large view Oxygen carrier (Hemoglobin)

Visualizing Particles in Motion

Our understanding of biotechnology will strengthen the more we look deeply and think about molecules.  We are lucky to live at a time when scientists have developed amazing tools for looking deeply at the detailed structures of  teeny-tiny particles (molecules!)

Links to the Inner Life of the Cell

A high quality version of this animation can be seen by following this link:

Inner Life of the Cell

For those of you, who want to improve your vocabulary, you can hear a professor comment on the images of the video, by clicking on one of the images on this link to the multimedia webpage of the Department of Molecular and Cell Biology at Harvard University. 

I've simplified and enlarged the story presented by the Harvard narrator to produce a more student-friendly version of the same story below:

A white blood cell (WBC) is on patrol in a small blood vessel (capillaries) near the surface of the body immediately under the skin.  It avoids being swept away in the strong current by using proteins that serve as grappling hooks to hold onto the cells that line the wall of blood vessel (endothelial cells).  Unseen in this video, the skin has been injured above the blood vessel and has been signaling for help.  The cells that line the blood vessel carry protein molecules that have the capability of signaling the white blood cells (WBC).  These proteins flip on a switch that lies on the surface of the WBC to tell the cell that a battle has begun with invading germs (microorganisms) in the nearby vicinity.

The video then zooms into the interior of the cell away from the oily cellular membrane.  As the camera zooms away from the surface, one can see the intracellular (inside the cell) matrix just below the membrane.  This matrix contains a network of proteins that strengthen the cell membrane, similar to the network of steel wires that used to be found embedded in old reinforced glass.

Zooming into the interior, we see one of the cytoskeleton element (f-actin) and then the same cytoskeleton being reassembled at the leading edge of the cell and disassembled (g-actin) at the retreating end.  This is but one mechanism that allows the WBC to move.  In a similar fashion, you also see a larger cytoskeletal element (microtubules) being formed and dissassembled at either end of the cell.

A molecular walker comes into view.  This molecular transport molecule (also known as a molecular motor, in this case, kinesin) uses the universal fuel of the cell (ATP) to power its legs and feet to move along the microtubules.  Behind this walker, a small bag (vesicle) of newly made proteins is being carried to the post office of the cell (the golgi) where the newly made proteins will be sorted and addressed. 

In the background, one can see that the microtubules radiate from two cylinders that lie close to the center of the cell.  These two cylinders serve as the Grand Central Terminal for this transport system.  They are called the centrioles.

Zooming past the centrioles we arrive at the center of the cell, the nucleus, which houses all the instructions that the cell needs for life.  Rocketing out of openings (nuclear pores) in the surface of the nucleus are messages that need to be decoded (messenger RNA).  These messages can be read like those magnetic tapes found in audio and video cassettes.  These molecular machines are made of proteins and RNA (ribosomes).   The messages themselves form into circles to allow the message to be read multiple times as the read head machinery makes several trips around the circle. 

Once made a cytoplasmic protein goes merrily on its way finding other proteins partners.  The camera shows one of the power plants of the cell worming its way around to another destination within the cell.  These power plants called mitochondria take the sugar you eat and convert it into a fuel that the molecular walker and other molecular machines can use.   

The next scene shows other proteins inserted into membranes or inserted into bags (vesicles) for delivery elsewhere (either in another cellular location or for a destination outside the cell).

The proteins destined for delivery are then carried by the walkers (kinesin) in the oily bags (vesicles) to the post office (golgi) for processing.  You can see several vesicles entering into the golgi from below and exiting from the golgi above.

Once the bag (vesicle) reaches the cell surface (membrane) the oily bag of the vesicle merges with the oily surface (membrane) of the cell.  This is similar to what soap bubbles do when they merge.  The contents of the vesicle are either attached to the membrane and remain as cell surface proteins or are released into the space outside the cell (extracellular matrix).  These released proteins often serve as cell signals (some of these are called hormones).  In this case, the WBC has most probably used the information in the nucleus to produce several proteins, the ones leaving the cell are most likely signals to recruit other WBC to the upcoming battle.  The ones that remain are likely to be signals to request that the cells lining the blood vessel (capillary endothelial cells) release the protein locks that lock each endothelial cell in place and prevent blood cells from escaping.

One sees a surface cell signalling protein on the WBC unfold to make contact with the endothelial cell above.  The video then zooms out to see the WBC reshape itself (recall the assembly and disassembly of the cytoskeleton) as it crawls through a gap in two endothelial cells that have released the  protein locks that tie them together (tight junctions).

This amazing animation is based on world-class research from around the world.  I have assembled a variety of links from scientific laboratories that work on some of the aspects of the cell and molecular biology illustrated in the animation.  Have fun exploring!


If YouTube isn't blocked, you can also check out this video.

PipeClleaner Animations of Kinesin
A fun look at how one scientist used claymation techniques to evaluate different models of proteins in motion.

Walking Molecule, Kinesin
In this movie you will see a protein that can walk! The surface below is a microtubule, part of the cytoskeleton (the miniature "bones" of the cell).

Viral attack!
Video of viruses swimming around inside a cell by hijacking actin comets. This video is sped up 15x.

A Molecular Hand Pulling a Molecular Rope
Imagine billions upon billions of these pulling together in a tug-of-war. Shrink these down about a billion times and you will have an approximation of what goes on when your muscles contract. Even though these are extremely tiny, trillions of them act together to provide you with tremendous strength.

A Rotating Molecular Motor
In this movie, you will see the image zoom down into a small motor embedded in the surface of a bacterium. The movie then shows details of the various components of this motor.

ASCB's Video Library
For more movies of cells, check out this video gallery of the American Society of Cell Biology. Caution: This did not work on my computer.

More information on the molecular motor in bacteria
This comprehensive website explains the structure of the bacterial molecular motor and includes a movie summarizing the research into this fascinatingly small motor.

Rotating Hooks
The motor above is connected to a hair-like thread called a flagella. The hooks seen here provide the connection. When the flagella whips around it provides thrust. Think of a propeller blade on a boat or a propeller on a plane, you get the idea.

Cells on the loose 2: A closer look
This is a series of time-compressed videos that show how cells move in a laboratory dish.

Molecular Workbench
We have used this software in class to view our dancing particles. This page describes the software and how to install it and how best to use it.

If your Internet connection is slow, I suggest that after you install Java onto your computer, you might want to use the Install MW without Java Web Start link. Once downloaded (which will take a long time the first time), the program will start much faster if it doesn't have to make a connection to the Internet before starting.

Download and install a 3D Molecular Viewer
Please follow these instructions to download and install Chime (a 3-D molecular viewer that works with your Internet browser, like Internet Explorer). I suggest you make the effort to also download and install Netscape Browser 4.8, which works the best with the Chime software.

Exploring DNA
Highly recommended for first-time users of Chime. This tutorial will teach you how to use the Chime 3D molecular viewer as you learn about DNA.

DNA Structure Tutorial
Once you have downloaded Chime and perhaps Netscape 4.8, you might have fun exploring the structure of DNA. You may not understand everything on this site, but remember the more you look, the more you understand. I'll be guiding you through the site in the future.

HIV protease inhibitor
If you really want to see some fancy advanced biotechnology, you will find this exploration on the design of a drug that fights AIDS. Remember to just push the buttons and say wow!

BioMolecular Explorer 3D
A selection of some of the most interesting molecules for a biotechnologist to know.

Molecular Visualization Resources
A large selection of some of the most interesting molecules to view.

Molecules in Motion
View this outstanding presentation to obtain an overview of protein structure.

Enzyme Activity
Here is an animated tutorial for learning the molecular concepts behind enzyme activity.

DNA visualizations
Outstanding DNA animations based on real scientific data.

Other Animations at WEHI-TV
Outstanding biomolecular animations from Australia

Gallery: EM Cyroscopy
Awesome movies of subcellular components, viruses etc from an EM Lab in Japan.

Video Tour of Cell's on the Move
A web presentation of cells on the move is provided by the Vic Small lab of the Austrian Academy of Sciences in Salzburg and Vienna (IMBA).

Green Globs in Motion
One of the movies that can be found on the Video Tour of Cell Motility Website described above.

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