Nucleic Acids: How Structure Conveys Information Chapter 9

Levels of structure in Nucleic Acids Primary – Order of bases in polynucleotide sequence Secondary – Three-dimensional conformation of the backbone Tertiary – Supercoiling of molecule Quaternary - Interaction between DNA and proteins Order of bases in DNA is the genetic code. It contains information necessary to produce the correct amino acid sequence in cell’s proteins

What are nucleotides? Monomers of Nucleic acids – Nucleotides Consists of nitrogenous base, sugar and phosphoric acid residue Covalently bonded RNA (Ribonucleic Acid) DNA (Deoxyribonucleic Acid)

Pyrimidine and Purine Bases

Other Bases Less common bases/Unusual bases Principally but not exclusively, in transfer RNAs Most of these bases are methylated

What are Nucleosides? Nucleoside: a compound that consists of D-ribose or 2-deoxy-D-ribose covalently bonded to a nucleobase by a β-N-glycosidic bond Lacks phosphate group It is a compound that contains a base linked to a sugar by a covalent bond or base forms a glycosidic linkage with sugar. When the sugar is β-D-ribose the resulting compound is ribonucleoside and when the sugar is β-D- deoxyribose then the resulting compound is deoxyribonucleoside. When phosphoric acid is esterified to one of the hydroxyl groups of the sugar portion of a nucleoside then a nucleotide is formed. Monophosphate, diphosphate or triphosphate

Nucleotides A nucleoside in which a molecule of phosphoric acid is esterified with an -OH of the monosaccharide, most commonly either the 3’-OH or the 5’-OH Polymerization leads to nucleic acids. Linkage is repeated (3’,5’-phosphodiester bond) Name based on parent nucleoside (any base ) with a suffix “monophosphate”

DNA - 1° Structure Deoxyribonucleic acids : a biopolymer that consists of a backbone of alternating units of 2-deoxy-D-ribose and phosphate the 3’-OH of one 2-deoxy-D-ribose is joined to the 5’-OH of the next 2-deoxy-D-ribose by a phosphodiester bond

DNA - 1° Structure “d” used to designate “deoxy” Primary Structure: the sequence of bases along the pentose-phosphodiester backbone of a DNA molecule base sequence is read from the 5’ end to the 3’ end A,G,C, and T

Secondary structure of DNA Double helix: a type of 2° structure of DNA molecules in which two antiparallel polynucleotide strands are coiled in a right-handed manner about the same axis The double helix model of DNA 2°structure was proposed by James Watson and Francis Crick in 1953

How is the base pairing of DNA complementary? A major factor stabilizing the double helix is base pairing by hydrogen bonding between T-A and between C-G T-A base pair comprised of 2 hydrogen bonds

How is the base pairing of DNA complementary? G-C base pair comprised of 3 hydrogen bonds

Are there other possible conformations of double helix DNA? A-DNA a right-handed helix, but thicker than B-DNA 11 base pairs per turn of the helix has not been found in vivo

Are there other possible conformations of double helix DNA? B-DNA considered the physiological form a right-handed helix 10 base pairs per turn (34Å) of the helix

Are there other possible conformations of double helix DNA? Z-DNA a left-handed double helix may play a role in gene expression Alternating purine and pyrimidine sequences

Z-form is derivative of B-form Produced by flipping one side of the backbone 180˚ without disturbing the backbone covalent bonds or hydrogen bonds

Differences between three forms Both A and B-DNA are right-handed helices • Z-DNA is left handed • Z-DNA occurs in nature, usually consists of alternating purine-pyrimidine bases • Methylated cytosine found also in Z-DNA

Tertiary structure of DNA Tertiary structure: the three-dimensional arrangement of all atoms of a nucleic acid; commonly referred to as supercoiling Circular DNA: a type of double-stranded DNA in which the 5’ and 3’ ends of each stand are joined by phosphodiester bonds Supercoiling- Further coiling and twisting of DNA helix

What are Topoisomerases? Enzymes that can change supercoiled state of DNA – TopoIsomerases Class I and Class II DNA gyrase

How does prokaryotic DNA supercoil into its tertiary structure? Class I: cut the phosphodiester backbone of one strand, pass the end through, and reseal Class II: cut both strands, pass some of the remaining DNA helix between the cut strands, and reseal DNA gyrase introduces negative supercoils into DNA

Super DNA Coiled Topology Double helix can be considered to a 2-stranded, right handed coiled rope Can undergo positive/negative supercoiling

How does eukaryotic DNA supercoil into its tertiary structure? Histone: a protein, particularly rich in the basic amino acids Lys and Arg; found associated with eukaryotic DNA five main types: H1, H2A, H2B, H3, H4 Chromatin: DNA molecules wound around particles of histones in a beadlike structure Topological changes induced by supercoiling accommodated by histone-protein component of chromatin.

Chromatin • Each “Bead” is a nucleosome • Nucleosome consists of: DNA wrapped around histone core

Denaturation of DNA Denaturation: disruption of 2° structure most commonly by heat denaturation (melting) absorbance at 260 nm Hyperchromicity midpoint of transition (melting) curve = Tm the higher the % G-C, the higher the Tm renaturation is possible on slow cooling

Denaturation and Renaturation of DNA Double helix unwinds when DNA is denatured Can be re-formed with slow cooling and annealing

Principal Kinds of RNA Six kinds of RNA – messenger RNA (mRNA) transfer RNA (tRNA) ribosomal RNA (rRNA) small nuclear RNA (snRNA) micro RNA (miRNA) small interfering (siRNA)

Structure of RNA RNA nucleotides joined by phosphodiester bonds between the 3’-OH of one pentose and the 5’-OH of the next the pentose unit is D-ribose the pyrimidine bases are uracil and cytosine RNA is single stranded

Central dogma theory

RNA molecules are classified according to their structure and function

Transfer RNA-tRNA the smallest kind of the three RNAs a single-stranded polynucleotide chain between 73-94 nucleotide residues carries an amino acid at its 3’ end intramolecular hydrogen bonding occurs in tRNA Also the shape of clover leaf which is considered as secondary structure of RNA. Shows hydrogen bonding among certain bases. The hydrogen bonded portions of the molecules are called stems and non-hydrogen bonded portions are called loops. Some of the loops have modified bases. Aminoacids bind to 3’ end of tRNA

Ribosomal RNA- rRNA Only a few types of rRNA exist in cells ribosomes consist of 60 to 65% rRNA and 35 to 40% protein prokaryotes and eukaryotes - ribosomes consist of two subunits analyzed by analytical ultracentrifugation - sedimentation coefficients - expressed in Svedberg units (S) a ribonucleic acid found in ribosomes, the site of protein synthesis. Among the subunits in pro and eukaryotes – ribosomes consist of two subunits – one is larger than the other. particles characterized by sedimentation coefficients .

Messenger RNA - mRNA A ribonucleic acid that carries coded genetic information from DNA to ribosomes for the synthesis of proteins Present in cells in small amounts (5-10 %) Very short-lived

Small nuclear RNA (snRNA) Found in nucleus of eukaryotes Small (100-200 nucleotides long) Forms complexes with protein - small nuclear ribonucleoprotein particles (snRNPs) snRNPs help with processing of initial mRNA transcribed from DNA recently discovered RNA - in nucleus of eukaryotes

Small interfering RNA (siRNA) Used in RNA interference Eliminate expression of an undesirable gene

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