MBoC Chapter 2: Weak Forces, Building Blocks, and pH

Biological Macromolecules and Weak Forces

• Biological macromolecules are mostly polymers of small organic molecules, including sugars, fatty acids, nucleotides, and amino acids.
• These molecules are composed of a handful of atoms, including carbon, nitrogen, hydrogen, and oxygen.

Properties of Water

• Water molecules are polar, with oxygen attracting electrons more strongly than hydrogen, resulting in a weak negative charge on oxygen and weak positive charges on hydrogen.
• This polarity enables water molecules to form weak non-covalent bonds, known as hydrogen bonds, which are responsible for many of water's unique properties.
• Hydrogen bonds in water are short-lived and rapidly broken by thermal motions of molecules.

Cohesive and Hydrophobic Properties

• Hydrogen bonding in water makes it cohesive, with high surface tension, and requires relatively high temperatures to be converted to a gas.
• Polar molecules that can form hydrogen bonds dissolve readily in water, while ions that can interact with water also dissolve readily.
• Non-polar or hydrophobic molecules cannot dissolve in water and are forced to interact with each other in aqueous solutions.

Carbon-Containing Molecules

• Nearly all molecules in cells are based on carbon, which can form large molecules because it can form four covalent bonds.
• The C-C bond is highly stable and is used to form diverse molecules.

Four Major Families of Small Organic Molecules

• Sugars
• Fatty acids
• Nucleotides
• Amino acids

Polymers and Macromolecules

• Sugars, nucleotides, and amino acids can be covalently linked together to form polymers.
• These long-chain macromolecules are largely responsible for the extraordinary properties of living organisms and constitute a large fraction of cellular mass.

Weak Non-Covalent Interactions

• Three kinds of weak non-covalent interactions play important roles in cells:
  • Electrostatic interactions (ionic bonds or salt bridges) between oppositely charged molecules.
  • Hydrogen bonds between molecules, which are stronger when all three atoms in the bond form a straight line.
  • Van der Waals interactions between electrons in neighboring atoms, which are highly distance-dependent.

Hydrophobic Effects

• Hydrophobic molecules are non-polar and cannot interact with water.
• Hydrophobic molecules displace water molecules and disrupt the hydrogen bonding network of water.
• Hydrophobic effects drive many important molecular interactions in cells, including formation of lipid bilayers, protein folding, and interactions between proteins.

Functional Groups

• Biological molecules have a number of functional groups that are used again and again in biochemical events.
• Common functional groups include:
  • Amines and amides
  • Carbonyl groups
  • Hydroxyl groups
  • Carboxyl groups
  • Esters
  • Phosphates
  • Sulfhydryl groups### Phosphate Groups and Acid Anhydrides
• Phosphate groups are often attached to proteins and can form a very stable structure with a carboxyl group or two or more phosphate groups, giving an acid anhydride.
• These compounds are easily hydrolyzed in the cell and are sometimes said to contain a "high-energy" bond.

Sulfhydryl Group

• The sulfhydryl group is a functional group found in the amino acid cysteine.
• It can exist in a reduced form or more rarely in an oxidized, cross-bridging form.

Phosphates and Water

• Inorganic phosphate is a stable ion formed from water and can dissolve in water.
• Phosphate groups can be attached to proteins and are often written as Pi.
• Water is an excellent solvent for many substances due to its polar bonds.

Hydrogen Ion Exchange

• Positively charged hydrogen ions (H+) can spontaneously move from one water molecule to another, creating two ionic species.
• pH is a measure of the concentration of hydrogen ions in a solution.

Acids and Bases

• Substances that release hydrogen ions into solution are called acids.
• Substances that reduce the number of hydrogen ions in a solution are called bases.
• pH is a measure of the acidity or basicity of a solution.
• Strong acids readily release a proton in water, whereas weak acids only partially dissociate their proton.

Example of Weak Acid

• The carboxyl group is an example of a weak acid, which dissociates to give a hydronium ion and a hydroxyl ion.### Acids and Bases

• A weak base reduces the number of H+ ions, making OH- ions that combine with H+ ions to form water.

• A strong base, like sodium hydroxide, directly removes H+ ions from water.

pH Scale

• pH is defined as the concentration of H+ ions.
• pH = -log10[H+] is used to provide a simple notation for the concentration of H+ ions.
• pH scale is a logarithmic scale used to measure the acidity of a solution.

Bases

• Bases are substances that reduce the number of H+ ions in a solution.
• Weak bases, like ammonia, contain an amino group (-NH2) and have a weak tendency to accept an H+ ion from water.
• Strong bases, like sodium hydroxide, directly combine with H+ ions.

Buffers

• Buffers resist changes in pH and maintain a solution within a tight pH range.
• Buffers are weak acids or bases that can bind or release H+ ions within a specific range.
• Buffers work best to maintain pH around their pKa.

Biological Importance

• The interior of the cell is kept close to pH 7 by the presence of buffers.
• Blood is buffered by carbonic acid, which releases a proton to form bicarbonate and H+ ions.
• Bicarbonate acts as a buffer by absorbing H+ ions released into the blood.

Laboratory Applications

• Numerous buffers are used in the laboratory to maintain the pH of solutions near physiological levels.
• Buffers are essential to maintain the pH of solutions in biological experiments.