Rucete ✏ Lehninger Principles of Biochemistry In a Nutshell
1.1 Cellular Foundations
This chapter introduces the unity and diversity of organisms at the cellular level, emphasizing the shared structural and biochemical features of all cells and their classification into three domains of life.
Cells as the Structural and Functional Units of Life
• All living organisms are made up of cells, which are the smallest units of life and can exist as single cells or as part of multicellular organisms.
• Each cell is surrounded by a plasma membrane, composed of lipids and proteins, providing a hydrophobic barrier and selective transport via specialized proteins.
• The cytoplasm consists of cytosol (a concentrated solution of enzymes, RNA, metabolites, coenzymes, and ions) and suspended particles, including organelles like mitochondria, chloroplasts, ribosomes, and proteasomes.
• Genetic material is housed in a nucleus (eukaryotes) or nucleoid (prokaryotes); the nucleus is membrane-bound while the nucleoid is not.
Cellular Dimensions and Diffusion
• Most cells are microscopic, with typical sizes from 1 to 100 micrometers.
• The lower size limit is determined by the minimal set of biomolecules required for life, while the upper limit is set by the efficiency of diffusion for nutrient and waste transport.
• Larger cells often have folded or convoluted surfaces to increase surface-to-volume ratio for improved exchange of materials.
Three Domains of Life
• Organisms are classified into three domains based on genetic sequence comparisons: Bacteria, Archaea, and Eukarya.
• Bacteria and Archaea are both single-celled, but differ in genetic, biochemical, and structural traits; Archaea often inhabit extreme environments.
• Eukaryotes (Eukarya) evolved from the same branch as Archaea and are more closely related to them than to Bacteria.
Energy Sources and Nutritional Classification
• Organisms are categorized by how they acquire energy and carbon: phototrophs use sunlight, chemotrophs use chemical fuels.
• Autotrophs can build all biomolecules from CO₂, while heterotrophs require preformed organic nutrients.
• Examples include cyanobacteria (photoautotrophs) and humans (chemoheterotrophs).
Bacterial and Archaeal Cell Structure
• Bacteria like E. coli have an inner plasma membrane, a protective peptidoglycan cell wall, and sometimes an outer membrane (in gram-negative species); Archaea have unique lipid membranes and structures for extreme conditions.
• The cytoplasm contains thousands of ribosomes, enzymes, metabolites, and genetic material; plasmids provide additional functions like antibiotic resistance.
• Bacteria may live as single cells, in biofilms, or form simple multicellular aggregates.
Eukaryotic Cell Structure and Organelles
• Eukaryotic cells are typically larger than prokaryotic cells and contain membrane-bound organelles, including nuclei, mitochondria, endoplasmic reticulum, Golgi apparatus, peroxisomes, lysosomes, and, in plant cells, chloroplasts and vacuoles.
• Cell fractionation techniques allow for the isolation and study of specific organelles and their functions.
• The cytoplasm may also contain nutrient storage granules and droplets.
Cytoskeleton and Cellular Organization
• The eukaryotic cytoskeleton consists of actin filaments, microtubules, and intermediate filaments, providing structure, shape, and movement for organelles and the cell as a whole.
• Cytoskeletal filaments are dynamic, constantly assembling and disassembling, regulated by proteins and intracellular signals.
• The endomembrane system (vesicles, organelles) enables dynamic transport and organization within the cell, supporting processes like exocytosis and endocytosis.
Hierarchy of Cellular Structures
• Cellular organization follows a hierarchy: small molecules → macromolecules → supramolecular complexes (e.g., chromatin, ribosomes) → organelles → cell.
• Macromolecules are joined by covalent bonds; supramolecular complexes are stabilized mainly by noncovalent interactions (hydrogen bonds, ionic interactions, van der Waals forces, hydrophobic effects).
In Vitro and In Vivo Studies
• Studying purified biomolecules in vitro reveals important details, but the true cellular environment (in vivo) is crowded and complex, which can alter the behavior and function of molecules.
• Functional understanding of cells requires considering the influences of cellular organization, crowding, and molecular interactions present only in living systems.
In a Nutshell
All cells, regardless of complexity, share essential structural and biochemical features: plasma membrane, cytosol, and genetic material. Organisms are classified into three domains based on genetic evidence. Cell size and internal complexity are shaped by diffusion and metabolic needs. Eukaryotic cells possess dynamic cytoskeletons and compartmentalized organelles. Studying components in isolation is valuable, but real cellular function is best understood within the living, organized, and crowded context of the cell.