DNA Is a Structure That Encodes Biological Information

A schematic shows three double-stranded DNA molecules against a white background. The sugar-phosphate backbone of the molecule in the middle of the frame is represented as a segmented grey cylinder coiled into a double helical shape. Base pairs are represented as twisted rectangular prisms connecting the two strands and resemble rungs on a ladder, each half of the rungs being a different color, either blue-orange or green-red. The different colors represent the different nucleotide bases that make up each pair. DNA molecules on the lower left and upper right resemble the molecule shown in the center, but are shown only in grey scale.

What do a human, a rose, and a bacterium have in common? Each of these things — along with every other organism on Earth — contains the molecular instructions for life, called deoxyribonucleic acid or DNA. Encoded within this DNA are the directions for traits as diverse as the color of a person's eyes, the scent of a rose, and the way in which bacteria infect a lung cell.

DNA is found in nearly all living cells. However, its exact location within a cell depends on whether that cell possesses a special membrane-bound organelle called a nucleus. Organisms composed of cells that contain nuclei are classified as eukaryotes, whereas organisms composed of cells that lack nuclei are classified as prokaryotes. In eukaryotes, DNA is housed within the nucleus, but in prokaryotes, DNA is located directly within the cellular cytoplasm, as there is no nucleus available.

But what, exactly, is DNA? In short, DNA is a complex molecule that consists of many components, a portion of which are passed from parent organisms to their offspring during the process of reproduction. Although each organism's DNA is unique, all DNA is composed of the same nitrogen-based molecules. So how does DNA differ from organism to organism? It is simply the order in which these smaller molecules are arranged that differs among individuals. In turn, this pattern of arrangement ultimately determines each organism's unique characteristics, thanks to another set of molecules that "read" the pattern and stimulate the chemical and physical processes it calls for.

What components make up DNA?

A labeled schematic shows the two basic components of a single nucleotide molecule. An elongated, red, vertical rectangle is labeled as the nitrogenous base. A gray rectangle, about half as long but twice as wide, is attached to the bottom of the red rectangle and represents a sugar molecule. The bottom-left corner of the sugar molecule is labeled the 3-prime side, and the bottom right corner of the sugar molecule is labeled the 5-prime side, or phosphate side.

Figure 1: A single nucleotide contains a nitrogenous base (red), a deoxyribose sugar molecule (gray), and a phosphate group attached to the 5' side of the sugar (indicated by light gray). Opposite to the 5' side of the sugar molecule is the 3' side (dark gray), which has a free hydroxyl group attached (not shown).

At the most basic level, all DNA is composed of a series of smaller molecules called nucleotides. In turn, each nucleotide is itself made up of three primary components: a nitrogen-containing region known as a nitrogenous base, a carbon-based sugar molecule called deoxyribose, and a phosphorus-containing region known as a phosphate group attached to the sugar molecule (Figure 1). There are four different DNA nucleotides, each defined by a specific nitrogenous base: adenine (often abbreviated "A" in science writing), thymine (abbreviated "T"), guanine (abbreviated "G"), and cytosine (abbreviated "C") (Figure 2).

Figure 2: The four nitrogenous bases that compose DNA nucleotides are shown in bright colors: adenine (A, green), thymine (T, red), cytosine (C, orange), and guanine (G, blue).

Although nucleotides derive their names from the nitrogenous bases they contain, they owe much of their structure and bonding capabilities to their deoxyribose molecule. The central portion of this molecule contains five carbon atoms arranged in the shape of a ring, and each carbon in the ring is referred to by a number followed by the prime symbol ('). Of these carbons, the 5' carbon atom is particularly notable, because it is the site at which the phosphate group is attached to the nucleotide. Appropriately, the area surrounding this carbon atom is known as the 5' end of the nucleotide. Opposite the 5' carbon, on the other side of the deoxyribose ring, is the 3' carbon, which is not attached to a phosphate group. This portion of the nucleotide is typically referred to as the 3' end (Figure 1). When nucleotides join together in a series, they form a structure known as a polynucleotide. At each point of juncture within a polynucleotide, the 5' end of one nucleotide attaches to the 3' end of the adjacent nucleotide through a connection called a phosphodiester bond (Figure 3). It is this alternating sugar-phosphate arrangement that forms the "backbone" of a DNA molecule.

Figure 3: All polynucleotides contain an alternating sugar-phosphate backbone. This backbone is formed when the 3' end (dark gray) of one nucleotide attaches to the 5' phosphate end (light gray) of an adjacent nucleotide by way of a phosphodiester bond.

How is the DNA strand organized?

Although DNA is often found as a single-stranded polynucleotide, it assumes its most stable form when double stranded. Double-stranded DNA consists of two polynucleotides that are arranged such that the nitrogenous bases within one polynucleotide are attached to the nitrogenous bases within another polynucleotide by way of special chemical bonds called hydrogen bonds. This base-to-base bonding is not random; rather, each A in one strand always pairs with a T in the other strand, and each C always pairs with a G. The double-stranded DNA that results from this pattern of bonding looks much like a ladder with sugar-phosphate side supports and base-pair rungs.

Note that because the two polynucleotides that make up double-stranded DNA are "upside down" relative to each other, their sugar-phosphate ends are anti-parallel, or arranged in opposite orientations. This means that one strand's sugar-phosphate chain runs in the 5' to 3' direction, whereas the other's runs in the 3' to 5' direction (Figure 4). It's also critical to understand that the specific sequence of A, T, C, and G nucleotides within an organism's DNA is unique to that individual, and it is this sequence that controls not only the operations within a particular cell, but within the organism as a whole.

A schematic shows 24 nucleotides arranged to form a double-stranded segment of DNA using grey horizontal cylinders as sugar molecules and colored vertical rectangles as nitrogenous bases.

Figure 4: Double-stranded DNA consists of two polynucleotide chains whose nitrogenous bases are connected by hydrogen bonds. Within this arrangement, each strand mirrors the other as a result of the anti-parallel orientation of the sugar-phosphate backbones, as well as the complementary nature of the A-T and C-G base pairing.

Figure Detail

$Rosalind Franklin used X-ray diffraction to obtain this image of DNA. Images like this one enabled the precise calculation of molecular distances within the double helix.$

Figure 5: Rosalind Franklin's X-ray diffraction image of DNA. Images like this one enabled the precise calculation of molecular distances within the double helix.

Beyond the ladder-like structure described above, another key characteristic of double-stranded DNA is its unique three-dimensional shape. The first photographic evidence of this shape was obtained in 1952, when scientist Rosalind Franklin used a process called X-ray diffraction to capture images of DNA molecules (Figure 5). Although the black lines in these photos look relatively sparse, Dr. Franklin interpreted them as representing distances between the nucleotides that were arranged in a spiral shape called a helix.

Around the same time, researchers James Watson and Francis Crick were pursuing a definitive model for the stable structure of DNA inside cell nuclei. Watson and Crick ultimately used Franklin's images, along with their own evidence for the double-stranded nature of DNA, to argue that DNA actually takes the form of a double helix, a ladder-like structure that is twisted along its entire length (Figure 6). Franklin, Watson, and Crick all published articles describing their related findings in the same issue of Nature in 1953.

Figure 6: The double helix looks like a twisted ladder.

How is DNA packaged inside cells?

Supercoiled DNA is tightly packed inside the chromosomes.

Figure 7: To better fit within the cell, long pieces of double-stranded DNA are tightly packed into structures called chromosomes.

Most cells are incredibly small. For instance, one human alone consists of approximately 100 trillion cells. Yet, if all of the DNA within just one of these cells were arranged into a single straight piece, that DNA would be nearly two meters long! So, how can this much DNA be made to fit within a cell? The answer to this question lies in the process known as DNA packaging, which is the phenomenon of fitting DNA into dense compact forms (Figure 7).

Chromatin

During DNA packaging, long pieces of double-stranded DNA are tightly looped, coiled, and folded so that they fit easily within the cell. Eukaryotes accomplish this feat by wrapping their DNA around special proteins called histones, thereby compacting it enough to fit inside the nucleus (Figure 8). Together, eukaryotic DNA and the histone proteins that hold it together in a coiled form is called chromatin.

A schematic shows coils of DNA wound around hundreds of nucleosomes. The DNA looks like grey thread bordering the nucleosomes, which look like red discs.

Figure 8: In eukaryotic chromatin, double-stranded DNA (gray) is wrapped around histone proteins (red).

DNA can be further compressed through a twisting process called supercoiling (Figure 9). Most prokaryotes lack histones, but they do have supercoiled forms of their DNA held together by special proteins. In both eukaryotes and prokaryotes, this highly compacted DNA is then arranged into structures called chromosomes. Chromosomes take different shapes in different types of organisms. For instance, most prokaryotes have a single circular chromosome, whereas most eukaryotes have one or more linear chromosomes, which often appear as X-shaped structures . At different times during the life cycle of a cell, the DNA that makes up the cell's chromosomes can be tightly compacted into a structure that is visible under a microscope, or it can be more loosely distributed and resemble a pile of string.

DNA forms a structure of coils within coils.

Figure 9: Supercoiled eukaryotic DNA.

How do scientists visualize DNA?

Figure 10: This karyotype depicts all 23 pairs of chromosomes in a human cell, including the sex-determining X and Y chromosomes that together make up the twenty-third set (lower right).

It is impossible for researchers to see double-stranded DNA with the naked eye — unless, that is, they have a large amount of it. Modern laboratory techniques allow scientists to extract DNA from tissue samples, thereby pooling together miniscule amounts of DNA from thousands of individual cells. When this DNA is collected and purified, the result is a whitish, sticky substance that is somewhat translucent.

To actually visualize the double-helical structure of DNA, researchers require special imaging technology, such as the X-ray diffraction used by Rosalind Franklin. However, it is possible to see chromosomes with a standard light microscope, as long as the chromosomes are in their most condensed form. To see chromosomes in this way, scientists must first use a chemical process that attaches the chromosomes to a glass slide and stains or "paints" them. Staining makes the chromosomes easier to see under the microscope. In addition, the banding patterns that appear on individual chromosomes as a result of the staining process are unique to each pair of chromosomes, so they allow researchers to distinguish different chromosomes from one another. Then, after a scientist has visualized all of the chromosomes within a cell and captured images of them, he or she can arrange these images to make a composite picture called a karyotype (Figure 10).