Biology - Molecules and Cells


 Terms and Concepts 



CHAPTER 3 - Parts of Cells




Because a cell does many different processes with unique and sensitive individual chemistry, it should not be surprising that such processes are often sealed away from the rest of the cell's interior by putting them into membrane-bound enclosures.  In pathway processes, advantage can be taken of another feature of cell membranes: proteins can be embedded in the membrane, and materials may be passed along an "assembly line" (or it could be for disassembly) of enzymes stuck into the membrane in the proper order to do, step-by-step and over and over.  Any organelle with a significant surrounding and/or inclusion of membrane is called a membrane-based organelle.

There are some organelles that are not membrane-based.  Ribosomes, a site for turning RNA code into protein sequences, and chromosomes the DNA storage complex, are examples.  These non-membrane organelles are commonly molecular complexes.  They may have complex functions, but the processes by which those functions are done are usually localized to the surfaces of the complex.  They may be in large membrane organelles (as chromosomes are in the nucleus), or near strategic cell features (ribosomes are often near where the protein they produce will be used).

Some functional parts of a eukaryote cell are extensions of the external membrane.  They will be treated here as cell extension organelles, although they are not always called "organelles" in some biology books.

The "soup" inside a cell, often so thick that it becomes a gel, has various names in various places.  In prokaryotes, its protoplasm.   In eukaryotes, the material between the cell membrane and the nuclear envelope is usually called cytoplasm, which sometimes is further divided, as cytosol is considered to be just outside the organelles.  The material inside the nucleus is usually called nucleoplasm.

Cells have characteristic shapes and sometimes the ability to change shape.  In a human, similar features would be a function of our skeletal systems.  In single cells, the term cytoskeleton is used for the network that provides shape and often movement.




There are many types of membrane-based organelles:

The nucleus is considered a type of membrane-based organelle, surrounded as it is by the doubled membrane called a nuclear envelope.  The outer membrane is generally considered continuous with the endoplasmic reticulum, described below.  There is some evidence that the endoplasmic reticulum "grows" from the nuclear envelope, but the reverse also has some experimental support.  Inside a nucleus, the local cytoskeleton, the nuclear matrix, is fairly dense, holding the nucleus in a fairly permanent shape and interacting with the processes going on in there.

All about the cell nucleus.

More on the nuclear envelope.

More on the nuclear matrix.

Vesicles, vacuoles, and other fairly simple sacs.  The inside of a cell may have many bubble-like membrane structures.  They can do simple work, like storing materials or carrying them from place to place:  the small versions of these bubbles would be vesicles, the large ones vacuoles.  Oddly enough for biological terms, there seems to be no set size range for either:  the smallest are definitely vesicles, the largest are vacuoles, but across the middle range either term may be used.  A few ones get special designations:


Food Vacuoles.  When items must be taken into a cell but are either too large, as when large cells eat smaller ones, or for which there is no other entrance, as for some molecules which have no carriers in the membrane, the items are surrounded by a membrane sphere "growing" out from the cell surface that buds into the cell interior in a process generally called endocytosis.  Proteins called clathrins are involved in closing a bit of membrane around a particular space.  More specifically, there is phagocytosis (Latin for "cell eating") when there is an obviously visible item taken in, and pinocytosis ("cell drinking," named because no items were seen in the vacuoles), sometimes called potocytosis.

Food vacuole formation (video).

Different types of endocytosis.

Another illustration.

Lysosomes.  These are often associated with food vacuoles.  They are tiny vesicles filled with digestive enzymes;  the enzymes are "dumped" into the food vacuoles, then activated to break down the contents for absorption.  Lysosomes may also be involved in a sequence by which cells kill themselves purposely, a process called apoptosis.  Apoptosis (the second "p" may or may not be pronounced) is very important in multicellular organisms:  lysosomes respond to a signal sent to, say, its worn-out cell by breaking and releasing digestive enzymes into the cell interior, killing it before it becomes dangerously defective.  It can happen when it shouldn't, too, leading to some degenerative diseases.   There also seems to be a wide range of lysosomes that are in the secretion business (called, logically, secretory lysosomes), an area just currently being researched.

More on lysosomes.

More on apoptosis.

Apoptosis role in disease.

Secretory lysosomes (abstract).

Central Vacuoles are used in some plant cells to sustain stiffness, being filled with water under pressure (turgor pressure).  In plants that wilt when they have been too long without water, it is central vacuoles rather than the network of cell walls that keep them upright.

Central vacuole (image).

Role in plants.

Peroxisomes are generally sites of some sort of complex metabolic function that just needs an isolated chamber of enzymes to work properly.  A lot of molecule breakdown for recycling occurs in peroxisomes.

More on peroxisomes.

Contractile Vacuoles are used to pump out water that floods into a cell by osmosis, a process covered later.  They are found mostly in unicellular animal-like fresh-water organisms.

Video of contractile vacuole.

Endoplasmic reticulum.  This is a network of membrane passages and outcroppings which may be integrated with sacs.  ER, as it's thankfully called most of the time, has a variety of functions, most of which should make sense:  

  • It can provide a way of getting materials quickly from one part of the cell to another.  A cell seems like a small place and a fast move for any molecule that has to get from here to there, but there is a lot of stuff potentially in the way.  Materials move through these channels or in tiny vesicles that bud off the ER.

  • It can store materials temporarily.

  • It can be a surface for enzyme-based reactions that seal off areas of activity or send materials on to where they will be used.

  • It can be a source of lipid-based materials, including new membranes in the cell and lipid-based hormones.  Its lipid nature makes it a logical place for this.

  • All of the above functions are  done on what appear to be plain membranes and the ER involved is called Smooth Endoplasmic Reticulum (SER).  ER can also be used as a site of protein synthesis, from ribosomes embedded in the membrane - this type of ER is called Rough Endoplasmic Reticulum (RER).  Proteins that need to be moved to particular places, or confined for a while, are built and dumped into the ER spaces or along the ER membrane.

More on endoplasmic reticulum (image shows connection to nucleus).


More on smooth endoplasmic reticulum.


More on rough endoplasmic reticulum.

Golgi Complex.  Also called Golgi Apparatus and Golgi Bodies.  These membrane-enclosed chambers take in materials and process them for export (a process called secretion) from the cell.  They often take the form of stacks of membrane discs, progressively smaller from those that start processing to those that end it by budding off and moving to the cell surface, where secretion-filled vesicles "flow" into the cell membrane and what was inside them gets released from the cell by exocytosis.  Secretions may be fully released into the environment, or be integrated into some cell-surrounding matrix, such as cell walls.

3 names, same thing -

Golgi Complex.

Golgi Apparatus.

Golgi Body.

Golgi animation.

Mitochondrion (plural mitochondria).  Usually there would be more than one in a cell, so knowing the plural form is useful.  They are the main site of aerobic respirationThey come in a variety of shapes, the most common being a stumpy cylinder.  Mitochondria have an external membrane and a highly-folded inner membrane (the folds are called cristae) embedded with enzymes upon which most of the aerobic reactions of respiration take place.  A mitochondrion (and the chloroplast discussed next) also has its own independent loop-shaped chromosome (with just a few locally-used specialty genes, not enough to make a whole mitochondrion) and its own ribosomes.  Mitochondria are also significant participants in many versions of apoptosis, and altered mitochondrial function appears to be associated with various cancerous changes in cells.

More on the mitochondrion.


Connection to ER (abstract).


Mitochondrial diseases:  modifying human embryos.

Plastids are chambers found in plant cells.  There are three types:  Leucoplasts used for storage of energy-source molecules such as starch;  Chromoplasts which contain colored pigments often involved in some light-capturing phase of photosynthesis or special coloring;  and Chloroplasts, where the process of photosynthesis takes place.  Proplastids, a kind of preliminary structure, may sometimes be considered yet another type, and there are a few more derived from leukoplasts. 

During photosynthesis, light energy is used to produce ATP molecules which are then used to construct sugar molecules from carbon dioxide and hydrogen obtained from water.  Chloroplasts have two outer membranes and several stacks of small disc-shaped membranes called thylakoids (also spelled thylacoids) inside.  Thylakoids are where light is used to make ATP, and the thick fluid (or unstacked membranes, there seems to be some disagreement about this) around them, called stroma, is where the ATP is used to build sugars.

Chloroplasts, like mitochondria, have prokaryote-like chromosomes and contain ribosomes.  This is a significant piece of evidence in support of the endosymbiosis theory.

Plastid types.


Chromoplast production.

More on chloroplasts.


High-level structural determination (article).


A researcher at Boston University in the 1960's, Lynn Margulis, noted structural similarities between mitochondria and certain types of aerobic bacteria;  from this she developed the endosymbiosis theory, which proposes that some cell organelles originated as independent prokaryotes that were taken in by larger cells, but which continued to function in there rather than being digested.  The internalized cells got the benefit of protection and mobility from the larger cell and provided a metabolic process, aerobic respiration, which was much more efficient in mobilizing energy from food than the anaerobic respiration of the host cell (similar cell-using-cell situations can still be found in nature).  This mutual-benefit relationship would be a symbiosis, and the contained cells would have been endosymbionts.  For almost two decades this theory was met with much resistance by the biological community (could it have been significant that Margulis was a female scientist in the 1960's?), but evidence accumulated:  the structures of mitochondria and, it turns out, chloroplasts as well, were incredibly similar to types of known prokaryotes, and eventually it was found that these organelles had prokaryotic ribosomes and chromosomes.  The endosymbiont theory is now widely accepted as explaining the evolutionary history of mitochondria and chloroplasts, and may apply to other cell inclusions such as flagella and centrioles.

Mitochondria also can be very active within the cell, fusing with each other then splitting apart again, a process which may cause cells in multicelled systems to wear out and initiate apoptosis.

More on Margulis' theories.


Margulis' obituary.


More on endosymbiosis.


More on the theory.



Chromosomes have already been discussed - and will be again - but they should be mentioned on this list because, like ribosomes and some others, they are molecular complexes that are generally considered organelles.

Also inside the nucleus is a type of molecular-complex organelle called the nucleolus.  There may be more than one in a nucleus.  As a complex, it includes proteins and strands of chromosomes involved in making ribosomal RNA and the proteins that can be assembled into ribosomes out in the cytoplasm.  There is accumulating evidence that there may be many other functions performed here as well.  The name is unfortunate - if you are not the best speller, still try to get this one right, since it is so close to "nucleus"!

Chromosome structure.


More on the nucleolus.


Nucleoli forming (quick video).


Nucleolus research.


Ribosomes are found in both prokaryotes and eukaryotes and even in mitochondria and chloroplasts.  They are complexes of RNA and protein that function in translating the nucleic acid sequences of DNA into the amino acid sequences of proteins.  Ribosomes may be floating loose in the cytoplasm (or assembled into clusters), where they mostly produce proteins used in the cell interior, or they may be embedded in Rough Endoplasmic Reticulum (RER), where they are often involved in proteins that will process through Golgi Complexes for secretion or proteins that will become part of membranes.

More on ribosomes.


Ribosome structure.

Microtubule-Organizing Centers (MTOCs) produce one of the important components in the cytoskeleton, microtubules.  They contain centrioles, a sort of microtubule template on which they build, and lots of associated proteins.  There are several sorts of MTOCs, different more because of where they are in cells and what the microtubules produced do than different in any structural way.  Different MTOCs include centrosomes in the cytoplasm of animal cells and basal bodies beneath the propulsive structures with microtubule cores, cilia or flagella.  The microtubules in these structure commonly are arranged in a ring of 9 microtubule pairs, with a pair at the center (called the 9 + 2 arrangement).  Plant cells have some microtubules but identifying MTOCs in them has been difficult.

Genome-oriented knowledge of yeast MTOC.

More on centrioles.

More on centrosomes.

More on cilia & flagella.

This is not the complete list, but these are the most common molecular-complex organelles.  Others are either very specialized or, due to integration into membranes and other features, not generally discussed in this group.




The cytoskeleton is involved in both providing cell structure and producing cell movements.  The components that make up the cytoskeleton fall into three main categories:  microtubules, microfilaments, and intermediate filaments.

Microtubules are, as the name implies, very tiny tubes.  A roundish protein called tubulin (actually two proteins in a complex dimer) is used to construct these structures, built at the base in Microtubule Organizing Centers and extending away from them.  The mode of construction seems to be incompletely understood - some sources say that they are constructed at both ends simultaneously, although one end grows much more quickly than the other.

Cytoskeleton overview.

Microtubule structure. 

Tubulin structure.

Microtubules can have a purely structural function, but they commonly are used for various sorts of movement.  When cells (or at least nuclei) divide, a network of microtubules called the spindle fibers radiate out from MTOCs at opposite ends of a cell, connect to double-stranded chromosomes, position them for separation and draw the separated strands away from each other.  Movement of molecules and organelles inside a cell is often along a system of microtubule "conveyor belts," using two proteins that can be linked to things and which can move along microtubules:  dynein and kinesin move in opposite directions.  And eukaryotic flagella and cilia have a core structure of nine pairs of microtubules around a central pair.  Dynein also functions here to achieve the types of movement necessary for these structures.

Mitosis animation.

Spindle fiber formation (video).

Dynein and kinesin.

Microfilaments also can function either structurally or in movement, but these are a much more important structural element than microtubules.  Cell shapes are determined by networks of microfilaments just under the membrane and/or crisscrossing the cytoplasm.  The protein component of microfilaments is actin, arranged in two twisted rope-like strings, which can interact with other proteins to produce movements such as ameba-like crawling, the pinching of a cell during division, and muscle cell contraction (where it interacts with the protein myosin).

More on microfilaments.

More on actin.

Myosin and actin (Video).

Intermediate filaments fit into the size range between microfilaments (which are about 7 nanometers across) and microtubules (about 25 nm).  There are currently six classes (maybe nine) of intermediate filaments, but more are probably yet to be discovered.  The classes are characterized by the types of proteins involved and usually the types of cells they are found in:  for instance, 2 classes of different keratin-protein intermediate filaments are found in animal epithelial (surface) cells, where they are important structural elements.  Several types are found in types of nerve cells and undergo changes during the progress of several diseases, leading to the question,  "Are the intermediate filament changes causing the disease or is the disease causing the IF changes?"  It also appears that these structures may be important in moving some organelles around and holding them in place once they get there.  The appearance of some types of intermediate filaments seems to occur in cells that are under physical stress.

More on intermediate filaments.


And more.


Intermediate filaments move mitochondria? (abstract)




A number of abilities of eukaryote cells lie in the various "outside" structures that can be produced by extending the cell membrane with different underlying protein complexes.  There are a few different kinds...

Pseudopods are distorted extensions of the cell membrane of differing thickness, produced by microfilaments and associated proteins in the submembrane network or matrix.  Amebas and our own white blood cell crawl by extending pseudopods, sticking them to surfaces with microfilaments that extend through the membrane, and then "pushing" the cytoplasm into the extension.  Pseudopods can be thick and short, but they can also be long and thin and act almost like tentacles, or almost anything in between.

Pseudopod image.

Ameba moving (sped-up video).

More video.

Different pseudopod shapes.

Flagella are relatively large, finger-like projections with a core structure of microtubules which are made in a MTOC called a basal body.  There are very rarely more than a dozen on a cell, and most flagellated cells have six or fewer.  Flagella occasionally are modified with additional structures, such as a membrane extension (making what is functionally a fin) or a comb or a combination of stiffened and free-moving sections.  A simple flagellum usually moves with a spinning motion that drives a cell like a propeller.  The vast majority of sperm cells swim using a flagellum.  In tissues with anchored flagellated cells, the flagella are used to move materials rather than the cells, although this function is much more commonly accomplished by cilia.  Monerans also may have flagella, but they have a very different internal structure, including one of the few true wheels found in nature.

Flagellar and ciliary motion.

Internal microtubule arrangement.

A flagellar fin-like "add-on."

Prokaryote flagellum.

Cilia are fairly tiny finger-like projections that, like flagella, also have a core structure of microtubules and basal bodies.  Cilia always appear on cells in large numbers - it's not unusual for unicellular ciliated animals to be completely covered with them.  They are too small to support additional structures, but cilia sometimes fuse in groups to form structures:  for instance, a few unicellular animals creep around on what look like legs but which are fused clusters of cilia.   Cilia can be used to move cells and are commonly used to move materials past cell surfaces, as happens in the mucus-lined airways of your breathing system:  the dust-catching mucus is moved across ciliated cells to the throat, where it is swallowed.  Cilia usually move in a highly-coordinated fashion, often with a sort of swimming stroke.  There are also many highly-modified types of cilia, many non-mobile, in multicelled systems.

Internal structure.


Fused cilia in cirri.


Ciliary stroke.

Microvilli look superficially like cilia:  they are also multiple small finger-like projections.  However, microvilli have a core of microfilaments rather than microtubules and have extremely limited movement ability;  this is because movement is not really their purpose.  Microvilli are found on cells that require lots of surface area to do their jobs, either because they are trying to absorb or release materials.  Microvilli cover the absorbing surface of an intestine or the outside of a tapeworm or the waste-processing tubes of a kidney.  What wiggling movement they can muster is probably to help move materials into and out of the limited spaces between them.

EM images of microvilli.

Scanning EM image.

Many cells with microvilli.




Cells can have materials built and attached to the membrane or just built around the cell.  These are sometimes lumped under the term extracellular matrix, but not all sources agree on how separate from the membrane the structures have to be to be included.  Some types:

Glycocalyx is a material attached to the molecules of the membrane, often carbohydrate strings, which help aid recognition and interactions between cells and may contribute to stability and protection.  Prokaryotes also have glycocalyx.

Glycocalyx of inner linings.

Cell junctions hold cells together.  There are several types, including tight junctions, which hold cells so closely that molecules cannot slip between them (very useful in things like skin);  adherens junctions that bind cells together tightly even against forces that would pull them apart (these hold heart muscle cells together);  gap junctions that are actually passageways between connected cells;  plasmodesmata are similar passageways that pass through the cell walls between plant cells.

A few junction types.

Tight junctions.

Adherens junction.

Gap junctions.


Cell Walls surround the membrane but are not necessarily bound to it;  they provide a reinforcing structure for plants and fungi and a protection for unicellular organisms.  They usually provide little barrier to the movement of molecules into and out of the cells, but that's the membrane's job.  For something like a plant, cell walls give it structure but the continuous connected pattern restricts mobility.  The nature of plant cell walls as cellulose has been discussed, but cell walls can be made of several materials, produced in golgi complexes in eukaryotes.  Plants, especially woody plants, may produce different types of cell walls, including an early soft version and a later more rigid one.  Cell walls are also a common feature on Monerans and Archaeans.  Many antibiotics kill bacteria by attacking their cell walls.

More on cell walls.

Plant cell wall molecules.

Fungus cell wall molecules.




A whole library of cell structure images.

And...a silly little game about cell parts.  Could be useful for learning the parts if you ignore the process. 


Terms and Concepts

In the order they were covered.

Organelle, Membrane-Based (Definition)  
   Molecular Complexes (Definition)  
Cell Extensions (Definition)  
Cytoskeleton (Definition)  
Organelles, Membrane-Based (List)  
Nuclear Matrix  
Nuclear Envelope  
Food Vacuoles  
Central Vacuoles  
Turgor Pressure  
Contractile Vacuoles  
Endoplasmic Reticulum  
Smooth Endoplasmic Reticulum  
Rough Endoplasmic Reticulum  
Golgi Bodies / Complex / Apparatus  
Aerobic Respiration  
Endosymbiosis Theory  
Margulis, Lynn  
Molecular Complex Organelles (List)  
Nuclear Complexes  
Cytoplasmic Molecular Complexes  
Microtubule-Organizing Centers (MTOCs)  
Basal Bodies  
Microtubule 9 + 2 Arrangement  
Cytoskeleton Components  
Spindle Fibers  
Intermediate Filaments  
Cell Extension Structures (List)  
Extracellular Matrix  
Cell Junctions  
Tight Junctions  
Adherens Junctions  
Gap Junctions  
Cell Walls



General Biology 2 - Molecules and Cells

Copyright 2013 - 2019, Michael McDarby.

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