Lecture 02 Chemistry for Biologists 2022

Periodic Table Overview

  • Elements categorized by:

    • Hydrogen

    • Alkali metals

    • Alkali earth metals

    • Transition metals

    • Poor metals

    • Nonmetals

    • Noble gases

    • Rare earth metals

Learning Objectives

Today’s lecture focuses on:

  1. Atoms and ions with specific numbers of electrons (e-, p+, n0)

  2. Compounds as two or more atoms bonded together

  3. Types of intramolecular bonds:

    • Metallic

    • Ionic

    • Covalent

  4. Valence electrons determining ion charge and bond types

  5. Compound shape dictated by bond type and atoms/ions involved

  6. Types of intermolecular bonds:

    • London Dispersion Forces (van der Waals)

    • Dipole-Dipole

    • Hydrogen Bonding

  7. Properties of water and discussion on concentration and moles

  8. Overview of organic molecules, polymers, and macromolecules (Upcoming Lecture 2b)

Human Cell Composition

  • The human body is estimated to have 10 trillion cells.

  • Length measurement conversion of cells and atoms:

    • 1 m = 10 µm = 0.01 mm = 0.001 cm = 0.00001 m

    • Size of a carbon atom: 170 pm = 0.00000000017 m

Understanding Atoms and Elements

Atoms

  • Smallest unit of matter retaining unique properties of the element:

    • Protons (p+) and Neutrons (n0) in the nucleus

    • Electrons (e-) in the surrounding cloud

    • Charge balance in atoms:

      • Protons are positive and neutrons have no charge

      • Equal numbers of protons and electrons yield a net charge of zero.

Elements

  • Atomic Number: Number of protons in an atom.

  • Atomic Mass: Protons + Neutrons (molecular weight).

  • Each proton and neutron ≈ 1.7 x 10^-24 grams (1 Da).

Molecules and Interactions

Formation of Molecules

  • Electrons interact and are arranged in quantized shells:

    • Max electrons per shell:

      • Shell 1: 2 e-

      • Shell 2: 8 e-

      • Shell 3: 18 e-

      • Continuing pattern through Shell 7.

Types of Molecules

  1. Hydrogen (H2): Single bond

  2. Oxygen (O2): Double bond

  3. Water (H2O): Single bonds; structure diagrams detailed.

  4. Methane (CH4): Formed by 4 hydrogen atoms satisfying carbon's valence.

Ion Formation

  • Ions:

    • Gain of electrons = Anions (negative charge)

    • Loss of electrons = Cations (positive charge)

  • Metals tend to lose electrons; non-metals gain them.

Types of Bonds

Ionic Bonds

  • Formed by the transfer of electrons between atoms creating oppositely charged ions:

  1. Sodium (Na) loses an electron.

  2. Chlorine (Cl) gains that electron to form Na+ and Cl-.

  • Resulting attraction forms sodium chloride (NaCl).

Covalent Bonds

  • Shared electrons between atoms:

    • Forms strong bonds and can be either:

      • Single bond (H2)

      • Double bond (O2)

Van der Waals and Intermolecular Bonds

  • Weaker bonds: Hydrogen bonds, Dipole-dipole, and London dispersion forces.

  • Discussed the significance of these in biological systems.

Water: The Biological Solvent

  • Water (H2O) is a polar covalent molecule.

  • Properties of water due to hydrogen bonding:

    • Excellent solvent for polar and ionic compounds.

    • Facilitates transport of ions and organic molecules.

Concentration and Moles

  • Concentration: Amount of substance in a specific volume.

  • Mole: Represents a large number of molecules (6.02 x 10^23).

  • Solutions typically measured in Molarity (mol/L).

Self-Ionization of Water

  • Water can self-ionize into hydronium (H3O+) and hydroxide (OH-) ions.

  • Significance of pH in biological systems:

    • Neutral water (pH = 7); acidic (pH < 7) and basic (pH > 7) conditions.

Energy and Biological Reactions

  • Energy is required to build covalent bonds.

  • Release of energy occurs when bonds are broken.

  • Related to cellular function and macromolecular processes.

Macromolecules Overview

Types of Macromolecules

  • Composed of multiple smaller molecules:

    • Carbohydrates

    • Proteins

    • Nucleic Acids (DNA/RNA)

    • Lipids

  • Structure dictated by the arrangement of monomers.

Organic vs Inorganic Compounds

  • Organic Compounds: Contain carbon and hydrogen (C-H bonds).

    • Examples: Sugars, DNA, methane.

  • Inorganic Compounds: Do not contain C-H bonds (e.g. salts, metals).

Functional Groups in Organic Molecules

  • Key elements combined (C, H, O, N) create functional groups:

    • Methyl, Amines, Aldehydes, Ketones, etc.

Revision Notes

  • Refer to QUT Readings on the LQB182 Blackboard for weekly textbook readings (Ch 2 to Ch 5.1 from Campbell Biology).