Chemistry in Living Organisms: Atoms to Macromolecules
The Building Blocks of Life: Atoms, Elements, and Life’s Chemistry
Everything living and nonliving is composed of matter; the smallest unit of matter is the atom.
Atoms form molecules; molecules form all organisms (hair strand to the nucleus of cells).
Key elements found in almost all living things and in many nonliving components of ecosystems include:
Hydrogen, Oxygen, Carbon, Nitrogen, Phosphorus, Calcium, Sodium, Potassium, Chloride (Cl).
These elements appear in both living organisms and nonliving components like seawater, soil, and the atmosphere.
Relative abundances vary by environment, but some elements exist in similar proportions across contexts (e.g., hydrogen and oxygen are prevalent in seawater and organisms).
Practical note: Later chapters will discuss plausible explanations for the origin of life on Earth; the elemental context is foundational for those discussions.
Subatomic Particles, Atoms, and Isotopes
Subatomic particles:
Electrons: negatively charged; orbit the nucleus of an atom.
Protons: positively charged; located in the nucleus.
Neutrons: no charge; located in the nucleus.
Electron speed in orbit: approx. 6.7 imes 10^{8} ext{ mph} (a scale that’s hard to visualize).
Electrons are arranged in shells around the nucleus. Each shell has a capacity:
First shell can hold up to 2 electrons.
Second shell can hold up to 8 electrons. (More shells exist for larger atoms.)
Atomic number Z = number of protons in the nucleus; determines the element.
Mass number A = total number of protons and neutrons in the nucleus: A = Z + N.
Isotopes:
Atoms of the same element (same Z) with different numbers of neutrons (different N).
Example: Hydrogen atoms can have different numbers of neutrons (protium, deuterium, tritium).
Isotopes differ in mass number but not in chemical identity (same Z).
Radioisotopes:
Isotopes with unstable nuclei that undergo radioactive decay over time (not influenced by environmental factors like pressure, temperature, or pH).
Decay is time-dependent and spontaneous; example: Carbon-14 (
^{14}{6} ext{C}) decays to Nitrogen-14 ( ^{14}{7} ext{N}) via radioactive decay.This process is used in dating and tracing but has nothing to do with environmental conditions alone.
Atomic Structure, Isotopes, and Mass/Atomic Numbers
Hydrogen example:
Hydrogen has Z=1 (one proton).
Isotopes differ by neutron count; but the number of protons remains 1.
Mass number vs atomic number:
Atomic number Z = protons = identity of the element.
Mass number A = ext{protons} + ext{neutrons} = Z + N.
In a periodic table entry, you may see:
A symbol for the element, the mass number A (upper left), and the element name.
Radiation and isotopes:
Radioisotopes decay independent of environmental conditions; a clock-like property of certain nuclei.
How Elements Differ: From Nuclei to Bonding
Elements differ by the number of protons in the nucleus (the atomic number Z).
When atoms have the same number of protons but different numbers of neutrons, they are isotopes of the same element.
Bonding basics (overview to connect to later sections):
Ionic bond: transfer of electrons; results in oppositely charged ions that attract.
Covalent bond: sharing of electrons between atoms.
Hydrogen bond: a weak bond between a partially positive hydrogen and a highly electronegative atom (e.g., H–O in water).
Electron configuration and chemical behavior:
The outer (valence) electrons determine an element’s reactivity and the type of bonds it forms.
Atoms tend to fill their outermost shell to achieve stability (often following the octet rule in main-group elements).
Water: A Polar Molecule Essential to Life
Water (H₂O) is polar:
Oxygen is more electronegative; the shared electrons spend more time around O than H, giving the O end a partial negative charge and the H ends a partial positive charge.
Polar molecules form hydrogen bonds between water molecules: the oxygen of one water molecule can attract the hydrogen of a neighboring water molecule.
Consequences of polarity and hydrogen bonding:
Cohesion and surface tension: water molecules stick together; surface layer resists breaking.
Adhesion and surface films: droplets and films on water surfaces exhibit cohesion.
High heat capacity and heat of vaporization: water requires substantial energy to break hydrogen bonds and, subsequently, covalent bonds when vaporizing.
Ice is less dense than liquid water due to expanded hydrogen bonding in the solid state; ice floats on liquid water and insulates bodies of water.
Water as a solvent: polar water dissolves many solutes (e.g., salts) but not nonpolar lipids; water is a universal solvent in biology.
Dissolution and solubility concepts:
Solvent: substance that dissolves solute (e.g., water).
Solute: substance that dissolves in a solvent (e.g., NaCl).
Salt dissolution: NaCl dissociates into Na⁺ and Cl⁻ ions in water; no net donation or removal of H⁺ or OH⁻ in the solution (definition of a salt).
pH and acid-base chemistry:
pH stands for the potential of hydrogen ions in a solution: ext{pH} ext{ measures } [ ext{H}^+].
Neutral pH is ext{pH} = 7; equal concentrations of hydrogen and hydroxide ions.
Acids increase [ ext{H}^+]; bases (alkaline) increase [ ext{OH}^-]; buffers resist pH changes by buffering additions/removals of H⁺ or OH⁻.
Buffers:
Substances that prevent large fluctuations in pH by donating or removing hydrogen ions as needed.
Example contexts: blood must stay near a specific pH; stomach requires a strongly acidic environment for digestion.
Environmental chemistry note:
Acid rain arises from sulfur dioxide and nitrogen oxides forming acids (e.g., sulfurous and nitric acids) with atmospheric water; leads to ecosystem and material damage.
Organic Molecules and Macromolecules (Biomolecules)
All organic molecules contain a carbon backbone; carbon-based backbones are central to macromolecules.
Macromolecules are large polymers built from monomers via dehydration synthesis (condensation): water is removed to form bonds.
Hydrolysis (adding water) breaks apart polymers into monomers.
Four major classes (macromolecules) in biology:
Carbohydrates
Lipids
Proteins
Nucleic acids
Carbohydrates: general features
Backbone formula approximation: ext{(CH}2 ext{O)}n, with carbon, hydrogen, and oxygen in roughly two hydrogens per carbon and one oxygen per carbon.
Functions: energy storage and structural roles; high-energy chemical bonds enable metabolism.
Monomers: monosaccharides (e.g., glucose, ribose, deoxyribose).
Disaccharides: sucrose, lactose, maltose (two monosaccharides joined by a glycosidic bond).
Polysaccharides: starch (plants), glycogen (animals), cellulose (plants), chitin (fungi and arthropods).
Structural vs storage roles arise from how glucose units are linked; the same monomer (glucose) forms different polysaccharides by linkage patterns.
Carbohydrates are generally high-energy and are preferred first in cellular energy metabolism due to easier breakdown and high energy content.
Lipids: general features
Contain carbon, hydrogen, and oxygen; the typical ratio approximates ext{C:H:O}
ot= ext{1:1:1}, but lipids are less polar and not water-soluble; many dissolve in nonpolar solvents (e.g., alcohols, ether).Higher energy content per gram than carbohydrates; stored energy is often used when carbohydrates are scarce.
Major categories:
Fats (triglycerides): glycerol backbone + three fatty acid chains; energy-dense and insulating; especially important for long-term energy storage and thermal insulation.
Saturated vs unsaturated fats:
Saturated fats: all single C–C bonds; fatty acid chains are straight and pack tightly; typically solid at room temperature.
Unsaturated fats: contain one or more C=C double bonds causing kinks; chains bend and are liquid at room temperature; examples include many plant fats (oils).
Trans fats: artificially produced fats with trans double bonds; not found in nature; generally more detrimental to health, associated with higher risk of cardiovascular disease; common in processed foods; less common in modern labeling but still present in some foods.
Phospholipids: glycerol backbone + phosphate group + two fatty acid tails; amphipathic (hydrophilic head, hydrophobic tails); form lipid bilayers essential for cell membranes.
Waxes: long-chain alcohols + fatty acids; protective coatings on leaves and skin to reduce water loss and provide protection.
Steroids: four-ring fused hydrocarbon skeleton; include hormones (e.g., estrogen, testosterone) and cholesterol; cholesterol is a membrane stabilizer and precursor to steroid hormones and vitamin D synthesis.
Phospholipids and the cell membrane
Phospholipid bilayer forms the basic structure of cellular membranes; hydrophilic heads face water environments (cytosol and extracellular space) while hydrophobic tails face inward away from water.
Membranes are dynamic, not rigid; lipids and proteins move within the bilayer to enable transport and signaling.
Proteins: versatile biomolecules
Functions include:
Hormones (some are proteins)
Antibodies (immune defense)
Transport proteins (e.g., hemoglobin carries oxygen; others move substances across membranes)
Enzymes (catalyze nearly all metabolic reactions; most are proteins)
Structural proteins (e.g., collagen in connective tissue; keratin in hair)
Monomers: amino acids (20 standard types).
Each amino acid has: amino group (–NH₂ or –NH₃⁺ in physiological pH), carboxyl group (–COOH), a central (alpha) carbon, a hydrogen, and a variable side chain (R group).
The R group determines the identity and properties of each amino acid.
Peptide bonds: link amino acids via a covalent bond between the carboxyl group of one amino acid and the amino group of the next (a condensation reaction; water is removed).
Dipeptide (two amino acids) and polypeptide (long chain) terminology.
Protein structure levels:
Primary structure: linear sequence of amino acids (single polypeptide chain).
Secondary structure: localized folding patterns (alpha helices and beta pleated sheets) stabilized by hydrogen bonds between backbone amide and carbonyl groups.
Tertiary structure: overall three-dimensional folding of a single polypeptide, stabilized by various interactions and sometimes disulfide bonds between cysteine residues.
Quaternary structure: arrangement of multiple polypeptide chains into a functional protein (e.g., hemoglobin has four subunits).
Denaturation: loss of three-dimensional structure and function due to disruption of bonds (e.g., heat, pH changes) — often irreversible for many proteins.
Prions (misfolded proteins): example of protein misfolding diseases (e.g., mad cow disease); prions induce normal proteins to adopt abnormal conformations, forming plaques that damage neural tissue.
Nucleic Acids: information storage and energy carriers
Monomers: nucleotides (each composed of a sugar, a phosphate group, and a nitrogenous base).
Nitrogenous bases for DNA: adenine (A), thymine (T), cytosine (C), guanine (G).
Nitrogenous bases for RNA: adenine (A), guanine (G), uracil (U), cytosine (C).
DNA: deoxyribonucleic acid; typically double-stranded, forming a double helix with a sugar–phosphate backbone and paired bases facing inward.
Base pairing rules (A pairs with T; C pairs with G) via hydrogen bonds.
Structure: two strands coiled in a right-handed helix; strands held together by hydrogen bonds between bases and by backbone interactions.
RNA: ribonucleic acid; usually single-stranded and can fold into complex structures; uses bases A, G, C, and uracil (U).
ATP (adenosine triphosphate): a nucleotide with three phosphate groups; energy-carrying molecule in cells.
Energy currency concept: energy stored in the phosphoanhydride bonds between phosphate groups.
Hydrolysis of the terminal phosphate releases energy that powers cellular work, converting ATP to ADP (and sometimes to AMP) depending on the reaction.
The language of heredity and the universal genetic code suggest common origin across life, since DNA-based information transfer is conserved across organisms.
The Four Macromolecule Classes in Depth
Carbohydrates (as energy sources and structural components)
Monosaccharides (single sugar units): glucose, ribose, deoxyribose.
Disaccharides: two monosaccharides linked together (e.g., sucrose, lactose, maltose).
Polysaccharides: many monosaccharide units; starch (plants, storage), glycogen (animals, storage), cellulose (plants, structural), chitin (fungi, exoskeletons).
Energy considerations: carbohydrates contain high-energy bonds and are typically metabolized first when available.
Lipids (energy storage, membranes, signaling)
Fats (triglycerides): glycerol + three fatty acids; high energy density; insulation and cushioning.
Saturated fats: no double bonds; straight chains; typically solid at room temperature; can contribute to arterial plaque with excessive intake.
Unsaturated fats: contain one or more double bonds; kinked chains; typically liquid at room temperature; generally healthier dietary fats.
Trans fats: artificially created by hydrogenating unsaturated fats; associated with higher health risks; not commonly found in natural foods and often subject to regulation.
Phospholipids: glycerol + two fatty acids + phosphate group; amphipathic; form lipid bilayers of cell membranes.
Waxes: long-chain alcohols and fatty acids; protective coatings (e.g., on plant leaves) to reduce water loss.
Steroids: four-ring hydrocarbon skeleton; include cholesterol (membrane component; precursor to steroid hormones and vitamin D synthesis); estrogen and testosterone are steroid hormones; others regulate various physiological processes.
Proteins (diverse functions and structures)
Functions include: hormones, antibodies, enzymes, transport proteins (e.g., hemoglobin), structural components (collagen, keratin).
Monomers: amino acids (20 standard types).
Amino acid structure: amino group (–NH₂), carboxyl group (–COOH), central (alpha) carbon, hydrogen, and a variable side chain (R).
Peptide bonds link amino acids; formation is a dehydration synthesis reaction; breaking is hydrolysis.
Protein structures:
Primary: linear amino acid sequence.
Secondary: alpha helices and beta pleated sheets formed by hydrogen bonds between backbone atoms.
Tertiary: three-dimensional folding stabilized by various interactions (hydrophobic effects, ionic bonds, hydrogen bonds, disulfide bonds).
Quaternary: assembly of multiple polypeptide chains into a functional protein (e.g., hemoglobin with four subunits).
Denaturation: loss of native structure and function due to environmental changes; many enzymes require proper tertiary structure to function.
Prions: misfolded proteins that can induce other proteins to misfold, causing neurodegenerative diseases (e.g., mad cow disease).
Nucleic Acids (genetic information and energy carriers)
DNA: deoxyribonucleic acid; double-stranded, helical structure; sugar backbone is deoxyribose; bases include A, T, C, G; base pairing is A–T and C–G via hydrogen bonds.
RNA: ribonucleic acid; typically single-stranded; bases include A, U, C, G; uses ribose sugar.
ATP: adenosine triphosphate; energy currency; consists of adenosine (adenine + ribose) plus three phosphate groups; energy is released when the bond between the second and third phosphate is hydrolyzed.
Key point: the genetic language (DNA) and metabolic energy language (ATP) are central to life across organisms, underscoring a shared biochemical foundation.
Real-World Connections and Practical Implications
Water’s properties underpin life-supporting processes: solvent capabilities enable nutrient transport; surface tension supports certain organisms at interfaces; ice insulation preserves aquatic ecosystems.
Nutrition and health: saturated vs unsaturated fats; trans fats’ health risks; cholesterol’s role in membranes and hormone synthesis.
Environmental health: acid rain impacts on ecosystems and infrastructure; buffers in blood and other fluids keep systems stable despite external fluctuations.
Disease and biology: prions illustrate how protein misfolding can cause severe pathology; proper protein folding is essential for function; enzyme activity underpins almost all metabolic pathways.
Medical and biotechnological relevance: understanding DNA structure informs genetics, forensic science, and biotechnology; ATP's role in energy transfer underlies metabolic engineering and physiology.
Summary of Key Formulas and Concepts (LaTeX-formatted)
Atomic number: Z= ext{number of protons}
Mass number: A=Z+N= ext{protons}+ ext{neutrons}
Electron shell capacities: first shell 2 electrons; second shell 8 electrons (simplified rule for basic chemistry).
pH scale: ext{pH} ext{ measures } [ ext{H}^+], ext{ neutral at } ext{pH}=7 ; acids increase [ ext{H}^+], bases increase [ ext{OH}^-].
Salt dissolution: NaCl → Na⁺ + Cl⁻ in water (no net change in [ ext{H}^+] or [ ext{OH}^-]).
Energy in bonds (metabolism): energy released when high-energy phosphate bonds in ATP are hydrolyzed; ATP → ADP + Pi releases usable energy for cellular work.
Polarity and hydrogen bonding: polar molecules (like water) form hydrogen bonds between molecules; the strength and number of such bonds contribute to water’s unique properties.
Quick Terminology recap
Atom, element, isotope, radioisotope
Ionic bond, covalent bond, hydrogen bond
Polar molecule, solvent, solute
Monomer, polymer, dehydration synthesis, hydrolysis
Carbohydrate, lipid, protein, nucleic acid
Monosaccharide, disaccharide, polysaccharide
Fatty acid (saturated vs unsaturated), triglyceride, phospholipid, wax, steroid
Amino acid, peptide bond, primary/secondary/tertiary/quaternary structure, denaturation, prion
DNA, RNA, ATP, nucleotide, base pairing (A–T, C–G), double helix