Atomic Structure, Chemical Bonds, and Water: Foundations for General Biology

Atomic Structure and Isotopes

Atoms and Their Components

Atoms are the basic units of matter, composed of protons, neutrons, and electrons. The arrangement of these subatomic particles determines the atom's identity and properties.

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

• Neutrons: Neutral particles in the nucleus. The number of neutrons can vary, resulting in different isotopes.

• Electrons: Negatively charged particles orbiting the nucleus in shells. The arrangement of electrons determines chemical reactivity.

Example: Carbon has 6 protons, and its most common isotopes are 12C, 13C, and 14C.

Electron Shells and Valence Electrons

Electrons occupy energy levels or shells around the nucleus. The outermost shell is called the valence shell and determines the atom's chemical behavior.

• Maximum electrons in the first shell: 2 electrons

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

• Electron pairing: Electrons fill shells in pairs, as shown in Lewis structures

Isotopes

An isotope is an alternative form of an atom with a different number of neutrons. Isotopes have the same chemical properties but different masses.

• Mass number: Sum of protons and neutrons

• Atomic number: Number of protons

• Isotope notation: $^{A}_{Z}X$ where A = mass number, Z = atomic number, X = element symbol

Example Table: Carbon Isotopes

Isotope	Number of electrons	Number of neutrons	Number of protons	Overall atomic charge	Can it be a reactant in photosynthesis?
12C	6	6	6	neutral	yes
13C	6	7	6	neutral	yes
14C	6	8	6	neutral	yes

Chemical Bonds

Electronegativity and Bond Types

Electronegativity is a measure of how strongly an atom attracts electrons in a chemical bond. The difference in electronegativity between two atoms determines the type of bond formed.

Bond Type	Electronegativity Difference
Pure covalent	< 0.4
Polar covalent	Between 0.4 and 1.8
Ionic	> 1.8

• Nonpolar covalent bond: Electrons shared equally between atoms (e.g., H2, O2).

• Polar covalent bond: Electrons shared unequally, creating partial charges (e.g., H2O, NH3, COOH).

• Ionic bond: Complete transfer of electrons, resulting in full charges (e.g., NaCl, MgCl2).

Lewis Structures and Molecular Geometry

Lewis structures represent the arrangement of electrons in molecules, showing bonds and lone pairs. Skeletal structures simplify the representation of molecules.

• CH4 (Methane): Tetrahedral geometry, equal sharing of electrons

• C2H6 (Ethane): Single bond between carbons, equal sharing

• C2H4 (Ethene): Double bond between carbons, equal sharing

• H2O (Water): Bent geometry, unequal sharing (polar)

Water: Structure and Properties

Polarity and Partial Charges

Water is a polar molecule due to the unequal sharing of electrons between oxygen and hydrogen. This creates partial positive ($ext{δ}^+$) and partial negative ($ext{δ}^-$) charges.

• Neutral molecule: Water has 10 protons and 10 electrons, resulting in no net charge.

• Partial charges: Oxygen is partially negative, hydrogens are partially positive.

Hydrogen Bonds

Hydrogen bonds are weak attractions between the partial positive charge of hydrogen (bonded to O, N, or F) and the partial negative charge of another electronegative atom. These bonds are crucial for the structure and properties of water and biological molecules.

• Hydrogen bond formation: Occurs between polar regions of molecules.

• Symbolization: Dotted lines are used to represent hydrogen bonds in diagrams.

Ionic Compounds in Water

When ionic compounds dissolve in water, ions are surrounded by water molecules, forming a hydration shell. This process breaks the ionic bond and allows ions to move freely in solution.

• Example: NaCl dissociates into Na+ and Cl- ions, each surrounded by water molecules.

Bond Energies and Biological Significance

Bond Energy Comparison

Bond energy is the amount of energy required to break a bond under physiological conditions. Covalent bonds are much stronger than ionic bonds in water.

Name	Basis of Interaction	Structure	Bond Energy (kcal/mol)
Ionic interaction	Attraction of opposite charges	Na+ ... Cl-	3-7
Covalent bond	Sharing of electron pairs	H-H	50-110
Hydrogen bond	Sharing of H atom	O-H ... O	3-7
Van der Waals interaction	Interaction of nonpolar substances	Temporary dipoles	1-2

• Covalent bonds: About 12 times stronger than ionic bonds in water.

• Ionic bonds: Easily broken in water due to complete electron transfer and hydration shell formation.

Levels of Biological Organization

Hierarchy of Organization

Biological systems are organized in a hierarchy from smallest to largest:

• Cell → Tissue → Organ → Organism → Population → Community

Example: Human muscle cell → muscle tissue → heart → human → group of humans → all living things in an area.

Additional info: Some explanations and examples have been expanded for clarity and completeness, including the significance of bond energies and the biological importance of water's polarity and hydrogen bonding.