Medical Biochemistry
Section 2 – chapter 2
I. Water
About 60% percent of the body weight in adults is water. 60% of the body water is
intracellular and 40% extracellular. Extracellular includes plasma and interstitial water.
Water has a dipolar nature which allows it to form hydrogen bonds, this property is
responsible for the role of water as a solvent. These are formed by electrons from the
oxygen atom that are unshared and give the oxygen atom a negative charge. The hydrogen
atoms are therefore positively charged. A hydrogen bond is defined as a weak noncovalent
bond between the hydrogen of one molecule and the more electronegative acceptor of the
other. So, organic molecules containing a lot of electronegative atoms can readily dissolve in
water.
Both extra- and intracellular fluids contain elektrolytes, a general term applied to
bicarbonate and inorganic anions and cations. They are unevenly distributed over the two
compartments and this distribution is mainly maintained by energy-requiring pumps.
Water is distributed between the different compartments according to the concentration of
solutes (proteins, ions etc.); this is called the osmolarity. Water can freely move between
the two compartments through the semipermeable membranes, but solutes cannot. Thus,
water will move from a compartment with low concentrations of solutes to a compartment
with high concentrations of solutes. The force it would take to keep water from moving
across the membrane under these conditions is called the osmotic pressure.
II. Acids and bases
Acids are compounds that donate a hydrogen ion (protons) to a solution. Bases are
compounds that accept them. An acid can also be defined as a substance that accepts a pair
of electrons to form a covalent bond and a base is a substance that can donate a pair of
electrons to form such a bond.
The concentration of hydrogen ions in a solution is usually denoted by the term pH.
pH= - log [H+]
The dissociation constant for water, Kd, expresses the relationship between the hydrogen
ion concentration, the hydroxide ion concentration and the concentration of water at
equilibrium.
The ion product of water, Kw, is always constant. So, a decrease in H+ must be accompanied
by a rise in OH-.
,A pH of 7 is called neutral because the concentrations of H+ and OH- are equal. Acidic
solutions have a greater hydrogen ion concentration and a lower hydroxide ion
concentration than pure water and are therefore pH<7.
Classification of weak and strong acids goes according to their degree of dissociation into a
hydrogen ion and a base. Strong acids dissociate completely in a solution. The tendency of
an acid to dissociate and donate a hydrogen ion to a solution is denoted by its Ka. The higher
the Ka, the greater the tendency to dissociate a proton.
The Henderson-Hasselbalch equation is the formula for the dissociation constant of a weak
acid into a convenient logarithmic equation.
III. Buffers
Buffers consist of a weak acid and its conjugate base. They cause a solution to resist changes
in pH when hydrogen ions or hydroxide ions are added. But it can only compensate for an
influx or removal of hydrogen ions within about 1 pH of its own pKa. If more hydrogen ions
were added the pH would fall rapidly because there is relatively little conjugate base
remaining.
IV. Metabolic acids and buffers
The major source of metabolic acid in the body is the gas CO2, produced mainly from the
fuel oxidation. CO2 dissolves in water to form H2CO3, or carbonic acid, which is a weak acid
that partially dissociates into H+ and HCO3-. Carbonic acid is both the major acid produced
by the body and its own buffer. The pKa is 3,8 so at the blood pH of 7,4 it is almost
completely dissociated but the amounts of CO2 are much greater than carbonic acid. The
dissociation of carbonic acid forces CO2 to dissociate to form new carbonic acid.
As pH falls, an individual will breathe more rapidly and expire more CO2 and for pH rises this
is vice versa. Thus, the rate of breathing contributes to regulation of pH through its effects
on the dissolved CO2 content of the blood.
The system described above cooperates with hemoglobin in buffering the blood and
transporting CO2 to the lungs.
Phosphate anions and proteins are the major buffers involved in maintaining a constant pH
in the intracellular fluids. Also, the transport of hydrogen ions out of the cell is important for
maintaining a constant pH.
The nonvolatile acid that is produced by the body is excreted in urine.
Section 2 – Chapter 3
I. Functional groups on biological compounds
Biological compounds consist mostly of carbon (C), nitrogen (N), hydrogen (H), oxygen (O),
sulfur (S) and phosphorus (P) joined by covalent bonds. The skeleton of such a structure
,consists of carbon atoms: one C-atom structures are called methyl, two ethyl, three
propionyl and so on. If the carbon chain is branched the prefix ‘iso’ is used.
Structures that are either straight or branched (like the
structures in this figure) are called aliphatic. When there
is a ring-structure present, the structure is called
aromatic.
But biochemical molecules are defined by their functional
groups, not their carbon skeleton. The functional groups
are mostly formed with the atoms named before. The
properties of the functional groups usually determine the
types of reactions that occur and the physiological role of
the molecule. For example: in carbon-hydrogen bonds, the electrons are shared equally and
the bonds are non-polar and relatively unreactive. In carbon-oxygen bonds, the electrons are
shared unequally and the bonds are polar and more reactive.
The names of the functional groups are often incorporated in the common name. For
example: the name of a compound that contains a hydroxyl (alcohol) might end in ‘-ol’, like
ethanol.
Oxidation is the loss of electrons and results in the loss of hydrogen atoms together with
one or two electrons or the gain of an oxygen atom or hydroxyl group.
Reduction is the gain of electrons and results in the gain of hydrogen atoms or loss of an
oxygen atom.
Acidic groups contain a proton that can dissociate, usually leaving the remainder of the
molecule as an anion with a negative charge. The major anionic substituents are groups with
the suffix ‘-ate’ which denotes a negative charge.
Compounds containing nitrogen are usually
basic and can acquire a positive charge.
Amines consist of nitrogen attached through
single bonds to hydrogen atoms and to one
or more carbon atoms. Primary amines have
a single carbon-atom attached to them,
secondary have two and so on.
Polar bonds are covalent bonds in which the electron cloud is denser around one atom (the
atom with the greater electronegativity) than the other. In non-polar bonds, the two
electrons in the covalent bond are shared almost equally.
, One consequence of the bond polarity is that, to be soluble in water, other molecules must
contain charged or polar groups that can associate with the partial positive and negative
charges of water. Polar groups or molecules are called hydrophilic and non-polar groups or
molecules hydrophobic.
Hydrophobic molecules tend to be pushed together in water as the water molecules
maximize the number of energetically favorable hydrogen bonds they can form with each
other.
Another consequence is that atoms with a negative charge will be attracted to atoms with a
positive charge and vice versa. These charges, partial or full, dictate the course of
biochemical reactions.
Nomenclature
There are two used systems to name biochemical chains. In the first one (the one we learned
in high school) you name number the carbon atoms starting with the most oxidized group. In
the second one, the carbons are given Greek letters, starting with the carbon next to the
most oxidized one.
II. Carbohydrates
Monosaccharides consist of a linear chain of
three or more carbon atoms, one of which
forms a carbonyl group via a double bond
with oxygen. The other carbon atoms
contain hydroxyl groups. The general
formula is: CnH2nOn, see the figure.
A carbon atom that contains four different chemical groups forms an asymmetrical (or
chiral) center. The groups can then be arranged to form two different isomers that are
mirror images of each other. They are
called D and L stereoisomers, which
have the same chemical formula but a
different arrangement. Most of the
sugars in human tissues belong to the
D series, thus they are assumed to be
D unless L is specifically added to the
name.
It is possible for a molecule to have
multiple asymmetrical carbon atoms,
in that case the molecule has 2^n
stereoisomers unless it has a plane of
symmetry. Epimers are stereoisomers
that differ in the position of the
Section 2 – chapter 2
I. Water
About 60% percent of the body weight in adults is water. 60% of the body water is
intracellular and 40% extracellular. Extracellular includes plasma and interstitial water.
Water has a dipolar nature which allows it to form hydrogen bonds, this property is
responsible for the role of water as a solvent. These are formed by electrons from the
oxygen atom that are unshared and give the oxygen atom a negative charge. The hydrogen
atoms are therefore positively charged. A hydrogen bond is defined as a weak noncovalent
bond between the hydrogen of one molecule and the more electronegative acceptor of the
other. So, organic molecules containing a lot of electronegative atoms can readily dissolve in
water.
Both extra- and intracellular fluids contain elektrolytes, a general term applied to
bicarbonate and inorganic anions and cations. They are unevenly distributed over the two
compartments and this distribution is mainly maintained by energy-requiring pumps.
Water is distributed between the different compartments according to the concentration of
solutes (proteins, ions etc.); this is called the osmolarity. Water can freely move between
the two compartments through the semipermeable membranes, but solutes cannot. Thus,
water will move from a compartment with low concentrations of solutes to a compartment
with high concentrations of solutes. The force it would take to keep water from moving
across the membrane under these conditions is called the osmotic pressure.
II. Acids and bases
Acids are compounds that donate a hydrogen ion (protons) to a solution. Bases are
compounds that accept them. An acid can also be defined as a substance that accepts a pair
of electrons to form a covalent bond and a base is a substance that can donate a pair of
electrons to form such a bond.
The concentration of hydrogen ions in a solution is usually denoted by the term pH.
pH= - log [H+]
The dissociation constant for water, Kd, expresses the relationship between the hydrogen
ion concentration, the hydroxide ion concentration and the concentration of water at
equilibrium.
The ion product of water, Kw, is always constant. So, a decrease in H+ must be accompanied
by a rise in OH-.
,A pH of 7 is called neutral because the concentrations of H+ and OH- are equal. Acidic
solutions have a greater hydrogen ion concentration and a lower hydroxide ion
concentration than pure water and are therefore pH<7.
Classification of weak and strong acids goes according to their degree of dissociation into a
hydrogen ion and a base. Strong acids dissociate completely in a solution. The tendency of
an acid to dissociate and donate a hydrogen ion to a solution is denoted by its Ka. The higher
the Ka, the greater the tendency to dissociate a proton.
The Henderson-Hasselbalch equation is the formula for the dissociation constant of a weak
acid into a convenient logarithmic equation.
III. Buffers
Buffers consist of a weak acid and its conjugate base. They cause a solution to resist changes
in pH when hydrogen ions or hydroxide ions are added. But it can only compensate for an
influx or removal of hydrogen ions within about 1 pH of its own pKa. If more hydrogen ions
were added the pH would fall rapidly because there is relatively little conjugate base
remaining.
IV. Metabolic acids and buffers
The major source of metabolic acid in the body is the gas CO2, produced mainly from the
fuel oxidation. CO2 dissolves in water to form H2CO3, or carbonic acid, which is a weak acid
that partially dissociates into H+ and HCO3-. Carbonic acid is both the major acid produced
by the body and its own buffer. The pKa is 3,8 so at the blood pH of 7,4 it is almost
completely dissociated but the amounts of CO2 are much greater than carbonic acid. The
dissociation of carbonic acid forces CO2 to dissociate to form new carbonic acid.
As pH falls, an individual will breathe more rapidly and expire more CO2 and for pH rises this
is vice versa. Thus, the rate of breathing contributes to regulation of pH through its effects
on the dissolved CO2 content of the blood.
The system described above cooperates with hemoglobin in buffering the blood and
transporting CO2 to the lungs.
Phosphate anions and proteins are the major buffers involved in maintaining a constant pH
in the intracellular fluids. Also, the transport of hydrogen ions out of the cell is important for
maintaining a constant pH.
The nonvolatile acid that is produced by the body is excreted in urine.
Section 2 – Chapter 3
I. Functional groups on biological compounds
Biological compounds consist mostly of carbon (C), nitrogen (N), hydrogen (H), oxygen (O),
sulfur (S) and phosphorus (P) joined by covalent bonds. The skeleton of such a structure
,consists of carbon atoms: one C-atom structures are called methyl, two ethyl, three
propionyl and so on. If the carbon chain is branched the prefix ‘iso’ is used.
Structures that are either straight or branched (like the
structures in this figure) are called aliphatic. When there
is a ring-structure present, the structure is called
aromatic.
But biochemical molecules are defined by their functional
groups, not their carbon skeleton. The functional groups
are mostly formed with the atoms named before. The
properties of the functional groups usually determine the
types of reactions that occur and the physiological role of
the molecule. For example: in carbon-hydrogen bonds, the electrons are shared equally and
the bonds are non-polar and relatively unreactive. In carbon-oxygen bonds, the electrons are
shared unequally and the bonds are polar and more reactive.
The names of the functional groups are often incorporated in the common name. For
example: the name of a compound that contains a hydroxyl (alcohol) might end in ‘-ol’, like
ethanol.
Oxidation is the loss of electrons and results in the loss of hydrogen atoms together with
one or two electrons or the gain of an oxygen atom or hydroxyl group.
Reduction is the gain of electrons and results in the gain of hydrogen atoms or loss of an
oxygen atom.
Acidic groups contain a proton that can dissociate, usually leaving the remainder of the
molecule as an anion with a negative charge. The major anionic substituents are groups with
the suffix ‘-ate’ which denotes a negative charge.
Compounds containing nitrogen are usually
basic and can acquire a positive charge.
Amines consist of nitrogen attached through
single bonds to hydrogen atoms and to one
or more carbon atoms. Primary amines have
a single carbon-atom attached to them,
secondary have two and so on.
Polar bonds are covalent bonds in which the electron cloud is denser around one atom (the
atom with the greater electronegativity) than the other. In non-polar bonds, the two
electrons in the covalent bond are shared almost equally.
, One consequence of the bond polarity is that, to be soluble in water, other molecules must
contain charged or polar groups that can associate with the partial positive and negative
charges of water. Polar groups or molecules are called hydrophilic and non-polar groups or
molecules hydrophobic.
Hydrophobic molecules tend to be pushed together in water as the water molecules
maximize the number of energetically favorable hydrogen bonds they can form with each
other.
Another consequence is that atoms with a negative charge will be attracted to atoms with a
positive charge and vice versa. These charges, partial or full, dictate the course of
biochemical reactions.
Nomenclature
There are two used systems to name biochemical chains. In the first one (the one we learned
in high school) you name number the carbon atoms starting with the most oxidized group. In
the second one, the carbons are given Greek letters, starting with the carbon next to the
most oxidized one.
II. Carbohydrates
Monosaccharides consist of a linear chain of
three or more carbon atoms, one of which
forms a carbonyl group via a double bond
with oxygen. The other carbon atoms
contain hydroxyl groups. The general
formula is: CnH2nOn, see the figure.
A carbon atom that contains four different chemical groups forms an asymmetrical (or
chiral) center. The groups can then be arranged to form two different isomers that are
mirror images of each other. They are
called D and L stereoisomers, which
have the same chemical formula but a
different arrangement. Most of the
sugars in human tissues belong to the
D series, thus they are assumed to be
D unless L is specifically added to the
name.
It is possible for a molecule to have
multiple asymmetrical carbon atoms,
in that case the molecule has 2^n
stereoisomers unless it has a plane of
symmetry. Epimers are stereoisomers
that differ in the position of the
