Transcript Chem 400 Biochemistry I

Properties of water
Polarity
Hydrogen bonding potential
Specific heat, heat of vaporization
Nucleophilic
Ionization
It is the unique combination of properties of water
that make it the perfect solvent for biological
systems. We will discuss each of these properties
in more detail.
Water and pH
Water - one of the most important molecules in life.
 70% of the bodies mass is water
 2/3 of total body water is intracellular (5566% body weight of men and 10% less for
women)
 The rest is interstitial fluid of which 25% is
in the blood plasma.
pH - The body tightly controls both the volume and
pH of water.
 The bicarbonate system is crucial for blood
maintenance
 changes of pH greater than 0.1 are dangerous
and can lead to coma -diabetics
Life on Earth would not be possible
without water
Its chemical and physical properties
actually defy some fundamental laws
of physics
Almost all biochemical reactions
require water!
Water is an ideal biological solvent
Water is close to a tetrahedral shape with the unshared
electrons on the two sp3-hybridized orbital are in two
corners and the hydrogen in others
Compared to a tetrahedron, CH4 (109o) or NH3 the bond
angle is smaller (109.5o and 107o vs.104.5o)
Due to the bent shape of the
molecule, there is an uneven
distribution of electrons.
It is a polar molecule,
-a dipole
Water is a polar molecule
•Water has a dipole
moment
•“like dissolves like”
Oxygen is more electronegative than
hydrogen so there is an uneven
distribution of charge in this H-O bond
Uneven distribution is called a dipole
and the bond is said to be polar
Water has hydrogen bonding
potential
H-bonds are noncovalent, weak
interactions
H2O is both a
Hydrogen donor
and acceptor
One H2O can form
up to four Hbonds
What makes this molecule important?
solvent ability - easily disrupts ionic compounds
– dielectric constant (D) is high (measure of the ability to keep
ions apart)
Coulombs Law - The force of attraction Kq1 q
2
F
=
between two charged pairs
Dr2
What makes this molecule important?
solvent ability - easily disrupts ionic compounds
– dielectric constant (D) is high (measure of the ability to keep
ions apart)
Coulombs Law - The force of attraction Kq1 q
2
F
=
between two charged pairs
– K = proportionality constant
» 8.99 x 109 J.M.C2
– q = charge and sign of ion
– D = 75.5 (water), 24.3 (EtOH)1.9
(Hexane), 2.4 (interior of protein).
Dr2
What makes this molecule important?
solvent ability - easily disrupts ionic compounds
– dielectric constant (D) is high (measure of the ability to keep
ions apart)
Kq q
Coulombs Law - The force of attraction
1 2
F
=
between two charged pairs
Dr2
– large electronegativity creates a
strong ionic type bond (dipole).
– Liquid water has a higher density
than solid water (ice). Is this
normal? Think of why this is
important?
– orderliness - solvating shells
– ability to take place in many
hydrogen bonds (up to 4 at a time)
What makes this molecule important?
solvent ability - easily disrupts ionic compounds
– dielectric constant (D) is high (measure of the ability to keep
ions apart)
Coulombs Law - The force of attraction Kq1 q
2
F
=
between two charged pairs
Dr2
- Strong nucleophile to prevent unwanted attack by
water, proteins often “hide”
reactions from water by creating
a hydrophobic core
Specific heat and heat of
vaporization is high for water due
to extensive H bonding
Water and H-bonds
High specific heat
Lots of heat is needed to break H-bonds
and raise H2O temperature. Therefore,
H2O is a good insulator.
High heat of vaporization
Lots of heat is needed to vaporize H2O.
Therefore, sweat cools.
Other bonds can also be Polar
Fig. 2.2
Water is nucleophilic
Water participates in many chemical reactions
– it is electron rich
– it is a weak nucleophile
– it is present in high concentration
Water weakly ionizes
CO2 buffers our blood
Water reacts with CO2 to form an
important blood buffer
We breath in and out gaseous CO2
In the blood, CO2 reacts with water to
form the buffering compound H2CO3 –
carbonic acid
Disturbances in blood
buffering system leads to
acidosis (pH below 7.1) or
alkalosis (pH above 7.6)
Bleeding in lungs – death!
“a few good men”
CO2 buffers our blood
Primary buffering compounds at physiological pH is H2CO3 (carbonic
acid) and HCO3- (bicarbonate)
CO2 buffers our blood
We will come back to
this after we talk about
pH and buffers
Noncovalent Bonds
The London dispersion force is the
weakest intermolecular force.
temporary attractive force that
results when the electrons in two
adjacent atoms occupy positions
that make the atoms form
temporary dipoles.
sometimes called an induced dipoleinduced dipole attraction.
cause nonpolar substances to
condense to liquids and to freeze
into solids when the temperature
is lowered sufficiently.
Noncovalent Bonds - London forces
Because of the constant motion of the electrons, an atom or molecule
can develop a temporary (instantaneous) dipole when its electrons
are distributed unsymmetrically about the nucleus.
A second atom or molecule, in turn, can be distorted by the
appearance of the dipole in the first atom or molecule (because
electrons repel one another) which leads to an electrostatic
attraction between the two atoms or molecules
Noncovalent Bonds - van
der Waals
the van der Waals force is the attractive or repulsive forces
between molecules (or between parts of the same
molecule) other than those due to covalent bonds or to the
electrostatic interaction of ions with one another or with
neutral molecules
The term includes:
dipole–dipole forces
London (instantaneous dipole–induced dipole) forces
induced-dipole induced-dipole (dispersion forces)
Noncovalent interactions in
biomolecules
Ionic
H-bond
van der Waals
Hydrophobic
Ionic>H-bond,
hydrophobic>van der Waals
Noncovalent Bonds – van der Waals
The major noncovalent
interactions in cells are
electrostatic (ionic),
hydrophobic, hydrogen bonds,
and van der Waals.
Remember:
London forces are minimal unless
tight association occurs
Most covalent bonds are 8 to 10
times stronger yet the overall
shape and effectiveness of
large molecules are due to the
much weaker non-covalent
bonds.
Ionic Bonds or salt bridges... into the
21st century?
 Simple magnetic attraction between
 Carboxy and amino groups, metals…
 The force of attraction (F) depends on distance and
relative shielding
 Water and salts weaken bond
 Strongest single noncovalent bond
Hydrogen bonds
result from the interactions of strong covalent bonds
between hydrogen and a highly electronegative atom (N
and O)
strongest bonds are when the arraignment is linear.
The hydrogen is “shared” by a the covalently bonded atom
and another electronegative atom
You must be able to identify the donor and acceptor
O H
O=C
N
H
O H
O
N H
O
O H
N
N H
N
O=C
Dipolar water
dissociates in
solution
-association of dipolar
water with typical
biological side groups
due to Hydrogen
bonding
-A-hydroxyl groups
-B-keto groups
-C-carboxylate ions
-D-ammonium ions
Van der Waals (dipole-induced interactions)
Next to London dispersion
forces, these are the
weakest of the nonionic
bonds but are important
due to the large number
of van der Waal
interactions in a protein
These bonds originate from
very small dipole moments
generated in atoms as
electrons move around
the nucleus.
Van der Waals
These are small ionic,
dipolar interactions
The energy of the
attraction is related to
the distance between
nuclei
The average separation
between atoms or
molecules is the sum of
the van der Waals radii
Van der Waals
Space filling models use the van der
Waal Radii to depict sizes
van der Waals in nature
The ability of geckos to climb on
sheer surfaces has been attributed
to van der Waals force
A gecko can hang on a glass surface
using only one toe. Efforts continue
to create a synthetic "gecko tape"
that exploits this knowledge
A recent study suggests that water
molecules of roughly monolayer
thickness (present on all surfaces)
also play a role
Hydrophobic interactions
The association of relatively
nonpolar molecular groups
in an aqueous
environment.
Driven by the order of
water entropy
– The lack of
interactions with a
polar molecules with
decreases the
randomness of the
order of water. ( an
increase in entropy)
Hydrophobic interactions
Water forms cage-like structure
around hydrocarbons forming
shells of highly ordered water
– Shell formation is due to
water forming hydrogen bonds
with each other
– Aggregation of hydrophobic
moleculules reduces total
surface area and results in
less order (increase in entropy)
– Minimization of the
hydrophobic portions of the molecule permits the water
max degrees of freedom (a minimization of entropy
increase)
Why are non-polar molecules insoluble in water?
Highly ordered water forms “cages: around
the hydrophobic lipid
Why are non-polar molecules insoluble in water?
A: It is energetically unfavorable to solvate a
non-polar molecule.
Non-polar (hydrophobic) compounds interfere
with the structure of water - HOW?
Water molecules surrounding a hydrophobic
molecule are ordered but cannot make hydrogen
bonds or ionic interactions to the non-polar
molecule.
Highly ordered water forms “cages: around
the hydrophobic lipid
This reduces the entropy (disorder) of water and
is thermodynamically unfavorable and is called
the hydrophobic effect.
Molecular associations are
often accompanied by the
release of water molecules
that are ordered at the
molecular surface.
Release of ordered
molecules is entropically
favorable.
By solvating themselves
through self association,
hydrophobic molecules,
decrease the level of order
of the system (shells of
hydration) entropy is
increased!
Highly ordered water
interacting with enz &
Substrate
Disorded
water
displaced by
interaction
Enzyme - Substrate interaction
stabilized by hydrophobic
interactions - less shells of
hydration for new complex
Thus nonpolar molecules aggregation is not due to attraction to other
hydrophobic compounds but due to inability to interact with water
Thus it is entropically favorable to have several hydrophobic pieces
come together so only on shell is formed. This is the hydrophobic
effect.
Very important in maintaining protein structure
– hydrophobic portions of proteins are solvated by “hiding” inside
the molecule away from the water.
This is the driving force for the formation of ampipathic molecules
forming lipid bilayers membranes and vesicles
The End
Any Questions?