic  tendency  of  liquids  to  acquire  least  amount  of  surface  area   possible   o   Water  has  a  greater  attraction  to  itself  than  to  other  surfaces,  liquid  or  air   •   Hydrophobic  effect:  tendency  of  nonpolar  substances  to  exclude  water  molecules  in   aqueous  solutions     Electronegativity:   •   Fluorine  is  most  electronegative     •   Electronegativity  decreases:  O,  Cl,  N,  S,  C,  H,  P…     Van  der  Waal’s  Forces   •   weak,  short-­‐lived  dipole  moments  flicker  back  and  forth  in  nonpolar  compounds   •   One  molecule  can  induce  a  similar  polarity  to  the  flickering  dipole  moment  and  can   weakly  hold  molecules  together   •   These  are  very  weak  &  transient  charges   •   Hydrophobic  effect  is  held  together  by  Van  der  Waal’s  forces     Hydrogen  bonds:   •   N—H  and  C  ==O  hydrogen  bonds  don’t  compete  well  w/  water,  therefore  they  are  used   to  hold  macromolecules  together   •   DNA  strands  are  held  together  by  covalent  bonds  and  2  separate  strands  are  held   together  by  non-­‐covalent  hydrogen  bonds   o   Stable  at  room  temp     Interactions  with  water   •   NaCl  interaction  is  strong  in  air  and  weak  in  water   •   Biological  molecules  are  dissolved  in  H O;  when  they  precipitate  out  they  create   2 pathological  conditions  for  humans  (i.e.  Kidney  stones)     Strength  of  Interactions   •   Covalent  >  electrostatic  >  hydrogen  bonds  >  van  der  Waal’s     o   Strength  depends  on  surroundings     pH   •   pH  affects  ionic  state  of  functional  groups  in  biological  molecules   •   carboxyl,  amino  and  phosphate  are  mostly  ionized  at  neutral  pH   •   Mediate  ionic  and  hydrogen  bonds  b/w  biological  molecules     Bond  Rotation   •   Single  bonds  can  rotate  freely  and  double  bonds  are  restrained  to  single  plane   o   Acids  lose  protons  above  their  pK  level  to  form  (-­‐)  charges   o   Bases  gain  protons  below  their  pK  level  to  form  (+)  charges   -­‐‑   covalent  bonds  link  macromolecule  units  together   -­‐‑   Noncovalent  bonds  link  multiple  proteins  together   -­‐‑   Hormones  synchronized  from  cholesterol  determine  M/F  sex  characteristics     Slideshow:   •   Two  strands  of  the  double  helix  are  held  together  by  non-­‐covalent  hydrogen  bonds   (indicated  with  dotted  lines)   •   The  additive  effect  of  many  hydrogen  bonds  produces  a  very  stable  double  helix   structure   •   [H][OH]  =  10^-­‐14   •   Carboxyl  (-­‐),  amino  (+)  and  phosphate  (-­‐)  are  mostly  ionized  at  neutral  pH     •   Covalent  bonds  link  together  macromolecules   •   Noncovalent  bonds  allow  macromolecules  to  interact  with  each  other     Lecture  3  –  Macromolecules     -­‐‑   Cells  are  densely  packed  with  macromolecules     -­‐‑   Surrounded  by  a  coat  of  carbohydrates   -­‐‑   All  living  cells  are  made  up  of  similar  stuff   -­‐‑   In  all  cells,  nucleic  acids  are  made  of  same  nucleotide  building  blocks   -­‐‑   All  plant  cell  walls  =  polysaccharides  +  carbohydrates  and  they  store  energy  in  form  of   starch   -­‐‑   In  all  cells,  proteins  are  made  of  same  amino  acid  building  blocks  with  phospholipid   membranes   -­‐‑   Carbohydrates  and  polysaccharides  vary  between  species  but  are  assembled  from   monosaccharides  in  similar  ways   -­‐‑   Humans  store  energy  as  glycogen     In  all  cells…   •   Nucleic  acids  are  made  of  the  same  nucleotide  building  blocks     •   Proteins  are  made  of  the  same  amino  acid  building  blocks   •   Membranes  are  made  of  similar  phospholipids   •   Carbohydrates  vary  between  species,  BUT  are  assembled  from  monosaccharides  in  the   same  fashion   •   We  attach  energy  to  proteins   •   Extracellular  matrix  is  rich  in  carbs   •   Plants  have  a  cell  wall  made  of  polysaccharides  and  carbohydrates     Synthesis  of  Macromolecules   •   Biosynthetic  processes  require  an  input  of  energy  to  build  polymers  –  provided  by  ATP     •   Synthesis  reactions  are  condensation  reactions  where  a  water  molecule  is  released  as  1   product   •   Broken  down  through  hydrolysis     Amino  Acids   •   RNA  =  ATP,  CTP,  UTP  &  GTP   •   Biosynthetic  processes  require  an  input  of  energy  to  build  polymers   •   Amino  acids  coupled  with  tRNA  in  ATP  dependent  reactions  and  used  to  build   polypeptides   •   Monosaccharide  +  nucleotides  =  carrier   o   I.e.)  glucose  reacts  with  UTP  to  form  UDP-­‐glucose   •   Covalent  bond  between  nucleotide  and  sugar   o   Glucose  is  transferred  to  growing  polysaccharide  chain     •   Synthesis  reactions  are  condensation  reactions  that  result  in  water  molecule   •   Macromolecules  are  broken  to  monomers  by  hydrolytic  reactions   •   Hydrolysis  à  consuming  a  water  molecule     ATP  Hydrolysis   •   H O 2  +  ATP  <-­‐>  ADP  +  inorganic  phosphate   •   Forward  reaction  has  –  deltaG  value   •   Reverse  reaction  has  +  deltaG  value   •   ATP  =  Adenosine  triphosphate   •   Chemical  energy  to  build  RNA  Polymer  comes  from  high  energy  phosphate  bonds  in   ATP,  UTP,  GTP  and  CTP  (nucleotide  phosphate  precursors)   •       ATP  Roles:     1.   Provides  energy  for  most  of  cell  +  activities  of  cell   2.   One  of  monomers  used  in  synthesis  of  RNA  and  after  conversion  to  deoxyATP  (dATP),   DNA   3.   Regulates  biological  pathways     Energy  Role:     •   3  phosphate  of  ATP  is  removed  by  hydrolysis,  free  energy  is  released  upon  formation   of  hydrolytic  products   •   ATP  stable  @  room  temp   •   Energy  is  required  to  break  terminal  phosphate  linkage   •   More  energy  is  released  as  H2O  molecule  is  consumed  to  form  ADP  and  phosphate   products   •   Average  free  energy  =  ~7.3  kcal/mol   •   Hydrolytic  reaction  has  highly  negative  free  energy   st nd •   Bond  between  1  and  2  phosphates  =  high  energy   RD o   Relatively  speaking  the  bonds  are  weak,  NOT  AS  STRONG  AS  THE  3  BOND     Human  Blood  Type   •   Varying  carbohydrate  structures  in  humans  =  different  blood  types   •   Cells  in  our  bodies  interact  through  carbohydrates     Energy  Storage   •   Mammals  store  energy  as  glycogen,  distribute  as  glucose  in  blood   •   Plants  store  energy  as  starch  +  distribute  as  sucrose  (sap)     Carbohydrate  Roles:   1.   Energy  storage   2.   Structural  support:   a.   Extracellular  matrix  of  animal  cells   b.   Cell  walls  of  plants  and  fungi   c.   Outer  membrane  of  bacteria   d.   Carbohydrates  are  polar  and  attract  water  to  plant  surface  to  prevent   dehydration   3.   Recognition   a.   Cell  to  cell  and  cell  to  pathogen  contact  mediated  by  carbohydrates  called   oligosaccharides  or  polysaccharides  when  linked  together  to  form  a  chain   b.   Protein  in  one  cell  or  virus  binds  to  a  specific  carbohydrate  structure  on  a  second   cell  à  flu  virus  binds  to  sialic  acid  sugar     Glycoproteins:  (important  for  Recognition,  cell  to  cell  contact)   -­‐‑   Protein  with  covalently  attached  chains  of  oligosaccharides   •   cell  surface  proteins  distinguish  species  and  even  individuals  within  species   •   Transplant  antigens  in  carbohydrates  lead  to  organ  rejections       Glucose  vs  Fructose:   •   stereoisomers  of  each  other   •   Glucose  =  aldehyde  sugar   •   Fructose  =  ketone  sugar   •   Both  are  hexose   •   Glucose  is  mostly  present  in  ring  structure  (sometimes  straight)   •   Incorporation  of  polysaccharide  locks  glucose  into  ring  resulting  in  new  chiral  carbon,   ONLY  in  ring   •   Linear  form  of  glucose  has  4  chiral  carbons,  ring  form  =  1  chiral  carbon   •   GLUCOSE  IS  ALWAYS  D-­‐STEREOISOMER   •   Ketose  sugars  will  always  generate  rings  through  reaction  of  carbonyl  @  second  carbon   th and  hydroxyl  @  5  carbon   •   Linear  form  of  glucose  always  has  4  chiral  carbons,  ring  form  =  5   •   Aldehyde  reducing  end  of  sugar   •   Chiral  carbons  have  2  stereoisomers  D  (most  sugars)  and  L  (most  amino  acids)     Stereoisomers   •   Proteins  look  for  specific  orientations  to  bind  to   •   Look  for  specific  stereoality  of  glucose   •   Glyceraldehyde  has  2  molecules  of  same  chemical  formula  and  2  possible  configurations   •   Biological  systems  typically  use  1  stereoisomer  even  when  2  are  possible   •   ALL  living  cells  use  D-­‐glucose     Diversifying  sugars   •   Rotate  around  chiral  carbons  2-­‐5  =  different  sugars   o   A  solution  of  glucose  will  contain  linear  and  ring  forms  AND  alpha  and  beta   stereoisomers  –  alpha  and  beta  get  locked  into  place  when  glucose  is  added  to   polysaccharide  chain     •   Solution  of  glucose  will  contain  linear  &  ring  forms,  alpha  and  beta  isomers   •   Rotation  around  carbon  1  of  aldehyde  will  yield  alpha  and  beta  isomers     Other  sugars   •   Triose,  tetrose,  pentose,  hexose  all  have  3,  4,  5,  6  carbons  respectively   o   All  possible  aldose  sugars   •   Cells  can  produce  many  different  sugars  with  the  same  chemical  formula  that  are   stereoisomers   •   Sialic  acid:  prominent  role  in  flu  infections     o   Flu  first  attacks  sialic  acids  on  cell  surface  proteins   o   Mammals  and  primates  have  slightly  different  structures  of  sialic  acids  which  is   believed  to  have  significance  in  evolution  of  humans   Formation  of  disaccharides   •   Found  in  plant  sap  and  used  to  distribute  chemical  energy     •   Table  sugar  =  mostly  sucrose   •   Only  monosugars  can  be  absorbed  into  intestines   •   High  fructose  corn  syrup  is  made  by  hydrolyzing  sucrose  and  adding  fructose     •   Galactose  and  glucose  can  cross  our  stomach  but  NOT  lactose   •   Lactose  intolerance  means  that  the  enzyme  that  cleaves  lactose  (lactase)  is  missing.   o   Even  though  alpha  and  beta  galactose  is  present  in  the  cell,  the  lactose   synthesizing  enzyme  will  only  use  the  beta  isomer.   •   Table  sugar  =  fructose  +  glucose  connected  through  C1  and  C2   UTP  +  Glucose  à  UDP-­‐glucose  +  Pi   UDP-­‐Glucose  +  fructose  à  Sucrose     Glycogen   •   Glucose  polymer,  short  term  storage  in  mammals’  livers   •   Glucose  =  energy  carrier  in  our  blood  stream  that  is  taken  up  by  cells  +  stored  as   glycogen     •   Enzyme  activates  glucose  by  combining  with  UTP  to  form  UDP  glucose     •   Structure  of  glucose  links  at  alpha  1  4  (linear)  and  alpha  1  6  (branched)  to  save   space     Starch  is  also  a  glucose  polymer  and  rarely  has  branches,  has  a  coiled  structure   •   Glucose  storage  in  plants   •   Glucose  polymer     Cellulose:     •   Cannot  be  digested,  only  by  termites  and  few  other  creatures   •   Linear  structure  to  allow  for  tight  packing   •   Chemical  linkage  allows  for  linear  polymers   •   Chains  of  beta  1à  4  linked  glucose   •   No  branches   •   Most  abundant  material  (aka  wood)   •   Subtle  chemical  differences  in  linkage  of  glucose  polymer  makes  huge  difference  in   properties  of  polysaccharides     Chitin:   •   abundant  and  tough  organic  material   •   Insect  +  crustacean  exoskeletons     Lecture  4:  Proteins  1     -­‐‑   Genes  =  units  of  heredity  and  molecularity   -­‐‑   Take  info  from  RNA  and  use  to  synthesize  protein   Nucleotides  à  amino  acids  à  3D  Protein  structure  (result  of  folding  linear  chains)     •   DNA  to  RNA  to  protein     •   Eukaryotic  cells  express  5000-­‐10,000  proteins     Proteins   •   Enzymes  that  mediate  all  biochemical  reactions   •   Structural  proteins  give  cells  their  shape  and  ability  to  move   •   Regulatory  proteins  help  cells  adapt  to  changing  environment   •   Defense  proteins     •   Carry  out  work  of  cell,  genes  code  for  proteins  that  synthesize  carbohydrates   •   Control  regulation  of  genes,  insure  appropriate  actions  take  place  @  right  time  and   place   •   Nutrient  storage:  seed  proteins,  albumens,  milk  proteins   •   Mobility  and  contractile  proteins:  actin-­‐myosin,  microtubules,  cilia,  flagella     ***  Defined  as  polymers  of  amino  acids  that  adopt  specific  3D  shapes     Collagen:  Principal  structural  protein  in  bone  +  connective  tissues   Carboxypeptidase:  digestive  enzyme   Insulin:  hormone  that  signals  need  to  store  nutrients   Hemoglobin:  oxygen  carrying  protein  in  blood     **  Same  20  amino  acids  are  building  blocks  for  nearly  every  protein  on  earth     Amino  Acids   •   Amino  group,  carboxyl  group  +  hydrogen  side  chain   •   Everything  is  covalently  bonded  to  alpha  carbon  (chiral  center)   •   Amino  acids  in  proteins  are  L-­‐isomers   •   Chemical  synthesis  of  amino  acids  will  give  you  an  equal  mix  of  L  and  D  stereoisomers   •   First  cell  chose  to  use  L-­‐amino  acids  and  all  organisms  inherited  this  trait   •   Only  L  amino  acids  synthesize  ribosomes   •   Polypeptides  grow  from  amino  to  carboxyl  terminals  (in  ribosomes)     Making  Bipolymers:   •   Condensation  reaction  that  produces  a  water  molecule   •   Process  is  reversible,  water  can  be  added  back  into  peptide  bond     Peptide  bond:     •   Chemical  bond  formed  between  2  molecules  when  the  carboxyl  group  of  1  molecule   reacts  with  amino  group  of  another  molecule   Carboxyl  +  amino  group  (4  charges)  à  polypeptide  (2  charges)   -­‐‑   covalently  bonded  by  peptide  bond   -­‐‑   Peptide  bond  (N-­‐H)  has  partial  resonance  structure,  the  single  bond  has  double  bond   character   -­‐‑   No  free  rotation  around  peptide  bond   -­‐‑   Carboxyl  group  carbon  becomes  carbonyl  (C=O)  group   -­‐‑   Carbonyl  and  NH  (amide)  groups  are  still  polar  and  engage  in  hydrogen  bonds     Polypeptide  synthesis:   Step  1:  requires  attaching  amino  acid  to  tRNA  molecule  (ATP  dependent  reaction)  then   transferring  amino  acid  to  the  growing  chain  on  a  ribosome   -­‐‑   unique  sequence  of  amino  acids  is  determined  by  genes   -­‐‑   Rotation  is  possible  on  each  side  of  alpha  carbon     -­‐‑   Peptide  bond  area  can  have  cis  or  trans  configuration  and  will  isomerize  spontaneously   in  solution     o   Trans  configuration  is  more  common  in  3D  structures  of  proteins   *  Sequence  of  amino  acids  determines  secondary  through  quaternary  structures       Lecture  5  –  Proteins  II   September  4 ,  2015     Elements  of  Protein  Structure   1.   Primary  –  sequence  of  amino  acids   2.   Secondary  –  alpha  helix  &  beta  sheet   3.   Tertiary  –  3D  conformation  of  a  polypeptide   4.   Quaternary  –  Subunit  composition   *  Must  assemble  in  correct  stoichiometry       Alpha  Helix   •   Most  compact  structure  that  a  polypeptide  can  form   •   Secondary  structure   •   Hydrogen  bonds  hold  alpha  helix  between  carbonyl  carbon  and  amine   •   3.6  amino  acids  per  turn   •   N  Terminus  =  amino  group   •   C  terminus  =  carboxyl  group   •   Certain  amino  acids  +  sequence  of  amino  acids  can  prevent  alpha  helix  from  forming   Beta  Sheet   •   Arrows  of  beta  sheet  show  direction  of  polarity   •   Most  spread  out  a  polypeptide  can  form   •   Antiparallel  beta  sheets  have  adjacent  backbones  that  run  in  opposite  directions   •   R  groups  alternate  what  side  of  the  antiparallel  sheet  they  are  going  to  be  on     •   Hydrogen  groups  are  on  the  inside  and  R  groups  on  the  outside  to  avoid  disruption  of   hydrogen  bonds   Porins   •   Made  of  beta  sheets  that  form  beta  barrel  structure   •   Hydrophobic  outside  and  hydrophilic  inside  =  water  filled  barrel   •   Beta  turns  reverse  orientation  of  polypeptide  chain   •   Found  in  outer  membrane  of  mitochondria   Ribbon  Diagram   •   Shows  how  polypeptide  backbone  winds  in  3D  space   •   All  proteins  have  different  structures  and  specific  folding  that  is  encoded  in  their  genes   •   Steric  influence  on  protein  folding   •   Ribbon  diagram  doesn’t  show  side  chains   •   Good  model  of  beta  strands   Turn  Structure:   •   Proline  =  beta  breaker,  alpha  helix  will  make  a  little  bend  but  won’t  break   o   Proline  is  a  side  chain  that  forms  a  covalent  bond   •   Correlation  coefficients  for  amino  acids  and  secondary  structural  elements  is  a  table   that  shows  tendency  to  find  amino  acid  side  chains  in  proteins     •   Negative  correlation  =  tend  not  to  find  specific  amino  acid  in  that  structure     4  Ways  of  depicting  tertiary  structure   1.   Backbone   2.   Ribbon   3.   Wire  (ball  and  stick)   4.   Space-­‐filling  –  most  accurate  way  to  view  a  protein   Domain  Organization:   •   Domains  are  completely  functionally  different     •   Not  all  proteins  have  domains,  some  have  1   •   Mutations  in  SRC  protein  indicate  a  likelihood  of  cancer   •   Domains:  independent  folding  unit  of  a  polypeptide  chain   o   Each  can  have  separate  binding   Coiled-­‐coil  domain  =  stabilized  by  hydrophobic  interactions   Amphipathic  helix:  has  hydrophobic  side  chains  spaced  every  3-­‐4  amino  acid  along  the  helix     Protein  Conformation:   •   Some  proteins  are  rigid,  some  undergo  serious  changes  in  order  to  carry  out  their   functions   •   When  conformation  changes,  function  changes   •   Porin  doesn’t  have  a  lot  of  flexibility   •   Calcium  pump  =  highly  dynamic     o   As  it  hydrolyzes  ATP  it  is  changing  conformations     Quaternary  Structure:   •   the  4  subunits  of  hemoglobin  alpha beta 2   2 •   polypeptides  =  subunits   •   subunits  held  together  by  ionic  bonds,  hydrogen  bonds  or  hydrophobic  interactions,   NOT  covalent  bonds   •   2  alphas  and  2  betas  are  each  coded  by  different  genes   •   Red  blood  cells  are  hemoglobin   •   Thousands  of  polypeptides  come  together  to  form  chains     Sickle  Cell  Anemia:   •   Red  blood  cells  hit  points  of  crisis  and  start  to  include  capillaries   •   Assemble  into  multimers  instead  of  tetrimers,  proteins  don’t  have  quaternary  structure     Nuclear  pore  and  ribosomes  are  examples  of  large  multisubunit  complexes   •   Ribosome  has  82  different  polypeptide  subunits  and  4  RNAs     Proteins  as  Higher  Order  Complexes   *  Form  cytoskeleton,  can  regulate  the  structures  in  new  cytoskeleton   •   Alpha  tubulin  and  beta  tubulin  assemble  into  a  heterodimer   Protein  Folding  and  Unfolding   •   When  unfolded,  proteins  will  precipitate  out  of  solution,  driven  by  hydrophobic   interactions   •   Ionic  detergents  disrupt  ionic  bonds  and  hydrophobic  interactions   •   Chaperones:  family  of  proteins  that  aid  in  protein  folding   •   pH  extremes  can  change  ionization  state  of  charged  side  chains   o   @  pH  10  amino  groups  lose  +  charge   o   @  pH  1,  carboxyl  groups  lose  negative  charge   •   Chaperones:  family  of  proteins  that  aid  in  protein  folding   •   Almost  all  genetic  diseases  are  caused  by  mutations  in  protein  structure   Protein  folding  &  Disease   •   Prions  are  infectious  protein  particles   •   Diseases  occur  due  to  aberrant  accumulation  of  misfolded  of  protein  –  Alzheimer’s,   Huntington’s,  Parkinson’s,  Creutzfeldt-­‐Jakob  disease     •   Genetic  diseases  caused  by  misfolding  of  altered  protein  causing  its  loss  of  function:   Cystic  fibrosis,  lysosomal  storage  disorders  (Tay-­‐Sachs),  Hemophilia,  muscular  dystrophy     Lecture  6  -­‐  Proteins  3:  Enzyme  Kinetics     •   RNA  Polymerase  =  enzyme   •   3D  Structure  of  proteins  so  it  can  interact  with  others     •   Can  bind  with  protons  to  macromolecules       Dissociation  Constant  (K )   d •   10 M  =  tight  interaction   •   10 M  =  weak  interaction   •   @  Equilibrium  can  be  calculated  by  [protein][ligand]/  [protein-­‐ligand  complex]   •   Enzymes  drive  our  metabolism     K M   •   Michaelis  constant   •   K foM  biological  interactions  range  from  10^-­‐3  (weak  affinity)  to  10^-­‐12  (strong  affinity)   Vmax:   •   related  to  turnover  number  of  an  enzyme;  #  of  substrate  molecules  converted  to   product  per  unit  time   •   For  every  enzyme  and  every  substrate,  you  can  define  specific  Vmax  for  each  one     •   Km  value  occurs  @  Vmax/2       Enzymes:     •   Catalyze  chemical  reactions     •   Added  to  reactions  to  increase  rate  exponentially   •   Extraordinary  for  the  rate  enhancing  to  do  it  at  ambient  pH,  pressure,  temperature  and   specificity   •   Most  things  are  stable  because  they  require  energy  to  overcome  activation  barrier   •   Ligand  +  enzyme  surfaces  are  a  lock  and  key  fit   •   Substrate  binds  @  active  site  where  catalysis  takes  place  and  only  4  enzymes   •   Ligand  site  is  the  term  used  for  active  site  in  proteins   •   Spontaneous  reactions  have  a  NEGATIVE  free  energy   •   Will  not  change  free  energy  of  a  reaction   •   pH  optimum  of  an  enzyme  usually  matches  the  native  environment  for  the  enzyme   o   Stomach  enzymes  =  very  acidic  pH  optimum   o   Cytosolic  enzymes  =  7.2  pH  optimum           Induced  Fit:   •   Some  proteins  are  rigid  and  some  are  flexible,  binding  site  is  sometimes  not  perfect   •   As  protein  binds  it  will  change  conformation  to  fit  into  the  site     •   This  puts  stress  onto  the  substrate  (like  a  spring)  and  requires  energy  because  bonds   need  to  be  broken     Hydrophobicity:   •   Corresponds  to  2  parts  à  hydrophobic  amino  acid  side  chain  will  bind  to  hydrophobic   parts   Active  Site:   •   complementary  in  shape,  charge,  hydrogen  bonding,  and  corresponds  to  hydrophobicity   •   Protein  folding  pattern  will  bring  active  site  residues  closer  and  into  precisely  structured   binding  pocket   •   Enzymes  best  bind  to  substrates  in  transition  states   •   Hexokinase  =  glycolytic  enzyme  that  adds  phosphate  group  to  glucose     Formation  of  Enzyme  Substrate  complex:   •   Transfer  of  phosphate  group  through  ATP  and  PEP  into  enzyme   •   Specific  binding  site  that  orients  substrates  to  bind  @  active  site   •   Can  alter  the  bond  angle     Inhibitors:   •   Competitive:  Looks  like  substrate  and  bonds  to  substrate,  which  blocks  the  active  site   •   Non-­‐Competitive:  Allosteric  inhibitor,  binds  to  different  place  on  enzyme  and  distorts   the  active  site,  they  bind  to  regulatory  site  on  enzyme   •   Many  drugs  are  inhibitors   •   Irreversible  inhibitors:  form  a  covalent  bond  with  active  site  residue  (amino  acid),  often   toxic   •   Reversible  inhibitors:  come  in  2  classes  based  on  whether  they  compete  for  substrate   binding  to  active  site   •   Allosteric  mechanism:  inhibitor  binds  at  a  site  distant  from  active  site,  common   mechanism  used  to  regulate  activity  of  an  enzyme     Protein  Synthesis:   •   Synthesis  would  stop  if  all  amino  acids  were  converted  to  the  same  thing   •   Feedback  inhibition:  lysine  levels  increase  when  it  is  synthesized  and  can  feedback  and   inhibit  the  starting  enzyme  @  a  certain  point  and  concentration,  important  for   maintaining  homeostasis     Chymotrypsin   •   Cleaves  peptide  bond  immediately  following  a  specific  side  chain   •   Active  site  residues  =  catalytic  residues   •   Negatively  charged  amino  acid  extracts  proton  off  of  syrine  (not  ionizable  amino  acid)   •   When  peptide  chain  leaves,  water  molecule  can  enter  site   •   Results  in  rearrangement  which  generates  a  new  molecule   •   Inhibits  rate  limiting  step     Lovastatin:     •   inhibits  initial  rate  limiting  enzyme  in  cholesterol  synthesis   •   Member  of  a  drug  class  of  statins  used  for  lowering  cholesterol   •   Inhibits  HMB  CoA  reductase   •   Inexpensive  generic  class  of  cholesterol  lowering  drugs  called  statins     Lecture  7:  Metabolism   September  9 ,  2015     •   Synthesis  of  carbohydrates  +  breaking  down  of  food  =  catabolic  break  down   •   Anabolic:  build  up   •   Definition:  Sum  of  all  chemical  reactions  in  cells     Disease  of  Metabolism:  Obesity   •   1985  CDC  started  tracking  data  for  clinical  obesity   •   most  of  diseases  in  US  are  influenced  by  obesity   •   Metabolic  disorders,  in  order  to  fix  need  to  understand  metabolism     Complementary  processes  of  photosynthesis  and  respiration   •   We  rely  on  plants  as  the  foundation  of  our  food  chain  –  photosynthesis   •   Plants  produce  all  food  indirectly  and  directly  –  they  feed  animals   •   Photosynthesis:  Remarkable  ability  of  a  plant  cell  to  take  CO  oxygen  2rom  the   atmosphere  and  convert  to  carbohydrate  and  sugar   o   Very  demanding  energetic  process   •   Using  sugars  to  do  work  =  respiration   o   Sugars  +  O2  à  H O2  +  CO 2   o   Deriving  energy  that  originally  started  as  sunlight  to  drive  all  metabolic  path   points     Carbon  Cycle:   •   Amount  of  CO2  in  our  atmosphere  is  moderated  by  plants   •   We  use  carbohydrates  fixed  by  plants  to  drive  our  energy  needs  and  society’s  needs   •   CO2  that  was  used  thousands  of  years  ago  is  now  fossil  fuels  that  are  used  today   •   29  billion  tons  of  CO2  released  per  year  into  the  atmosphere   •   Potential  for  dire  consequences  for  having  too  much  CO2  and  green  house  gas  in  our   atmosphere     Metabolic  Pathways:   •   Derive  energy  and  building  blocks  for  making  our  body  from  food   •   Macromolecules  =  food  that  we  eat   •   We  derive  amino  acids  from  proteins  and  also  plant  proteins   •   Plants  need  to  have  proteins  to  carry  out  their  metabolism   •   Polysaccharides  =  polymers  of  glucose  =  potatoes,  pasta   •   Ingest  a  polysaccharide  and  break  down  into  building  blocks   o   Same  with  proteins,  we  break  down  into  amino  acids   •   We  can  only  absorb  monomers,  we  can’t  absorb  big  proteins  and  polymers   •   We  can  only  synthesize  half  of  our  amino  acids;  we  can’t  make  a  lot  of  amino  acids   which  we  need  to  get  from  our  diet   •   All  food  that  we  eat  converge  onto  a  common  path  –  (Acetyl-­‐CoA)  which  is  used  and  fed   into  a  TCA  cycle  to  convert  into  another  cycle  and  then  used  to  make  ATP   •   Synthesize  ATP  to  derive  our  anabolic  processes     Cells  oxidize  sugars  in  a  step-­‐wise  fashion   •   A  lot  of  energy  is  stored  in  a  glucose  molecule   •   Glucose  =    -­‐686  kcal  /mol   •   Wood  burning  in  a  fire  releases  CO2  because  it  has  energy  in  it  (abiotic  burning  that  is   incompatible  with  life)   •   Rather  than  using  a  flame  to  overcome  activation  energy  of  glucose,  we  use  enzymes  in   stepwise  synthesis  of  glucose  to  get  the  energy   •   We  convert  glucose  step  by  step  and  release  small  packets  of  energy  along  the  way   (Step  path  in  slide  picture)   •   Put  in  7.2  kcal/mol  to  make  ATP  and  burn  7.2  kcal/mol  when  we  use  ATP   •   Fat  has  even  more  energy     •   Abiotic  burning:  Large  activation  energy  overcome  by  heat  from  fire     Oxidation  of  reduced  organic  molecules  liberates  high  energy  electrons   •   How  do  sugars  store  energy?  In  high  energy  bonds   •   C—H  and  C—C  are  HIGH  energy  bonds   •   Light  match  to  methane  =  heat,  natural  gas  that  we  use  to  heat  our  homes   o   Carries  energy  into  our  homes  and  we  are  releasing  it  by  burning  it   •   Carbon  molecule  is  being  oxidized,  not  completely  losing  but  the  electrons  are  being   drawn  away   •   We  add  electron  density  and  oxygen  in  to  produce  methane,  this  is  reduction  because   the  carbon  is  gaining  electron  density   •   Energy  required  to  break  bond  of  methane  is  LARGER  than  it  is  to  break  bond  of  CO2     Adenosine  Triphosphate  (ATP)   •   Energy  comes  from  oxidation  reactions  described  above     •   ATP  =  transient  storage  form,  constantly  making  and  burning   •   Make  and  consume  350  lbs.  of  ATP  per  day   •   If  we  are  alive,  we  are  maintaining  ATP  levels  much  higher  than  ADP  levels   o   This  is  to  be  metabolically  active   §   Maintaining  a  high  energy  level  so  that  we  can  drive  the  metabolic   processes  of  life   •   Phosphorus  doesn’t  exist  as  a  free  element  in  our  body  it  is  PHOSPHATE     NAD   •   Similarities  to  ATP   •   When  we  remove  electron  from  substrate  they  need  to  go  somewhere,  NAD  molecule  is   a  recipient  of  electrons  when  we  are  breaking  down  catabolic  reactions  (Food)   •   2  electrons  transferred  from  NAD to  NADH  which  carries  those  2  electrons     NADPH   •   Does  the  same  thing,  only  difference  is  there  is  a  phosphate   •   NADH  is  primarily  used  in  catabolic  reactions,  electron  accepter  when  we  break  down   stuff   •   NADPH  is  used  in  anabolic  reactions,  electron  donor  as  we  build  up  our   macromolecules,  when  we  synthesize  a  sugar  or  fat     Coenzyme  A  (CoA)   •   Acetyl  CoA  has  adenine,  ribose  and  2  phosphates.  2  carbons  –  1  fully  reduced  and  1  fully   oxidized   o   We  break  down  most  of  our  food  substances  to  2  carbons   o   See  this  a  lot  when  we  get  to  respiration     •   The  ATP  is  chosen  to  be  central  to  our  metabolism  and  almost  every  living  organism   uses  this     Breakdown  of  Glucose  to  harvest  energy   •   each  glucose  ~=  36  ATPs,  some  make  more  (38)  and  some  make  less  (30)   •   2  ATPs  come  from  glycolysis   •   34  ATPs  come  from  oxidation  of  pyruvate  to  H2O  and  CO2  in  the  mitochondria   •   Some  of  our  stored  energy  is  released  as  heat  when  we  burn  it  and  some  is  harvested  as   ATP     Overview  of  Glycolysis:   •   Cytosolic  pathway:     o   2  ATPs  invested  at  beginning  of  pathway   o   4  ATPs  produced  at  the  end   o   Net  yield  =  2  ATPs  (2  NADHs  and  2  pyruvates  per  glucose  molecule)   •   No  oxygen  is  required,  molecular  oxygen  isn’t  needed   •   Still  burn  glucose  and  make  ATP     Step  1  of  Glycolysis:  Priming  Step   •   Initial  investment   o   Activates  sugar   o   Traps  glucose  in  cell   o   Irreversible  enzymatic  reaction   §   Delta  G  is  large   •   Every  cell  on  our  body  and  most  in  this  planet  have  a  transport  protein  in  plasma   membrane  that  allows  glucose  to  enter   •   Glucose  can  enter  through  that  protein  and  exit   •   Cells  want  to  collect  glucose  to  use  for  metabolism  so  they  trap  it  by  phosphorylating   glucose  to  glucose  6-­‐phosphate  molecule  (it  is  not  glucose,  will  not  flow  back  out  of  the   cell)   o   By  doing  this  you  are  lowering  the  concentration  of  glucose     •   “irreversible”  means  that  hexokinase  cannot  catalyze  reverse  reaction,  doesn’t  mean   the  original  thing  can’t  be  reproduced   •   First  enzyme  that  phosphorylates  glucose  =  hexokinase   o   Can  also  phosphorylate  6  member  sugars     Step  2  of  Glycolysis:  Pay  Off  Step   •   Convert  glucose  to  fructose  through  rearrangement  of  the  bonds   •   Normalize  the  concentration  of  fructose  and  glucose  in  the  cell     Step  3:   •   Phosphofructokinase  (PFK)   •   Kinase  =  enzyme  that  transfers  phosphor  from  ATP  from  some  substrate   •   Producing  a  6  carbon  sugar  that  has  2  phosphates  (NOT  linked  together  so  called  a  1,6   bisphosphate)   •   This  is  the  major  regulated  step  in  glycolysis   •   Rate  limiting  step  –  slowest  step  in  the  pathway   o   Once  you  get  here  the  rest  of  the  process  is  relatively  fast   •   Irreversible  commitment   o   Up  until  this  point  there  are  ways  of  going  back  and  storing  the  sugar,  at  this  step   there  is  no  turning  back  ATP  is  going  to  be  burned   *****  know  all  INTERMEDIATES     Regulation  of  PFK  Activity   •   Feedback  inhibition     •   ATP  is  a  very  important  final  product  and  can  feed  back  when  levels  are  high  enough   and  inhibit  PTK   •   2  sites  that  bind  ATP,  one  is  regulatory  site.  When  ATP  is  in  regulatory  site  it  shuts  off   the  pathway  because  the  cell  doesn’t  need  anymore   •   ADP  stimulates  the  enzyme,  every  time  we  burn  ATP  we  are  producing  ADP       Step  4  &  5   •   Keep  in  mind  we  are  dealing  with  6  carbon  sugar  (fructose  and  glucose)   •   Enzyme  splits  6  carbon  sugar  into  two  3  carbon  sugars     Step  6  &  7   •   Start  to  harvest  energy  from  the  molecules   •   Oxidizing  bond  between  C:H  and  transferring  high  energy  electrons  onto  NAD  molecule   à  then  becomes  NADH  molecule   •   Coupled  to  incorporation  of  another  phosphate  onto  sugar,  the  phosphate  =  inorganic   phosphate  that  is  free  floating  in  the  cytosol     •   3  carbon  sugar  w/  2  phosphates  used  by  an  enzyme  that  will  transfer  P  onto  ADP  and   then  to  ATP   •   Substrate  level  phosphorylation   •   Produce  1  of  the  final  product  =  pyruvate     o   3  carbons   o   important  product  of  this  process   o   two  3  carbon  pyruvate  molecules,  has  reduced  hydrogens  associated  with  it   o   can  burn  this  and  get  another  34  ATPs  from  it   Phosphate  Transfer  potential   •   A  lot  of  other  molecules  that  have  more  energy  than  ATP     Lecture  8  –  Metabolism  II   September  11,  2015     •   Starchy  foods  are  polymers  of  glucose,  we  break  them  down  into  glucose  monomers   and  absorb  them   •   Table  sugar  =  disaccharide     Summary  of  Glycolysis   •   2  ATPs  invested  up  front   •   cytosolic  pathway   •   Typical  concentration  of  ATP  =  4.8  millimolar   •   Total  concentration  of  nucleotides  =  5  mM  and  that  doesn’t  change   •   As  ATP  levels  drop,  ADP  and  AMP  levels  go  up   •   NAD+  +  H+  +  2electrons  <-­‐>  NADH     Pyruvate  and  NADH  in  the  absence  of  oxygen  (exercising)   •   Can  still  produce  ATP  using  glycolysis  when  you  are  exercising  vigorously   •   Produce  lactate  during  that  process   •   Take  end  product  of  glycolysis  and  convert  to  ATP   + •   Generating  a  lot  of  ATP  through  glycolysis  and  NADH  at  the  expense  of  NAD   •   Yeast  cell  produces  Acetaldehyde  and  recycles  ATP     Not  exercising:   •   Pyruvate  goes  into  the  mitochondria       When  ATP  levels  are  high,  the  cell  has  enough  energy  and  as  new  energy  sources  come  in  it   doesn’t  want  to  convert  into  ATP  so  glucose  is  stored  as  glycogen,  goes  through  initial  steps  of   glycolysis  but  then  ATP  inhibits  the  primary  regulated  enzyme  of  pathway  so  that  glucose  is   stored  instead  of  converted     Liver  stores  glycogen  and  then  converts  into  energy  for  you  to  use     ATP  levels  begin  dropping,  AMP  and  ADP  start  to  stimulate  the  primary  regulatory  enzyme  of   the  pathway  and  starts  producing  energy     Overall  Reaction:   C 6 O 12  + 6  2ADP  +  2Pi  +  2NAD (consumed)     3  Enzyme  reactions  in  glycolysis  are  irreversible     Gluconeogenesis   •   Glycolytic  reactions  are  catalyzed  in  irreversible  fashion   •   When  ATP  levels  are  high  and  glucose  levels  are  low,  glucose  is  synthesized  from   pyruvate     The  Cori  Cycle   •   Recycling  of  lactic  acid  during  intensive  muscular  activity   •   Burn  in  muscles  comes  from  acidification  of  cells  and  burn  of  lactic  acid   •   Supplies  energy  to  muscles,  shifts  metabolic  burden  from  muscles  to  liver   •   Anaerobic   •   Animals  burst  into  a  sprint     Lactose   •   breaks  down  into  glucose  and  galactose   •   Break  down  disaccharide  into  monosaccharide  to  be  absorbed   •   Galactose  enters  glycolysis  at  glucose-­‐6-­‐phosphate   Table  Sugar/Sucrose   •   Sucrose  breaks  down  to  glucose  and  fructose   •   Hexokinase  (not  in  liver)  takes  fructose  and  makes  fructose-­‐6-­‐phosphate   o   Above  major  control  point  of  pathway   •   50/50  fructose  and  glucose   •   In  high  fructose  corn  syrup,  they  break  down  sugar  and  then  remix  it  together  in  60/40   ratio  of  fructose   o   Fructose  is  registered  in  our  taste  as  sweeter  than  glucose  and  sucrose   Liver   •   Everything  you  eat  goes  to  the  liver  first,  which  protects  the  body  from  the  toxins  that   we  eat     •   Liver  absorbs  majority  of  fructose  that  we  eat   •   Liver  doesn’t  make  hexokinase,  instead  makes  glucokinase,  which  is  specific  to  glucose   •   Glucokinase  can’t  phosphorylate  fructose,  that  is  separate  reaction   •   Preference  is  to  store  excess  energy  as  fat  because  it  is  a  long  term  energy  source


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