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University of Guelph
BIOC 2580
Pat Martin

BIOC*2580  Lecture  2:  Amino  Acid  Properties  -­‐   Polarity  and  Ionization  1 Synopsis:  Amino  acid  side  chains  may  be  classed  according  to  polarity,  hydrogen  bonding  ability   and  ionic  properties.  Biochemical  reactions  occur  in  aqueous  solution  at  close  to  neutral  pH.   Many   biochemical   substances   such   as   amino   acids   include   weak   acid   groups   such   as   carboxylates,  SH  or  phenolic  OH,  or  weak  bases  such  as  amines  or  some  ring  N  compounds.  The   behaviour  of  such  groups  is  highly  dependent  on  whether  they  are  protonated  or  deprotonated  .   REVIEW:    CHEM*1040  notes  regarding  weak  acids  and  bases.       Amino  acids  with  very  non-­‐polar  side  chains:    Ala,  Val,  Leu,  Ile,  Phe,  Met       These   side   chains   are   dominated   by   hydrocarbon,   i.e.   consists  only  of  C-­‐C  and  C-­‐H  bonds,  e.g.  Valine     Hydrocarbon   is  n on -­‐polar   and ydohoc,i   or   water   avoiding.       Polar  and  non-­‐polar  properties     Polarity   is   a   property   that   occurs   when   atoms   in   a   molecule   have   very   different   electronegativity.  Electronegativity  refers  to  the  tendency  of  a  nucleus  to  hold  electrons  (it   does  NOT  mean  possession  of  negative  charge).     very  electronegative      O  >  N  >  S    HC moderately  electronegative   Since   C   and   H   have   similar   electronegativity,   bonding   electrons   are  evenly  distributed   in   hydrocarbon  regions.  In  contrast,  O  and  N  are  more  electronegative,  and  in  bonds  such  as  O-­‐H   or  C=O,  electrons  shift  towards  the  electronegative  O  atom,  creating  a  dipole.  We  say  therefore   that  C=O  and  O-­‐H  are  polar,  while  C-­‐C  and  C-­‐H  are  non-­‐polar.         Non-­‐polar  groups  interact  well  with  each  other  and  poorly  with  polar  groups.    Hydrocarbon   regions  of  a  molecule  are  also  generally  chemically  unreactive.     Page  1  of  9   BIOC*2580  Lecture  2:  Amino  Acid  Properties  -­‐   Polarity  and  Ionization   2 Hydrocarbon  side  chains  are  described  as  hydrophobic,  i.e.  they  avoid  H O,  which  is  very 2  polar.   Hydrocarbon  side  chains  tend  to  cluster  together,  so  as  to  minimize  the  area  of  direct  contact   between   hydrocarbon   and   H O,   a   proper2y   known   as   the   hydrophobic   effect.   The   hydrophobicity  of  a  side  chain  is  simply  related  to  the  number  of  CH,  CH  or  CH 2groups.   3  Note:   methionine  has  one  S  atom  in  its  hydrocarbon  chain;  however  S  is  much  less  electronegative   than  O,  so  methionine  fits  in  the  very  non-­‐polar  class.         Amino  acids  with  moderately  non  polar  side  chains:  Gly,  Cys,  Pro,  Trp,  Tyr     Glycine  has  a  side  chain  that  is  simply  H  linked  directly  to  the  α-­‐carbon:  +NH CH CO -­‐ 3  2 2 Although  it's  a  non-­‐polar  bond,  it's  not  large  enough  to  make  the  whole  molecule  very  non-­‐ polar.   Note:  The  α-­‐carbon  of  all  other  natural  amino  acids  is  chiral,  with  L-­‐  configuration.     Glycine  is  the  only  non-­‐chiral  structure,  since  it  has  two  identical   H   substituents  on  the  α-­‐carbon.     Cysteine  has  the  side  chain  -­‐CH -­‐SH,2  which  is  not  very  polar,  because   S  is  much  less  electronegative  than  O.     Proline  is  unique  because  the  side  chain  links  back  to  the  -­‐N,  forming   a  5-­‐member  ring.     Tyrosine   and   tryptophan   are   the   most   hydrophobic   amino   acids,   based   on   their   total   surface   area   of   CH   atoms,   however   the   hydrophobicity  is  partly  offset  by  the  presence  of  a  polar  OH  group  in   Tyr  shown  at  right,  or  slightly  polar  NH  group  in  Trp,  so  overall,  these   two  amino  acids  are  only  somewhat  non-­‐polar.       Amino  acids  with  polar,  uncharged  side  chain:    Ser,  Thr,  Asn,  Gln       Ser  and  Thr  both  have  an  -­‐OH  group  on  the  side  chain.       Asn  and  Gln  both  have  amide  side  chains  -­‐CONH  derived  from  the  corresponding  carboxylates   2 Asp  and  Glu.       All  four  are  good  hydrogen  bond  formers,  with  little  hydrocarbon;  hence  they  are  polar.       Hydrogen  bonds  are  electrostatic  interactions  between  a  donor  consisting  of  the  dipole  of  a   polar  O-­‐H  or  N-­‐H  bond  and  an  acceptor,  consisting  of  an  available  lone  pair  of  electrons  on  a   nearby  N  or  O  atom  (which  may  be  on  different  molecule).     Page  2  of  9   BIOC*2580  Lecture  2:  Amino  Acid  Properties  -­‐   Polarity  and  Ionization  3   typical  H-­‐bond  donors   R 1N–H  -­‐  -­‐  2­   typical  H-­‐bond  acceptors     R 1O–H  -­‐  -­‐  2­     R 1O–H  -­‐  -­‐  2­   R 1N–H  -­‐  -­‐  2­     Typical  hydrogen  bonds  (or  H-­‐bonds)  are  about  5-­‐10%  as  strong  as  a  normal  covalent  bond,  and   are   not   permanent   bonds   like   covalent   bonds.   Instead   they   result   in   temporary   attractive   forces  that  help  hold  molecules  together.  Water  molecules  are  excellent  H-­‐bond  donors  and   acceptors;  so  polar  amino  acids  interact  well  with  H O.    H-­‐b2nding  attracts  H O  molecules  to 2   each  other,  and  this  makes  water  a  liquid  rather  than  a  gas  like  methane,  CH ,  whose  molecules   4 do  not  form  H-­‐bonds.     Biochemistry  is  concerned  with  how  molecules  function  in  living  cells,  which  is  an  aqueous   environment.   Hence   it   is   important   to   understand   how   various   biochemical   molecules   will   interact  with  H O. 2      Positively  charged  amino  acids:  Arg,  Lys,  His     These  side  chains  are  weak  bases,  fully  protonated  (Lys,  Arg)  or  partly  protonated  (His)  in   normal  biological  conditions,  pH  7.0-­‐7.4.   Although  the  side  chain  has  a  hydrocarbon  segment,  the  positive  charge  dominates  over  any   hydrophobic  effect.    Charged  amino  acids  are  very  polar.     + e.g.  Lysine  side  chain  is  -­‐CH 2­‐CH -­2CH -­‐C2 -­‐NH2   3     Negatively  charged  amino  acids:  Asp,  Glu       These  side  chains  are  carboxylate  groups,  normally  deprotonated  at  pH  7,  and  very  polar.       -­‐ Aspartate  side  chain  is      -­‐C2 -­‐COO       Glutamate  side  chain  is    -­‐CH -­‐CH -­‐COO   -­‐ 2 2   Two   amino   acids   with   oppositely   charged   side   chains   can   strongly   attract   each   other   by   electrostatic  interactions  known  as  salt  bridges  or  ion  pairs  (see  Lecture  7).    They  also  form   strong  H-­‐bonds  with  uncharged  H-­‐bond  donors  or  acceptors  including  H O.   2       Page  3  of  9   BIOC*2580  Lecture  2:  Amino  Acid  Properties  -­‐   Polarity  and  Ionization   Amino  acids  as  weak  electrolytes     Normal   biochemical   processes   occur   in   aqueous   solution   close   to   neutral   p H;   typical   physiological  pH  is  about  7.2  to  7.4,  and  pH  7.0  is  a  close  approximation.  Certain  functiona  l groups  found  in  biological  molecules,  in  particular  carboxylic  acids  or  amino  groups,  cang  ain  or   lose  H  depending  on  the  availability  of  hydrogen  ions  (or  protons)  in  the  solution.       + + pH  expresses  the  availability  of  H  pH  =  – 10  [H ]       Each  ionic  functional  group,  e.g.  amino  groups  or  carboxylic  acid  groups,  has  a  characteristic   constant,  pKa,  which  expresses  the  tendency  to  gain  or  lose  H.         The  Henderson  Hasselbalch  equation  relates  pH  to  pKa  and  the  state  of  ionization  :     deprotonated ⎧ [A ] ________________ pH=pK +log a 10 ⎨ [HA] }   protonated     ⎩   The  Henderson-­‐Hasselbalch  equation  allows  one  to  do  the  calculations  needed:       1. to  determine  the  pH  given  the  ionic  conditions  of  the  surroundings;   if  pK  and  the   € concentrations  are  known,  pH  can  be  calculated.   2. to  determine  the  degree  of  protonation  or  deprotonation  of  an  ionizable  functional   group  at  a  given  pH.  If  the  pH  aad  pK  are  known  ratio  of  concentrations  can  be   calculated,  and  this  means  we  can  work  out  what  the  state  of  an  "ionic"  functional  group   actually  is  at  a  given  pH.       For  each  amino  acid,  there  is   • an  α-­‐carboxylic  acid  (typical  pK  2.4 a ±  0.5)   • an  α-­‐amino  group  (typical  pK  9.6 a±  0.5)   • certain  amino  acids  also  have  a  side  chain  which  may  be  charged   o Not  all  amino  acids  have  a  side  chain  that  bears  a  charge!!     Exact  pK a  values  for  each  of  the  20  amino  acids  can  be  found  in  Lehninger  p.  73       Page  4  of  9   BIOC*2580  Lecture  2:  Amino  Acid  Properties  -­‐   Polarity  and  Ionization   The  Henderson-­‐Hasselbalch  equation  is  used  to  calculate  the  state  of  each  group  at  pH  7.0   ⎧ [A ] pH=pK +log a 10 ⎨ [HA] }       ⎩     Given  pK a  =  2.4  for  the  α-­‐carboxylic  acid  group,  we  can  calculate  the  ratio  of  anionic  carboxylate   € -­‐COO  to  neutral  carboxylic  acid  -­‐COOH  when  pH  =  7.0:       This  indicates  that  the  vast  majority  of  α-­‐carboxylic  acid  groups  are  fully  deprotonated  (i.e.  have   lost  H )  and  exist  in  the  carboxylate  ion  state  at  pH  7.0.     Given  pK a  =  9.6  for  the  α-­‐amino  group,     This  indicates  that  the  α-­‐amino  group  is  essentially  fully  protonated  (has  gained  H )  and  exists  in   + the  –NH 3  state  at  pH  7.0.     The  backbone  portion  of  a  free  amino  acid  at  pH  7  is  therefore  best  represented  as   + NH 3-­‐CHR-­‐COO -   When  an  amino  acid  is  linked  up  as  part  of  a  peptide  chain,  the  situation  is  di   -­‐  Theα amino   groups   and   α-­‐carboxylate   groups   combine   to   form   amide   or   peptide   bonds.   When   combined   as   an   amide,   the   α-­‐amino   groups   and   α-­‐carboxyl
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