BIOCHEMISTRY
Acids and Bases
Water and pH
I. Water
• Biochemical Importance
o Water is the predominant chemical component of living organisms.
o It has unique physical properties including:
▪ The ability to dissolve organic and inorganic molecules.
▪ The capacity to form hydrogen bonds.
o Water is an excellent nucleophile, meaning it is a reactant or product in metabolic reactions.
• Acidity
o Acidity is the concentration of protons in a solution.
o It is measured using the pH scale for aqueous solutions.
• Buffers
o Buffers are substances that resist changes in pH when a strong acid or base is added.
o They maintain the pH of extracellular fluid between 7.35 and 7.45.
o An example of a buffer is bicarbonate.
• Acidosis
o Acidosis occurs when blood pH is less than 7.35.
o Causes include diabetic ketosis and lactic acidosis.
• Alkalosis
o Alkalosis occurs when blood pH is more than 7.45.
o It can be caused by vomiting acidic gastric contents.
• Ideal Solvent
o A water molecule is shaped like a tetrahedron, with oxygen in the center and two hydrogen atoms
at the sides.
o The oxygen atom has a strong negative charge, while the hydrogen atoms have a partial positive
charge.
o This creates a strong dipole and a high dielectric coefficient.
▪ A dipole is a molecule with an electrical charge that is asymmetrically distributed.
▪ The dielectric coefficient is the ability to store an electric charge. Water has a high
dielectric coefficient because of its strong dipole.
II. Water Molecules Form H-bonds
• Hydrogen Bonding
o Hydrogen bonding occurs when a partially unshielded hydrogen nucleus interacts with an
unshared electron pair on another oxygen or nitrogen atom.
o It favors the self-association of water molecules into arrays.
o Hydrogen bonding influences the physical properties of water, such as its relatively high viscosity,
surface tension, and boiling point.
o Hydrogen bonds are relatively weak and transient compared to other bonds.
o They enable water to dissolve many other biomolecules.
III. Interaction with Water Influences Shape of Biomolecules
• Amphipathic Biomolecules
o Amphipathic biomolecules have regions that are rich in charged or polar groups as well as regions
that have hydrophobic characters.
• Hydrophobic Interactions
o Hydrophobic interactions describe the tendency for non-polar substances to self-associate.
o According to the 2nd Law of Thermodynamics, the optimal free energy of a hydrocarbon-water
mixture is a function of:
▪ Maximum enthalpy (from hydrogen bonding)
, BIOCHEMISTRY
Acids and Bases
▪ Highest entropy (maximum degree of freedom)
o Nonpolar molecules form droplets to:
▪ Minimize their exposed surface area
▪ Reduce the number of restricted water molecules
• Electrostatic Interaction
o Salt bridges are interactions between oppositely charged groups within or between biomolecules.
▪ They have the same strength as hydrogen bonds.
▪ They can act over large distances.
▪ They facilitate the binding of charged molecules and ions to proteins and nucleic acids.
o Van der Waals forces arise from attractions between transient dipoles.
▪ They are weaker than hydrogen bonds but are numerous.
▪ They act over very short distances.
• DNA Double Helix
o Covalent bonds hold each individual strand of DNA together.
o The two helical strands are held together by noncovalent interactions, specifically hydrogen bonds
between nucleotide bases.
o The outside of the DNA double helix is exposed to water and includes charged phosphate groups
and polar hydroxyl groups.
o The inside of the DNA double helix contains the hydrophobic nucleotide bases.
IV. Water as a Nucleophile
• Nucleophile and Electrophile
o A nucleophile is an electron-rich molecule.
o An electrophile is an electron-poor molecule.
• Hydrolysis
o Hydrolysis is the cleavage of amide, glycoside, or ester bonds.
o It is caused by a water nucleophilic attack.
• Enzymes
o Enzymes are protein catalysts that accelerate the rate of hydrolytic reactions.
o Proteases catalyze the hydrolysis of proteins.
o Nucleases catalyze the hydrolysis of phosphoester bonds in DNA and RNA.
• Ionization
o Water can act as both an acid and a base.
o During ionization, water molecules can form hydronium or hydroxide ions.
o 1 g of water contains 3.46 x 1022 molecules.
o The ion product of water (Kw) is equal to the concentration of hydrogen ions multiplied by the
concentration of hydroxide ions: Kw = [H+][OH-].
• Other Nucleophiles
o Other examples of nucleophiles include: water; the oxygen atoms of phosphates; alcohols;
carboxylic acids; the sulfur of thiols; and the nitrogen atom of amines and the imidazole ring of
histidine.
V. pH
• Definition and Formula
o pH is the negative log of the hydrogen ion concentration.
o The formula for pH is: pH = -log[H+].
• Relationship Between pH and Hydrogen Ion Concentration
o A high pH value indicates a low concentration of hydrogen ions.
o A low pH value indicates a high concentration of hydrogen ions.
• Acids
o Acids are proton donors.
o Strong acids completely dissociate into anions and protons.
Acids and Bases
Water and pH
I. Water
• Biochemical Importance
o Water is the predominant chemical component of living organisms.
o It has unique physical properties including:
▪ The ability to dissolve organic and inorganic molecules.
▪ The capacity to form hydrogen bonds.
o Water is an excellent nucleophile, meaning it is a reactant or product in metabolic reactions.
• Acidity
o Acidity is the concentration of protons in a solution.
o It is measured using the pH scale for aqueous solutions.
• Buffers
o Buffers are substances that resist changes in pH when a strong acid or base is added.
o They maintain the pH of extracellular fluid between 7.35 and 7.45.
o An example of a buffer is bicarbonate.
• Acidosis
o Acidosis occurs when blood pH is less than 7.35.
o Causes include diabetic ketosis and lactic acidosis.
• Alkalosis
o Alkalosis occurs when blood pH is more than 7.45.
o It can be caused by vomiting acidic gastric contents.
• Ideal Solvent
o A water molecule is shaped like a tetrahedron, with oxygen in the center and two hydrogen atoms
at the sides.
o The oxygen atom has a strong negative charge, while the hydrogen atoms have a partial positive
charge.
o This creates a strong dipole and a high dielectric coefficient.
▪ A dipole is a molecule with an electrical charge that is asymmetrically distributed.
▪ The dielectric coefficient is the ability to store an electric charge. Water has a high
dielectric coefficient because of its strong dipole.
II. Water Molecules Form H-bonds
• Hydrogen Bonding
o Hydrogen bonding occurs when a partially unshielded hydrogen nucleus interacts with an
unshared electron pair on another oxygen or nitrogen atom.
o It favors the self-association of water molecules into arrays.
o Hydrogen bonding influences the physical properties of water, such as its relatively high viscosity,
surface tension, and boiling point.
o Hydrogen bonds are relatively weak and transient compared to other bonds.
o They enable water to dissolve many other biomolecules.
III. Interaction with Water Influences Shape of Biomolecules
• Amphipathic Biomolecules
o Amphipathic biomolecules have regions that are rich in charged or polar groups as well as regions
that have hydrophobic characters.
• Hydrophobic Interactions
o Hydrophobic interactions describe the tendency for non-polar substances to self-associate.
o According to the 2nd Law of Thermodynamics, the optimal free energy of a hydrocarbon-water
mixture is a function of:
▪ Maximum enthalpy (from hydrogen bonding)
, BIOCHEMISTRY
Acids and Bases
▪ Highest entropy (maximum degree of freedom)
o Nonpolar molecules form droplets to:
▪ Minimize their exposed surface area
▪ Reduce the number of restricted water molecules
• Electrostatic Interaction
o Salt bridges are interactions between oppositely charged groups within or between biomolecules.
▪ They have the same strength as hydrogen bonds.
▪ They can act over large distances.
▪ They facilitate the binding of charged molecules and ions to proteins and nucleic acids.
o Van der Waals forces arise from attractions between transient dipoles.
▪ They are weaker than hydrogen bonds but are numerous.
▪ They act over very short distances.
• DNA Double Helix
o Covalent bonds hold each individual strand of DNA together.
o The two helical strands are held together by noncovalent interactions, specifically hydrogen bonds
between nucleotide bases.
o The outside of the DNA double helix is exposed to water and includes charged phosphate groups
and polar hydroxyl groups.
o The inside of the DNA double helix contains the hydrophobic nucleotide bases.
IV. Water as a Nucleophile
• Nucleophile and Electrophile
o A nucleophile is an electron-rich molecule.
o An electrophile is an electron-poor molecule.
• Hydrolysis
o Hydrolysis is the cleavage of amide, glycoside, or ester bonds.
o It is caused by a water nucleophilic attack.
• Enzymes
o Enzymes are protein catalysts that accelerate the rate of hydrolytic reactions.
o Proteases catalyze the hydrolysis of proteins.
o Nucleases catalyze the hydrolysis of phosphoester bonds in DNA and RNA.
• Ionization
o Water can act as both an acid and a base.
o During ionization, water molecules can form hydronium or hydroxide ions.
o 1 g of water contains 3.46 x 1022 molecules.
o The ion product of water (Kw) is equal to the concentration of hydrogen ions multiplied by the
concentration of hydroxide ions: Kw = [H+][OH-].
• Other Nucleophiles
o Other examples of nucleophiles include: water; the oxygen atoms of phosphates; alcohols;
carboxylic acids; the sulfur of thiols; and the nitrogen atom of amines and the imidazole ring of
histidine.
V. pH
• Definition and Formula
o pH is the negative log of the hydrogen ion concentration.
o The formula for pH is: pH = -log[H+].
• Relationship Between pH and Hydrogen Ion Concentration
o A high pH value indicates a low concentration of hydrogen ions.
o A low pH value indicates a high concentration of hydrogen ions.
• Acids
o Acids are proton donors.
o Strong acids completely dissociate into anions and protons.
