The Elements and Molecules of Living Systems

The Chemical Elements of Cells and Organisms

Biochemistry explores the chemical basis of life, focusing on the elements and molecules that constitute living cells. The periodic table can be used to highlight the elements most relevant to biological systems.

• First Tier Elements: These are abundant and able to form covalent bonds, including the elements of water (H, O) and carbon skeletons (C).

• Second Tier Elements: Includes phosphorus (P) and sulfur (S), along with important anions/cations (such as Na+, K+, Ca2+, Mg2+) involved in transport and cellular potentials.

• Third and Fourth Tier Elements: Metals such as Fe, Zn, Cu, Mn, Co, Mo, Ni, Se, which play indispensable roles mostly as cofactors in enzymes and other proteins.

Properties of Carbon in Biochemistry

Carbon is central to biochemistry due to its unique chemical properties:

• Abundance and Versatility: Carbon is abundant and can bond with many other elements, forming diverse structures.

• Polarizability: Carbon's electrons are polarizable, allowing for a variety of chemical interactions.

• Compatibility with Water: Carbon-based molecules can interact with water, which is essential for life.

Water Solubility of Molecules

One key question in biochemistry is whether a molecule is water-soluble. This depends on the molecule's structure and the presence of polar or charged groups.

• Polar Molecules: Molecules with polar groups (e.g., -OH, -NH2) tend to be water-soluble.

• Nonpolar Molecules: Molecules with large nonpolar regions (e.g., hydrocarbons) are generally insoluble in water.

• Examples: Amino acids, sugars, and nucleotides are typically water-soluble due to their polar functional groups.

The Origin of Biomolecules and Cells

Biomolecules such as proteins, nucleic acids, and polysaccharides are formed by the self-assembly of smaller molecules. This process is governed by predictable chemical rules and does not require external guidance.

• Macromolecules: Large molecules formed by the condensation of smaller units (monomers).

• Condensation Reactions: Chemical reactions where two molecules combine, releasing a small molecule such as water.

• Self-Assembly: The spontaneous organization of molecules into structured arrangements, such as cell membranes or protein complexes.

Emergent Complexity in Biochemistry

Emergent complexity refers to the appearance of new and more complex properties in a system as a result of simple interactions among its parts. In biochemistry, life itself is considered an emergent phenomenon.

• Emergence: Complex behaviors or properties arise from the collective interactions of simpler components.

• Examples: The formation of cell membranes, protein folding, and metabolic networks.

• Application: Understanding emergence helps explain how life arises from non-living molecules.

Key Terms and Definitions

• Macromolecule: A large molecule composed of repeating subunits (e.g., proteins, nucleic acids).

• Condensation: A chemical reaction that joins two molecules with the loss of a small molecule (often water).

• Cofactor: A non-protein chemical compound required for the biological activity of some proteins.

• Emergence: The process by which complex systems and patterns arise out of a multiplicity of relatively simple interactions.

Relevant Equations

• General Condensation Reaction:

• Water Solubility (Polarity):

Additional info: The notes reference a video on emergence and encourage students to predict outcomes of self-assembly, illustrating the concept of emergent complexity in biological systems.