Lecture2&3-AminoAcids

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Unformatted text preview: BIOC*2580
Lectures
2
&
3:
Amino
acid
properties
 
 1 Synopsis:
Each
amino
acid
has
a
unique
side
chain.
Since
the
 α‐amino/
α‐carboxylate
core
is
 constant,
it's
the
side
chain
R
 which
determines
the
specific
properties
of
a
particular
amino
 acid
 and
 what
 role
 it
 plays
 in
 a
 protein.
 Side
 chains
 may
 be
 classed
 according
 to
 polarity,
 hydrogen
bonding
ability
and
ionic
properties.

 
 READ:

Lehninger
5th
ed
p.43‐66,
71‐87
(4th
ed
p.60‐69,
75‐88)

 REVIEW:

CHEM*1040
notes
regarding
electronegativity
and
Lewis
structures.
 
 Structural
layout
of
amino
acids
 
 Amino
 acids
 in
 a
 peptide
 chain
 have
 identical
 backbone
 but
 unique
 side
 chains
 R.
 Specific
 properties
of
a
protein
are
determined
by
 the
particular
functional
groups
present
in
the
side
 chains.

The
amino
acid
glutamate
(Glu
for
short)
is
an
example.
 
 In
 biochemical
 nomenclature,
 Greek
 letters
 identify
the
carbon
atoms
of
the
 structural
 core
 of
 an
 amino
 acid,
 as
 in
 the
example
at
left:

 
 Functional
groups
are
 labeled
 according
 to
 the
 core
 atom
 to
 which
 they
 are
 attached,
 e.g.
 α ‐amino,
 α ‐carboxylate,
 γ ‐carboxylate.
 
 The
 α‐amino
 and
 α‐ carboxylate
 become
 linked
 up
 in
 the
 peptide
bonds
making
up
the
backbone.
 
 The
side
chain
properties
that
have
most
influence
on
the
behaviour
of
the
protein
include:
 
 • polarity

 • hydrogen
bonding
ability

 • charge
 
 There
are
twenty
different
amino
acids
commonly
found
in
protein
chains,
described
by
a
full
 name,
a
three‐letter
abbreviation,
or
a
single
letter
symbol.

Full
structures
of
amino
acids
and
 other
 properties
 can
 be
 found
 in
 Lehninger
 p.73‐75
 (4th
 ed
 p.78‐79)
 and
 on
 the
 amino
 acids
 Euchre
deck
(available
online).
 You
 should
 be
 prepared
 to
 reproduce
 the
 structures
 of
 the
 amino
 acid
 constituents
 of
 proteins
 and
 the
 complete
 covalent
 structures
 of
 proteins,
 and
 to
 know
 the
 single‐
 and
 three‐letter
abbreviations
for
the
amino
acids.
 Page
1
of
6
 BIOC*2580
Lectures
2
&
3:
Amino
acid
properties
 
 Classification
of
amino
acids
by
properties
 
 The
"inverted
pyramid"
below
is
a
convenient
memory
aid
which
groups
amino
acids
 according
to
common
properties
and
structures.

I
have
also
created
a
Euchre
deck
of
the
 amino
acids
and
nucleotides
in
DNA.

If
you
play
euchre,
try
these
cards
out!

 
 6
amino
acids
with
very
non
polar
side
chains:
 
 Alanine
 Valine
 Leucine
 Isoleucine
 Phenylalanine
 Methione
 Ala,
A
 Val,
V
 Leu,
L
 Ile,
I
 Phe,
F

 Met,
M
 
 
 5
amino
acids
with
medium
to
moderately
non
polar
side
chains:
 
 Glycine
 Cysteine
 Proline
 Tryptophan
 Gly,
G

 Cys,
C

 Pro,
P
 Trp,
W
 
 
 
 
 
 
 4
amino
acids
with
very
large
or
very
small
side
chains:
 
 Serine
 Threonine
 Asparagine
 Ser,
S
 Thr,
T
 Asn,
N
 
 
 Page
2
of
6
 Tyrosine
 Tyr,
Y
 
 Glutamine
 Gln,
Q

 
 
 2 BIOC*2580
Lectures
2
&
3:
Amino
acid
properties
 
 3
amino
acids
with
positively
charged
side
chains:
 
 Histidine
 Lysine
 His,
H
 Lys,
K
 
 Arginine
 Arg,
R
 
 
 2
amino
acids
with
negatively
charged
side
chains:
 
 Aspartate
 Glutamate
 Asp,
D
 Glu,
E

 
 
 
 
 
 
 
 And,
just
for
the
record,
here
are
the
4
aces
in
the
euchre
deck:
 
 4
nucleotides
in
DNA
 
 Guanine
 Cytosine
 Thymine
 Adenine
 G
 C
 T
 A
 
 (You
are
NOT
expected
to
reproduce
the
structures
of
the
nucleotides
for
the
midterm)
 
 Page
3
of
6
 3 BIOC*2580
Lectures
2
&
3:
Amino
acid
properties
 
 4 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
 non‐polar
 and
 hydrophobic,
 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
>
C
≈
H 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.
 
 Hydrocarbon
side
chains
are
described
as
hydrophobic,
i.e.
not
attracted
to
H2O,
which
is
very
 polar.
 Hydrocarbon
 side
 chains
 tend
 to
 cluster
 together,
 so
 as
 to
 minimize
 the
 area
 of
 direct
 contact
 between
 hydrocarbon
 and
 H2O,
 a
 property
 known
 as
 the
 hydrophobic
 effect.
 The
 hydrophobicity
of
a
side
chain
is
simply
related
to
the
number
of
CH,
CH2
or
CH3
groups.

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.
 Page
4
of
6
 BIOC*2580
Lectures
2
&
3:
Amino
acid
properties
 
 5 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
a‐carbon:
+NH3CH2CO2‐

 Although
 it's
 a
 non‐polar
 bond,
 it's
 not
 large
 enough
 to
 make
 the
 whole
 molecule
 very
 nonpolar.
 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
 
 ‐CH2‐SH,
 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
 (shown
 on
 the
 right),
 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
‐CONH2
derived
from
the
corresponding
carboxylates
 Asp
and
Glu.

 
 All
four
are
good
hydrogen
bond
formers,
with
little
hydrocarbon,
hence
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).

 
 typical
H‐bond
donors
 R1N–H
‐
‐
‐:OR2
 typical
H‐bond
acceptors
 
 R1O–H
‐
‐
‐:NR2
 
 R1O–H
‐
‐
‐:OR2
 R1N–H
‐
‐
‐:NR2
 
 Page
5
of
6
 BIOC*2580
Lectures
2
&
3:
Amino
acid
properties
 
 6 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
H2O.

H‐bonding
attracts
H2O
to
each
other,
 and
 this
 makes
 water
 a
 liquid
 rather
 than
 a
 gas
 like
 methane,
 CH4,
 whose
 molecules
 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
H2O.
 
 
 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
‐CH2‐CH2‐CH2‐CH2‐NH3+

 
 
 Negatively
charged
amino
acids:
Asp,
Glu

 
 These
side
chains
are
carboxylate
groups,
normally
deprotonated
at
pH
7,
and
very
polar.

 
 Aspartate
side
chain
is


‐CH2‐CO2‐

 
 Glutamate
side
chain
is

‐CH2‐CH2‐CO2‐
 
 Two
 amino
 acids
 with
 oppositely
 charged
 side
 chains
 can
 strongly
 attract
 each
 other
 by
 electrostatic
 interactions
 known
 as
 salt
 bridges
 or
 ion
 pairs.
 
 They
 also
 form
 strong
 H‐bonds
 with
uncharged
H‐bond
donors
or
acceptors
including
H2O.
 
 Page
6
of
6
 ...
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This note was uploaded on 09/21/2011 for the course BIOOC 2580 taught by Professor Douger during the Fall '10 term at University of Guelph.

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