Levels of Organisation

Learning Outcomes

  • Describe an atom and how atomic structure affects interactions between atoms.

  • Compare the ways in which atoms combine to form molecules and compounds.

  • Distinguish among the major types of chemical reactions that are important for studying physiology.

  • Describe the crucial role of enzymes in metabolism.

  • Distinguish between inorganic compounds and organic compounds.

  • Explain how the chemical properties of water make life possible.

  • Explain pH and discuss its importance.

Atoms and Atomic Structure

Matter

  • Defined as anything that takes up space and has mass.

  • Composed of atoms, which join together to form chemicals displaying diverse characteristics.

  • The chemical characteristics of these compounds dictate physiological functions at molecular and cellular levels.

Subatomic Particles

  • Protons: Positive charge, approximately 1 mass unit.

  • Neutrons: Neutral charge, approximately 1 mass unit.

  • Electrons: Negative charge, very low mass compared to protons and neutrons.

Atomic Structure

  • Atomic Number: The number of protons in an atom determines its identity and chemical properties.

  • Nucleus: Contains protons and neutrons.

  • Electron Cloud: Spherical region surrounding the nucleus where electrons reside.

  • Electron Shell: A two-dimensional model representing energy levels within the electron cloud.

Example: Hydrogen Atom

  • The three-dimensional model of a hydrogen atom depicts the electron cloud formed by a single electron.

Principal Elements in the Human Body (Table 2-1)

Major Elements

  • Oxygen (O): 65% – Component of water and necessary for respiration.

  • Carbon (C): 18.6% – Found in all organic molecules.

  • Hydrogen (H): 9.7% – Component of water and most compounds.

  • Nitrogen (N): 3.2% – Found in proteins and nucleic acids.

  • Calcium (Ca): 1.8% – Found in bones; important for functions such as muscle contraction.

  • Phosphorus (P): 1.0% – Found in nucleic acids and high-energy compounds.

  • Potassium (K): 0.4% – Vital for membrane functions.

Trace Elements

  • Elements found in small amounts, including sodium, chlorine, magnesium, sulfur, iron, iodine, and various essential trace elements.

Isotopes and Atomic Weight

  • Element Definition: A pure substance made of one kind of atom; defined by its atomic number.

  • Isotopes: Variants of elements characterized by differing mass numbers (number of protons + neutrons).

  • Radioisotopes: Unstable isotopes that exhibit radioactive decay.

    • Decay Rate: Expressed in terms of half-life.

  • Atomic Weight: Average mass of all isotopes of an element, where 1 mole equals its atomic weight in grams.

Electrons and Energy Levels

  • Electrons in the outer electron cloud influence an atom's reactivity.

  • Electrons are arranged in shells or energy levels that fill in order from lowest to highest.

  • The outermost shell is termed the valence shell, pivotal for bonding.

Examples of Electron Arrangement

  • Hydrogen (H): Atomic number 1, with 1 electron in its first energy level.

  • Helium (He): Atomic number 2, with 2 electrons filling the first energy level.

  • Lithium (Li): Atomic number 3, with 3 electrons, where the first shell holds 2, and the second shell has 1.

  • Neon (Ne): Atomic number 10, with a complete filling in the first two shells (2 in the first and 8 in the second).

Molecules and Compounds

Chemical Bonds

  • Molecule: Formed by two or more atoms joined by strong bonds.

  • Compound: Formed by two or more different elements joined by strong or weak bonds.

  • Not all molecules qualify as compounds, and vice-versa.

  • Molecular Weight: The sum of atomic weights of all atoms in a molecule.

Chemical Notation and Reactions

  • The representation of atomic and molecular amounts using symbols; for instance, H represents one atom of hydrogen, while H₂ indicates two hydrogen atoms.

  • Chemical reactions entail reactants transforming into products, represented by equations.

  • Conservation of Atoms: Chemical reactions rearrange atoms without creating or destroying them.

Ions

  • An ion is formed when an atom gains or loses one or more electrons, thereby acquiring a charge.

    • Cations: Positive ions formed when electrons are lost (e.g., Na⁺).

    • Anions: Negative ions formed when electrons are gained (e.g., Cl⁻).

Types of Chemical Bonds

  • Ionic Bonds: Formed from the attraction between cations and anions.

  • Covalent Bonds: Result from electron sharing between atoms; can be single, double, or triple.

    • Nonpolar Covalent Bonds: Equal sharing of electrons.

    • Polar Covalent Bonds: Unequal sharing due to differing pulls, leading to partial charges.

  • Hydrogen Bonds: Weaker bonds based on charge attractions, significant in water's properties.

States of Matter

  • Solid: Defined shape and volume.

  • Liquid: Defined volume, takes shape of container.

  • Gas: Changes both volume and shape.

Chemical Reactions

Key Concepts

  • Chemical reactions involve the formation or breaking of bonds:

    • Reactants: Substances entering a reaction.

    • Products: Substances produced by a reaction.

    • Metabolism: All chemical reactions in the body.

Energy in Reactions

  • Energy: The ability to do work, classified into types such as kinetic (motion) and potential (stored).

  • Chemical Energy: Potential energy stored in chemical bonds.

Types of Chemical Reactions

  • Decomposition: AB → A + B (e.g., Hydrolysis: AB + H₂O → AH + BOH).

  • Synthesis: A + B → AB (includes Dehydration Synthesis: AH + BOH → AB + H₂O).

  • Exchange: AB + CD → AD + CB.

  • Reversible Reactions: A + B ↔ AB, in dynamic equilibrium.

Enzymes

Function and Characteristics

  • Enzymes serve as catalysts, lowering activation energy required for reactions; essential in metabolism.

    • Types:

    • Exergonic: Releasing energy.

    • Endergonic: Absorbing energy.

  • Enzymes maintain specificity for substrates and work under specific conditions.

Cofactors and Enzyme Function

  • Cofactors: Non-protein substances that aid enzyme functionality, including minerals and vitamins.

  • Factors affecting enzymes include temperature and pH, where extremes can cause denaturation.

Glycoproteins and Proteoglycans

  • Glycoproteins: Large proteins combined with smaller carbohydrates, serving multiple functions.

  • Proteoglycans: Composed of large polysaccharides and polypeptides increasing fluid viscosity.

Nucleic Acids

Nucleic Acids Structure and Function

  • Large organic molecules (e.g., DNA, RNA).

  • DNA: Carries genetic information, directs protein synthesis.

  • RNA: Involved in protein synthesis and the intermediary process.

Nucleotide Structure

  • Comprising a pentose sugar, phosphate group, and nitrogenous base (A, G, T, C for DNA; U replaces T in RNA).

Comparison of DNA and RNA (Table 2-6)

  • DNA and RNA differ in structure (double helix vs. single strand), sugar types (deoxyribose vs. ribose), and nitrogenous bases.

High-Energy Compounds

Description

  • High-energy compounds such as ATP are crucial for cellular processes.

  • Phosphorylation: Adding a phosphate group to a molecule to yield a high-energy bond.

  • ATP: Principal energy currency in cells; consists of adenosine and three phosphate groups.