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BIOL 4087 Exam 1
Chapter 2: Water
Overview of Water
Noncovalent interactions
o Hydrogen bonds
o Electrostatic interactions
o Van der Waals interactions
Ionization of water
o pH
o Buffers
Most proteins like to be in a very narrow pH range (blood is)
o Henderson-Hasselbalch equation
Used for pH problems
Water
Water is 60-75% of weight of most organisms (don’t have to know number)
Water is the solvent of life
o Determines the shape and the interactions of biological molecules
Water is a polar molecule
o Fig. 2.1A
o Shape of water molecule is bent structure
o Oxygen is electronegative so has a slight negative charge and hydrogens a
slight positive charge
Noncovalent interactions
o Hydrogen bond is longer which means it is the weaker bond compared to a
covalent bond
o Noncovalent interactions are weaker than covalent bonds because they are
longer
o Covalent bond in water is between the hydrogen and oxygen
470 kj/mol
o Hydrogen bond between two different H2O molecules
23 kj/mol (weaker)
o In ice, there are 4 hydrogen bonds and in liquid water there are about 3.4
hydrogen bonds
o In general:
Noncovalent interactions are weak ( 4-20 kj/mol)
Because they are so weak, they are reversible at body temperature
which causes them to by dynamic
Easy to make and break at body temp (37C)
The sum of many makes a strong interaction
,2
Demonstrated in the structure of DNA, RNA, protein, and
membranes
o In DNA, bases hydrogen bond
Types of Noncovalent interactions:
o Hydrogen bonds
o Electrostatic interactions
o Van der Waals interactions
Hydrogen bonds (~20 kj/mol)
o Hydrogen bonds with nitrogen and oxygen (occasionally with fluorine)
Hydrogen likes to give up electrons and nitrogen and oxygen like to
pull electrons to themselves
o Forms between nitrogen and oxygen (electronegative) and hydrogen is
covalently bound to another nitrogen and oxygen **** know this
If want to know if hydrogen bond, just look for nitrogen or oxygen
o Hydrogen bonds are directional
They are stronger when lined up in straight line when compared to if
the molecule/bond is at an angle
Direction matters!
Linear hydrogen bonds are strongest
o Water is a good solvent for polar molecules (oxygen or nitrogen) (like
dissolves like)
Electrostatic interactions (~20 kj/mol)
o Aka: salt bridges or ionic bonds
o F= QQ/Er^2 (don’t need to learn equation)
r = distance
Q = charge
E = dielectric constant
H2O = 78.5
o Water attenuates the charge so that the force between
water molecules isn’t as strong
o Water masks the chargers and allows salt to dissolve in
water
Benzene = 4.6
Vacuum = 1
As pull charge apart, force between two charges decreases
Opposite charges attract, like charges repel
o Water is a good solvent for ions because of high dielectric constant which
masks the charges from each other
Van der Waals interactions (2-4 kj/mol)
o Transient dipole inducted interactions
o Not a very strong interaction, weak
o As you bring two atoms closer to one another, the transient dipole starts and
induce an attraction but then as you get closer, there is a repulsion
, 3
So there is a sweet spot (Fig. 1-10)
Sweet spot where there is an attraction and no repulsion from the
electron cloud
o Geckos have 500,000 fine hairs on their toes
Each hair has 100s of projections which are called spatulae
Gecko puts foot on the wall and little hairs go into the imperfections
on the walls which forms Van der Waals interactions
If you have 100s X 500,000, enough Van der Waals to lift gecko up wall
Because each little interaction is weak, this allows the gecko to lift up
feet and walk along wall
o HIV protease (enzyme)
Virus needs the protease in order to replicate
Drug companies are intensely interested in Van der Waals because
that’s how they design new drugs
Water and Amphipathic Molecules
Amphipathic is part hydrophobic and part hydrophilic
Sodium stearate
o Stearate is saturated fatty acid
o Charged head group and hydrophobic tail
o If put in water, the sodium dissociates and forms a micelle (cluster)
Carboxylic acid (hydrophilic) can hydrogen bond with water so head
out and tail in
pH
Ionization of water
o Water dissociates into a proton and a hydroxide
o Keq = [H+][OH-]/[H2O]
[H2O] = 55.5M
o Ion product Kw = [H+] [OH-] = 10^-14 at 25C
pH = -log[H+] *** memorize and do calculations***
o pH 4 = 10^-4M of H+
o pH 5 = 10^-5M of H+
Neutral solution
o [H+] = [OH-]
o [H+][H+] = 10^-14
o [H+] = 10^-7M
o pH of 7
Acids and Bases
o Strong acids or bases dissociate when put in water
HCl H+ + Cl-
NaOH Na+ + OH-
o Weak acids and bases partially dissociate
BIOL 4087 Exam 1
Chapter 2: Water
Overview of Water
Noncovalent interactions
o Hydrogen bonds
o Electrostatic interactions
o Van der Waals interactions
Ionization of water
o pH
o Buffers
Most proteins like to be in a very narrow pH range (blood is)
o Henderson-Hasselbalch equation
Used for pH problems
Water
Water is 60-75% of weight of most organisms (don’t have to know number)
Water is the solvent of life
o Determines the shape and the interactions of biological molecules
Water is a polar molecule
o Fig. 2.1A
o Shape of water molecule is bent structure
o Oxygen is electronegative so has a slight negative charge and hydrogens a
slight positive charge
Noncovalent interactions
o Hydrogen bond is longer which means it is the weaker bond compared to a
covalent bond
o Noncovalent interactions are weaker than covalent bonds because they are
longer
o Covalent bond in water is between the hydrogen and oxygen
470 kj/mol
o Hydrogen bond between two different H2O molecules
23 kj/mol (weaker)
o In ice, there are 4 hydrogen bonds and in liquid water there are about 3.4
hydrogen bonds
o In general:
Noncovalent interactions are weak ( 4-20 kj/mol)
Because they are so weak, they are reversible at body temperature
which causes them to by dynamic
Easy to make and break at body temp (37C)
The sum of many makes a strong interaction
,2
Demonstrated in the structure of DNA, RNA, protein, and
membranes
o In DNA, bases hydrogen bond
Types of Noncovalent interactions:
o Hydrogen bonds
o Electrostatic interactions
o Van der Waals interactions
Hydrogen bonds (~20 kj/mol)
o Hydrogen bonds with nitrogen and oxygen (occasionally with fluorine)
Hydrogen likes to give up electrons and nitrogen and oxygen like to
pull electrons to themselves
o Forms between nitrogen and oxygen (electronegative) and hydrogen is
covalently bound to another nitrogen and oxygen **** know this
If want to know if hydrogen bond, just look for nitrogen or oxygen
o Hydrogen bonds are directional
They are stronger when lined up in straight line when compared to if
the molecule/bond is at an angle
Direction matters!
Linear hydrogen bonds are strongest
o Water is a good solvent for polar molecules (oxygen or nitrogen) (like
dissolves like)
Electrostatic interactions (~20 kj/mol)
o Aka: salt bridges or ionic bonds
o F= QQ/Er^2 (don’t need to learn equation)
r = distance
Q = charge
E = dielectric constant
H2O = 78.5
o Water attenuates the charge so that the force between
water molecules isn’t as strong
o Water masks the chargers and allows salt to dissolve in
water
Benzene = 4.6
Vacuum = 1
As pull charge apart, force between two charges decreases
Opposite charges attract, like charges repel
o Water is a good solvent for ions because of high dielectric constant which
masks the charges from each other
Van der Waals interactions (2-4 kj/mol)
o Transient dipole inducted interactions
o Not a very strong interaction, weak
o As you bring two atoms closer to one another, the transient dipole starts and
induce an attraction but then as you get closer, there is a repulsion
, 3
So there is a sweet spot (Fig. 1-10)
Sweet spot where there is an attraction and no repulsion from the
electron cloud
o Geckos have 500,000 fine hairs on their toes
Each hair has 100s of projections which are called spatulae
Gecko puts foot on the wall and little hairs go into the imperfections
on the walls which forms Van der Waals interactions
If you have 100s X 500,000, enough Van der Waals to lift gecko up wall
Because each little interaction is weak, this allows the gecko to lift up
feet and walk along wall
o HIV protease (enzyme)
Virus needs the protease in order to replicate
Drug companies are intensely interested in Van der Waals because
that’s how they design new drugs
Water and Amphipathic Molecules
Amphipathic is part hydrophobic and part hydrophilic
Sodium stearate
o Stearate is saturated fatty acid
o Charged head group and hydrophobic tail
o If put in water, the sodium dissociates and forms a micelle (cluster)
Carboxylic acid (hydrophilic) can hydrogen bond with water so head
out and tail in
pH
Ionization of water
o Water dissociates into a proton and a hydroxide
o Keq = [H+][OH-]/[H2O]
[H2O] = 55.5M
o Ion product Kw = [H+] [OH-] = 10^-14 at 25C
pH = -log[H+] *** memorize and do calculations***
o pH 4 = 10^-4M of H+
o pH 5 = 10^-5M of H+
Neutral solution
o [H+] = [OH-]
o [H+][H+] = 10^-14
o [H+] = 10^-7M
o pH of 7
Acids and Bases
o Strong acids or bases dissociate when put in water
HCl H+ + Cl-
NaOH Na+ + OH-
o Weak acids and bases partially dissociate
