Chapter Four

Chapter 4: Evolutionary Origin of Cells and Their General Features

General Overview of the Chapter

  • Cell Theory:

    • All living things are composed of one or more cells.

    • Cells are the smallest units of living organisms.

    • New cells arise only from pre-existing cells through the process of cell division (Latin phrase: Omnis cellula e cellula).

  • Key Concepts Covered:

    • General features of cells

    • Origin of living cells on Earth

    • Microscopy (to be reviewed independently)

    • Overview of cell structure

    • The cytosol

    • The nucleus and endomembrane system

    • Semiautonomous organelles

    • Systems biology of cells: a summary

Understanding Cells

  • Cells can specialize in shape and function.

    • Example of differentiation:

    • Muscle cells: specialized for contraction

    • Nerve cells: specialized for information processing and transmission

    • Pancreatic beta cells: specialized for the production and release of insulin

    • Despite diverse specializations, all cells share fundamental commonalities.

    • This chapter aims to provide a comprehensive understanding of cells as the basic units of life.

Composition of Cells

  • Cells are complex collections of various molecules with distinct functions:

    • DNA: Stores genetic material

    • RNA: Plays a role in protein production

    • Proteins: Major contributors to the structure and function of living cells.

4.1: Origin of Cells - Four Overlapping Stages

  1. Formation of Nucleotides and Amino Acids:

    • These molecules were produced before the existence of cells.

  2. Polymerization:

    • Nucleotides and amino acids polymerized to form DNA, RNA, and proteins.

  3. Enclosure in Membranes:

    • The polymers became enclosed in membranes.

  4. Acquisition of Cellular Properties:

    • The enclosed polymers developed cellular properties leading towards living cells.

RNA World Hypothesis

  • Describes the early role of RNA:

    • Functions of RNA:

    • Information Storage

    • Self-Replication

    • Catalytic Activity (as ribozymes)

    • Importance of DNA and proteins: They cannot perform all three functions as efficiently as RNA.

Stages Leading to Cellular Life

Stage 1: Origin of Organic Molecules

  • Reducing Atmosphere Hypothesis:

    • Geological data indicates an atmosphere rich in water vapor, hydrogen (H₂), methane (CH₄), and ammonia (NH₃) with little free oxygen.

    • Methane and ammonia can easily donate electrons.

    • Stanley Miller's experiments replicated this atmosphere with electrical discharges to form organic precursors (HCN, CH₂O), amino acids, sugars, DNA bases, and lipids, contributing to the theory of prebiotic synthesis.

  • Extraterrestrial Hypothesis:

    • Suggests that organic carbon was delivered to Earth via meteorites, containing amino acids and nucleic acid bases.

    • Critics argue that such compounds would be largely destroyed in intense heating and impacts.

  • Deep-Sea Vent Hypothesis:

    • Proposes that biologically significant molecules may form in thermal gradients between hot vent water and cold ocean water.

    • Supported by findings of complex biological communities harnessing chemical energy from vents rather than sunlight.

Stage 2: Organic Polymers

  • Mechanisms from Stage 1 facilitated the synthesis and accumulation of small organic molecules on early Earth.

  • Prebiotic polymerization in aqueous solutions is typically unfeasible due to competing hydrolysis reactions.

  • Experiments demonstrated the possibility of forming nucleic acid polymers and polypeptides on the surface of clay.

Stage 3: Formation of Boundaries

  • Definition of Protobionts:

    • Aggregates of prebiotically produced molecules and macromolecules with a boundary (lipid bilayer) to maintain a distinct internal chemical environment.

    • Characteristics include:

    • Boundary separating external and internal environments

    • Polymers within containing informational capability

    • Catalytic functions attributable to these polymers

    • Capability of self-replication

Stage 4: The RNA World

  • Dominant scientific consensus favors RNA as the first macromolecule within protobionts based on its notable functions.

Microscopy Techniques

  • Key microscopy methods include Transmission Electron Microscopy (TEM) and Scanning Electron Microscopy (SEM).

  • Visual examples of samples were provided (dimensions: 140.8 μm, 56.8 μm).

4.3: Cell Structure and Function

  • Life is categorized into two main types based on cell structure:

    • Prokaryotes:

    • Characterized by simple structures, lack of membrane-enclosed nucleus.

    • Includes Bacteria and Archaea.

    • Eukaryotes:

    • More complex structure with internal membranes forming organelles and a membrane-bound nucleus.

Prokaryotic Cells

  • Simple structural design analogous to a “studio apartment.”

  • Lack membrane-enclosed nuclei and other compartments.

Types of Prokaryotes

  • Bacteria:

    • Small size (1 μm - 10 μm diameter), abundant in environments, most non-pathogenic.

  • Archaea:

    • Similar size, less common and often inhabit extreme environments.

Inside a Typical Bacterial Cell

  • Cytoplasm:

    • Contents of the plasma membrane, described as “loose jello.”

  • Nucleoid Region:

    • Localized area of DNA distribution.

  • Ribosomes:

    • Organelles for protein synthesis.

Outside a Typical Bacterial Cell

  • Cell Wall:

    • Provides support and protection.

  • Glycocalyx:

    • Protects against desiccation and aids in immune evasion.

  • Appendages:

    • Pili for attachment, flagella for movement.

Eukaryotic Cells

  • More organized structure:

    • DNA located in membrane-bound nucleus.

    • Compartmentalization allows specialized functions.

    • Compared to a “4-bedroom house.”

Characteristics Determining Cell Function

  • All cells within a single organism contain identical DNA but produce diverse cell types.

  • Proteome:

    • The unique set of proteins expressed by cells; influences structure and function.

    • Gene regulation determines expression, amount, timing, amino acid sequence, and post-translational modifications of proteins.

    • Healthy versus cancerous cells exhibit differing proteomes.

Cell Functionality - Cellular Factory Analogy

  • The cell functions analogously to a factory, primarily for protein production.

    • Various organelles and structures facilitate this function: ribosomes serve as workbenches for protein synthesis, etc.

Structures in Eukaryotic Cells

  • Key components:

    • Cytosol: The liquid component of the cytoplasm where many metabolic reactions occur.

    • Cytoskeleton: Structural framework consisting of microtubules, intermediate filaments, and actin filaments.

    • Plasma Membrane: Outer boundary regulating material transport.

    • Nucleus: Contains genetic material and is the site for ribosome synthesis.

    • Other Organelles: Specific membrane-bound compartments with specialized functions.

Cytoskeleton Detail

  • Composed of three types of filaments:

    1. Microtubules:

    • Hollow and cylindrical, approximately 25 nm in diameter.

    1. Intermediate Filaments:

    • Twisted structure, roughly 10 nm in diameter providing cellular strength.

    1. Actin Filaments (Microfilaments):

    • Thin fibers about 7 nm in diameter, involved in cell movement and shape.

  • Flagella and Cilia:

    • Flagella: Longer structures, typically singular or in pairs composed of a 9 + 2 microtubule arrangement.

    • Cilia: Shorter than flagella, often covering cell surfaces, also composed of a 9 + 2 arrangement.

Motor Proteins

  • Proteins utilizing ATP for energy-driven movements.

  • Functioning analogous to walking along filaments with distinct parts: head, hinge, and tail.

  • Types of movements controlled by motor proteins include:

    • Carrying cargo along filaments

    • Filament movement relative to anchored motor proteins

    • Static actions causing filament bending.

Nucleus and Endomembrane System

  • Endomembrane System:

    • Network of membranes enclosing the nucleus, ER, Golgi apparatus, lysosomes, vacuoles, and plasma membrane.

    • Membranes may connect directly or transport materials via vesicles.

Nucleus Explained

  • Known as the control center of the cell.

    • Houses chromosomes (DNA and protein in chromatin form).

    • Consists of nuclear matrix for organization and protection of genetic material.

    • Ribosome assembly occurs in the nucleolus, a specific part of the nucleus.

Endoplasmic Reticulum (ER)

  • Composed of networks of membranes that form tubules or cisternae.

    • Rough ER: Studded with ribosomes; involved in protein synthesis and sorting.

    • Smooth ER: Lacks ribosomes; involved in detoxification, carbohydrate metabolism, calcium balance, and lipid synthesis.

Golgi Apparatus

  • Stack of flattened membranes, not directly continuous with the ER.

  • Functionally serves as a processing and sorting facility for proteins (analogous to a mailroom).

Lysosomes

  • Specialized vesicles containing enzymes (acid hydrolases) for hydrolysis reactions, acting as the cell’s waste disposal system.

  • Autophagy: Recycling cellular components through endocytosis.

Vacuoles

  • Diverse functions across cell types and conditions; primarily involved in storage and support in plants (e.g., central vacuoles).

  • Other types include contractile vacuoles in protists and phagocytic vacuoles in white blood cells.

Peroxisomes

  • Enzymatic reactions catalyze the breakdown of molecules.

  • Notable for oxidation reactions generating hydrogen peroxide, which is further processed by catalase within peroxisomes.

Plasma Membrane

  • The outer boundary of cells acting as a gate.

    • Selectively permeable, allowing controlled transport of substances and facilitating signal reception.

Semiautonomous Organelles

  • Organelles like mitochondria and chloroplasts that can grow and divide, but still depend on cellular components for function.

Mitochondria

  • Known as the powerhouses of the cell, responsible for ATP production through cellular respiration.

    • Composed of outer and inner membranes, an intermembrane space, and a mitochondrial matrix.

Chloroplasts

  • Site of photosynthesis in plants, featuring membranes and thylakoid structures.

    • Chloroplasts contain chlorophyll and conduct energy capture for organic molecule synthesis.

    • Endosymbiotic origins traced from cyanobacteria.

Endosymbiosis Theory

  • Suggests mitochondria originated from purple bacteria (α-proteobacteria) and chloroplasts from cyanobacteria.

  • Evidence includes the presence of their own DNA and division through binary fission.

Multicellular Organisms

  • Characterized by multiple cells, benefiting from specialization and division of labor.

    • Larger genomes allow diverse proteomes, enabling complex cellular communication and attachment formats.

Extracellular Matrix (ECM) and Cell Walls

  • ECM: A secreted network material providing structural support and organization in plants and animals (e.g., bone and cartilage).

  • Functions of ECM:

    • Offer mechanical strength, tissue organization, and facilitate cell signaling.

Proteins within ECM

  • Adhesive Proteins: Fibronectin and laminin bind ECM components and cells.

  • Structural Proteins: Collagen and elastin provide strength and elasticity, respectively.

  • Collagen formation involves synthesis into precursors followed by assembly into fibrils and fibers.

Polysaccharides in Animal ECM

  • Major component includes glycosaminoglycans (GAGs), which resist compression and impact the gel-like properties.

    • Examples include chondroitin sulfate and hyaluronic acid, vital for tissues such as cartilage and skin.