Prokaryotes – Bacteria and Archaea

Overview of Prokaryotes

Prokaryotes are unicellular organisms that lack a membrane-bound nucleus and other organelles. They are divided into two domains: Bacteria and Archaea. Prokaryotes are among the most abundant and diverse organisms on Earth, occupying a wide range of habitats.

• Bacteria: One of the two main prokaryotic domains, characterized by the presence of peptidoglycan in their cell walls.

• Archaea: The other prokaryotic domain, lacking peptidoglycan and often inhabiting extreme environments.

• Peptidoglycan: A polymer that forms a mesh-like layer outside the plasma membrane of most bacteria, providing structural support.

• Outer membrane: Found in Gram-negative bacteria, this additional membrane provides extra protection.

Cell Structure and Classification

• Gram stain: A laboratory technique used to classify bacteria based on their cell wall composition.

• Gram-positive bacteria: Have thick peptidoglycan layers and stain purple.

• Gram-negative bacteria: Have thin peptidoglycan layers and an outer membrane; stain pink/red.

• Capsule: A sticky, protective layer outside the cell wall that aids in adherence and evasion of host defenses.

• Fimbriae/Pili: Hair-like appendages that help bacteria adhere to surfaces or other cells.

• Flagella: Long, whip-like structures used for movement.

• Endospore: A resistant, dormant cell formed by some bacteria to survive harsh conditions.

• Nucleoid: Region in prokaryotic cells where the DNA is located.

• Plasmid: Small, circular DNA molecules that replicate independently of the chromosome.

Reproduction and Genetic Variation

• Binary fission: Asexual reproduction in prokaryotes, resulting in two identical cells.

• Genetic recombination: The exchange of genetic material, increasing diversity.

• Transformation: Uptake of foreign DNA from the environment.

• Transduction: Transfer of DNA via bacteriophages (viruses that infect bacteria).

• Conjugation: Direct transfer of DNA between two bacterial cells via a pilus.

Metabolic Diversity and Adaptations

• Metabolic diversity: Prokaryotes can be photoautotrophs, chemoautotrophs, photoheterotrophs, or chemoheterotrophs.

• Extremophiles: Archaea that thrive in extreme environments.

• Thermophiles: Live in very hot environments.

• Halophiles: Thrive in highly saline environments.

• Methanogens: Produce methane as a metabolic byproduct; often found in anaerobic environments.

Classification Systems

• Three-domain system: Classification of life into Bacteria, Archaea, and Eukarya based on genetic and biochemical differences.

Table: Comparison of Gram-Positive and Gram-Negative Bacteria

Protists

Overview of Protists

Protists are a diverse group of mostly unicellular eukaryotes that do not fit into the plant, animal, or fungal kingdoms. They exhibit a wide range of nutritional strategies and life cycles.

• Photoautotroph: Organisms that use light energy to synthesize organic compounds.

• Heterotroph: Organisms that obtain nutrients by consuming other organisms.

• Mixotroph: Organisms capable of both photosynthesis and heterotrophy.

Endosymbiosis and Evolution

• Endosymbiosis: A symbiotic relationship in which one organism lives inside the cell of another; crucial in the evolution of mitochondria and plastids.

• Primary endosymbiosis: The engulfment of a prokaryote by a eukaryotic cell, leading to the origin of mitochondria and chloroplasts.

• Secondary endosymbiosis: A eukaryotic cell engulfs another eukaryotic cell that already contains an endosymbiont.

• Alphaproteobacteria: The likely ancestor of mitochondria.

• Cyanobacteria: The likely ancestor of chloroplasts.

Major Protist Groups

• Brown algae, Red algae, Green algae: Multicellular protists important in aquatic ecosystems.

• Diatoms: Unicellular algae with silica cell walls.

• Dinoflagellates: Marine protists, some of which cause harmful algal blooms.

• Slime molds: Fungus-like protists that exhibit unique life cycles.

Fungi

Structure and Nutrition

Fungi are heterotrophic eukaryotes that absorb nutrients from their environment using hydrolytic enzymes. They play key roles as decomposers, parasites, and mutualists.

• Hyphae: Thread-like filaments that make up the body of a fungus.

• Mycelium: A network of hyphae that forms the main body of the fungus.

• Fruiting body: The reproductive structure that produces spores.

• Molds: Rapidly growing, asexually reproducing fungi.

• Yeasts: Unicellular fungi that reproduce by budding.

Fungal Life Cycles

• Plasmogamy: Fusion of cytoplasm from two parent mycelia.

• Heterokaryon: A fungal cell with two or more genetically distinct nuclei.

• Karyogamy: Fusion of nuclei from two parent cells.

• Meiosis and Mitosis: Processes for spore production and growth.

• Budding: Asexual reproduction in yeasts.

Fungal Symbioses

• Mycorrhizae: Symbiotic associations between fungi and plant roots.

• Arbuscular mycorrhizal fungi: Penetrate plant root cells.

• Ectomycorrhizal fungi: Surround root cells but do not penetrate.

• Lichens: Symbiotic associations between fungi and photosynthetic organisms (algae or cyanobacteria).

• Soredia: Small clusters of fungal hyphae and algal cells that serve as reproductive units in lichens.

Animal Form and Function and Homeostasis

Levels of Organization

Animals are organized into hierarchical levels: cells, tissues, organs, and organ systems. Each level contributes to the structure and function of the organism.

• Anatomy: Study of structure.

• Physiology: Study of function.

• Adaptation: Evolutionary process that increases fitness.

• Acclimatization: Short-term physiological adjustment to environmental changes.

Animal Tissues

• Epithelial tissue: Covers body surfaces and lines cavities; functions in protection, absorption, and secretion.

• Connective tissue: Supports and binds other tissues (e.g., bone, blood, cartilage).

• Muscle tissue: Responsible for movement; includes skeletal, cardiac, and smooth muscle.

• Nervous tissue: Conducts electrical impulses; composed of neurons and glial cells.

Homeostasis and Regulation

• Homeostasis: Maintenance of a stable internal environment.

• Conformer: Organism whose internal conditions vary with the environment.

• Regulator: Organism that maintains internal stability despite external changes.

• Homeostatic system: Consists of a sensor, integrator, and effector.

• Negative feedback: A control mechanism that reduces the stimulus (e.g., body temperature regulation).

Thermoregulation

• Endothermic: Generate heat internally (e.g., mammals, birds).

• Ectothermic: Rely on external sources for heat (e.g., reptiles, amphibians).

• Vasodilation: Widening of blood vessels to increase heat loss.

• Vasoconstriction: Narrowing of blood vessels to reduce heat loss.

• Countercurrent exchange: Mechanism for conserving heat by transferring it between fluids flowing in opposite directions.

• Physical processes of heat exchange: Radiation, Evaporation, Convection, Conduction.

Nervous System

Structure and Function of Neurons

• Neuron: Basic unit of the nervous system; transmits electrical signals.

• Dendrite: Receives signals from other neurons.

• Axon: Conducts impulses away from the cell body.

• Synapse: Junction between neurons where communication occurs.

• Neurotransmitter: Chemical messenger released at synapses.

• Glial cells: Support and protect neurons.

Electrical Properties of Neurons

• Resting potential: The membrane potential of a neuron at rest, typically around -70 mV.

• Sodium-potassium pump (Na+/K+ pump): Maintains resting potential by pumping 3 Na+ out and 2 K+ in per ATP hydrolyzed.

• Action potential: Rapid change in membrane potential that travels along the axon.

• Threshold: The critical level to which a membrane potential must be depolarized to initiate an action potential.

• Depolarization: Membrane potential becomes less negative.

• Repolarization: Return to resting potential.

• Hyperpolarization: Membrane potential becomes more negative than resting.

• Voltage-gated ion channels: Open or close in response to changes in membrane potential.

• Refractory period: Time during which a neuron cannot fire another action potential.

• Saltatory conduction: Rapid transmission of nerve impulses along myelinated axons, jumping from node to node.

• Myelin sheath: Insulating layer around axons.

• Nodes of Ranvier: Gaps in the myelin sheath where action potentials are regenerated.

Synaptic Transmission

• Chemical synapse: Neurotransmitters cross the synaptic cleft to transmit signals.

• Electrical synapse: Direct passage of ions through gap junctions.

• Excitatory postsynaptic potential (EPSP): Depolarizes the postsynaptic membrane, increasing the likelihood of firing.

• Inhibitory postsynaptic potential (IPSP): Hyperpolarizes the postsynaptic membrane, decreasing the likelihood of firing.

• Summation: Integration of multiple EPSPs and IPSPs (spatial and temporal).

Organization of the Nervous System

• Central nervous system (CNS): Brain and spinal cord.

• Peripheral nervous system (PNS): Nerves outside the CNS.

• Sensory neurons: Carry information to the CNS.

• Interneurons: Connect neurons within the CNS.

• Motor neurons: Carry signals from the CNS to effectors.

• Gray matter: Neuron cell bodies and unmyelinated fibers.

• White matter: Myelinated axons.

• Cerebrospinal fluid: Cushions and nourishes the CNS.

• Cranial nerves: Emerge from the brain.

• Spinal nerves: Emerge from the spinal cord.

Autonomic Nervous System (ANS)

• Sympathetic division: Prepares the body for 'fight or flight'.

• Parasympathetic division: Promotes 'rest and digest' activities.

• Enteric division: Controls the gastrointestinal system.

Major Brain Regions

• Forebrain: Includes cerebrum, thalamus, hypothalamus.

• Midbrain: Involved in sensory and motor functions.

• Hindbrain: Includes cerebellum, medulla oblongata, pons.

• Cerebrum: Responsible for higher brain functions.

• Cerebral cortex: Outer layer of the cerebrum; involved in perception, thought, and voluntary movement.

• Thalamus: Relay center for sensory information.

• Hypothalamus: Regulates homeostasis and endocrine functions.

• Cerebellum: Coordinates movement and balance.

• Medulla oblongata: Controls vital functions (e.g., breathing, heart rate).

• Pons: Connects different parts of the brain; involved in sleep and respiration.

• Brainstem: Includes midbrain, pons, and medulla; controls basic life functions.

• Limbic system: Involved in emotion and memory (includes amygdala and hippocampus).

• Amygdala: Processes emotions.

• Hippocampus: Involved in memory formation.

Muscles

Types of Muscle Tissue

• Skeletal muscle: Voluntary, striated muscle attached to bones.

• Cardiac muscle: Involuntary, striated muscle found in the heart.

• Smooth muscle: Involuntary, non-striated muscle found in walls of organs.

Muscle Structure

• Muscle fiber: Single muscle cell.

• Myofibril: Bundles of actin and myosin filaments within muscle fibers.

• Sarcomere: Functional unit of muscle contraction, defined by Z lines.

• Actin: Thin filament protein.

• Myosin: Thick filament protein.

• Z line: Boundary of a sarcomere.

• M line: Center of the sarcomere.

Sliding Filament Model

Muscle contraction occurs when myosin heads bind to actin filaments and pull them toward the center of the sarcomere, shortening the muscle.

• Tropomyosin and Troponin complex: Regulatory proteins that control access of myosin to actin.

• Sarcoplasmic reticulum (SR): Stores and releases calcium ions (Ca2+).

• Transverse tubules (T-tubules): Conduct action potentials into the muscle fiber.

Muscle Contraction Process

1. Action potential arrives at the neuromuscular junction.

2. Acetylcholine (ACh) is released, triggering an action potential in the muscle fiber.

3. Action potential travels along T-tubules, causing SR to release Ca2+.

4. Ca2+ binds to troponin, shifting tropomyosin and exposing binding sites on actin.

5. Myosin heads bind to actin, performing a power stroke using ATP.

6. ATP is required for myosin head detachment and re-cocking.

Muscle Fiber Types

• Slow-twitch fibers: Contract slowly, resist fatigue, rely on aerobic metabolism.

• Fast-twitch fibers: Contract quickly, fatigue rapidly, rely on anaerobic metabolism.

Comparison Table: Muscle Types

Key Equations

• Nernst equation (for equilibrium potential):

• Resting membrane potential (Goldman-Hodgkin-Katz equation):