Understanding Atoms, Molecules, and Cells: A Primer

Posted on Mar 5, 2025 in Chemistry

Atom: The Basic Unit

An atom is the smallest unit of a chemical element that retains its identity and properties and cannot be divided by chemical processes.

Atomic Structure

  • Proton: A subatomic particle with a positive (+) charge.
  • Neutron: An uncharged subatomic particle.
  • Electron: A subatomic particle with a negative (-) charge.

Chemical Elements and Bonds

A chemical element is a substance that cannot be decomposed by chemical reactions. Substances are formed by molecules of a single type, such as O, O2, and O3.

  • Atomic Number: The number of protons.
  • Mass Number: The number of protons plus neutrons.

Elements in living organisms include CHON (Carbon, Hydrogen, Oxygen, Nitrogen).

Chemical Bonds

A chemical bond is the union between two or more atoms to form molecules.

  • Ionic Bond: A bond between a metal and a nonmetal, with an electronegativity difference greater than or equal to 1.7. (The most electronegative atom takes the electron from the less electronegative atom.)
  • Electronegativity: A measure of an atom’s attraction to another atom to steal electrons.
  • Covalent Bond: The union between two non-metal atoms with an electronegativity difference less than 1.7. This occurs when polarity in the union is not large enough.
  • Binding Energy: Energy released when a bond is formed from the atoms that form it. Strong bonds, like ionic and covalent bonds, are more stable than weak bonds, such as the H-bridge.

Mass Formula: The sum of all atoms appearing in the formula.

Isotopes and Molecules

  • Isotope: Atoms of the same element with different atomic masses because they have different numbers of neutrons.
  • Molecule: Two or more parts of matter that can exist freely, clusters of atoms held together by bonds (forces of attraction).
  • Compound: Substances consisting of molecules of different kinds of atoms.
  • Valence: The ability of a bonding atom, the number of electrons being shared, donated, or accepted by an atom.

Ions and Biological Molecules

  • Ion: A chemical species of electrically charged atoms or molecules, either positive (+) or negative (-).
  • Cation: A chemical species of an atom or molecule with a positive (+) charge, given by the loss of electrons.
  • Anion: A chemical species of an atom or molecule with a negative (-) charge, given by electron gain.

BK (Biochemistry): The science that studies the chemical components of all living things (the basics of life): proteins, carbohydrates, lipids, and nucleic acids. All living things generally contain C: CHONPS.

Cells: The Building Blocks of Life

A cell is the morphological and functional unit of all living things. It is the smallest element that can be considered living.

  • Unicellular: Organisms with one cell, e.g., protozoa and bacteria.
  • Multicellular: Living organisms that have a variable number of cells.

Cellular Components

  • Peroxisomes: Spherical organelles found in plant cells with a membrane and important metabolic enzymes (catalase and peroxidase), which detoxify the cell by degrading catabolized hydrogen peroxide (H2O2) and free radicals that can damage cellular components.
  • Vacuoles: Sacs of fluid in the plant cell with a membrane called tonoplast, containing a solution of mineral salts, sugars, and amino acids. They store many compounds: sugars and amino acids (temporary warehouse), have enzymes, and may function as lysosomes, containing Anthocyanin, a pigment that gives color.
  • Chloroplasts: The site of photosynthesis, bounded by an envelope formed by two membranes called thylakoids and stroma. These organelles contain molecules necessary to convert light energy into chemical energy through two stages: the light stage and the dark stage.
  • Light Phase: Takes place in the thylakoid and is responsible for converting light energy into chemical energy and generating NADPH.
  • Dark Phase: Occurs in the stroma and is responsible for fixing CO2 through the Calvin cycle.
  • Photosynthesis: The process by which plants, some bacteria, and protists use the energy of sunlight to produce carbohydrates, in which the cell becomes ATP.

H2O enters the root and leaves and is carried by cells called xylem and phloem. CO2 enters through a call aperture stroma, flanked by two cells.