Fundamentals of Biological Molecules and Chemical Bonds

Introduction to Chemical Bonds in Biology

Ionic and Covalent Bonds

Chemical bonds are essential for the structure and function of biological molecules. The two main types are ionic and covalent bonds.

• Ionic bonds: Formed when electrons are transferred from one atom to another, resulting in oppositely charged ions that attract each other. There is no sharing of electrons.

• Covalent bonds: Involve the sharing of electron pairs between atoms, creating a stable balance of attractive and repulsive forces.

Electrons, Protons, and Charge

• Electrons: Negatively charged subatomic particles involved in chemical bonding.

• Protons: Positively charged subatomic particles found in the nucleus of atoms.

Hydrogen Bonds

Hydrogen bonds are weak interactions that occur between a hydrogen atom covalently bonded to an electronegative atom (such as oxygen, fluorine, or nitrogen) and another electronegative atom.

• Example: The bond between hydrogen and oxygen in water molecules.

Properties of Water

Emergent Properties of Water

Water exhibits several unique properties due to its polarity and ability to form hydrogen bonds.

• Cohesion: Water molecules stick to each other.

• High heat capacity: Water can absorb a lot of heat before its temperature rises.

• Good solvent: Water dissolves many substances due to its polarity.

Water Structure and Behavior

• Liquid water: Molecules are highly packed but can move past each other.

• Solid water (ice): Molecules are less packed and expand, making ice less dense than liquid water.

Kinetic Energy

• Kinetic energy: The energy of motion, which increases with temperature.

Specific Heat

• Specific heat: The amount of heat required to raise or lower the temperature of 1 gram of water by 1 degree Celsius.

Acids, Bases, and pH

pH Scale and Definitions

The pH scale measures the concentration of hydrogen ions (H+) in a solution.

• Acidic solution: pH lower than 7; high hydrogen ion concentration.

• Basic (alkaline) solution: pH higher than 7; low hydrogen ion concentration.

• Neutral solution: pH = 7.

Macromolecules in Biology

Dehydration and Hydrolysis Reactions

• Dehydration: Forms covalent bonds between monomers to build polymers by removing water.

• Hydrolysis: Breaks down covalent bonds in polymers by adding water.

Carbohydrates

Carbohydrates are organic molecules composed of carbon, hydrogen, and oxygen. They serve as energy sources and structural components.

• Monosaccharides: Single carbohydrate units or monomers (e.g., glucose).

• Oligosaccharides: 2–20 linked sugar units.

• Polysaccharides: More than 20 linked sugar units; form complex polymers (e.g., starch, cellulose).

Proteins

Proteins are polymers made of amino acid monomers. They perform a wide range of functions in cells, including catalysis, structure, and signaling.

• Primary structure: The sequence and number of amino acids in a polypeptide chain.

• Secondary structure: Local folding into alpha helices or beta sheets, stabilized by hydrogen bonds.

• Tertiary structure: The overall 3D shape of a single polypeptide chain.

• Quaternary structure: The association of multiple polypeptide chains to form a functional protein complex.

Nucleic Acids

Nucleotides and Nucleic Acid Structure

Nucleic acids, such as DNA and RNA, store and transmit genetic information. Their monomers are nucleotides.

• Nucleotides: Consist of three components:

  1. Phosphate group

  2. Pentose sugar (deoxyribose in DNA, ribose in RNA)

  3. Nitrogenous base

Base Pairing in DNA and RNA

• DNA base pairs: Adenine (A) pairs with Thymine (T); Cytosine (C) pairs with Guanine (G).

• RNA: Contains Uracil (U) instead of Thymine (T).

Lipids

Properties and Types of Lipids

Lipids are hydrophobic molecules that do not form polymers. They are important for energy storage, membrane structure, and signaling.

• Hydrophobic: Lipids do not mix with water due to their nonpolar nature.

• Phospholipids: A class of lipids that contain a phosphate group; major components of cell membranes.

Summary Table: Types of Biological Macromolecules

Macromolecule	Monomer	Bond Type	Main Functions
Carbohydrates	Monosaccharides	Glycosidic bonds	Energy storage, structure
Proteins	Amino acids	Peptide bonds	Catalysis, structure, signaling
Nucleic Acids	Nucleotides	Phosphodiester bonds	Genetic information storage and transfer
Lipids	Fatty acids, glycerol (not true polymers)	Ester bonds	Energy storage, membranes, signaling