Biology and the Chemical Basis of Life

Foundations of Biology and the Study of Life

• Biology is the scientific study of living things, referred to as organisms.
• The term is derived from the Greek words "bios" (meaning life) and "logos" (meaning study).
• Biology is an empirical science rooted in systematic observations, the formulation of hypotheses, predictions, and both observational and experimental testing.
• The field encompasses many areas of inquiry, including the structure, function, growth, origin, evolution, and distribution of living organisms.

Defining Characteristics of Living Organisms

Living organisms are distinguished from the nonliving world by several universal characteristics:

• Cellular Composition: Organisms consist of one or more cells.
• Energy Laws: All organisms are constructed and governed by the same laws of physics and energy.
• Metabolism: Organisms engage in metabolism, which is the capacity to acquire and use energy and materials from their surroundings to survive, maintain themselves, grow, and reproduce more cells.
• Responsiveness: Organisms sense and make controlled responses to changes in both their internal and external environments.
• Heritability: Instructions encapsulated in DNA (deoxyribonucleic acid) provide the capacity for growth and reproduction.
• Evolution: The characteristics that define a specific population change over time through evolution.

The Molecular Level and DNA

• Intellectual distinctions between living and nonliving entities emerge at the molecular level. Unlike living organisms, inanimate objects such as rocks are never composed of nucleic acids, proteins, carbohydrates, and lipids.
• In nature, only living cells are capable of synthesizing these specific biological molecules.
• The cell is the smallest unit of life and contains DNA, the signature molecule of life.
• DNA Functions:
  • Holds assembly instructions for various proteins constructed from smaller subunits called amino acids.
  • Works in conjunction with RNAs (ribonucleic acids) to translate DNA instructions into proteins.
• Enzymes: These are specialized proteins that act as "worker molecules." When provided with an energy boost, they build, split, and rearrange the molecules of life.
• Energy: Defined as the capacity to do work, energy is the driving force behind all molecular events within a cell.

Levels of Biological Organization

Biological complexity is organized into twelve distinct, hierarchical levels:

1. Subatomic Particle: Fundamental units such as electrons, protons, and neutrons.
2. Atom: The smallest unit of an element that retains the properties of that element.
3. Molecule: A unit consisting of two or more bonded-together atoms of the same or different elements.
4. Organelle: A membrane-bound internal compartment designated for specialized chemical reactions within a cell.
5. Cell: The smallest unit with the capacity to live and reproduce, either independently or as part of a multicelled organism.
6. Tissue: An organized aggregation of cells and substances functioning together in a specialized activity.
7. Organ: A structural unit where tissues combine in specific patterns and amounts to perform a common task.
8. Organ System: Two or more organs interacting chemically, physically, or both to contribute to the survival of the organism.
9. Multicelled Organism: An individual consisting of interdependent cells organized into tissues, organs, and organ systems.
10. Population: A group of individuals of the same species occupying a designated area.
11. Community: All populations of all species occupying the same area.
12. Ecosystem: A community interacting with its physical environment.
13. Biosphere: All regions of the Earth's crust, waters, and atmosphere that sustain life.

Interdependencies and Energy Flow

• Nutrients: Types of atoms or molecules that play essential roles in growth and survival which an organism cannot produce for itself.
• Producers: Organisms, such as plants, that acquire energy and simple raw materials from the environment to manufacture their own food (e.g., through photosynthesis).
• Consumers: Organisms, including animals, most fungi, many protists, and bacteria, that cannot make their own food. They obtain energy and nutrients indirectly by eating producers and other organisms.
• Decomposers: Organisms that break down dead material; some nutrients released during decomposition cycle back to producers.
• One-Way Energy Flow: Energy enters the ecosystem (mainly from sunlight), flows through producers and then consumers, and eventually leaves the ecosystem, primarily as heat. Energy does not cycle; it flows in one direction.

Chemical Basis of Life: Elements and Atoms

• Element: A fundamental form of matter that occupies space, has mass, and cannot be broken down into a different form of matter by ordinary physical or chemical means.
• Essential Elements: The most common elements in living organisms are Oxygen, Carbon, Hydrogen, and Nitrogen. Lesser amounts of Calcium, Phosphorus, Potassium, and Sulfur are also present.
• Atomic Components:
  • Proton ($p^+$): A positively charged particle found in the atomic nucleus. The number of protons determines the atomic number. A lone proton without an electron is a hydrogen ion ($H^+$).
  • Electron ($e^-$): A negatively charged particle occupying specific volumes of space (orbitals) around the nucleus. Electrons can be transferred or shared between atoms.
  • Neutron: An uncharged particle in the nucleus (except in hydrogen). The mass number is the sum of protons and neutrons.
• Isotope: Forms of an element's atoms that differ in their number of neutrons.
• Ion: An atom that has gained or lost one or more electrons, resulting in a net negative or positive charge.

Molecules, Mixtures, and Solutions

• Molecule: Two or more atoms of the same or different elements bonded together.
• Compound: A molecule composed of two or more different elements in unvarying proportions (e.g., $H_2O$).
• Mixture: An intermingling of two or more elements in proportions that can and usually do vary.
• Solute: Any molecule or ion that dissolves in a solvent. Dissolution occurs when water molecules cluster around ions or molecules to keep them dispersed in the fluid.
• Hydrophilic Substances: "Water-loving" polar molecules that readily dissolve in water.
• Hydrophobic Substances: "Water-dreading" nonpolar molecules that strongly resist dissolving in water.

Properties of Water and pH

• Temperature-Stabilizing Effects: Cells rely on water to absorb heat released by metabolism. Without hydrogen bonds, cells would essentially "cook in their own juices." Temperature measures molecular motion.
• Evaporation: The process where heat energy converts liquid water into a gaseous state.
• Cohesion: The capacity of water to resist rupturing when placed under tension (stretched).
• Solvent Properties: Water's polarity makes it an excellent solvent for ions and other polar molecules.
• Acids: Substances that release hydrogen ions ($H^+$) when dissolved in water.
• Bases: Substances that accept hydrogen ions ($H^+$) when dissolved in water.
• Buffers: Compounds that help maintain pH by accepting or donating hydrogen ions.
• Salts: Compounds that release ions other than $H^+$ or $OH^-$ when dissolved in water.
• pH Scale: A measure of the concentration of hydrogen ions in a substance.

Carbohydrates

• Carbohydrates are the most abundant biological molecules and generally consist of Carbon, Hydrogen, and Oxygen in a $\frac{1}{2}{1}$ ratio, represented by the formula $(CH_2O)$.
• Monosaccharides: Simple sugars consisting of one monomer. They dissolve easily in water and serve as the main energy source (e.g., Ribose and Deoxyribose).
• Oligosaccharides: Short-chain carbohydrates ("Oligo" means a few).
  • Disaccharides: Consist of two sugar units.
  • Lactose: Milk sugar containing one glucose and one galactose unit.
  • Sucrose: The most plentiful sugar in nature, consisting of glucose and fructose.
• Polysaccharides: Complex carbohydrates made of straight or branched chains of many sugar monomers. Examples include cellulose, starch, and glycogen.

Lipids

• Lipids are nonpolar hydrocarbons that resist dissolution in water but dissolve in nonpolar substances. They function as energy stores and structural materials.
• Fats and Fatty Acids: Consist of glycerol attached to one, two, or three fatty acids. Triglycerides (neutral fats) have a glycerol head and three fatty acid tails and serve as major energy reservoirs.
• Phospholipids: Consist of a glycerol backbone, two fatty acid tails, and a hydrophilic head with a phosphate group. They are the primary components of cell membranes (lipid bilayers).
• Sterols/Steroids: Lipids lacking fatty acids, featuring a rigid backbone of four fused carbon rings.
  • Cholesterol: Common in animal tissues and nerve cell membranes; precursor for other steroids.
  • Bile Acids/Salts: Remodeled from cholesterol to assist in fat emulsification and digestion.
  • Hormones: Adrenocortical hormones (cortisol, aldosterone) involved in stress; female reproductive hormones (estrogen, progesterone); male reproductive hormone (testosterone); and Ecdysone (causes molting in arthropods).
  • Vitamin D2 (Calciferol): Facilitates calcium and phosphate absorption in the small intestine.
• Waxes: Firm, water-repelling lubricating substances with long-chain fatty acids (e.g., beeswax used for honeycombs).

Proteins and Amino Acids

• Protein Levels of Structure:
  • Primary: The specific sequence of amino acids along a polypeptide chain.
  • Secondary: Local regions that fold or twist into helical coils, sheet-like arrays, and loops.
  • Tertiary: Polypeptide chains organized into domains, which are structurally stable, compact units with distinct functions.
  • Quaternary: Two or more polypeptide chains joined together by hydrogen bonds, covalent bonds, and disulfide bridges.
• Classifications by Structure:
  • Fibrous Proteins: Polypeptide chains in long strands; stable and insoluble in water; serve structural functions (e.g., collagen in bone, keratin in hair).
  • Globular Proteins: Polypeptide chains rolled into spherical shapes; relatively unstable and soluble in water; serve metabolic functions (e.g., enzymes, antibodies, hemoglobin, insulin).
• Classifications by Composition:
  • Simple Proteins: Pure proteins containing no other substances.
  • Conjugated Proteins: Consist of a protein portion and a non-protein prosthetic group.
• Functions: Enzymes, hormones, structural formation, and respiratory substrates.
• Denaturation: The breaking of weak bonds (like hydrogen bonds) that disrupts the three-dimensional shape of a protein. This is caused by changes in temperature and pH.

Nucleotides and Nucleic Acids

• Nucleotides: Small organic compounds containing a five-carbon sugar, a phosphate group, and a nitrogenous base. They serve as energy carriers, chemical messengers between cells and cytoplasm, and subunits for coenzymes and nucleic acids.
• DNA Structure:
  • Consists of two polynucleotide strands arranged in an anti-parallel fashion (opposite directions).
  • Sugar is deoxyribose.
  • Coiled into a double helix held by hydrogen bonds between nitrogenous bases.
  • Base Pairing: Adenine (A) pairs with Thymine (T); Guanine (G) pairs with Cytosine (C).
• RNA Structure:
  • Single-stranded with ribose sugar.
  • Bases include Adenine (A), Guanine (G), Cytosine (C), and Uracil (U) instead of Thymine.
  • Three Types:
    • ribosomal RNA (rRNA): Component of ribosomes for protein synthesis.
    • Messenger RNA (mRNA): Carries information for making proteins.
    • transfer RNA (tRNA): Delivers amino acids to protein factories (ribosomes).
• Nitrogenous Bases:
  • Purines: Double-ringed (Adenine, Guanine).
  • Pyrimidines: Single-ringed (Thymine, Cytosine, Uracil).