Introduction to Basic Chemistry for Biology

The Periodic Table and Elements

  • The periodic table contains approximately 118118 different elements.
  • This table is dynamic, meaning new elements can be discovered, potentially leading to significant scientific recognition.
  • All living organisms, from bacteria to humans, are composed of elements.
  • Specific elements form the major components of living things, with others present in smaller amounts.

Atoms and Their Fundamental Components

  • Elements are essentially made up of atoms.
  • Atoms combine to form molecules, which then make up organelles and cells.
  • Determining Compound Properties: The properties of a compound are determined by the characteristics of its constituent atoms and how they bond.
  • Atomic Structure: Atoms can be broken down into three subatomic particles:
    • Protons: Positively charged (++.) Located in the nucleus.
    • Neutrons: Neutrally charged (no charge). Located in the nucleus.
    • Electrons: Negatively charged (−-). Orbit the nucleus in shells.
  • Nucleus: The center of an atom, comprised of protons and neutrons, making the core of the atom somewhat positively charged.
  • Electron Shells: Electrons surround the nucleus in distinct shells and largely determine an atom's characteristics and how it will bond with other atoms.
  • The interaction of positive and negative charges allows atoms to bond together to form compounds, which in turn build larger structures (e.g., properties of water discussed in Chapter 3).

Matter vs. Life

  • Organisms are Composed of Matter: All living things are made of matter.
  • Smallest Unit of Matter: Atoms are defined as the smallest unit of matter.
  • Smallest Unit of Life: Cells are the smallest unit of life.
  • Distinction: There is a clear difference between matter and life.
    • Living: Cells are living (e.g., organisms).
    • Non-living: Matter can be non-living (e.g., water, sun, rocks). Non-living things do not grow, reproduce, or exhibit other characteristics of life.
  • Understanding these foundational concepts in chemistry is crucial for comprehending biology, analogous to building a structure brick by brick.

Elements and Compounds in Living Organisms

  • Matter is Made of Elements: As seen in the periodic table (e.g., carbon, hydrogen, oxygen, nitrogen, gold, silver, lithium).
  • Compounds as Emergent Properties: Elements combine to form compounds. This is an example of emergent properties, where new characteristics arise from the arrangement and interaction of simpler components (e.g., bike parts forming a functional bike).
  • Example: Sodium ($\text{Na}$) and Chlorine ($\text{Cl}$) are individual elements. When combined, they form Sodium Chloride ($\text{NaCl}$), which is table salt. Pure sodium is not consumable, but salt is.
  • Essential Elements for Living Things: All living organisms are primarily composed of four main elements (making up 96%96 \% of their mass):
    • CHON: Carbon ($\text{C}$), Hydrogen ($\text{H}$), Oxygen ($\text{O}$), Nitrogen ($\text{N}$).
  • Secondary Elements: Another 4%4 \% of living matter consists of:
    • Calcium ($\text{Ca}$), Phosphorus ($\text{P}$), Potassium ($\text{K}$), Sulfur ($\text{S}$). These are important for various biological functions (e.g., calcium for bones, potassium for preventing cramps).
  • Trace Elements: Elements comprising less than 1%1 \% of an organism's mass.
    • These include elements like Iron ($\text{Fe}$), Manganese ($\text{Mn}$), Selenium ($\text{Se}$), Silicon ($\text{Si}$), Fluorine ($\text{F}$), Copper ($\text{Cu}$), and Iodine ($\text{I}$).
    • Low iron levels, for instance, can lead to fatigue.

Atomic Weight and Isotopes

  • Each element has a specific atomic weight.
  • Isotopes: Atoms of the same element that have a fluctuating weight due to a change in the number of neutrons. The number of protons remains constant for a given element.
  • Radiometric Dating: This technique is used to determine the age of ancient objects like fossils and rocks.
    • It calculates the number of half-lives that have passed since the object was formed by measuring the radioactivity emanating from it.
    • Half-life values can range from seconds or days to billions of years.
    • This method provides scientific evidence for the age of the Earth and the existence of prehistoric life.

Electronegativity, Polarity, and Bonds

  • Electronegativity: This is a key concept defining an atom's attraction for electrons.
    • Elements have varying electronegativity values (the more electronegative an atom, the stronger its pull on electrons).
    • For example, Oxygen ($\text{O}$) has a higher electronegativity than Hydrogen ($\text{H}$) due to its larger atomic mass of 1616 compared to Hydrogen's atomic mass of 11.
    • This difference in electronegativity drives atoms to attract and pull electrons, influencing how they bond.
  • Polarity: Describes the uneven or even distribution of electron charge within a molecule.
    • Polar: Uneven distribution of charge, meaning one atom in a compound is more electronegative than others (e.g., water ($\text{H}_2\text{O}$), where oxygen is more electronegative than hydrogen).
    • Nonpolar: Even distribution of charge, with no significant difference in electronegativity, leading to a balanced molecule.
  • Bonds: These are the forces that hold atoms together to form compounds.
    • Ionic Bonds: Formed by the strong attraction between oppositely charged ions (positive and negative). These are considered strong bonds (e.g., Sodium Chloride ($\text{NaCl}$)).
    • Covalent Bonds: The strongest type of bond, involving the sharing of electron pairs between atoms (e.g., the bonds between oxygen and hydrogen within a single water molecule).
    • Hydrogen Bonds: The weakest type of bond, typically an attraction between a hydrogen atom in one molecule and an electronegative atom (like oxygen or nitrogen) in another molecule (e.g., the bonds between water molecules).

Chemical Reactions

  • Basic Equation: Chemical reactions are represented by equations similar to mathematical equations: Reactants →\rightarrow Products.
  • Reactants: The starting materials or ingredients that enter into a chemical reaction.
  • Products: The substances formed as a result of a chemical reaction. The arrow in the equation points towards the products.
  • Reversibility: Chemical reactions are often reversible, meaning the arrow can point in both directions (↔\leftrightarrow).
    • This implies that products can become reactants and vice-versa, depending on the conditions.
    • This mechanism allows for both the building up and breaking down of substances.
  • Example: Photosynthesis: A crucial biological chemical reaction.
    • Reactants: Carbon Dioxide ($\text{CO}2$), Water ($\text{H}2\text{O}$), and Sunlight energy.
    • Products: Glucose (plant food) and Oxygen ($\text{O}_2$).
    • Plants use this process to produce their own food and release oxygen, which benefits the environment and other living organisms.