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Notes on Prokaryotic and Eukaryotic Cells, Membranes, and Metabolism

Cell Membrane: Fluid Mosaic Model

  • The cell membrane is composed of phospholipids and proteins. It is very fluid and dynamic; proteins are not locked in place and can migrate within the membrane.
  • Fluidity refers to the dynamic movement of membrane components.
  • Mosaic refers to the mixture of many different types of phospholipids and proteins making up the membrane.
  • Composition: roughly half phospholipids and half proteins.
  • Proteins have various roles: integral proteins (e.g., channels that move substances in/out) and peripheral proteins (e.g., receptors that monitor the environment, such as glucose).
  • The membrane’s structure supports selective transport and communication with the environment.

Transport Across the Membrane

  • Transport is categorized as passive or active.
  • Passive transport:
    • No energy is required (ATP not used).
    • Movement from high concentration to low concentration (down the concentration gradient).
    • Small, nonpolar molecules (e.g., O2) can diffuse directly across the membrane.
    • Larger or charged molecules require facilitating proteins (facilitated diffusion): example is glucose transport via a specific channel that recognizes glucose; glucose binds to the transporter and is carried into the cell.
    • Even charged, small ions like K^+ require specific facilitating proteins to move down their gradient.
  • Active transport:
    • Moves substances from low concentration to high concentration (up the gradient).
    • Requires energy, usually from ATP.
    • Example: glucose transport that moves outside-to-inside against the gradient; the transporter binds glucose and ATP; energy release drives transport; ATP becomes ADP in the process.
    • ATP hydrolysis provides the energy for active transport; represented as the ATP → ADP + P_i energy release.
  • Key terms:
    • Facilitating protein (channel/protein) specificity: channels are highly specific for their substrates (e.g., glucose channel only translocates glucose).
    • The energy currency (ATP) is used to power active transport and other cellular processes.

Cytoplasm and Prokaryotic Cell Structure

  • Prokaryotic cytoplasm contains:
    • Intracellular materials: carbohydrates, proteins, lipids, nucleotides, DNA, RNA.
    • Inclusion bodies for storage.
    • 70S ribosomes (not 80S; see later for comparison with eukaryotes).
    • Cytoskeleton (distinct from eukaryotic cytoskeleton).
    • Enzymes for glycolysis and the TCA cycle, DNA replication, transcription, translation, etc.
  • Metabolic pathways (glycolysis and TCA cycle) occur in the cytoplasm for prokaryotes; other metabolic pathways also operate in the cytoplasm.
  • Prokaryotes lack membrane-bound organelles (no true nucleus, mitochondria, etc.); this is known as the absence of compartmentalization.
  • Cytoplasm is a busy site where energy extraction and synthesis of cellular components occur concurrently.

Eukaryotic Cells: Size and Compartmentalization

  • Eukaryotic cells are larger on average than prokaryotes. Typical sizes: about 10 μm to 50–100 μm (plants, animals, fungi, protozoa).
  • Eukaryotes possess membrane-bound organelles, enabling compartmentalization of processes (e.g., glycolysis in cytosol, TCA cycle in mitochondria, transcription/translation in nucleus/cytosol).
  • Prokaryotes do not have true organelles; everything largely happens in the cytoplasm.

Take-Home Activity: Organelles and Their Functions (Eukaryotic cells)

  • Task: Provide a very short definition of what each organelle does (e.g., mitochondria – Powerhouse; chloroplast – photosynthesis).
  • Example definitions:
    • Mitochondria: Powerhouse; generates ATP.
    • Chloroplasts: Site of photosynthesis.
    • Ribosomes: Protein synthesis (translation).
    • Other organelles to be introduced later; focus now on functional intuition rather than full structure.
  • Note: In later discussions, more detail on specific structures (e.g., flagella, mitochondrial structures) will be covered.

Ribosomes: Size Difference and Implications for Antibiotics

  • Prokaryotic ribosomes: 70S.
  • Eukaryotic ribosomes: 80S.
  • Function is the same (protein synthesis/translation), but structural differences exist.
  • Implication: Many antibiotics selectively target prokaryotic 70S ribosomes and do not affect eukaryotic 80S ribosomes, allowing selective toxicity.

Metabolism: Overview and Goals

  • Metabolism comprises two major stories:
    1) Energy extraction: converting nutrients into usable energy in the form of ATP.
    2) Growth: building cellular components (membranes, proteins, capsules, glycocalyx, slime layer, pili, flagella, peptidoglycan) to enable cell growth and division (binary fission).
  • Microbes require nutrients: carbon, nitrogen, sulfur sources, minerals, and energy sources to grow and reproduce.
  • The host body is a source of raw materials for invading microbes; microbes cause disease by growing and damaging host tissues, not by “wanting” to harm the host.
  • Microbes harvest energy by extracting energy from molecules (carbohydrates, lipids, proteins, nucleotides) via controlled breakdown reactions (glycolysis, TCA cycle) and then store energy as ATP for cellular processes.
  • ATP serves as the universal energy currency for driving cellular processes, including enzymatic reactions, transport, and biosynthesis.

ATP: The Universal Energy Currency

  • ATP: adenosine triphosphate; a nucleotide with:
    • Adenosine base attached to a ribose sugar and three phosphate groups.
    • The three phosphates are linked by high-energy (phosphoanhydride) bonds; energy is stored in these bonds and released on hydrolysis.
  • Hydrolysis of ATP releases energy used to drive endergonic processes and metabolic reactions.
  • Key forms of ATP regeneration:
    • Substrate-level phosphorylation: direct transfer of a high-energy phosphate to ADP to form ATP.
    • Example (generic):
      ext{ADP} + ext{P}_i
      ightarrow ext{ATP}
    • Oxidative phosphorylation: energy from NADH/FADH2 electrons transferred through the electron transport chain to generate ATP.
    • Photophosphorylation: ATP production during photosynthesis (not covered in this course).
  • ATP hydrolysis also converts ATP to ADP, releasing energy used for cellular work.
  • Illustration: ATP acts as a universal cash currency for the cell; enzymes and molecular machines recognize and use ATP to perform work.
  • Analogy used in class: ATP is the cell’s cash alongside a metaphor about converting energy-rich molecules into usable energy; the goal is to siphon electrons (high-potential energy) to generate ATP efficiently.

How Cells Access Energy from Molecules: Redox Chemistry

  • Metabolism involves redox reactions: the transfer of electrons from donors to acceptors.
  • Concepts:
    • Oxidation: loss of electrons (donor).
    • Reduction: gain of electrons (acceptor).
    • Redox reactions are coupled: when one molecule is oxidized, another is reduced.
    • High-potential electrons are the ones that can be used to make ATP; low-potential electrons are not useful for energy capture.
  • Electron shuttles (carriers) transport high-potential electrons between reactions:
    • NAD^+/NADH (nicotinamide adenine dinucleotide).
    • NADP^+/NADPH (nicotinamide adenine dinucleotide phosphate).
    • FAD/FADH_2 (flavin adenine dinucleotide).
  • Functional view: These carriers act like taxis (or Uber rides) that move high-potential electrons from donors (e.g., glycolysis intermediates) to acceptors (e.g., the electron transport chain) and return to cycle.
  • Oxidized vs reduced states (nomenclature):
    • NAD^+ (oxidized, empty taxi) vs NADH (reduced, taxi with passengers).
    • The same logic applies to NADP^+/NADPH and FAD/FADH_2.
  • Important note: The focus is on electrons with high potential energy; balancing hydrogens is for charge balance, not the energy-carrying part.
  • Quick conceptual framework: NAD^+ picks up electrons to become NADH; NADH donates electrons to the electron transport chain (ETC) and becomes NAD^+ again, continuing the cycle.

Do Zero-Calorie Energy Drinks Really Boost Metabolism? A Conceptual Aside

  • Zero-calorie energy drinks often contain B vitamins (e.g., B3, B6, B_12), which are precursors to electron shuttles.
  • The idea (in the discussion) is that consuming these vitamins could increase the cellular capacity to generate electron shuttles (NAD^+/NADH, NADP^+/NADPH) and thus potentially influence ATP production.
  • In practice, absorption efficiency and bioavailability vary; not all consumed vitamins are converted to shuttles in sufficient quantities to dramatically alter metabolism.
  • Caffeine in energy drinks is a stimulant, not the energy source per se; it affects brain chemistry and perception of wakefulness, not ATP yield. The body’s actual energy currency remains ATP and its production via glycolysis, TCA, and oxidative phosphorylation.
  • The discussion also notes that many nutrition products use this as a marketing claim; actual metabolic gain depends on multiple factors including absorption, regulation, and overall energy balance.

Glucose Energy: Where Is the Energy in a Bond?

  • The energy in glucose and other nutrients comes from chemical bonds, which are formed by electrons in different shells and orbitals; electrons in higher energy shells have greater potential energy.
  • When bonds are broken, high-energy electrons are released and can be captured by electron shuttles to form ATP.
  • Free roaming electrons are dangerous (free radicals) and can damage biomolecules; antioxidants in foods (e.g., berries) help neutralize free radicals by scavenging electrons.
  • In metabolism, controlled, multi-step pathways (glycolysis, TCA cycle) harvest energy gradually, which is safer and more efficient for the cell than a single, massive energy release.

Catabolic vs Anabolic Metabolism

  • Catabolic pathways (catabolism): break down complex molecules into simpler ones, releasing energy that is captured as ATP and reduced cofactors (e.g., NADH, FADH_2).
    • Examples: breakdown of carbohydrates, lipids, proteins to generate ATP.
  • Anabolic pathways (anabolism): synthesize complex molecules from simpler ones; consume energy (ATP).
    • Examples: building proteins from amino acids, polysaccharides from monosaccharides, lipids from fatty acids and glycerol.
  • The two types are interconnected: ATP produced in catabolism drives anabolic biosynthesis; thus metabolism alternates between energy production and biosynthesis depending on cellular needs.
  • Nutritional inputs in the environment serve as building blocks and energy sources; nutrients include carbohydrates, proteins, complex lipids, nucleotides, minerals, etc.

Glycolysis, TCA Cycle, and Energy Harvesting (Overview)

  • Microbes extract energy by controlled breakdown of energy-rich molecules via glycolysis and the TCA cycle, feeding electrons to the ETC via carriers like NADH and FADH_2.
  • The electron transport chain then uses these high-potential electrons to generate ATP (oxidative phosphorylation).
  • In prokaryotes, these pathways occur in the cytoplasm; in eukaryotes, many steps occur in organelles (cytosol for glycolysis; mitochondria for TCA and ETC).
  • The lecture emphasizes the overlap with other courses but notes key differences between prokaryotic and eukaryotic implementations of these pathways.

Enzymes: Catalysts of Metabolic Reactions

  • Enzymes are required to catalyze biological reactions at physiologically relevant temperatures and to overcome activation energy barriers.
  • Without enzymes, many essential reactions would occur too slowly to sustain life at body temperature.
  • Example: lactose (milk sugar) is a disaccharide of glucose and galactose connected by a glycosidic bond; enzymes (lactase) hydrolyze lactose into glucose and galactose.
  • The rate of non-enzymatic hydrolysis at room temperature would require impractically high temperatures (e.g., ~300°F) to occur quickly, which would kill the organism. Enzymes enable rapid reactions at ambient temperatures.

Protein Structure and Function: Four Levels

  • Proteins are chains of amino acids; in prokaryotes, average protein length ~300 amino acids (humans have larger proteins).
  • Protein structure determines function: shape and folding are critical.
  • Four levels of structure:
    • Primary structure: linear sequence of amino acids from N-terminus to C-terminus (e.g., Met–Val–Trp–Ala–…).
    • Secondary structure: local folding patterns stabilized by hydrogen bonds; two common forms are:
    • Alpha helix (α-helix)
    • Beta pleated sheet (β-pleated sheet)
    • Tertiary structure: overall 3D folding of a single polypeptide, determined by interactions among R-groups (hydrogen bonds, ionic bonds, disulfide bridges, hydrophobic effects).
    • Quaternary structure: assembly of multiple polypeptide chains into a functional unit (e.g., hemoglobin has four subunits).
  • Consequences of structure:
    • The same set of atoms arranged differently yields different proteins with distinct functions (e.g., glucose vs. fructose have the same formula but different structures and properties).
    • Correct folding is essential for function; misfolding leads to loss of function.
  • Example: Hemoglobin is composed of four polypeptide chains that must fold properly at secondary, tertiary, and quaternary levels to transport oxygen and carbon dioxide.
  • The analogy: a truck key fits a specific ignition; if the shape is wrong, it won’t start. Similarly, a protein must have the correct 3D shape to function.

Why Enzymes Are Essential in Metabolism

  • Enzymes lower the activation energy of reactions, enabling them to proceed at biologically meaningful rates at normal body temperatures.
  • This enables life as we know it, as cellular chemistry would be too slow otherwise.
  • Lactose example (revisited): the lactose-to-glucose/galactose hydrolysis is enzyme-catalyzed, speeding digestion in the gut.

Quick Recap: Key Takeaways for Metabolism and Cell Biology

  • The cell membrane is a fluid mosaic of phospholipids and proteins, enabling dynamic transport and signaling.
  • Transport across membranes occurs via passive (no energy) or active (energy-dependent) processes; facilitated diffusion permits selective movement of certain molecules.
  • Prokaryotic cells lack true organelles and have a cytoplasm that houses all major metabolic processes; they have 70S ribosomes and smaller genome organization.
  • Eukaryotic cells are larger and compartmentalized with membrane-bound organelles (e.g., mitochondria, chloroplasts) that specialize functions; they have 80S ribosomes.
  • Metabolism comprises energy extraction (catabolism) and growth/building (anabolism); ATP is the universal energy currency, produced via substrate-level phosphorylation, oxidative phosphorylation, and, in photosynthetic organisms, photophosphorylation.
  • Redox reactions move high-potential electrons through electron shuttles (NAD^+/NADH, NADP^+/NADPH, FAD/FADH_2); energy is conserved in ATP after the electrons reach the ETC.
  • Enzymes catalyze metabolic reactions, enabling rapid biochemistry at physiological temperatures and lowering activation energy; protein structure (primary–quaternary) is tightly linked to function.
  • Antibiotics often target prokaryotic ribosomes (70S) specifically, leaving eukaryotic ribosomes (80S) largely unaffected.
  • The body and metabolism involve a cascade of tightly regulated processes; nutrition, energy balance, and enzymatic control all shape cellular growth and health.