Chemistry of Life: Atomic Structure, Macromolecules, and Metabolic Processes

Fundamental Atomic Structure

• Subatomic Particles Comparison: All atoms are constructed from three primary subatomic particles: protons, neutrons, and electrons.     * Protons:         * Charge: $+1$         * Relative Mass: $1837$         * Location: Located within the nucleus.         * Properties: Protons have a positive charge that is equal in magnitude to the negative charge of an electron.     * Neutrons:         * Charge: $0$         * Relative Mass: $1842$         * Location: Located within the nucleus.         * Properties: They are neutral and have a mass approximately equal to that of a proton. Both are nearly $2000$ times heavier than an electron.     * Electrons:         * Charge: $-1$         * Relative Mass: $1$         * Location: Reside outside the nucleus in the "mostly empty space" of the atom.

• Atomic Architecture:     * The nucleus contains protons and neutrons, which are collectively referred to as nucleons.     * The nucleus holds almost all the mass of the atom but is approximately $100,000$ times smaller than the total size of the atom.     * Electron Cloud: Electrons move so rapidly that their specific location is никогда certain. This region of rapid movement is known as the electron cloud.

Foundations of Organic and Inorganic Molecules

• Organic Molecules:     * These are the molecules that constitute living things.     * Elemental Composition: Made mostly of Carbon ($C$), Hydrogen ($H$), Oxygen ($O$), and Nitrogen ($N$), frequently including Sulfur ($S$) and Phosphorus ($P$).     * Size: Generally large molecules.     * Defining Characteristic: They always contain carbon and can be synthesized by both living and non-living things.

• Inorganic Molecules:     * Function: Can participate in the metabolism of living things but do not build the structures of living things.     * Size: Very small molecules.     * Defining Characteristic: Generally do not contain carbon.     * Examples: Water ($H_2O$), Ammonia ($NH_3$), and Carbon Dioxide ($CO_2$). Even though Carbon Dioxide contains carbon, it is classified as inorganic.

• The Special Nature of Carbon:     * Carbon atoms are capable of forming $4$ covalent bonds.     * Carbon can bond with other carbon atoms to form long, branching chains, facilitating the creation of large organic molecules.     * Carbon Skeletons: Also called carbon "backbones," these are the carbon-containing structures of large organic molecules.     * Polymers and Monomers: Large organic molecules are called polymers, which are constructed by connecting smaller units called monomers.

Hydrocarbons: Classification and Behavior

• Chemical Structure: Hydrocarbons consist exclusively of carbon and hydrogen atoms.     * Each carbon atom forms $4$ bonds.     * Each hydrogen atom forms $1$ bond.

• Polarity and Solubility:     * Carbon-hydrogen bonds are non-polar.     * Hydrocarbons are hydrophobic because water is polar. Since hydrocarbons lack polarity, they are not attracted to water and will not mix or dissolve in it.

• Saturated vs. Unsaturated Hydrocarbons:     * Saturated Hydrocarbons: Every carbon atom is bonded to four different atoms. No new atoms can be added to the chain.     * Unsaturated Hydrocarbons: Contain some carbon-carbon double or triple bonds. These bonds can be broken and replaced with single bonds to add additional atoms to the chain.     * Structural Kinks: The presence of carbon-carbon double bonds creates "kinks" in the hydrocarbon chain.

• Fossil Fuels: Examples of hydrocarbons formed from decaying organic matter.

The Four Categories of Biological Macromolecules

• All macromolecules are built on a hydrocarbon backbone.

• The Three Polymers:     1. Proteins: Built from Amino acids.     2. Carbohydrates: Built from Simple sugars (monosaccharides).     3. Nucleic acids: Built from Nucleotides.

• The Non-Polymer:     4. Lipids: These are large biological molecules but do not consist of polymers.

Protein Structure and Function

• Elemental Composition: Carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur.

• Biological Roles: Proteins serve as the "machines" of the organism, acting as enzymes, transporters, and structural components.

• Nomenclature: Also referred to as peptides and polypeptides.

• Amino Acid Foundation:     * Proteins are chains constructed from $20$ different amino acids.     * Virtually all life on Earth uses the same set of $20$ amino acids.     * Peptide Bonds: The specific bonds that link neighboring amino acids.

• Amino Acid Components:     1. Amino group ($-NH_2$).     2. Carboxyl group ($-COOH$).     3. Side chain (R-group): The unique side chain determines the specific properties of each amino acid.

• Four Levels of Protein Structure: Shape is critical to function. A protein's shape is determined by:     1. Primary Structure     2. Secondary Structure     3. Tertiary Structure     4. Quaternary Structure

Carbohydrate Properties

• Composition: Compounds consisting of carbon and water (atoms of carbon, hydrogen, and oxygen).

• Classification:     * Monosaccharides: Simple sugars with the general formula $(C_x H_{2x} O_x)$.     * Disaccharides: Two monosaccharides bonded together.     * Polysaccharides: Long chains combining many monosaccharides.

• Functions: Simple sugars act as fuel for work, raw materials for carbon backbones, and monomers for larger carbohydrates.

• Solubility: Sugars contains many polar hydroxyl ($OH^-$) groups, making them highly soluble in water.

Nucleic Acids and Nucleotides

• Composition: Consist of carbon, hydrogen, oxygen, nitrogen, and phosphorus.

• Function: Storing genetic information and directing the cell in protein synthesis.

• Types of Nucleic Acids:     * DNA: Deoxyribonucleic Acid.     * RNA: Ribonucleic Acid. The three main types are Messenger RNA ($mRNA$), Transfer RNA ($tRNA$), and Ribosomal RNA ($rRNA$).

• Nucleotide Structure: The monomers of nucleic acids consist of:     1. A sugar.     2. A nitrogenous base.     3. A phosphate group.

• Bonding: Phosphodiester bonds connect nucleotides and are formed through dehydration synthesis reactions.

Lipid Specialization and Phospholipids

• Major Functions: Energy storage, major components of cell membranes, and various metabolic activities.

• Physical Chemistry of Lipids:     * Hydrophobic Lipids: Fats and oils (will not mix with water).     * Amphiphilic Lipids: Molecules possessing both a hydrophobic "tail" and a hydrophilic "head."

• Triglycerides: Common fat storage molecules.     * Structure: One single glycerol bonded to three fatty acids.     * Fatty Acids: Carboxylic acids with very long carbon chains; they vary in length and the number/location of double bonds.

• Phospholipids and Cell Membranes:     * Structure: Includes $2$ fatty acids and $1$ phosphate group.     * The phosphate group is polar and hydrophilic (forms hydrogen bonds with water).     * The fatty acid chains are non-polar and hydrophobic.     * Membrane formation: In an aqueous environment, polar heads orient toward the exterior and interior of the cell, while hydrophobic tails orient toward each other to form a nonpolar interior layer.

• Saturated vs. Unsaturated Lipids:     * Saturated Lipids: Maximum number of hydrogen atoms, no double bonds, solid at room temperature.     * Unsaturated Lipids: One or more double bonds, liquid at room temperature. Can be converted to solid saturated lipids via hydrogenation (adding hydrogen).

Principles of Chemical Bonding

• Covalent Bonding: Electrons are shared between atoms to form molecules. There are two subtypes:     1. Covalent Networks: Large compounds of repeating units all covalently bonded (e.g., diamond ($C_n$) or quartz ($(SiO_2)_n$)).     2. Molecules: Smaller compounds of one or more elements (e.g., $H_2O$, $O_2$).

• Ionic Bonding: Forms between positive and negative ions.     * They do not form discrete molecules but creates compounds with specific ratios of ions.     * Formula Unit: The lowest-term ratio of atoms in an ionic compound (e.g., $NaCl$, $HCl$).

• Metallic Bonding: Occurs between large numbers of metal atoms.     * Electrons are shared across many atoms, forming a "sea of electrons" that move freely.

Intermolecular Forces (IMFs)

• Van der Waals Forces:     1. Dipole-Dipole Interactions: Occur between polar molecules with permanent dipoles. The positive end of one is attracted to the negative end of another. Stronger polarity leads to higher boiling and melting points.     2. Hydrogen Bonding: A particularly strong dipole-dipole interaction occurring when Hydrogen ($H$) is bonded to Nitrogen ($N$), Oxygen ($O$), or Fluorine ($F$). The small radius and high electronegativity of $N$, $O$, and $F$ expose the hydrogen nucleus.     3. London Dispersion Forces (LDFs): Occur in all molecules (polar and non-polar) due to constant electron motion. This creates instantaneous dipoles and induced dipoles.

• Polarizability: The tendency of an electron cloud to distort. Larger molecules with more electrons have higher polarizability and stronger LDFs.

• Ion-Dipole Interactions: Occur between ions and polar molecules. These are not Van der Waals forces. They are responsible for ionic substances dissolving in polar solvents.

The Molecular Structure and Properties of Water

• Formation: Two hydrogen atoms ($1$ electron each) bond with one oxygen atom ($6$ valence electrons). Through covalent bonding, each Hydrogen achieves $2$ valence electrons and Oxygen achieves $8$.

• Polarity: Oxygen has more protons and a stronger electric force than Hydrogen, pulling the shared electrons closer to the Oxygen nucleus. This results in the oxygen side being slightly negative and the hydrogen side being slightly positive.

• Specific Properties of Water:     * Intermolecular forces between water molecules are hydrogen bonds.     * High Specific Heat: It takes a signficant amount of energy to change the temperature of water.     * Solubility: Water's polarity allows it to dissolve most substances.     * Cohesion and Adhesion: Water attracts other water molecules (cohesive) and other types of molecules (adhesive) due to polarity.     * Biological Medium: Provides the environment for almost all biological chemical reactions.

Passive Transport Mechanisms

• Definition: Movement of molecules, ions, solutes, and water through a cell membrane with the concentration gradient and without free energy input.

• Types:     * Diffusion: Random movement of particles from high to low concentration.     * Osmosis: The net flow of water molecules through a semi-permeable membrane into an area of higher solute concentration.     * Facilitated Diffusion: Diffusion that requires the assistance of an integral membrane protein.     * Thermosynthesis: Biological reactions using free energy from a temperature gradient to occur when they normally would not.

The Four Laws of Thermodynamics and Entropy

• Zeroth Law: Defines temperature. Heat flows from objects at higher temperature to those at lower temperature until they reach thermal equilibrium.

• First Law: Statement of conservation of energy. Energy of the universe is constant; it can only be converted into forms like chemical, gravitational, kinetic, electromagnetic, or nuclear.

• Second Law: Deals with entropy ($S$). For spontaneous/irreversible processes, the entropy of the universe increases (\Delta S > 0). For reversible processes, $\Delta S = 0$.

• Third Law: Establishes that the entropy of a perfect crystal at absolute zero ($0\,K$) is zero.

• Definitions of Entropy ($S$):     1. Measure of the number of energetically equivalent ways a system can be arranged.     2. Measure of disorder in a system.     3. Measure of the degree to which energy is dispersed and unable to do work.

Metabolic Pathways and Chemical Reactions

• Metabolism: All chemical reactions in an organism to obtain or use energy. Reactions are catalyzed by specific enzymes.

• Anabolic Pathways:     * Function: Combine building blocks to create large molecules.     * Characteristics: Not spontaneous; require energy; products are more complex than reactants.     * Entropy: Decrease life's entropy, but increase the entropy of the surroundings (total universe entropy still increases).     * Example: Photosynthesis.     * Mechanism: Dehydration Synthesis (two monomers combine, a water molecule is removed, and a polymer is formed).

• Catabolic Pathways:     * Function: Break down large molecules into smaller blocks.     * Characteristics: Release energy; products are less complex than reactants.     * Entropy: Increase entropy of life and the environment.     * Example: Cellular Respiration (breaking down glucose).     * Mechanism: Hydrolysis (a water molecule is added to cause a molecule to split; $H$ and $OH$ groups combine with the resulting products).

Oxidation and Reduction (REDOX)

• Definition: Reactions involving the transfer of electrons between species.

• Oxidation: The loss of electrons ($LEO$). The oxidation state increases. In a chemical equation, electrons are shown as products ($Na_{(s)} \rightarrow Na^+_{(aq)} + e^-$).

• Reduction: The gain of electrons ($GER$). The oxidation state decreases. In a chemical equation, electrons are shown as reactants ($Mg^{2+}<em>{(aq)} + 2e^- \rightarrow Mg</em>{(s)}$).

• Mnemonic: "LEO the lion says GER."

• Example Reaction: $Cu_{(s)} + Ag^+<em>{(aq)} \rightarrow Cu^+</em>{(aq)} + Ag_{(s)}$     * Copper ($Cu_{(s)}$) is oxidized (loses an electron).     * Silver ion ($Ag^+_{(aq)}$) is reduced (gains an electron).