Organelles & compartmentalisation

Why a cell needs rooms

A eukaryotic cell (the kind that makes up plants, animals, fungi and protists) is packed with organelles, structures that each do a particular job. Most of them are wrapped in their own membrane. Splitting the cell into membrane-bound spaces like this is called compartmentalisation.

Compartments make a cell more efficient in three main ways. First, they concentrate things: the enzymes and substrates for one pathway are packed into a small space, so they meet each other far more often than if they were spread through the whole cell.

Second, they keep incompatible reactions apart. A lysosome is a bag of digestive enzymes that break down worn-out parts and engulfed bacteria. Its inside is kept acidic, at about pH 4.5–5, by proton pumps in its membrane, while the surrounding cytosol sits at about pH 7.2. The enzymes work best in acid, so the rest of the cell isn't digested.

Third, a membrane lets a cell build a gradient: a difference in concentration between two sides. Mitochondria and chloroplasts both store energy as a pile-up of protons on one side of an internal membrane, and use it to make ATP. Without a closed compartment, there would be nothing to hold the protons back.

A quick tour

• Nucleus: holds the cell's DNA. It's surrounded by the nuclear envelope, a double membrane pierced by nuclear pores that control what passes in and out, such as RNA heading to the cytoplasm. Inside, a dense region called the nucleolus assembles ribosome subunits.
• Ribosomes: build proteins. Free ribosomes in the cytosol make proteins that stay in the cytosol. Ribosomes bound to the ER make proteins that will be secreted, placed in the plasma membrane, sent to lysosomes, or kept in the ER or Golgi.
• Endoplasmic reticulum (ER): a maze of membrane sacs and tubes. Rough ER is studded with ribosomes and folds and modifies new proteins. Smooth ER has no ribosomes; it makes lipids and steroid hormones, detoxifies drugs and stores Ca²⁺.
• Golgi apparatus: a stack of flattened sacs that modifies, sorts and ships proteins and lipids.
• Mitochondria: double-membraned organelles where aerobic respiration makes most of the cell's ATP. The inner membrane is folded into cristae.
• Chloroplasts (plants and algae): double-membraned organelles that carry out photosynthesis, with stacks of membrane sacs called thylakoids.
• Peroxisomes: single-membraned sacs that break down fatty acids and detoxify poisons.
• Vacuoles: storage sacs. Plant cells have a large central vacuole that helps keep the cell firm.

The endomembrane system: following a secreted protein

The nuclear envelope, ER, Golgi, lysosomes, vesicles and plasma membrane together form the endomembrane system. They're linked either directly or by vesicles, small membrane bubbles that bud off one compartment and fuse with another. Here is the path Palade's radioactive proteins took, filled in with what we've learnt since:

1. 1Translation starts on a free ribosome in the cytosol. The first stretch of the new protein is a signal peptide, a short "address label" that means "send me to the ER".
2. 2As the signal peptide pokes out of the ribosome, a particle called the signal recognition particle (SRP) grabs it and briefly pauses translation.
3. 3SRP docks the ribosome onto a receptor on the rough ER. The growing protein is threaded through a channel into the ER's interior (the lumen), and translation resumes. Because targeting happens while the protein is still being made, this is called co-translational targeting. An enzyme then snips off the signal peptide.
4. 4In the ER lumen the protein folds, and many proteins get short sugar chains attached.
5. 5The protein is packed into a transport vesicle, which buds off the ER and fuses with the cis face of the Golgi, the side facing the ER.
6. 6Moving through the Golgi, the protein is modified further (for example, its sugar chains are trimmed and extended) and tagged for its destination.
7. 7At the trans face, the side facing the plasma membrane, it's packed into a secretory vesicle.
8. 8The vesicle fuses with the plasma membrane and releases the protein outside the cell. This is exocytosis.

Proteins that belong in the plasma membrane follow the same route, except that they stay embedded in the vesicle's membrane. When the vesicle fuses, they become part of the plasma membrane. Lysosome enzymes also travel ER → Golgi, but they're tagged and sorted into vesicles bound for lysosomes instead.

Where did mitochondria and chloroplasts come from?

Mitochondria and chloroplasts are odd organelles. They aren't made by the endomembrane system, and they behave a lot like bacteria living inside the cell. In the 1960s the American biologist Lynn Margulis pulled together the evidence for an old, then unpopular, idea: that these organelles really were once free-living bacteria. The idea is called endosymbiosis, meaning one organism living inside another.

The story goes like this. An ancestral host cell took in an aerobic bacterium and, instead of digesting it, kept it. The two came to depend on each other, and the bacterium became the mitochondrion. Later, a cell that already had mitochondria took in a photosynthetic cyanobacterium, which became the chloroplast. Here is the evidence:

• Two membranes. The inner membrane matches the bacterium's own plasma membrane; the outer one is thought to come from the host's engulfing membrane.
• Their own DNA, in a circular chromosome like a bacterium's, rather than the linear chromosomes of the nucleus.
• Their own ribosomes, built on the bacterial pattern rather than the cytosolic one. Chloroplast ribosomes are 70S like bacteria's; mitochondrial ribosomes vary in size between groups, but are still bacterial in design.
• They divide by fission, like bacteria. A cell can't make a mitochondrion from scratch; new ones only come from existing ones.
• Their genes are bacterial. Comparing DNA sequences places mitochondrial genes among the alpha-proteobacteria and chloroplast genes among the cyanobacteria.

Key terms

Compartmentalisation

Dividing the cell into membrane-bound spaces so that different reactions and conditions can be kept separate.

Endomembrane system

The linked membranes of the nuclear envelope, ER, Golgi, lysosomes, vesicles and plasma membrane.

Rough ER / smooth ER

ER with ribosomes that makes and folds proteins / ER without ribosomes that makes lipids, detoxifies and stores Ca²⁺.

Golgi apparatus

Stacked membrane sacs that modify, sort and package proteins; it receives from the ER at its cis face and ships from its trans face.

Signal peptide

A short sequence at the start of a protein that directs the ribosome to the ER.

Vesicle

A small membrane bubble that carries material between compartments or to the plasma membrane.

Lysosome

An acidic, membrane-bound sac of digestive enzymes.

Endosymbiosis

The theory that mitochondria and chloroplasts descend from bacteria that once lived inside a host cell.

Check yourself

Try answering in your head before you open each answer.

• 1.A mutation deletes the signal peptide from the gene for insulin, a secreted hormone. Where would the mutant protein end up, and would it be released from the cell?Show answerHide

  Without a signal peptide, SRP never recognises it, so the ribosome stays free and finishes the protein in the cytosol. It never enters the ER, Golgi or secretory vesicles, so it isn't released.

• 2.A lysosome springs a small leak into the cytosol. Why doesn't this usually digest the cell from the inside?Show answerHide

  Lysosomal enzymes work best at about pH 4.5–5. The cytosol is about pH 7.2, where they're much less active. The acid compartment is what makes them dangerous; outside it they're mostly switched off. (A massive rupture can still harm the cell.)

• 3.An antibiotic blocks bacterial-type ribosomes but not the eukaryotic cytosolic ones. In a plant cell, which organelles would you expect to be affected, and why?Show answerHide

  Chloroplasts and mitochondria, because they have their own ribosomes built on the bacterial pattern, a leftover of their endosymbiotic origin. You'd predict they'd struggle to make the proteins their own genomes encode, while proteins made by cytosolic ribosomes would be unaffected. (How strongly a given drug hits organelle ribosomes varies, since they aren't identical to bacterial ones.)