Cellular Structure, Proteins, and Metabolic Pathways

Microscopic Dimensions and Cellular Scale

• Structural Dimensions of Biological Entities:

  • Period at the end of a printed sentence: approximately $1000\,\mu\text{m}$ ($1\,\text{mm}$) in diameter.

  • Typical human cell: $10\,\mu\text{m} - 100\,\mu\text{m}$ in diameter.

  • Mitochondrion: $1.0\,\mu\text{m}$ in diameter.

  • Lysosomes, peroxisomes, and intracellular vesicles: $0.1\,\mu\text{m} - 1.0\,\mu\text{m}$.

  • Ribosome: $0.01\,\mu\text{m} - 0.1\,\mu\text{m}$ ($10\,\text{nm} - 100\,\text{nm}$).

  • Globular protein molecule: $0.001\,\mu\text{m} - 0.01\,\mu\text{m}$ ($1\,\text{nm} - 10\,\text{nm}$).

  • Hydrogen atom: $0.0001\,\mu\text{m}$ ($0.1\,\text{nm}$).

• Detection Ranges of Microscopic Instruments:

  • Unassisted human eye: Resolves structures down to approximately $100\,\mu\text{m}$.

  • Light microscope: Resolves objects from $0.2\,\mu\text{m}$ up to over $100\,\mu\text{m}$.

  • Electron microscope: Resolves structural details from $0.001\,\mu\text{m}$ ($1\,\text{nm}$) up to $100\,\mu\text{m}$.

  • Scanning tunneling microscope: Resolves atomic structures smaller than $0.001\,\mu\text{m}$ ($0.1\,\text{nm}$).

Cellular Compartmentalization: Cytoplasm versus Cytosol

• Definition of Compartments:

  • Cytoplasm: The entire internal cellular region excluding the nucleus, comprising both the membrane-bound organelles and the fluid medium.

  • Cytosol: The unbound liquid phase or fluid portion of the cytoplasm that surrounds the cell organelles.

Plasma Membrane Structure and Dynamics

• Functions of Membranes:

  • Act as selective barriers that regulate the passage of substances into and out of the cell, as well as between cytosol and internal organelles.

  • Detect chemical extracellular messengers and signaling molecules.

  • Form mechanical junctions that link adjacent cells together.

  • Anchor cells directly to the extracellular matrix (ECM).

• Phospholipid Bilayer Structure:

  • Composed of amphipathic phospholipids organized in a double layer.

  • Nonpolar fatty acid hydrocarbon chains aggregate in the interior core to minimize contact with water.

  • Polar phosphate head groups are oriented outward toward the aqueous intracellular and extracellular fluids.

  • Cholesterol molecules are interspersed within the phospholipid bilayer of the plasma membrane to regulate and maintain membrane fluidity across variable temperature conditions.

• Membrane Protein Classifications:

  • Integral Membrane Proteins: Amphipathic molecules that associate closely with the nonpolar fatty acid chains. Transmembrane proteins span the entire lipid bilayer, possessing nonpolar regions within the membrane interior and polar hydrophilic segments exposed to aqueous fluids on either side (often featuring an extracellular $-\text{NH}_2$ or $-\text{COOH}$ terminal region).

  • Peripheral Membrane Proteins: Hydrophilic proteins that do not interact with the hydrophobic core of the bilayer. Located exclusively at the membrane surfaces, bound non-covalently to integral membrane proteins.

• Fluid-Mosaic Model:

  • The structure of the membrane is a dynamic mosaic of proteins freely floating or migrating laterally within a flexible, fluid phospholipid matrix embedded with cholesterol.

Cell Junctions and Extracellular Adhesion

• Integrins:

  • Specialized transmembrane proteins that mediate cell-matrix and cell-cell interactions.

  • Bind to specific adhesion proteins within the extracellular matrix and link them to structural components in adjacent cell membranes.

• Desmosomes:

  • Characterized by plasma membranes separated by a intercellular space of approximately $20\,\text{nm}$.

  • Feature localized protein accumulations called dense plaques on the inner cytoplasmic membrane faces, which serve as anchoring sites for intermediate filaments (such as keratin).

  • Transmembrane proteins called cadherins extend into the extracellular space to interlock with cadherins extending from adjacent cell membranes, forming strong mechanical attachments.

• Tight Junctions:

  • Join adjacent plasma membranes directly together, leaving no extracellular space between cell faces.

  • Extend in a continuous circumferential belt around the entire apical boundary of epithelial cells.

  • Form impermeable barriers that completely block the extracellular pathway (paracellular diffusion) between cells, forcing molecules to pass through cells via the selective transcellular pathway.

  • Polarize epithelial tissues into an apical side facing the lumen and a basolateral side facing the blood supply.

• Gap Junctions:

  • Direct protein channel complexes that link the cytosol of adjacent cells.

  • Hexameric protein assemblies called connexins from neighboring membranes align end-to-end to build a continuous aqueous channel.

  • Channel pore diameter of $1.5\,\text{nm}$ permits selective passage of small ions and hydrophilic molecules, while preventing passage of large proteins or macromolecules.

Cell junctions = cell ↔ cell connections

Imagine cells are people standing next to each other:

• Tight junctions = Ziploc seal → cells are sealed tightly together so substances can’t leak between them. Example: intestinal lining.

• Desmosomes = strong snaps/buttons → physically hold cells together so they don’t rip apart when stretched. Example: skin and heart tissue.

• Gap junctions = little tunnels → channels connect neighboring cells so ions and small molecules can pass directly between them. This lets cells communicate. Example: heart cells coordinating contractions.

Gap junctions occur between two neighboring cells, right where their cell membranes meet.

Picture it like this:

Cell 1 | membrane → 🔘 GAP JUNCTION 🔘 ← membrane | Cell 2

Nuclear Organization and Protein Synthesis Machinery

• Structural Features of the Nucleus:

  • Houses genetic information stored in double-stranded DNA molecules required for cellular inheritance and protein expression.

  • DNA binds tightly to specialized proteins called histones, forming a complex termed chromatin.

  • During cellular division, chromatin condenses into distinct, tightly coiled structures termed chromosomes.

• Nuclear Envelope and Nucleolus:

  • The nucleus is enclosed by a nuclear envelope consisting of two concentric lipid bilayers.

  • The inner and outer nuclear membranes join at localized sites to form nuclear pores, controlling macromolecular transport between nucleoplasm and cytoplasm.

  • The nuclear membrane is structurally continuous with the endoplasmic reticulum.

  • The nucleolus is a dense, non-membrane-bound sub-nuclear region containing DNA sequences coding for ribosomal RNA (rRNA), responsible for assembling ribosomal subunits before exporting them to the cytoplasm.

• Ribosomes:

  • Composed of structural ribosomal RNA (rRNA) and specific proteins.

  • Function as protein synthesis sites, operating either free in the cytosol or bound to the cytoplasmic surface of the endoplasmic reticulum.

Endomembrane System and Organelle Function

• Rough Endoplasmic Reticulum (RER):

  • Continuous network of flattened membrane sacs studded with bound ribosomes on its cytosolic surface.

  • Processes and packages newly synthesized proteins into transport vesicles destined for routing to the Golgi apparatus.

• Smooth Endoplasmic Reticulum (SER):

  • Lacks bound ribosomes.

  • Site of lipid and steroid hormone synthesis.

  • Contains enzymes that detoxify harmful organic molecules and metabolic waste products.

  • Serves as the primary intracellular storage compartment for calcium ions ($\text{Ca}^{2+}$).

• Golgi Apparatus:

  • Consists of flattened, membrane-bound sacs (cisternae).

  • Receives transport vesicles carrying newly synthesized proteins at its cis (receiving) face.

  • Chemically modifies, sorts, and packages proteins into distinct transport vesicles that bud off the trans (shipping) face toward the plasma membrane, secretory vesicles, or lysosomes.

• Lysosomes:

  • Membrane-enclosed vesicles filled with acidic fluid and hydrolytic digestive enzymes.

  • Digest cellular waste, engulfed bacteria, foreign material, and damaged intracellular organelles via autophagy.

• Peroxisomes:

  • Membrane-bound organelles that consume molecular oxygen ($\text{O}_2$) to oxidize organic substrates and strip away hydrogen atoms.

  • Perform catabolism of long-chain fatty acids into two-carbon units used in energy metabolic pathways.

  • Generate hydrogen peroxide ($\text{H}_2\text{O}_2$) as a metabolic byproduct, which is enzymatically converted to water and oxygen.

• Mitochondria:

  • Principal sites of cellular respiration, converting energy extracted from nutrient fuels into adenosine triphosphate (ATP).

  • Bound by a double membrane: a smooth outer membrane and an inner membrane deeply folded into shelf-like cristae.

  • The innermost fluid filled compartment enclosed by the inner membrane is called the matrix.

Cytoskeletal Architecture and Motility

• Cytoskeletal Filament Types:

  • Actin Filaments (Microfilaments):

  • Diameter: $7\,\text{nm}$.

  • Subunit: G-actin (globular actin) polymerizing into helical chains.

  • Functions: Cell movement, determination and modification of cell shape, cytokinesis during cell division, and muscle contraction.

  • Intermediate Filaments:

  • Diameter: $10\,\text{nm}$.

  • Subunits: Fibrous protein polymers including keratin, desmin, and lamin.

  • Functions: Provide mechanical tensile strength, maintain cellular structural integrity under mechanical stress, and anchor the cell nucleus.

  • Microtubules:

  • Diameter: $25\,\text{nm}$.

  • Subunit: $\alpha$- and $\beta$-tubulin heterodimers assembled into hollow cylindrical tubes.

  • Microtubules originate from the centrosome, a microtubule-organizing center containing a pair of perpendicular centrioles.

  • Provide rigid intracellular tracks along which motor proteins (e.g., kinesin) walk to transport secretory vesicles and organelles.

• Cilia and Flagella:

  • Cilia: Hair-like, motile cell surface projections composed of a central core of microtubules arranged in a characteristic $9+2$ array with contractile proteins, producing sweeping surface fluid movements (e.g., respiratory tract epithelial lining).

  • Flagella: Single, long motile extensions possessing a $9+2$ microtubule structural arrangement, generating propulsive motility (e.g., sperm cells).

Gene Expression: Transcription, Processing, and Translation

• DNA Structure and Complementary Base Pairing:

  • DNA exists as a double-stranded, right-handed double helix.

  • Composed of four nucleotide bases: Adenine ($\text{A}$), Thymine ($\text{T}$), Cytosine ($\text{C}$), and Guanine ($\text{G}$).

  • Complementary pairing rules dictating double-strand linkage: Adenine pairs exclusively with Thymine ($\text{A-T}$), and Cytosine pairs exclusively with Guanine ($\text{C-G}$).

  • A gene is defined as a specific nucleotide sequence along a DNA molecule containing instructions for synthesizing a specific polypeptide chain.

• Genetic Code and Codons:

  • The genetic code is read as a triplet code consisting of three-base sequences on mRNA termed codons.

  • Four nucleotide bases organized into three-letter combinations yield $4^3 = 64$ possible codons.

  • Degeneracy: Individual amino acids are encoded by more than one distinct codon.

  • Start codon: $\text{AUG}$ (codes for Methionine).

  • Stop codons: $\text{UAA}$, $\text{UAG}$, and $\text{UGA}$.

• Transcription and Pre-mRNA Processing:

  • RNA polymerase reads DNA

  • RNA polymerase “grabs” free nucleotides to build primary RNA transcript (DNA mirror like)

  • specific transcription factors bind to a promoter base sequence on the template strand of DNA.

  • Transcription proceeds along the template strand producing a primary RNA transcript (pre-mRNA) until a stop signal is reached.

  • Primary RNA transcripts contain protein-coding regions (exons) interspersed with non-coding regions (introns).

  • Nuclear RNA splicing performed by spliceosome complexes excises introns and ligates exons together to generate functional mRNA. (cuts off the non coding pieces)

  • Processed mRNA exits the nucleus through nuclear pores into the cytosol.

• Translation and Post-Translational Splicing:

  • mRNA binds to a ribosome composed of small and large subunits.

  • Transfer RNA (tRNA) molecules carrying specific amino acids dock at active ribosomal sites by binding their specific anticodon sequence to complementary mRNA codons.

  • The ribosome moves along the mRNA molecule in the direction of synthesis, elongating the growing amino acid chain.

  • Post-translational splitting: A single translated polypeptide precursor can undergo enzymatic cleavage to generate multiple distinct functional protein molecules (e.g., Protein 1 split into Protein 2 and Protein 3). (the final proteins get editited from the ribosome and modified through processes such as phosphorylation, glycosylation, or ubiquitination, which can influence their activity, stability, and interactions with other cellular components.

Protein Biophysics: Ligand Binding, Specificity, and Affinity

• Principles of Ligand-Protein Interaction:

  • Ligand: Any molecule or ion that binds non-covalently to a specific region on a protein face.

  • Binding Site: The specialized binding pocket or domain on a protein structural surface that accommodates the ligand.

  • Binding is non-covalent and induces a conformational change in protein structure, altering its functional activity (activation or inhibition).

• Chemical Specificity:

  • The capability of a protein's binding site to bind specific ligands based on spatial shape, charge distribution, and structural complementarity.

  • High chemical specificity sites bind only a single specific ligand molecule; low specificity sites can bind families of structurally related molecules.

• Binding Affinity:

  • The thermodynamic strength of chemical binding between a ligand and a protein site, governing the rate of dissociation.

  • High-affinity binding sites bind ligands tightly at low ligand concentrations.

  • Low-affinity binding sites require significantly elevated ligand concentrations to achieve equivalent binding site occupation.

Metabolic Pathways and Cellular Bioenergetics

• Enzymes as Biological Catalysts:

  • Enzymes are protein catalysts that increase chemical reaction rates by lowering the activation energy ($\text{E}_a$) required to reach reaction transition states.

  • Reactants binding to enzyme active sites are termed substrates.

• Adenosine Triphosphate (ATP) Hydrolysis:

  • ATP consists of adenine, ribose, and three inorganic phosphate groups.

  • Energy is released through the cleavage of terminal phosphoanhydride bonds via hydrolysis:     $\text{ATP} + \text{H}_2\text{O} \rightarrow \text{ADP} + \text{P}_i + \text{H}^+ + \text{Energy}$

• Glycolytic Pathway (Cytosolic Metabolism):

  • Occurs entirely within the cytoplasm.

  • Stored in the skeletal muscle and liver

  • Converts $1\text{ molecule of glucose } (6\text{ carbons})$ into $2\text{ molecules of pyruvate } (3\text{ carbons})$.

  • Energy Investment Phase: Consumes $2\text{ ATP}$ molecules in early priming steps.

  • Energy Yielding Phase: Produces $4\text{ ATP}$ molecules and reduces $2\text{ NAD}^+$ to $2\text{ NADH}$ (carrying high-energy electrons).

  • Net Yield: $2\text{ ATP}$ and $2\text{ NADH}$ per glucose molecule.

  • In anaerobic environments or oxygen-deprived conditions, pyruvate is converted in the cytosol to lactate.

• Transition Reaction and Krebs Cycle (Mitochondrial Matrix):

  • Pyruvate diffuses into the inner mitochondrial compartment (matrix).

  • Transition Reaction: Pyruvate is converted into Acetyl Coenzyme A (Acetyl CoA), releasing $\text{CO}_2$ waste and reducing additional $\text{NAD}^+$ to $\text{NADH}$.

  • Acetyl CoA enters the Krebs Cycle (Citric Acid Cycle).

  • Oxidation of acetyl groups yields $\text{ATP}$ (via GTP conversion), releases $\text{CO}_2$, and reduces electron carrier coenzymes to $\text{NADH}$ and $\text{FADH}_2$ ($\text{Coenzyme-2H}$).

  • Using Acetyl CoA to produce NADH and FADH2 to be used in an transport chain

• Oxidative Phosphorylation and Electron Transport:

  • High-energy electrons carried by $\text{NADH}$ and $\text{FADH}_2$ are transferred to cytochrome proteins forming the electron transport chain in the inner mitochondrial membrane.

  • Energy released during electron transfer fuels proton pumps, creating a proton gradient that drives ATP synthase to form ATP.

  • Molecular oxygen ($\text{O}_2$ ) acts as the final terminal electron acceptor, combining with free hydrogen ions to produce water ($\text{H}_2\text{O}$).

• Integrated Fuel Metabolism Summary:

  • Carbohydrate Breakdown: Glycogen $\leftrightarrow$ Glucose $\rightarrow$ Glycolysis $\rightarrow$ Pyruvate $\rightarrow$ Acetyl CoA $\rightarrow$ Krebs Cycle.

  • Triglyceride Breakdown: Fats break down into Glycerol (which feeds directly into the glycolytic pathway) and Fatty Acids (which undergo breakdown to Acetyl CoA).

  • Protein Degradation: Proteins hydrolyze into free Amino Acids. Removal of nitrogen groups via deamination ($\text{R-NH}_2 \rightarrow \text{NH}_3 \rightarrow \text{Urea}$ ) yields carbon skeletons that enter as Pyruvate, Acetyl CoA, or Krebs Cycle intermediates.