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The Information in DNA Is Decoded by Transcription

A schematic shows a region of DNA in a horizontal position. A green blob representing RNA polymerase is shown synthesizing a complementary RNA strand in a right to left direction. A transparent green globular structure, representing the enzyme RNA polymerase, is bound to a several-nucleotide long region along the DNA strand. To the left of RNA polymerase, a single-stranded DNA molecule is present; to the right of RNA polymerase, the single-stranded DNA molecule is paired with a complementary strand of RNA. On the DNA strand, the sugar-phosphate backbone is depicted as a segmented grey cylinder; on the RNA strand, the sugar-phosphate backbone is depicted as a segmented white cylinder. Nitrogenous bases are represented as colored vertical rectangles attached to each segment on the sugar-phosphate backbone. On the DNA strand, the nitrogenous bases are either red, blue, green, or orange; on the RNA strand, the red nucleotides have been replaced by yellow nucleotides. The region of DNA bound by RNA polymerase is visible inside the transparent enzyme at a higher magnification. Six nucleotides in this region are bound to six complementary nucleotides arranged above and in parallel to the single strand. About a half dozen individual nucleotides float in the background.

DNA is essentially a storage molecule. It contains all of the instructions a cell needs to sustain itself. These instructions are found within genes, which are sections of DNA made up of specific sequences of nucleotides. In order to be implemented, the instructions contained within genes must be expressed, or copied into a form that can be used by cells to produce the proteins needed to support life.

The instructions stored within DNA are read and processed by a cell in two steps: transcription and translation. Each of these steps is a separate biochemical process involving multiple molecules. During transcription, a portion of the cell's DNA serves as a template for creation of an RNA molecule. (RNA, or ribonucleic acid, is chemically similar to DNA, except for three main differences described later on in this concept page.) In some cases, the newly created RNA molecule is itself a finished product, and it serves an important function within the cell. In other cases, the RNA molecule carries messages from the DNA to other parts of the cell for processing. Most often, this information is used to manufacture proteins. The specific type of RNA that carries the information stored in DNA to other areas of the cell is called messenger RNA, or mRNA.

How does transcription proceed?

Transcription begins when an enzyme called RNA polymerase attaches to the DNA template strand and begins assembling a new chain of nucleotides to produce a complementary RNA strand. There are multiple types of types of RNA. In eukaryotes, there are multiple types of RNA polymerase which make the various types of RNA. In prokaryotes, a single RNA polymerase makes all types of RNA. Generally speaking, polymerases are large enzymes that work together with a number of other specialized cell proteins. These cell proteins, called transcription factors, help determine which DNA sequences should be transcribed and precisely when the transcription process should occur.

Initiation

A schematic shows two horizontal strands of DNA against a white background, one in the lower half of the image and one arcing in the upper half. A transparent green globular structure, representing the enzyme RNA polymerase, is bound to a several-nucleotide-long region along the lower DNA strand on the right side. The sugar-phosphate backbone is depicted as a segmented grey cylinder half as long and twice as wide as the nitrogenous bases. Nitrogenous bases are represented as blue, orange, red, or green vertical rectangles attached to each segment of the sugar-phosphate backbone. About three dozen individual nucleotides float in the background. Two individual nucleotides are visible inside the transparent enzyme at a higher magnification.

Figure 1: Transcription begins when RNA polymerase binds to the DNA template strand.

The first step in transcription is initiation. During this step, RNA polymerase and its associated transcription factors bind to the DNA strand at a specific area that facilitates transcription (Figure 1). This area, known as a promoter region, often includes a specialized nucleotide sequence, TATAAA, which is also called the TATA box (not shown in Figure 1)

Strand elongation

Figure 2: RNA polymerase (green) synthesizes a strand of RNA that is complementary to the DNA template strand below it.

Once RNA polymerase and its related transcription factors are in place, the single-stranded DNA is exposed and ready for transcription. At this point, RNA polymerase begins moving down the DNA template strand in the 3' to 5' direction, and as it does so, it strings together complementary nucleotides. By virtue of complementary base- pairing, this action creates a new strand of mRNA that is organized in the 5' to 3' direction. As the RNA polymerase continues down the strand of DNA, more nucleotides are added to the mRNA, thereby forming a progressively longer chain of nucleotides (Figure 2). This process is called elongation.

A schematic compares a single-stranded DNA molecule with a single-stranded RNA molecule with a similar sequence. Both RNA and DNA contain nitrogenous bases, represented by vertical colored rectangles, attached to a sugar-phosphate backbone, represented as a segmented cylinder. There are two major differences between the composition of RNA and DNA strands. The sugar in the DNA strand is deoxyribose, represented by a grey cylinder, whereas the sugar in the RNA strand is ribose, represented by a white cylinder. In addition, the nitrogenous base thymine (red) in the DNA strand is replaced by uracil (yellow) in the RNA strand.

Figure 3: DNA (top) includes thymine (red); in RNA (bottom), thymine is replaced with uracil (yellow).

Three of the four nitrogenous bases that make up RNA — adenine (A), cytosine (C), and guanine (G) — are also found in DNA. In RNA, however, a base called uracil (U) replaces thymine (T) as the complementary nucleotide to adenine (Figure 3). This means that during elongation, the presence of adenine in the DNA template strand tells RNA polymerase to attach a uracil in the corresponding area of the growing RNA strand (Figure 4).

A schematic shows two rows of nucleotides. Each individual nucleotide is represented as an elongated, vertical, colored rectangle (a nitrogenous base) bound at one end to a grey horizontal cylinder (a sugar molecule). The top row of nucleotides is from RNA, with an A-C-U-G base sequence. The bottom row of nucleotides is from DNA, with a T-G-A-C base sequence.

Figure 4: A sample section of RNA bases (upper row) paired with DNA bases (lower row). When this base-pairing happens, RNA uses uracil (yellow) instead of thymine to pair with adenine (green) in the DNA template below.

Interestingly, this base substitution is not the only difference between DNA and RNA. A second major difference between the two substances is that RNA is made in a single-stranded, nonhelical form. (Remember, DNA is almost always in a double-stranded helical form.) Furthermore, RNA contains ribose sugar molecules, which are slightly different than the deoxyribosemolecules found in DNA. As its name suggests, ribose has more oxygen atoms than deoxyribose.

Thus, the elongation period of transcription creates a new mRNA molecule from a single template strand of DNA. As the mRNA elongates, it peels away from the template as it grows (Figure 5). This mRNA molecule carries DNA's message from the nucleus to ribosomes in the cytoplasm, where proteins are assembled. However, before it can do this, the mRNA strand must separate itself from the DNA template and, in some cases, it must also undergo an editing process of sort.

A schematic shows two strands of DNA against a white background, each going from the lower left to the upper middle of the frame. A transparent green globular structure, representing the enzyme RNA polymerase, is bound to a several-nucleotide-long region along the lower DNA strand. The sugar-phosphate backbone of the DNA is depicted as a segmented grey cylinder. Nitrogenous bases are represented as colored vertical rectangles attached to each segment on the sugar-phosphate backbone. A newly synthesized RNA strand is shown in the foreground of the illustration. It snakes down to the RNA polymerase. In the RNA strand, uracil, represented by a yellow base, has been inserted in place of thymine.

Figure 5: During elongation, the new RNA strand becomes longer and longer as the DNA template is transcribed. In this view, the 5' end of the RNA strand is in the foreground. Note the inclusion of uracil (yellow) in RNA.

Termination and editing

A schematic shows a single-stranded region of RNA on a white surface that has had a loop, or intron, removed.

Figure 6: In eukaryotes, noncoding regions called introns are often removed from newly synthesized mRNA.

Figure Detail

As previously mentioned, mRNA cannot perform its assigned function within a cell until elongation ends and the new mRNA separates from the DNA template. This process is referred to as termination. In eukaryotes, the process of termination can occur in several different ways, depending on the exact type of polymerase used during transcription. In some cases, termination occurs as soon as the polymerase reaches a specific series of nucleotides along the DNA template, known as the termination sequence. In other cases, the presence of a special protein known as a termination factor is also required for termination to occur.

A schematic shows a chain of eight adenine nucleotides standing upright on a white surface. An elongated, green, vertical rectangle represents the adenine base. A grey cylinder, about half as long but twice as wide as the base, is attached to the top of the green rectangle and represents a sugar-phosphate molecule. Each grey cylinder is connected to the grey cylinder adjacent to it.

Figure 7: In eukaryotes, a poly-A tail is often added to the completed, edited mRNA molecule to signal that this molecule is ready to leave the nucleus through a nuclear pore.

Once termination is complete, the mRNA molecule falls off the DNA template. At this point, at least in eukaryotes, the newly synthesized mRNA undergoes a process in which noncoding nucleotide sequences, called introns, are clipped out of the mRNA strand. This process "tidies up" the molecule and removes nucleotides that are not involved in protein production (Figure 6). Then, a sequence of adenine nucleotides called a poly-A tail is added to the 3' end of the mRNA molecule (Figure 7). This sequence signals to the cell that the mRNA molecule is ready to leave the nucleus and enter the cytoplasm.