11  Mitochondrial and Organelle Genomes

11.1 Genomes Within Genomes

11.1.1 A Surprising Discovery

Here’s something amazing: You don’t just have ONE genome! You actually have multiple genomes inside your cells!

Your genomes:

  1. Nuclear genome - In the nucleus (the main one we’ve been talking about)

  2. Mitochondrial genome - In mitochondria (tiny power plants)

  3. Chloroplast genome - In chloroplasts (if you’re a plant—sorry, you’re not! 🌱)

Think of it like:

  • Your cell is a factory

  • The factory has a main office with blueprints (nuclear genome)

  • But the power plant and solar panels have their own instruction manuals too!

11.2 The Endosymbiotic Theory

11.2.1 How Did This Happen?

Why do mitochondria have their own DNA? The answer is one of biology’s coolest stories!

11.2.2 The Big Idea

The endosymbiotic theory explains that:

  • Billions of years ago, one cell swallowed another cell

  • Instead of digesting it, they formed a partnership

  • The swallowed cell became mitochondria (and chloroplasts in plants)

  • This partnership was so successful that it became permanent!

“Endosymbiotic” means:

  • Endo = inside

  • Symbiotic = living together (mutually beneficial)

  • So: “living together inside”

11.2.3 The Story: How It Probably Happened

About 2 billion years ago:

  1. A big cell (early eukaryote) is swimming around

  2. A small bacterium (that’s good at making energy) is nearby

  3. The big cell engulfs the bacterium (like eating it)

  4. But doesn’t digest it! (Maybe it couldn’t, or maybe the bacterium was protected)

  5. The bacterium survives inside and keeps making energy

  6. Win-win situation:

    • Bacterium gets protection and food

    • Big cell gets lots of energy (ATP)

  7. They become dependent on each other

  8. Over millions of years, the bacterium becomes mitochondria!

Think of it like:

  • You hire a chef to live in your house

  • They make all your meals

  • Eventually, they become part of the family

  • Now you can’t imagine life without them!

11.2.4 Evidence for Endosymbiotic Theory

How do we know this actually happened? Lots of evidence!

1. Mitochondria have their own DNA

  • Separate from nuclear DNA

  • More similar to bacterial DNA than eukaryotic DNA

  • Circular, like bacterial chromosomes!

2. Mitochondria have double membranes

  • Inner membrane: From the original bacterium

  • Outer membrane: From when it was engulfed

  • Like a bag inside a bag!

3. Mitochondria are the same size as bacteria

  • About 1-2 micrometers

  • Perfect size match!

4. Mitochondria divide independently

  • They reproduce by splitting (binary fission)

  • Just like bacteria!

  • Not controlled by the nucleus

5. Mitochondrial ribosomes are like bacterial ribosomes

  • Different from cytoplasmic ribosomes

  • Similar size and structure to bacterial ribosomes

6. Some antibiotics affect mitochondria

  • Antibiotics that target bacteria also affect mitochondria

  • Because mitochondria are basically modified bacteria!

7. DNA comparisons show mitochondria are related to specific bacteria

  • Most closely related to alpha-proteobacteria

  • Like finding a long-lost cousin!

11.2.5 Who Discovered This?

Lynn Margulis (1938-2011):

  • Proposed the endosymbiotic theory in 1967

  • Most scientists didn’t believe her at first!

  • Kept collecting evidence

  • Eventually proved she was right

  • Now her theory is accepted by all scientists

Her story teaches us: Good science and persistence can change our understanding of life!

11.3 The Human Mitochondrial Genome

11.3.1 Basic Facts

Size: Only about 16,500 base pairs

  • Compare to nuclear genome: 3.2 billion base pairs

  • That’s 200,000 times smaller!

Shape: Circular (like bacteria!)

  • Nuclear DNA: Linear chromosomes

  • Mitochondrial DNA: One circular chromosome

Location: Inside mitochondria (in the cytoplasm, outside the nucleus)

How many copies:

  • Each mitochondrion has 2-10 copies of its genome

  • Each cell has hundreds to thousands of mitochondria

  • So each cell has thousands of copies of the mitochondrial genome!

Think of it like:

  • Nuclear genome: One master copy in a safe

  • Mitochondrial genome: Thousands of backup copies everywhere!

11.3.2 Organization

The mitochondrial genome is VERY compact:

  • 37 genes total (compared to ~20,000 nuclear genes)

  • No introns (like bacterial genes!)

  • Very little non-coding DNA (super efficient)

  • Some genes overlap! (to save space)

It’s like a perfectly optimized, minimalist instruction manual!

11.3.3 What Genes Does It Have?

The 37 mitochondrial genes include:

13 genes for proteins:

  • All involved in making energy (ATP)

  • Part of the electron transport chain

  • Essential for cellular respiration

22 genes for tRNAs:

  • Transfer RNAs needed for making proteins inside mitochondria

2 genes for rRNAs:

  • Ribosomal RNAs needed for mitochondrial ribosomes

That’s it! Only 37 genes!

11.3.4 What Happened to the Other Genes?

Mitochondria used to be bacteria with thousands of genes. Where did they go?

Three fates:

  1. Moved to the nucleus (most genes)

    • Over time, genes transferred from mitochondria to nucleus

    • Now encoded in nuclear DNA

    • Proteins made in cytoplasm, then imported to mitochondria

  2. Lost completely (genes no longer needed)

    • Living inside a cell, mitochondria didn’t need some genes anymore

    • Like getting rid of camping gear when you move into a house

  3. Stayed in mitochondria (essential genes)

    • The 37 genes that are still there

    • Probably stayed because they’re needed immediately in mitochondria

Think of it like:

  • A company outsourcing most tasks to headquarters (nucleus)

  • Keeping only the most essential operations in-house (mitochondria)

11.4 Inheritance of Mitochondrial DNA

11.4.1 You Got It From Your Mom!

Here’s something special: You inherit mitochondrial DNA only from your mother!

Why?

  • Egg cells have lots of mitochondria (thousands!)

  • Sperm cells have very few mitochondria (in the tail)

  • When sperm fertilizes egg, usually only the sperm nucleus enters

  • Even if some sperm mitochondria enter, they’re quickly destroyed

  • So all your mitochondria come from the egg (mom)!

Think of it like:

  • Mom provides the house and all the furniture (mitochondria)

  • Dad just brings his suitcase (nucleus)

11.4.2 Implications

Maternal inheritance means:

  • You share mitochondrial DNA with your mom, her mom, her mom’s mom, etc.

  • All the way back through your maternal line

  • Your siblings have the same mitochondrial DNA

  • But your dad’s mitochondrial DNA wasn’t passed to you

Uses:

  • Tracing maternal ancestry: Tracking maternal lineages through history

  • “Mitochondrial Eve”: The most recent common maternal ancestor of all humans (~150,000 years ago)

  • Family relationships: Confirming maternal relatives

11.5 Functions of Mitochondrial DNA Genes

11.5.1 Why Are These Genes So Important?

The 13 protein-coding genes in mitochondrial DNA are all involved in one crucial process: Making ATP (cellular energy)!

11.5.2 The Electron Transport Chain

Mitochondria make ATP using a complex of proteins called the electron transport chain.

Think of it like:

  • A series of machines in a factory

  • Passing electrons from one to the next

  • Using the energy to make ATP (cellular energy)

The 13 mitochondrial genes encode:

  • 7 subunits of Complex I

  • 1 subunit of Complex III

  • 3 subunits of Complex IV

  • 2 subunits of Complex V (ATP synthase)

But wait! The electron transport chain has many more proteins than 13!

The rest come from nuclear genes:

  • Made in the cytoplasm

  • Imported into mitochondria

  • Assembled with the mitochondrial-encoded proteins

It’s a team effort! Nuclear and mitochondrial genomes work together!

11.5.3 Why Keep Genes in Mitochondria?

Scientists wondered: Why keep any genes in mitochondria? Why not move them all to the nucleus?

Possible reasons:

  1. Rapid response: Genes in mitochondria can respond quickly to energy needs

  2. High expression needed: These genes need to be made in huge amounts

  3. Hydrophobic proteins: Some proteins are too “water-hating” to cross membranes easily

  4. Gene regulation: Keeping them local allows better control

  5. Redox regulation: Some proteins need to be made near reactive oxygen species

11.6 Mitochondrial Diseases

11.6.1 When Mitochondrial DNA Goes Wrong

Mutations in mitochondrial DNA can cause diseases:

Characteristics of mitochondrial diseases:

  • Affect high-energy organs most (brain, muscle, heart)

  • Maternal inheritance (passed from mom)

  • Variable severity (depends on ratio of mutant to normal mitochondria)

  • Can appear at any age

Examples:

  • MELAS: Stroke-like episodes, seizures

  • LHON: Vision loss

  • Leigh syndrome: Neurological problems

Why variable severity?

  • Cells have thousands of mitochondria

  • Some might have mutant DNA, some normal DNA

  • Ratio determines severity

  • Different tissues can have different ratios!

This is called heteroplasmy (mixed population of mitochondrial DNA).

11.7 Chloroplasts: The Plant Power Source

11.7.1 Photosynthesis Factories

Plants (and algae) have another type of organelle with its own genome: chloroplasts!

Chloroplasts:

  • Make food using sunlight (photosynthesis)

  • Contain chlorophyll (green pigment)

  • Also originated from endosymbiosis!

  • Captured from cyanobacteria (photosynthetic bacteria)

11.7.2 Chloroplast Genome

Size: About 120,000-200,000 base pairs

  • Larger than mitochondrial genome

  • But still much smaller than nuclear genome

Genes: About 100-120 genes

  • Photosynthesis genes

  • Some ribosomal and transfer RNA genes

  • Similar to cyanobacteria genes

Also circular like mitochondrial DNA and bacteria!

11.7.3 Double Endosymbiosis?

Plants actually had TWO endosymbiotic events:

  1. First: Acquired mitochondria (like all eukaryotes)

  2. Second: Acquired chloroplasts (only in plants and algae)

Some organisms even had a third endosymbiotic event (capturing algae that already had chloroplasts)!

It’s endosymbiosis all the way down! 🌀

11.8 Key Takeaways

  • Mitochondria and chloroplasts have their own genomes (separate from nuclear genome)

  • Endosymbiotic theory: These organelles were once free-living bacteria

    • Engulfed by early eukaryotic cells

    • Formed permanent beneficial partnerships

  • Evidence: Double membranes, circular DNA, bacterial-like ribosomes, independent division

  • Lynn Margulis proposed and proved the endosymbiotic theory

  • Human mitochondrial genome:

    • 16,500 base pairs (very small)

    • Circular (like bacteria)

    • 37 genes (13 protein-coding, 22 tRNA, 2 rRNA)

    • All protein genes involved in energy production

  • Maternal inheritance: Mitochondrial DNA comes only from your mother

  • Mitochondrial genes encode parts of the electron transport chain

  • Most original genes either moved to nucleus or were lost

  • Mutations in mitochondrial DNA can cause diseases

  • Chloroplasts (in plants) also have their own genome from a second endosymbiotic event

Sources: Information adapted from Nature Scitable (Origin of Mitochondria), Ask A Biologist (Endosymbiotic Theory), university cell biology textbooks, and mitochondrial genomics research.