How to Make a Cell

Biologists have long pondered whether life can be reduced to discrete chemicals or, conversely, whether those same chemicals could be used to re-assemble an organism from scratch. But doing this has proven extremely difficult. Nobody has yet made a living cell by mixing together inert molecules.¹

And for good reason! A cell is a complicated object. Even the simplest kinds are made from thousands of different proteins, metabolites, RNA and DNA packed into a lipid membrane. These components move around quickly. Each protein collides with trillions of water molecules per second. For this reason (and others), some researchers think that biology is “irreducibly” complex; cells cannot be accurately simulated on a computer, let alone built from scratch.

But still, life tames this complexity. Cells beget cells by turning simple molecules, such as sugars and nitrogen, into more complex ones, beating back the tides of entropy. Or, as the Austrian physicist Erwin Schrödinger wrote in his classic 1944 book, What Is Life?, cells refuse to succumb to chaos “by eating, drinking, breathing and (in the case of plants) assimilating.” Cells are an advanced form of nanotechnology, mixing and matching atoms to build life anew.²

To appreciate why life is so miraculous, we first need to take an inventory. What is a cell made of? How many atoms — and how much energy — does it take to build a new one? By tallying the parts, it will become clear why humans can strip cells apart and understand each piece in isolation, while struggling to put the pieces back together.

It’s easiest to build an inventory for Escherichia coli because that microbe has been studied more than any other. It is the subject of more than 100,000 published research papers. Scientists have studied many types of E. coli, too, from “flesh-eating” variants to engineered strains that act as living “camera film.”

Even within a single species like E. coli, though, there is no one-size-fits-all cell. Instead, there is a positive correlation between how quickly a cell grows and its size; larger cells have higher growth rates.

In 2015, researchers measured this directly for E. coli, using a microfluidic device called a “Mother Machine” that traps single cells and tracks them for many generations.³ They grew thousands of cells in seven different types of growth media, from nutrient-rich broths to minimal media, and saw the cells double anywhere from 1.2 to 3.5 times per hour. For each condition, they also measured the average volume of each “daughter” cell, finding an exponential relationship between growth rate and size. Cells in the nutrient-rich media were about six times larger, by volume, than cells in the nutrient-starved ones.⁴

Pick one of those cells, then, and take it apart. What is it made from?

About 70 percent of its mass is water. The other 30 percent — the so-called “dry mass” — is everything else: DNA, RNA, proteins, lipids, and so on. DNA makes up just 3 percent of dry mass, yet encodes all the information needed for the cell to grow, divide, adapt, and evolve.⁵ The bulk of a cell’s dry mass — 55 percent — is protein, or large molecules that catalyze reactions, form structural scaffolds, and control which genes ought to switch “on” or “off.” About 20 percent is RNA, 10 percent is lipids, and the rest is ions, signaling molecules, and miscellany.⁶

Proteins make up most of the dry mass for a few reasons. First, there are lots of them, and each protein is heavy. A single E. coli cell has about two million proteins in total, each with hundreds of amino acids. A typical 300-amino-acid protein weighs around 33 kilodaltons (kDa), equal to the mass of 50 base pairs of DNA.⁷

Why are proteins so big? For one, larger proteins fold faster than smaller ones due to cooperativity, where one part of the protein coaxes another part to snap into place.⁸ Also, enzymes — the proteins that speed up chemical reactions by a factor of 10¹⁰ or more — often need extra bulk to build pockets, or cavities that are shaped in such a way that only certain molecules can enter and reach the active site. The enzyme that attaches tyrosine to its tRNA, for example, prefers tyrosine over phenylalanine — a molecule that differs by just one oxygen atom — by more than 100,000 to one.

Cells have millions of proteins floating around at any moment, but only a few thousand types. Protein copy numbers span five or six orders of magnitude, meaning that cells might have just one copy of protein A and a million copies of protein B. This distribution is long-tailed; about one hundred protein types make up the vast majority of a cell’s dry mass!⁹

In the 1970s, most biologists thought that EF-Tu, a protein that delivers tRNAs to the ribosome during protein synthesis, was the most abundant protein. This makes sense, because each E. coli has tens of thousands of ribosomes, each stitching together about 20 amino acids per second. It makes sense, then, that cells need a lot of EF-Tu to keep up!

But in 1979, a paper in Cell found that — no — the most abundant protein in E. coli is actually Braun’s lipoprotein, or Lpp, with over 700,000 copies per cell. Lpp is a small protein that staples a cell’s outer membrane to its peptidoglycan layer, thus preventing blistering and leaking.¹⁰

Still, many other abundant molecules in E. coli are involved in protein synthesis. But, oddly enough, most of the machinery used to make proteins is not protein at all.

About 20 percent of the cell’s dry mass is RNA. And of that RNA, the majority is ribosomal RNA.¹¹ Ribosomes are two-thirds RNA by mass. Each ribosome has long threads of RNA inside, together stretching about 4,500 nucleotides in length. Assuming there are 20,000 ribosomes in an average E. coli, that means there are about ten-times more ribonucleotides just in ribosomes than all the DNA in the cell.

Lipids, finally, make up about 10 percent of a cell’s dry weight. There are about 2 × 10⁷ lipids in each membrane, or roughly 30 million lipid molecules per E. coli, packed into two continuous bilayers that stretch around the entire cell. If the E. coli cell membrane were pressed into a flat sheet, it would cover about 6 µm² of space and it would take about 10,000 of these cell membranes, stitched together, to cover the period at the end of this sentence.

All of this leads to a final question: How much energy is needed to make all these molecules? How much energy is burned when a cell builds a cell?

One might assume it's a lot! After all, a cell holds millions of proteins, each one stitched together from individual amino acids.¹² Making each amino acid, and then joining them, costs a great deal of energy. The same goes for DNA, RNA, lipids, and every other molecule.¹³

The actual amount of energy required is surprisingly small — at least from a macroscopic view. Scientists recently used computational models to estimate the energy cost of assembling every part of a single cell. They drew on experimental data to quantify E. coli’s molecules, then applied a group-contribution algorithm to calculate the standard Gibbs free energy needed to build each type. Adding these numbers together, the researchers arrived at the minimum energy required to build an E. coli: 9.54 × 10⁻¹¹ joules, or about 0.1 nanojoules. That is ten billion times less than the energy needed to lift an apple one meter off the ground.¹⁴

Zoom into a single cell, though, and the same number feels quite large. Each molecule of ATP, the energy-storage molecule, releases about 5 × 10⁻²⁰ Joules when it breaks apart, meaning about 2 billion of them are needed to “build” a cell.¹⁵ Each glucose molecule can 'burn' to make 30 ATP during aerobic respiration, so one cell costs about 60 million glucose molecules.¹⁶

But these estimates assume 'perfect' efficiency. In truth, a cell wastes energy at every step. Stitching together each amino acid theoretically requires just one ATP, for example, but actually demands four. Proofreading during DNA and protein synthesis costs energy, too, and the cell loses some as heat. The reality is that measured growth yields put the actual cost of a cell at roughly 5–10× the minimum, meaning 10–20 billion ATP or about one billion sugar molecules are needed to build each E. coli.¹⁷

We now have a nearly complete list of the molecules in a cell, along with estimates of the energy needed to assemble them. And yet, even if one gathers all the right molecules in the right quantities, we still couldn’t arrange them to "create life."

I can walk across the street from my Berkeley apartment and buy some of the same ingredients the chefs at The French Laundry cook with. But could I assemble them into Oysters & Pearls, or any other award-winning dish? I'm sure my wife would love it if I could, but I can't. I don't know how to cook the ingredients, how to set the heat, or how to feel when a sauce has thickened enough to pull it off the stove.

Cells have the same problem, except the cooking happens at a speed we can scarcely imagine. Sugar molecules fly through a cell at 460 miles per hour, and each protein is bombarded by 10¹³ water molecules per second. Every number in this essay, then, is an average of this blur. Bulk measurements can tell us a cell has two million proteins, but not where any of them are, what they are touching, or what they will do in the next millisecond.

And this makes life all the more remarkable. Despite the chaos, a cell holds everything in check. It runs thousands of reactions at once, in the same small volume, without the reagents interfering with one another. Then it builds a second copy of itself — in some species, in under ten minutes — from nothing but sugar and salts and simple building blocks.

Part of the reason we have not tamed this complexity, I suspect, is that our tools are too narrow. To measure a cell's contents, we typically kill it: we grind up billions of bacteria, separate the pieces, and weigh what comes out. The result is an average across a population of corpses. What we need instead are new ways to watch single cells across space and time. We ought to build sensors for every molecule, tracking what each one is doing, where it is going, and how it is changing, continuously and noninvasively, as the cell grows and divides.

That is the dream, at least. A list of ingredients is inherently static, and it is only by capturing how each piece moves and interacts that a catalog of parts might become a recipe for a cell.