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CHY 204 (10)
Chapter 8


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Ryerson University
CHY 204
Mario Estable

CHAPTER 8: NUCLEOTIDES & NUCLEIC ACIDS 8.1 Some Basics -Nucleotides are constituents of nucleic acids: DNA & RNA. A segment of a DNA molec that contains the info req for synthesis of a func biological product, whether pro/RNA is a gene. The storage & transmission of bio info are the only known func of DNA. RNAs have broader range of functions & several classe: ribosomal RNAs (rRNAs; components of ribosomes which carry out synthesis of pro), messenger RNAs (mRNAs; intermediaries carrying genetic infor from 1/more genes to a ribosome where the corresponding pro can be synthesized), transfer RNAs (tRNAs; adapter molec that translate info in mRNA to specific seq of aa). -Nucleotides & nucleic acids have characteristic bases & pentoses: Nucleotides have 3 components: 1) nitrogenous base (A, C, T, G, U) 2) a pentose & 3) a phosphate. Nucleosides only have all except the phosphate group. The nitrogenous bases are either pyrimidines (1 ring; C,T (DNA), U (RNA)) & purines (2 rings; A,G). The base of a nucleotide is joined covalently at N-1 of pyrimidines & N-9 of purines. In soln, the straight chain (aldehyde) & ring (beta furanose) forms of free ribose are in equil; RNA contains only the ring form, B-D-ribofuranose vs. deoxyribose undergoes similar intercoversion in soln but DNA exists solely as B-2’-deoxy-D-ribofuranose. -The 4 major deoxyribonucleotides (deoxyribonucleoside 5’-monoP) in DNA: deoxyadenylate (A,dA,dAMP), deoxyguanylate (G,dG, dGMP), deoxythymidylate (T, dT, dTMP) & deoxycytidine (C, dC, dCMP). The 4 major nucleotides (ribonucleoside 5’-monoP) in RNA: adenylate, guanylate, uridylate & cytidylate. Both DNA & RNA contain some minor bases. In DNA, most common of these are methylated forms of the major bases & in some viral DNAs, certain bases may be hydroxymethylated or glycosylated. Cells contain nucleotides w/ P groups in posn other than on 5’ C, eg. Adenosine 5’-monoP & adenosine 2’,3’-cyclic monoP (cAMP) -Phosphodiester bonds link successive nucleotides & nucleic acids: the successive nucleotides of both DNA & RNA are covalently linked via P group bridges in which the 5’-P group of 1 nucleotide is joined to 3’ –OH group of the next creating a phosphodiester linkage. The backbones of both DNA & RNA are hydrophilic b/c the –OH groups of the sugar residues H bonds w/ H2O; the P groups w/ a pKa of 0 completely ionize & neg charged at pH of 7 which are neutralized by ionic interactions w/ pos charges on pro, metal ions & polyamines. The covalent backbone of DNA & RNA is subject to slow, nonenzymatic hydrolysis of the phosphodiester bonds. RNA is hydrolyzed rapidly under alkaline conditions while DNA doesn’t. DNA is more stable than RNA b/c the 2’ OH of RNA acts as a nucleophile in an intramolec displacement; the 2’,3’-cyclicmonoP derivative is further hydrolyzed to a mixture of 2’ & 3’ monoP derivatives; DNA lacks 2’ OH thus are stable under similar conditions (hydrolysis of RNA under alkaline conditions). Oligonucleotides are short nucleic acids w/ <50 nucleotides vs. polynucleotides have >50. Primers are synthetic short oligos. -The properties of nucleotide bases affect 3D structure of nucleic acids: Free pyrimidine ^ purine bases may exist in 2/more tautomeric forms depending on pH; tautomers are isomers that interconvert by chemical rxn by switching single bonds to double bonds. All nucleotide bases absorb UV light & nucleic acids are charcterized by a strong absorption at wavelengths near 260nm. Because of multiple resonance bonds in bases, they absorb light w/ a maxima at 260nm. Purines & pyrimidines are hydrophobic & relatively insoluble in H2O at near neutral pH of cell; at acidic/alkaline bases, they become charged & solubility w/ H2O inc. The stacking of bases involve hydrophobic interactions & combination of van der Waals & dipole-dipole interactions b/c bases; base stacking helps minimize contact of bases w/ H2O which are very important in 3D structure of nucleic acids. The func groups of purines/pyrimidines are ring N, carbonyl groups & exocyclic amino groups; Watson & Crick defines A has 2 H bonds w/ T or U & G has 3 H bonds w/ C (which is why separation of DNA strands is harder the higher the ratio of G-C to A-T). Timeline: 1928-Griffith showed that something was transforming 1944-Avery, MacLeod & McCarty repeated Griffith’s transformation showing that DNA was able to do the transformation 1952-Hershey & Chase further proved that DNA was genetic material in bacteriophages 1953-Watson & Crick presented the double helix model publication 1975-Fred Sanger developed dideoxy-sequencing 1977-Fred Sanger published first whole genome of X174 2000-Venter & Collins seq the human genome 2007-Venter makes synthetic baterial genome 8.2 Nucleic acid structure -The primary structure of nucleic acid is its covalent structure & nucleotide seq; secondary structure is any reg, stable structure taken up by some or all of the nucleotides in a nucleic acid; the tertiary structure is the complex folding of large chromosomes w/in eukaryotic chromatin & bacterial nucleoids. -DNA is a double helix that stores genetic info: DNA was first isolated & characterized by Freidrich Miescher in 1868. Avery, MacLeod & McCarty found that DNA extracted from a virulent strain of Streptococcus pneumonaie & injected into a nonvirulent strain of same bacterium formed the nonvirulent strain into a virulent one thus they concluded that DNA from the virulent strain carried the genetic info for virulence. Erwin Chagraff & colleagues found that 4 nucleotide bases of DNA occur in diff ratios in the DNAs of diff organisms & the amts are closely related; Chagraff’s rules state: 1. DNA base composition is species-specific 2. Diff tissues of same species have same base composition 3. Base composition of an individual w/in a species is stable throughout life 4. # of A = # of T; # of C= # of G, in all species, ie. A+G=T+C -Rosalind Franklin & Maurice Wilkis used xray diffraction to know more about DNA’s structure which produced an x-ray diffraction pattern; from this pattern, it was found that DNA molecules are helical w/ 2 periodicities along their long axis, a primary one of 3.4 A & 2ndary one of 34 A. Watson & Crick used this info to form their double helix; it consists of 2 identical helical DNA chains wound around the same axis to form a right handed double helix. The offset pairing of 2 strands create major & minor groove on the surface of the duplex. DNA is antiparallel; the vertically stacked bases inside the double helix are 3.4 A apart, the 2ndary repeat dist of ~34A was accounted for by the presence of 10 base pairs each complete turn of the double helix; in aq solns, there are 10.5 base pairs per helical turn. The anitparallel strands are complementary to each other; DNA double helix is held together by H bonding & base-stacking interactions. The structure can be replicated by separating the 2 strands & synthesizing a complementary strand for each. -Avery’s experiments (1944): 1) Live encapsulated virulent bacteria is injected into the mouse & mouse died, thus Encapsulated bacteria is lethal. 2) Live nonecapsulated nonvirulent bacteria is injected into the mouse & it lives, thus non-encapsulated bacteria is not lethal. 3) Live encapsulated virulent bacteria that is heated forming heat-killed virulent bacteria is injected into the mouse & it lives, thus heating kills & eliminates virulence. 4) If the heat killed virulent bacteria is mixed w/ live nonecapsulated nonvirulent bacteria & injected into the mouse, it dies thus the dead virulence fact
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