7  What is a Genome?

7.1 Your Complete Instruction Manual

7.1.1 Defining the Genome

A genome is the complete set of genetic instructions for building and running a living organism. It’s like having the ENTIRE library of instruction manuals for your body!

Think of it like:

  • 📚 A complete encyclopedia (all volumes together)

  • 🗺️ A complete set of maps for a whole country

  • 💿 The master copy of all the software that runs your body

Your genome includes:

  • All of your DNA

  • All of your genes

  • All of your chromosomes

  • Everything needed to make YOU!

7.1.2 Genome Size

Different organisms have genomes of different sizes:

Measured in “base pairs” (the rungs on the DNA ladder):

  • Humans: ~3.2 billion base pairs

  • Mouse: ~2.5 billion base pairs

  • Fruit fly: ~140 million base pairs

  • E. coli (bacteria): ~4.6 million base pairs

  • Virus: As small as 5,000 base pairs

Bigger organisms don’t always have bigger genomes! (We’ll learn why in the C-value paradox chapter)

7.2 Haploid vs. Diploid

7.2.1 Understanding Sets of Chromosomes

Remember that humans have 46 chromosomes? Well, there’s more to the story!

Diploid (2 sets):

  • Having TWO complete sets of chromosomes

  • One set from mom, one set from dad

  • Most of your cells are diploid

  • Humans have 46 chromosomes (23 pairs)

  • Symbol: 2n (where n = 23 for humans)

Haploid (1 set):

  • Having only ONE complete set of chromosomes

  • Your egg and sperm cells are haploid

  • Humans have 23 chromosomes (no pairs)

  • Symbol: n (where n = 23 for humans)

7.2.2 Why Do We Have Both?

Think of it like a card game:

  • Your body cells need two complete decks (diploid) to work properly

  • Your egg or sperm cells have only one deck (haploid)

  • When egg and sperm combine, the baby gets two decks again!

Mom’s egg (23) + Dad’s sperm (23) = Baby (46 chromosomes)

This is why you get traits from both parents!

7.2.3 Backup Copies

Having two copies of each chromosome is helpful:

  • If one gene is broken, you usually have a backup copy

  • It’s like having a spare tire in your car

  • This is why recessive diseases need two broken copies to show up

7.3 Coding and Non-Coding DNA

7.3.1 Not All DNA Is the Same

Here’s a surprise: Only about 1-2% of your DNA actually codes for proteins!

So what’s the rest doing?

7.3.2 Coding DNA (Genes)

Coding DNA = DNA that has instructions for making proteins

  • These are your genes

  • About 20,000-25,000 genes in humans

  • They’re like the actual recipes in your cookbook

  • They tell cells how to make proteins

Example: The gene for making insulin (the protein that controls blood sugar)

7.3.3 Non-Coding DNA

Non-coding DNA = DNA that doesn’t code for proteins

But “non-coding” does NOT mean “useless”! This DNA has many important jobs:

1. Regulatory Regions (we’ll discuss these next)

  • Control when and where genes are turned on

2. Spacers

  • DNA between genes

  • Like margins and spacing in a book

3. Introns

  • Parts of genes that get removed before making proteins

  • Like deleted scenes in a movie

4. Repetitive DNA

  • Repeated sequences

  • Some help organize chromosomes

  • Some are ancient viral DNA

5. RNA genes

  • Code for RNA molecules that do jobs (but don’t make proteins)

  • Examples: tRNA, rRNA

6. Structural DNA

  • Helps organize and package DNA

  • Like the table of contents in a book

7.4 Regulatory Elements: The Control Switches

7.4.1 Turning Genes On and Off

Genes need to be controlled! You wouldn’t want your stomach making proteins that belong in your eyeball!

Regulatory elements are like light switches that turn genes on and off.

7.4.2 Types of Regulatory Elements

1. Promoters 🚦

  • Located right before a gene

  • Signal where to START reading the gene

  • Like a “Start Here” sign

How they work:

  • Special proteins bind to promoters

  • This signals: “Start making mRNA from this gene!”

  • Like pressing a start button

2. Enhancers 🔊

  • Can be far away from the gene they control

  • INCREASE gene activity (make more protein)

  • Like turning up the volume

How they work:

  • Special proteins bind to enhancers

  • DNA loops around so the enhancer touches the gene

  • This boosts protein production

3. Silencers 🔇

  • The opposite of enhancers

  • DECREASE gene activity (make less protein)

  • Like turning down the volume or muting

4. Operators (mainly in bacteria)

  • Act like on/off switches

  • Can completely block gene reading

  • Part of bacterial gene regulation systems (like the lac operon)

7.4.3 Why Regulation Matters

Think about your different cells:

  • Brain cells need different proteins than muscle cells

  • Eye cells need different proteins than stomach cells

  • All these cells have the SAME genes!

  • But different genes are turned on in different cells

It’s like having the same cookbook in every room of your house, but only using certain recipes in the kitchen, different ones in the workshop, etc.

7.5 “Junk DNA” vs. Functional Non-Coding DNA

7.5.1 The Junk DNA Story

When scientists first sequenced the human genome, they were shocked:

  • Only 1-2% codes for proteins

  • What about the other 98%?

Some scientists called it “junk DNA”—useless leftover DNA from evolution.

But they were WRONG!

7.5.2 Not Junk After All!

Scientists now know that much of “junk DNA” is actually very important:

What “Junk DNA” Actually Does:

  1. Gene Regulation 🎛️

    • Controls when and where genes are turned on

    • Contains enhancers and silencers

  2. Chromosome Structure 📦

    • Helps organize and package DNA

    • Contains centromeres (where chromosomes attach during cell division)

    • Contains telomeres (protective caps on chromosome ends)

  3. Evolution Playground 🧬

    • Provides raw material for evolution

    • New genes can form from “junk DNA”

    • Like a spare parts bin for evolution to work with

  4. Produces Functional RNAs 📝

    • Some non-coding DNA makes RNA that does jobs (without making protein)

    • Examples: microRNAs that regulate genes

  5. Protection 🛡️

    • Spacing between genes can protect them

    • Like bubble wrap protecting fragile items

7.5.3 The Onion Test

Here’s a funny way to think about it:

Question: Does an onion need 5 times more genes than you to be an onion?

Answer: No! Onions have bigger genomes than humans, but they’re not more complex!

This proves that genome size isn’t everything. Much of the “extra” DNA in onions probably IS junk!

In humans, though, most of our non-coding DNA seems to have functions we’re still discovering.

7.5.4 How We Know It’s Functional

Scientists discovered non-coding DNA is important because:

  • It’s conserved (stays similar across many species through evolution)

  • If it were truly junk, evolution would have deleted it

  • Mutations in non-coding DNA can cause diseases

  • Non-coding DNA is transcribed into RNA (sign of activity)

Think of it like:

  • If a recipe ingredient has been used for 1000 years, it’s probably important!

  • If people have tried removing it and the dish failed, it’s definitely important!

7.6 The Genome’s Organization

7.6.1 It’s Not Random!

Your genome isn’t just randomly scattered DNA. It’s organized like a well-planned library:

1. Chromosomes = Different books

  • 23 different chromosomes (in one set)

  • Each chromosome has different genes

2. Genes = Chapters in the books

  • Each gene is a separate instruction

  • Genes can be different sizes

3. Regulatory Regions = Table of contents and index

  • Help find and control genes

4. Non-Coding Regions = Margins, spacing, footnotes

  • Organize and support the main content

7.7 Comparing Genomes

7.7.1 What We Learn from Comparisons

Comparing genomes between species tells us amazing things:

Humans vs. Chimpanzees:

  • 96% identical

  • The 4% difference makes us human!

  • Shows we share a recent common ancestor

Humans vs. Mice:

  • 90% of genes are similar

  • Why mice are good for medical research

  • Many mouse genes can be swapped with human genes!

Humans vs. Fruit Flies:

  • 60% of genes are similar

  • Even insects share our basic genetic toolkit

  • Disease genes are often similar

Humans vs. Bananas:

  • 50% of genes are similar

  • Shows all life on Earth is related

  • We share basic cellular machinery with plants!

7.7.2 The Universal Genome Features

Almost all genomes have:

  • DNA as genetic material (some viruses use RNA)

  • Genes that code for proteins

  • Regulatory elements

  • A genetic code (with rare exceptions)

This shows all life on Earth is related—we’re all part of the same family tree!

7.8 Key Takeaways

  • Genome = All of an organism’s DNA, genes, and chromosomes

  • Diploid = Two sets of chromosomes (most body cells); Haploid = One set (egg and sperm)

  • Coding DNA (~1-2% in humans) = Genes that code for proteins

  • Non-coding DNA (~98% in humans) = Doesn’t code for proteins but has many important functions

  • Regulatory elements control gene activity:

    • Promoters = Start signals

    • Enhancers = Volume up

    • Silencers = Volume down

    • Operators = On/off switches (bacteria)

  • “Junk DNA” is mostly NOT junk—it has important regulatory and structural functions

  • Genomes are organized like libraries with books (chromosomes), chapters (genes), and organizational elements

  • Comparing genomes shows all life is related

Sources: Information adapted from NHGRI Genome Glossary, Nature Education, Khan Academy, and current genomics research on non-coding DNA function.