Chapter 8 Nucleotides and Nucleic Acids Roles of nucleotides o Energy currency in metabolic transactions o The essential chemical links in the response of cells to hormone and o The structural components of an array of enzyme cofactors and other extracellular stimuli metabolic intermediates o Constituents of nucleic acids 8 1 Some Basics Gene for the synthesis of a functional biological product a segment of a DNA molecule that contains the information required Only known functions of DNA o Storage of biological information o Transmission of biological information Classes of RNA o Ribosomal RNAs rRNAs components of ribosomes Ribosomes are the complexes that carry out the synthesis of proteins o Messenger RNAs mRNAs intermediaries that carry genetic information from one or a few genes to a ribosome where the corresponding proteins can be synthesized the information of mRNA into a specific sequence of amino acids tRNAs adapter molecules that faithfully translate o Transfer RNAs Nucleotides and Nucleic Acids Have Characteristic Bases and Pentoses Nucleotides have three components o A nitrogenous base o A pentose o A phosphate o Pyrimidine o Purine Nucleoside Nitrogenous bases are derivatives of two parent compounds a nucleotide without a phosphate group 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 Thymine Uracil Two kinds of pentoses the pyrimidine that is in both DNA and RNA the other pyrimidine in DNA the other pyrimidine in RNA o DNA contains 2 deoxy D ribose o RNA contains D ribose Deoxyribonucleotides Ribonucleotides the structural units of RNAs DNA and RNA also contain some minor bases the structural units of DNA o DNA has the methylated forms of the major bases o In some viral DNAs certain bases may be hydroxymethylated or glucosylated o Ribonucleoside 2 3 cyclic monophosphates Cells also contain nucleotides with phosphate groups in positions other than on the 5 carbon intermediates o Ribonucleoside 3 monophosphates of RNA by certain ribonucleases end products of the hydrolysis isolatable o Adenosine 3 5 cyclic monophosphate cAMP o Guanosine 3 5 cyclic monophosphate cGMP Phosphodiester Bonds Link Successive Nucleotides in Nucleic Acids Phosphodiester linkage nucleotide to the 3 hydroxyl group of the next nucleotide a bond between the 5 phosphate group of one The backbones of both DNA and RNA are hydrophilic Oligonucleotide a short nucleic acid o Polymers containing 50 or fewer nucleotides Polynucleotide a longer nucleic acid The Properties of Nucleotide Bases Affect the Three Dimensional Structure of Nucleic Acids All nucleotide bases absorb UV light The bases are hydrophobic and relatively insoluble in water at cell pH Pyrimidines and purines are aromatic o At acidic or alkaline pH the bases become charged and their solubility Bases can stack via hydrophobic interactions van der Waals forces and in water increases dipole dipole interactions o Helps minimize the contact of the bases with water o Stabilizes the 3D structure of nucleic acids Base pairs A to T and G to C o Permits the duplication of genetic information 8 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 structure DNA Is a Double Helix That Stores Genetic Information Chargaff s rules another o The base composition of DNA generally varies from one species to o DNA specimens isolated from different tissues of the same species have the same base composition o The base composition of DNA in a given species does not change with an organism s age nutritional state or changing environment o 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 strands in DNA and minor grooves are created by the offset pairing of the two Three hydrogen bonds form between G and C and only two form between A and T Different pairing of bases destabilizes DNA structure Parallel Antiparallel directions when the 3 5 phosphodiester bonds run in the same direction when the 3 5 phosphodiester bonds run in opposite o DNA is antiparallel wherever adenine occurs in one chain thymine is found in Complementary 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 interactions DNA 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 deoxyribose o Rotation about the contiguous bonds that make up the phosphodeoxyribose backbone o 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 Syn o Anti Pyrimidines are restricted to the anti conformation because of steric interference B DNA the most stable structure for a random sequence B form DNA DNA molecule under physiological conditions A form favored in many solutions that are relatively devoid of water o The helix is wider and the number of base pairs per helical turn is 11 o The plane of base pairs is rotated about 20o with respect to the helix o Deepens the major groove while making the minor groove shallower o Most short DNA molecules tend to crystallize axis Z form o Left handed o 12 base pairs per helical turn o More slender and elongated o DNA backbone is zig zag o Purine residues flip to syn conformation o Major groove is barely apparent and minor groove is narrow and deep A DNA might not occur in cells but Z DNA does Certain DNA Sequences Adopt Unusual Structures a word phrase or sentence that is spelled identically read regions of DNA with twofold symmetry over two strands Palindrome either forward or backward Inverted repeats of DNA o Self complementary
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