《分子生物学》名词解释The genome is the complete set of sequences in the genetic material of an organism. It includes the sequence of each chromosome plus any DNA in organelles.A gene (cistron) is the segment of DNA specifying production of 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).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.A replication fork (Growing point) is the point at which strands of parental duplex DNA are separated so that replication can proceed. A complex of proteins including DNA polymerase is found at the fork.A DNA polymerase is an enzyme that synthesizes a daughter strand(s) of DNA (under direction from a DNA template). Any particular enzyme may be involved in repair or replication (or both).RNA polymerases are enzymes that synthesize RNA using a DNA template (formally described as DNA-dependent RNA polymerases).A deoxyribonuclease (DNAase) is an enzyme that attacks bonds in DNA. It may cut only one strand or both strands.Ribonucleases (RNAase) are enzymes that cleave RNA. They may be specific for single-stranded or for double-stranded RNA, and may be either endonucleases or exonucleases.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.Endonucleases cleave bonds within a nucleic acid chain; they may be specific for RNA or for single-stranded or double-stranded DNA.Denaturation of protein describes its conversion from the physiological conformation to some other (inactive) conformation.Renaturation describes the reassociation of denatured complementary single strands of a DNA double helix.Annealing of DNA describes the renaturation of a duplex structure from single strands that were obtained by denaturing duplex DNA.Hybridization describes the pairing of complementary RNA and DNA strands to give an RNA-DNA hybrid.The Tm is the midpoint of the temperature range for denaturation.Spontaneous mutations occur in the absence of any added reagent to increase the mutation rate, as the result of errors in replication (or other events involved in the reproduction of DNA) or by environmental damage.The 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 of spontaneous mutations and their removal by repair systems, and is characteristic for any species.Mutagens increase the rate of mutation by inducing changes in DNA sequence, directly or indirectly.Induced mutations result from the action of a mutagen. The mutagen may act directly on the bases in DNA or it may act indirectly to trigger a pathway that leads to a change in DNA sequence.Abortive initiation describes a process in which RNA polymerase starts transcription but terminates before it has left the promoter. It then reinitiates. Several cycles may occur before the elongation stage begins.A point mutation is a change in the sequence of DNA involving a single base pair.A transition is a mutation in which one pyrimidine is replaced by the other and/or in which one purine is replaced by the other.A transversion is a mutation in which a purine is replaced by a pyrimidine or vice versa.Base mispairing is a coupling between two bases that does not conform to the Watson-Crick rule, e.g., adenine with cytosine, thymine with guanine.An insertion is the addition of a stretch of base pairs in DNA. Duplications are a special class of insertions.A transposon (transposable element) is a DNA sequence able to insert itself (or a copy of itself) at a new location in the genome, without having any sequence relationship with the target locus.A deletion is the removal of a sequence of DNA, the regions on either side being joined together except in the case of a terminal deletion at the end of a chromosome.Revertants are derived by reversion of a mutant cell or organism to the wild-type phenotype. Forward mutations inactivate a wild-type gene.A back mutation reverses the effect of a mutation that had inactivated a gene; thus it restores wild type.A true reversion is a mutation that restores the original sequence of the DNA.Second-site reversion occurs when a second mutation suppresses the effect of a first mutation.Suppression occurs when a second event eliminates the effects of a mutation without reversing the original change in DNA.A suppressor is a second mutation that compensates for or alters the effects of a primary mutation.The one gene : one enzyme hypothesis summarizes the basis of modern genetics: that a gene is a stretch of DNA coding for a single polypeptide chain.Frameshift mutations arise by deletions or insertions that are not a multiple of 3 base pairs and change the frame in which triplets are translated into protein. The term is inappropriate outside of coding sequences.A reading frame is one of the three possible ways of reading a nucleotide sequence. Each reading frame divides the sequence into a series of successive triplets. There are three possible reading frames in any sequence, depending on the starting point. If the first frame starts at position 1, the second frame starts at position 2, and the third frame starts at position 3.An open reading frame (ORF) is a sequence of DNA consisting of triplets that can be translated into amino acids starting with an initiation codon and ending with a termination codon.Processing of RNA describes changes that occur after its transcription, including modification of the 5 and 3 ends, internal methylation, splicing, or cleavage.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.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).A cis-acting site affects the activity only of sequences on its own molecule of DNA (or RNA); this property usually implies that the site does not code for protein.The 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.A retrovirus is an RNA virus with the ability to convert its sequence into DNA by reverse transcription.Reverse transcription is synthesis of DNA on a template of RNA. It is accomplished by the enzyme reverse transcriptase.An exon is any segment of an interrupted gene that is represented in the mature RNA product.An intron (Intervening sequence) is a segment of DNA that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it.A transcript is the RNA product produced by copying one strand of DNA. It may require processing to generate a mature RNA.A superfamily is a set of genes all related by presumed descent from a common ancestor, but now showing considerable variation.The genome is the complete set of sequences in the genetic material of an organism. It includes the sequence of each chromosome plus any DNA in organelles.The transcriptome is the complete set of RNAs present in a cell, tissue, or organism. Its complexity is due mostly to mRNAs, but it also includes noncoding RNAs.The proteome is the complete set of proteins that is expressed by the entire genome. Because some genes code for multiple proteins, the size of the proteome is greater than the number of genes. Sometimes the term is used to describe complement of proteins expressed by a cell at any one time.Defining the contents of a genome essentially means making a map. We can think about mapping genes and genomes at several levels of resolution:A genetic (or linkage) map identifies the distance between mutations in terms of recombination frequencies. It is limited by its reliance on the occurrence of mutations that affect the phenotype. Because recombination frequencies can be distorted relative to the physical distance between sites, it does not accurately represent physical distances along the genetic material.A linkage map can also be constructed by measuring recombination between sites in genomic DNA. These sites have sequence variations that generate differences in the susceptibility to cleavage by certain (restriction) enzymes. Because such variations are common, such a map can be prepared for any organism irrespective of the occurrence of mutants. It has the same disadvantage as any linkage map that the relative distances are based on recombination.A restriction map is constructed by cleaving DNA into fragments with restriction enzymes and measuring the distances between the sites of cleavage. This represents distances in terms of the length of DNA, so it provides a physical map of the genetic material. A restriction map does not intrinsically identify sites of genetic interest. For it to be related to the genetic map, mutationshave to be characterized in terms of their effects upon the restriction sites. Large changes in the genome can be recognized because they affect the sizes or numbers of restriction fragments. Point mutations are more difficult to detect.The ultimate map is to determine the sequence of the DNA. From the sequence, we can identify genes and the distances between them. By analyzing the protein-coding potential of a sequence of the DNA, we can deduce whether it represents a protein. The basic assumption here is that natural selection prevents the accumulation of damaging mutations in sequences that code for proteins. Reversing the argument, we may assume that an intact coding sequence is likely to be used to generate a protein.Polymorphism (more fully genetic polymorphism) refers to the simultaneous occurrence in the population of genomes showing variations at a given position. The original definition applied to alleles producing different phenotypes. Now it is also used to describe changes in DNA affecting the restriction pattern or even the sequence. For practical purposes, to be considered as an example of a polymorphism, an allele should be found at a frequency > 1% in the population.Single nucleotide polymorphism (SNP) describes a polymorphism (variation in sequence between individuals) caused by a change in a single nucleotide. This is responsible for most of the genetic variation between individuals.Restriction fragment length polymorphism (RFLP) refers to inherited differences in sites for restriction enzymes (for example, caused by base changes in the target site) that result in differences in the lengths of the fragments produced by cleavage with the relevant restriction enzyme. RFLPs are used for genetic mapping to link the genome directly to a conventional genetic marker.DNA fingerprinting analyzes the differences between individuals of the fragments generated by using restriction enzymes to cleave regions that contain short repeated sequences. Because these are unique to every individual, the presence of a particular subset in any two individuals can be used to define their common inheritanceThe C-value paradox describes the lack of relationship between the DNA content (C-value) of an organism and its coding potential.Nonrepetitive DNA shows reassociation kinetics expected of unique sequences.Repetitive DNA behaves in a reassociation reaction as though many (related or identical) sequences are present in a component, allowing any pair of complementary sequences to reassociate.A transposon (transposable element) is a DNA sequence able to insert itself (or a copy of itself) at a new location in the genome, without having any sequence relationship with the target locus.Selfish DNA describes sequences that do not contribute to the genotype of the organism but have self-perpetuation within the genome as their sole function.The transcriptome is the complete set of RNAs present in a cell, tissue, or organism. Its complexity is due mostly to mRNAs, but it also includes noncoding RNAs.Housekeeping genes (Constitutive gene) are those (theoretically) expressed in all cells because they provide basic functions needed for sustenance of all cell types.Luxury genes are those coding for specialized functions synthesized (usually) in large amounts in particular cell types.A gene family consists of a set of genes whose exons are related; the members were derived by duplication and variation from some ancestral gene.A translocation is a rearrangement in which part of a chromosome is detached by breakage or aberrant recombination and then becomes attached to some other chromosome.A gene cluster is a group of adjacent genes that are identical or related.Nonreciprocal recombination (unequal crossing-over) results from an error in pairing and crossing-over in which nonequivalent sites are involved in a recombination event.It produces one recombinant with a deletion of material and one with a duplication.Satellite DNA (Simple-sequence DNA) consists of many tandem repeats (identical or related) of a short basic repeating unit.Minisatellite DNAs consist of ~10 copies of a short repeating sequence. the length of the repeating unit is measured in 10s of base pairs. The number of repeats varies between individual genomes.An aminoacyl-tRNA is a tRNA linked to an amino acid. The COOH group of the amino acid is linked to the 3- or 2-OH group of the terminal base of the tRNA.Aminoacyl-tRNA synthetases are enzymes responsible for covalently linking amino acids to the 2- or 3-OH position of tRNA.A cap is the structure at the 5 end of eukaryotic mRNA, introduced after transcription by linking the terminal phosphate of 5 GTP to the terminal base of the mRNA. The added G (and sometimes some other bases) are methylated, giving a structure of the form 7MeG5ppp5Np . . .A cap 0 at the 5 end of mRNA has only a methyl group on 7-guanine.A cap 1 at the 5 end of mRNA has methyl groups on the terminal 7-guanine and the 2-O position of the next base.A cap 2 has three methyl groups (7-guanine, 2-O position of next base, and N6 adenine) at the 5 end of mRNA.The wobble hypothesis accounts for the ability of a tRNA to recognize more than one codon byunusual (non-G·C, non-A·T) pairing with the third base of a codon.Proofreading refers to any mechanism for correcting errors in protein or nucleic acid synthesis that involves scrutiny of individual units after they have been added to the chain.The leader of a protein is a short N-terminal sequence responsible for initiating passage into or through a membrane.Self-assembly refers to the ability of a protein (or of a complex of proteins) to form its final structure without the intervention of any additional components (such as chaperones). The term can also refer to the spontaneous formation of any biological structure that occurs when molecules collide and bind to each other.Chaperones（分子伴侣）are a class of proteins which bind to incompletely folded or assembled proteins in order to assist their folding or prevent them from aggregating.Protein sorting (targeting) is the direction of different types of proteins for transport into or between specific organelles.A signal sequence is a short region of a protein that directs it to the endoplasmic reticulum for co-translational translocation.The signal recognition particle (SRP) is a ribonucleoprotein complex that recognizes signal sequences during translation and guides the ribosome to the translocation channel. SRPs from different organisms may have different compositions, but all contain related proteins and RNAs.Signal peptidase is an enzyme within the membrane of the ER that specifically removes the signal sequences from proteins as they are translocated. Analogous activities are present in bacteria, archaebacteria, and in each organelle in a eukaryotic cell into which proteins are targeted and translocated by means of removable targeting sequences. Signal peptidase is one component of a larger protein complex.Retrograde translocation (Reverse translocation) is the translocation of a protein from the lumen of the ER to the cytoplasm. It usually occurs to allow misfolded or damaged proteins to be degraded by the proteasome.The transmembrane region (transmembrane domain) is the part of a protein that spans the membrane bilayer. It is hydrophobic and in many cases contains approximately 20 amino acids that form an α-helix. It is also called the transmembrane domain.A transmembrane protein (Integral membrane protein) extends across a lipid bilayer. A hydrophobic region (typically consisting of a stretch of 20-25 hydrophobic and/or uncharged aminoa acids) or regions of the protein resides in the membrane. Hydrophilic regions are exposed on one or both sides of the membrane.An anchor (stop-transfer) (often referred to as a "transmembrane anchor") is a segment of a transmembrane protein which resides in the membrane.The TOM complex (TOM) resides in the outer membrane of the mitochondrion and is responsible for importing proteins from the cytosol into the space between the membranes.The TIM complex (TIM) resides in the inner membrane of mitochondria and is responsible for transporting proteins from the intermembrane space into the interior of the organelle.The periplasm (or periplasmic space) is the region between the inner and outer membranes in the bacterial envelope.Signal peptidase is an enzyme within the membrane of the ER that specifically removes the signal sequences from proteins as they are translocated. Analogous activities are present in bacteria, archaebacteria, and in each organelle in a eukaryotic cell into which proteins are targeted and translocated by means of removable targeting sequences. Signal peptidase is one component of a larger protein complex.The nuclear envelope is a layer of two concentric membranes (inner and outer nuclear membranes) that surrounds the nucleus and its underlying intermediate filament lattice, the nuclear lamina. The nuclear envelope is penetrated by nuclear pores. The outer membrane is continuous with the membrane of the rough endoplasmic reticulum.A nuclear pore complex (NPC) is a very large, proteinaceous structure that extends through the nuclear envelope, providing a channel for bidirectional transport of molecules and macromolecules between the nucleus and the cytosol.A nuclear localization signal (NLS) is a domain of a protein, usually a short amino acid sequence, that interacts with an importin, allowing the protein to be transported into the nucleus.A nuclear export signal (NES) is a domain of a protein, usually a short amino acid sequence, which interacts with an exportin, resulting in the transport of the protein from the nucleus to the cytoplasm.Ubiquitin has a highly conserved sequence of 76 amino acids. It is linked via its COOH group to the ε NH2 group of a lysine residue in a target protein.The proteasome is a large complex with an interior cavity that degrades cytosolic proteins previously marked by covalent addition of ubiquitin.A promoter is a region of DNA where RNA polymerase binds to initiate transcription.Startpoint (startsite) (Startsite) refers to the position on DNA corresponding to the first baseincorporated into RNA.Initiation describes the stages of transcription up to synthesis of the first bond in RNA. This includes binding of RNA polymerase to the promoter and melting a short region of DNA into single strands.Elongation is the stage in a macromolecular synthesis reaction (replication, transcription, or translation) when the nucleotide or polypeptide chain is being extended by the addition of individual subunits.Termination is a separate reaction that ends a macromolecular synthesis reaction (replication, transcription, or translation), by stopping the addition of subunits, and (typically) causing disassembly of the synthetic apparatus.The holoenzyme (complete enzyme) is the complex of five subunits including core enzyme (α2ββ and σ) factor that is competent to initiate bacterial transcription.An open complex describes the stage of initiation of transcription when RNA polymerase causes the two strands of DNA to separate to form the "transcription bubble".Tight binding of RNA polymerase to DNA describes the formation of an open complex (when the strands of DNA have separated).The ternary complex in initiation of transcription consists of RNA polymerase and DNA and a dinucleotide that represents the first two bases in the RNA product.Abortive initiation describes a process in which RNA polymerase starts transcription but terminates before it has left the promoter. It then reinitiates. Several cycles may occur before the elongation stage begins.Conserved positions are defined when many examples of a particular nucleic acid or protein are compared and the same individual bases or amino acids are always found at particular locations.A consensus sequence is an idealized sequence in which each position represents the base most often found when many actual sequences are compared.A terminator is a sequence of DNA that causes RNA polymerase to terminate transcription.Antitermination is a mechanism of transcriptional control in which termination is prevented at a specific terminator site, allowing RNA polymerase to read into the genes beyond it.Readthrough at transcription or translation occurs when RNA polymerase or the ribosome, respectively, ignores a termination signal because of a mutation of the template or the behavior of an accessory factor.Intrinsic terminators are able to terminate transcription by bacterial RNA polymerase in the absence of any additional factors.Rho-dependent terminators are sequences that terminate transcription by bacterial RNA polymerase in the presence of the rho factor.Rho factor is a protein involved in assisting E. coli RNA polymerase to terminate transcription at certain terminators (called rho-dependent terminators).Polarity refers to the effect of a mutation in one gene in influencing the expression (at transcription or translation) of subsequent genes in the same transcription unit.Antitermination is a mechanism of transcriptional control in which termination is prevented at a specific terminator site, allowing RNA polymerase to read into the genes beyond it.Antitermination proteins allow RNA polymerase to transcribe through certain terminator sites.Immediate early phage genes in phage lambda are equivalent to the early class of other phages. They are transcribed immediately upon infection by the host RNA polymerase.Delayed early genes in phage lambda are equivalent to the middle genes of other phages. They cannot be transcribed until regulator protein(s) coded by the immediate early genes have been synthesized.A trans-acting product can function on any copy of its target DNA. This implies that it is a diffusible protein or RNA.A cis-acting site affects the activity only of sequences on its own molecule of DNA (or RNA); this property usually implies that the site does not code for protein.A structural gene codes for any RNA or protein product other than a regulator.A regulator gene codes for a product (typically protein) that controls the expression of other genes (usually at the level of transcription).A repressor is a protein that inhibits expression of a gene. It may act to prevent transcription by binding to an operator site in DNA, or to prevent translation by binding to RNA.The operator is the site on DNA at which a repressor protein binds to prevent transcription from initiating at the adjacent promoter.A transcription factor is required for RNA polymerase to initiate transcription at specific promoter(s), but is not itself part of the enzyme.An operon is a unit of bacterial gene expression and regulation, including structural genes and control elements in DNA recognized by regulator gene product(s).Induction refers to the ability of bacteria (or yeast) to synthesize certain enzymes only when their substrates are present; applied to gene expression, it refers to switching on transcription as a result of interaction of the inducer with the regulator protein.Basal level The level of response from a system in the absence of a stimulus is its basal level. (The basal level of transcription of a gene is the level that occurs in the absence of any specific activation.)Repression describes the ability of bacteria to prevent synthesis of certain enzymes when their products are present; more generally, refers to inhibition of transcription (or translation) by binding of repressor protein to a specific site on DNA (or mRNA).An inducer is a small molecule that triggers gene transcription by binding to a regulator protein.A corepressor is a small molecule that triggers repression of transcription by binding to a regulator protein.Gratuitous inducers resemble authentic inducers of transcription but are not substrates for the induced enzymes.Allosteric regulation describes the ability of a protein to change its conformation (and therefore activity) at one site as the result of binding a small molecule to a second site located elsewhere on the protein.Coordinate regulation refers to the common control of a group of genes.Autogenous control describes the action of a gene product that either inhibits (negative autogenous control) or activates (positive autogenous control) expression of the gene coding for it.Glucose repression (Catabolite repression) describes the decreased expression of many bacterial operons that results from addition of glucose.Inducer exclusion describes the inhibition of uptake of other carbon sources into the cell that is caused by uptake of glucose.CRP activator (CAP activator) is a positive regulator protein activated by cyclic AMP. It is needed for RNA polymerase to initiate transcription of many operons of E. coli.Adenylate cyclase is an enzyme that uses ATP as a substrate to generate cyclic AMP, in which 5 and 3 positions of the sugar ring are connected via a phosphate group.Attenuation describes the regulation of bacterial operons by controlling termination of transcription at a site located before the first structural gene.An attenuator is a terminator sequence at which attenuation occurs.The leader peptide is the product that would result from translation of a short coding sequence used to regulate transcription of the tryptophan operon by controlling ribosome movement.Ribosome stalling describes the inhibition of movement that occurs when a ribosome reaches a codon for which there is no corresponding charged aminoacyl-tRNA.RNA interference (RNAi) describes the technique in which double-strand RNA is introduced into cells to eliminate or reduce the activity of a target gene. It is caused by using sequences complementary to the double-stranded RNA sequences to trigger degradation of the mRNA of the gene.RNA silencing describes the ability of a dsRNA to suppress expression of the corresponding gene systemically in a plant.Cosuppression describes the ability of a transgene (usually in plants) to inhibit expression of the corresponding endogenous gene.Lytic infection of a bacterium by a phage ends in the destruction of the bacterium with release of progeny phage.Lysis describes the death of bacteria at the end of a phage infective cycle when they burst open to release the progeny of an infecting phage (because phage enzymes disrupt the bacterium's cytoplasmic membrane or cell wall). The same term also applies to eukaryotic cells; for example, when infected cells are attacked by the immune system.Prophage is a phage genome covalently integrated as a linear part of the bacterial chromosome.Lysogeny describes the ability of a phage to survive in a bacterium as a stable prophage component of the bacterial genome.Integration of viral or another DNA sequence describes its insertion into a host genome as a region covalently linked on either side to the host sequences.Induction of prophage describes its entry into the lytic (infective) cycle as a result of destruction of the lysogenic repressor, which leads to excision of free phage DNA from the bacterial chromosome.The excision of phage or episome or other sequence describes its release from the host chromosome as an autonomous DNA molecule.。