• Biomolecules

    Biomolecules

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Nucleotides

ribose and deoxyribose structural modelsPossibly the first biomolecules to support life, nucleic acids store and transfer cellular information and transfer energy in all living organisms. Deoxyribonucleic acid, better known as DNA, stores hereditary information in small segments called genes inside long polymer strands. Ribonucleic acid (RNA) delivers gene information from DNA to create functional products. Other RNA molecules are active, three-dimensional products that provide enzymatic or regulatory functions inside cells. An enormous body of evidence suggests that RNA was the original molecule of life due to RNA’s ability to both store hereditary information and provide functional activity as enzymes.

Each component of nucleic acid structure plays an important role in DNA and RNA’s ability to store and transmit information during a cell’s life and to deliver a copy into offspring. Nucleic acids are polymers of individual nucleotide monomers. Each nucleotide is composed of three parts: a 5-carbon sugar, a phosphate group, and a nitrogenous base. Only two 5-carbon sugars are found in nature: ribose and deoxyribose. Deoxyribose is a ribose derivative in which an oxygen atom is missing from one carbon; the carbon was deoxygenated. DNA contains deoxyribose nucleotides while RNA contains ribose nucleotides. DNA is more stable than RNA because of the reduction in reactive oxygen atoms.

nucleotide model showing phosphate, 5-carbon sugar, and nitrogenous baseA 5-carbon sugar (ribose or deoxyribose) forms the central molecule in a nucleotide. By convention, the carbon atoms in the sugar are numbered from the original carbonyl position on the chain using a number plus the prime symbol (‘). For example, a nitrogenous base is attached to the 1’ (pronounced “one prime”) carbon position, which was originally the sugar’s carbonyl group. A phosphate group is attached to the 5’ carbon position, the carbon atom that is outside the sugar ring.

Each nucleotide includes one nitrogenous base, attached to the 1’ carbon of the sugar. A nitrogenous base is an organic molecule containing both carbon and nitrogen atoms. The name nitrogenous base signifies that several nitrogen atoms act as bases in solution. In nucleic acids, nitrogenous bases contain either one ring or two fused rings. Purines are double-ring nitrogenous bases found in nature and include adenine and guanine. Thymine, cytosine and uracil are pyrimidines, single-ring nitrogenous bases found in nature.

The sugar and nitrogenous base present in a nucleotide define the nucleotide and its functional role. Because the sugar and phosphate are similar structural components in all nucleotides, scientists frequently use a shorthand notation to identify a nucleotide by naming only the structural model of an ATP moleculeunique nitrogenous base present. For example, “adenine” may refer to the nitrogenous base alone or to a nucleotide containing adenine, depending on the context. Similarly, a nucleotide is often called a “base,” a shorthand reference to the presence of a nitrogenous base in the nucleotide structure.

Like monosaccharides, nucleotides and short nucleotide chains perform important cellular functions. Adenosine triphosphate (ATP) is an important energy carrier in living organisms. ATP is composed of adenine, a ribose sugar, and three phosphate groups bonded sequentially. The bonding of three anionic phosphate groups in a row forces several negative ions into close proximity, an unfavorable state. Reactions that remove the outermost phosphate group (forming adenosine diphosphate, or ADP) release energy for use in other chemical reactions. Dinucleotides such as NAD+, NADP+, and FAD act as coenzymes, delivering energy by transferring electrons from one reaction to another.

 

Building Nucleotides

In this activity, you will select components of a nucleotide and place them in the correct position to form covalent bonds.

 

Nucleic Acid Structure and Function

model of a DNA polymerDNA polymers store hereditary information for each living organism. The unique structure of a DNA polymer provides a template for identification and delivery of the information inside each gene and for accurate replication of DNA during cell division. RNA polymers perform a variety of cellular functions, including delivering DNA messages to synthesize proteins and acting as enzymes or regulatory molecules in many cellular processes. Although less complex than protein structure, RNA polymers frequently form three-dimensional structures specific to their function. Interactions between the nitrogenous bases in DNA and RNA polymers form the basis for the structure, function, and accurate replication of nucleic acids.

Nucleic acids are formed by repeated dehydration synthesis reactions between nucleotides. During dehydration synthesis, a phosphodiester linkage forms between the phosphate group of one nucleotide and the sugar of another nucleotide. Using the chemical convention for carbon numbering in nucleotides, the phosphate group is the 5’ end of a nucleotide because it is bonded to the 5’ carbon of the sugar. Phosphodiester linkages form between the 5’ end of one nucleotide and the 3’ hydroxyl group of another nucleotide, forming a polymer with one open 5’ end and one open 3’ end.

phosphodiester linkages modelInside cells, nucleic acid synthesis occurs by formation of new phosphodiester linkages at the 3’ end of a growing polymer. Although all biomolecule polymers are synthesized in only one direction, the 5’ to 3’ nature of nucleic acid polymers is of particular relevance to many cellular processes, including DNA replication, protein synthesis, and DNA damage repair. Understanding how DNA polymers form is vital to analyzing DNA replication and gene expression in living cells.

Phosphodiester linkages form between the phosphate and sugar segments of each nucleotide, leaving the nitrogenous bases free to interact with one another. Because some nitrogenous bases contain oxygen in addition to nitrogen, hydrogen bonds easily form between separate bases in a specific pattern. DNA polymers form paired strands in which the nitrogenous bases act like a zipper, binding the two strands together.

nitrogenous bases in a DNA moleculeStructurally, nitrogenous bases in a polymer tend to pair in an anti-parallel pattern, meaning that two paired strands of nucleic acid sit in opposite directions. If one strand is viewed from the 5’ end towards the 3’ end, the other strand is sitting 3’ to 5’ in order to form the maximum number of hydrogen bonds. The nucleotide pairs on opposing strands that form hydrogen bonds are frequently called base pairs. In DNA, polymers are almost exclusively found in long, paired anti-parallel strands forming the famous double helix.

All DNA nucleotides contain the sugar deoxyribose and one of four different nitrogenous bases: adenine, guanine, cytosine, or thymine. With only four different nucleotides, it seems impossible that DNA could encode enough information to produce the millions of different proteins and functional RNA molecules that yield such a vast diversity of living organisms. However, the order and choice of nucleotides allows an almost infinite number of possible sequences. Imagine creating a 5-nucleotide chain using only the 4 DNA nucleotides. With these parameters, up to 1,024 possible polymers exist. Imagine how many different polymer sequences are possible for the shortest human chromosome, which is fifty million nucleotides long!

RNA nucleotides are defined by the sugar ribose, and contain a slightly different set of nitrogenous bases: adenine, guanine, cytosine, and uracil. RNA molecules do not contain thymine. Unlike DNA, RNA is usually present in a single-stranded form. Many single-stranded RNA molecules bend and twist into a three-dimensional structure that includes some hydrogen bonding between nucleotides in the same strand. As with protein structure, the three-dimensional structure of an RNA molecule specifies a unique function in cells, including enzyme catalysis.

 

Joining Neucleotides

In this activity, you will select the nucleotide and position to form a phosphodiester linkage.

 

Nucleic Acids: DNA and RNA

Use this activity to compare and contrast the structural and functional attributes typically found in DNA and RNA.

 

Additional Resources

Websites

Nucleic Acids
Learn why a DNA molecules is shaped like a twisted ladder.