Principles of Biochemistry: The Cell and Water – Foundations for Life

Chapter 1: Biochemistry and the Language of Chemistry

The Unit of Biological Organization: The Cell

The cell is the fundamental unit of life, providing compartmentalization and organization necessary for biological processes. Understanding cellular structure and function is essential for grasping the chemical basis of life.

• Compartmentation: Formation of distinct compartments within cells protects from adverse environmental forces and allows for the maintenance of high local concentrations of biological molecules. This enhances the efficiency of chemical reactions such as polymerization.

• Types of Cells: There are three main types of cells:

  1. Bacterial

  2. Archaeal

  3. Eukaryotic

  Bacterial and archaeal cells are collectively referred to as prokaryotic cells due to their similarities.

Distinguishing Characteristics of Living Systems

Living systems are defined by several essential attributes that distinguish them from nonliving matter:

• Program: Organized plan for constitution and regeneration, encoded in DNA.

• Improvisation: Ability to change the program as surroundings change (evolution).

• Compartmentation: Ability to be separate from the environment via membranes.

• Energy: Ability to maintain order despite overall positive entropy.

• Regeneration: Compensation for environmental wear and tear (repair mechanisms).

• Adaptability: Ability to respond to environmental changes.

• Seclusion: Operation of processes and pathways in isolation.

Comparison of Prokaryotic and Eukaryotic Cells

Cells are classified based on structural and functional differences:

Feature	Prokaryotes	Eukaryotes
Nuclear Envelope	Absent	Present (Nucleus)
Size	~1 μm	10–100 μm
Genetic Material	Single circular DNA	Multiple linear DNA molecules
Organelles	Lack organelles and cytoskeleton	Contain organelles and cytoskeleton
Cellularity	Unicellular	Often multicellular

Prokaryotes

• Exhibit varied and highly adaptable metabolisms.

• Fast growth rate; size ranges from 1–10 μm.

• Three basic shapes: spheroidal (cocci), rodlike (bacilli), and helically coiled (spirilla).

• No specific compartmentation inside the cell, but metabolic functions occur in specific regions of the cytoplasm.

Eukaryotes

• Include plants, animals, fungi, protozoans, yeasts, and some algae.

• Cells are 10 times larger than prokaryotes (10–100 μm).

• Surrounded by a plasma membrane composed of lipids and proteins, serving as a chemical barrier.

• Contain internal membranes and compartments (organelles), which allow for separation of biological functions.

• Most enzymes are compartmentalized within organelles.

Major Eukaryotic Organelles and Their Functions

• Cytoplasm/Cytosol: Site of metabolic processes; cytosol is the cytoplasm minus organelles.

• Nucleus: Site of DNA/RNA synthesis.

• Peroxisomes: Breakdown of long-chain fatty acids and detoxification.

• Cytoskeleton: Provides cell shape and mobility.

• Endoplasmic Reticulum (ER): Site of protein synthesis.

• Lysosomes: Degrade polymers into monomers.

• Golgi Apparatus: Site of protein modification.

• Mitochondria: Site of oxidative energy production.

Chapter 2: Chemical Foundation of Life (Water)

Physical and Chemical Properties of Water

Water is central to biochemistry, influencing the structure and function of biological molecules through its unique physical and chemical properties.

• Physical Properties: Water is a polar molecule (H2O) with two hydrogen atoms bonded to an oxygen atom.

• The O–H bond distance is 0.958 Å, and the H–O–H bond angle is 104.5°.

• Oxygen atom has four sp3 hybrid orbitals forming a tetrahedral geometry; two corners are occupied by hydrogen atoms, and two by lone electron pairs.

• Greater repulsion between electron pairs causes the bond angle to deviate from the ideal tetrahedral angle of 109.5°.

Water Molecules Form Hydrogen Bonds

Hydrogen bonding is a key feature of water, resulting from its polarity and the uneven distribution of electrons.

• Oxygen has a partial negative charge (δ-), and hydrogen has a partial positive charge (δ+).

• Electrostatic attraction between O and H leads to directional intermolecular associations known as hydrogen bonds.

Hydrogen Bond Donors and Acceptors

• Donor: A molecule or functional group that supplies a hydrogen atom for a hydrogen bond.

• Acceptor: A molecule or functional group that provides the lone pair of electrons to which the hydrogen atom is attracted.

Donor	Acceptor	Distance (nm)	Comment
O–H	O	0.28–0.31	Strong hydrogen bond, common in water and alcohols
N–H	O	0.28–0.31	Common in proteins and nucleic acids
O–H	N	0.28–0.31	Less common, but possible in some biomolecules
N–H	N	0.28–0.31	Rare, but can occur in nucleic acids

Key Equations

• Bond angle in water: $\angle \mathrm{H-O-H} = 104.5^\circ$

• O–H bond length: $0.958\ \mathrm{\AA}$

Example: Hydrogen Bonding in Water

Each water molecule can form up to four hydrogen bonds with neighboring water molecules, resulting in a highly cohesive and structured liquid. This property is critical for the unique behavior of water in biological systems, such as its high boiling point and solvent capabilities.

Additional info: Hydrogen bonding is also responsible for the secondary and tertiary structures of proteins and the double helix structure of DNA.