Name: genes, introns, and regulatory dna
Uploaded: 2026-08-26T08:20:12.834Z
Duration: 2 min 39 s
Channel: JoVE

K12 Standards

Pennsylvania State Academic Standards

9-12

Life Science

Structure and Function

3.1.9-12.A

Organization of Genes

Inside the nucleus, genetic material is tightly packaged, and human genes have a distinct and organized structure.Human cells contain over 20,000 genes arranged along chromosomes. These genes make up a small fraction of the DNA. They are separated by long stretches of noncoding DNA that do not code for proteins.Each gene contains coding regions along with regulatory DNA sequences that control when, where, and how much the gene is expressed. A key component of this regulatory region is the promoter, a specific DNA sequence that marks the start site of transcription. It provides a binding site for proteins required for RNA synthesis.Transcription factors bind to the promoter first. They help position RNA polymerase at a nearby transcription start site, where RNA synthesis begins using the DNA strand as a template.RNA polymerase reads the DNA template strand in the 3 prime to 5 prime direction and builds a complementary RNA strand in the 5 prime to 3 prime direction as it moves along the DNA. It continues until it reaches a termination sequence. At this point, RNA synthesis stops.Between the start and end of the gene are regions called exons and introns. Both regions are copied into the initial RNA transcript during transcription.Introns are removed from the RNA transcript through RNA splicing. The remaining exons are joined together to form a mature messenger RNA that encodes proteins.Other noncoding DNA elements, such as silencers and enhancers, also help control gene expression. Repressor proteins bind to silencer sequences and block RNA polymerase from binding, which inhibits transcription. Enhancers increase transcription by binding activator proteins, which interact with promoter-bound transcription factors to help RNA polymerase bind.So, each gene includes promoters, exons, introns, and regulatory elements that together help control protein expression in a cell.

organization of genes

The genomes of eukaryotes can be structured in several functional categories. A strand of DNA is comprised of genes and intergenic regions. Genes themselves consist of protein-coding exons and non-coding introns. Introns are excised once the sequence is transcribed to mRNA, leaving only exons to code for proteins.<h4>Eukaryotic Genes Are Separated by Intergenic Regions</h4>In eukaryotic genomes, genes are separated by large stretches of DNA that do not code for proteins. However, these intergenic regions carry important elements that regulate gene activity, for instance, the promoter where transcription starts, and enhancers and silencers that fine-tune gene expression. Sometimes these binding sites can be located far away from the associated gene.<h4>Protein-Coding Exons Are Interspersed by Introns</h4>As researchers investigated the process of gene transcription in eukaryotes, they realized that the final mRNA that codes for a protein is shorter than the DNA it is derived from. This difference in length is due to a process called splicing. Once pre-mRNA has been transcribed from DNA in the nucleus, splicing immediately removes introns and joins exons together. The result is protein-coding mRNA that moves to the cytoplasm and is translated into protein.<h4>The Number of Introns per Gene Can Vary Significantly</h4>One of the largest human genes, DMD, is over two million base pairs long. This gene encodes the muscle protein dystrophin. Mutations in DMD cause muscular dystrophy, a disorder characterized by progressive muscle deterioration. This gene contains 79 exons and 103 introns. On the other end of the spectrum lies the histone H1A gene&#x2014;it is one of the smallest genes in the human genome at only 781 base pairs long with one exon and no introns.<h4>Introns Carry Important Functions</h4>Are introns garbage DNA that needs to be removed? Interestingly, introns can carry elements that are important for gene regulation. Furthermore, the cutting of the initial transcript and re-joining of exons allows DNA sequences to be shuffled. This process of mixing and matching exons is known as alternative splicing. It makes it possible to produce several protein variants from a single coding sequence.<h4>The Vast Majority of the Human Genome Does Not Code for Proteins</h4>Did you know that 99% of your genome does not code for proteins? In the early days of genome research, biologists coined the catchy term &#x2018;junk DNA&#x2019; for these seemingly non-functional sequences. Meanwhile, we have learned that a large portion of non-coding DNA does carry important functions. At least 9% of the human genome is involved in gene regulation&#x2014;that is nine times more than protein-coding sequences.

Overview

The genomes of eukaryotes can be structured in several functional categories. A strand of DNA is comprised of genes and intergenic regions. ...

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DNA Structure and Function

KEY TERMS AND CONCEPTS

genes, introns, and regulatory dna

Eukaryotic genes are arranged within DNA along with non-coding regions that help control gene activity. A DNA strand includes genes and intergenic regions, which are the stretches between genes. These regions do not code for proteins, but they can contain important regulatory elements such as promoters, enhancers, and silencers.

A gene itself is not a single continuous coding block. It usually contains protein-coding exons and non-coding introns. After DNA is transcribed into pre-mRNA in the nucleus, splicing removes the introns and joins the exons together. The shorter mRNA then moves to the cytoplasm, where it is translated into protein.

The number of introns in a gene can vary a lot. The human DMD gene is more than two million base pairs long and encodes dystrophin, a muscle protein. Mutations in DMD can cause muscular dystrophy, a disease that leads to progressive muscle deterioration. This gene has 79 exons and 103 introns. In contrast, the histone H1A gene is only 781 base pairs long and has one exon and no introns.

Introns are not always useless DNA. Some introns contain elements that help regulate genes. They also support alternative splicing, a process that mixes and matches exons after transcription. This lets one coding sequence produce several protein variants.

Most of the human genome does not code for proteins. Early genome research called many of these sequences junk DNA, but scientists now know that much of this non-coding DNA has important roles. At least 9% of the human genome is involved in gene regulation, which is far more than the protein-coding portion.

Genes, Introns, and Regulatory DNA

the dna helix

How DNA Stores Genetic Information

DNA stores genetic information that is passed from one generation to the next in organisms and most viruses. It is built from two strands of nucleotides that twist together into a double helix. The story of how scientists uncovered this structure developed step by step over nearly a century. Each DNA strand is made of nucleotides. A nucleotide contains the sugar deoxyribose, a phosphate group, and one of four nitrogen bases: adenine (A), guanine (G), cytosine (C), or thymine (T). Adenine and...

dna packaging

Chromatin and Histones in DNA Packing

Eukaryotic cells must pack long DNA molecules into the nucleus, and chromatin makes that possible. DNA wraps around proteins called histones to form nucleosomes, which are the main unit of DNA packaging. Nucleosomes then coil into compact chromatin fibers. The amount of DNA in a cell is much larger than it first seems. A single human skin cell has about 3 billion base pairs of DNA, and if that DNA were stretched out in a line, it would be about 2 meters long. With about 50 trillion cells in...

Eukaryotic genes are arranged within DNA along with non-coding regions that help control gene activity. A DNA strand includes genes and intergenic regions, which are the stretches between genes. These regions do not code for proteins, but they can contain important regulatory elements such as promoters, enhancers, and silencers. A gene itself is not a single continuous coding block. It usually contains protein-coding exons and non-coding introns. After DNA is transcribed into pre-mRNA in the...

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Chromosome Stains for Detecting Disorders

Chromosome staining helps scientists find genetic disorders by showing the number and physical features of chromosomes. These features appear after DNA condenses into chromosomes during mitosis. Cytogeneticists then stop mitosis and stain the chromosomes to study their banding pattern. The pattern reveals details such as chromosome number, shape, and type. A chromosome description like this is called a karyotype. To create one, scientists take an image of the stained chromosomes and identify...

replication in prokaryotes

How Prokaryotic DNA Is Copied

Prokaryotic DNA is copied through a coordinated process with three main stages: initiation, elongation, and termination. It begins when initiator proteins bind to the single origin of replication, or ori, on the cell’s circular chromosome. The DNA then copies around the circle in both directions, starting from two replication forks, and this produces two DNA molecules. Several proteins work together to open and protect the DNA during replication. Topoisomerase cuts one side of the...

replication in eukaryotes

Eukaryotic DNA Copying and Telomeres

Eukaryotic DNA copying is tightly regulated and must duplicate many linear chromosomes before cell division. The process is highly conserved and uses many proteins with specialized roles. It moves through initiation, elongation, and termination, and it ends with two complete sets of chromosomes in the nucleus. Eukaryotic replication shares basic steps with prokaryotic DNA replication, but the larger genome and linear chromosomes require more proteins. Replication begins at multiple origins of...

proofreading

DNA Polymerase Fixes Replication Errors

DNA polymerase helps copy DNA and fix mistakes during replication. It adds nucleotides in a sequence that matches the template DNA strand. The enzyme also has a higher affinity for the correct base, which helps keep DNA replication accurate. As new genomic DNA is made, it is synthesized in the 5’ to 3’ direction. In many cells, DNA polymerases have different jobs in this process. DNA polymerase delta and DNA polymerase epsilon can proofread when nuclear DNA is being copied. These polymerases...

mismatch repair

DNA Mismatch Repair in Replication

DNA mismatch repair fixes copying errors that happen during DNA replication. When DNA polymerase makes a mistake, the cell can detect a wrong base pair, such as A with G or T with C, and replace it with the correct nucleotide. This repair system works in both prokaryotes and eukaryotes and depends on several proteins. The Mutator protein family plays a central role in this process. In bacteria such as Escherichia coli, MutS first binds the mismatch. MutL then helps identify which strand is the...

nucleotide excision repair

DNA Damage Repair by Excision

DNA damage repair by excision protects cells from mutagens that can change DNA. Exposure to environmental mutagens can create bulky lesions that bend the double helix or block transcription. If these changes are not repaired, they can lead to mutations and may contribute to cancer or disease, depending on which DNA sequences are affected. Nucleotide excision repair, or NER, is the process that detects and removes this kind of damage. Specialized proteins scan the DNA for a damaged region, then...

mutations

DNA Changes From Point Mutations to UV Damage

Mutations are changes in the DNA sequence. They can happen by chance during DNA copying, or they can be caused by environmental factors such as radiation and chemicals. Scientists also describe mutations by how much DNA they affect, how they change a protein, and whether they happen in body cells or germline cells. Some mutations affect only one nucleotide, which is a point mutation. When a point mutation falls inside a gene, the outcome depends on how the amino acid sequence changes. A silent...

transcription

Transcription and Gene Control

Transcription and gene control explain how cells make RNA from DNA and decide which genes are active. RNA polymerase copies a DNA sequence into RNA, and this is the first step in making a protein from a gene. Many other proteins and control sequences help make messenger RNA, or mRNA, correctly. In eukaryotes, the DNA is first copied into a primary RNA, also called pre-mRNA. This RNA can then be processed into mature mRNA, which serves as the template for protein synthesis. In prokaryotes such...

translation

Protein Synthesis and mRNA Decoding

Protein synthesis begins when ribosomes decode messenger RNA (mRNA) and build a chain of amino acids. This final step of gene expression is called translation. The finished chain is a polypeptide, which can later become a functional protein. Proteins are often called the building blocks of life because they make up much of the body, from muscle fibers to hairs and immune system parts. The instructions for each protein are encoded in genes found in the DNA of every cell. In biology, the central...

bacterial transformation

Griffith’s Mouse Experiment and DNA

Bacterial transformation explains how DNA can move into bacteria and change their traits. Frederick Griffith first noticed this in 1928 while studying pneumonia-causing Streptococcus pneumoniae in mice. He compared one pathogenic strain with one non-pathogenic strain and found that only the pathogenic strain killed the host mice. Griffith made an unexpected discovery when he killed the pathogenic bacteria and mixed their remains with live, non-pathogenic bacteria. The mixture killed the mice,...

key terms and concepts

Explore how eukaryotic genes are organized with exons, introns, intergenic regions, and regulatory DNA, plus how splicing and alternative splicing work.

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Genes, Introns, and Regulatory DNA

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