Essential Concepts in General Biology: Atoms, Molecules, and Biological Macromolecules

Atoms, Subatomic Particles, and Chemical Bonds

The Three Subatomic Particles and Their Significance

Atoms are the fundamental units of matter, composed of three main subatomic particles:

• Protons: Positively charged particles found in the nucleus; determine the atomic number and identity of an element.

• Neutrons: Neutral particles in the nucleus; contribute to atomic mass and isotopic variation.

• Electrons: Negatively charged particles orbiting the nucleus; involved in chemical bonding and reactions.

Example: A carbon atom has 6 protons, 6 neutrons, and 6 electrons.

Types of Chemical Bonds and How They Form

Chemical bonds are forces that hold atoms together in molecules and compounds. The main types include:

• Ionic Bonds: Formed when electrons are transferred from one atom to another, resulting in oppositely charged ions (e.g., NaCl).

• Covalent Bonds: Formed when two atoms share one or more pairs of electrons (e.g., H2O).

• Hydrogen Bonds: Weak attractions between a hydrogen atom covalently bonded to an electronegative atom (like O or N) and another electronegative atom.

Example: Water molecules are held together by hydrogen bonds.

Importance of Hydrogen Bonding to the Properties of Water

• Hydrogen bonds give water its unique properties, such as high specific heat, cohesion, adhesion, and surface tension.

• These properties are essential for life, influencing climate, cellular processes, and the structure of biomolecules.

Example: Water's high heat capacity helps regulate Earth's temperature.

Properties of Water and Their Contribution to Life on Earth

• Cohesion and Adhesion: Allow water to move through plant vessels (capillary action).

• High Specific Heat: Stabilizes temperatures in organisms and environments.

• Solvent Abilities: Water dissolves many substances, facilitating biochemical reactions.

• Density of Ice: Ice is less dense than liquid water, allowing aquatic life to survive under ice layers.

Interpreting a pH Scale

• The pH scale measures the concentration of hydrogen ions ($[H^+]$) in a solution.

• Scale ranges from 0 (most acidic) to 14 (most basic), with 7 being neutral.

Formula:

$pH = -\log_{10}[H^+]$

Biological Systems and Chemical Properties

pH Changes in Biological Systems

• Enzyme activity and cellular processes are sensitive to pH changes.

• Organisms maintain homeostasis by regulating internal pH.

Importance of Buffers in Biological Systems

• Buffers are substances that minimize changes in pH by absorbing or releasing hydrogen ions.

• They are crucial in maintaining stable pH in blood and cellular fluids.

Example: The bicarbonate buffer system in human blood.

Properties of Carbon That Make It Important

• Carbon can form four covalent bonds, allowing for diverse and complex molecules.

• It forms the backbone of organic molecules, including carbohydrates, lipids, proteins, and nucleic acids.

Dehydration and Hydrolysis Reactions with Organic Compounds

• Dehydration Synthesis: Joins monomers by removing a water molecule, forming polymers.

• Hydrolysis: Breaks polymers into monomers by adding water.

Example: Formation and breakdown of starch in plants.

Macromolecules: Structure and Function

Sequence and Subcomponents of the 4 Groups of Organic Compounds

• Carbohydrates: Monosaccharides (simple sugars) form polysaccharides (e.g., starch, cellulose).

• Lipids: Glycerol and fatty acids form triglycerides and phospholipids.

• Proteins: Amino acids form polypeptides and functional proteins.

• Nucleic Acids: Nucleotides form DNA and RNA.

The sequence and composition of subunits determine the properties and functions of each macromolecule.

Cellular Functions of Carbs, Lipids, Proteins, and Nucleic Acids

• Carbohydrates: Provide energy and structural support.

• Lipids: Store energy, form cell membranes, and act as signaling molecules.

• Proteins: Serve as enzymes, structural components, and signaling molecules.

• Nucleic Acids: Store and transmit genetic information.

Changes in Organic Molecules Affecting Function

• Alterations in structure (e.g., sequence of amino acids in proteins) can change function.

• Mutations or chemical modifications may disrupt normal biological activity.

Structural Levels of Proteins and Their Functional Impact

• Primary Structure: Sequence of amino acids.

• Secondary Structure: Local folding (α-helices, β-sheets) stabilized by hydrogen bonds.

• Tertiary Structure: Overall 3D shape of a polypeptide.

• Quaternary Structure: Association of multiple polypeptide chains.

Changes at any level can affect protein function.

Protein Shape (Conformation) and Denaturation

• Protein function depends on its specific 3D shape (conformation).

• Denaturation: Loss of structure due to heat, pH, or chemicals, leading to loss of function.

Example: Cooking an egg denatures egg white proteins.

Directionality in Polymers

• Polymers like nucleic acids and proteins have directionality, meaning they have distinct ends.

• Nucleic acids: 5' and 3' ends refer to carbon positions in the sugar-phosphate backbone.

• Proteins: Amino (N-) and carboxyl (C-) termini.

Directionality is essential for processes like DNA replication and protein synthesis.

Summary Table: Macromolecules and Their Properties

Macromolecule	Monomer	Bond Type	Main Functions
Carbohydrates	Monosaccharide	Glycosidic linkage	Energy storage, structure
Lipids	Glycerol & Fatty acids	Ester bond	Energy storage, membranes
Proteins	Amino acid	Peptide bond	Enzymes, structure, signaling
Nucleic Acids	Nucleotide	Phosphodiester bond	Genetic information