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BIOC 2580
Pat Martin

BIOC*2580  Lecture  1:  Biological  Macromolecules   Amino  Acids  1 Synopsis:   Molecules   of   interest   to   biochemists   may   be   classified   as  small   molecules   and   macromolecules.   Small   molecules   are   similar   to   those   encountered   in   conventional   organic   chemistry,  and  are  important  in  metabolism,  which  we  deal  with  in  the  second  ha lf  of  the  course.   Macromolecules  are  huge  by  comparison  -­‐  molar  masses  from  10  to  over  10  g.mol .    What  makes   it  possible  to  comprehend  structures  of  this  magnitude  is  their  modular  construction  from  much   simpler  smaller  molecular  units.  The  basis  of  macromolecule  assembly  is  the  reversible  formation   of  certain  kinds  of  bonds,  e.g.  ester  or  amide  bonds  to  link  up  smaller  subunits  into  long  chains.       Proteins  are  chains  of  linked  amino  acids.    Each  amino  acid  has  a  unique  side  chain.  Since  the  α-­‐ amino/α-­‐carboxylate  core  is  constant,  the  side  chain  R  determines  the  specific  properties  of  a   particular  amino  acid  and  the  role  it  plays  in  a  protein.       REVIEW:    CHEM*1040  notes  regarding  electronegativity  and  Lewis  structures  .   Classes  of  molecules  found  in  biochemistry:     Small  molecules   • Sugars,  amino  acids,  nucleotides,  fatty  acids,  simple  carboxylic  acid  derivatives   • Interconversions  of  small  molecules  may  be  used  to  store  or  release  energy,  which  is  the   basis  of  metabolism   • Particular  kinds  of  small  molecules  ma y  serve  as  building  blocks  for   macromolecules     Macromolecules   • Proteins,  made  as  chains  of  amino  acids   • Nucleic  acids,   made  as  chains  of  nucleotides   • Polysaccharides,  made  as  chains  of  simple  sugars     Proteins   form   complex   structures   capable   of   many   functions,   including   structural   components   of   cells,   catalysis   of   reactions   and   communication   processes.   For   this   reason,   the   first   half   of   the   semester   will   focus   on   proteins  and  their  role.     For  example,  myoglobin  (right)  is  a  protein  that  stores  O 2  in   muscle  tissue.     –1 Typical  protein  molecules  have  molecular  masses  between  10  000  and  100  000  g.mol ,  so  they   contain  literally  thousands  of  atoms.  Myoglobin  has  a  molecular  mass  of  16  500  g.mol   .  –1   Because   proteins   and   other   macromolecules   are   so   large,   biochemists  use   a   unit   called   the   -­‐1 –1 kiloDalton  (kDa).    One  Dalton  is  simply  1  g.mol ,  so  11  000  g.mol  becomes  11  kDa.    Typical   proteins  are  therefore  between  10  and  100  kDa,  while  myoglobin  is  16.5  kDa.    The  largest  known   single  protein  molecule  is  titin  at  10  000  kDa.   Page  1  of  7   BIOC*2580  Lecture  1:  Biological  Macromolecules   2 Amino  Acids   The  building  block  principle  of  macromolecule  structure     Proteins  are  chains  of  linked  amino  acids:   Each   protein   has   a   unique   sequence   of   different  amino  acids,  and  a  well-­‐defined   size   and   structure.   The   arrangement   of   amino   acids   in   the   chain   determines   the   properties  and  function  of  the  protein.  A   protein  of  100  amino  acids  has  a  mass  of  about  11  000  g.mol ,  about  110  g.mol  per  amino  acid.   4   7 -­‐1 Proteins  are  between  10  and  10  000  kDa    (10 to  10  g.mol ).       Two  other  kinds  of  macromolecule  will  be  dealt  with  later  in  the  semester:     1. A  polysaccharide  is  a  chain  of  sugars:      Most  polysaccharides,  e.g.  starch,  are   simple  repetitive  structures  of  one  or   two   sugars,   with   no   definite   size.   Some   polysaccharides   are   used   for   storage  of  sugars;  others  act  in  simple   structural  roles.       2. Nucleic  acids  DNA  and  RNA  are  a  bit  more  complex:       The  backbone  is  simple  and  repetitive;  but  different  bases  are  attached  giving  nucleic  acids   unique  and  characteristic  sequences.  The  repeating  unit,  base  +  sugar  +  phosphate  is  called   a  nucleotide.   Page  2  of  7   BIOC*2580  Lecture  1:  Biological  Macromolecules   Amino  Acids   3 Bonding  between  subunits       The   types   of   bond   that   link   subunits   in   macromolecules   are   formed   by   a   process   called   condensation,  since  the  process  involves  elimination   of  the  elements  of  H O.   2     e.g   amino   acids   contain   both   carboxylic   acid   and   amino   groups,   and   these   allow   the   formation   of   an   amide  bond  by  condensation:             The  converse  of  condensation  is  the  attack  of  H O  on   2 the  amide  bond,  which  restores  the  original  carboxylic   acid  and  amino  group  and  thus  unlinks  the  two  units.   This  is  called  hydrolysis.     The  carbonyl  group  C=O  of  the  amide  is  the  point  of   weakness  that  allows  H O  to  at2ack.       Bonds  formed  by  condensation  and  broken   by  hydrolysis:         carboxylic  acid  +  amino  group    n    amide       carboxylic  acid    +    alcohol        n          ester   Page  3  of  7   BIOC*2580  Lecture  1:  Biological  Macromolecules   Amino  Acids  4 Proteins  are  chains  of  amino  acids     Twenty  different  amino  acids  are  found   in  proteins.  They  have  in  common  the   following   structure,   distinguished   by   different  side  chain  groups,  shown  as  R.     Each   amino   acid   has   an  amino   group   and  a  carboxylate  group,  and  can  thus   form   either   end   of   an   amide   bond.   (What's  different  about  the  amino  acid  proline?  -­‐  look  it  up  and  find  out!)     After  removal  of  the  H O  2n  condensation,  the  portion  of  the  amino  acid  found  in  the  chain  is  called   an  amino  acid  residue.     Large  numbers  of  amino  acids  can  be  strung   together  in  a  chain:     Each  
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