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The cell

Last updated: January 21, 2021

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The cell is the basic structural and functional unit of living organisms. While unicellular organisms (e.g., bacteria, protozoa) consist of a single cell capable of sustaining life, multicellular organisms (e.g., animals, land plants) consist of numerous highly specialized and diverse cells organized into various types of tissue. Cells are surrounded by a membrane composed of a lipid bilayer with embedded proteins. Depending on their cell structure, organisms are classified as prokaryotes or eukaryotes. Prokaryotes, which encompass the domains of the Bacteria and the Archaea, are unicellular organisms that lack membrane-bound organelles such as a nucleus and mitochondria (see bacteria overview). Eukaryotes are unicellular and multicellular organisms with a cell or cells containing various specialized, membrane-bound organelles such as nuclei and mitochondria.

Cell types are classified as either prokaryotic or eukaryotic. Prokaryotes are unicellular organisms that encompass the domains of Bacteria and Archaea. They consist of a single cytoplasm-filled compartment enclosed by a cell membrane. Eukaryotes contain a nucleus and other membrane-bound cell organelles. Eukaryotes encompass all multicellular organisms as well as some unicellular ones (protozoa). Eukaryotic cells are larger (100–10,000-fold) than prokaryotic cells and have a significantly more complex structure.

Overview of the eukaryote and prokaryote cell structure
Factor Eukaryotes (humans, protozoa, animals, and plants) Prokaryotes (archaea and bacteria)
  • Present
  • Absent

Location of DNA

DNA storage form
Amount of noncoding DNA
  • 70–98% (lower gene density)
  • 5–25% (higher gene density)
  • Present
  • Absent
  • 80S
  • 70S

Cell membrane

Cell wall
  • Only in plants, fungi, and algae
  • Membranes separate cellular compartments within the cytosol
  • No compartmentalization
Locomotive structures (flagellum)
  • Consist of bundles of microtubules and the motor protein dynein, surrounded by a plasma membrane
  • Consist of repeating subunits of the protein flagellin (filament), a hook, and a motor complex that is anchored in the cell membrane

Prokaryotic cells do not have a nucleus.

Both prokaryotes and eukaryotes have cell membranes. The cell membrane provides a boundary between the outside environment and the cell interior and is an essential component of living systems. Eukaryotic cells also have intracellular membranes that envelop individual organelles and enable specialized processes to occur in separation from cytoplasmic processes. Furthermore, most prokaryotic and plant cells possess a cell wall, which envelops the cell membrane, stabilizes, and protects cells from the outside environment.

Cell membrane structure

The cell membrane (or plasma membrane) is composed of an asymmetric lipid bilayer with embedded or attached membrane proteins. The synthesis of membrane components occurs in the smooth endoplasmic reticulum (SER).

Lipid bilayer

  • Structure: consists of amphiphilic lipids such as phospholipids or sphingolipids, which possess a polar head (e.g., phosphate, sphingosine) and hydrophobic tails (fatty acids).
    • Distribution of nonpolar and polar groups: In an aqueous solution, the nonpolar hydrocarbon tails face inward, while the polar heads form a boundary to water in both directions. As a result, stable lipid bilayers develop, forming a spherical entity (e.g., cells or vesicles).
    • Distribution of membrane lipids: The different types of lipids are distributed asymmetrically between the two leaflets of the membrane.
      • Outer lipid layer: rich in phosphatidylcholine and sphingomyelin
      • Inner lipid layer: rich in phosphatidylserine, phosphatidylethanolamine, and phosphatidylinositol
  • Characteristics
    • Permeability
      • Almost impermeable to polar molecules
      • Highly permeable to nonpolar molecules and water
    • Fluidity: The fluidity of the membrane lipid bilayer changes depending on the composition of bilayer and the temperature of the environment.
      • Unsaturated fatty acids increase membrane fluidity.
      • Cholesterol and glycolipids; (i.e., lipids with a carbohydrate attached by a glycosidic covalent bond) stabilize the membrane.
    • Diffusion (transport): The fluidity of the lipid bilayer allows for movement of individual molecules within the membrane.
      • Lateral (parallel) diffusion: Individual lipid molecules diffuse freely within the lipid bilayer.
      • Transverse diffusion : very slow; requires enzymatic support by flippases, floppases, or scramblases (phospholipid translocators)
        • Flippases: move phospholipids from the outer to the inner surface
        • Floppases: move phospholipids from the inner to the outer surface
        • Scramblases: move phospholipids in both directions
      • Facilitated diffusion: diffusion of molecules across the cell membrane via carrier proteins, channel proteins, or ions (e.g., glucose and fructose transport into cells via GLUT transporters)

Membrane proteins

Examples of asymmetrically distributed membrane components
Integral membrane proteins Transmembrane proteins
Integral monotopic proteins
Peripheral membrane proteins Extracellularly directed
Intracellularly directed

Because of their fluidity, membranes are also permeable to water and some small molecules like O2, even without the use of specific channels or transporters. Accordingly, they are described as semipermeable.


Membrane functions

  • Protects the cell from the external environment
  • Transport of substances from the inside to the outside of the cell or from the outside to the inside of the cell
  • Signal transduction: conversion of extracellular signals into intracellular reactions
  • Cell identification
    • Every cell expresses specific proteins on its surface that are mostly glycosylated (glycoproteins).
    • These glycoproteins are highly specific for each cell type and allow self cells to be distinguished from one another as well as from foreign cells.
  • Electrical excitability
    • Generation of an electrochemical gradient across the membrane creates a membrane potential.
    • Excitation activates voltage-gated ion channels, temporarily decreasing the negative membrane potential (depolarization).
  • Cell junctions: formed by anchor proteins (cell adhesion molecules), which are anchored to the cytoskeleton and protrude outside of the cell

Cellular organelles are compartments within cells that are enveloped by a membrane and have a highly specific function. Eukaryotes contain numerous organelles, whereas prokaryotes lack compartmentalization.

Overview of the most important cell organelles
Cellular organelles Structure Function
  • Double membrane
Endoplasmic reticulum (ER)
  • Branched membrane system
  • Synthesis of proteins, membrane components, etc.
Golgi apparatus
  • Enveloped, disc-shaped vesicle system
  • Modification and packaging of products for export out of the cell
  • Double membrane
  • Intramembranous space
  • Matrix
  • Energy production
  • Various metabolic pathways
  • Small enveloped vesicles
  • Loaded with hydrolytic enzymes
  • Degradation of foreign and self molecules
  • Small enveloped vesicles
  • Loaded with various enzymes such as catalases


The nucleus is the control center of the cell. It is surrounded by a double membrane and contains all of the cell's genetic material, except for the mitochondrial DNA.

Nuclear envelope

The nuclear membrane consists of an inner and outer membrane, each composed of a lipid bilayer.

Nuclear content


The endoplasmic reticulum (ER) is an extensive network of membranes that is directly connected to the outer nuclear membrane. The ER forms a channel system of elongated cavities. The most important function is the synthesis of cellular components and cell export products. The ER can be microscopically and functionally differentiated into the rough and smooth ER.


  • Membranous channel system
  • In direct contact with the outer nuclear membrane
  • Composed of two microscopic and functionally different regions:
    • Rough endoplasmic reticulum (RER): characterized by ribosomes that are bound to the surface
    • Smooth endoplasmic reticulum (SER): without surface ribosomes



Enveloped, disc-shaped, slightly curved vesicle system with two sides:

  • Cis-Golgi face (convex side)
    • Bends slightly around the ER
    • Membrane vesicles from the ER that are loaded with proteins are received at the cis-Golgi side.
  • Trans-Golgi face (concave side)


Vesicular trafficking proteins

Defective labeling of lysosomal acid hydrolases in the Golgi apparatus leads to I-cell disease.

To remember that COPII facilitates anterograde (forward) transport from the rough endoplasmatic reticulum to the Golgi apparatus and COPI facilitates retrograde (backward) transport, think: “Two cops (COPII) go for (forward) a coffee to go (to the Golgi apparatus). One cop (COPI) goes back (backward) to the rough (rough ER) neighborhood.”



  • Intracellular sorting and transport system
    • Early endosomes
      • Internalize materials from outside the cell via plasma membrane invagination
      • Recycle receptors (e.g., LDL receptor) and transport them back to the cell surface membrane
      • Can receive vesicles from the Golgi apparatus and send them back
    • Late endosomes: fuse with lysosomes and thereby allow for lysosomal degradation of endosomal content

Mitochondria are often described as the powerhouses of the cell because of their central role in the synthesis of ATP, a vital source of energy for the body. They are composed of a double membrane, intramembranous space, and matrix. Various mitochondrial types can be differentiated based on the inner membrane structure.


The structure and DNA of mitochondria resemble the structure and DNA of prokaryotes. Mitochondria are believed to have been prokaryotes originally that evolved into endosymbionts living inside eukaryotes (see symbiogenesis).

Mitochondrial membrane

There are two, highly specialized mitochondrial membranes that surround the mitochondrion. They provide the framework for the electron transport chain and ATP production.

Outer membrane

  • Structure: smooth
  • Permeability: interspersed with pores, highly permeable for various molecules

Inner membrane

  • Structure: convoluted
  • Permeability: impermeable, especially to ions; however the inner membrane contains many different highly specific transport proteins
  • Characteristic component: cardiolipin (stabilizes the enzymes of oxidative phosphorylation)

Types of inner mitochondrial membranes

  • Mitochondrial cristae
    • Thin invaginations (cristae) of the inner membrane
    • Present in most cells
  • Tubular mitochondria
    • Inner membrane forms tubules
    • Mainly in cells that produce steroids

Carriers of the inner mitochondrial membrane

Specific transporters regulate the transport of substances through the inner membrane.

  • Functional mechanism: antiporter of two molecules
  • Examples
    • Malate-aspartate shuttle : transport of reducing equivalents
    • Carnitine-acylcarnitine translocase
    • Glutamate aspartate transporter

In the malate-aspartate shuttle, only the electrons of NADH and not NADH itself are transported across the inner mitochondrial membrane.

Mitochondrial matrix


“If you cite (cytoplasm) my article, I might (mitochondria) give you a HUG”: Heme synthesis, the Urea cycle, and Gluconeogenesis take place in both, the cytoplasm and the mitochondria, think: “If you cite (cytoplasm) my article, I might (mitochondria) give you a HUG”.

Heme synthesis, the urea cycle, and gluconeogenesis take place in both the cytoplasm and the mitochondria.


The DNA and ribosomes of mitochondria and prokaryotes have many similarities. The discovery of this resulted in the endosymbiotic theory of mitochondrial evolution, which is that mitochondria were originally independent prokaryotic bacteria with the special ability to produce energy through oxidative phosphorylation and were eventually engulfed by eukaryotic cells. As a result, the prokaryotic cells lost parts of their DNA and their ability to live independently, while the eukaryotic host cell became dependent on the energy produced by the incorporated bacterium.

Lysosomes can be regarded as the cell's waste disposal system. Their main function is intracellular digestion (e.g., the degradation of polymers into monomers).


  • Small, spherical organelles that are surrounded by a lipid bilayer and filled with digestive hydrolytic enzymes, which are responsible for the degradation of macromolecules

The main enzyme stored in lysosomes is acidic phosphatase.


Intracellular degradation of macromolecules

  • Process
    1. Primary lysosomes are vesicles with newly synthesized hydrolytic enzymes that bud from the Golgi apparatus.
    2. They fuse with vesicles that contain digestive materials, e.g., endosomes, phagosomes, and thereby form secondary lysosomes.
    3. The hydrolytic enzymes in the secondary lysosomes degrade the macromolecules.
    4. Cleavage products are emptied into the cytosol and can be reused for new synthesis processes.
    5. Residual bodies: lipid-rich, undigested material (lipofuscin) left over from macromolecule degradation is expelled from the cell or stored in the cytosol in residual bodies.
  • Origin of macromolecules
    • Endocytosis
      • Receptor-mediated endocytosis: Endocytic vesicles from the plasma membrane fuse first with early endosomes and later with lysosomes.
      • Phagocytosis: Particles are engulfed and taken up by phagocytic cells, forming phagosomes.
    • Autophagy: Autophagosomal membranes fuse and form an autophagosome that sequesters intracellular debris (e.g., proteins, lipids, cell organelles). It later fuses with lysosomes in order to degrade the macromolecules.

Lysosomes play an important role in adaptive immunity. Antigen-presenting cells (e.g., macrophages, dendritic cells) internalize antigens and degrade them through proteolysis within lysosomes. Afterwards, the resulting peptides are loaded onto MHC class II molecules, delivered to the cell surface and presented to naive T cells.


In the event of severe cellular damage, lysosomes release their contents into the cytosol, causing the cell to disintegrate (apoptosis).


Peroxisomes are spherical organelles surrounded by a single membrane; they play a key role in fatty acid oxidation and the biosynthesis and degradation of specific molecules.


  • Relatively small, round, membrane-enclosed vesicles


Zellweger syndrome is caused by impaired peroxisome formation, which results in the accumulation of cytotoxic hydrogen peroxide within the cells.

Refsum disease is caused by insufficient α-oxidation of branched-chain fatty acids.

Adrenoleukodystrophy is caused by insufficient β-oxidation of very-long-chain fatty acids.


The cytosol, also termed matrix, is part of the cytoplasm and enclosed by the cell membrane. In prokaryotes, almost all metabolic pathways occur directly in the cytosol. In eukaryotes, several of these processes occur in cell organelles that are separated from the cytosol by a membrane (compartmentalization).


  • Water, dissolved ions, and small molecules (70%)
  • Proteins, e.g., enzymes involved in metabolic pathways (30%)


The cytoplasm surrounds the nucleus and consists of the cytosol and the cell organelles.

Heme synthesis, the urea cycle, and gluconeogenesis take place in both the cytoplasm and the mitochondria.


Ribosomes are very large molecule complexes of RNA and proteins that are located in the cytosol, on the cytosolic side of the rough endoplasmic reticulum (rER) and within the mitochondria. The ribosome is the site of protein synthesis (translation).




Cytosolic proteins (such as tubulin) are synthesized on free ribosomes. Lysosomal and membrane proteins are synthesized on ribosomes of the rER.

  • Definition: a network of filaments (protein fibers) that extends throughout the cytosol.
  • Functions
    • Stability and movement of the cell and its organelles
    • Transport processes within the cell
    • Essential for cell division
  • Structure
    • Filaments
    • Accessory proteins
      • Responsible for various functions of the cytoskeleton (e.g., motion, attachment and detachment of monomers)
      • Motor proteins: important accessory proteins responsible for filament motion
Cytoskeletal elements
Filament Structure Accessory protein Function

Actin filaments (microfilaments)

  • Diameter ∼ 7 nm
  • Monomer
    • G-Actin
    • Polymerize to F-Actin filaments through ATP consumption
  • A double helix of two polymer actin strands forms the actual filament.
Intermediate filaments (IFs)
  • Cell stability


The spectrin-based cytoskeleton of RBCs is deficient in hereditary spherocytosis.

Intermediate filaments can be used as immunohistochemical tumor markers to detect the origin of a neoplasm.

To remember drugs that disrupt microtubules, think “Microtubules Get Constructed Very Poorly”: Mebendazole, Griseofulvin, Colchicine, Vincristine/Vinblastine, Paclitaxel.

Negative end Near Nucleus, while Positive end Points to the Periphery: The negative end of the microtubule is oriented towards the nucleus and the positive end is oriented towards the periphery of the cell.

Kin (keen) to go out (anterograde), Dying to come back home (retrograde). Kinesin transports anterograde (from – → +) along the microtubule. Dynein transports retrograde (from + → –) along the microtubule.

The cells of the body are connected to other cells and the surrounding structures by cell-cell junctions and cell-matrix junctions. The type and number of junctions varies between different cell types. While red blood cells do not form cell junctions, epithelial cells are tightly connected to one another and to the basal lamina.

Occluding junctions

Anchoring junctions (adhering junctions)

Anchoring junctions are mechanical attachments between cells. Several forms can be differentiated according to function.

Adherens junction (zonula adherens, belt desmosome)

Desmosomes (macula adherens, spot desmosome)


Communicating junctions

Communicating junctions permit the passage of electrical or chemical signals.

  • Gap junction (nexus): intercellular channels that connect two cells
    • Structure: formed by the interaction of the connexons of two neighboring cells
      • Connexon: composed of six membrane-spanning proteins (connexins) with a central pore
    • Occurrence/function
  • Synapse: areas where signals or action potentials are transmitted from a presynaptic to a postsynaptic structure (e.g., neurons, muscle)

Auto-antibodies directed against components of the cell junctions are formed in autoimmune blistering diseases, e.g., in pemphigus vulgaris (antidesmosome antibodies) and bullous pemphigoid (antihemidesmosome antibodies).

CADherins are CAlcium dependent ADhesion proteins.

  1. Goljan EF. Rapid Review Pathology. Elsevier Saunders ; 2018
  2. Gartner LP. Textbook of Histology. Elsevier ; 2017