Chapter 8 – Nucleotides and Nucleic Acids- Roles of nucleotides:o Energy currency in metabolic transactionso The essential chemical links in the response of cells to hormone and other extracellular stimulio The structural components of an array of enzyme cofactors and metabolic intermediateso Constituents of nucleic acids8.1 Some Basics- Gene – a segment of a DNA molecule that contains the information required for the synthesis of a functional biological product- Only known functions of DNA:o Storage of biological informationo Transmission of biological information- Classes of RNA:o Ribosomal RNAs (rRNAs) – components of ribosomes Ribosomes are the complexes that carry out the synthesis of proteinso Messenger RNAs (mRNAs) – intermediaries that carry genetic information from one or a few genes to a ribosome, where the corresponding proteins can be synthesizedo Transfer RNAs (tRNAs) – adapter molecules that faithfully translate the information of mRNA into a specific sequence of amino acidsNucleotides and Nucleic Acids Have Characteristic Bases and Pentoses- Nucleotides have three components:o A nitrogenous baseo A pentoseo A phosphate- Nucleoside – a nucleotide without a phosphate group- Nitrogenous bases are derivatives of two parent compounds:o Pyrimidine o Purine - The base of the nucleotide is joined covalently in an N--glucosyl bond to the 1’ carbon of the pentose and the phosphate is esterified to the 5’ carbon.- Two major purine bases in DNA and RNA:o Adenine o Guanine - Cytosine – the pyrimidine that is in both DNA and RNA- Thymine – the other pyrimidine in DNA- Uracil – the other pyrimidine in RNA- Two kinds of pentoses:o DNA contains 2’-deoxy-D-riboseo RNA contains D-ribose- Deoxyribonucleotides – the structural units of DNA- Ribonucleotides – the structural units of RNAs- DNA and RNA also contain some minor baseso DNA has the methylated forms of the major baseso In some viral DNAs, certain bases may be hydroxymethylated or glucosylated- Cells also contain nucleotides with phosphate groups in positions other than on the 5’ carbon:o Ribonucleoside 2’,3’-cyclic monophosphates – isolatable intermediateso Ribonucleoside 3’-monophosphates – end products of the hydrolysis of RNA by certain ribonucleaseso Adenosine 3’,5’-cyclic monophosphate (cAMP)o Guanosine 3’,5’-cyclic monophosphate (cGMP)Phosphodiester Bonds Link Successive Nucleotides in Nucleic Acids- Phosphodiester linkage – a bond between the 5’-phosphate group of one nucleotide to the 3’-hydroxyl group of the next nucleotide- The backbones of both DNA and RNA are hydrophilic- Oligonucleotide – a short nucleic acido Polymers containing 50 or fewer nucleotides- Polynucleotide – a longer nucleic acidThe Properties of Nucleotide Bases Affect the Three-Dimensional Structure of Nucleic Acids- Pyrimidines and purines are aromatic- All nucleotide bases absorb UV light- The bases are hydrophobic and relatively insoluble in water at cell pHo At acidic or alkaline pH the bases become charged and their solubility in water increases- Bases can stack via hydrophobic interactions, van der Waals forces, and dipole-dipole interactions.o Helps minimize the contact of the bases with watero Stabilizes the 3D structure of nucleic acids- Base pairs – A to T and G to Co Permits the duplication of genetic information8.2 Nucleic Acid Structure- Primary structure of a nucleic acid is its covalent structure and nucleotide sequence- Any stable structure is the secondary structure- The complex folding of large chromosomes within eukaryotic chromatin and bacterial nucleoids is tertiary structureDNA Is a Double Helix That Stores Genetic Information- Chargaff’s rules:o The base composition of DNA generally varies from one species to anothero DNA specimens isolated from different tissues of the same species have the same base compositiono The base composition of DNA in a given species does not change with an organism’s age, nutritional state, or changing environmento In all cellular DNAs the number of adenosine residues is equal to the number of thymidine residues and the number of guanosine residues is equal to the number of cytidine residues. The sum of the purine residues equals the sum of the pyrimidine residues- The furanose ring of each deoxyribose is in the C-2’ endo conformation- Major grooves and minor grooves are created by the offset pairing of the two strands in DNA- Three hydrogen bonds form between G and C and only two form between A and T- Different pairing of bases destabilizes DNA structure- Parallel – when the 3’,5’-phosphodiester bonds run in the same direction- Antiparallel – when the 3’,5’-phosphodiester bonds run in opposite directionso DNA is antiparallel- Complementary – wherever adenine occurs in one chain, thymine is found in the other and when guanine occurs in one chain, cytosine is found in the other- DNA double helix is held together by hydrogen bonding between complementary base pairs and base-stacking interactionsDNA Can Occur in Different Three-Dimensional Forms- Considerable rotation is possible around several types of bonds in the sugar-phosphate backbone and thermal fluctuation can produce bending, stretching and unpairing of the strands- Structural variation in DNA reflects three things:o The different possible conformations of the deoxyriboseo Rotation about the contiguous bonds that make up the phosphodeoxyribose backboneo Free rotation about the C-1’-N-glycosyl bond- Purines are restricted to two stable conformations with respect to deoxyribose due to steric constraints:o Syno Anti- Pyrimidines are restricted to the anti conformation because of steric interference- B-form DNA (B-DNA) – the most stable structure for a random-sequence DNA molecule under physiological conditions- A form – favored in many solutions that are relatively devoid of watero The helix is wider and the number of base pairs per helical turn is 11o The plane of base pairs is rotated about 20o with respect to the helix axiso Deepens the major groove while making the minor groove shallowero Most short DNA molecules tend to crystallize- Z form :o Left-handedo 12 base pairs per helical turno More slender and elongatedo DNA backbone is zig-zago Purine residues flip to syn conformationo Major groove is barely apparent and minor groove is narrow and deep- A-DNA might not occur
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