The Chemistry of Life
MODULE 2.3 CHEMICAL REACTIONS
CHEMICAL NOTATION
A chemical reaction is defined as occurring whenever:
A chemical bond is formed, broken, or rearranged.
Electrons are transferred between two or more atoms or molecules.
Chemical notation refers to:
A series of symbols and abbreviations that demonstrate what occurs in a reaction.
Chemical equation: the basic form of chemical notation consisting of two parts:
Reactants: located on the left side of the equation and represent the starting ingredients which will undergo the reaction.
Products: located on the right side of the equation and represent the results of the chemical reaction.
CHEMICAL REACTIONS
Reversible reactions:
Can proceed in either direction, denoted by two arrows pointing in opposite directions (↔).
Irreversible reactions:
Proceed from left to right, denoted by a single arrow (→).
Example:
CO2 + H20→ H2CO3 (where carbon dioxide + water yields carbonic acid).
ENERGY AND CHEMICAL REACTIONS
Energy: Defined as the capacity to do work or to put matter into motion or to fuel chemical reactions.
Two general forms of energy:
Potential energy: Stored energy that can be released to do work later.
Kinetic energy: Energy released from potential energy that is in motion; every atom possesses kinetic energy due to being in constant motion, with faster-moving atoms possessing greater energy.
Three forms of energy in human body:
Chemical energy: Found in bonds between atoms and drives most chemical processes.
Electrical energy: Generated by the movement of charged particles or ions.
Mechanical energy: Directly transferred from one object to another.
Energy must be invested for chemical reactions to occur:
Endergonic reactions: Require input of energy from another source; products contain more energy than reactants as energy was invested for the reaction to proceed.
Exergonic reactions: Release excess energy; products have less energy than reactants.
HOMEOSTASIS AND TYPES OF CHEMICAL REACTIONS
Three fundamental processes to maintain homeostasis in the body:
Breaking down molecules.
Converting energy in food to usable form.
Building new molecules.
Three basic types of chemical reactions:
Catabolic reactions (decomposition reactions):
Involves breaking down a large substance into smaller substances.
General chemical notation: AB→ A + B
Typically, exergonic due to the breaking of chemical bonds.
Exchange reactions:
Occur when one or more atoms from reactants are exchanged for each other.
General chemical notation: AB + CD→ AD + BC
Example: HCl + NaOH→ H2O + NaCl
Anabolic reactions (synthesis reactions):
Occur when small, simple subunits are united by chemical bonds to form larger, more complex substances.
General chemical notation: A + B→ AB
These reactions are endergonic and fueled by chemical energy.
REACTION RATES AND ENZYMES
Activation energy (Ea): Energy required for atoms to collide with enough energy to overcome electron repulsion and react.
Analogy for chemical reactions:
Activation energy must be supplied for reactants to reach their transition states (to the top of the "energy hill") in order to react and form products (fall down the hill).
Factors that increase reaction rate:
Concentration: Higher concentration increases the chance of successful collisions between reactants.
Temperature: Raising temperature increases kinetic energy, resulting in more forceful effective collisions.
Properties of reactants: Particle size and state of matter influence reaction rates:
Smaller particles move faster and possess more energy compared to larger particles.
Reactant particles in gas phase generally have higher kinetic energy than those in solid or liquid phase.
Catalyst: A substance that increases reaction rate by lowering activation energy without being consumed or altered.
Enzymes: Biological catalysts, mostly proteins, that:
Speed up reactions by lowering activation energy.
Are highly specific for individual substrates (substances that can bind to the enzyme’s active site).
Do not alter the reactants or products.
Are not permanently altered in reactions they catalyze.
Induced-fit mechanism:
Describes the interaction between the enzyme and its substrate, where the binding of the substrate causes a shape change that reduces the energy of activation, allowing the transition state to proceed to final products.
MODULE 2.4 INORGANIC COMPOUNDS: WATER, ACIDS, BASES, AND SALTS
BIOCHEMISTRY
Biochemistry: The chemistry of life.
Inorganic compounds: Typically, do not contain carbon bonded to hydrogen (e.g., water, acids, bases, and salts).
Organic compounds: Contain carbon bonded to hydrogen.
WATER
Water (H2O) constitutes approximately 60–80% of the human body mass and has several essential properties:
High heat capacity: Absorbs heat without a significant change in temperature.
Carries heat: Evaporates and carries heat when changing from a liquid to a gas.
Cushions and protects: Due to relatively high density.
Acts as a lubricant: Reduces friction between adjacent surfaces.
Solvent Properties:
Water is considered the body’s primary solvent (often called the universal solvent) because many solutes will dissolve in it entirely or partially.
Water is a polar covalent molecule with:
Oxygen pole: Partially negative (δ-).
Hydrogen pole: Partially positive (δ+).
This polarity allows water molecules to engage with certain solutes, surrounding them and keeping them apart.
Hydrophilic solutes:
Those that have fully or partially charged ends and can dissolve in water (ionic and polar covalent solutes).
Hydrophobic solutes:
Those without charged ends that do not dissolve in water (e.g., uncharged nonpolar covalent molecules like oils and fats).
ACIDS AND BASES
Study of acids and bases commonly reduces to understanding the hydrogen ion (H+).
Dissociation in water: Water molecules may break into hydrogen ions (H+) and hydroxide ions (OH-).
Definitions:
Acid: A hydrogen ion or proton donor; increases the number of hydrogen ions in a solution when added (e.g., HCl).
Base (alkali): A hydrogen ion acceptor; reduces the number of hydrogen ions in a solution when added (e.g., NaHCO3).
pH SCALE
pH scale: Ranges from 0–14 and represents the concentration of hydrogen ions in a solution:
pH = 7: Neutral solution (equal numbers of H+ and OH-).
pH < 7: Acidic solution (H+ outnumbers OH-).
pH > 7: Basic or alkaline solution (OH- outnumbers H+).
Buffer: A chemical system that resists pH changes, preventing large swings in pH when acids or bases are added.
Blood pH must remain within a narrow range to maintain homeostasis: Natural ranges are:
Blood pH: 7.35–7.45
Intracellular pH: 7.2
SALTS AND ELECTROLYTES
Salt: Any metal cation and nonmetal anion held together by ionic bonds.
Salts dissolve in water to form ions called electrolytes that can conduct electrical current.
MODULE 2.5 ORGANIC COMPOUNDS: CARBOHYDRATES, LIPIDS, PROTEINS, AND NUCLEOTIDES
MONOMERS AND POLYMERS
Organic compounds in the body consist of polymers built from monomer subunits:
Monomers: Single subunits that can combine to create larger structures (polymers) through:
Dehydration synthesis: An anabolic reaction that links monomers and releases a molecule of water in the process.
Hydrolysis: A catabolic reaction that uses water to break up polymers into smaller subunits.
CARBOHYDRATES
Carbohydrates: Composed of carbon, hydrogen, and oxygen, primarily functioning as fuel with some structural roles.
Types of carbohydrates:
Monosaccharides (3 to 7 carbons): The basic building blocks; common monosaccharides include glucose, fructose, galactose, ribose, and deoxyribose.
Disaccharides: Formed by the union of two monosaccharides through dehydration synthesis.
Polysaccharides: Composed of many monosaccharides linked by dehydration synthesis.
Example: Glycogen is the storage polymer of glucose, primarily found in skeletal muscle and liver cells.
Some polysaccharides are attached to proteins or lipids to form glycoproteins and glycolipids with various functions in the body.
LIPIDS
Lipids: A group of hydrophobic molecules primarily composed of carbon and hydrogen, including fats and oils.
Fatty acids:
Lipid monomers consisting of 4 to 20 carbon atoms that may have 0, 1, or multiple double bonds between carbon atoms.
Types of fatty acids:
Saturated fatty acids: Solid at room temperature; contain no double bonds between carbon atoms.
Monounsaturated fatty acids: Generally liquid at room temperature; contain one double bond between two carbons.
Polyunsaturated fatty acids: Liquid at room temperature; contain multiple double bonds between carbons.
Triglyceride: Composed of three fatty acids linked to glycerol via dehydration synthesis; serves as a storage polymer for fatty acids (also known as neutral fat).
Phospholipids: Composed of a glycerol backbone, two fatty acid tails, and a phosphate head instead of a third fatty acid; amphiphilic in nature, essential for forming cellular membranes.
Steroids: Nonpolar molecules with a four-ring hydrocarbon structure; cholesterol is a steroid that serves as the precursor for all other steroids.
PROTEINS
Proteins: Macromolecules serving various functions including:
Enzymatic activity.
Structural roles.
Involvement in movement.
Participation in the body's defenses.
Possible fuel source.
Amino acids: The 20 different monomers linked by peptide bonds to form polypeptides.
Peptides: Formed from two or more amino acids linked together by peptide bonds through dehydration synthesis.
Examples:
Dipeptides: Composed of two amino acids.
Tripeptides: Composed of three amino acids.
Polypeptides: Composed of ten or more amino acids.
Protein structure: Comprised of one or more polypeptide chains folded into specific shapes crucial for functionality. The levels of protein structure are:
Primary structure: Sequence of amino acids in a polypeptide chain.
Secondary structure: Refers to segments of primary structure folded in specific ways (alpha helix and beta-pleated sheet) held together by hydrogen bonds.
Tertiary structure: The overall three-dimensional shape of the peptide chain, maintained by interactions among R groups.
Quaternary structure: The arrangement of multiple polypeptide chains into a single functional protein.
Protein denaturation: The process of altering a protein's shape due to factors such as heat, pH changes, or exposure to chemicals, disrupting the stabilizing interactions, leading to loss of function.
NUCLEOTIDES AND NUCLEIC ACIDS
Nucleotides: The monomers of nucleic acids, essential components of genetic material, consisting of:
A nitrogenous base (purines: adenine (A) and guanine (G); pyrimidines: cytosine (C), uracil (U), and thymine (T)).
A five-carbon sugar (ribose or deoxyribose).
A phosphate group.
Adenosine triphosphate (ATP): A nucleotide structure comprising adenine, ribose, and three phosphate groups, serving as the primary source of chemical energy in the body.
ATP is synthesized from adenosine diphosphate (ADP) and a phosphate group (Pi) utilizing energy derived from oxidation of fuels like glucose.
DNA: A large macromolecule consisting of two long chains forming a double helix, which contains genes providing the instructions for protein synthesis.
The backbone is made of deoxyribose sugar alternates with phosphate groups, with hydrogen bonds forming between complementary base pairs (A pairs with T, G pairs with C).
RNA: A single strand of nucleotides, vital for protein synthesis, containing ribose sugar and uracil instead of thymine. RNA transcribes the genetic code from DNA and translates it into protein.