Nucleic acids Universal constituents of living matter. They are concerned with the storage, transmission and transfer of genetic information. Vytášek 2008 Presentation is only for internal purposes of 2nd Medical faculty

Nucleic acids polymers in molar mass in the range 20kDa to 4GDa or more two basic types : DNA and RNA during last twenty years rapid development – molecular biology and genetics, genetic engineering etc.

Components of nucleic acids phosphoric acid (H 3 PO 4 ) pentose (5 carbon sugar) D-ribose 2-deoxy-D-ribose (RNA)(DNA)

heterocyclic bases (nucleobases) pyrimidine uracil thymine cytosine (RNA) (DNA) purine adenine guanine

Nucleoside consists of a pentose (ribose or deoxyribose) linked via a  -N-glycosidic bond to a ring nitrogen of nucleobase. Adenosine guanosine cytidine

Nucleotide consists of nucleoside which is esterified by phosphoric acid at either 5´ (usually and exclusively in nucleic acids) or 3´- hydroxyl group of pentose moiety. Nucleotide is monomeric unit of polymeric nucleic acids (polynucleotides) deoxyribonucleotides – dAMP, dGMP, dTMP and dCMP (monomers of DNA) ribonucleotides – AMP, GMP, UMP and CMP (monomers of RNA) AMP

Nucleic acid is polynucleotide chain which contains mononucleotides linked by phosphodiester bonds. 5´-OH group of nucleotide is joined to 3´- OH group of another nucleotide by phosphodiester bond polynucleotide chain contains 5´- and 3´- end and by convention nucleic acid sequence is written from 5´ to 3´ end

RNA

DNA

Most DNAs exist as double-helix (duplex) structures.

Double-helix (duplex) structure of DNA double helix is stabilized by hydrogen bonds of base pairs (A-T, G-C) but also by other forces (van der Waals forces, dipol- dipol interactions, repulsive forces of negatively charged phosphoryl groups etc) denaturation of DNA involves separation of complementary strands DNA renaturation is the formation of duplex structure from single strands

The RNA family

Messenger RNA (mRNA) transfer of information in a gene (DNA) to the protein synthetizing machinery very heterologous in size and stability, each molecule is template for specific protein sequence translation of mRNA to protein begins from 5´-terminus the most of mRNA molecules contains polyA tail at the 3´-hydroxyl teminus (attached adenylate residues)

5´-end is capped

Transfer RNA (tRNA) carries amino acids to the template for protein synthesis small molecules (about 75 nucleotides) at least 20 species of tRNA in every cell corresponding to each of 20 amino acids

Ribosomal RNA (rRNA) integral component of ribosome (specific cytoplasmatic structure for proteosynthesis from mRNA templates) the bulk of cellular RNA three rRNAs 28S 18S and 5,8S catalytic (enzyme like) activity during creation of peptidyl bond

Small interfering RNAs (siRNAs) around 22 nucleotides in length mediate the recently discovered phenomenon of RNA interference (RNAi) mediate the downregulation of gene expression - binding to specific mRNAs labelled them for destruction by enzymes called endonucleases

MicroRNAs (miRNAs) 22–24 nucleotides in length downregulate gene expression - binding to messenger RNAs (mRNAs) causes preventing mRNAs from being translated into proteins

Gene silencing in mammals by microRNAs and small interfering RNAs Nature Rev. Genet. 3, 737–747 (2002)

Small nucleolar RNAs (snoRNAs) important for the biosynthesis of rRNAs, modify ribosomal RNAs (rRNAs) by organizing the cleavage of the long pre- rRNA into its functional subunits (18S, 5.8S and 28S molecules)

Small nuclear RNAs (snRNAs) are constituents of the cellular machinery (spliceosome) that helps to produce mRNA removing the non-coding regions (introns) of genes and piecing together the coding regions (exons) to be translated into proteins some of these snRNAs have been shown to be the functional enzymes in the splicing reaction

Ribozyme an RNA molecule that catalyzes a chemical reaction from ribonucleic acid enzyme (called also RNA enzyme) many natural ribozymes catalyze either the hydrolysis of one of their own phosphodiester bonds or the hydrolysis of bonds in other RNA

Chemical differences between DNA and RNA DNA RNA carbohydratedeoxyriboseribose pyrimidine base thyminuracil structuredouble-helix single helix stability at high pH resistentcleaved

Estimation of nucleic acids content of phosphorus (bulk of pure nucleic acids) content of bases (absorption of UV light) content of pentose estimation of native chains by intercalating stains

Ethidium bromide intercalation

Intercalation induces structural distortions