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Lodish H, Berk A, Zipursky SL, et al. Molecular cabinet Biology. Fourth edition. Brand-new York: W. H. Freeman; 2000.


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DNA and also RNA have good chemical similarities. In their primarystructures both are straight polymers (multiple chemistry units) composed of monomers (single chemistry units), referred to as nucleotides. Cellular RNAs range inlength from less than one hundreds to countless thousands that nucleotides. Moving DNAmolecules can be as long as numerous hundred million nucleotides. These huge DNAunits in association through proteins can be stained through dyes and visualized in thelight microscope as chromosomes.


Polymerization of Nucleotides develops Nucleic Acids

DNA and also RNA each consists of just four various nucleotides. Every nucleotideshave a usual structure: a phosphate group attached by aphosphoester bond come a pentose (a five-carbon sugar molecule)that subsequently is attached to one organic base (Figure 4-1a). In RNA, the pentose isribose; in DNA, that is deoxyribose (Figure 4-1b). The only other difference inthe nucleotides the DNA and also RNA is that among the four organic bases differsbetween the 2 polymers. The bases adenine, guanine, and cytosine are discovered inboth DNA and RNA; thymine is found only in DNA, and also uracil is found only in RNA.The bases are frequently abbreviated A, G, C, T, and U, respectively. For conveniencethe single letters are likewise used when lengthy sequences the nucleotides space writtenout.


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Figure 4-1

All Nucleotides have a usual structure. (a) Chemical framework of adenosine 5′-monophosphate (AMP),a nucleotide the is current in RNA. All nucleotides are composed ofa phosphate moiety, containing up to three phosphate groups, linkedto the (more...)


The base contents of main point acids room heterocyclic compounds with the ringscontaining nitrogen and carbon. Adenine and also guanine are purines, i m sorry contain a pair offused rings; cytosine, thymine, and uracil are pyrimidines, i beg your pardon contain a single ring (Figure 4-2). The acidic character ofnucleotides is because of the existence of phosphate, i beg your pardon dissociates at the pHfound inside cells, freeing hydrogen ions and also leaving the phosphate negativelycharged (see number 2-22). Because thesecharges tempt proteins, many nucleic acids in cells are associated withproteins. In nucleotides, the 1′ carbon atom that the sugar (ribose ordeoxyribose) is attached to the nitrogen at position 9 that a purine(N9) or at place 1 that a pyrimidine (N1).


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Figure 4-2

The chemical frameworks of the primary bases in nucleicacids. In main point acids and also nucleotides, nitrogen 9 of purines and nitrogen1 the pyrimidines (red) space bonded come the 1′ carbon ofribose or deoxyribose.


Cells and also extracellular fluids in organisms contain tiny concentrations that nucleosides, combinations of a baseand a sugar without a phosphate. Nucleotides are nucleosides that have actually one, two,or three phosphate teams esterified at the 5′ hydroxyl.Nucleoside monophosphates have a solitary esterifiedphosphate (see figure 4-1a),diphosphates contain a prophosphate group


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and triphosphates have actually a third phosphate. Table 4-1 lists the names of the nucleosides andnucleotides in nucleic acids and also the various creates of nucleoside phosphates. Aswe will watch later, the nucleoside triphosphates are provided in the synthetic ofnucleic acids. However, these compounds additionally serve many other functions in thecell: ATP, because that example, is the many widely used power carrier in the cell (seeFigure 2-25), and also GTP dram crucialroles in intracellular signaling and acts as an energy reservoir, particularlyin protein synthesis.


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When nucleotides polymerize to type nucleic acids, the hydroxyl team attached tothe 3′ carbon that a sugar of one nucleotide develops an ester bond to thephosphate of one more nucleotide, eliminating a molecule of water:


This condensation reaction is similar to that in which a peptide bond is formedbetween two amino mountain (Chapter3). Thus a single nucleic acid strand is a phosphate-pentose polymer (apolyester) with purine and pyrimidine bases together side groups. The web links betweenthe nucleotides are referred to as phosphodiesterbonds. Choose a polypeptide, a nucleic acid strand has actually an end-to-endchemical orientation: the 5′ end hasa complimentary hydroxyl or phosphate group on the 5′ carbon the its terminalsugar; the 3′ finish has a freehydroxyl team on the 3′ carbon the its terminal street (Figure 4-3). This directionality, add to thefact that synthesis proceeds 5′ come 3′, has given rise to theconvention that polynucleotide sequences are written and read in the5′ → 3′ direction (from left come right); forexample, the sequence AUG is assumed to it is in (5′)AUG(3′).(Although, strictly speaking, the letters A, G, C, T, and also U stand for bases,they are also often used in diagrams to stand for the totality nucleotidescontaining this bases.) The 5′ → 3′directionality of a nucleic acid strand is really important building ofthe molecule.


Figure 4-3

Alternative methods of representing nucleic mountain chains, in thiscase a single strand the DNA containing only three bases: cytosine(C), adenin (A), and also guanine (G). (a) Chemical framework of the trinucleotide CAG. Keep in mind the freehydroxyl group at the 3′ (more...)


The linear sequence that nucleotides linked by phosphodiester bond constitutes theprimary structure of main point acids. Together we talk about in the following section,polynucleotides have the right to twist and also fold into three-dimensional conformationsstabilized by noncovalent bonds; in this respect, castle are comparable topolypeptides. Back the major structures the DNA and RNA are generallysimilar, your conformations are fairly different. Uneven RNA, i m sorry commonlyexists together a solitary polynucleotide chain, or strand, DNA contains two intertwinedpolynucleotide strands. This structural difference is critical to the differentfunctions that the two types of main point acids.


Native DNA Is a twin Helix of complementary Antiparallel Chains

The modern-day era of molecular biology began in 1953 once James D. Watson andFrancis H. C. Crick proposed correctly the double-helical framework of DNA,based top top the evaluation of x-ray diffraction fads coupled with cautious modelbuilding. A closer look in ~ the “thread that life,” as the DNAmolecule is occasionally called, reflects why the exploration of its an easy structuresuggests that function.

DNA consists of two linked polynucleotide strands that windtogether through an are to form a structure regularly describedas a double helix. The 2 sugar-phosphate backbones space on theoutside that the double helix, and the bases project right into the interior. Theadjoining bases in each strand stack on optimal of one an additional in parallel planes(Figure 4-4a). The orientation that thetwo strands is antiparallel; the is, their 5′ →3′ directions space opposite. The strands are organized in precise registerby a continual base-pairing between the two strands: A is paired with T throughtwo hydrogen bonds; G is paired through C through three hydrogen binding (Figure 4-4b). This base-paircomplementarity is a an effect of the size, shape, and chemicalcomposition of the bases. The presence of hundreds of such hydrogen bond in aDNA molecule contributes significantly to the security of the dual helix.Hydrophobic and van der Waals interactions between the stacked surrounding basepairs likewise contribute to the stability of the DNA structure.


Figure 4-4

Two representations of contacts in ~ the DNA doublehelix. (a) Space-filling model of B DNA, the most common kind of DNA incells. The sugar and phosphate residual water (gray) in every strand formthe backbone, i beg your pardon is traced by a red line, showing the helicaltwist (more...)


To keep the geometry that the double-helical structure shown in figure 4-4a, a bigger purine (A or G) mustpair through a smaller sized pyrimidine (C or T). In natural DNA, A nearly alwayshydrogen bonds with T and also G through C, developing A·T and also G·Cbase bag often referred to as Watson-Crick basic pairs. Twopolynucleotide strands, or regions thereof, in which every the nucleotides formsuch basic pairs are said to it is in complementary. However, in theory and in fabricated DNAs otherinteractions can occur. For example, a guanine (a purine) can theoreticallyform hydrogen bonds through a thymine (a pyrimidine), bring about only a minordistortion in the helix. The an are available in the helix additionally would allowpairing between the two pyrimidines cytosine and thymine. Return thenonstandard G·T and also C·T base pairs are typically not foundin DNA, G·U base pairs space quite common in double-helical regionsthat kind within otherwise single-stranded RNA.

Two polynucleotide strands can, in principle, form either a right-handed or aleft-handed helix (Figure 4-5). Becausethe geometry that the sugar-phosphate backbone is more compatible with the former,natural DNA is a right-handed helix. The x-ray diffraction sample of DNAindicates the the stacked bases are on regular basis spaced 0.34 nm apart follow me thehelix axis. The helix renders a finish turn every 3.4 nm; therefore there are about10 pairs per turn. This is described as the B form of DNA,the normal kind present in most DNA follow me in cells (Figure 4-6a). ~ above the outside of B-form DNA, the spacesbetween the linked strands type two helical grooves of different widthsdescribed together the major groove and the minorgroove (see figure 4-4a). Consequently,part of each base is available from outside the helix to both small and largemolecules that tie to the DNA by contacting chemical groups within the grooves.These two binding surface of the DNA molecule are offered by various classes ofDNA-binding proteins.


Figure 4-5

Two feasible helical develops of DNA are mirror images of eachother. The geometry the the sugar-phosphate backbone that DNA reasons naturalDNA to be right-handed. (Right-handed andleft-handed are defined by convention.)


Figure 4-6

Models of miscellaneous DNA structures that are recognized to exist. The sugar-phosphate backbone of each chain is ~ above the exterior in allstructures (one red and also one blue) with the bases (silver) orientedinward. Side views are displayed at the top, and views along the (more...)


In enhancement to the major B form of DNA, three added structures have actually beendescribed. In very low humidity, the crystallographic framework of B DNA changesto the A form; RNA-DNA and RNA-RNA helices additionally exist in thisform. The A type is an ext compact 보다 the B form, having actually 11 bases per turn, andthe stack bases room tilted (Figure4-6b). Brief DNA molecules composed of alternative purine-pyrimidinenucleotides (especially Gs and Cs) take on an different left-handedconfiguration rather of the normal right-handed helix. This structure is calledZ DNA because the bases seem come zigzag as soon as viewed indigenous theside (Figure 4-6c). It is entirelypossible that both A-form and also Z-form stretches of DNA exist in cells.

Finally, a triple-stranded DNA framework can also exist at the very least in the testtube, and possibly during recombination and DNA repair. For example, whensynthetic polymers of poly(A) and also polydeoxy(U) space mixed, a three-strandedstructure is developed (Figure 4-6d).Further, long homopolymeric stretches of DNA written of C and also T residues in onestrand and A and also G residues in the other deserve to be targeted by brief matchinglengths the poly(C+T). The fabricated oligonucleotide deserve to insert as athird strand, binding in a sequence-specific path by so-calledHoogsteen base pairs. Details cleavage the the DNA at thesite whereby the triple helix ends deserve to be accomplished by it is registered a chemicalcleaving agent (e.g., Fe2+-EDTA) to the shortoligodeoxynucleotide that renders up the 3rd strand. Together reactions may beuseful in researching site-specific DNA damages in cells.

By much the most important modifications in typical B-form DNA come around as aresult the protein binding to certain DNA sequences. Although the multitude ofhydrogen and also hydrophobic bonds between the polynucleotide strands providestability to DNA, the twin helix is somewhat flexible about its long axis.Unlike the α helix in proteins (see number 3-6), there room no hydrogen bonds in between successive residuesin a DNA strand. This prop- erty permits DNA to bend once complexed v aDNA-binding protein. Crystallographic analyses of protein bound come particularregions the DNA have conclusively demonstrated departures native the standard B-DNAstructure in protein-DNA complexes. Two instances of DNA deformed by call withproteins are displayed in figure 4-7. Thespecific DNA-protein contacts that occur in this tightly tied complexes havethe ability both come untwist the DNA and also to bending the axis that the helix. AlthoughDNA in cells most likely exists in the B form most the the time, details regionsbound come protein plainly depart native the traditional conformation.


Figure 4-7

Bending of OF DNA result from protein binding. (a) A direct DNA (left) is displayed binding a repressorprotein encoded by bacteriophage 434 (center); theresulting bending in the DNA (right) is easily seen bycomparison with the linear molecule. Binding (more...)


DNA have the right to Undergo Reversible Strand Separation

In DNA replication and in the copying of RNA native DNA, the strands that the helixmust separate at least temporarily. As we discuss later, throughout DNA synthesistwo brand-new strands space made (one replicated from each of the original strands),resulting in two dual helices the same with the initial one. In the situation ofcopying the DNA design template to do RNA, the RNA is released and the 2 DNAstrands reassociate v each other.

The unwinding and also separation the DNA strands, referred to as denaturation, or“melting,” have the right to be induced experimentally. Because that example, if asolution of DNA is heated, the thermal power increases molecule motion,eventually break the hydrogen bonds and other forces that stabilize thedouble helix, and the strands different (Figure4-8). This melting of DNA alters its absorb of ultraviolet (UV)light (in the 260-nm range), i beg your pardon is routinely used to measure up DNAconcentration due to the fact that of the high absorbance of UV irradiate by nucleic mountain bases.Native double-stranded DNA absorbs about one-half as lot light at 260 nm asdoes the equivalent amount the single-stranded DNA (Figure 4-9a). Thus, as DNA denatures, its absorption of UVlight increases. Close to the denaturation temperature, a small increase intemperature causes an abrupt, near simultaneous, lose of the multiple, weak,cooperative interactions holding the 2 strands together, so that denaturationrapidly wake up throughout the whole length the the DNA.


Figure 4-9

Light absorption and temperature in DNA denaturation. (a) melt of doubled-stranded DNA have the right to be monitored through theabsorption the ultraviolet irradiate at 260 nm. As areas ofdouble-stranded DNA unpair, the absorption of light by those regionsincreases virtually (more...)


The melt temperature, Tm, at which the strands ofDNA will separate counts on numerous factors. Molecules that contain a greaterproportion of G·C bag require greater temperatures come denaturebecause the 3 hydrogen bond in G·C pairs make them an ext stablethan A·T pairs through two hydrogen bonds (see number 4-4b). Indeed, the portion of G·Cbase pairs in a DNA sample have the right to be estimated from itsTm (Figure4-9b). In addition to heat, services of low ion concentrationdestabilize the twin helix, leading to it to melt at reduced temperatures. DNA isalso denatured by exposure to other agents the destabilize hydrogen bonds, suchas alkaline solutions and also concentrated remedies of formamide or urea:


The single-stranded DNA molecule that an outcome from denaturation type random coilswithout a regular structure. Lowering the temperature or enhancing the ionconcentration reasons the two complementary strands to reassociate right into a perfectdouble helix (see number 4-8). The extentof such renaturation is dependent on time, the DNAconcentration, and the ionic content of the solution. 2 DNA strands notrelated in succession will remain as random coils and also will not renature and, mostimportant, will not substantially inhibit complementary DNA companion strands fromfinding each other. Denaturation and renaturation of DNA room the basis ofnucleic acid hybridization, apowerful method used to research the relatedness of two DNA samples and also todetect and isolate certain DNA molecules in a mixture containing numerousdifferent DNA assignment (Chapter7).


Many DNA Molecules room Circular

All prokaryotic genomic DNAs and also many famous DNAs room circular molecules. CircularDNA molecules likewise occur in mitochondria, which are present in nearly alleukaryotic cells, and in chloroplasts, i m sorry are existing in plants and also someunicellular eukaryotes.

Each that the two strands in a circular DNA molecule develops a closeup of the door structurewithout complimentary ends. Simply as is the situation for direct DNA, elevated temperature oralkaline pH damage the hydrogen bonds and other interactions the stabilizedouble-helical one DNA molecules. Unlike direct DNA, however, the twostrands of circular DNA can not unwind and also separate; attempts to melt together DNAresult in an interlocked, tangled massive of single-stranded DNA (Figure 4-10a).


Figure 4-10

Denaturation of circular DNA. (a) If both strands space closed circles, denaturation disrupts thedouble helix, but the two solitary strands end up being tangled about eachother and also cannot separate. (b) If one or both strands space nicked,however, the two strands (more...)


Only if a native circular DNA is nicked (i.e., one of thestrands is cut), will the two strands unwind and separate as soon as the molecule isdenatured. In this case, among the separated strands is circular, and also the otheris direct (Figure 4-10b). Nicking ofcircular DNA occurs naturally throughout DNA replication and also can be inducedexperimentally v a short concentration that deoxyribonuclease (a DNA-degradingenzyme), for this reason that only a solitary phosphodiester bond in the molecule is cleaved.The examine of circular DNA molecule lacking free ends an initial uncovered thecomplicated geometric shape changes that the double-stranded DNA molecule mustundergo once the strands are not free to separate.


Local Unwinding the DNA root cause Supercoiling

So far we have described DNA together a long continual helical structure that deserve to havelocal perturbations, especially due to protein binding. In addition, when thetwo end of a DNA molecule space fixed, the molecule exhibits a superstructureunder certain conditions. This occurs when the base pairing is interrupted and alocal an ar unwinds. The stress induced through unwinding is relieved by twisting ofthe dual helix top top itself, developing supercoils (Figure 4-11). Unwinding and subsequentsupercoiling occurs during replication, transcription, and binding the manyproteins to circular DNAs or to long DNA loops whose end are resolved withineukaryotic chromosomes. Supercoiling is recognized and regulated through enzymescalled topoisomerases. Together discussedin later chapters, this enzymes have an essential role in both DNA replicationand the warrior of DNA into RNA.


Figure 4-11

Supercoiling in electron micrographs that DNA isolated indigenous theSV40 virus. When isolated SV40 DNA is separated from its associated protein, theDNA duplex is underwound and assumes the supercoiled configuration(form I). If one strand is nicked, the strands (more...)


RNA molecule Exhibit differed Conformations and also Functions

As detailed earlier, the major structure of RNA is generally comparable to that ofDNA; however, the street component (ribose) the RNA has second hydroxylgroup at the 2′ position (see Figure4-1b), and also thymine in DNA is changed by uracil in RNA (see number 4-2). The hydroxyl group onC2 of ribose provides RNA more chemically labile 보다 DNA andprovides a chemically reactive team that takes part in RNA-mediated enzymaticevents. As a an outcome of this lability, RNA is cleaved into mononucleotides byalkaline solution, vice versa, DNA is not. Choose DNA, RNA is a lengthy polynucleotidethat can be double-stranded or single-stranded, direct or circular. It deserve to alsoparticipate in a hybrid helix created of one RNA strand and also one DNA strand;this hybrid has a slightly different conformation 보다 the common B type ofDNA.

Unlike DNA, i m sorry exists primarily in a single, very long three-dimensionalstructure, the dual helix, the various species of RNA exhibition differentconformations. Distinctions in the sizes and also conformations of the miscellaneous typesof RNA allow them to carry out certain functions in a cell. The simplestsecondary structures in single-stranded RNAs are formed by pairing ofcomplementary bases. “Hairpins” are created by pairing ofbases in ~ ≈5 – 10 nucleotides of eachother, and “stem-loops” through pairing that bases the areseparated by ≈50 to several hundred nucleotides (Figure 4-12a). These straightforward folds cancooperate to type more facility tertiary structures, among which is termed a“pseudoknot” (Figure4-12b).


Figure 4-12

RNA second and tertiary structures. (a) Stem-loops, hairpins, and other secondary structures can form bybase pairing between distant complementary segments of an RNAmolecule. In stem-loops, the single-stranded loop (dark red) betweenthe base-paired (more...)


As questioned in detail later, tRNA molecules adopt a well-definedthree-dimensional style in equipment that is critical in protein synthesis.Larger rRNA molecules also have locally well identified three-dimensionalstructures, with much more flexible web links in between. Secondary and tertiarystructures also have been well-known in mRNA, particularly near the end ofmolecules. These recently found structures are under energetic study. Clearly,then, RNA molecules are choose proteins in the they have actually structured domainsconnected by much less structured, functional stretches.

The folded domains of RNA molecules not only are structurally analogous to theα helices and also β strands uncovered in proteins, however in part casesalso have catalytic capacities. Such catalytic RNAs, called ribozymes, can reduced RNA chains. SomeRNA domains additionally can catalyze RNA splicing, a remarkableprocess in i m sorry an internal RNA sequence, an intron, is cut and also removed and the two resulting chains,the exons, space sealed together.This procedure occurs during formation that the majority of practical mRNAmolecules in eukaryotic cells, and also occurs in bacteria and archaea.Remarkably, part RNAs bring out self-splicing, through thecatalytic activity residing in the intron sequence. The mechanisms of splicingand self-splicing are discussed in information in chapter 11. As noted later in this chapter, rRNA isthought to play a catalytic function in the formation of peptide bonds duringprotein synthesis.

In this chapter, we emphasis on the functions of mRNA, tRNA, and also rRNA in geneexpression — the process of getting theinformation in DNA converted into proteins. In later chapters we will encounterother RNAs, often linked with proteins, that get involved in other cellfunctions.

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