A Tour of the Cell

A Tour of the Cell

Ayush Noori | EduSTEM Advanced Biology

  • All organisms are made of cells , the simplest collections of matter that can be considered a living entity, and the basic structural and functional mechanisms of every organism.
  • Common features of all cells:
    • Bounded by a plasma membrane – a semipermeable, selective barrier.
    • Filled with cytosol – a semifluid, jellylike substance.
    • Contain chromosomes – carry genes in the form of DNA.
    • Contain ribosomes, complexes of rRNA and protein which translate proteins according to instructions from genes.

Prokaryotes and Eukaryotes:

  • Cells are of two distinct types – prokaryotes and eukaryotes .
    • Bacteria and Archaea (domains) are prokaryotes, while protists, fungi, animals, and plants are all eukaryotes.
    • Interior of both cells is called the cytoplasm.
  • Eukaryotes:
    • DNA is in the nucleus, which is bounded by a double membrane.
    • Membrane-bound organelles of specialized form and function are suspended in cytosol.
    • Typically larger than prokaryotic cells, usually 10-100 µm in diameter.
  • Prokaryotes:
    • DNA is concentrated in a region not membrane-enclosed, called the nucleoid.
    • Lack organelles, but instead contain specific protein regions for various processes.
    • Typical bacteria (prokaryotic cells) are 1-5 µm in diameter.

Metabolic Size Limits on Cells:

  • The plasma membrane is the selective barrier that allows passage of enough oxygen, nutrients and waste to service the entire cell.
    • Consists of a phospholipid bilayer with various attached or embedded membrane proteins (with hydrophobic projections into the lipid bilayer) and carbohydrate side chains.
  • For every square micrometer of membrane, only a limited number of solutes can cross the plasma membrane per second. Therefore, each unit of intracellular volume requires a certain surface area of membrane to sustain function.
  • As a cell increases in size, the surface area grows proportionately less than its volume, therefore cells accommodate by:
    • Microscopic size.
    • Narrow, elongated shapes.
    • Long, thin projections such as microvilli (increase SA without increase in V).
    • Having more cells, not larger cells.

The Nucleus:

  • On average 5 µm in diameter, the nucleus contains most of the genes in the eukaryotic cell.
    • The nucleus directs protein synthesis by synthesizing messenger RNA (mRNA) according to instructions provided by the DNA. The mRNA is transported to the cytoplasm via the nuclear pores, where ribosomes translate the genetic message into the primary structure of the polypeptide.
  • Enclosed by the nuclear envelope , double membrane (two bilayers separated by 20-40 nm).
    • Envelope is perforated by nuclear pore structures about 100 nm in diameter.
    • Pore structures are lined by protein structures called pore complexes , regulate entry and exit of proteins, RNAs, and large macromolecules to and from the nucleus.
    • Nuclear side of the envelope is lined by the nuclear lamina (except at the pores), a netlike array of protein filaments (intermediate filaments in animal cells) which provide mechanical support.
    • The nuclear matrix , a network of protein fibers extending through the interior, helps provide support and organize genetic material.
    • The DNA in the nucleus is organized into units called chromosomes , each containing one long DNA molecule.
      • The complex of DNA and proteins making up chromosomes is called chromatin .
    • In the nucleolus , rRNA (ribosomal RNA) is synthesized from instructions in the DNA, and proteins from the cytoplasm are assembled with rRNA to form the large and small subunits of ribosomes.


  • Ribosomes are the cellular compo will nents that carry out protein synthesis.
    • They are complexes made of ribosomal RNAs (rRNAs) and proteins and are built from the large subunit and a small subunit.
  • Free ribosomes are suspended in the cytosol, while bound ribosomes are attached to the outside of the endoplasmic reticulum or nuclear envelope.
    • Ribosomes can play either role at different times.
    • Most proteins made on free ribosomes function within the cytosol.
    • Most proteins made on bound ribosomes are destined for insertion into membranes, packaging within organelles, or for export from the cell.
  • Cells that specialize in protein secretion have high proportions of bound ribosomes.

The Endomembrane System:

  • The endomembrane system of the eukaryotic cell includes many organelles such as the nuclear envelope, the endoplasmic reticulum, the Golgi apparatus, lysosomes, various kinds of vesicles and vacuoles, and the plasma membrane.
  • The endomembrane system performs a variety of tasks in the cell, including:
    • Synthesis of proteins.
    • Transport of proteins into membranes and organelles or out of the cell.
    • Metabolism and movement of lipids.
    • Detoxification of poisons.
  • The membranes of the system are connected through either direct physical continuity or by the transfer of vesicles.

The Endoplasmic Reticulum:

  • The endoplasmic reticulum (ER) consists of a network of membranous tubules and sacs called cisternae , and accounts for more than half the total membrane in many eukaryotic cells.
  • The ER membrane separates the internal compartment of the ER, called the ER lumen or cisternal space, from the cytosol. The membrane is continuous with the nuclear envelope.
  • There are two distinct, connected regions of the ER: the smooth ER and rough ER .
  • Smooth ER:
    • The outer surface lacks ribosomes.
    • Smooth ER functions include:
      • Synthesis of lipids including oils, new membrane phospholipids, and steroids such as sex hormones (cells which are secrete hormones are rich in smooth ER).
      • Metabolism of carbohydrates.
      • Detoxification of drugs and poisons (such as barbiturates) by adding hydroxyl groups to make them more soluble.
      • Storage of calcium ions, the membrane pumps calcium ions from the cytosol into the ER lumen, and release of calcium from the smooth ER can trigger different cellular responses.
  • Rough ER:
    • The outer surface is studded with ribosomes.
    • Bound ribosomes thread synthesized polypeptides through membrane pores directly into the rough ER lumen as they are translated.
    • In the ER, these secretory glycoproteins fold and covalently bind to carbohydrates.
    • Secretory proteins are packaged in transport vesicles which bud from the transitional ER.
    • The rough ER also makes membrane phospholipids and membrane proteins.

The Golgi Apparatus:

  • The Golgi apparatus acts as a warehouse for receiving, sorting, shipping, and manufacturing products of the endoplasmic reticulum, and is extensive in cells specialized for secretion.
  • The Golgi apparatus consists of a group of associated, flattened membranous sacs called cisternae . Vesicles transfer material between parts of the Golgi and other structures.
  • The Golgi stack has distinct structural directionality, the cis face is located near the ER and receives transport vesicles from the ER, while the trans face gives rise to vesicles that pinch off and travel to other sites.
  • Functions include:
    • Modification of carbohydrates of glycoproteins as they pass through the Golgi.
    • Manufacturing some macromolecules such as pectins and non-cellulose polysaccharides.
  • The cisternal maturation model suggests that the cisternae (especially those on the outer ends) progress forward from the cis to the trans face.
  • Before vesicles body from the trans face of the Golgi, molecular identification tags such as phosphate groups are added to Golgi products to aid in sorting.


  • A lysosome is a membranous sac of hydrolytic enzymes that many eukaryotic cells use to hydrolyze and digest macromolecules.
    • Lysosomal enzymes work in and the acidic environment of lysosomes.
  • Amoebas, unicellular eukaryotes, and some human cells (macrophages) eat by engulfing smaller organisms or food particles, a process called phagocytosis . The resulting food vacuole then fuses with the lysosome, whose enzymes digest the food, and digestion products pass into the cytosol.
  • Lysosomes also recycle the cells own organic material via autophagy , where a damaged organelle become surrounded by a double membrane, which in turn fuses with the lysosome.
  • People with inherited lysosomal storage diseases lack a functioning hydrolytic enzyme normally present in lysosomes. In Tay-Sachs disease, a lipid-digesting enzyme is impaired, causing pathogenic accumulation of lipids in the brain.


  • Vacuoles are large vesicles derived from the ER and Golgi and selectively transport solutes to maintain different intravacuolar compositions than the cytosol.
  • Types and functions of vacuoles:
    • Food vacuoles are formed by phagocytosis.
    • Some unicellular eukaryotes in hypotonic environments use contractile vacuoles to pump excess water out of the cell.
    • Some hydrolytic vacuoles perform enzymatic hydrolysis in plants and fungi.
    • Plant vacuoles often store important organic compounds, or defensive (and unpalatable) compounds, as well as pigments.
    • In mature plant cells, smaller vacuoles coalesce to form a large central vacuole , which is filled with cell sap, the plant cells main repository of inorganic ions such as potassium and chloride. The central vacuole also absorbs water, allowing the cell to grow.


  • Mitochondria , generally 1-10 µm long, are the sites of cellular respiration , the metabolic process that uses oxygen to drive the generation of ATP by extracting energy from sugars, fats, and other fuels.
  • Bounded by two phospholipid bilayers, a smooth outer membrane , and a convoluted inner membrane with infoldings called cristae (and associated circular DNA molecules).
    • Cristae give the inner membrane a large surface area, thus enhancing the productivity of cellular respiration.
  • The two bilayers divide the mitochondria into two internal compartments – the outer intermembrane space and the inner mitochondrial matrix .


  • Chloroplasts , generally 3-6 µm long and found in plants and algae, are the sites of photosynthesis , which converts solar energy to chemical energy by absorbing sunlight and using it to drive the synthesis of organic compounds such as sugars from carbon dioxide and water. They contain the chlorophyll, along with other molecules for photosynthesis.
  • Bounded by two phospholipid bilayers, an outer and inner membrane .
  • The chloroplast has three internal compartments – the outer, narrow intermembrane space , the inner stroma , and the thylakoid space inside thylakoids. This compartmental organization allows for photosynthesis.
    • Flattened, interconnected sacs called thylakoids are suspended in the stroma and stacked into grana .
    • The stroma also contains chloroplast DNA and ribosomes.
  • The chloroplast is a member of a family of related plant organelles called plastids .
    • Other types include the amyloplast , a colorless organelle that stores amylose in roots and tubers, and the chromoplast , which has pigments that give fruits and flowers their orange and yellow hues.

Thylakoids which connect two separate grana are called stromal lamellae . DNA is stored in chloroplasts and mitochondria as nucleoids, are is compacted 10,000-fold.

Endosymbiotic Theory:

  • The endosymbiotic theory states that an early ancestor of eukaryotic cells engulfed an oxygen-using nonphotosynthetic prokaryotic cell, and eventually the engulfed cell formed a relationship with the host, becoming an endosymbiont. Over evolutionary time, the two cells became a single eukaryotic cell with the mitochondrion.
  • Similarly, the eukaryotic cell with the mitochondrion may have been taken up a photosynthetic prokaryote, becoming the ancestor of eukaryotic cells that contain chloroplasts.
  • Structural features of mitochondria and chloroplasts which support the endosymbiotic theory:
    • Mitochondria and chloroplasts have two membranes surrounding them, akin to ancient engulfed prokaryotes.
    • Mitochondria and chloroplasts contain their own ribosomes and circular DNA molecules called nucleoids associated with their inner membranes.
    • Mitochondria and chloroplasts are autonomous organelles that grow and reproduce within a cell.

Mitochondria are descended from α-Proteobacteria, while chloroplasts are descended from cyanobacteria.


  • Peroxisomes are specialized organelles which contain enzymes that remove hydrogen atoms from various substrates and transfer them to oxygen (O2), producing hydrogen peroxide (H2­O­2), which is then converted to water.
  • These reactions can be used to break down fatty acids into smaller molecules or detoxify alcohol and other harmful compounds, among various other functions.
    • Specialized peroxisomes called glyoxysomes are found in the fat-storing tissues of plant seeds, and initiate the conversion of fatty acids to sugar, until the seedling can produce its own sugar.

Schrader et al: https://www.sciencedirect.com/science/article/pii/S0925443911002997?via%3Dihub

Peroxisomes can form by growth and division (fission) from pre-existing ones or can also arise from the ER. Signaling cascades are largely unelucidated, however key players in division are known. The nuclear receptor Peroxisome Proliferator Activated Receptor α (PPARα) is the responsible mediator for changing the expression of peroxisomal genes.

Please see Figure 3 from the paper, outlining the model of peroxisome growth and division - elongation (growth), constriction, and final fission (division). (a) Peroxisomal membrane remodeling via Pex11p is induced by the insertion of an amphipathic helix into one leaflet of the lipid bilayer which causes membrane asymmetry and bending. Subsequently, the extension grows and acquires a specific set of PMPs (peroxisomal membrane proteins, e.g. Pex11pβ, Fis1), before it constricts and starts to import predominantly newly synthesized matrix proteins. Pex11pβ and the Mff-DLP1 complex concentrate at the sites of constriction. (b) Cytosolic DLP1 is recruited by the membrane receptor Mff. After targeting, DLP1 self-assembles into large ring-like structures that hydrolyze GTP and sever the peroxisomal membrane via a dynamin-like action. (DLP1 protein is a GTPase, and upon GTP hydrolysis severs the new peroxisome from the parent membrane via a “twisting” conformational change.) Fis1 may fulfil a regulatory function.

The Cytoskeleton:

  • The cytoskeleton is a network of protein fibers extending throughout the cytoplasm.
  • The eukaryotic cytoskeleton is composed of three types of molecular structures: microtubules (thickest), microfilaments (thinnest), and intermediate filaments.
  • Functions of the cytoskeleton include:
    • Providing mechanical support to the cell to maintain its shape, more important for animal cells.
    • Some forms of cell motility (changes in cell location and movements of cell parts) involve interaction of the cytoskeleton with motor proteins .
      • Motor proteins can “walk” vesicles along microtubules.
    • Manipulating the plasma membrane to allow phagocytosis.


  • Microtubules , structured as hollow tubes with a 25 nm diameter and 15 nm lumen, are polymers of tubulin, which is a dimer consisting of α-tubulin and β-tubulin.
    • One end of the microtubule (called the “plus end”) can accumulate and release tubulin dimers at a much higher rate than the other.
  • Functions of microtubules include acting as compression-resisting “girders”, guiding vesicles, cell motility in cilia and flagella, chromosome movements in cell division, and organelle movements.
  • In animal cells, microtubules grow from a centrosome , a region near the nucleus.
    • Within the centrosome is a pair of centrioles (each about 250 nm in diameter), each composed of nine sets of triplet microtubules arranged in a ring, the “9 + 0” pattern . The centrioles help organize microtubule assembly.
  • In eukaryotes, specialized microtubules are responsible for the beating of cilia and flagella , extensions which project from some cells and propel eukaryotes through water. Cilia and flagella also propel fluid over the surface of tissue, such as the lining of the trachea or the cilia lining the oviducts.
    • Motile cilia occur in large numbers, while flagella are limited and longer than cilia.
    • Flagella have undulating motions while cilia have alternating power and recovery strokes.
    • A single cilium, called the primary cilium , can also act as an antenna for a cell.
    • Cilia and flagella share a common structure, nine doublets of microtubules arranged in a ring with two microtubules in the center (the “9 + 2” pattern ), sheathed in an extension of the plasma membrane.
      • The assembly is anchored in the cell by a basal body, which has a “9 + 0” pattern (with triplets instead of doublets ). Centrioles and nonmotile cilia also have a “9 + 0” pattern.
      • Dynein motor proteins use ATP to “walk” along the microtubule of the doublet adjacent to which it is attached, creating bending movements.
      • The doublets are held together by cross-linking proteins and radial spokes.

Schatten and Simerly: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4576973/

“Cartwheels” are the subcentriolar centers of the centrioles and are largely composed of the SAS6 and BLD10/CEP135 proteins. They might supplant centriolar function in acentriolar cells.

“More challenges, recently insurmountable, can now be addressed. If the centrosome is an MTOC cloud organized by the centriole, are directed motors, MT-binding proteins, chromosomes, and RAN truly sufficient to organize accurate bipolar spindles without centrioles? Might nanoscopic cartwheels, from which centrioles do not grow, be at the acentriolar centrosome core?”


  • Microfilaments are structured as thin solid rods – two intertwined strands of actin with a 7 nm diameter. They can form branched structures.
  • Functions of microfilaments include acting as tension-bearing elements, changes in cell shape, muscle contraction, cytoplasmic streaming in plant cells, amoeboid cell motility, and division of animal cells.
    • Cortical microfilaments give the outer cytoplasmic layer, called the cortex , structure.
    • In intestinal cells, microfilaments make up the core of microvilli.
    • Actin microfilaments interact with thicker filaments of a protein called myosin , to which walk along the filaments to cause contractions of muscle cells.
  • In some cells, the cell crawls along the surface using actin-myosin interactions by extending cellular extensions called pseudopodia (specifically called filopodia in macrophages).
  • In plant cells, actin-protein interactions contribute to cytoplasmic streaming , a circular flow of cytoplasm with cells.

Intermediate Filaments:

  • Intermediate filaments are structured as fibrous proteins (such as keratins) coiled into cables with an 8-12 nm diameter.
    • Intermediate filaments are only found in the cells of some eukaryotes, including vertebrates, and can vary in composition.
  • Functions of intermediate filaments include acting as tension-bearing elements, anchorage of the nucleus and other organelles, and the formation of the nuclear lamina.
    • Intermediate filament networks are more permanent fixtures than microfilaments and microtubules, act as the framework of the cell.
    • Intermediate filaments can anchor the microfilaments of the intestinal cell microvilli.

Cell Walls of Plants:

  • The cell wall is an extracellular structure of cells, ranging from 0.1 µm to several micrometers, it is made of microfibrils of the polysaccharide cellulose. The cellulose microfibrils are synthesized by cellulose synthase and secreted to the extracellular space where along with a matrix of other polysaccharides and proteins, they form the cell wall.
  • Functions of the cell wall include protecting the plant cell, maintaining shape, preventing excessive uptake of water, holding the plant up against the force of gravity.
  • A young plant cell first creates a thin primary cell wall , which is glued to other cell walls by pectins in the middle lamella . Mature cells may add a secondary cell wall between the plasma membrane and the primary wall, consisting of several laminated layers (as in wood).

The Extracellular Matrix (ECM) of Animal Cells:

  • Though animal cells lack cell walls, they have an elaborate extracellular matrix (ECM) , consisting of collagen (a glycoprotein, accounts for about 40% of the total protein the human body) embedded in a network of proteoglycans .
    • Proteoglycans consist of a small core protein with carbohydrate chains covalently attached (total 95% carbohydrate), and form proteoglycans complexes when proteoglycans become noncovalently attached to a single long polysaccharide.
    • ECM glycoproteins such as fibronectin bind to transmembrane receptor proteins called integrins and connect the plasma membrane to the ECM.
    • On the cytoplasmic side, integrins bind to microfilaments of the cytoskeleton.
  • Functions of the extracellular matrix include cell-to-cell communication (such as in embryonic migration) and nuclear gene regulation via chemical and mechanical signaling pathways.

Cell Junctions:

  • Plant cell walls are perforated with plasmodesmata , channels which connect adjacent cells through which cytosol can pass.
  • In animals, there are three main types of cell junctions: tight junctions , desmosomes , and gap junctions . All three types are especially common in epithelial tissue, which lines the external and internal surfaces of the body.
    • At tight junctions, the plasma membranes of neighboring cells are tightly bound together by specific proteins, forming continuous seals which prevent leakage of extracellular fluid across a layer of epithelial cells, such as in skin cells or the intestine.
    • Desmosomes (one type of anchoring junction) are made of keratin intermediate filaments in cells such as muscle cells, and function like rivets, fastening cells together in strong sheets.
    • Gap junctions (or communicating junctions) provide cytoplasmic channels from one cell to an adjacent cell, akin to plasmodesmata in plants.

With these courses, we hope to further our mission to make high-quality STEMX education accessible for all. For questions or support, please feel free to reach out to me at anooristudent@outlook.com.

Best Regards,

Ayush Noori

EduSTEM Boston Chapter Founder


  1. NCBI PubMed

The premier source of past and present medical literature. Most supplemental information in Extensions is available via PubMed. When searching PubMed, be sure to use the “Free full text,” and “Sort by: Best Match” filters to find relevant and accessible results.

  1. RCSB Protein Data Bank (PDB)

A large database of useful 3D structures of large biological molecules, including proteins and nucleic acids. Use the search bar to find a molecule of interest, which can then be examined using the Web-based 3D viewer.