Bio 340 - Exam 2 Terms And Definitions

chromosomal fragment without a centromere which will be lost during nuclear division

polyploid individual or species whose chromosomes derive from two or more closely related species

conditions in which the somatic chromosomes complement of an individual is NOT an exact multiple of the haploid number (n) of chromosomes found in gametes of the species due to addition or loss of one or more whole chromosomes

polyploid individual or species in which all chromosomes derive from the same places

a structurally altered chromosome carrying one or more inversions or translocations that is used to maintain detrimental recessive mutants in the homolog with normal gene order by "crossover suppression", i.e., production of inviable crossovers. A dominant mutant marker is usually incorporated into a balancer chromosome to make its presence visible

change in the normal number or structure of chromosomes

mutation in the structure of a chromosome

see balancer chromosome

a mutation caused by the loss, or deletion, of part of a chromosome

use of overlapping deletions (deficiencies) to locate a gene on a chromosomal or genetic map

one with two centromeres that forms an anaphase bridge during nuclear division which breaks, causing deleted and duplicated chromosomal regions in daughter nuclei

condition in which the somatic chromosome complement is 2n, or twice the number of chromosomes found in gametes of the species

the syndrome expressed by humans having the abnormal karyotype 47, +21

a chromosomal aberration in which a segment of a chromosome is repeated

condition in which the somatic chromosome complement of an individual is a multiple of the species' full monoploid set of chromosomes (x)

inherited type of down syndrome caused by a translation of chromosome 21 to an autosome, usually chromosome 14, which results in trisomy for most of chromosome 21

increase in the copy number of a gene. gene amplification can occur by differential replication of a gene within a chromosome, by chromosomal duplication, by replication of whole chromosomes (polyteny), or by extrachromosomal replication (e.g., ribosomal gene amplification)

a chromosomal aberration in which a segment of the chromosome is reversed. a paracentric inversion does not include the centromere in the inverted segment, while a pericentric inversion does.

three nucleotide sequences amplified from 10-50 copies up to 1000 copies in or near a gene, i.e., Fragile x Syndrome and Huntington Disease

aneuploid condition in which the somatic chromosome complement is 2n-1

aneuploid condition in which the somatic chromosome complement is 2n-2 due to the loss of one pair of homologs

mutation that can be mapped to a single locus; at the molecular level, the substitution, deletion, or addition of a single nucleotide par in the DNA of a gene

euploidy in which the somatic chromosome complement is 3x or greater

a change in the expression of a gene resulting from a change in its position within the genome. Variegated position effect appears as a mosaic pattern caused by an instability in the phenotypic expression of a gene moved to a new position, e.g., into or adjacent to heterochromatic

aneuploid condition in which the somatic chromosome complement is 2n+2, one set of homologous chromosomes having two additional homologs.

a chromosomal aberration in which a segment of one chromosome is transferred to another. the most common is a reciprocal translocation in which non-homologous chromosomes have exchanged segments

a DNA sequence capable of moving (transposing0 from one location to another in a genome. Some TEs are called "jumping genes"

euploidy in which the somatic chromosome complement is 3x

aneuploid condition in which the somatic chromosome complement is 2n+1. in double trisomic individuals, two different pairs of homologous chromosomes have an extra homolog, i.e., 2n+1+1

crossing over associated with asymmetrical pairing of duplicate genes in individuals homozygous for the duplication, and resulting in three gene copies in one crossover product and one copy in the other.

in bacteria, a transient condition required for transformation when the cell can bind and take up foreign DNA molecules; a competent cell is able to take up exogenous DNA and thereby be transformed.

the temporary union of two sexually reproducing unicellular organisms for the transfer of DNA; in E. coli, DNA transfer is unidirectional, from the donor call (F+ or Hfr) to the recipient cell (F-)

a circular genetic element in bacteria that can self-replicate (autonomous replication) in the cytoplasm or integrate into the bacterial chromosome and replicate with the chromosome

a male bacterial cell containing fertility factor in its cytoplasm.

a female bacterial cell containing a fertility factor

a fertility factor (F) that contains a portion of the bacterial chromosome.

a bacterial episome whose presence confers donor ability (maleness) during conjugation

see transduction

a bacterial cell exhibiting a high frequency of recombination due to a chromosomally integrated F factor that can mobilize and transfer all or part of the host chromosome to a recipient F- cell.

the spectrum of strains of a given bacterial species that a given strain of phage can infect; host range is determined by the array of restriction endonucleases produced by the bacterium in its defense against viral infection.

in a Hfr X F- cross, a technique by that breaks apart donor and recipient cells at specific times during conjugation, allowing only a given amount of DNA to be transferred; the bacterial genes can be mapped (in minutes) by determining the order in which donor genes enter recipient cells

disintegration of a cell brought about by the rupture of its membrane, e.g., by a virus

the process by which the DNA of an infecting phage becomes repressed and integrated into the host bacterium's chromosome

see temperate phage

see temperate phage

a bacterial cell in which a segment of its genome is duplicated in a fragment brought in by transformation, transduction, or conjugation.

a clear area on an otherwise opaque lawn of bacteria caused by infection and lysis of cells by a phage; each plaque represents the growth of one phage, so counting plagues is a way of counting viable phage particles.

extrachromosomal, circular DNA molecule that self replicates in the cytoplasm of a bacterium and may contain genetic information; a cell may contain one or more plasmids, which may segregate to daughter cells during cell division.

a phage genome integrated into the chromosome of a lysogenic bacterium.

a DNA molecule formed by joining two different molecules; DNA or gene splicing is done in vitro usually, ligating DNAs from different organisms.

nuclease derived from microorganisms that recognices specific nucleotide sequences in DNA and cleaves or nicks the molecule at those site; restriction enzymes that cleave both DNA strags are used to construct recombinant DNA molecules

see transduction

a virus that can integrate into the host bacterial chromosome as a prophage that congers lysogeny upon the host cell; while in the lysogenic phase - or pathway, lytic activity of the virus is repressed, but, upon entering the lytic phase, it leaves the chromosomes and multiplies, killing the host cell.

in bacteria, virus-mediated gene transfer from one cell to another. The transducing phage in specialized transduction produces particles carrying only specific regions of host genome, i.e., adjacent to one to a few sites of insertion into the bacterial chromosomes; in generalized transduction, any part of the host chromosomes can be packaged at random into transducing phage and transferred upon lysis of the host cell into a new bacterium, where it can enter the genome of the new host cell by non-reciprocal recombination

heritable change in a cell or an organism brought about by the uptake of foreign (exogenous), non-viral DNA such as a plasmid. Transformation in bacteria permits the non-reciprocal genetic recombination of exogenous genes into the host genome, requiring a physiological uptake mechanism (e.g., as in pneumococci) or a non-physiological mechanism (e.g., E coli). Transformation in eukaryotes is the conversion of cultured cells to a malignant phenotype, usually through infection by a tumor virus or by a virus-transmitted oncogene.

a phase or virus that infects and lyses the host bacterial cell.

a unit of measurement equal to 0.1 nanometer

parallel arrangement of two linear structures (molecules) which have opposite orientations

sequences within a gene that encode biological information

in nucleic acid chemistry, the mutual affinity of two nucleotides, or two polynucleotides, that enables them to unite by hydrogen bonding; e.g., complementary bases in a pair of nucleotides or complementary strands in a DNA double helix

non-ionic chemical bond formed by electron-sharing; e.g., the phosphodiester bonds in the backbone of nucleic acids that connect the 5'-carbon of one pentose sugar to the 3' carbon of the pentode in the adjacent nucleotide

double stranded DNA that has lost its three-dimensional structure that has been separated into single strands by breakage of hydrogen bonds

the pentose (5-carbon) sugar in DNA

an enzyme that degrades DNA into oligonucleotides or nucleotides by breaking its sugar-phosphate bonds

the genetic material of prokaryotes and eukaryotes, the most viruses, that is typically composed of two polynucleotide chains which are united into a double helic. DNA exists in several different conformations, e.g., A-form, B-form, and Z-form; recently, a triplex form was described.

a method of hybridizing DNA probes to regions in genomic DNA containing dispersed, hyper-variable arrays of short tandem repeats with a core sequence; each probe represents a tandem repeat of one of the core sequences.

genetically active chromatic that stains lightly during interphase and lies in dispersed regions of eukaryotic chromosomes

darkly staining chromatic in regions of chromosomes that remain condensed during interphase and are, for the most part, genetically inert

proteins complexed with chromosomal DNA that are rich in basic amino acids (arginine and lysine)

a weak, electrostatic, non-covalent linkage formed when a hydrogen atom is shared by two electronegative atoms such as oxygen or nitrogen

unit of measure equal to 1 X 10^(-9) meter

a weak organic acid composed of phosphate groups, pentose sugar groups, and nitrogenous bases (purines and pyrimidines)

a purine or pyrimidine base covalently linked to a deoxyribose or ribose sugar molecule

a nucleoside phosphate, i.e., a nucleoside covalently linked to a phosphate

a pair of nucleotides within opposite strands of duplex DNA that are held together by H-bonds formed between their complementary base pairs (bp), A-T, and G-C

a short polynucleotide chain

in nucleic acids, a segment of DNA in which the sequence of bases on the same strand, or on complementary strands, reads the same from a central axis of symmetry, e.g. simple palindrome -GGA|AGG-, or inverted repeat -GGA|TCC-, -CCT|AGG-. Palindromes may form a stem-loop or hairpin structures; in DNA, these may serve as recognition sites for cleavage by restriction endonucleases.

a single-stranded molecule composed of nucleotides covalently linked end to end

a class of nitrogenous organic bases with a double ring structure found in nucleic acids; DNA and RNA contain the purines adenine and quanine

a class of nitrogenous organic bases with a single ring structure found in nucleic acids; DNA contains the pyrimidines cytosine and thymine, while RNA contains uracil instead of thymine

a RNA virus that, upon infection of its animal host, uses reverse transcripts to synthesize DNA complementary to its own genome.

a nucleic acid that is usually singe-stranded and contains the sugar ribose and the pyrimidine uracil

the five-carbon sugar in RNA

any enzyme that cleaves phosphodiester bonds in RNA

a form of double-stranded DNA in which tension due to over-winding or under-winding of the double helix causes it to coil upon itself and form a superhelix that is table in DNA without free ends, e.g., circular DNA

a method used to determine the three-dimensional crystalline structure of molecules based on diffraction (scattering) patterns produced when X-rays pass through them and are recorded on a photographic film.

double-stranded, circular DNA consisting almost entirely of unique sequences and with uniform distribution of G-C nucleotide pairs; there are no histones associated with the bacterial chromosome, but certain DNA-binding proteins (e.g., HU and H) are presumed to provide structural stability

the "110 A fiber" or ("11 nm fiber") is the primary structural fiber of chromatin seen in interphase nuclei; it is composed of nucleosomes held together by linker DNA sequences. The "300 A Fiber" (or "30 nm fiber") is the secondary level of chromatin organization seen in partly condensed mitotic or meiotic chromatics and formed by folding and/or supercoiling of the primary fiber into a solenoid with 6 nucleosomes per turn. at the tertiary level, the 300 A fiber is folded into DNA loops about a central axis ("scaffold") producing a highly condensed metaphase chromatid with a diameter of =700 nm.

("sticky ends") - ends of DNA duplex that are cut in a staggered pattern enabling them to hydrogen-bond with complementary base sequences from other similarly formed ends. for example, cohesive ends (cos) of linear lambda phage, unite by base pairing to produce a circular DNA molecule.

see levels of organization of chromatin fibers.

the paired histone proteins - histone 1 (H2a), histone 2 (H2b), histone 3 (H3), and histone 4 (H4) - that comprise the histone octomer (8) of a nucleosome's core.

in genomic DNA renaturation analysis, a parameter that expresses the product of initial DNA concentration (C0T in moles) and renaturation time (t in seconds) per liter. A C0T curve is used to determine the renaturation rate of DNA by graphing the amount of renatured DNA relative to C0T and hence giving a measure of the proportion of repetitive sequences in double-stranded DNA.

genomic DNA pattern formed by spacers composed of a middle repetitive DNA sequence interspersed with unique copy DNA sequences (genes): may be long or short pattern

a type of large repetitive DNA sequence in eukaryotic genomes, especially in higher organisms, e.g. the 6-kb KpnI sequence

the DNA linking two nucleosomes together

The major band formed when genomic DNA is centrifuged in a cesium chloride gradient; it contains unique and moderately repetitive sequences

an enzyme that breaks bonds in nuclei acid molecules

the repeating basic unit of eukaryotic chromosomes which consists of a core of 8 histones (core particle) wrapped around by about two coils of DNA 146 base pairs long.

process by which denatured DNA or protein is restored to its normal three-dimensional structure through restoration of hydrogen bonds.

any DNA sequence occurring repeatedly in chromosomal DNA either as highly repetitive (low C0T) or moderately repetitive (middle C0T) sequences.

nuclear DNA that separates from bulk nuclear DNA as one or more distinct minor bands during cesium chloride density gradient centrifugation; sDNA consists of short, tandem repeats of simple sequence DNA (highly repetitive) and derives from centromeric heterochromatic in animals and plants (excepting lower fungi).

a type of small repetitive DNA sequence in eukaryotic genomes, especially in higher organisms, e.g., 300-bp Alu sequence.

see unique-sequence DNA

a non-coding base sequence located between genes in eukaryotic DNA (or between coding segments of poly-cistronic mRNA in prokaryotes)

a closed double-stranded DNA molecule that is twisted upon itself, e.g., the covalently closed circular DNA of a bacterial chromosome.

a DNA sequence with a high C0T value that occurs only once in a haploid genome; it includes single copy genes.

a mode of replication where both Y-forks move and replicate DNA

a regulatory system for controlling progression through the cell cycle. In eukaryotes it involves cyclins and protein kinases.

a model for DNA replication that would result in one progeny duplex containing both parental strands and the other only newly synthesized strands.

replication of the leading strand in semiconservative DNA synthesis, in which 5'---->3' polymerization continues uninterrupted in the same direction as strand separation at the base of the Y-fork.

a measure of the specific volume and degree of hydration of a molecule, compound or particle, as expressed by the proportion of its weight/volume

a method for separating macromolecules based on centrifugal force and a gradient in the concentration of the solvent containing them. nucleic acid dissolved in cesium chloride (CsCl) separate according to their buoyant densities when subjected to high speed centrifugation; centrifugal force produces a CsCl gradient in which nucleic acid molecules sediment but stop migrating when they attain equilibrium at a position in the gradient where their density equals that of the CsCl. (macromolecules can be separated according to their sedimentation velocity when centrifuged in a preformed sucrose gradient)

deoxyribonucleoside with three phosphate groups at its 5' and (e.g., dATP, dGTP, dCTP, and dTTP) that provide high energy for DNA polymerization.

replication of the lagging strand in semiconservative DNA synthesis, in which 5'--->3' polymerization is directionally opposite to strand separation in the Y-fork; to rectify this, DNA synthesis is interrupted and reinitiated repeatedly, resulting the formation of Okazaki fragments.

a model for DNA replication that would result in progeny duplexes containing dispersed fragments of the parental strands due to multiple cleavages of the parental strands during replication

a DNA topoisomerase that reduces molecular tension in a DNA double helix caused by positive supercoiling building up in advance of a migrating replication fork; DNA gyrase makes double-stranded breaks to relax the duplex, and then seals them.

an enzyme that catalyzes covalent bond formation between the 5' phosphoryl end of one polynucleotide chain and the 3'-hydroxyl end of another chain during DNA replication; it also serves as a DNA repair enzyme by restoring broken sugar-phosphate bonds in the backbone of DNA strains. (some DNA ligases can join two double-stranded DNA molecules)

see polymerase

an enzyme that breaks internal phosphodiester bonds in a single- or double-stranded nucleic acids; it is usually specific for either DNA or RNA.

an enzyme that removes a terminal nucleotide in a polynucleotide chain by cleaving the terminal phosphodiester bond, thus removing one nucleotide at a time. Exonucleases are usually specific for either the 3'- or 5'-terminus, for DNA or RNA, and often for single- or double-stranded nucleic acids.

an enzyme that participates in DNA replication by unwinding double-stranded DNA in or near the replication fork.

see discontinuous replication

see continuous replication

an enzyme that breaks phosphodiester bonds in a polynucleotide (see DNase, exonuclease and endonuclease)

one of the short polynucleotide strands produced during discontinuous replication of the lagging strand of DNA synthesis.

the site at which the two strands of the parental DNA duplex are separated to allow replication of each strand.

an enzyme that catalyzes covalent bonding of nucleotides during nucleic acid synthesis or repair, e.g., DNA polymerases and RNA polymerases. during DNA replication in E.coli, DNA polymerase III holoenzyme (active form of DNA Pol III) is the major catalyst for 5'-->3' chain elongation; it also proof-reads through exonuclease activities (both 5'--->3' and 3'--->5') by excising/replacing incorrect base pairs. DNA Polymerase I also has both types of exonuclease activity and serves in proofreading; it plays major roles in DNA replication by removing the RNA primer and filling the gap through its 5'--->3' polymerase activity. (along with DNA ligase, DNA Pol I also serves as a repair enzyme to restore DNA damaged by UV lights or other radiations) DNA polymerase II has 5'--->3' polymerase activity but only 3'--->5' exonuclease activity.

a short RNA (sometimes single-stranded DNA) segment that provides a 3'-hydroxyl growing point for polymerization to ensue.

an RNA polymerase that uses DNA as the template to synthesize the RNA primer used to initiate DNA replication

a multi-enzyme complex containing primase activity that assembles at a specific site on a single strand of DNA in E. coli migrates 5'--->3', and at intervals synthesizes and RNA primer through its primase activity.

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the initiation site for DNA replication, i.e., the base sequence at which strand separation occurs so that DNA synthesis can begin.

a DNA molecule that contains a replication origin

the multi-peptide/enzyme complex that forms at a replication fork and includes a primosome, DNA polymerase III holoenzyme, and other enzymes involved in DNA synthesis.

a mode of DNA replication in which the growing point (replication fork) rolls around a circular template and, with each pass around the circle, produces a linear strand of newly formed DNA. The linear strand can serve as a new template and, when cut free, form another circular template.

a mode of double-stranded DNA replication that results in progeny molecules containing both a parental and a newly synthesized DNA strand.

replication of double-stranded DNA in which the newly synthesized leading strand undergoes continuous replication, while the lagging strand is replicated by discontinuous replication

a tetrameric protein at the base of a replication fork that stabilizes the fork by maintaining strand separation and protecting against degradation.

an enzyme composed of a protein and RNA that functions like a reverse transcriptase in that it uses its RNA as template for the synthesis of telomeric DNA

a single-stranded DNA or RNA molecule that specifies the nucleotide sequence in a complementary strand produced during nucleic acid synthesis.

a mode of replication where one Y-fork remains as a fixed swivel and the second replicates

the DNA structure where the two single strands have separated to allow DNA synthesis.

in models for recombination, migration of the cross bridge (branch) along the two heteroduplex strands created by an exchange.

early model for crossing over based by synchronous breakage of non-sister chromatids at homologous sites, after chromatid replication, followed by strand exchange and reunion of broken ends

branched DNA structure formed by the first strand exchange during crossing over.

an unsupported early model for crossing over that assumed the exchange occurs between two non-sister chromatids as they are being replicated, when each bends toward and copies the opposite homolog.

nonreciprocal recombination in which one allele of a gene directs the conversion of its partner allele to its own form during meiosis. The directed conversion is thought to result from correction of a DNA mismatch caused during crossing over and heteroduplex formation.

see homologous recombination

a DNA double helix formed by annealing complementary single strands from different sources; they may show loops or buckles if a structural difference exists between the strands. heteroduplexes may form as intermediate products in a recombinational event.

a popular model to explain homologous recombination that invokes the concept of heteroduplex DNA formation following simultaneous breaks at the same relative positions in homologous, non-sister DNA strands during crossing over.

recombination that requires little if any sequence similarity between the recombining DNAs and is therefore not site-specific

recombination that requires extensive sequence similarity (i.e., homology) between the recombining DNAs

a one-way recombination event where the recipient gives nothing back to the donor

a single-stranded DNA-dependent ATPase that catalyzes strand exchange to form heteroduplex joints and mediates several steps in general genetic recombination, including the search for homology in double-stranded DNA, homologous pairing, and strand transfer. RecA plays a role in the SOS response to DNA damage.

crossing over in homologous recombination that results in an exchange of DNA segments

recombination mediated by a specific recombination system that occurs between two specific sequences that need not be homologous.