Cell Membranes and Compartments

From CellBiology
Eukaryotic Cell Physical Compartments


Membrane cartoon

A major difference between eukayotes and prokaryotes is the presence of physical compartments (membrane bound) within the cell. These compartments allow the separation/specialization of processes within the cell. There also exist within each of these physical compartments, functional compartments where specific processes may occur or are restricted too. This lecture is an introduction to compartments within the cell and membranes. The key components are: cell compartments, membrane structure, membrane models, membrane specializations.

Lecture Slides: 2017 Lecture PDF

Lecture Archive: 2016 | 2015 | 2014 | 2013 2012 | 2010 | 2009 | 2008 | 1/page 2007 (viewing only) 43 pages, 1.4 Mb


  • Understand the concept of separate intracellular spaces
  • Understand the structure of membranes
  • Brief understanding of history of membrane models
  • Understand the difference between physical and functional compartments
  • Brief understanding of membrane specializations


Cork Bark by Robert Hooke 1665
  • Robert Hooke (1635-1703)
    • used early microscopes to view cork tree bark
    • was the first to use the term CELL
  • Robert Brown 1825
    • identified nuclei in plant cells
  • Theodor Schwann (1810 - 1882)
    • together with Matthias Schleiden (plants) developed the cell theory in 1839

Cell Theory

    • All organisms consist of one or more cells
    • The cell is the basic unit of structure for all cells
    • All cells arise only from preexisting cells

Plasma Membrane Images

The cell membrane (plasma membrane or plasmalemma) encloses or covers all cell types and is 7 nanometers (7 x 109 M) thick. Begin by some different ways of looking microscopically at membranes.

Membrane - Light Micrograph

CellB35x10L2.jpg Eo104le.jpg

Membrane - Fluorescent Micrograph

Candida albicans.jpg

Yeast - Candida albicans



Membrane - Scanning Electron Micrograph

Red White Blood cells.jpg Mycobacterium tuberculosis bacteria.jpg

  • thickness 3.5 nm

Membrane - Transmission Electron Micrograph

Plasma and Organelle Membranes CDCcandida.jpg

Links: Block-Face Scanning Electron Microscopy to Reconstruct Three-Dimensional Tissue Nanostructure Denk W, Horstmann H (2004) Serial Block-Face Scanning Electron Microscopy to Reconstruct Three-Dimensional Tissue Nanostructure. PLoS Biol 2(11): e329


Eukaryotic Cell Physical Compartments
  • Physical Compartments
    • membrane bound
    • Nucleus, Cytoplasm, Organelles
    • cell nomenclature based upon presence or absence of these compartments (eukaryotic, prokaryotic)
  • Functional Compartments
    • spatial localization
    • targeting
    • activation and inactivation
    • signaling

Major Cellular Compartments

Proposed model for organelle membrane evolution
  • Nucleus (nuclear) - contains a single organelle compartment
  • Cytoplasm (cytoplasmic) - contains many organelle compartments

Organelle Number/Volume

  • How many organelles?
  • How much space within the cell do they occupy?
  • Are all the cells the same?

Take a typical mammalian liver cell....

Liver Structure

Table 12-1. Relative Volumes Occupied by the Major Intracellular Compartments in a Liver Cell (Hepatocyte)

Table 12-2. Relative Amounts of Membrane Types in Two Kinds of Eucaryotic Cells

Compartments are Dynamic

Movies showing flexibility of membranes and their changing shape and size.

Microfilament movie 1.jpg
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Integrin movie 1-icon.jpg
 ‎‎Adhesion Integrin
Page | Play


Fluidity of the Lipid Bilayer

Nuclear Compartment

  • Nuclear matrix - consisting of Intermediate filaments (lamins)
  • Nucleoli (functional compartment - localised transcription DNA of RNA genes)
  • Chromosomes (DNA and associated proteins)

(MH - you will not see chromosomes in interphase nuclei only during mitosis, more in the Nucleus Lecture)

Cytoplasmic Compartment

  • Cytoplasmic Organelles
    • Membrane bound structures
    • Endoplasmic reticulum, golgi apparatus, mitochondria, lysosomes, peroxisomes, vesicles
  • Cytoskeleton
    • 3 filament systems
  • Cytoplasmic “structures”
    • Ribosomes
    • DNA -> mRNA -> Protein
    • Proteins
    • Receptors, signaling, metabolism, structural
    • Viruses, bacteria, prionsl
  • Functional compartments
    • occur in nucleus, cytoplasm, in organelles and outside organelles
    • signaling, metabolic reactions, processing genetic information, cytoskeleton dynamics, vesicle dynamics

Membrane Functions

  • Form compartments
  • Allow “specialization”
  • Metabolic and biochemical
  • Localization of function
  • Regulation of transport
  • Detection of signals
  • Cell-cell communication
  • Cell Identity

Plasma Membrane Image

EM - Cell (Plasma) and Organelle Membranes

Cell (Plasma) encloses or covers or cell types.

Tem cellstructures2.jpg

Cell (Plasma) and Organelle Membranes

Membrane Components

Model of Cell (plasma) membrane structure
  • phospholipids, proteins and cholesterol
  • first compartment formed
  • prokaryotes (bacteria) just this 1 compartment
  • eukaryotic cells many different compartments

Membrane model 02.jpg

Membrane size


  • membranes contain phospholipids, glycolipids, and steroids
  • The main lipid components include:
    • phosphatidylcholine (~50%)
    • phosphatidylethanolamine (~10%)
    • phosphatidylserine (~15%)
    • sphingolipids (~10%)
    • cholesterol (~10%)
    • phosphatidylinositol (1%).
Polar Head
1 2
Non-Polar Hydrocarbon Tail

Amphipathic - having both hydrophilic and hydrophobic properties. (phospholipids, cholesterol, glycolipids).

Links: Three views of a cell membrane | MCB Schematic diagram of typical membrane proteins in a biological membrane

Phospholipid Orientation

Figure 2-22. Phospholipid structure and the orientation of phospholipids in membranes

Phospholipid Bilayer
  • A liposome (lipid vesicle) is a small aqueous compartment surrounded by a lipid bilayer.
  • A micelle is a small compartment surrounded by a single lipid layer.
Phospholipid Orientation

Membranes History

  • 1890 Charles Overton
    • selective permeation of membranes
    • non-polar pass through (lipid soluble)
    • polar refractory
    • lipids present as a coat
  • 1905 Irving Langmuir
    • lipids faced with heads towards water away from organic solvents
  • 1925 Gorter and Grendel
    • monolayer of lipid isolated from rbc
    • twice (2x) surface area of cell (bilayer)
  • 1930-40 Danielle-Davson
    • Proteins coat a bilayer with polar “pores”
  • 1960s Robertson
    • Modification with glycoprotein on one side, therefore asymmetric
  • 1972 Singer and Nicholson
    • proteins “floating” within lipid bilayer like a “liquid” surface
  • 1975 Unwin and Henderson
    • integral membrane proteins
    • both hydrophobic and hydrophilic
    • alternating -phobic and -philic represent trans-membrane loops
    • glycoprotein carbohydrate groups on outer surface
Links: MCB - Freeze fracturing can separate the two phospholipid leaflets that form every cellular membrane | MCB - Solubilization of integral membrane proteins by nonionic detergents

Membranes Recent History

Morphology and_ interaction between lipid domains
  • 1997 Simons - cholesterol to form rafts that move within the fluid bilayer
  • “Membrane Rafts” “A new aspect of cell membrane structure is presented, based on the dynamic clustering of sphingolipids and cholesterol to form rafts that move within the fluid bilayer. It is proposed that these rafts function as platforms for the attachment of proteins when membranes are moved around inside the cell and during signal transduction.”
  • saturated lipids and cholesterol form liquid-ordered domains

Lipid rafts

Lipid rafts

Cartoon of different raft roles

Links: PMID20044567 | Fig. 1 Evolution of the raft concept for subcompartmentalization in cell membranes

Membrane Proteins

Protein Layer-Lipid-Protein Island Model
Membrane model 03.jpg Membrane model 04.jpg
Outside Inside
Links: Protein Layer-Lipid-Protein Island Model | Membrane size | Outside | Inside | PMID 24806512
  • 20-30% of the genome encodes membrane proteins PMID 9568909
  • Proteins can be embedded in the inner phospholipid layer, outer phospholipid layer or span both layers
  • Some proteins are folded such that they span the membrane in a series of “loops”

Two major protein transmembrane structures

  1. α-helical - ubiquitously distributed
  2. β-barrel - outer membranes of Gram-negative bacteria, chloroplasts, and mitochondria

Membrane Protein Functions

  • transport channels
  • enzyme reactions
  • cytoskeleton link
  • cell adhesion
  • cell identity

Links: MCB Topologies of some integral membrane proteins synthesized on the rough ER

Membrane Glycoproteins

  • Glycoproteins are proteins which have carbohydrate groups (sugars) attached
  • to produce these proteins go through a very specific cellular pathway of organelles (secretory pathway)
  • to reach the cell surface where they are either secreted (form part of the extracellular matrix)
  • or are embedded in the membrane with the carbohydrate grouped on the outside surface (integral membrane protein)
  • distribution of glycoproteins have functional effects (motility, migration, channel distribution, signalling) PMID 24040379

Membrane Cholesterol

Model of Cell (plasma) membrane structure
  • Small molecule embedded between the phospholipid molecules and regulates lipid mobility (MH - see rafts)
  • Cholesterol can be at different concentrations in different regions of plasma membrane
  • lateral organization of membranes and free volume distribution
  • may control membrane protein activity and "raft” formation
  • fine tuning of membrane lipid composition, organization/dynamics, function
  • bacterial membranes (except for Mycoplasma and some methylotrophic bacteria) have no sterols, they lack the enzymes required for sterol biosynthesis.

Links: MBoC Figure 10-9. Cholesterol in a lipid bilayer

Bacterial Membranes

(MH - covered this in previous Lecture)

  • Bacteria with double membranes (Example: E. coli)
    • inner membrane is the cell's plasma membrane
    • Gram Negative do not retain dark blue dye used in gram staining
  • Bacteria with single membranes (Example: staphylo-cocci and streptococci)
    • thicker cell walls
    • Gram Positive because they do retain blue dye
    • single membrane comparable to inner (plasma) membrane of gram negative bacteria

Membrane Fluidity

Neutrophil activation membrane reorganisation
  • fusion of 2 cells
  • FRAP
  • membrane domains (polarized cells)
    • epithelia - apical, basal and lateral domains

Tubular Bridges

Bronchial epithelial bridge

(cytonemes and tunneling nanotubes, TNTs) - New membrane structures identified that can facilitate transfer of cellular signals and components over large distances (hundreds of microns) representing the longest direct connections between cells in vitro and in vivo.

File:Bronchial epithelial bridge.mov

ER to Golgi FRAP-icon.jpg
Page | Play


Links: FRAP | MBC - Membrane Fluidity

Membrane Curvature

There can be both direct and indirect bending of the lipid bilayer.[1]

Direct membrane bending Indirect membrane bending
Direct membrane bending within the lipid bilayer PMID27528656.jpg Indirect membrane bending within the lipid bilayer PMID27528656.jpg

Membrane Specializations

  • plasma membrane cytoskeleton
  • different directly under membranes
  • adhesion complexes
  • absorbtive and secretory
  • synaptic junctions
  • fenestrations

This range of membrane specializations will be covered in detail in later Lectures.

Liver sinusoidal endothelial cell fenestrations.jpg

Super resolution imaging of Liver sinusoidal endothelial cell (LSEC) fenestrations.[2]

Liver sinusoidal endothelial cells (LSECs)[3] act as a filter between blood and the hepatocytes and are highly fenestrated cells (contain transcellular pores with diameters between 50 to 200 nm). The small sizes of the fenestrae have so far prohibited any functional analysis with standard and advanced light microscopy techniques.

labeled LSEC movie

Adhesion Specializations

A series of different types of proteins and cytoskeleton associations forming different classes of adhesion junctions (MH - covered in detail in a lecture 8)

  • Desmosomes ( = macula adherens)
  • Adherens Junctions ( = zonula adherens)
  • Septate Junctions
  • Tight Junctions
  • Gap Junctions

Covered in Cell Junctions

Membrane Transport

Three major forms of transport across the membrane

  • Passive - Simple diffusion
  • Facilitated - transport proteins
  • Active - transport proteins for nutrient uptake, secretion, ion balance
Links: Figure 17-13The secretory pathway of protein synthesis and sorting

Ion Channels

Cell potassium channels
  • phospholipid impermeable to ions in aqueous solution
  • protein channels permit rapid ion flux
  • 1960’s structure and function, ionophores (simple ion channels)
  • common structural motif alpha helix
  • 75 + different ion channels
  • Allosteric proteins - conformation regulated by different stimuli
  • opening/closing, “gating” of ions

Ion Channel Types

  • 3 rapid + 1 slow gate (gap junction)
    • Voltage-gated - propogation of electrical signals along nerve, muscle
    • Ligand-gated - opened by non-covalent, reversible binding of ligand between nerve cells, nerve-muscle, gland cells
    • Mechanical-gated - regulated by mechanical deformation
    • Gap junction - allow ions to flow between adjacent cells open/close in response to Ca2+ and protons

Apoptosis and Membranes

  • programmed cell death
  • membrane "blebbing" encloses cellular component fragments

Link: Time-lapse movie of human HeLa cells undergoing apoptosis PMID: 18073771 | Example of early apoptotic blebbing PMID:16129889

Membrane Transport Disease

  • Cystic Fibrosis
    • 1989 Collins (US), Tsui and Riordan (Canada)
    • Chloride channel protein mutation
    • point mutant, folded improperly, trapped and degraded in ER

Historic Papers

Below are some example historical research finding related to cell membranes from the JCB Archive and other sources.

1957 The invention of freeze fracture EM and the determination of membrane structure Russell Steere introduces his home-made contraption for freeze fracture electron microscopy (EM), and Daniel Branton uses it to conclude that membranes are bilayers.

1971 Spectrin is peripheral S. Jonathan Singer, Garth Nicolson, and Vincent Marchesi use red cell ghosts to provide strong evidence for the existence of peripheral membrane proteins.

1992 Lipid raft idea is floated Gerrit van Meer and Kai Simons get the first hints of lipid rafts based on lipid sorting experiments.

Links: Sorted JCB Archive -Membranes JCB Archive

  1. <pubmed>27528656</pubmed>
  2. <pubmed>26549018</pubmed>
  3. <pubmed>26549018</pubmed>



Search Online Textbooks



Vertebrate membrane proteins: structure, function, and insights from biophysical approaches. Müller DJ, Wu N, Palczewski K. Pharmacol Rev. 2008 Mar;60(1):43-78. Epub 2008 Mar 5. Review. PMID: 18321962

PLoS Articles

Studying the Nucleated Mammalian Cell Membrane by Single Molecule Approaches

Nagy PD, Strating JRPM, van Kuppeveld FJM (2016) Building Viral Replication Organelles: Close Encounters of the Membrane Types. PLoS Pathog 12(10): e1005912. doi:10.1371/journal.ppat.1005912

Holdbrook DA, Huber RG, Piggot TJ, Bond PJ, Khalid S (2016) Dynamics of Crowded Vesicles: Local and Global Responses to Membrane Composition. PLoS ONE 11(6): e0156963. doi:10.1371/journal.pone.0156963

Strahl H, Turlan C, Khalid S, Bond PJ, Kebalo J-M, Peyron P, et al. (2015) Membrane Recognition and Dynamics of the RNA Degradosome. PLoS Genet 11(2): e1004961. doi:10.1371/journal.pgen.1004961


Membrane Terms

  • adhesion junction membrane specialization allowing either cell-cell or cell-extracellular matrix adhesion generally in multicellular organisms.
  • bilayer having two layers, refers to the 2 lipid layers of a single membrane.
  • blebbing a plasma membrane change often associated with apoptosis. The underlying cell cytoskeleton is disrupted leading to a the bubbling of the plasma membrane, which will enclose cytoplasmic and nuclear components.
  • cholesterol small steroid metabolite that decreases membrane motility involved in many membrane functions (endocytosis, membrane rafts). Bacterial membranes (except for Mycoplasma and some methylotrophic bacteria) have no sterols, they lack the enzymes required for sterol biosynthesis.
  • cytonemes thin, actin-based extensions that project from cells and allow cell-cell communication.
  • electron microscopy a microscope technique that uses beams of electrons instead of light to generate high resolution images of cellular components. This technique historically gave the first images of the membrane bilayer structure.
  • electron tomography an electron microscopic technique to generate a three dimensional (3-D) image from any electron microscopy specimen.
  • flippases enzymes that catalyze rapid translocation of phospholipids across the endoplasmic reticulum membrane. Required for balanced growth of both halves of the bilayer.
  • flotillin (flotillin-1 and -2) protein that is ubiquitously enriched in detergent resistant membranes (membrane rafts).
  • FRAP - Fluorescence Recovery After Photobleaching is a method used to study the dynamics of lipids and proteins in artificial and cellular membrane systems.
  • functional compartment a specialized region formed within a cell which is not limited by a membrane, compared to a "structural compartment".
  • Gram negative term used to describe bacteria which do not retain the Gram dye when stained. These are bacteria with double membranes, the inner membrane is the cell's plasma membrane (Example: E. coli).
  • Gram positive term used to describe bacteria which do retain the Gram dye when stained. These are bacteria with single membranes and thicker cell wall (Example: staphylo-cocci and streptococci).
  • lipids the basic molecules forming the lipid bilayer as phospholipids, glycolipids, and steroids. The main lipid components include phosphatidylcholine (~50%), phosphatidylethanolamine (~10%), phosphatidylserine (~15%), sphingolipids (~10%), cholesterol (~10%), and phosphatidylinositol (1%). Medical Microbiology - Plasma (Cytoplasmic) Membranes
  • liposome (lipid vesicle) is a small aqueous compartment surrounded by a lipid bilayer.
  • membrane cytoskeleton the components of the cell cytoskeleton that directly underly either the cell (plasma) and nuclear membranes.
  • micelle is a small compartment surrounded by a single lipid layer.
  • phospholipid the basic molecule forming the lipid bilayer of a typical membrane (see also lipid).
  • raft (lipid rafts, membrane raft) term used to describe stabilized regions that form within membranes. These rafts "float" within the lipid membrane and are formed by cholesterol altering (stabilizing) the fluidity of the local membrane.
  • structural compartment a specialized region formed within a cell which is limited by a membrane, compared to a "functional compartment".
  • trogocytosis process of T and B cells capture antigens via membrane fragments of antigen presenting cells (APC).
  • vesicle general term given to any membrane enclosing material within the cytoplasm.
  • protein-to-lipid ratio the analysis of membranes by separating the 2 main components. For example, bacterial plasma membranes are approximately 3:1, close to those for mitochondrial membranes.

External Links

External Links Notice - The dynamic nature of the internet may mean that some of these listed links may no longer function. If the link no longer works search the web with the link text or name.



  • A myosin V moves yeast secretory vesicles Secretory vesicles actively move to the site of exocytosis in yeast. Schott et al. find that multiple secretory vesicles often follow the same linear track and frequently enter and cross the bud. This movement requires the activity of the myosin-V heavy chain encoded by the MYO2 gene. When the predicted lever arm of this motor is progressively shortened (with the most extreme example being the 0IQ mutant), the vesicle movements are progressively slowed.
  • Rapid cycling of lipid rafts to and from the Golgi Nichols et al. detect rapid cycling of lipid raft markers between the plasma membrane and the Golgi. Through selective photobleaching, they are able to study transport either out from the Golgi to the plasma membrane, or in from the plasma membrane to the Golgi.
  • Membrane docking at the immunological synapse requires Rab27a Stinchcombe et al. find that normal membrane docking of lytic granules at the immunological synapse is defective in cells lacking Rab27a. In cells lacking other Rab proteins, polarization of the secretory granules is incomplete.
  • Visualizing the location and dynamics of exocytosis Schmoranzer et al. use total internal reflection (TIR) fluorescence microscopy to visualize exocytosis in mammalian cells (e.g., see event on left side of video). The analysis reveals that there are no preferred sites for constitutive exocytosis in this system.
  • Visualizing the location and dynamics of exocytosis Toomre et al. use a combination of TIR microscopy (green, labeling molecules close to or at the membrane) and standard fluorescence microscopy (red, for molecules further from the membrane) to visualize trafficking to and fusion with the plasma membrane during exocytosis. Red dots turn yellow then green as they approach the membrane, and then explode in a burst of light as they fuse with the plasma membrane during exocytosis. The transport containers appear to be partially anchored at the membrane before fusion, and can undergo either partial or complete fusion events.

PLoS Movies

Online Movies

2017 Course Content


Lectures: Cell Biology Introduction | Cells Eukaryotes and Prokaryotes | Cell Membranes and Compartments | Cell Nucleus | Cell Export - Exocytosis | Cell Import - Endocytosis | Cytoskeleton Introduction | Cytoskeleton - Microfilaments | Cytoskeleton - Microtubules | Cytoskeleton - Intermediate Filaments | Cell Mitochondria | Cell Junctions | Extracellular Matrix 1 | Extracellular Matrix 2 | Cell Cycle | Cell Division | Cell Death 1 | Cell Death 2 | Signal 1 | Signal 2 | Stem Cells 1 | Stem Cells 2 | Development | 2017 Revision

2017 Laboratories: Introduction to Lab | Fixation and Staining |

2017 Projects: Group 1 - Delta | Group 2 - Duct | Group 3 - Beta | Group 4 - Alpha

Dr Mark Hill 2015, UNSW Cell Biology - UNSW CRICOS Provider Code No. 00098G