Lodish H. - Molecular Cell Biology (5ed, Freeman, 2003) (794361), страница 46
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Finally, the same enzyme joins (ligates) the two ends of the broken strand.Another type of enzyme, topoisomerase II, makes breaks inboth strands of a double-stranded DNA and then religatesthem. As a result, topoisomerase II can both relieve torsional stress and link together two circular DNA moleculesas in the links of a chain.Although eukaryotic nuclear DNA is linear, long loops ofDNA are fixed in place within chromosomes (Chapter 10).Thus torsional stress and the consequent formation of supercoils also could occur during replication of nuclear DNA.As in bacterial cells, abundant topoisomerase I in eukaryoticnuclei relieves any torsional stress in nuclear DNA thatwould develop in the absence of this enzyme.Many DNA Molecules Are CircularMany prokaryotic genomic DNAs and many viral DNAs arecircular molecules.
Circular DNA molecules also occur inmitochondria, which are present in almost all eukaryotic4.1 • Structure of Nucleic Acids(a) Supercoiled(b) Relaxed circle107 EXPERIMENTAL FIGURE 4-7 DNAsupercoils can be removed by cleavageof one strand. (a) Electron micrograph ofSV40 viral DNA. When the circular DNA ofthe SV40 virus is isolated and separated fromits associated protein, the DNA duplex isunderwound and assumes the supercoiledconfiguration.
(b) If a supercoiled DNA isnicked (i.e., one strand cleaved), the strandscan rewind, leading to loss of a supercoil.Topoisomerase I catalyzes this reaction andalso reseals the broken ends. All the supercoilsin isolated SV40 DNA can be removed by thesequential action of this enzyme, producingthe relaxed-circle conformation. For clarity, theshapes of the molecules at the bottom havebeen simplified.Different Types of RNA Exhibit VariousConformations Related to Their FunctionsAs noted earlier, the primary structure of RNA is generallysimilar to that of DNA with two exceptions: the sugar component of RNA, ribose, has a hydroxyl group at the 2 position (see Figure 2-14b), and thymine in DNA is replaced byuracil in RNA.
The hydroxyl group on C2 of ribose makesRNA more chemically labile than DNA and provides achemically reactive group that takes part in RNA-mediatedcatalysis. As a result of this lability, RNA is cleaved intomononucleotides by alkaline solution, whereas DNA is not.Like DNA, RNA is a long polynucleotide that can be doublestranded or single-stranded, linear or circular. It can also participate in a hybrid helix composed of one RNA strand andone DNA strand.
As noted above, RNA-RNA and RNADNA double helices have a compact conformation like the Aform of DNA (see Figure 4-4b).Unlike DNA, which exists primarily as a very long double helix, most cellular RNAs are single-stranded and exhibita variety of conformations (Figure 4-8). Differences in thesizes and conformations of the various types of RNA permitthem to carry out specific functions in a cell. The simplestsecondary structures in single-stranded RNAs are formed bypairing of complementary bases. “Hairpins” are formed bypairing of bases within ≈5–10 nucleotides of each other, and“stem-loops” by pairing of bases that are separated by >10 toseveral hundred nucleotides. These simple folds can cooperate to form more complicated tertiary structures, one ofwhich is termed a “pseudoknot.”As discussed in detail later, tRNA molecules adopt a welldefined three-dimensional architecture in solution that is crucial in protein synthesis.
Larger rRNA molecules also havelocally well-defined three-dimensional structures, with moreflexible links in between. Secondary and tertiary structuresalso have been recognized in mRNA, particularly near theends of molecules. Clearly, then, RNA molecules are likeproteins in that they have structured domains connected byless structured, flexible stretches.The folded domains of RNA molecules not only arestructurally analogous to the helices and strands found inproteins, but in some cases also have catalytic capacities.Such catalytic RNAs are called ribozymes.
Although ribozymes usually are associated with proteins that stabilizethe ribozyme structure, it is the RNA that acts as a catalyst.Some ribozymes can catalyze splicing, a remarkable processin which an internal RNA sequence is cut and removed, andthe two resulting chains then ligated. This process occursduring formation of the majority of functional mRNA molecules in eukaryotic cells, and also occurs in bacteria and archaea. Remarkably, some RNAs carry out self-splicing, withthe catalytic activity residing in the sequence that is removed.The mechanisms of splicing and self-splicing are discussedin detail in Chapter 12.
As noted later in this chapter, rRNA108CHAPTER 4 • Basic Molecular Genetic Mechanisms FIGURE 4-8 RNA secondary(a) Secondary structureand tertiary structures. (a) Stem-loops,hairpins, and other secondary structurescan form by base pairing betweendistant complementary segments ofan RNA molecule. In stem-loops, thesingle-stranded loop between the basepaired helical stem may be hundredsor even thousands of nucleotides long,whereas in hairpins, the short turn maycontain as few as four nucleotides.(b) Pseudoknots, one type of RNAtertiary structure, are formed byinteraction of secondary loops throughbase pairing between complementarybases (green and blue). Only basepaired bases are shown.
A secondarystructure diagram is shown at right.[Part (b) adapted from P. J. A. Michiels et al.,2001, J. Mol. Biol. 310:1109.](b) Tertiary structure3Hairpin3Loop1Stem1Double-helicalstem region5Stem-loopplays a catalytic role in the formation of peptide bonds during protein synthesis.In this chapter, we focus on the functions of mRNA,tRNA, and rRNA in gene expression. In later chapters wewill encounter other RNAs, often associated with proteins,that participate in other cell functions.KEY CONCEPTS OF SECTION 4.1Structure of Nucleic AcidsDeoxyribonucleic acid (DNA), the genetic material, carries information to specify the amino acid sequences ofproteins. It is transcribed into several types of ribonucleicacid (RNA), including messenger RNA (mRNA), transferRNA (tRNA), and ribosomal RNA (rRNA), which function in protein synthesis (see Figure 4-1).■Both DNA and RNA are long, unbranched polymers ofnucleotides, which consist of a phosphorylated pentoselinked to an organic base, either a purine or pyrimidine.■The purines adenine (A) and guanine (G) and the pyrimidine cytosine (C) are present in both DNA and RNA.
Thepyrimidine thymine (T) present in DNA is replaced by thepyrimidine uracil (U) in RNA.■Stem2Loop25Pseudoknotside and the two sugar-phosphate backbones on the outside (see Figure 4-3). Base pairing between the strands andhydrophobic interactions between adjacent bases in thesame strand stabilize this native structure.The bases in nucleic acids can interact via hydrogenbonds. The standard Watson-Crick base pairs are G·C, A·T(in DNA), and A·U (in RNA). Base pairing stabilizes thenative three-dimensional structures of DNA and RNA.■Binding of protein to DNA can deform its helical structure,causing local bending or unwinding of the DNA molecule.■Heat causes the DNA strands to separate (denature).The melting temperature Tm of DNA increases with thepercentage of G·C base pairs. Under suitable conditions, separated complementary nucleic acid strands willrenature.■Circular DNA molecules can be twisted on themselves,forming supercoils (see Figure 4-7).
Enzymes called topoisomerases can relieve torsional stress and remove supercoils from circular DNA molecules.■Cellular RNAs are single-stranded polynucleotides, someof which form well-defined secondary and tertiary structures (see Figure 4-8). Some RNAs, called ribozymes, havecatalytic activity.■Adjacent nucleotides in a polynucleotide are linked byphosphodiester bonds. The entire strand has a chemical directionality: the 5 end with a free hydroxyl or phosphategroup on the 5 carbon of the sugar, and the 3 end witha free hydroxyl group on the 3 carbon of the sugar (seeFigure 4-2).4.2 Transcription of Protein-CodingGenes and Formation ofFunctional mRNANatural DNA (B DNA) contains two complementary antiparallel polynucleotide strands wound together into a regular right-handed double helix with the bases on the in-The simplest definition of a gene is a “unit of DNA that contains the information to specify synthesis of a single polypeptide chain or functional RNA (such as a tRNA).” The vast■■1094.2 • Transcription of Protein-Coding Genes and Formation of Functional mRNAmajority of genes carry information to build protein molecules, and it is the RNA copies of such protein-coding genesthat constitute the mRNA molecules of cells.
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