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Chapter 6 · Part 10 of 10
  1. Chapter overview
  2. 1Energy and the laws of thermodynamics
  3. 2Free energy and the direction of reactions
  4. 3How ATP powers endergonic reactions
  5. 4How enzymes speed up reactions
  6. 5Enzyme speed, affinity, and inhibitors
  7. 6Enzyme helpers, conditions, and ribozymes
  8. 7Breaking down and building up molecules
  9. 8Redox reactions and NADH
  10. 9How cells regulate metabolic pathways
  11. 10Recycling proteins and organelles

Recycling proteins and organelles

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Most of a cell’s large molecules are temporary. DNA is the exception: cells keep it intact and pass it on when they divide. Others, such as RNA, proteins, lipids, and polysaccharides (long sugar chains), last a relatively short time before they’re broken down and their parts reused.

Half-life and why recycling pays

How long a type of molecule lasts is described by its half-life: the time it takes for half (50%) of that type of molecule in a cell to be broken down and recycled. Take mRNA, the RNA copy of a gene that serves as instructions for building a protein. In bacteria, mRNA molecules have an average half-life of about 5 minutes. In eukaryotic cells they tend to last longer, from 30 minutes to 24 hours, and some last many days.

Recycling matters because building molecules from scratch is expensive. Making the building blocks of larger molecules, such as the amino acids in proteins or the nucleotides in RNA, takes a lot of energy. By reusing them, organisms save that energy, which helps them compete in their environments.

The proteasome breaks down proteins

Cells continually get rid of proteins that are faulty or no longer needed. The work is done by proteases, enzymes that cut the bonds between neighboring amino acids.

In eukaryotes and archaea, the main site of protein breakdown is the proteasome, a large protein complex. Its core is a hollow cylinder of four stacked rings, each built from seven protein subunits. In eukaryotes, a cap at each end of the core controls which proteins get in.

A protein is marked for destruction with ubiquitin, a small protein that serves as a tag. The process runs like this:

  1. A string of ubiquitin molecules is covalently attached to the target protein.
  2. The ubiquitin tag directs the protein to a proteasome cap, which has binding sites for ubiquitin.
  3. Enzymes in the cap unfold the protein and feed it into the core’s central cavity. The ubiquitins are removed on the way in and released into the cytosol to be reused.
  4. Proteases inside the core break the protein into small peptides (short chains of amino acids) and individual amino acids.
  5. The peptides and amino acids are released back into the cytosol, and the amino acids are used to build new proteins.
Ubiquitinreleasedfor reuse Targetprotein Unfoldedprotein Proteasome core Cap Cap Peptides Amino acids
Figure 6.7 The ubiquitin chain delivers its target to the proteasome, but only the target protein enters the core. The ubiquitin tag is removed at the entrance and used again. Inside, proteases cut the protein into peptides and amino acids.

Why tag proteins with ubiquitin

Ubiquitin tagging serves three purposes:

Autophagy recycles whole organelles

Proteasomes handle single proteins. For something as large as a worn-out organelle (a membrane-enclosed compartment with a specific job, such as a mitochondrion), cells turn to lysosomes. A lysosome is a membrane-bound sac of acid hydrolases, digestive enzymes that break down proteins, carbohydrates, nucleic acids, and lipids. Lysosomes digest material the cell has taken in from outside by endocytosis (Chapter 5), and they digest the cell’s own material too.

Digesting the cell’s own material this way is autophagy, from the Greek for “eating oneself.” It happens in three stages:

  1. A membrane tubule grows and wraps around the worn-out organelle until it encloses it in a double membrane. The enclosed package is an autophagosome.
  2. The autophagosome fuses with one or more lysosomes.
  3. Lysosomal enzymes digest the contents, and the resulting small molecules are recycled back into the cytosol.

Autophagy lets a cell reuse the parts of an entire organelle instead of making every one of its molecules from scratch.

Cytosol Worn-outorganelle Doublemembrane Autophagosome Lysosome Digestiveenzymes Smallmoleculesrecycled
Figure 6.8 A double membrane wraps around the worn-out organelle and seals it inside an autophagosome, with no digestion yet. The autophagosome then fuses with a lysosome. Only then do the lysosome’s enzymes digest the contents, and the small molecules they release return to the cytosol for reuse.
Check yourselfWhat is the difference between what a proteasome breaks down and what autophagy breaks down?

A proteasome breaks down individual proteins that have been tagged with ubiquitin. Autophagy handles larger material, such as a whole worn-out organelle, by enclosing it in an autophagosome that fuses with lysosomes. In both cases the small molecules produced are recycled.

Practice questions

  1. 1 of 4

    A cell has 1,000 copies each of two different mRNAs. mRNA A has a half-life of 5 minutes, and mRNA B has a half-life of 10 hours. If the cell stops making both, what will be true an hour later?

  2. 2 of 4

    Cells constantly break down old proteins and reuse the amino acids to build new ones. What is the main advantage of this recycling?

  3. 3 of 4

    A mutation keeps the enzymes that attach ubiquitin from recognizing improperly folded proteins. What is the most likely result?

  4. 4 of 4

    Two strains of yeast are identical except that strain A reuses the nucleotides from its broken-down mRNAs, while strain B must build every nucleotide from smaller molecules. If the strains compete for a limited food supply, which will likely do better?