Interactions in aqueous systems
Lehninger 8th edition: Chapter 2: p. 43-49; p. 53-64, Chapter 3: p. 70-83; p. 90-92,
Chapter 4: p. 106-125
Water is very important for life. Water makes up ≥70% of an organisms
total weight. It is the medium in which life on earth began. Many
biochemical reactions are studied in aqueous solutions.
There are several types of interactions in aqueous systems;
Hydrogen bonds: This is a bond that occurs between a hydrogen (H)
atom that is covalently bonded to a highly electronegative atom
(Oxygen (O) or nitrogen (N)). This electronegative atom pulls the
electrons towards itself, making it slightly more negative: δ-. The
hydrogen atom then becomes slightly positive: δ+. The positive
hydrogen on one molecule is then attracted to the negative O,
N or F of another molecule. These bonds are also stronger when
donor-hydrogen-acceptor are in a straight line. Examples of this
bond are in water, but they also hold two strands of DNA
together and help proteins maintain shape.
When water becomes ice, the hydrogen bonds have a nearly
perfect tetrahedral arrangement. 1 water molecule can form
multiple hydrogen bonds with other water molecules; 3.4 bonds in
water, 4 bonds in ice.
Ionic interactions: In this bond, oppositely charged ions attract.
However, unlike in hydrogen bonds, the atoms carry full charged rather
than partial charges. Examples are table salt: Na+ bound to Cl-. These
can be strong, but are weaker in aqueous systems, as water molecule
shield the charges.
Van der Waals interactions: The weakest of all interactions. These
bonds occur when adjacent uncharged atoms come close enough that
their outer electron clouds barely touch. This induces charge
fluctuations that result in nonspecific, nondirectional attraction. So this
is a distance-dependant interaction between atoms or molecules.
These are all weak interactions in comparison to:
Covalent bonds: In this bond, atoms share one or more pairs of
electrons.
Individually, interactions such as Hydrogen bonds and Van der Waals
interactions are very weak, but in large numbers they play a crucial role
in maintain structure and functions of biological molecules like proteins
and DNA.
Ways to test the strength of bonds are, for example, is to measure the
distance between atoms with spectroscopy. In this way, the molecules can
be visualized, and it becomes clear that with covalent bonds, the distance
,between the atoms is much smaller (0.0965 nm) than with hydrogen
bonds (0.177 nm). Another way to measure the strength of the bond is to
measure the amount of energy needed to break it apart; 470 kJ/mol for
covalent vs. 23 kJ/mol for hydrogen bonds.
Hydrogen bonds however, are stronger when the donor-hydrogen-acceptor
are in a straight line.
Water as a solvent
Hydrophilic compounds have a strong interaction with water. They are
often polar compounds, which can have ionic interactions. They can be
solved in water very easily. Examples are salts; water dissolves salts by
hydrating and stabilizing ions.
Hydrophobic compounds are repelled by water; nonpolar compounds are
often hydrophobic. These non-polar molecules interact with each other;
we call these hydrophobic interactions. Water molecules stick to each
other, and do not give space to non-polar compounds. Or, to put it
differently, hydrophobic compounds do not form solute-water interactions.
No hydrogen bonds are formed.
There are also molecules with both hydrophobic and hydrophilic
properties; these are called amphipathic. An example of amphipathic
compounds are lipids, which can form micelles. Micelles are a roughly
spherical structure with the hydrophobic tails packed in the centre and the
hydrophilic heads forming the outer surface in contact with water. This
micelle formation happens because the hydrophobic tails are held
together by hydrophobic interactions; they aggregate and reduce the
amount of surface exposed to water. The polar heads face outwards,
where they can interact with water through hydrogen bonding.
To summarize; many biomolecules can easily be dissolved in water due to
their charge or polarity (hydrophilic compounds). Nonpolar compounds
cannot be readily dissolved in water (hydrophobic compounds); they need
nonpolar solvents (e.g. chloroform). Compounds with both hydrophobic
and hydrophilic groups are called amphipathic compounds and have
important biological functions.
Noncovalent (weak) interactions among biomolecules in aqueous solvents
are (from strong to weak); ionic interactions, hydrogen bonds,
hydrophobic interactions and Van der Waals interactions.
Ionization of water, weak acids and weak bases
Strong acids, such as HCl, or H2SO4, or strong bases, such as NaOH, could
destroy cells. Therefor, they are not very useful in the biological system. In
biochemistry, weak bases and acids are found more often. Weak acids and
,bases cannot fully ionize. Instead, they form an equilibrium: A + B ↔ C +
D.
The equilibrium constant, Keq, describes the position of any chemical
reaction. This can be calculated as follows:
[ Products ]eq [ A ]eq ∙ [ B ]eq
K eq = or K eq =
[ Reactants ]eq [ C ] eq ∙ [ D ]eq
A video to explain how to calculate: The Equilibrium Constant
Water is special, as it can both be a weak acid as a weak base: it can
ionize to either H+ (acid) or OH- (base). This can be written in two ways:
H2O ↔ H+ + OH-, or 2H2O ↔ H3O + OH-.
This is because of the hydrogen bonds that form between the water
molecules, that can cause a proton to hop from one molecule to another.
As water has this special equilibrium, it is sometimes referred to as Kw
instead of Keq. A video to explain Kw.
At 25 ⁰C, the Kw = 10-14. In equilibrium, H+ and OH- would have the same
concentration. This could then be written as Kw = 10-14 = [H+]2 = [OH-]2.
Or, simplified: 10-7 = [H+] = [OH-].
This means that the concentration of both H+ and OH- is 10-7 M; a neutral
pH.
Kw is a constant. This also means that if H+ is very low, OH-
must be very low, and the other way around. This is the basis
of the pH scale. At higher temperatures however, Kw
increases because the self-ionization of water is an
endothermic equilibrium. Heating shifts the balance towards
the right; their concentrations are increased, but they are still
equal. The pH thus stays the same.
Weak acids can donate H+. Weak bases can accept an H+.
They are then in equilibrium. An example is the acid Acetic
Acid, CH3COOH, which can donate an H+. It then becomes
CHCOO, which is a base; it can accept an H+.
The total hydrogen concentration [H+] can be measured and is expressed
as the pH of a solution. The p is pH simply means “the negative logarithm
of’. pH = -log [H+]
The pH scale is logarithmic; this means that the difference in a single pH
unit indicates a 10-fold difference in H+ concentration.
, pH measurements are very important in biochemistry, as they affect the
structure and function of proteins (e.g. enzymes). The pH of blood and
urine is also a diagnostic marker.
To summarize: Strong acids/bases are completely ionized in aqueous
solutions. Each acid had a specific tendency to lose protons in a solution,
the stronger the acid, the easier a proton will dissociate. The equilibrium
constant defines this tendency to lose protons. It can also be referred to
as the Ka; the Acid Dissociation constant.
The Pka is an intrinsic property of an acid.
pH can also be expressed in the format of
pKa. The stronger the acid, the higher it’s
Ka, and the lower the pKa.
HA is a general abbreviation for a weak acid. Not to be confused with HAc
(=Acetic Acid).
Henderson-Hasselbalch equation
The equation to calculate the Ka, can be modified to calculate the [H+].
K a =¿ ¿ ¿
With this, the pH can be calculated, and the pKa
pH=−log¿ ¿
pH= p K a + log ¿ ¿ ¿
With this, the pH, pKa, and the ratio proton donor/acceptor can be
calculated.
A video to explain logarithms: Logarithms
The pKa is an intrinsic property of an acid. With this, it can be determined
how relatively strong or weak an acid is.
The pKa can can be measured using an acid-base titration by identifying
the half-equivalence point. The main principle here, is that the pKa is the
pH at which half of the acid has been neutralized. The titration experiment
would go as follows:
A solution of a weak acid, such as HA, with a
known concentration is prepared, and the pH is
measured. It will attempt to achieve the following
equilibrium:
HA ↔ H+ +A-.
A base, such as NaOH, is added slowly, while the
pH is measured. The OH- of this base will combine
with the free H+ and create H2O. As free H+ is
removed, HA will dissociate further.
The pH at which 50% of the weak acid has been
dissociated (the midpoint), is equal to the pKa.
Lehninger 8th edition: Chapter 2: p. 43-49; p. 53-64, Chapter 3: p. 70-83; p. 90-92,
Chapter 4: p. 106-125
Water is very important for life. Water makes up ≥70% of an organisms
total weight. It is the medium in which life on earth began. Many
biochemical reactions are studied in aqueous solutions.
There are several types of interactions in aqueous systems;
Hydrogen bonds: This is a bond that occurs between a hydrogen (H)
atom that is covalently bonded to a highly electronegative atom
(Oxygen (O) or nitrogen (N)). This electronegative atom pulls the
electrons towards itself, making it slightly more negative: δ-. The
hydrogen atom then becomes slightly positive: δ+. The positive
hydrogen on one molecule is then attracted to the negative O,
N or F of another molecule. These bonds are also stronger when
donor-hydrogen-acceptor are in a straight line. Examples of this
bond are in water, but they also hold two strands of DNA
together and help proteins maintain shape.
When water becomes ice, the hydrogen bonds have a nearly
perfect tetrahedral arrangement. 1 water molecule can form
multiple hydrogen bonds with other water molecules; 3.4 bonds in
water, 4 bonds in ice.
Ionic interactions: In this bond, oppositely charged ions attract.
However, unlike in hydrogen bonds, the atoms carry full charged rather
than partial charges. Examples are table salt: Na+ bound to Cl-. These
can be strong, but are weaker in aqueous systems, as water molecule
shield the charges.
Van der Waals interactions: The weakest of all interactions. These
bonds occur when adjacent uncharged atoms come close enough that
their outer electron clouds barely touch. This induces charge
fluctuations that result in nonspecific, nondirectional attraction. So this
is a distance-dependant interaction between atoms or molecules.
These are all weak interactions in comparison to:
Covalent bonds: In this bond, atoms share one or more pairs of
electrons.
Individually, interactions such as Hydrogen bonds and Van der Waals
interactions are very weak, but in large numbers they play a crucial role
in maintain structure and functions of biological molecules like proteins
and DNA.
Ways to test the strength of bonds are, for example, is to measure the
distance between atoms with spectroscopy. In this way, the molecules can
be visualized, and it becomes clear that with covalent bonds, the distance
,between the atoms is much smaller (0.0965 nm) than with hydrogen
bonds (0.177 nm). Another way to measure the strength of the bond is to
measure the amount of energy needed to break it apart; 470 kJ/mol for
covalent vs. 23 kJ/mol for hydrogen bonds.
Hydrogen bonds however, are stronger when the donor-hydrogen-acceptor
are in a straight line.
Water as a solvent
Hydrophilic compounds have a strong interaction with water. They are
often polar compounds, which can have ionic interactions. They can be
solved in water very easily. Examples are salts; water dissolves salts by
hydrating and stabilizing ions.
Hydrophobic compounds are repelled by water; nonpolar compounds are
often hydrophobic. These non-polar molecules interact with each other;
we call these hydrophobic interactions. Water molecules stick to each
other, and do not give space to non-polar compounds. Or, to put it
differently, hydrophobic compounds do not form solute-water interactions.
No hydrogen bonds are formed.
There are also molecules with both hydrophobic and hydrophilic
properties; these are called amphipathic. An example of amphipathic
compounds are lipids, which can form micelles. Micelles are a roughly
spherical structure with the hydrophobic tails packed in the centre and the
hydrophilic heads forming the outer surface in contact with water. This
micelle formation happens because the hydrophobic tails are held
together by hydrophobic interactions; they aggregate and reduce the
amount of surface exposed to water. The polar heads face outwards,
where they can interact with water through hydrogen bonding.
To summarize; many biomolecules can easily be dissolved in water due to
their charge or polarity (hydrophilic compounds). Nonpolar compounds
cannot be readily dissolved in water (hydrophobic compounds); they need
nonpolar solvents (e.g. chloroform). Compounds with both hydrophobic
and hydrophilic groups are called amphipathic compounds and have
important biological functions.
Noncovalent (weak) interactions among biomolecules in aqueous solvents
are (from strong to weak); ionic interactions, hydrogen bonds,
hydrophobic interactions and Van der Waals interactions.
Ionization of water, weak acids and weak bases
Strong acids, such as HCl, or H2SO4, or strong bases, such as NaOH, could
destroy cells. Therefor, they are not very useful in the biological system. In
biochemistry, weak bases and acids are found more often. Weak acids and
,bases cannot fully ionize. Instead, they form an equilibrium: A + B ↔ C +
D.
The equilibrium constant, Keq, describes the position of any chemical
reaction. This can be calculated as follows:
[ Products ]eq [ A ]eq ∙ [ B ]eq
K eq = or K eq =
[ Reactants ]eq [ C ] eq ∙ [ D ]eq
A video to explain how to calculate: The Equilibrium Constant
Water is special, as it can both be a weak acid as a weak base: it can
ionize to either H+ (acid) or OH- (base). This can be written in two ways:
H2O ↔ H+ + OH-, or 2H2O ↔ H3O + OH-.
This is because of the hydrogen bonds that form between the water
molecules, that can cause a proton to hop from one molecule to another.
As water has this special equilibrium, it is sometimes referred to as Kw
instead of Keq. A video to explain Kw.
At 25 ⁰C, the Kw = 10-14. In equilibrium, H+ and OH- would have the same
concentration. This could then be written as Kw = 10-14 = [H+]2 = [OH-]2.
Or, simplified: 10-7 = [H+] = [OH-].
This means that the concentration of both H+ and OH- is 10-7 M; a neutral
pH.
Kw is a constant. This also means that if H+ is very low, OH-
must be very low, and the other way around. This is the basis
of the pH scale. At higher temperatures however, Kw
increases because the self-ionization of water is an
endothermic equilibrium. Heating shifts the balance towards
the right; their concentrations are increased, but they are still
equal. The pH thus stays the same.
Weak acids can donate H+. Weak bases can accept an H+.
They are then in equilibrium. An example is the acid Acetic
Acid, CH3COOH, which can donate an H+. It then becomes
CHCOO, which is a base; it can accept an H+.
The total hydrogen concentration [H+] can be measured and is expressed
as the pH of a solution. The p is pH simply means “the negative logarithm
of’. pH = -log [H+]
The pH scale is logarithmic; this means that the difference in a single pH
unit indicates a 10-fold difference in H+ concentration.
, pH measurements are very important in biochemistry, as they affect the
structure and function of proteins (e.g. enzymes). The pH of blood and
urine is also a diagnostic marker.
To summarize: Strong acids/bases are completely ionized in aqueous
solutions. Each acid had a specific tendency to lose protons in a solution,
the stronger the acid, the easier a proton will dissociate. The equilibrium
constant defines this tendency to lose protons. It can also be referred to
as the Ka; the Acid Dissociation constant.
The Pka is an intrinsic property of an acid.
pH can also be expressed in the format of
pKa. The stronger the acid, the higher it’s
Ka, and the lower the pKa.
HA is a general abbreviation for a weak acid. Not to be confused with HAc
(=Acetic Acid).
Henderson-Hasselbalch equation
The equation to calculate the Ka, can be modified to calculate the [H+].
K a =¿ ¿ ¿
With this, the pH can be calculated, and the pKa
pH=−log¿ ¿
pH= p K a + log ¿ ¿ ¿
With this, the pH, pKa, and the ratio proton donor/acceptor can be
calculated.
A video to explain logarithms: Logarithms
The pKa is an intrinsic property of an acid. With this, it can be determined
how relatively strong or weak an acid is.
The pKa can can be measured using an acid-base titration by identifying
the half-equivalence point. The main principle here, is that the pKa is the
pH at which half of the acid has been neutralized. The titration experiment
would go as follows:
A solution of a weak acid, such as HA, with a
known concentration is prepared, and the pH is
measured. It will attempt to achieve the following
equilibrium:
HA ↔ H+ +A-.
A base, such as NaOH, is added slowly, while the
pH is measured. The OH- of this base will combine
with the free H+ and create H2O. As free H+ is
removed, HA will dissociate further.
The pH at which 50% of the weak acid has been
dissociated (the midpoint), is equal to the pKa.
