3.2 Eukaryotic Cell Organelles and Their Functions

Eukaryotic cells contain specialized compartments called organelles, each handling specific tasks like energy production, protein synthesis, and waste breakdown. Understanding what each organelle does and how they work together is the foundation for everything else in cell biology.

Membrane-Bound Organelles

The Nucleus

The nucleus stores the cell's DNA and controls gene expression, making it the directive center of the cell. It's surrounded by a nuclear envelope, a double membrane that separates nuclear contents from the cytoplasm.

• Nuclear pores perforate the envelope and selectively allow molecules like mRNA and proteins to pass in and out
• The nucleolus is a dense region inside the nucleus where ribosomal RNA (rRNA) is made and ribosomal subunits are assembled
• DNA is organized with histone proteins into a complex called chromatin, which condenses into visible chromosomes during cell division

The nuclear envelope is continuous with the endoplasmic reticulum, which matters for understanding how proteins move through the cell.

Mitochondria

Mitochondria generate most of the cell's ATP through cellular respiration, breaking down glucose and other organic molecules. Their structure reflects this function.

• Double membrane: the outer membrane is smooth, while the inner membrane folds into cristae that increase surface area for the electron transport chain
• The matrix (inner compartment) contains enzymes for the citric acid cycle
• Mitochondria have their own DNA and ribosomes, which is strong evidence for the endosymbiotic theory: the idea that mitochondria descended from free-living bacteria that were engulfed by an ancestral cell

Chloroplasts

Found only in plant cells and some algae, chloroplasts capture light energy and convert it to chemical energy through photosynthesis.

• Also a double-membrane organelle, with an internal system of thylakoid membranes arranged in stacks called grana
• Thylakoids contain chlorophyll and other pigments that absorb light for the light-dependent reactions
• The stroma, the fluid surrounding the thylakoids, is where the Calvin cycle fixes $CO_2$ into glucose
• Like mitochondria, chloroplasts have their own DNA and ribosomes, supporting the endosymbiotic theory

The Endomembrane System

The endomembrane system is a set of interconnected organelles that work together to synthesize, modify, package, and transport proteins and lipids.

Endoplasmic Reticulum (ER): A network of membrane-bound channels and sacs extending from the nuclear envelope.

• Rough ER is studded with ribosomes on its cytoplasmic surface. Proteins made here are modified (folded, glycosylated, or given disulfide bonds) and then shipped to the Golgi apparatus.
• Smooth ER lacks ribosomes and handles lipid synthesis, detoxification of drugs and poisons, and calcium ion storage.

Golgi Apparatus: A stack of flattened membrane sacs (cisternae) that receives products from the ER.

1. Proteins and lipids arrive at the cis face (receiving side) in transport vesicles from the ER
2. As they move through the Golgi stacks, they're further modified (e.g., carbohydrate chains are trimmed or added)
3. At the trans face (shipping side), finished products are sorted and packaged into vesicles headed for the plasma membrane, lysosomes, or secretion outside the cell

Lysosomes: Single-membrane organelles packed with digestive enzymes (hydrolases) that operate at an acidic pH. They break down worn-out organelles, cellular debris, and engulfed foreign particles like bacteria. This recycling function is essential for cell maintenance.

Vacuoles: Large, membrane-bound sacs used for storage. In plant cells, the central vacuole can occupy most of the cell's volume, storing water, ions, and pigments while maintaining turgor pressure (the internal pressure that keeps the plant cell rigid against the cell wall).

Peroxisomes

Peroxisomes are single-membrane organelles that carry out oxidation reactions. They break down fatty acids and amino acids, and in the process generate hydrogen peroxide ($H_2O_2$), which is toxic. The enzyme catalase inside the peroxisome quickly converts $H_2O_2$ into water and oxygen, preventing cell damage.

Protein Synthesis Machinery

Ribosomes

Ribosomes are the sites where mRNA is translated into proteins. They're not membrane-bound, so they aren't technically organelles in the same sense, but they're essential to every cell.

• Composed of rRNA and proteins, organized into a large subunit and a small subunit that join together during translation
• Free ribosomes float in the cytoplasm and typically make proteins that function within the cytosol
• Bound ribosomes are attached to the rough ER and generally produce proteins destined for membranes, organelles, or secretion outside the cell
• The two types are interchangeable; it's the signal sequence on the growing polypeptide that determines where a ribosome ends up

Cellular Structure and Division

The Cytoskeleton

The cytoskeleton is a dynamic network of protein filaments that gives the cell its shape, enables movement, and organizes internal transport. Three types of filaments make up the system, each with distinct roles:

Microtubules and microfilaments are dynamic, constantly assembling and disassembling. Intermediate filaments are more stable and act like internal cables that reinforce the cell.

Centrosomes and Cell Division

The centrosome is the main microtubule-organizing center (MTOC) of animal cells. It consists of two centrioles (short cylinders of microtubules arranged in a 9+0 pattern) surrounded by pericentriolar material that nucleates microtubule growth.

During cell division:

1. The centrosome duplicates during S phase
2. The two centrosomes migrate to opposite poles of the cell
3. They organize the mitotic spindle, a structure of microtubules that attaches to chromosomes and pulls them apart during mitosis