Nucleic Acids and the Genetic Information

Deoxyribonucleic acid (DNA) is the fundamental hereditary material. It stores and preserves the genetic information that determines the physical characteristics and various functions of living organisms. Ribonucleic acid (RNA) is involved in the transcription and translation of DNA for the synthesis of proteins. Nucleotides are the building blocks of DNA and RNA and both molecules are composed of a chain of nucleotides. Nucleotides are capable of storing energy and reducing power. A nucleotide is made up of three basic units: phosphoric acid, a pentose sugar, and a nitrogenous base. The pentose used is ribose if the polynucleotide is RNA and is deoxyribose if the polynucleotide is DNA. The nitrogenous bases can be separated into two groups, purines and pyrimidines. Adenine (A) and guanine (G) are the two purines found in both DNA and RNA. The pyrimidine common to both DNA and RNA is cytosine (C). Thymine (T) is used in DNA and uracil (U) is used in the formation of RNA. The basic structure of the deoxyribonucleotides and ribonucleotides is shown in Figure 1.

DNA Structure

The DNA molecule takes the form of a double stranded helix with a uniform diameter. The sugar (deoxyribose) phosphates bound by phosphodiester bonds lie on the outside of the helix. The nitrogenous bases point toward the center. Complementary bases of the two polynucleitde strands are paired in the molecule and held together by hydrogen bonds. Adenine (A) pairs with thymine (T) sharing two hydrogen bonds and cytosine (C) pairs with guanine (G) sharing three hydrogen bonds. The two strands run in opposite directions in the molecule. As shown in Figure 2, the phosphate groups connect to the 3’ carbon and the 5’ carbon of the successive sugar molecules. So one strand extends from the 5’ carbon to the 3’carbon, while the other extends from the 3’ carbon to the 5’ carbon when matched together. Figure 2 shows a general portion of the DNA structure within the helix formation. The base sequence represents the genetic information need for protein synthesis.

RNA Structure

The RNA molecule consists of one polynucleotide strand with ribose as the successive sugar. Phosphodiester bonds bind the phosphate and sugar molecules. The nitrogenous bases of the molecule include adenine, uracil, guanine, and cytosine.

Replication of DNA

Replication involves the generation of new DNA from original DNA. The process is semi-conservative meaning that each of the two strands in the parent molecule unwind, separate, serve as a template for a new complementary strand and form new bonds with that strand. The process is briefly described as follows: The double helix unwinds and the strands separate creating a replication fork. The replication fork is a moving Y-shaped structure that indicates the region of new strand formation. DNA polymerase III catalyzes the replication of both strands. New paired nucleotides are added to the 3’ end of the original polynucleotide chain so the molecule grows from the 5’ to 3’ direction. A short RNA strand called a primer begins the new strands. The replication process is smooth for one of the strands because initially its 3’ end is exposed. This strand is referred to as the leading strand. For the other strand, the lagging strand, the 5’ end is exposed and synthesis takes place in discontinuous fragments. The 5’ end of the nucleotide is added to the 3’ end of the new strand, however the DNA is being constructed in the opposite direction with respect to the movement of the replication fork. These shorter, backward stretches of new DNA with gaps between them are called Okazaki fragments. The RNA primer is removed and the gaps are filled by DNA polymerase I while DNA ligase links the fragments together. The mechanism of DNA replication is illustrated in Figure 3.

In bacterial cells DNA replication only occurs at one point, the origin of replication. In eukaryotic cells, the chromosomes (DNA with additional integrated proteins) have many origins of replication for the various genes.

Polymerase Chain Reaction

The polymerase chain reaction (PCR) is a powerful technique that is used to amplify replication of DNA molecules. It is capable of producing billions of copies of a DNA sequence of interest within hours whereas conventional cloning usually takes days to weeks. The process is cyclic so the steps are continually repeated. First, the strands are denatured by heat (94° C) in order to get two separate strands. DNA primers are added to the 3’ end of the target sequence. The researcher needs to know approximately the initial 20 bases at the 3’ end so he/she can introduce the appropriate complementary primer. Temperature resistant DNA polymerase is used to catalyze the synthesis of the new complementary strands, the strands rewind and the cycle is repeated. Completion of one cycle doubles the amount of DNA from the previous sequence.

Automated PCR machines can be found in many research laboratories. The technique can be used to diagnose diseases, analyze ancient DNA that has been preserved and to make identifications from hairs and bodily fluids during criminal investigations.

The Central Dogma of Biology

The central dogma of biology describes the relationship between DNA, RNA, and protein synthesis and is represented by the graphic below.

The DNA molecule stores information. That information can be replicated to generate identical molecules or transcribed to produce RNA molecules of various functions. The information stored by the RNA molecules can then be translated to synthesize the proteins that mediate all the structural and metabolic functions of the cell.

Transcription

The transcription process can produce three types of RNA, messenger, transfer, and ribosomal. Messenger RNA (m-RNA) carries the genetic information from chromosomes to ribosomes. Transfer RNA (t-RNA) transports specific amino acids to the site of protein synthesis on the ribosomes. Ribosomal RNA (r-RNA) is a major component of the ribosome structure (~65%). RNA polymerase catalyzes the construction of RNA from DNA. Transcription is initiated at a specific DNA sequence called the promoter region. The DNA molecule unwinds and RNA polymerase reads one of the two strands in the 3’ to 5’ direction. Elongation of RNA along the template strand takes place in the 5’ to 3’ direction. Nucleotides are added to the new RNA molecule so the nitrogenous bases are complementary to the DNA template strand. Uracil (U) is complementary to adenine (A) and cytosine (C) is complementary to guanine (G). As the transcribed RNA is released the DNA strands rewind. Transcription stops at a specific DNA sequence called the transcription terminator. The procedural events for transcription in prokaryotic and eukaryotic cells can differ slightly.

Translation

The exchange of information between different cellular machinery is mediated through a language called the genetic code. The code is made up of three letter sequences called codons and uses a total of four letters, A, G, U and C. The codons represent a specific amino acid. The code is considered degenerate because more than one codon can be used to indicate the same amino acid. The genetic code is provided in Figure 4.

There are three codons that do not encode for an amino acid but serve as indicators for the stopping points of translation. These chain terminators are UAA, UAG, and UGA and usually occur at the end of each transcribed gene. Translation is initiated when the ribosome attaches to a messenger RNA molecule. The start codon is always AUG or GUG. A transfer RNA molecule with the anticodon to match and encoded amino acid attached enters a specific site of the ribosome. This begins the chain of amino acids that define the primary structure of the new protein. The ribosome continues to move along the m-RNA, codon by codon, and a new t-RNA enters the ribosome adding a new amino acid to the chain. As this process continues, the protein chain elongates. Translation is terminated when a stop codon is reached and the new protein, final t-RNA, and ribosome units dissociate. The resulting protein can be modified through the addition of phosphorous, lipids, sugars, or other compounds.

Back to Table of Contents
Forward to Nucleic Acids and the Genetic Information HW