What is a gene?
A gene is a section of DNA that holds the instructions to make one functional product. Most genes code for a protein; some code only for an RNA, such as tRNA or rRNA.
Genes sit on chromosomes at fixed places called loci (singular locus). Different versions of the same gene are alleles.
DNA has two strands. When a gene is used, RNA polymerase reads one strand, the template strand, from 3′ to 5′ and builds RNA from 5′ to 3′. The other strand, the coding strand, has the same sequence as the RNA (except T in DNA is U in RNA). The DNA before the start of a gene is called upstream; after it, downstream.
Parts of a gene: promoter, coding region, terminator
- Promoter: a DNA sequence just upstream of the gene where RNA polymerase (helped by proteins) binds. It sets where transcription starts and which strand is read. Many eukaryotic promoters contain a TATA box; bacterial promoters have short sequences about 10 and 35 bases upstream.
- Coding region: the part that carries the message. In the mRNA it begins with a start codon (AUG) and ends with a stop codon (UAA, UAG or UGA). Each three-base codon stands for one amino acid.
- Untranslated regions (UTRs): short stretches of mRNA before the start codon (5′ UTR) and after the stop codon (3′ UTR). They are copied but not turned into protein; they help ribosomes bind and control how long the mRNA lasts.
- Terminator: a sequence at the end of the gene that makes RNA polymerase stop and let go.
- Regulatory sequences: switches such as operators (bacteria) and enhancers or silencers (eukaryotes) that control how much the gene is used. Enhancers can be thousands of bases away.
Prokaryotic genes and eukaryotic genes
| Prokaryotes (bacteria) | Eukaryotes (animals, plants, fungi) | |
|---|---|---|
| Introns | Almost never; genes are continuous | Common; genes are split into exons and introns |
| Grouping | Related genes often in an operon, sharing one promoter and operator | Each gene usually has its own promoter |
| mRNA | Polycistronic: one mRNA, several proteins | Monocistronic: one mRNA, one protein (usually) |
| Processing | None; translation can start while transcription is still going on | Pre-mRNA is capped, spliced and given a poly-A tail in the nucleus |
| Where | Cytoplasm (no nucleus) | Transcription in nucleus, translation in cytoplasm |
Exons are the parts that remain in mature mRNA (mostly coding). Introns are copied into pre-mRNA but removed before translation. In many human genes, introns are much longer than exons.
Splicing and alternative splicing
In eukaryotes the whole gene, exons and introns, is first transcribed into pre-mRNA (primary transcript). Then it is processed:
- A 5′ cap (a modified G) is added to the front. It protects the RNA and helps ribosomes bind.
- Splicing: a machine called the spliceosome cuts out the introns and joins the exons end to end.
- A poly-A tail (a chain of about 200 A bases) is added to the 3′ end. It protects the mRNA and helps it leave the nucleus.
Alternative splicing: the same pre-mRNA can be spliced in different ways, keeping different sets of exons. So one gene can make several related proteins. This helps explain how humans make far more kinds of protein than their roughly 20,000 protein-coding genes.
Bacteria cannot splice. That is why a human gene placed into bacteria must be a copy made from mature mRNA (called cDNA), with no introns.
Genes and the genome
The genome is all the genetic material of an organism (or one set of it). The human genome has about 3.1 billion base pairs in each set of 23 chromosomes, but only about 20,000 protein-coding genes.
- Only about 1–2% of human DNA codes for protein. The rest includes introns, regulatory switches, genes for RNA, repeated sequences and DNA whose job is still being studied.
- Bacterial genomes are small and packed: most of the DNA is coding (often about 85–90%), with very little space between genes.
- Genome size does not match how complex an organism is: some plants and amoebas have far more DNA than humans.
- Mitochondria and chloroplasts also carry small circular genomes of their own.
Projects that read whole genomes (like the Human Genome Project, finished in 2003) help find disease genes and compare species.
Try it: edit a 'gene sentence'
Write this on paper: START-the-xqzv-cat-bbbb-sat-STOP. The real words are exons; the nonsense groups (xqzv, bbbb) are introns. Cross out the introns and join what is left: 'the cat sat'. Now try 'alternative splicing': keep a different set of words to make a new sentence. In the 3D, step 5 lets you add or remove introns and see how the mRNA length compares with the gene length.
Key formulas and definitions
- Gene = promoter + (5′ UTR + coding region + 3′ UTR) + terminator
- Eukaryotic gene: exon – intron – exon – intron – exon …
- Pre-mRNA → cap + splicing (introns out, exons joined) + poly-A tail → mature mRNA
- Prokaryote operon: one promoter + operator + several genes → one polycistronic mRNA
- Template strand is read 3′→5′; RNA is made 5′→3′; coding strand = RNA sequence (T → U)
- Genome = all the DNA of an organism; gene = one functional unit inside it
Worked examples
1. A eukaryotic gene has 4 exons (150, 200, 100, 250 bases) and 3 introns (1000, 800, 1200 bases). How long are the pre-mRNA and the mature mRNA coding part?
Pre-mRNA (exons + introns) = 150 + 200 + 100 + 250 + 1000 + 800 + 1200 = 3700 bases. Mature mRNA (exons only) = 700 bases. Most of the transcript was intron.
2. The coding strand reads 5′-ATG GCT TAA-3′. Write the mRNA and the template strand.
mRNA has the same sequence as the coding strand with U for T: 5′-AUG GCU UAA-3′. The template strand is complementary and antiparallel: 3′-TAC CGA ATT-5′.
3. A human insulin gene is put straight into a bacterium, but no working insulin is made. Why?
The human gene has introns. Bacteria have no spliceosome, so they cannot remove the introns, and the protein made would be wrong. Scientists use cDNA made from mature mRNA instead.
4. Three enzymes for using one sugar are made together in a bacterium from a single mRNA. Explain how.
The three genes lie side by side in an operon with one promoter. RNA polymerase transcribes them as one polycistronic mRNA, and ribosomes start translation at each gene's own start codon, making three proteins.
Common mistakes
- Thinking introns are translated. Introns are copied into pre-mRNA but cut out before translation.
- Saying exons are 'all coding'. Exons also include the UTRs, which stay in mRNA but are not translated.
- Thinking a gene and a genome are the same. A gene is one unit; the genome is all the DNA.
- Believing bacteria have introns and splice like us. Prokaryotic genes are continuous and are not spliced.