The biological realm encompasses an extraordinary range of sizes, from macroscopic organisms visible to the naked eye to the intricate molecular machinery operating at the nanoscale. To truly grasp nanobiology, understanding the spatial relationships between these diverse structures is fundamental to comprehending biological processes and the immense complexity of biological systems. This post will explore the relative sizes of key biological components – proteins, DNA, viruses, bacteria, cells, and tissues – and discuss how advanced microscopy techniques, specifically Atomic Force Microscopy (AFM) and Electron Microscopy (EM), enable their visualization and characterization. Our goal is to make this experience accessible as early as high school, using our intuitive and affordable AFMs.

To appreciate the power of AFM and EM, it’s essential to first establish a sense of scale within the biological world. We typically measure these structures using units like micrometers (µm) and nanometers (nm). For reference, a human hair is approximately 50-100 µm in diameter (about a tenth of a millimeter). A strand of DNA, on the other hand, is 2 nm in diameter (roughly 50,000 times smaller than a hair). A single glucose molecule is about 1 nm in diameter.

These raw dimensions are difficult to conceptualize. To help put them into perspective, here’s an analogy by “magnifying” everything a million times: If DNA was the width of twine, a human cell would be the size of a house, the nucleus the living room, a bacterium would be a desk, a virus would be a soccer ball, a protein a marble. Your human body could stretch across the entire United States.

• Tissues: These are organized groups of cells working together to perform specific functions (e.g., muscle tissue, nervous tissue). Tissues are macroscopic structures, often ranging from millimeters to centimeters, and are generally visible to the naked eye. While their cellular and extracellular components require microscopy (like histology using light microscopy), tissues themselves build up to form an entire organism.
• Cells: As the fundamental units of life, cells vary considerably in size. Animal cells, for instance, commonly range from 10 to 100 µm in diameter and are easily observed using standard light microscopy. A fibroblast cell for example looks a bit like a sunny side up egg, about 20 µm wide and 10 µm tall. See our cheek cell data.
• Bacteria: These prokaryotic organisms are generally smaller than eukaryotic cells, typically measuring between 1 and 10 µm. While some larger bacteria can be resolved with high-power light microscopes, detailed structural analysis often requires more advanced techniques. A typical pill-shaped bacterium (bacilli) like E. coli is approximately 1 x 2 µm. In nature they form communities called bacterial biofilms.
• Viruses: Considerably smaller than bacteria, viruses are obligate intracellular parasites, typically falling between 20 and 400 nm. Their nanoscale dimensions place them beyond the resolution limits of conventional light microscopy, but well within the resolution of AFM and EM.
• Proteins: These essential macromolecules, responsible for a vast array of biological functions, are often measured in nanometers. Individual protein molecules can be just a few nanometers in size. For example, hemoglobin with a mass of 64 kDa is 6 x 5 x 5 nm. Collagen fibers (a protein polymer) on the other hand can be hundreds of nm wide and many microns long.
• DNA: The genetic material, DNA, is a double helix with a remarkably consistent width of approximately 2 nm. Each rung in the helix is 0.34 nm and the helix completes a turn in 10 rungs (10 base pairs = 3.4 nm). Visualizing the structure of DNA at this resolution is best done by AFM.
• Small biomolecules: These are often around 1 kDa and consist of carbohydrates, amino acids, lipids and other metabolites. Glucose is 1 nm in diameter, a phospholipid in a membrane is about 2 nm long.

Single-stranded DNA molecules, the genome of the bacteriophage M13.

A cheek cell (epithelial cell) with bacteria on its surface.

Given the nanoscale dimensions of many crucial biological structures, specialized microscopy techniques are required for their investigation. AFM and EM are two such powerful tools that provide unparalleled insights into the micro- and nanoscale world.

• Electron Microscopy (EM): Electron microscopes use beams of electrons to illuminate samples, forming an image by the scattering of electrons by the sample. Compared to light microscopes, which use photons, the shorter wavelength of electrons allows EMs to achieve significantly higher resolution and magnification—up to millions of times. This capability makes EM indispensable for visualizing the fine details of tissues, cells, and even the structure of proteins, revealing both their external shape and internal organization. Scanning and transmission electron microscopes (SEM, TEM) are highly complex instruments that operate under high vacuum to generate and maintain an electron beam, typically restricting their use to expert scientists.
• Atomic Force Microscopy (AFM): AFM is a scanning probe microscopy technique that generates a 3D topographic map of a sample’s surface. It employs a sharp tip, typically made of silicon or silicon nitride, attached to a cantilever. Think of it like tapping your fingertip over your desk, but with a nanoscale “finger”! As the tip scans across the surface, it interacts with the sample through atomic forces. A laser system monitors the deflection of the cantilever, and this data is used to construct an image of the surface topography with nanoscale resolution. AFM can resolve individual molecules and small aggregates, making it particularly well-suited for studying proteins, DNA, and other nanoscale features. It can also visualize larger structures such as viruses, bacteria, and cells. AFM provides direct information about the height and shape of structures on a surface, offering a different perspective compared to the projection images often obtained with EM. A significant advantage of AFM is its ability to image samples in liquid environments, allowing for the observation of biological processes, such as protein aggregation, under more physiological conditions. For many samples, AFM sample preparation can be relatively straightforward and rapid, taking approximately 30 minutes for a liquid-to-dry process. Because of its different principle and design, an AFM is easier to operate, making it possible to train high school and undergraduate students to use it independently.

The great thing about having hands-on access to nanobiology data is that it allows us to explore this nano-world beyond the theoretical information found in cell biology textbooks. It opens our eyes to the awe-inspiring complexity of biological systems, from a “simple” virus or bacterium to eukaryotic cells, and even complex tissues like the brain or liver. If you’re interested in backing this up with numbers, check out bionumbers.hms.harvard.edu.

Atomic Force Microscopy and Electron Microscopy are complementary techniques that open windows into the otherwise invisible world of biological structures at the nanoscale and microscale. While EM excels at providing high-resolution images of the overall morphology and internal details of viruses, bacteria, and cells, AFM offers unique capabilities for visualizing surface topography, resolving individual molecules, and observing dynamic processes like protein aggregation with nanoscale precision. By employing these powerful tools, scientists can continue to unravel the complexities of life at its most fundamental levels.

• Comparing TEM, SEM, and AFM
• Teaching serendipity and nanobiology with an AFM and eggshells
• AFM of biofilms