Lecture1-Biomolecules

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Unformatted text preview: BIOC*2580
Lecture
1:
Biological
Macromolecules
 
 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
 half
 of
 the
 course.
 Macromolecules
 are
 by
 comparison
 huge
 ‐
 molar
 mass
 from
 104
 to
 over
 109
 g.mol‐1.

 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.

 
 Reading:
Lehninger’s
Principles
of
Biochemistry,
5th
ed
p.
11‐14
(4th
ed
p.
12‐16,
75‐88)
 
 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
may
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
 semester
 will
 focus
 on
 proteins
and
their
role.
 
 For
example,
myoglobin
is
a
protein
that
stores
 O2
in
 muscle
tissue.
 
 Typical
 protein
 molecules
 have
 masses
 between
 10
 000
 and
 100
 000
 g.mol–1,
 so
 they
 contain
 literally
 thousands
of
atoms.
Myoglobin
is
16
500
g.mol
–1.
 
 Because
 proteins
 and
 other
 macromolecules
 are
 so
 large,
 biochemists
 use
 a
 unit
 called
 the
 kiloDalton
 (kDa).
 
 One
 Dalton
 is
 simply
 1
 g.mol‐1,
 so
 11
 000
 g.mol–1
 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
4
 BIOC*2580
Lecture
1:
Biological
Macromolecules
 
 The
building
block
principle
of
macromolecule
structure
 2 
 
 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–1,
 about
 110
 g.mol–1
 per
 amino
 acid.
 proteins
 are
 between
 10
 and
 10
 000
 kDa

(104
to
107
g.mol‐1).
 
 
 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
4
 BIOC*2580
Lecture
1:
Biological
Macromolecules
 
 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
H2O.
 

 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
H2O
 on
 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
H2O
to
attack.
 
 
 Bonds
formed
by
condensation
and
broken
 by
hydrolysis:


 
 carboxylic
acid
+
amino
group

 

amide
 
 
 aldehyde



+




alcohol






 




glycoside
 
 carboxylic
acid

+

alcohol



 




ester
 Page
3
of
4
 3 BIOC*2580
Lecture
1:
Biological
Macromolecules
 
 Proteins
are
chains
of
amino
acids
 4 
 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
 H2O
in
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
 amino
 acid
 in
 the
 chain
 can
 have
 a
 different
 side
 chain
 R;
 these
 give
 the
 protein
 molecule
as
a
whole
its
unique
properties.
 
 On
 average,
 each
 amino
 acid
 contributes
 about
 110
Da
to
the
molar
 mass
of
a
protein.
 153
 amino
 acids
 make
 up
 the
 16.5
 kDa
 myoglobin
molecule.

 Some
terminology
to
learn:

 
 One
end
of
the
chain
has
an
amino
acid
with
an
uncombined
amino
group,
usually
protonated;
 this
is
called
the
 N‐terminal
amino
acid.
The
other
end
has
an
amino
acid
with
an
uncombined
 carboxylate
group,
and
is
called
the
C‐terminal
amino
acid.

 
 Amino
 acid
 chains
 linked
 in
 this
 way
 are
 called
 peptide
 chains;
 the
 amide
 bonds
 linking
 them
are
called
peptide
bonds.
 
 A
polypeptide
is
a
large
peptide
chain,
usually
the
complete
amino
acid
chain
of
a
protein.
 Typical
proteins
are
several
hundred
amino
acids
long.

 Poly
=
Greek
for
"many"
 
 An
oligopeptide
is
a
smaller
peptide
chain,
often
applied
to
a
fragment
of
a
larger
protein

 Oligo
=
Greek
for
"a
few"
 Page
4
of
4
 ...
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