Chapter 1

Chapter 1Chapter 1

Genes are DNA

DNA 是遗传物质DNA 为双螺旋DNA 的复制是半保留的通过碱基配对进行核酸杂交突变改变了 DNA 的序列突变集中于热点顺反子是单个 DNA 片断多重等位基因的种类DNA 的物理交换导致重组遗传密码是三联体细菌的基因和蛋白是共线性的顺式作用点和反式作用分子遗传信息可由 DNA 或者 RNA 提供

本章主要内容

Figure 1.1 A brief history of genetics.

1.1 Introduction

Genes are DNA

Avirulent mutants of a virus have lost the capacity to infect a host cell productively, that is, to make more virus.Transfection of eukaryotic cells is the acquisition of new genetic markers by incorporation of added DNA.Transforming principle is DNA that is taken up by a bacterium and whose expression then changes the properties of the recipient cell.

1.2 DNA is the genetic material

Figure 1.2 The transforming principle is DNA.


Figure 1.3 The genetic material of phage T2 is DNA.


Figure 1.4 Eukaryotic cells can acquire a new phenotype as the result of transfection by added DNA.


Antiparallel strands of the double helix are organized in opposite orientation, so that the 5′ end of one strand is aligned with the 3′ end of the other strand.Base pairing describes the specific (complementary) interactions of adenine with thymine or of cytosine with thymine in a DNA double helix (the former is replaced by adenine with uracil in double helical RNA).Complementary base pairs are defined by the pairing reactions in double helical nucleic acids (A with T in DNA or with U in RNA, and C with G).Supercoiling describes the coiling of a closed duplex DNA in space so that it crosses over its own axis.

1.3 DNA is a double helix

Figure 1.5 A polynucleotide chain consists of a series of 5 ￠ -3 ￠ sugar-phosphate links that form a backbone from which the bases protrude


Figure 1.6 The double helix maintains a constant width because purines always face pyrimidines in the complementary A-T and G-C base pairs. The sequence in the figure is T-A, C-G, A-T, G-C.


Figure 1.7 Flat base pairs lie perpendicular to the sugar-phosphate backbone.


Figure 1.8 The two strands of DNA form a double helix.


DNA polymerases are enzymes that synthesize a daughter strand(s) of DNA (under direction from a DNA template). May be involved in repair or replication.DNAases are enzymes that attack bonds in DNA.Endonucleases cleave bonds within a nucleic acid chain; they may be specific for RNA or for single-stranded or double-stranded DNA.Exonucleases cleave nucleotides one at a time from the end of a polynucleotide chain; they may be specific for either the 5′ or 3′ end of DNA or RNA.Parental strands of DNA are the two complementary strands of duplex DNA before replication.

1.4 DNA replication is semicon-servative

Replication fork is the point at which strands of parental duplex DNA are separated so that replication can proceed.Ribonucleases are enzymes that degrade RNA. Exo(ribo)nucleases work progressively, typically degrading one base at a time from the 3′ end toward the 5 ′ end. Endo(ribo)nucleases make single cuts within the RNA chain.RNA polymerases are enzymes that synthesize RNA using a DNA template (formally described as DNA-dependent RNA polymerases).RNAases are enzymes that degrade RNA.Semiconservative replication is accomplished by separation of the strands of a parental duplex, each then acting as a template for synthesis of a complementary strand.


Figure 1.9 Base pairing provides the mechanism for replicating DNA.


Figure 1.10 Replication of DNA is semiconservative.


Figure 1.11 The replication fork is the region of DNA in which there is a transition from

the unwound parental duplex to the newly replicated daughter duplexes.

1.4 DNA replication is semiconservative

Denaturation of DNA or RNA describes its conversion from the double-stranded to the single-stranded state; separation of the strands is most often accomplished by heating.Hybridization is the pairing of complementary RNA and DNA strands to give an RNA-DNA hybrid.Melting of DNA means its denaturation.Melting temperature of DNA is the mid-point of the transition when duplex DNA to denatured by heating to separate into single strands. Renaturation is the reassociation of denatured complementary single strands of a DNA double helix.

1.5 Nucleic acids hybridize by base pairing

Figure 1.12 Base pairing occurs in duplex DNA and also in intra- and inter-molecular interactions in single-stranded RNA (or DNA).

1.5

Nucleic acids hybridize by base pairing

Figure 1.13 Denatured single strands of DNA can renature to give the duplex form.

1.5


Figure 1.14 Filter hybridization establishes whether a solution of denatured DNA (or RNA) contains sequences complementary to the strands immobilized on the filter.

1.5


Background level of mutation describes the rate at which sequence changes accumulate in the genome of an organism. It reflects the balance between the occurrence spontaneous mutations and their remomval by repair systems, and is characteristic for any species.Deletions are generated by removal of a sequence of DNA, the regions on either side being joined together.result from the action of a mutagen (which may act directly on the bases in DNA) or indirectly, but in either case the result is a change in the sequence of DNA. are identified by the presence of an additional stretch of base pairs in DNA.

1.6 Mutations change the sequence of DNA

Leaky mutants have some residual function, either because the mutant protein is partially active (in the case of a missense mutation), or because a small amount of wild-type protein is made (in the case of a nonsense mutation).Mutagens increase the rate of mutation by inducing changes in DNA sequence, directly or indirectly.Point mutations are changes involving single base pairs.Revertants are derived by reversion of a mutant cell or organism.Spontaneous mutations occur as the result of natural effects, due either to mistakes in DNA replication or to environmental damage.


Suppression describes the occurrence of changes that eliminate the effects of a mutation without reversing the original change in DNA.Suppressor (extragenic) is usually a gene coding a mutant tRNA that reads the mutated codon either in the sense of the original codon or to give an acceptable substitute for the original meaning.Transition is a mutation in which one pyrimidine is substituted by the other or in which one purine is substituted for the other.Transversion is a mutation in which a purine is replaced by a pyrimidine or vice versa.


Figure 1.15 Mutations can be induced by chemical modification of a base.


Figure 1.16 Mutations can be induced by the incorporation of base analogs into DNA.


Back mutation reverses the effect of a mutation that had inactivated a gene; thus it restores wild type.Forward mutations inactivate a wild-type gene.Hotspot is a site at which the frequency of mutation (or recombination) is very much increased.Modified bases are all those except the usual four from which DNA (T, C, A, G) or RNA (U, C, A, G) are synthesized; they result from postsynthetic changes in the nucleic acid.Neutral substitutions in a protein are those changes of amino acids that do not affect activity.Silent mutations do not change the product of a gene.

1.7 Mutations are concentrated at hotspots

Figure 1.17 Spontaneous mutations occur throughout the lacI gene of E. coli, but are concentrated at a hotspot.


Figure 1.18 The deamination of 5-methylcytosine produces thymine (causing C-G to T-A transitions), while the deamination of cytosine produces uracil (which usually is removed and then replaced by cytosine).


Figure 1.15 Mutations can be induced by chemical modification of a base.


Cistron is the genetic unit defined by the cis/trans test; equivalent to gene.Complementation group is a series of mutations unable to complement when tested in pairwise combinations in trans; defines a genetic unit (the cistron).Gene (cistron) is the segment of DNA involved in producing a polypeptide chain; it includes regions preceding and following the coding region (leader and trailer) as well as intervening sequences (introns) between individual coding segments (exons).One gene : one enzyme hypothesis is the basis of modern genetics: that a gene is a stretch of DNA coding for a single polypeptide chain.

1.8 A cistron is a single stretch of DNA

Figure 1.19 Genes code for proteins; dominance is explained by the properties of mutant proteins. A recessive allele does not contribute to the phenotype because it produces no protein (or protein that is nonfunctional).


Figure 1.20 The cistron is defined by the complementation test. Genes are represented by bars; red stars identify sites of mutation.


Gain-of-function mutation represents acquisition of a new activity. It is dominant.Leaky mutants have some residual function, either because the mutant protein is partially active (in the case of a missense mutation), or because a small amount of wild-type protein is made (in the case of a nonsense mutation).Loss-of-function mutation inactivates a gene. It is recessive.Null mutation completely eliminates the function of a gene, usually because it has been physically deleted.Polymorphism refers to the simultaneous occurrence in the population of genomes showing allelic variations (as seen either in alleles producing different phenotypes or-for example-in changes in DNA affecting the restriction pattern).

1.9 The nature of multiple alleles

Figure 1.19 Genes code for proteins; dominance is explained by the properties of mutant proteins. A recessive allele does not contribute to the phenotype because it produces no protein (or protein that is nonfunctional).


Figure 1.21 The w locus has an extensive series of alleles, whose phenotypes

extend from wild-type (red) color to complete lack of pigment.


Figure 1.22 The ABO blood group locus codes for a galactosyltransferase whose specificity determines the blood group.


Bivalent is the structure containing all four chromatids (two representing each homologue) at the start of meiosis.Breakage and reunion describes the mode of genetic recombination, in which two DNA duplex molecules are broken at corresponding points and then rejoined crosswise (involving formation of a length of heteroduplex DNA around the site of joining).Chiasma (pl. chiasmata) is a site at which two homologous chromosomes appear to have exchanged material during meiosis.Crossing-over describes the reciprocal exchange of material between chromosomes that occurs during meiosis and is responsible for genetic recombination.Hybrid DNA is another term for heteroduplex DNA.

1.10 Recombination occurs by physical exchange of DNA

Figure 1.23 Chiasma formation is responsible for generating recombinants.


Figure 1.24 Recombination involves pairing between complementary strands of the two parental duplex DNAs.


Figure 1.13 Denatured single strands of DNA can renature to give the duplex form.


Codon is a triplet of nucleotides that represents an amino acid or a termination signal.Frameshift mutation results from an insertion or deletion that changes the phase of triplets, so that all codons are misread after the site of mutation.Genetic code is the correspondence between triplets in DNA (or RNA) and amino acids in protein.Initiation codon is a special codon (usually AUG) used to start synthesis of a protein.ORF is an open reading frame; presumed likely to code for a protein.>Reading frame is one of three possible ways of reading a nucleotide sequence as a series of triplets.Suppressor (extragenic) is usually a gene coding a mutant tRNA that reads the mutated codon either in the sense of the original codon or to give an acceptable substitute for the original meaning.Termination codon is one of three (UAG, UAA, UGA) that causes protein synthesis to terminate.

1.11 The genetic code is triplet-- Key terms

Figure 1.25 Frameshift mutations show that the genetic code is read in triplets from a fixed starting point.

1.11

The genetic code is triplet

Figure 1.26 An open reading frame starts with AUG and continues in triplets to a termination codon. Blocked reading frames may be interrupted frequently by termination codons.

1.11 The genetic code is triplet

Coding region is a part of the gene that represents a protein sequence.Leader of a protein is a short N-terminal sequence responsible for passage into or through a membrane.RNA splicing is the process of excising the sequences in RNA that correspond to introns, so that the sequences corresponding to exons are connected into a continuous mRNA.Trailer is a nontranslated sequence at the 3´ end of an mRNA following the termination codon.Transcription is synthesis of RNA on a DNA template.Translation is synthesis of protein on the mRNA template.

1.12 The relationship between coding sequences and proteins

Figure 1.27 The recombination map of the tryptophan synthetase gene corresponds with the amino acid sequence of the protein.

1.12

The relationship between coding sequences and proteins

Figure 1.28 RNA is synthesized by using one strand of DNA as a template for complementary base pairing.


Figure 1.29 The gene may be longer than the sequence coding for protein.


Figure 1.30 Gene expression is a multistage process.

1.12


Figure 2.10 Interrupted genes are expressed via a precursor RNA. Introns are removed when the exons are spliced together. The mRNA has only the sequences of the exons.

1.12


Figure 5.16 Eukaryotic mRNA is modified by addition of a cap to the 5 ￠ end and poly(A) to the 3 ￠ end.

1.12


cis- configuration describes two sites on the same molecule of DNA.Trans- configuration of two sites refers to their presence on two different molecules of DNA (chromosomes).

1.13 cis-acting sites and trans-acting molecules

Figure 1.20 The cistron is defined by the complement-ation test. Genes are represented by bars; red stars identify sites of mutation.


Figure 1.31 Control sites in DNA provide binding sites for proteins; coding regions are expressed via the synthesis of RNA.


Figure 1.32A cis-acting site controls the adjacent DNA but does not influence the other allele.


Figure 1.33 A trans-acting mutation in a protein affects both alleles of a gene that it controls.


Central dogma describes the basic nature of genetic information: sequences of nucleic acid can be perpetuated and interconverted by replication, transcription, and reverse transcription, but translation from nucleic acid to protein is unidirectional, because nucleic acid sequences cannot be retrieved from protein sequences.

Prion is a proteinaceous infectious agent, which behaves as an inheritable trait, although it contains no nucleic acid. Examples are PrPSc, the agent of scrapie in sheep and bovine spongiform encephalopathy, and Psi, which confers an inherited state in yeast.Reverse transcription is synthesis of DNA on a template of RNA; accomplished by reverse transcriptase enzyme.Scrapie is a infective agent made of protein.Virion is the physical virus particle (irrespective of its ability to infect cells and reproduce).Viroid is a small infectious nucleic acid that does not have a protein coat.

1.14 Genetic informationcan be provided by DNA or RNA

Figure 1.34 The central dogma states that information in nucleic acid can be perpetuated or transferred, but the transfer of information into protein is irreversible.

1.14 Genetic information can be provided by DNA or RNA

Figure 1.35 Double-stranded and single-stranded nucleic acids both replicate by synthesis of complementary strands governed by the rules of base pairing.


Figure 1.36 The amount of nucleic acid in the genome varies over an enormous range.


Figure 1.37 PSTV RNA is a circular molecule that forms an extensive double-stranded structure, interrupted by many interior loops. The severe and mild forms differ at three sites.


1. Two classic experiments proved that DNA is the genetic material. 2. DNA is a double helix consisting of antiparallel strands in which the nucleotide units are linked by 53 phosphodiester bonds. 3. A stretch of DNA may code for protein.4. A chromosome consists of an uninterrupted length of duplex DNA that contains many genes. 5. A gene may have multiple alleles. Recessive alleles are caused by a loss-of-function.

1.15 Summary

6. A mutation consists of a change in the sequence of A·T and G·C base pairs in DNA. 7. The natural incidence of mutations is increased by mutagens. 8. Forward mutations occur at a rate of ~106 per locus per generation; back mutations are rarer. 9. Although all genetic information in cells is carried by DNA, viruses have genomes of double-stranded or single-

stranded DNA or RNA.

1.15 Summary

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