Origins of Cell Compartmentalization: Study Guide (Biology 2.10)

Two ways to organize a cell

All cells share a plasma membrane, cytoplasm, ribosomes and DNA. Beyond that, life uses two broad designs. Prokaryotic cells (bacteria and archaea) are usually small and have few or no internal membranes. Eukaryotic cells (protists, fungi, plants and animals) are usually much larger and are packed with membrane-bound organelles. This topic asks two questions. How do the two designs divide up a cell’s work? And where did the organelles of eukaryotes come from?

Inside a prokaryotic cell

Prokaryotes typically lack membrane-bound organelles. Their insides are still not a uniform soup. Different regions have different structures and jobs.

• Nucleoid. The main DNA molecule, usually one circular chromosome, is gathered in one region of the cytoplasm. No membrane surrounds it.
• Ribosomes. Prokaryotic ribosomes are smaller than the ribosomes in the cytosol of a eukaryotic cell, but they do the same job: they make proteins.
• The plasma membrane as a work surface. A prokaryote has no mitochondria, so the proteins that make ATP during aerobic respiration sit in its plasma membrane. The membrane does the job of the mitochondrial inner membrane.
• Specialized internal structures. Cyanobacteria (photosynthetic bacteria) have internal thylakoid membranes where the light-capturing reactions happen. Some bacteria also have carboxysomes: compartments bounded by a protein shell, not a membrane, that hold the carbon-fixing enzyme rubisco. These are exceptions and special cases, which is why the rule says prokaryotes typically lack internal membranes.

Because prokaryotes are small, their large surface area relative to volume lets the plasma membrane serve the whole cell. A large eukaryotic cell could not rely on its plasma membrane alone.

Inside a eukaryotic cell

Eukaryotic cells keep a whole system of internal membranes that partition the cell into regions, each specialized for particular jobs: the nucleus, the ER, the Golgi complex, vesicles, lysosomes and vacuoles, plus mitochondria and, in plants and algae, chloroplasts. As you saw in Topic 2.9, these membranes keep competing reactions apart and add surface area for membrane-bound reactions.

Feature	Prokaryotic cell	Eukaryotic cell
Plasma membrane	yes	yes
Ribosomes	yes, smaller type	yes, larger type in the cytosol; smaller type inside mitochondria and chloroplasts
Where the main DNA is	nucleoid region, no membrane	nucleus, inside a double nuclear envelope
Membrane-bound organelles	typically none	many
Where ATP is made by aerobic respiration	plasma membrane	inner membrane of mitochondria
Where light is captured (if photosynthetic)	plasma membrane or internal thylakoids (cyanobacteria)	thylakoid membranes inside chloroplasts
Specialized internal regions	yes (nucleoid, ribosomes, protein-shelled compartments in some)	yes, mostly bounded by membranes

Similarities: both have a plasma membrane, ribosomes, DNA and specialized regions with specialized jobs. Differences: eukaryotes partition the cell with internal membranes and membrane-bound organelles; prokaryotes typically do not.

Endosymbiosis: where mitochondria and chloroplasts came from

Endosymbiosis means one organism living inside the cell or body of another. In the case of these organelles, the partnership came to benefit both sides. The endosymbiotic theory states that mitochondria and chloroplasts evolved from prokaryotes that were once free-living. The American biologist Lynn Margulis set out the microbiological evidence for it in a 1967 paper, building on older ideas.

The sequence explains a pattern you can see today. Almost all eukaryotes have mitochondria (or reduced remnants of them), but only plants, algae and a few other protists have chloroplasts. That fits mitochondria being acquired first, by the common ancestor of eukaryotes, and chloroplasts later, by one lineage that already had mitochondria. The partnership helped both sides: the host gained a very efficient way to make ATP (and later to capture light), and the guest gained a protected, food-rich home.

The evidence

A strong claim rests on several independent lines of evidence. Each one below would be hard to explain if mitochondria and chloroplasts had formed from the host’s own membranes.

Observation about mitochondria and chloroplasts	Why it supports endosymbiosis
They have two membranes.	Fits a prokaryote (inner membrane) enclosed in a membrane from the host when it was taken in (outer membrane).
They contain their own DNA, usually a small circular molecule, as bacteria do.	Free-living prokaryotes carry their own circular chromosome. Human mitochondrial DNA has 16,569 base pairs and 37 genes.
They have their own ribosomes, which are more like bacterial ribosomes than like those in the eukaryotic cytosol.	Leftover protein-making machinery from the ancestor. Some antibiotics that act on bacterial ribosomes also slow protein synthesis inside mitochondria.
New ones form only by splitting existing ones, in a way that resembles bacterial binary fission.	A cell cannot build a mitochondrion from scratch; it must inherit one, as you would expect from a former organism.
Their DNA sequences are most similar to those of particular bacterial groups: mitochondria to a group called alphaproteobacteria, chloroplasts to cyanobacteria.	Sequence similarity shows shared ancestry, and it points to a specific ancestor for each organelle.
Their inner membrane has proteins and enzymes similar to those in bacterial plasma membranes.	The inner membrane is the descendant of the ancestor’s plasma membrane.

Since then: dependence. Over a very long time, most of the guest’s genes moved to the host’s nucleus or were lost. Human mitochondrial DNA now codes for just 13 proteins (its other genes code for RNA). Hundreds of the proteins a mitochondrion needs are coded in the nucleus, made in the cytosol and imported. That is why modern mitochondria and chloroplasts cannot live outside a cell, even though their ancestors did.

What about the other internal membranes? (Background.) The ER, the Golgi complex and the nuclear envelope do not show the set of evidence in the table: none has a small, separate genome of its own or bacteria-like ribosomes inside. A widely used hypothesis is that they formed from inward folds of an ancestral cell’s plasma membrane that later pinched off. Notice how the same kinds of evidence let you tell the two origins apart. That is the skill this topic tests: using evidence to support, or reject, a claim about where a structure came from.

Worked example 1: using sequence data to identify an ancestor

Question. A scientist compares the sequence of a ribosomal RNA gene from the mitochondria of a fictional fungus with three other sequences, over 1,450 aligned positions. The data are fictional.

Compared with	Identical positions
a free-living alphaproteobacterium	1,073
a free-living cyanobacterium	841
the fungus’s own cytosolic ribosomal RNA gene (in the nucleus)	667

(a) Calculate the percentage identity for each comparison. (b) Use the data to support a claim about the origin of the fungus’s mitochondria.

(a) Percentage identity = identical positions ÷ positions compared × 100.

1. Alphaproteobacterium: 1,073 ÷ 1,450 × 100 = 74.0%.
2. Cyanobacterium: 841 ÷ 1,450 × 100 = 58.0%.
3. The fungus’s own nuclear gene: 667 ÷ 1,450 × 100 = 46.0%.

(b) Claim, evidence, reasoning.

• Claim: the fungus’s mitochondria descend from an alphaproteobacterium-like prokaryote.
• Evidence: the mitochondrial gene matches the alphaproteobacterium at 74.0% of positions, more than the cyanobacterium (58.0%) and much more than the fungus’s own nuclear gene (46.0%).
• Reasoning: sequences change slowly over generations, so the more similar two sequences are, the more recently they shared an ancestor. If mitochondria had formed from the host cell’s own parts, their genes should be most like the host’s nuclear genes. They are least like them.

Check the limits. One gene is not enough. Biologists compare many genes from many species. Also note the comparison is with a modern bacterium, a distant cousin of the true ancestor, not the ancestor itself.

Worked example 2: an antibiotic experiment

Question. Animal cells are grown in three dishes with an amino acid that carries a radioactive label. New proteins pick up the label, so the radioactivity (in counts per minute) measures protein synthesis. Mitochondria are separated from the rest of the cell, and each part is measured. Drug K blocks bacterial ribosomes; drug C blocks the ribosomes of the eukaryotic cytosol. The data are fictional.

Treatment	Mitochondria / counts per minute	Rest of cell / counts per minute
No drug (control)	4,800	52,000
Drug K	390	50,400
Drug C	4,650	2,100

(a) For each drug, calculate the percentage of control protein synthesis that remains in each part of the cell. (b) Explain how the results support the endosymbiotic theory.

(a) Percentage remaining = treated ÷ control × 100.

1. Drug K, mitochondria: 390 ÷ 4,800 × 100 = 8.1% (so 91.9% inhibited).
2. Drug K, rest of cell: 50,400 ÷ 52,000 × 100 = 96.9%.
3. Drug C, mitochondria: 4,650 ÷ 4,800 × 100 = 96.9%.
4. Drug C, rest of cell: 2,100 ÷ 52,000 × 100 = 4.0%.

(b) The two drugs give a mirror-image pattern. The drug that blocks bacterial ribosomes almost stops protein synthesis inside mitochondria but barely affects the rest of the cell. The drug that blocks cytosolic ribosomes does the reverse. So mitochondrial ribosomes behave like bacterial ribosomes, not like the cell’s own cytosolic ones. That is what the theory predicts if mitochondria descend from bacteria and kept their own protein-making machinery.

Why both drugs matter. With drug K alone, someone could argue that it simply damages mitochondria in some general way. Drug C shows the mitochondria can still make protein when only cytosolic ribosomes are blocked. Each drug acts as a control for the other.

Biological consequence. This is why some antibiotics that target bacterial ribosomes can have side effects on human cells: they can slow protein synthesis in mitochondria too.

Common misconceptions

• “Prokaryotes have nothing inside them.” They lack membrane-bound organelles, but they have a nucleoid, ribosomes and, in some species, internal membranes or protein-shelled compartments.
• “Prokaryotes cannot respire aerobically because they have no mitochondria.” Many do. The proteins sit in their plasma membrane instead.
• “Mitochondria today are bacteria living in our cells.” They descend from bacteria but have lost most of their genes and cannot live on their own.
• “Plants have chloroplasts instead of mitochondria.” Plants have both. Chloroplasts were added to cells that already had mitochondria.
• “The double membrane alone proves endosymbiosis.” No single observation proves it. The theory is strongly supported because several independent lines of evidence agree.
• “A higher percentage identity means the organisms are the same.” It means a more recent shared ancestor, not identity.

Where this leads

Mitochondria and chloroplasts return in Unit 3, where you will follow cellular respiration and photosynthesis across their membranes. The next topic is Enzymes. First, test yourself with the practice questions, then use the revision notes and the checklist.