8  Prokaryotic vs Eukaryotic Genomes

8.1 Two Fundamentally Different Cell Types

8.1.1 The Great Divide in Life

All life on Earth falls into two main categories based on cell structure:

  1. Prokaryotes - Simple cells WITHOUT a nucleus

  2. Eukaryotes - Complex cells WITH a nucleus

Think of it like:

  • Prokaryotes = Studio apartment (everything in one room)

  • Eukaryotes = House with many rooms (compartments for different activities)

8.1.2 Who Are the Prokaryotes?

Prokaryotes include:

  • 🦠 Bacteria (like E. coli, strep throat bacteria)

  • 🌡️ Archaea (extremophiles that live in hot springs, salt lakes, etc.)

Prokaryotes are:

  • Usually single-celled

  • Very small (0.1-5 micrometers)

  • Found everywhere on Earth

  • The first life forms (existed 3.5 billion years ago!)

8.1.3 Who Are the Eukaryotes?

Eukaryotes include:

  • 🧍 Animals (including you!)

  • 🌳 Plants

  • 🍄 Fungi (mushrooms, yeast)

  • 🦠 Protists (amoebas, algae)

Eukaryotes are:

  • Can be single-celled or multicellular

  • Larger (10-100 micrometers)

  • More complex

  • Evolved about 2 billion years ago

8.2 Chromosome Organization

8.2.1 Prokaryotic Chromosome Organization

The Nucleoid:

  • Prokaryotes don’t have a nucleus!

  • Their DNA floats in a region called the nucleoid

  • “Nucleoid” means “nucleus-like” but it’s NOT a true nucleus

  • No membrane surrounds the DNA

  • It’s like having your valuables in a pile instead of in a safe

Shape:

  • Usually ONE circular chromosome

  • Shaped like a loop or ring

  • Much smaller than eukaryotic chromosomes

  • Some bacteria also have small extra DNA circles called plasmids

Organization:

  • DNA is compact but not as organized as eukaryotic DNA

  • Uses special proteins to help fold and organize DNA

  • Like a loose coil of rope

8.2.2 Eukaryotic Chromosome Organization

The Nucleus:

  • Eukaryotes have a true nucleus

  • Membrane surrounds and protects the DNA

  • Like keeping valuables in a locked safe

  • Keeps DNA separate from the rest of the cell

Shape:

  • MULTIPLE linear chromosomes

  • Shaped like straight lines (not circles!)

  • Humans have 46 chromosomes

  • Organized in pairs

Organization:

  • Highly organized and compact

  • DNA wraps around special proteins called histones

  • Forms structures called nucleosomes (we’ll discuss this more in the next chapter!)

  • Like a well-organized library with labeled shelves

8.3 Histones vs. Histone-Like Proteins

8.3.1 What Are Histones?

Histones are special proteins that help organize DNA in eukaryotes.

Think of histones like:

  • 🎁 Spools that DNA wraps around

  • 📦 Packaging materials that keep DNA organized

  • 🏗️ Scaffolding that gives structure

Key facts:

  • DNA wraps around histones like thread on a spool

  • This helps compact 2 meters of DNA into a tiny nucleus!

  • Histones also help control which genes are turned on or off

  • Very ancient proteins (barely changed over millions of years)

8.3.2 Histone-Like Proteins in Prokaryotes

Prokaryotes don’t have true histones (with a few exceptions).

Instead, they have histone-like proteins:

  • Similar job (organizing DNA)

  • Different structure

  • Not as sophisticated as true histones

  • Like having a simple organizer instead of a fancy filing system

Examples:

  • HU proteins

  • IHF proteins

  • H-NS proteins

These proteins help:

  • Compact the DNA

  • Organize the nucleoid

  • Regulate some genes

8.4 Gene Structure Differences

8.4.1 Prokaryotic Genes Are Simple

Prokaryotic gene structure:

  • Genes are continuous (no interruptions)

  • DNA sequence goes straight from start to finish

  • Like reading a sentence without any gaps: “Thecatsat”

No introns:

  • The entire gene codes for protein

  • No extra stuff to remove

  • Simple and efficient!

8.4.2 Eukaryotic Genes Are Complex

Eukaryotic gene structure:

  • Genes are split up into pieces

  • Have introns (removed) and exons (kept)

  • Like a sentence with gaps: “The … cat … sat”

Introns and Exons:

  • Exons = EXpressed regions (kept in final mRNA, used to make protein)

  • Introns = INTervening regions (removed, not used)

Why have introns?

  • Allows alternative splicing (making different proteins from one gene)

  • Provides flexibility

  • Allows evolution to create new genes

Think of it like:

  • Having extra footage when making a movie

  • You can edit it different ways to make different versions!

8.4.3 Complete Eukaryotic Gene Structure

A complete eukaryotic gene has much more than just exons and introns!

8.4.3.1 The Full Picture

[Promoter]--[5'UTR]-[Exon1]-[Intron1]-[Exon2]-[Intron2]-[Exon3]--[3'UTR]-[Poly-A signal]
     ↑                ↑                                      ↑           ↑
   Start          Start                                  Stop      Transcription
Transcription   Translation                           Translation      Stop

```

Key components:

1. Promoter (Upstream):

  • Located before the gene (upstream)

  • Binding site for RNA polymerase

  • Position and orientation dependent (must be in right place and direction!)

  • Contains elements like TATA box, CAAT box

  • Without promoter = no transcription!

2. 5’ UTR (5’ Untranslated Region):

  • Part of mRNA but NOT translated into protein

  • Between transcription start site and translation start (ATG)

  • Contains regulatory sequences

  • Affects mRNA stability and translation efficiency

  • Called “5 prime UTR” because it’s at the 5’ end

3. Exons (we covered these):

  • Coding sequences

  • First and last exons are always present

  • Internal exons may be alternatively spliced

  • Important: First exon and last exon also contain UTR sequences!

4. Introns (we covered these):

  • Non-coding sequences

  • Removed during RNA splicing

  • Contain splice sites at boundaries

5. 3’ UTR (3’ Untranslated Region):

  • Part of mRNA but NOT translated into protein

  • Between stop codon and poly-A tail

  • Contains regulatory sequences

  • microRNA binding sites often here

  • Affects mRNA stability and localization

  • Called “3 prime UTR” because it’s at the 3’ end

6. Poly-A Signal:

  • Short sequence (like AAUAAA in RNA)

  • Signals where to add poly-A tail

  • Usually 10-30 nucleotides before poly-A tail

  • Essential for mRNA stability!

Common Student Mistake: Many students draw incomplete ORFs (Open Reading Frames) by forgetting that:

  • ORF starts at START codon (ATG) in first exon

  • ORF ends at STOP codon in last exon

  • ORF can be interrupted by introns

  • UTRs are NOT part of the ORF!

8.4.4 Open Reading Frames (ORFs)

What’s an ORF?

  • A stretch of DNA that could code for a protein

  • Starts with a START codon (ATG)

  • Ends with a STOP codon (TAA, TAG, or TGA)

  • No STOP codons in the middle

Why it matters:

  • Scientists look for ORFs to find potential genes

  • Like looking for sentences that start with a capital letter and end with a period

In prokaryotes:

  • ORFs are usually complete genes

  • Easy to identify genes

In eukaryotes:

  • ORFs can be interrupted by introns

  • Harder to identify complete genes

8.5 mRNA Differences

8.5.1 Polycistronic mRNA (Prokaryotes)

Polycistronic = One mRNA codes for MULTIPLE proteins

Think of it like:

  • One ticket gets you into multiple movies

  • One message contains multiple instructions

How it works:

  • Multiple genes are transcribed together

  • One long mRNA molecule

  • Multiple START and STOP codons

  • Makes several different proteins from one mRNA

  • Very efficient!

Example: The lac operon in bacteria makes one mRNA that codes for 3 different proteins!

8.5.2 Monocistronic mRNA (Eukaryotes)

Monocistronic = One mRNA codes for ONE protein

Think of it like:

  • One ticket for one movie

  • One message contains one instruction

How it works:

  • Each gene is transcribed separately

  • One mRNA molecule per gene

  • One protein made per mRNA

  • More control, but less efficient

Why different?

  • Eukaryotes have more complex regulation needs

  • Allows independent control of each gene

  • More flexible but requires more energy

8.6 Operons and Gene Regulation

8.6.1 What Is an Operon?

An operon is a group of genes controlled together (found mainly in prokaryotes).

Think of an operon like:

  • 🎼 A orchestra playing together (all start and stop together)

  • 📦 A bundle of products (controlled as one package)

  • 🚦 Multiple traffic lights synchronized

8.6.2 The Famous Lac Operon

The lac operon in E. coli bacteria is the most famous example!

The Setup:

  • E. coli bacteria can eat lactose (milk sugar)

  • But making lactose-digesting proteins is expensive (uses energy)

  • So bacteria only make these proteins when lactose is present

The Genes: The lac operon has 3 genes that work together:

  • lacZ - Makes an enzyme that breaks apart lactose

  • lacY - Makes a protein that brings lactose into the cell

  • lacA - Makes an enzyme that modifies lactose

How It Works:

When there’s NO lactose:

  1. A repressor protein sits on the operator (like a lock)

  2. RNA polymerase can’t read the genes

  3. No proteins are made

  4. Saves energy!

When lactose IS present:

  1. Lactose binds to the repressor protein

  2. Repressor falls off the operator (lock opens!)

  3. RNA polymerase can now read the genes

  4. Proteins are made

  5. Bacteria can eat lactose!

Think of it like:

  • A vending machine that only turns on when you insert money

  • No point wasting electricity when nobody’s using it!

8.6.3 Why Operons Are Efficient

Advantages for prokaryotes:

  • Coordinate related genes (turn on/off together)

  • Save energy (don’t make proteins you don’t need)

  • Quick response to environmental changes

  • Simple control system

Why eukaryotes don’t use operons much:

  • Eukaryotes have more complex needs

  • Need independent control of genes

  • Have more sophisticated regulation systems

  • Can afford to be less efficient (more resources available)

8.7 Summary of Key Differences

Feature Prokaryotes Eukaryotes
Nucleus No nucleus (nucleoid) True nucleus with membrane
Chromosomes 1 circular chromosome Multiple linear chromosomes
DNA packaging Histone-like proteins True histones
Gene structure Continuous (no introns) Split (introns + exons)
mRNA type Polycistronic (multiple proteins) Monocistronic (one protein)
Gene organization Often in operons Rarely in operons
Size Small (0.1-5 μm) Large (10-100 μm)
Gene regulation Simple (operons) Complex (multiple levels)

8.8 Why These Differences Matter

8.8.1 Different Lifestyles

Prokaryotes:

  • Need to respond quickly to environment

  • Limited resources

  • Simple, efficient gene regulation

  • Like a small, agile speedboat

Eukaryotes:

  • More complex needs

  • Can afford sophisticated regulation

  • More flexible gene expression

  • Like a large ship with many specialized compartments

8.8.2 Evolution

These differences show:

  • Prokaryotes evolved first (simpler design)

  • Eukaryotes evolved from prokaryotes (more complex design)

  • Both strategies are successful (bacteria are everywhere!)

  • Complexity isn’t always better (bacteria thrive with simplicity)

8.8.3 Applications

Understanding these differences helps us:

  • Make medicines: Antibiotics target prokaryotic features

  • Genetic engineering: Use bacteria to make proteins (insulin, vaccines)

  • Understand diseases: Know how bacteria work differently from human cells

  • Study evolution: See how complex life evolved from simple life

8.9 Key Takeaways

  • Prokaryotes = Simple cells without nucleus (bacteria, archaea)

  • Eukaryotes = Complex cells with nucleus (animals, plants, fungi)

  • Nucleoid vs. Nucleus: Prokaryotes have DNA in nucleoid; eukaryotes in nucleus

  • Circular vs. Linear: Prokaryote chromosomes are circular; eukaryote chromosomes are linear

  • Histone-like vs. Histones: Both organize DNA, but histones (eukaryotes) are more sophisticated

  • Continuous vs. Split genes: Prokaryotic genes have no introns; eukaryotic genes have introns and exons

  • Polycistronic vs. Monocistronic: Prokaryotic mRNA codes for multiple proteins; eukaryotic for one

  • Operons: Groups of genes controlled together (mainly in prokaryotes)

  • Lac operon: Classic example of gene regulation in bacteria

  • These differences reflect different evolutionary strategies and lifestyles

Sources: Information adapted from Khan Academy Biology, Nature Scitable, Biology LibreTexts (Comparing Prokaryotic and Eukaryotic Cells), and molecular biology textbooks.

Key components:

1. Promoter (Upstream):

  • Located before the gene (upstream)

  • Binding site for RNA polymerase

  • Position and orientation dependent (must be in right place and direction!)

  • Contains elements like TATA box, CAAT box

  • Without promoter = no transcription!

2. 5’ UTR (5’ Untranslated Region):

  • Part of mRNA but NOT translated into protein

  • Between transcription start site and translation start (ATG)

  • Contains regulatory sequences

  • Affects mRNA stability and translation efficiency

  • Called “5 prime UTR” because it’s at the 5’ end

3. Exons (we covered these):

  • Coding sequences

  • First and last exons are always present

  • Internal exons may be alternatively spliced

  • Important: First exon and last exon also contain UTR sequences!

4. Introns (we covered these):

  • Non-coding sequences

  • Removed during RNA splicing

  • Contain splice sites at boundaries

5. 3’ UTR (3’ Untranslated Region):

  • Part of mRNA but NOT translated into protein

  • Between stop codon and poly-A tail

  • Contains regulatory sequences

  • microRNA binding sites often here

  • Affects mRNA stability and localization

  • Called “3 prime UTR” because it’s at the 3’ end

6. Poly-A Signal:

  • Short sequence (like AAUAAA in RNA)

  • Signals where to add poly-A tail

  • Usually 10-30 nucleotides before poly-A tail

  • Essential for mRNA stability!

Common Student Mistake: Many students draw incomplete ORFs (Open Reading Frames) by forgetting that:

  • ORF starts at START codon (ATG) in first exon

  • ORF ends at STOP codon in last exon

  • ORF can be interrupted by introns

  • UTRs are NOT part of the ORF!

8.9.1 Open Reading Frames (ORFs)

What’s an ORF?

  • A stretch of DNA that could code for a protein

  • Starts with a START codon (ATG)

  • Ends with a STOP codon (TAA, TAG, or TGA)

  • No STOP codons in the middle

Why it matters:

  • Scientists look for ORFs to find potential genes

  • Like looking for sentences that start with a capital letter and end with a period

In prokaryotes:

  • ORFs are usually complete genes

  • Easy to identify genes

In eukaryotes:

  • ORFs can be interrupted by introns

  • Harder to identify complete genes

8.10 mRNA Differences

8.10.1 Polycistronic mRNA (Prokaryotes)

Polycistronic = One mRNA codes for MULTIPLE proteins

Think of it like:

  • One ticket gets you into multiple movies

  • One message contains multiple instructions

How it works:

  • Multiple genes are transcribed together

  • One long mRNA molecule

  • Multiple START and STOP codons

  • Makes several different proteins from one mRNA

  • Very efficient!

Example: The lac operon in bacteria makes one mRNA that codes for 3 different proteins!

8.10.2 Monocistronic mRNA (Eukaryotes)

Monocistronic = One mRNA codes for ONE protein

Think of it like:

  • One ticket for one movie

  • One message contains one instruction

How it works:

  • Each gene is transcribed separately

  • One mRNA molecule per gene

  • One protein made per mRNA

  • More control, but less efficient

Why different?

  • Eukaryotes have more complex regulation needs

  • Allows independent control of each gene

  • More flexible but requires more energy

8.11 Operons and Gene Regulation

8.11.1 What Is an Operon?

An operon is a group of genes controlled together (found mainly in prokaryotes).

Think of an operon like:

  • 🎼 A orchestra playing together (all start and stop together)

  • 📦 A bundle of products (controlled as one package)

  • 🚦 Multiple traffic lights synchronized

8.11.2 The Famous Lac Operon

The lac operon in E. coli bacteria is the most famous example!

The Setup:

  • E. coli bacteria can eat lactose (milk sugar)

  • But making lactose-digesting proteins is expensive (uses energy)

  • So bacteria only make these proteins when lactose is present

The Genes: The lac operon has 3 genes that work together:

  • lacZ - Makes an enzyme that breaks apart lactose

  • lacY - Makes a protein that brings lactose into the cell

  • lacA - Makes an enzyme that modifies lactose

How It Works:

When there’s NO lactose:

  1. A repressor protein sits on the operator (like a lock)

  2. RNA polymerase can’t read the genes

  3. No proteins are made

  4. Saves energy!

When lactose IS present:

  1. Lactose binds to the repressor protein

  2. Repressor falls off the operator (lock opens!)

  3. RNA polymerase can now read the genes

  4. Proteins are made

  5. Bacteria can eat lactose!

Think of it like:

  • A vending machine that only turns on when you insert money

  • No point wasting electricity when nobody’s using it!

8.11.3 Why Operons Are Efficient

Advantages for prokaryotes:

  • Coordinate related genes (turn on/off together)

  • Save energy (don’t make proteins you don’t need)

  • Quick response to environmental changes

  • Simple control system

Why eukaryotes don’t use operons much:

  • Eukaryotes have more complex needs

  • Need independent control of genes

  • Have more sophisticated regulation systems

  • Can afford to be less efficient (more resources available)

8.12 Summary of Key Differences

Feature Prokaryotes Eukaryotes
Nucleus No nucleus (nucleoid) True nucleus with membrane
Chromosomes 1 circular chromosome Multiple linear chromosomes
DNA packaging Histone-like proteins True histones
Gene structure Continuous (no introns) Split (introns + exons)
mRNA type Polycistronic (multiple proteins) Monocistronic (one protein)
Gene organization Often in operons Rarely in operons
Size Small (0.1-5 μm) Large (10-100 μm)
Gene regulation Simple (operons) Complex (multiple levels)

8.13 Why These Differences Matter

8.13.1 Different Lifestyles

Prokaryotes:

  • Need to respond quickly to environment

  • Limited resources

  • Simple, efficient gene regulation

  • Like a small, agile speedboat

Eukaryotes:

  • More complex needs

  • Can afford sophisticated regulation

  • More flexible gene expression

  • Like a large ship with many specialized compartments

8.13.2 Evolution

These differences show:

  • Prokaryotes evolved first (simpler design)

  • Eukaryotes evolved from prokaryotes (more complex design)

  • Both strategies are successful (bacteria are everywhere!)

  • Complexity isn’t always better (bacteria thrive with simplicity)

8.13.3 Applications

Understanding these differences helps us:

  • Make medicines: Antibiotics target prokaryotic features

  • Genetic engineering: Use bacteria to make proteins (insulin, vaccines)

  • Understand diseases: Know how bacteria work differently from human cells

  • Study evolution: See how complex life evolved from simple life

8.14 Key Takeaways

  • Prokaryotes = Simple cells without nucleus (bacteria, archaea)

  • Eukaryotes = Complex cells with nucleus (animals, plants, fungi)

  • Nucleoid vs. Nucleus: Prokaryotes have DNA in nucleoid; eukaryotes in nucleus

  • Circular vs. Linear: Prokaryote chromosomes are circular; eukaryote chromosomes are linear

  • Histone-like vs. Histones: Both organize DNA, but histones (eukaryotes) are more sophisticated

  • Continuous vs. Split genes: Prokaryotic genes have no introns; eukaryotic genes have introns and exons

  • Polycistronic vs. Monocistronic: Prokaryotic mRNA codes for multiple proteins; eukaryotic for one

  • Operons: Groups of genes controlled together (mainly in prokaryotes)

  • Lac operon: Classic example of gene regulation in bacteria

  • These differences reflect different evolutionary strategies and lifestyles

Sources: Information adapted from Khan Academy Biology, Nature Scitable, Biology LibreTexts (Comparing Prokaryotic and Eukaryotic Cells), and molecular biology textbooks.