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Biomolecules Lecture 1 and 2
Biomolecules Lecture 1 and 2
Instructor
Dr.
Noor
Hassan
Assistant
Prof.
KTH,
Royal
Ins;tute
of
Technology
Stockholm
Sweden
Email:
n_hassank@yahoocom
Amino
Acids,
Pep;des
and
Proteins
Amino
Acids
and
Pep;des
Learning
goals:
• To know the structure and naming of all 20 protein amino acids
• To
know
the
structure
and
proper;es
of
pep;des
and
the
par;cularly
the
structure
of
the
pep;de
bond.
• Ioniza;on behavior of amino acids and pep;des at different pH’s.
• To
know
the
general
pKa’s
of
amino
acids:
their
carboxyls,
aminos,
the
R-‐
group
weak
acids.
Proteins:
Enzymes,
Binding
Proteins,
Structural
Proteins
–
all
made
from
Amino
Acids
Amino
Acids:
Building
Blocks
of
Protein
A
Amino
Acids:
ClassificaBon
Common
amino
acids
can
be
placed
in
five
basic
groups
depending
on
their
R
subsBtuents:
•
Nonpolar,
aliphaBc
(7)
•
AromaBc
(3)
•
Polar,
uncharged
(5)
•
PosiBvely
charged
(3)
•
NegaBvely
charged
(2)
Key to Structure. Covalent Structures and Abbreviations of the “Standard” Amino
Acids of Proteins, Their Occurrence, and the pK Values of Their Ionizable Groups
ConBnued
Spectrophotometry
UV
light
AbsorpBon
by
Proteins
–
due
to
2
Amino
Acids
Cysteine
can
form
Disulfide
Bonds
Uncommon
Amino
Acids
Amino
acids
in
Proteins
Can
be
Reversibly
Modified
A
Non
Protein
Amino
Acids
Toxic
Amino
Acids
The
isoelectronic
point
or
isoionic
point
is
the
pH
at
which
the
amino
acid
does
not
migrate
in
an
electric
field,
i.e.
amino
acid
is
electrically
neutral,
the
zwiUerion
form
is
dominant
(net
zero
charge)
pI
is
given
by
the
average
of
the
pKas
that
involve
the
zwi]erion.
Amino
acids
with
neutral
side
chains
These
amino
acids
are
characterised
by
two
pKas
:
pKa1
and
pKa2
for
the
carboxylic
acid
and
the
amine
respec;vely.
The
isoelectronic
point
will
be
halfway
between,
or
the
average
of,
these
two
pKas,
i.e.
pI
=
1/2
(pKa1
+
pKa2).
At
very
acidic
pH
(below
pKa1)
the
amino
acid
will
have
an
overall
+ve
charge
and
at
very
basic
pH
(above
pKa2
)
the
amino
acid
will
have
an
overall
-‐ve
charge.
For
the
simplest
amino
acid,
glycine,
pKa1=
2.34
and
pKa2
=
9.6,
pI
=
5.97.
Amino
acids
with
acidic
side
chains
• The
pI
will
be
at
a
lower
pH
because
the
acidic
side
chain
introduces
an
"extra"
nega;ve
charge.
So
the
neutral
form
exists
under
more
acidic
condi;ons
when
the
extra
-‐ve
has
been
neutralised.
• For
example:
• aspar;c
acid
shown
below,
the
neutral
form
is
dominant
between
pH
1.88
and
3.65,
pI
is
halfway
between
these
two
values,
i.e.
pI
=
1/2
(pKa1
+
pKa3),
so
pI
=
2.77.
Amino
acids
with
basic
side
chains
The
pI
will
be
at
a
higher
pH
because
the
basic
side
chain
introduces
an
"extra"
posi;ve
charge.
So,
his;dine,
the
neutral
form
is
dominant
between
pH
6.00
and
9.17,
pI
is
halfway
between
these
two
values,
i.e.
pI
=
1/2
(pKa2
+
pKa3),
so
pI
=
7.59.
pKax
+
pKay
pI
=
2
+ CH3 CH3
+ CH3
H3N CO2H H3N CO2 H2N CO2 pKa1
+
pKa2
pI
=
H pKa1 H pKa2 H 2
low pH (2.3) (9.7)
high pH
pI
=
6.0
37
Electrophoresis:
separa;on
of
polar
compounds
based
on
their
mobility
through
a
solid
support.
The
separa;on
is
based
on
charge
(pI)
or
molecular
mass.
+ _
+ _
_ _ _ _ + + + +
Amino
acids
are
linked
together
by
covalent
pep;de
bonds
PepBde
Bond
FormaBon
By
conven;on,
pep;de
sequences
are
wriUen
len
to
right
from
the
N-‐terminus
to
the
C-‐
O R2 O R4 O R6 O terminus
H H H H
N N N N
N N N N
H H H H
R1 O R3 O R5 O R7
CharacterisBcs
of
pepBde
bond
The
amide
(pep;de)
bond
has
C=N
double
bond
character
due
to
resonance
resul;ng
in
a
planar
geometry
O R2 _
H H O R2
N N H H restricts rotations resistant to
N + N
N N hydrolysis
R1 H O R1 H O
amide bond
The
N-‐H
bond
of
one
amide
linkage
can
form
a
hydrogen
bond
with
the
C=O
of
another.
O
H N
R
N H O N H N-‐O
distance
2.85
-‐
3.20
Å
O
R
N H O
R
H N H N op;mal
N-‐H-‐O
angle
is
180
°
O O
Disulfide
bonds:
the
thiol
groups
of
cysteine
can
be
oxidized
to
form
disulfides
(Cys-‐S-‐S-‐Cys)
1/2 O2 H2O NH2
NH2 S CO2H
2 HO2C S
SH
HO2C NH2
H2
R6 O R8 O R10 R9 O R11 O R13
H H H H H H
N N N N N N
N N N N N N
H H H H H H
O O R9 O O O R12 O
HS S
1/2 O2
SH S
R1 O O R5 H2 R1 O O R5
H H H H H H
N N N N N N
N N N N N N
H H H H H H
O R2 O R4 O O R2 O R4 O
Structure
of
a
Simple
PepBde
Proper;es
of
pep;de/protein
depends
on
the
amino
acid
sequence
Gly-‐Lys-‐Ala
Ala-‐Gly-‐Lys
Ser-Gly-Tyr-Ala-Leu or SGYAL
Naming
pepBdes:
start
at
the
N-‐terminus
A
PepBdes:
A
Variety
of
FuncBons
•
Hormones
and
pheromones
–
insulin
(think
sugar)
–
oxytocin
(think
childbirth)
–
sex-‐pepBde
(think
fruit
fly
maBng)
•
NeuropepBdes
–
substance
P
(pain
mediator)
•
AnBbioBcs
–
polymyxin
B
(for
Gram
–
bacteria)
–
bacitracin
(for
Gram
+
bacteria)
48
Secondary
structure
of
proteins
-‐
α
helix
H
bond
between
the
N-‐H
of
every
pep;de
bond
to
the
C=O
of
the
next
pep;de
bond
of
the
same
chain.
R
groups
are
not
involved.
(Pitch)
Secondary
structure
of
proteins
-‐
α
helix
α-helix: 3.6 amino acids per coil, 5.4 Å
C
3.6
AA
5.4
Å
N
50
Secondary
Structural
level
of
Pep;des
and
Proteins.
β-‐sheet:
Two
or
more
extended
pep;de
chain,
in
which
the
amide
backbones
are
associated
by
hydrogen
bonded
N
→
C
an9-‐parallel
loop
R H O R H O R H O R
or
N N N O
turn
N N N N
N
→
C
H O R H O R H O R H O
O H R O H O H R O H
N N N N
O
C
←
N
N N N
R O H R O H R O H R
C
←
N
parallel
N
→
C
O R H O R H O R H O
N
→
C
H
N N N N
N N N O
R H O R H O R H O R
crossover
O R H O R H O R H O
H
N N N N
N N N O
N
→
C
R H O R H O R H O R
N
→
C
51
Secondary
structure
of
proteins
–
β sheet
Polypep;de
chains
are
held
together
by
H
bonds
between
N-‐H
group
of
one
polypep;de
chain
and
C=O
group
of
the
other
chain
(e.g.
in
the
protein
fibroin
-‐
abundant
in
silk)
TerBary
Structure
level
of
Proteins
myoglobin
pdb code: 1WLA
Bacteriorhodopsin
pdb
code:
1AP9
An;-‐parallel
Parallel
β-‐sheets
β-‐sheets
carbonic
anhydrase
of
lec;n
pdb
code:
1QRM
pdb code: 2LAL
TerBary
Structure
of
polypepBdes
and
Proteins.
Pro • Ile • Lys • Tyr • Leu • Glu • Phe • Ile • Ser • Asp • Ala • Ile • Ile • His •Val • His • Ser • Lys
54
Primary
structure
(sequence
of
amino
acids)
determines
the
structure
of
a
protein
Fig.4-‐5:
In
water,
hydrophobic
aa
cluster
inside
a
folded
protein,
away
from
solvent.
Why?
α helices
can
wrap
around
one
another
by
interac;ons
between
their
hydrophobic
side
chains
to
form
a
stable
coiled-‐coil.
[Fig.
4-‐16]
e.g.
α
kera;n
in
the
skin
and
myosin
in
muscles
Ter;ary
structure
of
proteins
• 3D
conforma;on
or
shape
• Depends
on
the
proper;es
of
the
R
groups
of
amino
acid
residues
• Fold
spontaneously
or
with
the
help
of
molecular
chaperones
• Stabilized
by
covalent
and
non-‐covalent
bonds
Molecular
chaperone
proteins
assist
folding
of
other
proteins
[Horton
et
al.
Principles
of
Biochemistry,
2nd
ed.]
Many
proteins
are
composed
of
separate
func;onal
domains
e.g.
bacterial
catabolite
protein
(CAP).
Protein
domain:
a
segment
(100
–
250
aa)
of
a
polypep;de
chain
that
fold
independently
into
a
stable
structure
[Fig.
4-‐19]
Noncovalent
bonds
help
protein
folding
Covalent
disulfide
bonds
between
adjacent
cysteine
side
chains
help
stabilize
a
favored
protein
conforma;on
Quaternary
structure
of
proteins
hemoglobin,
a
protein
in
red
blood
cells,
has
four
sub
units
(two
copies
each
of
α-‐
and
β-‐globins
containing
a
heme
molecule
Proteins
are:
•
coenzymes
- organic
cofactors
-
NAD+
in
lactate
dehydrogenase
•
prostheBc
groups
- covalently
a]ached
cofactors
- heme
in
myoglobin
•
other
modificaBons
Things
to
Know
by
Now
1. Know
Structure
and
chemistry
of
all
20
amino
acids.
2. Approximate
pKa
of
amino
acid
ionizable
groups
and
their
ionizaBon
state
at
different
pH’s.