Foundations of Biochemistry

What is Biochemistry?

Biochemistry is the study of the chemical processes and substances that occur within living organisms. It explores the molecular mechanisms that underlie the structure, function, and regulation of biological macromolecules and cellular processes.

• Definition: The chemistry of life, focusing on the molecules and reactions that enable living systems to grow, reproduce, and respond to their environment.

• Scope: Includes synthesis and breakdown of biomolecules, energy production, defense mechanisms, reproduction, communication, and environmental sensing.

• Evolutionary Context: Higher organisms have evolved by adapting and utilizing a limited set of chemical reactions over millions of years.

Cells: The Functional Units of Life

General Characteristics of Cells

Cells are the basic structural and functional units of all living organisms. Despite diversity, all cells share certain fundamental features.

• Cell Membrane: Composed of phospholipids, sterols, and proteins, forming a selective barrier.

• Cytoplasm: The internal solution (cytosol) containing cellular machinery.

• Genetic Material: DNA is the hereditary material, organized differently in prokaryotes and eukaryotes.

• Eukaryotes: DNA is organized as chromosomes within a nucleus.

• Prokaryotes: DNA is circular and located in the cytoplasm, not enclosed by a nucleus.

Domains of Life

Classification of Organisms

All living organisms are classified into three domains based on cellular organization and genetic relationships.

• Bacteria (Eubacteria): Includes gram-positive and gram-negative bacteria, cyanobacteria, and others found in soil, water, and as symbionts.

• Archaea (Archaebacteria): Includes extremophiles such as methanogens and thermophiles.

• Eukarya (Eukaryotes): Includes fungi, plants, animals, and protists.

Additional info: The three-domain system is based on differences in ribosomal RNA sequences and fundamental cellular structures.

Classifying Organisms by Environment and Energy Sources

Environmental Adaptations

Prokaryotes have evolved to survive in a wide range of environments, including extreme conditions.

• Aerobic: Organisms that require oxygen-rich environments.

• Anaerobic: Organisms that thrive in environments devoid of oxygen.

• Some prokaryotes are facultative, able to survive in both aerobic and anaerobic conditions.

Energy and Carbon Sources

Organisms are also classified by how they obtain energy and carbon for growth.

• Phototrophs: Obtain energy from light.

• Chemotrophs: Derive energy from chemical compounds.

• Autotrophs: Fix carbon from carbon dioxide (CO2).

• Heterotrophs: Obtain carbon from organic compounds.

Additional info: These classifications can be combined (e.g., photoautotrophs, chemoheterotrophs) to describe an organism's metabolic strategy.

Types of Cells

Common Features and Diversity

All cells share certain core features, but their structures and organization can vary significantly.

• Membrane-bound: All cells are enclosed by a lipid bilayer membrane.

• Genetic Information: DNA is used for storage of genetic information.

• Protein Synthesis: Ribosomes are responsible for synthesizing proteins.

• Lipid Bilayers: Form the cytoplasmic membrane barrier.

Bacteria

Structure and Function

Bacteria are single-celled prokaryotic organisms with unique structural features.

• No Membrane-bound Organelles: Cellular processes occur in the cytoplasm.

• Cell Envelope: Structure varies by bacterial class (e.g., gram-positive, gram-negative, cyanobacteria, archaebacteria).

• Pili: Hair-like structures used for adhesion to surfaces.

• Flagella: Tail-like structures that propel the bacterium.

Additional info: The Gram stain differentiates bacteria based on cell wall structure, which affects antibiotic susceptibility.

Animal & Plant Cells

Similarities and Differences

Animal and plant cells are both eukaryotic and share many structural features, but also have distinct differences.

• Protein Synthesis: Proteins are synthesized at the rough endoplasmic reticulum (ER).

• Lipids are synthesized at the smooth ER.

• Protein Export: Proteins are processed and exported by the Golgi apparatus.

• Genetic Material: DNA is housed in the nucleus.

• Cytoskeleton: Composed of protein filaments, involved in cell shape and intracellular transport.

Additional info: Plant cells have additional structures such as cell walls and chloroplasts, which are not found in animal cells.