Difficulty: Intermediate | Prerequisites: DNA structure, gene expression, biotechnology applications (Part 1 of these notes).
This section moves from what we can do with genomes (biotechnology, covered in Part 1) to what genomes look like and how they change over evolutionary time. You will need a working understanding of DNA replication, mutations, meiosis, and crossing over. The core question here is: if all organisms share a common ancestor, how do genomes expand, diversify, and reorganise themselves? The answers involve gene duplication, transposable elements, chromosomal rearrangements, and comparative analysis across species.
Genomes vary enormously in size and gene density, and most of the human genome does not code for protein. Transposable elements, gene duplication, exon shuffling, and chromosomal rearrangements drive genome evolution. Comparing genomes across species reveals conserved genes that clarify evolutionary relationships and developmental biology.
Bioinformatics
The application of computational methods to store, manage, and analyse large biological datasets, especially genomic sequences. Think of it as the branch of biology that relies on algorithms and databases rather than test tubes.
Gene annotation
The process of identifying protein-coding genes within a DNA sequence and assigning functions to them, often by comparing them to characterised genes in other species.
Systems biology
An approach that studies how genes, proteins, and other molecules interact as integrated networks within biological systems, rather than examining each component in isolation.
Gene density
The number of genes per unit length of DNA. Humans and other mammals have notably low gene density because most of their genome consists of introns and non-coding sequences.
Non-coding DNA
Regions of the genome that do not encode proteins, rRNAs, or tRNAs. In humans, this accounts for roughly 98.5% of the genome. Includes regulatory sequences, introns, pseudogenes, and repetitive DNA.
Pseudogene
A former gene that has been rendered inactive by accumulated mutations. It remains in the genome as a non-functional relic. In simple terms, it is a broken copy of a gene that no longer produces a working protein.
Transposable element (TE)
A stretch of DNA that can move from one location to another within the genome. Also called "jumping genes." Found in both prokaryotes and eukaryotes.
Transposon
A type of transposable element that moves via a DNA intermediate, using a transposase enzyme. Can relocate by a cut-and-paste or copy-and-paste mechanism.
Retrotransposon
A type of transposable element that moves via an RNA intermediate, using reverse transcriptase to convert the RNA back into DNA before insertion at a new site.
Multigene family
A group of genes that arose by duplication of an ancestral gene. Members may be identical (e.g. rRNA gene clusters) or divergent (e.g. the globin gene families on chromosomes 11 and 16).
Exon shuffling
The recombination of exons from different genes during meiosis, creating new genes with novel combinations of functional domains.
Exon duplication
An error in meiosis that copies an exon onto one chromosome while deleting it from the homologous chromosome, potentially giving a gene extra functional modules.
Hox genes
A family of regulatory genes that control body plan development and segment identity in animals. They are highly conserved across species, from fruit flies to humans.
Polyploidy
A condition in which an organism has more than two complete sets of chromosomes, often resulting from errors in meiosis. Common in plants and a driver of speciation.
Bioinformatics applies computational tools to biological data. Complete genome sequences now exist for humans, chimpanzees, many bacteria, fruit flies, and thousands of other organisms.
Comparing genomes across organisms provides insights into evolution and biological processes. If a gene in an unknown organism looks like a well-studied gene in another species, that similarity can hint at function.
Gene annotation is the process of scanning a genome sequence to identify which stretches are protein-coding genes, using sequence-comparison algorithms and known gene databases.
Systems biology moves beyond individual genes. Instead of asking "what does gene X do?", it asks "how do genes X, Y, and Z interact within the cell?" Scientists compile catalogues of genes and proteins and study their functional integration, often using tools like DNA microarrays to measure expression of thousands of genes simultaneously.
Genome size varies widely across life:
Most bacteria and archaea: 1 to 6 Mb (megabases, i.e. millions of base pairs).
Most plants and animals: genomes greater than 100 Mb.
Humans: approximately 3,000 Mb (3 billion base pairs).
Gene density is inversely related to genome complexity:
Humans and other mammals have the lowest gene density of any organisms, meaning fewer genes per unit length of DNA.
The reason: introns (non-coding sequences within genes) and vast stretches of non-coding DNA between genes.
The human genome is mostly non-coding:
98.5% of the human genome does not code for proteins, rRNAs, or tRNAs.
Gene regulatory sequences account for about 5% of the genome.
Introns account for about 20%.
The remaining non-coding DNA between genes includes:
Pseudogenes: former genes rendered inactive by mutations. They no longer produce functional protein but persist in the genome.
Repetitive DNA: sequences present in multiple copies throughout the genome. Some repetitive DNA is highly conserved across species, suggesting it has functional importance even though it does not encode protein.
The high level of sequence conservation of some non-coding DNA across distantly related organisms is one of the clearest signals that "junk DNA" is not all junk.
Transposable elements (TEs) are stretches of DNA that can move from one location to another within the genome. They exist in both prokaryotes and eukaryotes.
Two major types:
Transposons move via a DNA intermediate using a transposase enzyme. Two mechanisms:
Cut-and-paste: the transposon is excised from its original location and inserted at a new target site. The original site loses the element.
Copy-and-paste: the transposon is copied, and the copy is inserted at a new site. The original remains in place.
Retrotransposons move via an RNA intermediate. The element is first transcribed into RNA, then reverse transcriptase converts the RNA back into DNA, which is inserted at a new genomic location. This is always a copy-and-paste process, so retrotransposons tend to increase in number over time.
How transposable elements contribute to genome evolution:
They facilitate recombination and crossing over by providing homologous sequences at different chromosomal locations.
Insertion within a protein-coding sequence can block protein production (a loss-of-function mutation).
Insertion within a regulatory sequence can increase or decrease expression of a nearby gene.
They can carry genes or groups of genes to new positions in the genome.
They can create new sites for alternative splicing in RNA transcripts, potentially generating new protein variants from existing genes.
The basis of all genomic change is mutation. The earliest forms of life likely carried only the genes necessary for survival and reproduction. Over evolutionary time, duplication and diversification expanded gene repertoires.
Diversification through chromosomal changes:
Chromosomal rearrangements (including crossing over) are thought to contribute to the generation of new species.
Accidents in meiosis can lead to polyploidy, where an organism ends up with extra complete sets of chromosomes. Genes in the extra sets can then diverge by accumulating mutations, potentially acquiring novel functions.
Chromosomal alterations also matter. After humans and chimpanzees diverged from a common ancestor, two ancestral chromosomes fused in the human lineage. This is why humans have 23 pairs of chromosomes (n=23) while chimps have 24 (n=24).
Multigene families:
Chromosomal changes can turn a single gene into a multigene family.
Identical multigene families: clusters of identical DNA sequences, typically arranged in tandem. The rRNA genes are the standard example, with hundreds of copies needed to meet the cell's demand for ribosomal RNA.
Nonidentical multigene families: related but distinct genes expressed at different times or in different tissues. The globin gene families (alpha-globin on chromosome 16, beta-globin on chromosome 11) are the textbook example. An ancestral globin gene duplicated, the copies mutated independently, transposed to different chromosomes, and duplicated further, producing a family of oxygen-carrying proteins expressed at different developmental stages.
Evolution of genes with novel functions:
Some duplicated genes diverge so much that their protein products perform entirely different functions from the ancestral gene. The duplication frees one copy from selective pressure, allowing it to accumulate mutations that may, occasionally, produce a useful new protein.
Exon duplication and exon shuffling:
Exon duplication results from errors in meiosis. An exon is duplicated on one chromosome and deleted from the homologous chromosome, giving one gene extra functional modules.
Exon shuffling occurs when errors in meiotic recombination mix and match exons from different genes (or different positions within the same gene), creating new gene architectures. The tissue plasminogen activator (TPA) gene, which encodes a protein that dissolves blood clots, is a classic example: it contains exons derived from the EGF gene, the fibronectin gene, and the plasminogen gene.
Comparing distantly related species:
Highly conserved genes have changed very little over hundreds of millions of years. Their conservation signals that they perform essential functions under strong selective pressure.
Conserved genes clarify evolutionary relationships among species that diverged long ago.
Because these genes are so similar, findings from model organisms (yeast, fruit flies, mice) can be applied to human biology.
Widespread conservation of developmental genes:
Hox genes are crucial regulators of body structure and segment identity. They are conserved across animals, from insects to mammals.
Related sequences appear in regulatory genes of yeast, plants, and even prokaryotes.
Small changes in the regulatory sequences of certain genes can lead to major changes in body form, which is one of the key insights of evolutionary developmental biology (evo-devo).
Comparing closely related species:
Genomes of closely related species tend to be organised similarly in terms of gene order and chromosome structure.
Human and chimpanzee genomes differ by about 1.2% at single base pairs and by about 2.7% when insertions and deletions are included.
Despite this genetic closeness, phenotypic differences between humans and chimps are significant, suggesting that regulatory changes (not just protein-coding changes) drive much of the divergence.
Comparing genomes within a species:
Within humans, genetic variation arises from SNPs, inversions, deletions, duplications, and environmental influences on gene expression.
Humans have relatively low within-species genetic variation compared to many other organisms.
These variations are useful for studying both human evolution (migration patterns, population history) and human health (disease susceptibility, drug response).
"Non-coding DNA is junk." The term "junk DNA" is outdated. While much non-coding DNA has no known function, regulatory sequences, conserved non-coding elements, and transposable elements all play roles. Conservation of non-coding sequences across distantly related species is strong evidence of function.
"More DNA means more genes." Genome size does not correlate neatly with gene count or organism complexity. Some plants have far larger genomes than humans but fewer genes. The difference lies in the amount of repetitive and non-coding DNA.
"Transposable elements are parasites with no benefit." While TEs can disrupt genes, they also drive genome evolution by facilitating recombination, creating new regulatory sites, and enabling exon shuffling.
"Humans and chimps are 98.8% identical, so the remaining 1.2% is trivial." That 1.2% represents roughly 35 million single-nucleotide differences, and the 2.7% from insertions and deletions adds further divergence. Small percentage differences across a 3-billion-base-pair genome translate to substantial absolute change.
⚠️ Know the difference between transposons (DNA intermediate, transposase) and retrotransposons (RNA intermediate, reverse transcriptase). Exams love this comparison.
⚠️ Be able to explain the five ways transposable elements contribute to genome evolution (recombination, blocking protein production, altering regulation, carrying genes, creating new splicing sites).
⚠️ Understand the globin gene family as the textbook example of multigene family evolution: ancestral gene, duplication, mutation, transposition to different chromosomes, further duplication.
⚠️ Know the key genome statistics: human genome is 3,000 Mb, 98.5% non-coding, regulatory sequences 5%, introns 20%.
⚠️ Human vs. chimp: 1.2% difference at single base pairs, 2.7% with insertions/deletions, n=23 vs. n=24 (chromosome fusion).
⚠️ Exon shuffling and the TPA gene are commonly tested. Be ready to explain how exons from three different genes ended up in one.
True or false: Retrotransposons use a DNA intermediate to move within the genome.
Answer: False. Retrotransposons use an RNA intermediate and reverse transcriptase.
Fill in the blank: Humans have ______ Mb in their genome, of which approximately 98.5% is non-coding.
Answer: 3,000.
True or false: Pseudogenes are active genes that code for regulatory proteins.
Answer: False. Pseudogenes are former genes rendered inactive by mutations.
Fill in the blank: The alpha-globin gene family is found on chromosome ______, and the beta-globin gene family is on chromosome ______.
Answer: 16; 11.
True or false: Highly conserved genes are useful for studying evolutionary relationships between distantly related species.
Answer: True.
Q: Explain the difference between transposons and retrotransposons.
A: Transposons move via a DNA intermediate using transposase, by either cut-and-paste or copy-and-paste. Retrotransposons move via an RNA intermediate: they are transcribed into RNA, then reverse transcriptase converts the RNA back into DNA for insertion at a new site. Retrotransposons always copy themselves (they never leave the original site), so they tend to accumulate.
Q: Why do humans have low gene density compared to bacteria?
A: Because the human genome contains large amounts of introns within genes and non-coding DNA between genes (pseudogenes, repetitive sequences, regulatory elements). Bacteria have compact genomes with little non-coding DNA.
Q: Describe how the globin multigene families evolved from a single ancestral gene.
A: An ancestral globin gene duplicated. The two copies accumulated mutations independently. One copy transposed to a different chromosome. Further duplications and mutations on each chromosome produced the alpha-globin family (chromosome 16) and the beta-globin family (chromosome 11), with different members expressed at different developmental stages.
Q: What is exon shuffling, and why is the TPA gene a good example?
A: Exon shuffling occurs when errors in meiotic recombination mix exons from different genes into a single gene. The TPA (tissue plasminogen activator) gene contains exons from the EGF gene, the fibronectin gene, and the plasminogen gene, making it a mosaic product of recombination events.
Q: Why is the conservation of non-coding DNA across distantly related species considered evidence that the DNA has a function?
A: If a non-coding sequence had no function, mutations in it would accumulate freely over evolutionary time and the sequence would diverge. High conservation implies that natural selection is preserving the sequence because it serves a role (likely regulatory).
This material builds directly on the biotechnology applications covered in Part 1 of these notes. The tools used in biotechnology (CRISPR, recombinant DNA) exploit the same genomic features discussed here: transposable elements, gene duplication, and non-coding regulatory regions.
Comparative genomics connects to evolutionary biology and phylogenetics. The concept of conserved genes and Hox genes links to developmental biology and evo-devo. Gene duplication and exon shuffling connect to protein evolution and the origin of novel protein domains.
Bioinformatics, gene annotation, systems biology, genome size, gene density, non-coding DNA, junk DNA, pseudogene, repetitive DNA, transposable elements, jumping genes, transposon, retrotransposon, transposase, reverse transcriptase, cut-and-paste transposition, copy-and-paste transposition, genome evolution, gene duplication, multigene family, globin genes, alpha-globin, beta-globin, Hox genes, exon shuffling, exon duplication, TPA gene, tissue plasminogen activator, polyploidy, chromosomal rearrangement, comparative genomics, conserved genes, human-chimp genome comparison, SNPs, insertions and deletions, DNA microarray, evo-devo, developmental genes