Introduction to Biochemistry: Atomic Structure, Chemical Bonds, and Water

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Introduction to Biochemistry

Overview

Biochemistry explores the chemical processes and substances that occur within living organisms. Understanding atomic structure and chemical bonding is fundamental to studying the molecules that make up cells and their interactions, especially in aqueous environments.

Key elements in cells: Carbon (C), Oxygen (O), Nitrogen (N), and Hydrogen (H)
Focus: Atomic structure, types of chemical bonds, electronegativity, and the properties of water

Basic Atomic Structure

Subatomic Particles

Atoms are the basic units of matter, composed of three types of subatomic particles:

Protons: Positively charged particles located in the nucleus
Neutrons: Neutral particles located in the nucleus
Electrons: Negatively charged particles found in orbitals surrounding the nucleus

Each element is defined by its number of protons (atomic number).

Electron Shells and Orbitals

Orbitals: Regions around the nucleus where electrons are likely to be found; each orbital can hold up to 2 electrons.
Electron shells: Energy levels containing one or more orbitals; shells are filled in order of increasing energy.
Example: Hydrogen has one shell (1 electron), Carbon has two shells (6 electrons).

Chemical Bonds

Stability and Bond Formation

Atoms are most stable when their outermost electron shell is full. Atoms achieve stability by sharing or transferring electrons, resulting in chemical bonds.

Covalent bond: Atoms share electron pairs (e.g., H2, O2).
Ionic bond: Electrons are transferred from one atom to another, creating oppositely charged ions that attract each other (e.g., NaCl).

Number of Bonds and Unpaired Electrons

The number of covalent bonds an atom can form equals the number of unpaired electrons in its outermost shell.

Carbon: 4 bonds
Nitrogen: 3 bonds
Oxygen: 2 bonds
Hydrogen: 1 bond

Covalent Bonds in Biological Molecules

Elements of Life

Cells are primarily composed of carbon, oxygen, nitrogen, and hydrogen. These elements form stable covalent bonds, which are essential for the structure and function of biological molecules.

Types of Covalent Bonds

Nonpolar covalent bond: Equal (or nearly equal) sharing of electrons; no partial charges (e.g., C-H, O2).
Polar covalent bond: Unequal sharing of electrons; partial charges develop (e.g., O-H, N-H).

Electronegativity

Electronegativity is the tendency of an atom to attract electrons in a bond. The difference in electronegativity between two atoms determines bond polarity.

Relative electronegativities: O > N > C ≈ H

If the difference is large, the bond is polar; if small or zero, the bond is nonpolar.

Polar and Nonpolar Covalent Bonds

Definitions and Examples

Nonpolar covalent bond: Electrons are shared evenly; bond is symmetrical (e.g., C-H, C-C).
Polar covalent bond: Electrons are shared unevenly; bond is asymmetrical. The more electronegative atom has a partial negative charge (δ-), the other a partial positive charge (δ+).

Example: In water (H2O), oxygen is more electronegative than hydrogen, so the O-H bonds are polar.

Water: Structure and Properties

Polarity of Water

Water is a polar molecule due to the difference in electronegativity between oxygen and hydrogen, resulting in partial charges on each atom.

Oxygen: δ- (partial negative)
Hydrogen: δ+ (partial positive)

Hydrogen Bonds

Hydrogen bonds are weak attractions between a δ+ hydrogen atom and a δ- atom (usually oxygen or nitrogen) in another molecule.

Hydrogen bonds are shown as dotted lines in diagrams.
They are essential for the structure of water, DNA, and proteins.

Water as the "Solvent of Life"

Water is an excellent solvent due to its polarity.
A solute dissolved in a solvent forms a solution.
Chemical reactions occur more readily in aqueous solutions.

Polar vs Nonpolar Molecules

Hydrophilic and Hydrophobic Molecules

Hydrophilic molecules: Contain polar covalent bonds; interact with water (e.g., sugars, salts).
Hydrophobic molecules: Contain mostly nonpolar covalent bonds; do not interact with water (e.g., oils, fats).

Example: Glucose is hydrophilic and dissolves in water; octane is hydrophobic and does not.

Exceptions

Some molecules, like carbon dioxide (CO2), have polar bonds but are nonpolar overall due to their symmetrical shape, causing the dipoles to cancel out.

Ionic Bonds

Formation and Properties

Formed when electrons are transferred from one atom to another, creating ions.
Cation: Positively charged ion (lost electrons)
Anion: Negatively charged ion (gained electrons)
Ionic bond: Attraction between a cation and an anion (e.g., NaCl)

Charged ions dissolve readily in water due to interactions with water's partial charges.

The Electron-Sharing Continuum

Bond Types Spectrum

Chemical bonds exist on a continuum based on how electrons are distributed:

Equal sharing: Nonpolar covalent (e.g., H2)
Unequal sharing: Polar covalent (e.g., H2O, NH3)
Full transfer: Ionic (e.g., NaCl)

Bond Type	Electron Distribution	Example
Nonpolar Covalent	Equal sharing	H2, O2, C-H
Polar Covalent	Unequal sharing	H2O, NH3, O-H
Ionic	Full transfer	NaCl, KBr

Key Terms and Definitions

Atom: Smallest unit of an element, composed of protons, neutrons, and electrons.
Element: Substance consisting of one type of atom.
Molecule: Two or more atoms held together by covalent bonds.
Electronegativity: Atom's ability to attract electrons in a bond.
Hydrogen bond: Weak attraction between a hydrogen atom and an electronegative atom.
Hydrophilic: Water-loving; interacts with water.
Hydrophobic: Water-fearing; does not interact with water.

Summary Table: Properties of Bonds

Bond Type	Strength	Polarity	Example
Covalent (Nonpolar)	Strong	Nonpolar	O2, CH4
Covalent (Polar)	Strong	Polar	H2O, NH3
Ionic	Moderate (weaker in water)	Full charges	NaCl
Hydrogen Bond	Weak (individually)	Partial charges	Between H2O molecules

Key Equations

Electronegativity difference (ΔEN):

General rule:

If → Nonpolar covalent If → Polar covalent If → Ionic

Applications and Examples

Water's role in biology: Solvent for biochemical reactions, temperature regulation, transport of substances.
Hydrogen bonding: Stabilizes DNA double helix, protein secondary structure, and properties of water.
Polarity and solubility: Determines whether molecules are hydrophilic or hydrophobic, affecting cell membrane structure and function.