Notes on Nucleic Acids and Nucleotides

DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are nucleic acids which are polymers of nucleotides. Electron carries such as FAD, NAD, and NADP are dinucleotides. High energy phosphate carriers such as ATP, CTP, GTP, and UTP are single nucleotides.

The Nucleotide Structure Nucleotides are the basic components of nucleic acids. Each nucleotide consists of three components: 1. Pentose Sugar: Each nucleotide contains a five-carbon sugar. The pentose is ribose for ATP, FAD, NAD, NADP, and RNA. The pentose is deoxyribose for DNA. 2. Nitrogenous Base: Each nucleotide contains one nitrogenous base which may be either a purine or a pyrimidine. Pyrimidines consist of a 6-membered ring containing C and N (i.e. cytosine, uracil, and thymine) Purines consist of a 6-membered ring fused to a 5-membered ring (i.e. adenine and guanine) 3. Phosphate Group: Each nucleotide contains one (MP), two (DP), or three (TP) phosphate groups. The letter code for the nitrogenous base plus the letter code for the number of phosphate groups can be used to designate a nucleotide (ex. A nucleotide with adenine and two phosphate groups is ADP). If more than one phosphate group is attached to the nucleotide, the extra phosphates are weakly bonded to the nucleotide and can be easily hydrolyzed to release the energy used to make the bonds and make that energy available to other processes in the cell. Due to the higher number of bonds in triphosphate nucleotides, triphosphate groups are the primary energy source. UTP => used in biosynthetic reactions involving addition of sugars. GTP => used to provide energy for protein shape changed by G proteins involved in receptor-triggered reaction sequences and protein synthesis. Positional Nomenclature Locations of atoms on nucleotides are specified relative to the carbon atoms in the pentose ring. 1. The purine or pyrimidine is attached to the 1 C on the sugar. 2. The phosphate group is attached to the 5 C on the sugar. 3. The hydroxyl group on the 3 C on the sugar is reacted with the phosphate group on the adjacent nucleotide when a nucleotide is added to a DNA or RNA chain.

Nucleotide Base Pairing Nucleotides may base pair with complementary nucleotides by forming H bonds between their nitrogenous bases. Stable base pairs consist of a purine paired with a pyrimidine. Two patterns of base pairing occur naturally. An adenine base pairs with uracil or thymine by forming two hydrogen bonds. A guanine base pairs with cytosine by forming three hydrogen bonds. There are three nucleotide functions in cells: - Nucleotide triphosphates transport energy from energy-generating chemical reactions to energyconsuming reactions within the same cell. - Nucleotide triphosphates serve as monomers for the synthesis of RNA and DNA. - Nucleotides may be modified into chemical signals for use within a cell. RNA Structure RNA is a polymer of ribonucleotides. The purine bases in RNA are adenine and guanine while the pyrimidine bases in RNA are cytosine and uracil. RNA consists of a single linear chain of nucleotides. However, RNA chains may fold and form base pairs between regions of the same chain where complementary sequences occur. RNA Functions Messenger RNA (mRNA) codes for the amino acid sequence (primary structure) of polypeptide chains in proteins. Transfer RNA (tRNA) carries amino acids (as aminoacyl groups on the tRNA) into protein synthesis and uses the nucleotide sequence in a mRNA to determine where to insert the amino acid carried by the tRNA in the forming polypeptide chain. Ribosomal RNA (rRNA) form the structural framework for the ribosomal subunits, and a loop of one of the rRNA molecules appears to be capable of catalyzing the formation of peptide. Several ribonucleicprotein (RNP) particles contains small RNA molecules are involved in RNA and protein processing. Small nuclear ribonucleicproteins (snRNPs) which contain RNA molecules remove introns (DNA regions within a gene that is not translated into a protein) from mRNA in eukaryotes. DNA Structure DNA is made of deoxyribonucleotides. The purine bases in DNA are adenine and guanine. The pyrimidine bases in DNA are cytosine and thymine. The nucleotides within a single DNA chain or strand are joined by covalent bonds linking the 3 carbon on one nucleotide with the phosphate on the 5 carbon of the adjacent nucleotide. A DNA molecule usually consists of two linear chains of nucleotides and is referred to as double-stranded (although some viruses have single-stranded DNA).

The two chains or strands in a DNA molecule are paired by H bonds between complementary base pairs (A-T, G-C). Genetic Information Flow in Cells Genetic information (genotype) is stored in cells in the form of the sequence of deoxyribonucleotides in DNA. The double-stranded nature of DNA allows repair of damage as long as both strands are not damaged in the same location. Genetic information is transmitted from cell to cell during mitosis and from parent to offspring since the deoxyribonucleotide sequence in newly formed DNA molecules during DNA replication. Conversion of genetic information into a cellular phenotype requires a sequence of events. Transcription (RNA Synthesis). The deoxyribonucleotide sequence in regions of DNA (genes) codes for the ribonucleotide sequence in mRNA. The bases in RNA can hydrogen bond to the bases in DNA, so one base in DNA specifies one base (complementary to it) in RNA. Translation (Protein Synthesis). The ribonucleotide sequence in regions of DNA (genes) codes for (serves as a template for) the ribonucleotide sequence in mRNAs codes for the amino acid sequence in proteins (polypeptides). A three nucleotide codon in the mRNA base pairs with the complementary three nucleotide anticodon on an aminoacyl tRNA to allow the aminoacyl group on the aminoacyl tRNA to be added to the polypeptide being synthesized. A three nucleotide unit in mRNA functions as one codon to specify one amino acid in a polypeptide (a polypeptide in turn forms all or part of a protein). The proteins form cellular structures and/or perform or catalyze cell functions. Proteins directly or indirectly produce the phenotype of a cell. Protein Structure Proteins are made of 20 different types of amino acids which share a common backbone structure consisting of an amino group covalently bonded to a carboxylic acid (carboxyl) group. Each of the 20 different types of amino acids differs in the side chain structure attached to the alpha carbon. One amino acid in a polypeptide chain in a protein is specified by a sequence of three nucleotides in a messenger RNA (mRNA). This three nucleotide codon is translated through the mediation of a transfer RNA (tRNA). The amino acid sequence of each polypeptide chain (its primary structure) interacts with the polypeptides environment and with other functional components in the cell. In which the polypeptide was made to determine further modifications and eventual assembly of a functional protein.

Protein Function Structural proteins form all or parts of cell structures such as ribosomes, chromosomes, mitotic spindles, and cell membranes. Enzymes are almost all proteins and are required to catalyze most chemical reactions in cells, including DNA synthesis, RNA synthesis, protein synthesis, carbohydrate synthesis, and lipid synthesis. Most cellular reactions will not occur under normal intracellular conditions without access to the appropriate enzyme. Transport proteins serve as carriers or channels to allow molecules to move across cell membranes. Signal or regulatory proteins respond to changes in a cell by changing their interactions with critical components such as DNA, thereby altering cell functions.