Introduction to Biochemistry

Introduction to Biochemistry

• Living organisms are composed of molecules following physical and chemical laws of matter.
• Living matter displays unique characteristics that sharply contrast with non-living matter despite both being made of inanimate molecules.

Identifying Characteristics of Living Matter

• Living organisms exhibit complexity and high organization, with cells containing intricate internal structures made of complex molecules.
• Each component of a living organism has a specific function, including macroscopic structures and chemical compounds within cells.
• Organisms can extract and transform energy from their environment to build and maintain structures from simple materials and perform work, such as locomotion.
• Living organisms possess the ability to replicate precisely.

Biochemistry and the Living State

• There is a radical difference between living and non-living matter, primarily in how molecules interact to sustain life.
• The goal of biochemistry is to uncover how inanimate molecular collections in living organisms work together to create and maintain life.

Biomolecules

• Living organisms consist mainly of organic compounds primarily containing carbon, often with nitrogen.
• E. coli serves as a model organism containing approximately 5,000 different compounds, including around 3,000 proteins and 1,000 nucleic acids.
• Macromolecules like proteins and nucleic acids form the bulk of organic material in cells and boast high molecular weights.
• Humans possess over 100,000 distinct proteins, with no protein molecule from E. coli being identical to human proteins.
• Cell macromolecules are constructed from simple building blocks, emphasizing molecular simplicity across cell types.

Axioms of Molecular Organization

• First Axiom: Simplicity exists in cellular molecular organization.
• Second Axiom: All living organisms share a common ancestor due to the identical nature of building-block biomolecules.
• Third Axiom: Each species' identity is maintained by its unique sets of proteins and nucleic acids.
• Fourth Axiom: Living organisms exhibit molecular economy, containing the fewest types of molecules necessary for life and species identity.

Energy Transformations in Living Cells

• According to the 2nd Law of Thermodynamics, all processes increase entropy or disorder in the environment.
• The 1st Law asserts that energy cannot be created or destroyed; living organisms only transform energy from one form to another.
• Living organisms interact with their environment, resulting in increased disorder while maintaining their internal orderliness.

Thermodynamic Principles

• Living organisms are open systems, constantly exchanging energy and matter with their surroundings.
• They function in a steady state, with rates of energy and matter transfer balanced.
• Living cells are isothermal and cannot utilize heat as a work source—energy is instead absorbed and transformed into chemical energy for work at constant temperature.

Chemical Reactions in Living Cells

• Enzymatic reactions yield 100% efficiency without by-products, with each enzyme responsible for a specific reaction.
• Metabolic reactions connect in network pathways, allowing energy transfer through sequences of reactions.
• Seventh Axiom: Specificity in molecular interactions arises from structural complementarity (e.g., enzyme-substrate "lock and key" fit).

Energy Sources in Living Cells

• Photosynthetic cells utilize sunlight as energy while heterotrophic cells derive energy from organic molecules.
• ATP serves as the primary energy carrier in cells, converting into ADP during energy transfer and regeneration when absorbing energy.

Self-Regulation of Cell Reactions

• Metabolism regulation occurs through feedback inhibition, stopping production when an end-product accumulates.
• Cells adjust enzyme synthesis to optimize metabolic efficiencies.

Self-Replication of Living Organisms

• Genetic information is highly stable and serves as the blueprint for cellular organisms, encoded in DNA through nucleotide sequences.
• Structural complementarity allows one DNA strand to dictate the replication of a complementary strand, ensuring accuracy.
• DNA can experience breaks or mutations, which are typically repaired or may provide beneficial evolutionary adaptations.

Additional Notes

• Genetic information, while minute in size, is hugely complex and critical for organismal identity and function.
• Stability and redundancy in genetic coding enhance reliable inheritance and adaptation.