Atomic Structure and Elements

Subatomic Particles and Atomic Structure

Understanding the structure of atoms is fundamental to chemistry and microbiology. Atoms are composed of three main subatomic particles: protons, neutrons, and electrons.

• Protons: Positively charged particles located in the nucleus. The number of protons defines the atomic number and the element.

• Neutrons: Neutral particles also found in the nucleus. The number of neutrons plus protons gives the atomic mass.

• Electrons: Negatively charged particles that orbit the nucleus in electron shells (energy levels).

Isotopes are atoms of the same element with different numbers of neutrons, resulting in different atomic masses.

Electron configuration refers to the arrangement of electrons in an atom's electron shells. The chemical properties of an atom are largely determined by the number of electrons in its outermost shell (valence electrons).

Elements and the Periodic Table

Elements are pure substances consisting of only one type of atom. The periodic table organizes elements by increasing atomic number and groups elements with similar chemical properties together.

• Atomic Number: Number of protons in the nucleus.

• Atomic Mass: Sum of protons and neutrons.

• Valence Electrons: Electrons in the outermost shell, important for chemical bonding.

Chemical Bonds and Molecules

Types of Chemical Bonds

Chemical bonds form when atoms share or transfer electrons to achieve stable electron configurations. The main types of chemical bonds are:

• Ionic Bonds: Formed when electrons are transferred from one atom to another, resulting in oppositely charged ions that attract each other. Example: NaCl (sodium chloride).

• Covalent Bonds: Formed when two atoms share one or more pairs of electrons. Covalent bonds can be:

  • Nonpolar Covalent Bonds: Electrons are shared equally between atoms (e.g., O2).

  • Polar Covalent Bonds: Electrons are shared unequally, resulting in partial charges (e.g., H2O).

• Hydrogen Bonds: Weak attractions between a hydrogen atom covalently bonded to an electronegative atom (like oxygen or nitrogen) and another electronegative atom. Important in the structure of water and biological macromolecules.

Properties of Water

Water is essential for life and has unique properties due to its polar covalent bonds and ability to form hydrogen bonds.

• Cohesion and Adhesion: Water molecules stick to each other (cohesion) and to other substances (adhesion).

• High Specific Heat: Water can absorb a lot of heat before changing temperature.

• Solvent Properties: Water dissolves many substances, making it a universal solvent.

• pH: Measure of hydrogen ion concentration; water can act as an acid or base.

Chemical Reactions

Types of Chemical Reactions

Chemical reactions involve the making and breaking of chemical bonds, resulting in the formation of new substances.

• Synthesis (Anabolic) Reactions: Two or more simple substances combine to form a more complex product. Example:

• Decomposition (Catabolic) Reactions: A complex molecule breaks down into simpler substances. Example:

• Exchange (Transfer) Reactions: Parts of molecules are exchanged to form new products. Example:

Exergonic reactions release energy, while endergonic reactions require energy input.

Macromolecules and Biological Molecules

Inorganic vs. Organic Molecules

Inorganic molecules generally do not contain carbon-hydrogen (C-H) bonds (e.g., water, salts). Organic molecules contain C-H bonds and are the basis of life (e.g., carbohydrates, proteins, lipids, nucleic acids).

Macromolecules: Structure and Function

Macromolecules are large, complex molecules essential for life. They are typically formed by the polymerization of smaller subunits (monomers).

• Monomers: Small building blocks (e.g., amino acids, monosaccharides, nucleotides).

• Polymers: Large molecules made by joining monomers (e.g., proteins, polysaccharides, nucleic acids).

• Dehydration Synthesis: Reaction that joins monomers by removing water.

• Hydrolysis: Reaction that breaks polymers into monomers by adding water.

Major Classes of Biological Macromolecules

Enzymes

Enzymes are biological catalysts, usually proteins, that speed up chemical reactions in cells by lowering the activation energy required. They are highly specific for their substrates and can be regulated by various factors.

• Active Site: The region of the enzyme where the substrate binds and the reaction occurs.

• Function: Facilitate metabolic reactions essential for life.

Functional Groups in Organic Molecules

Functional groups are specific groups of atoms within molecules that determine the chemical properties and reactions of those molecules.

• Hydroxyl (-OH): Found in alcohols and carbohydrates.

• Carboxyl (-COOH): Found in amino acids and fatty acids.

• Amino (-NH2): Found in amino acids.

• Phosphate (-PO4): Found in nucleic acids and ATP.

• Sulfhydryl (-SH): Found in some amino acids (e.g., cysteine).

Summary Table: Macromolecules and Their Components

Key Definitions

• Atom: The smallest unit of an element that retains its chemical properties.

• Molecule: Two or more atoms bonded together.

• Ion: An atom or molecule with a net electric charge due to the loss or gain of electrons.

• pH: A measure of the hydrogen ion concentration in a solution; scale ranges from 0 (acidic) to 14 (basic).

• Isotope: Atoms of the same element with different numbers of neutrons.

Additional info:

• Understanding these chemistry fundamentals is essential for studying microbiology, as all cellular processes are based on chemical interactions.

• Reviewing the structure and function of macromolecules will aid in understanding microbial metabolism and genetics.