H. Lodish - Molecular Cell Biology (5ed, Freeman, 2003) (796244), страница 43
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In this chapter we cover the three processes thatlead to production of proteins ( 1 – 3 ) and the process forreplicating DNA ( 4 ). Because viruses utilize host-cell machinery,they have been important models for studying these processes.During transcription of a protein-coding gene by RNA polymerase( 1 ), the four-base DNA code specifying the amino acid sequenceof a protein is copied into a precursor messenger RNA (premRNA) by the polymerization of ribonucleoside triphosphatemonomers (rNTPs). Removal of extraneous sequences and othermodifications to the pre-mRNA ( 2 ), collectively known as RNAprocessing, produce a functional mRNA, which is transported to thecytoplasm.
During translation ( 3 ), the four-base code of the mRNA isdecoded into the 20–amino acid “language” of proteins. Ribosomes,the macromolecular machines that translate the mRNA code, arecomposed of two subunits assembled in the nucleolus from ribosomal RNAs (rRNAs) and multiple proteins (left). After transport to thecytoplasm, ribosomal subunits associate with an mRNA and carryout protein synthesis with the help of transfer RNAs (tRNAs) andvarious translation factors.
During DNA replication (4 ), which occursonly in cells preparing to divide, deoxyribonucleoside triphosphatemonomers (dNTPs) are polymerized to yield two identical copies ofeach chromosomal DNA molecule. Each daughter cell receives oneof the identical copies.In this chapter, we first review the basic structures andproperties of DNA and RNA.
In the next several sectionswe discuss the basic processes summarized in Figure 4-1:transcription of DNA into RNA precursors, processing ofthese precursors to make functional RNA molecules, translation of mRNAs into proteins, and the replication of DNA.Along the way we compare gene structure in prokaryotesand eukaryotes and describe how bacteria control transcription, setting the stage for the more complex eukaryotictranscription-control mechanisms discussed in Chapter 11.After outlining the individual roles of mRNA, tRNA, andrRNA in protein synthesis, we present a detailed descriptionof the components and biochemical steps in translation.
Wealso consider the molecular problems involved in DNA repli-cation and the complex cellular machinery for ensuring accurate copying of the genetic material. The final section ofthe chapter presents basic information about viruses, whichare important model organisms for studying macromolecularsynthesis and other cellular processes.4.1 Structure of Nucleic AcidsDNA and RNA are chemically very similar. The primarystructures of both are linear polymers composed ofmonomers called nucleotides. Cellular RNAs range in lengthfrom less than one hundred to many thousands of nucleotides. Cellular DNA molecules can be as long as several4.1 • Structure of Nucleic Acidshundred million nucleotides. These large DNA units in association with proteins can be stained with dyes and visualized in the light microscope as chromosomes, so namedbecause of their stainability.A Nucleic Acid Strand Is a Linear Polymerwith End-to-End DirectionalityDNA and RNA each consist of only four different nucleotides.Recall from Chapter 2 that all nucleotides consist of anorganic base linked to a five-carbon sugar that has a phosphate group attached to carbon 5.
In RNA, the sugar is ribose;in DNA, deoxyribose (see Figure 2-14). The nucleotides usedin synthesis of DNA and RNA contain five different bases.The bases adenine (A) and guanine (G) are purines, which con-(a)5 end(b)OOOPCO3H2C 5COHOOH555HO3H3Phosphodiesterbond3GPHHAPO5 C-A-G 3OH2C 5HHOH3OOH2C 5GOH3 endNative DNA Is a Double Helix of ComplementaryAntiparallel StrandsHPHtain a pair of fused rings; the bases cytosine (C), thymine (T),and uracil (U) are pyrimidines, which contain a single ring (seeFigure 2-15). Both DNA and RNA contain three of thesebases—A, G, and C; however, T is found only in DNA, andU only in RNA.
(Note that the single-letter abbreviations forthese bases are also commonly used to denote the entire nucleotides in nucleic acid polymers.)A single nucleic acid strand has a backbone composed ofrepeating pentose-phosphate units from which the purine andpyrimidine bases extend as side groups. Like a polypeptide, anucleic acid strand has an end-to-end chemical orientation: the5 end has a hydroxyl or phosphate group on the 5 carbonof its terminal sugar; the 3 end usually has a hydroxyl groupon the 3 carbon of its terminal sugar (Figure 4-2).
This directionality, plus the fact that synthesis proceeds 5 to 3, hasgiven rise to the convention that polynucleotide sequences arewritten and read in the 5n3 direction (from left to right); forexample, the sequence AUG is assumed to be (5)AUG(3). Aswe will see, the 5n3 directionality of a nucleic acid strandis an important property of the molecule.
The chemical linkagebetween adjacent nucleotides, commonly called a phosphodiester bond, actually consists of two phosphoester bonds, oneon the 5 side of the phosphate and another on the 3 side.The linear sequence of nucleotides linked by phosphodiester bonds constitutes the primary structure of nucleic acids.Like polypeptides, polynucleotides can twist and fold intothree-dimensional conformations stabilized by noncovalentbonds. Although the primary structures of DNA and RNAare generally similar, their three-dimensional conformationsare quite different.
These structural differences are criticalto the different functions of the two types of nucleic acids.HOPhosphodiesterbondAO103HH3OHH▲ FIGURE 4-2 Alternative representations of a nucleic acidstrand illustrating its chemical directionality. Shown here is asingle strand of DNA containing only three bases: cytosine (C),adenine (A), and guanine (G). (a) The chemical structure shows ahydroxyl group at the 3 end and a phosphate group at the 5end. Note also that two phosphoester bonds link adjacentnucleotides; this two-bond linkage commonly is referred to as aphosphodiester bond.
(b) In the “stick” diagram (top), the sugarsare indicated as vertical lines and the phosphodiester bonds asslanting lines; the bases are denoted by their single-letter abbreviations. In the simplest representation (bottom), only the basesare indicated. By convention, a polynucleotide sequence is always written in the 5n3 direction (left to right) unless otherwise indicated.The modern era of molecular biology began in 1953 whenJames D. Watson and Francis H.
C. Crick proposed thatDNA has a double-helical structure. Their proposal, basedon analysis of x-ray diffraction patterns coupled with carefulmodel building, proved correct and paved the way for ourmodern understanding of how DNA functions as the geneticmaterial.DNA consists of two associated polynucleotide strandsthat wind together to form a double helix. The two sugarphosphate backbones are on the outside of the double helix,and the bases project into the interior. The adjoining bases ineach strand stack on top of one another in parallel planes(Figure 4-3a).
The orientation of the two strands is antiparallel; that is, their 5n3 directions are opposite. The strandsare held in precise register by formation of base pairs between the two strands: A is paired with T through two hydrogen bonds; G is paired with C through three hydrogenbonds (Figure 4-3b). This base-pair complementarity is aconsequence of the size, shape, and chemical compositionof the bases.
The presence of thousands of such hydrogenbonds in a DNA molecule contributes greatly to the stability104CHAPTER 4 • Basic Molecular Genetic Mechanisms(a)(b)353CH3O POHHNONT NH N AO5CH25OOOOCH2OO POOOG NHCH2OOOCH2MajorgrooveOOON CNHHOPHHNP OOOHNH OO POOONA N HTCH2OOOOCH2POHNH OO POC N HNGOOMinorgrooveO5 CH253▲ FIGURE 4-3 The DNA double helix. (a) Space-filling modelof B DNA, the most common form of DNA in cells. The bases(light shades) project inward from the sugar-phosphate backbones(dark red and blue) of each strand, but their edges are accessiblethrough major and minor grooves. Arrows indicate the 5’n3’direction of each strand. Hydrogen bonds between the bases arein the center of the structure. The major and minor groovesof the double helix.
Hydrophobic and van der Waals interactions between the stacked adjacent base pairs further stabilize the double-helical structure.In natural DNA, A always hydrogen bonds with T andG with C, forming A·T and G·C base pairs as shown in Figure 4-3b. These associations between a larger purine andsmaller pyrimidine are often called Watson-Crick base pairs.Two polynucleotide strands, or regions thereof, in which allthe nucleotides form such base pairs are said to be complementary. However, in theory and in synthetic DNAs otherbase pairs can form. For example, a guanine (a purine) couldtheoretically form hydrogen bonds with a thymine (a pyrimidine), causing only a minor distortion in the helix.
The spaceavailable in the helix also would allow pairing between thetwo pyrimidines cytosine and thymine. Although the nonstandard G·T and C·T base pairs are normally not found inDNA, G·U base pairs are quite common in double-helicalregions that form within otherwise single-stranded RNA.Most DNA in cells is a right-handed helix. The x-ray diffraction pattern of DNA indicates that the stacked bases areregularly spaced 0.36 nm apart along the helix axis. TheHNHOOOCH2OOP5OO3are lined by potential hydrogen bond donors and acceptors(highlighted in yellow).
(b) Chemical structure of DNA doublehelix. This extended schematic shows the two sugar-phosphatebackbones and hydrogen bonding between the Watson-Crickbase pairs, AT and GC. [Part (a) from R. Wing et al., 1980, Nature287:755; part (b) from R. E. Dickerson, 1983, Sci.
Am. 249:94.]helix makes a complete turn every 3.6 nm; thus there areabout 10.5 pairs per turn. This is referred to as the B formof DNA, the normal form present in most DNA stretches incells. On the outside of B-form DNA, the spaces between theintertwined strands form two helical grooves of differentwidths described as the major groove and the minor groove(see Figure 4-3a).
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