General Biology: Chemical Bonds, Water Properties, and Biomolecules Study Guide

Chemical Bonds in Biology

Types of Chemical Bonds

Chemical bonds are forces that hold atoms together in molecules and compounds. Understanding their properties is essential for studying biological molecules.

• Ionic Bonds: Formed when electrons are transferred from one atom to another, resulting in oppositely charged ions that attract each other. Strengths: Strong in solid state, weaker in aqueous solutions. Example: Sodium chloride (NaCl).

• Covalent Bonds: Formed when atoms share pairs of electrons. Strengths: Very strong and stable. Example: Water (H2O), methane (CH4).

• Hydrogen Bonds: Weak attractions between a hydrogen atom covalently bonded to an electronegative atom (like O or N) and another electronegative atom. Strengths: Individually weak, collectively strong. Example: Between water molecules, in DNA base pairing.

• Van der Waals Interactions: Weak, transient attractions due to temporary dipoles in molecules. Strengths: Weakest type, but important in large molecules. Example: Stabilization of protein structures.

Additional info: Polar covalent bonds occur when electrons are shared unequally, creating partial charges (e.g., in water).

Properties of Water

Emergent Properties of Water

Water exhibits unique properties that are crucial for life due to its molecular structure and hydrogen bonding.

• Cohesion: Water molecules stick to each other via hydrogen bonds, allowing for surface tension and transport in plants.

• Adhesion: Water molecules stick to other substances, aiding capillary action.

• High Specific Heat: Water can absorb or release large amounts of heat with little temperature change, stabilizing environments.

• Ice Floats: Solid water (ice) is less dense than liquid water due to hydrogen bonds forming a lattice structure.

Additional info: Water is an excellent solvent for polar and ionic substances.

Why Ice Floats on Water

Ice floats because its molecular structure forms a crystalline lattice due to hydrogen bonding, making it less dense than liquid water.

• In liquid water, molecules are closer together.

• In ice, hydrogen bonds hold molecules apart in a hexagonal pattern.

pH and Water Chemistry

The pH of water can change when acids or bases are added. pH is a measure of hydrogen ion concentration.

• Adding Acid: Increases H+ concentration, lowers pH.

• Adding Base: Decreases H+ concentration (or increases OH-), raises pH.

Diagram: Use a pH scale to show changes from neutral (pH 7) to acidic (<7) or basic (>7).

Carbon and Molecular Diversity

Carbon's Versatility

Carbon can form many different molecules due to its ability to make four covalent bonds with other atoms, including itself.

• With 3 carbons and 3 hydrogens, many combinations are possible.

• Double bonds and branching increase diversity.

Example: Propane (C3H8), cyclopropane, and other isomers.

Chemical Isomers

Isomers are molecules with the same molecular formula but different structures.

• Structural Isomers: Differ in covalent arrangement of atoms.

• Cis-Trans Isomers: Differ in spatial arrangement around double bonds.

• Enantiomers: Mirror images due to asymmetric carbon.

Real-world example: Glucose and fructose (structural isomers); cis and trans fatty acids (cis-trans isomers); L- and D-amino acids (enantiomers).

Polymer Formation and Breakdown

Dehydration and Hydrolysis Reactions

Polymers are formed and broken down by specific chemical reactions.

• Dehydration Synthesis: Monomers are joined by removing a water molecule.

• Hydrolysis: Polymers are broken down by adding water.

Equation:

$\text{Monomer}_1 + \text{Monomer}_2 \xrightarrow{\text{Dehydration}} \text{Polymer} + H_2O$

$\text{Polymer} + H_2O \xrightarrow{\text{Hydrolysis}} \text{Monomer}_1 + \text{Monomer}_2$

Biomolecules: Sugars and Lipids

Glucose, Fructose, and Aldehyde/Ketone Structures

Glucose (an aldehyde sugar) and fructose (a ketone sugar) both have the formula C6H12O6 but differ in structure.

• Glucose: Aldehyde group at carbon 1.

• Fructose: Ketone group at carbon 2.

Diagram: Draw glucose with a terminal CHO group; fructose with a C=O group on the second carbon.

Phospholipids and Water Interaction

Phospholipids are major components of cell membranes, consisting of a hydrophilic (water-attracting) head and hydrophobic (water-repelling) tails.

• Phospholipids form bilayers in water, with heads facing outward and tails inward.

• Substituting a fatty acid with a phosphate group creates the hydrophilic head.

Diagram: Show a phospholipid with a phosphate head and two fatty acid tails.

Amino Acids and Protein Structure

Components of an Amino Acid

Amino acids are the building blocks of proteins, each containing:

• A central carbon (alpha carbon)

• An amino group (-NH2)

• A carboxyl group (-COOH)

• A hydrogen atom

• A variable R group (side chain)

Levels of Protein Structure

Proteins have four levels of structure, each contributing to their function.

• Primary Structure: Sequence of amino acids linked by peptide bonds.

• Secondary Structure: Local folding into alpha helices and beta sheets via hydrogen bonds.

• Tertiary Structure: Overall 3D shape formed by interactions among R groups (hydrophobic interactions, ionic bonds, disulfide bridges).

• Quaternary Structure: Association of multiple polypeptide chains.

Additional info: Protein function depends on its structure; denaturation disrupts function.

Summary Table: Types of Chemical Bonds

Bond Type	Formation	Strength	Example
Ionic	Electron transfer	Strong (solid), weak (aqueous)	NaCl
Covalent	Electron sharing	Very strong	H2O
Hydrogen	Attraction between H and electronegative atom	Weak (individually)	DNA base pairs
Van der Waals	Temporary dipoles	Very weak	Protein folding