Eukaryotic Cell Structure and Function

Microscopy parameters:
- Magnification: Ratio of an object's image size to its real size.
- Resolution: Measure of the clarity of an image.
- Contrast: Difference in brightness between light and dark areas.
Light Microscopes (LM): Pass visible light through a specimen and glass lenses to magnify up to approximately $1,000\times$ .
Electron Microscopes (EM):
- Scanning Electron Microscopy (SEM): Focuses an electron beam onto a specimen surface to reveal 3D topography.
- Transmission Electron Microscopy (TEM): Directs an electron beam through a specimen to study internal ultrastructure.

Universal cellular features:
- Plasma membrane (selective barrier).
- Cytosol (semifluid substance).
- Chromosomes (carry genetic material).
- Ribosomes (synthesize proteins).
Prokaryotic cells:
- DNA located in an unbound, non-enclosed region called the nucleoid.
- Lack membrane-enclosed organelles.
- Examples include bacteria such as Corynebacterium diphtheriae.
Eukaryotic cells:
- DNA enclosed in a double-membrane-bound nucleus.
- Cytoplasm contains diverse membrane-bound organelles.
- Generally larger than prokaryotic cells due to surface area-to-volume ratio constraints on metabolism.

Nucleus:
- Contains most cellular DNA and genes.
- Bounded by a double membrane known as the nuclear envelope, perforated by nuclear pores.
- DNA is organized with histone proteins into chromatin, which condenses into distinct chromosomes during cell division.
- Nucleolus: Dense region within the nucleus responsible for ribosomal RNA (rRNA) synthesis.
Ribosomes:
- Protein-synthesizing complexes composed of rRNA and protein subunits (large and small subunits).
- Free ribosomes: Function while suspended in the cytosol.
- Bound ribosomes: Attached to the exterior of the endoplasmic reticulum or nuclear envelope.

Components: Nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, and plasma membrane (connected directly or via transport vesicles).
Endoplasmic Reticulum (ER):
- Smooth ER: Synthesizes lipids, metabolizes carbohydrates, detoxifies drugs and poisons, and stores calcium ions.
- Rough ER: Studded with ribosomes; synthesizes secretory proteins (glycoproteins) and membrane components.
Golgi Apparatus:
- Flattened membranous sacs called cisternae.
- Receives transport vesicles at the cis face, modifies products of the ER, sorts them, and dispatches vesicles from the trans face.
Lysosomes:
- Membranous sacs containing hydrolytic enzymes operating in acidic cellular conditions.
- Perform phagocytosis (digestion of engulfed foreign particles/food) and autophagy (recycling cell organelles).
Vacuoles:
- Food vacuoles (formed by phagocytosis).
- Contractile vacuoles (pump excess water out of freshwater protists).
- Central vacuole (found in plant cells for storage, water retention, and structural support).

Endosymbiont Theory: Mitochondria and chloroplasts originated when an ancestral eukaryotic host cell engulfed an oxygen-using nonphotosynthetic prokaryote and a photosynthetic prokaryote, establishing an endosymbiotic relationship.
Mitochondria:
- Sites of cellular respiration converting energy to usable ATP.
- Enclosed by two membranes; inner membrane is folded into cristae to maximize surface area and surrounds the mitochondrial matrix.
Chloroplasts:
- Plant and algal organelles belonging to the plastid family; sites of photosynthesis.
- Contain flattened sacs called thylakoids (stacked into grana) surrounded by a fluid matrix called stroma.
Peroxisomes:
- Specialized metabolic compartments that transfer hydrogen to oxygen, forming hydrogen peroxide ( $H_2O_2$ ), which is subsequently broken down into water.
- Function in fatty acid breakdown and cellular detoxification.

Cytoskeleton: Network of structural fibers extending throughout the cytoplasm to provide support, maintain cell shape, and facilitate movement via motor proteins powered by ATP.
Microtubules:
- Thickest fibers, composed of tubulin dimers.
- Grow out from the centrosome (containing a pair of centrioles in animal cells).
- Direct organelle movement and form motility structures like cilia and flagella ( $9+2$ doublet arrangement attached to a $9+0$ triplet basal body).
Microfilaments (Actin Filaments):
- Thinnest fibers, composed of twisted double chains of actin.
- Form a cortex inside the plasma membrane to support cell shape.
- Interact with myosin motor proteins for muscle cell contraction, amoeboid movement via pseudopodia, and cytoplasmic streaming in plant cells.
Intermediate Filaments:
- Medium-sized, durable fibers that reinforce cell shape and anchor organelles (such as the nucleus) in place.

Cell Walls of Plants:
- External rigid layer composed of cellulose microfibrils embedded in polysaccharides and proteins.
- Protects the cell, maintains shape, and prevents excessive water uptake.
Extracellular Matrix (ECM) of Animal Cells:
- Meshwork of glycoproteins, primarily collagen, proteoglycan complexes, and fibronectin.
- Connects to cell membrane receptor proteins called integrins to regulate cellular behavior and signaling.
Plant Cell Junctions:
- Plasmodesmata: Channels penetrating cell walls that connect cytoplasms of adjacent plant cells to pass water, solutes, RNA, and proteins.
Animal Cell Junctions:
- Tight Junctions: Press membranes of neighboring cells tightly together to seal fluid leaks across cell layers.
- Desmosomes: Anchoring junctions that rivet cells together into strong structural sheets.
- Gap Junctions: Communicating junctions providing cytoplasmic channels for ions and small molecules between cells.