Information and recycling machines

The previous lesson covered machines that make force and motion. This one covers the machines that act on polymers — reading and copying DNA and RNA, and building, unfolding, and recycling proteins. They are some of the largest and most intricate machines in the cell.

As before, use the mode toggle (top-right) to switch representations and explode to separate the subunits.

Nucleic-acid machines

These act on DNA and RNA — copying, unwinding, untangling, reading, and cutting.

Polymerases synthesise new strands while tracking along a template. DNA polymerase copies DNA during replication; below it is caught with a gapped DNA and an incoming nucleotide poised opposite the template base.

RNA polymerase reads a DNA template and writes a complementary RNA strand, one base at a time. This one is frozen mid-transcription, with the DNA and a short nascent RNA threaded through its cleft (the thin strands, coloured separately from the protein).

Helicases unwind double-stranded nucleic acids, burning ATP to pry the two strands apart. Many are rings that thread one strand through a central channel and reel it in, unzipping the duplex ahead.

Six subunits form the ring; the single DNA strand runs down the middle. Explode the chains to see the six-fold assembly clearly.

Topoisomerases relieve the torsional stress that builds up as DNA is unwound: they cut one or both strands, let the DNA swivel or pass through the break, then reseal it. Here the enzyme is clamped right around the double helix.

The ribosome is the cell's master copier — it translates mRNA into protein, ratcheting along the message codon by codon. It is a ribozyme: two-thirds of it is RNA, and the catalytic site that joins amino acids is built from RNA, not protein. It is also enormous — the structure below has ~150,000 atoms, so (like the flagellar motor) it loads only as mmCIF and is shown as a surface.

Look for the two interlocking subunits: the small subunit that reads the mRNA and the large subunit that forges the peptide bonds. The messenger threads through the neck between them.

CRISPR-Cas9 is a programmable machine — biology's, then ours. A short guide RNA loaded into the Cas9 protein steers it to a matching DNA sequence, which the two nuclease domains then cut. Reprogram the guide and you retarget the scissors; that simple idea became the dominant gene-editing tool and the 2016/2020 Nobel story.

The protein folds into two lobes that close like a clamp around the RNA–DNA duplex sitting in the central channel; switch to ball-and-stick to pick out the guide RNA paired with its DNA target.

The spliceosome completes the set but is too large and shape-shifting to freeze in one snapshot: it is a dynamic assembly of RNAs and proteins that finds introns in pre-mRNA, excises them, and stitches the exons together — rebuilding itself anew on every intron.

Degradation and folding machines

The cell must also take proteins apart and help them fold.

The proteasome is a self-contained shredder: a barrel of four stacked seven-membered rings whose cutting sites face inward, so digestion happens in a sealed chamber. In cells it is capped by AAA+ motors that recognise tagged proteins, unfold them, and thread the chain inside.

Chaperonins do the opposite job. GroEL/GroES is a double-ringed cage with a detachable lid: it encloses a struggling protein in a quiet chamber and gives it a private, ATP-paced chance to fold correctly without clumping.

The two stacked seven-membered rings are GroEL; the small dome is the GroES lid. The RuBisCO lesson follows this chamber through a full folding cycle.

Synthetic molecular machines

A separate world: not evolved but designed by chemists. These are tiny organic molecules — not the megadalton complexes above — so they don't live in the structural databases this viewer draws from, but they obey the same principle of biased, fuel-driven motion.

• Rotaxanes — a ring threaded onto a molecular axle between two stoppers; the ring can be driven to shuttle between docking stations.
• Catenanes — interlocked rings that can be made to rotate relative to one another, like links in a chain.
• Molecular motors and switches — Feringa's light-driven rotor turns unidirectionally in 360° steps. The distinction matters: a switch flips back and forth (no net work), a motor completes a cycle and does net work.

This field won the 2016 Nobel Prize in Chemistry (Sauvage, Stoddart, Feringa) — proof that the design rules biology discovered can be rebuilt from scratch on the bench.

Across both lessons the same blueprint keeps reappearing: an energy source, a repeating conformational cycle, and a built-in direction that turns random molecular jiggling into useful, one-way work. Next, the RuBisCO case study follows a single enzyme and the whole crew of machines biology built just to assemble it.