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Biology for AP® Courses

16.1 Regulation of Gene Expression

Biology for AP® Courses16.1 Regulation of Gene Expression

Learning Objectives

In this section, you will explore the following question:

  • How does prokaryotic gene regulation differ from eukaryotic gene regulation?

Connection for AP® Courses

Structure and function in biology result from the presence of genetic information and the correct expression of this information. In the chapter on DNA structure and function, we explored how genes are translated into proteins, which in turn determine the nature of the cell. But how does a cell know when to “turn on” its DNA? With few exceptions, each cell in your body contains identical genetic information. If each cell has the same exact DNA make up, how is it that a liver cell differs from a nerve or muscle cell?

As we will discover, although each cell shares the same genome and DNA sequence, each cell does not express exactly the same genes. Many factors determine when and how genes are expressed in a given cell. Even the type of chromosome a gene is located on, like whether it is a sex chromosome or not, can determine its expression pattern, as can mutations or changes in DNA sequence and other external factors. In prokaryotes, gene expression is regulated primarily at the level of transcription, when DNA is copied into RNA. However, eukaryotes have evolved regulatory mechanisms in gene expression at multiple levels. In all cases, regulation of gene expression determines the type and amount of protein produced in the cell. Errors in regulatory processes can result in many human diseases and conditions, including cancer.

Gene expression regulation occurs at different points in prokaryotes and eukaryotes. Prokaryotic organisms express their entire genome in every cell, but not necessarily all at the same time. In general, a gene is expressed only when its specific protein product is needed. Remember that each cell in an organism carries the same DNA as every other cell. Yet cells of eukaryotic organisms each express a unique subset of DNA depending on cell type. To express a protein, DNA is first transcribed into RNA, which is then translated into proteins. In prokaryotic cells, transcription and translation occur almost simultaneously. In eukaryotic cells, transcription occurs in the nucleus, separate from the translation that occurs in the cytoplasm along ribosomes attached to endoplasmic reticulum. As stated above, gene expression in prokaryotes is regulated at the level of transcription, whereas in eukaryotes, gene expression is regulated at multiple levels, including the epigenetic (DNA), transcriptional, pre- and post-transcriptional, and translational levels.

The science of epigenetics studies heritable changes in the genome that do not affect the underlying DNA gene sequences.

The content presented in this section supports the learning objectives outlined in Big Idea 3 of the AP® Biology Curriculum Framework. The AP® learning objectives merge essential knowledge content with one or more of the seven science practices. These objectives provide a transparent foundation for the AP® Biology course, along with inquiry-based laboratory experiences, instructional activities, and AP® exam questions.

Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes.
Enduring Understanding 3.B Expression of genetic information involves cellular and molecular mechanisms.
Essential Knowledge 3.B.1 Gene regulation results in differential gene expression, leading to cell specialization
Science Practice 7.1 The student can connect phenomena and models across spatial and temporal scales.
Learning Objective 3.18 The student is able to describe the connection between the regulation of gene expression and observed differences between different kinds of organisms.

For a cell to function properly, necessary proteins must be synthesized at the proper time. All cells control or regulate the synthesis of proteins from information encoded in their DNA. The process of turning on a gene to produce RNA and protein is called gene expression. Whether in a simple unicellular organism or a complex multi-cellular organism, each cell controls when and how its genes are expressed. For this to occur, there must be a mechanism to control when a gene is expressed to make RNA and protein, how much of the protein is made, and when it is time to stop making that protein because it is no longer needed.

Although genetic differences between species and between individuals within a species are often responsible for phenotypic differences, another mechanism that can create phenotypic differences is differences in gene expression. For example, although every cell in an organism contains the same genes, the bone cells in the organism appears different from the fat cells due to differences in which genes are expressed by which cell. Similarly, although mice and humans share approximately 97.5% of their genes, they are very different organisms because different genes are turned on at different times during development and in different cells. Even organisms that share 100% identity in their genomes (a.k.a clones) can eventually appear different if they express their genes differently in response to different environmental conditions, for example. Even among humans, identical twins can possess different birthmarks, wrinkles, or other features that arise during development sometimes due to differential gene expression.

The regulation of gene expression conserves energy and space. It would require a significant amount of energy for an organism to express every gene at all times, so it is more energy efficient to turn on the genes only when they are required. In addition, only expressing a subset of genes in each cell saves space because DNA must be unwound from its tightly coiled structure to transcribe and translate the DNA. Cells would have to be enormous if every protein were expressed in every cell all the time.

The control of gene expression is extremely complex. Malfunctions in this process are detrimental to the cell and can lead to the development of many diseases.

Teacher Support

Ask students what genes are present in the DNA in a muscle cell and skin cell. Ask them if the same genome is present in every cell in the body, how do the cells have different properties. For example, discuss red blood cells, which lose their nucleus during development. This video gives an overview of gene regulation in prokaryotes and eukaryotes.

Prokaryotic versus Eukaryotic Gene Expression

To understand how gene expression is regulated, we must first understand how a gene codes for a functional protein in a cell. The process occurs in both prokaryotic and eukaryotic cells, just in slightly different manners.

Prokaryotic organisms are single-celled organisms that lack a cell nucleus, and their DNA therefore floats freely in the cell cytoplasm. To synthesize a protein, the processes of transcription and translation occur almost simultaneously. When the resulting protein is no longer needed, transcription stops. As a result, the primary method to control what type of protein and how much of each protein is expressed in a prokaryotic cell is the regulation of DNA transcription. All of the subsequent steps occur automatically. When more protein is required, more transcription occurs. Therefore, in prokaryotic cells, the control of gene expression is mostly at the transcriptional level.

Eukaryotic cells, in contrast, have intracellular organelles that add to their complexity. In eukaryotic cells, the DNA is contained inside the cell’s nucleus and there it is transcribed into RNA. The newly synthesized RNA is then transported out of the nucleus into the cytoplasm, where ribosomes translate the RNA into protein. The processes of transcription and translation are physically separated by the nuclear membrane; transcription occurs only within the nucleus, and translation occurs only outside the nucleus in the cytoplasm. The regulation of gene expression can occur at all stages of the process (Figure 16.2). Regulation may occur when the DNA is uncoiled and loosened from nucleosomes to bind transcription factors (epigenetic level), when the RNA is transcribed (transcriptional level), when the RNA is processed and exported to the cytoplasm after it is transcribed (post-transcriptional level), when the RNA is translated into protein (translational level), or after the protein has been made (post-translational level).

Prokaryotic cells do not have a nucleus, and DNA is located in the cytoplasm. Ribosomes attach to the mRNA as it is being transcribed from DNA. Thus, transcription and translation occur simultaneously. In eukaryotic cells, the DNA is located in the nucleus, and ribosomes are located in the cytoplasm. After being transcribed, pre-mRNA is processed in the nucleus to make the mature mRNA, which is then exported to the cytoplasm where ribosomes become associated with it and translation begins.
Figure 16.2 Prokaryotic transcription and translation occur simultaneously in the cytoplasm, and regulation occurs at the transcriptional level. Eukaryotic gene expression is regulated during transcription and RNA processing, which take place in the nucleus, and during protein translation, which takes place in the cytoplasm. Further regulation may occur through post-translational modifications of proteins.

The differences in the regulation of gene expression between prokaryotes and eukaryotes are summarized in Table 16.1. The regulation of gene expression is discussed in detail in subsequent modules.

Differences in the Regulation of Gene Expression of Prokaryotic and Eukaryotic Organisms
Prokaryotic organismsEukaryotic organisms
Lack nucleusContain nucleus
DNA is found in the cytoplasmDNA is confined to the nuclear compartment
RNA transcription and protein formation occur almost simultaneouslyRNA transcription occurs prior to protein formation, and it takes place in the nucleus. Translation of RNA to protein occurs in the cytoplasm.
Gene expression is regulated primarily at the transcriptional levelGene expression is regulated at many levels (epigenetic, transcriptional, nuclear shuttling, post-transcriptional, translational, and post-translational)
Table 16.1

Evolution Connection

Evolution of Gene Regulation

Prokaryotic cells can only regulate gene expression by controlling the amount of transcription. As eukaryotic cells evolved, the complexity of the control of gene expression increased. For example, with the evolution of eukaryotic cells came compartmentalization of important cellular components and cellular processes. A nuclear region that contains the DNA was formed. Transcription and translation were physically separated into two different cellular compartments. It therefore became possible to control gene expression by regulating transcription in the nucleus, and also by controlling the RNA levels and protein translation present outside the nucleus.

Some cellular processes arose from the need of the organism to defend itself. Cellular processes such as gene silencing developed to protect the cell from viral or parasitic infections. If the cell could quickly shut off gene expression for a short period of time, it would be able to survive an infection when other organisms could not. Therefore, the organism evolved a new process that helped it survive, and it was able to pass this new development to offspring.

Cytochrome c is an important component of the electron transport chain, a part of cellular respiration, and it is normally located in the cellular organelle, the mitochondrion. This protein has a heme prosthetic group, and the heme's central ion alternately reduces and oxidizes during electron transfer. Because this essential protein’s role in producing cellular energy is crucial, it has changed very little over millions of years. Protein sequencing has shown that there is a considerable amount of cytochrome c amino acid sequence homology among different species. In other words, we can assess evolutionary kinship by measuring the similarities or differences among various species’ DNA or protein sequences.
Cytochrome c oxidase is a highly conserved protein found in bacteria and in the mitochondria of eukaryotes. Based on your knowledge of evolutionary relationships, which of the following statements would you expect to be true of the cytochrome c oxidase protein sequence?
  1. The bacterial protein will be more similar to the human protein than the yeast protein.
  2. The yeast protein will be more similar to the human protein than the bacterial protein.
  3. The bacterial protein will be more similar to the yeast protein than the human protein.
  4. The bacterial and yeast proteins will share a similar sequence, but the human protein will be unrelated.

Science Practice Connection for AP® Courses

Think About It

How does controlling gene expression alter the overall protein level in the cell?

Teacher Support

The question is an application of Learning Objective 3.18 and Science Practice 7.1 because students are asked to describe the connection between genes, gene expression (i.e., transcription and translation), and how the production of different proteins can result in cell specialization and differences between organisms.


The cell controls which proteins are expressed and to what level each protein is expressed in the cell. Prokaryotic cells alter the transcription rate to turn genes on or off. This method will increase or decrease protein levels in response to what is needed by the cell. Eukaryotic cells change the accessibility (through epigenetic mechanisms), transcription, or translation of a gene. This will alter the amount of RNA and the lifespan of the RNA to alter the amount of protein that exists. Eukaryotic organisms are much more complex and can manipulate protein levels by changing many stages in the process.

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