Genomes and Their Evolution – Part Two

Coding vs. Non-coding DNA and how it differs between Prokaryotes and Eukaryotes 

Coding DNA Regions: DNA sequences that contain instructions for producing proteins. 

Non-Coding DNA: DNA sequences that do not code for proteins but may have other functions, such as regulating gene expression or maintaining chromosome structure. 

Prokaryotes: Over 90% of their DNA codes for proteins, meaning very little DNA is non-coding.

Eukaryotes: Much of their DNA is non-coding, with only about 1.5% of human DNA coding for proteins.

Key Concept: Eukaryotes, such as humans, contain much more non-coding DNA than bacteria. 

What Are Transposable Elements? 

Who is Barbara McClintock?

Transposable Elements: Segments of DNA that can move to different locations within a genome within a cell. 

• They make up approximately 20–50% of mammalian genomes. 

• They can change gene function and influence genome evolution. 

Barbara McClintock discovered transposable elements while studying corn (maize). 

• She discovered that transposable elements (moving DNA) could insert themselves into genes controlling corn colour. 

Two Types of Transposable Elements in eukaryotes  

What are Transposons ?

They can move in two ways. 

What is the Cut-and-Paste Mechanism ?

What is the Copy-and-Paste Mechanism ?

Transposons: DNA segments that move to new locations within a genome using a

They can move in two ways. 

Cut-and-Paste Mechanism 

1. The transposon is removed from its original location. 

2. It moves to another location in the genome. 

3. The total number of copies stays the same. 

Result: Changes the location of the transposon without increasing the number of copies. 

Copy-and-Paste Mechanism 

1. The original transposon is copied. 

2. The new copy moves to another location. 

3. The original transposon remains in place. 

Result: Increases the number of transposon copies in the genome. 

(image is of copy and paste mechanism) **increases amount of genetic material**

Two Types of Transposable Elements in eukaryotes  

What is Retrotransposons ?

what is their process?

Retrotransposons: Transposable elements that move through an RNA intermediate. 

Process: 

1. The retrotransposon DNA is copied into RNA. 

2. Enzyme Reverse transcriptase converts the RNA back into a DNA copy. 

3. The new DNA copy is inserted elsewhere in the genome. 

4. The original retrotransposon remains in place. 

Result: Increases the number of retrotransposon copies in the genome.  **increases amount of genetic material**

The two common transposable elements in humans?

Alu Elements and LINE-1 (L1) 

Length, percentage in human genome, number of copies, possible function

Element	Alu Elements	LINE-1 (L1)
Length	Approximately 300 nucleotides.	Much longer than Alu.
Percentage of human genome	Approximately 10%.	Approximately 17%.
Number of copies	Lecture estimates approximately 20 million.	Approximately 1 million.
Possible function	Helps regulate gene expression.	May contribute to neuron development.

Key Concept: Transposable elements are not necessarily useless DNA. Some may contribute to important biological functions. 

How Do Transposable Elements Affect Genomes? 

Gene inactivation

Changes in gene expression:

Process of unequal crossing over:

genes normally line up correctly with matching sequences

Although repetitive DNA can cause confusion when crossing over because similar DNA sequences may line up incorrectly.

Process of unequal crossing over: Transposable elements can provide matching DNA sequences that cause chromosomes to align incorrectly during meiosis. 

Process: 

1. Two non-sister chromatids align incorrectly at repetitive sequences. 

2. Crossing over occurs between these misaligned sequences. 

3. One chromatid receives an extra copy of a gene. 

4. The other chromatid loses that gene. 

This results in: 

• Gene duplication on one chromatid. 

• Gene deletion on the other. 

transposable elements cause genetic changes that are usually harmful, but some are beneficial and can be passed on through natural selection, contributing to evolution.

Gene inactivation: A transposable element inserting into an exon can disrupt a gene and prevent it from producing a functional protein. 

Changes in gene expression: A transposable element inserting into regulatory DNA can increase or decrease rates of gene expression. 

What Is Repetitive DNA? 

What are the three types and how do they work?

Transposable elements

Large-Segment Duplications

Simple Sequence DNA + Short Tandem Repeats

Repetitive DNA: DNA sequences that appear multiple times throughout the genome.  

These other classes of repetitive DNA found in genomes likely occur as a result of errors in DNA replication or in DNA recombination. 

Transposable elements: DNA sequences that can move around the genome. Can change gene function and genome structure. (5-6% of human genome)

Large-Segment Duplications: scattered copies of long sequences that are copied from one region of the genome to another, either on the same chromosome or on different chromosomes.  

Simple Sequence DNA: Short DNA sequences repeated consecutively (each copy is one after another). (2–500 nucleotides long, 3% human genome)

Why Is Simple Sequence DNA Important? 

It may help maintain chromosome structure and genome integrity. 

Ex. ATGCA – ATGCA – ATGCA – ATGCA 

Short Tandem Repeats: Simple sequence DNA in which each repeating unit contains only 2–5 nucleotides. 

• They are useful for constructing genetic profiles. 

Genome structure can change through several mechanisms

What are Chromosomal Translocations ?

Human vs. Mouse Chromosomes 

Chromosomal Translocation: When a chromosome segment moves to another chromosome

Genome Rearrangement Example: Human vs. Mouse Chromosomes 

• Parts of human chromosome 16 correspond to regions spread across four mouse chromosomes. 

• This provides evidence that chromosomal rearrangements occurred during evolution. 

Result: Changes the arrangement of genetic material. 

Genome structure can change through several mechanisms

What are Chromosomal Fusions ?

Humans vs. Chimpanzees 

How Can Chromosome Rearrangements Lead to New Species? 

Chromosomal Fusion: When two chromosomes join together to form one chromosome. 

Example: Human Chromosome 2

• Humans have one chromosome (chromosome 2) that matches two separate chromosomes in chimpanzees.

• Scientists believe these two chromosomes fused together in a human ancestor.

• Telomere-like and centromere-like sequences in human chromosome 2 provide evidence of this fusion.

Result: Changes chromosome number and organization. 

How Can Chromosome Rearrangements Lead to New Species? 

Individuals with different chromosome arrangements may produce living offspring that are sterile (cannot reproduce) because their chromosomes cannot pair properly during meiosis. 

Genome structure can change through several mechanisms

What is Whole-Genome Duplication ?

Whole-Genome Duplication: When an organism gains an extra copy of its entire genome = the duplication of the entire genome. This can happen because of nondisjunction that results in polyploidy.  

Nondisjunction: The failure of chromosomes to separate properly during cell division. 

Haploid (n)	One set of chromosomes.
Diploid (2n)	Two sets of chromosomes.
Polyploid (3n or more)	Three or more sets of chromosomes.

Why is it important?

1. The entire genome is copied.

2. Original genes continue their normal functions.

3. Extra gene copies can accumulate mutations.

4. Some develop new functions or traits, contributing to evolution.

Key Point: Often harmful, but more tolerated in plants and can lead to new species.

Genome structure can change through several mechanisms

Duplication or Deletion of Chromosomal Regions 

Chromosomal Duplication: When a chromosome segment is copied, producing additional genetic material. 

Chromosomal Deletion: When a chromosome segment is lost. 

These changes can happen through unequal crossing over during meiosis. 

Process 

1. Homologous chromosomes align incorrectly. 

2. Crossing over occurs. 

3. One chromosome gains extra DNA. 

4. The other chromosome loses DNA. 

Result: Genes or entire chromosome regions can be duplicated or deleted. 

Genome structure can change through several mechanisms

DNA Polymerase Slippage 

Process and possible results

DNA Polymerase Slippage: When DNA polymerase temporarily loses its position during replication, causing repeated DNA sequences to become misaligned and repeat numbers in short tandem repeats 

How Does It Work? 

1. DNA polymerase is copying a repetitive DNA sequence.

2. When DNA polymerase falls off. It temporarily separates new strand from the template. 

3. The newly synthesized strand realigns incorrectly. 

4. Replication continues. 

Possible Results: 

Misalignment	Result
Newly synthesized strand slips backward (Expansion)	Extra repeat added (duplication) (Contraction).
Newly synthesized strand slips forward	Repeat lost (deletion).

Key Concept: DNA polymerase slippage changes the number of repeated DNA sequences. 

What Are Multigene Families? 

Two types: identical, non identical

Multigene Family: A group of two or more similar genes that evolved from a common ancestral gene and produce RNA or proteins with similar but slightly different functions. 

Types of Multigene Families 

Type	Description	Example
Identical genes	Multiple copies with identical sequences, often clustered together. Usually have RNA as final product.	Ribosomal RNA genes.
Non-identical genes	Similar genes that accumulated mutations and developed slightly different functions.	Globin genes.

Identical Gene Families: Ribosomal RNA 

Ribosomal RNA (rRNA): RNA that forms part of ribosomes, which make proteins.

Why are there multiple copies?

1. Having hundreds or thousands of rRNA gene copies allows cells to produce lots of rRNA quickly.

2. Multiple RNA polymerases can transcribe the same gene at once, increasing rRNA production.

Key Point: More rRNA gene copies = faster rRNA production = more ribosomes for protein synthesis.

Non-Identical Gene Families: Globin Genes 

What are globin gene? what do they produce

Globin Gene Families: Globin genes are a family of related but non-identical genes that produce slightly different globin proteins, which help transport oxygen in the blood.

alpha and beta globin families

What are pseudogenes, and how do they form?

Pseudogenes: DNA sequences that were once functional genes but accumulated mutations and no longer produce functional proteins.

• Sometimes duplicated genes become pseudogenes instead of developing new functions.

What is sequence alignment, and why are amino acid sequences often used?

Sequence Alignment: A method used to compare DNA or protein sequences to identify similarities and evolutionary relationships.

How it works:

1. Scientists compare sequences of amino acids (letters represent amino acids; dashes represent gaps).

2. More similarities = more closely related proteins.

Why use amino acid sequences?

• amino acid sequences often change more slowly than DNA sequences, making evolutionary relationships easier to identify.

Evolution of Genes with Completely New Protein Functions 

Gene duplication followed by mutation can also produce proteins with completely different functions. 

How Did They Evolve?

1. An ancestral lysozyme gene was duplicated.

2. One copy kept its original function.

3. The other gained mutations, eventually becoming alpha-lactalbumin.

Evidence: Both proteins have similar 3D structures and amino acid sequences.

What are exon duplication, deletion, and shuffling, and how do they contribute to evolution?

Exons: Parts of genes that remain in mature RNA after splicing.

Mechanism	Explanation
Exon Duplication	An exon is copied, adding an extra segment.
Exon Deletion	An exon is removed, removing a segment.
Exon Shuffling	Exons from different genes are rearranged or exchanged, creating new combinations.

How does exon shuffling happen?

1. rearrange exons between non-allelic genes.

2. The new combination of exons may produce a protein with a different structure or function.

Key Point: Changing exon combinations can create proteins with new structures and functions, contributing to evolution.