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498 Cards in this Set
- Front
- Back
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C-value paradox
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among eukaryotes, there is no consistent relationship between the dna content of the haploid genome and the metabolic developmental, or behavioral complexity of the organism
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purines
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double ring structured bases (Adenine and Guanine)
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pyrimidines
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single ring-ring structures bases (Thymine and Cytosine)
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nucleoside
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a base chemically linked to one molecule of sugar deoxydribose
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nucleotide
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phosphate group attached to a sugar molecule attached to the base
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polynucleotide chain
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phosphate attached to the 5' carbon of one sugar linked to the hydroxyl group attached to the 3' carbon of the next sugar in line (ncleotides joined together)
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phosphodiester bonds
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chemical bonds that bond the sugar components of the adjacent nucleotides that are linked through the phosphate groups
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5' end
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the end that terminates in a phosphate
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3' end
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the end that terminates in a hydroxyl
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hydrogen bond
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a weak bond in which two negatively charged atoms share a hydrogen atom
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antiparallel
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the orientation of the two strands of double stranded nucleic acid molecules;; (the 5' to 3' orientation)
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daughter strand
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the newly replicated complimentrary strand
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parental strand
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the strand being replicated
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template
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a strand of nucleic acid whose base sequence is copied in a polymerization reaction to produce either a complementrary DNA or an RNA strand
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semiconservative replication
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the usual form of replication in which one strand of dna serves as a template for another
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Mathew Meselson and Franklin Stahl in 1958
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the expiriment that showed DNA replication was semiconservative by using bacteria in a heavy N-containing medium and replicating their DNA several generations.
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theta replication
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bidirectional replicaion of a circular dna molecule, starting from a single origin of replication
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replication origin
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the position long a molecule at which DNA replication begins
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replication fork
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the region on dna molecule where the parental strands are separating and new strands are being sythesized
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initiation
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the process of generaing a new replication fork
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rolling-circle replication
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a mode of replication in which a circular parent molecule produces a linear branch of newly formed dna
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helicase
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protein that hydrolyzes ATP to drive the unwinding reaction
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single stranded DNA binding protein (SSB)
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binds single-stranded DNA tightly and cooperatively and it has an affinity for single stranded DNA at least 1000-fold greater than that for double stranded DNA
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gyrase
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a type of topoisomerase II that cleaves and rejoins both strands of a DNA duplex to relieve torsional stress
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ribose
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identical to deoxyribose of DNA except for the presence of an -OH group on the 2' carbon atom
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RNA polymerase
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An enzyme that makes RNA by copying the base sequence of a DNA strand
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primer
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in nucleic acids, a short RNA or single-stranded DNA segment that functions as a growing point in polymerization
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primosome
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the enzyme complex that forms the RNA primer for DNA replication. Multienzyme complex composed of 15 to 20 polypeptide chains
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DNA polymerase
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the enzyme that forms the sugar-phosphate bond between adjacent nucleotides in a new DNA acid chain.
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editing function or proofreading function
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The activity of DNA polymerases that removes incorrectly incorporated nucleotides
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precursor fragments (okazaki fragment)
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any of the short strands of DNA produced during discontinuous replication of the lagging strand
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leading strand
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DNA strand whose complement is synthesized as a continuous unit
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lagging strand
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the DNA strand whose complement is synthesized in short fragments that are ultimately joined together
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DNA ligase
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an enzyme that catalyzes formation of a covalent bond between adjacent 5' P and 3' OH termini in broken polynucleotide strand of double-stranded DNA
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Denaturation
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Separation of DNA strands (i.e. heating them up)
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Renaturation
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DNA strands coming together (i.e. when the heat is lowered in a solution)
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3 uses and methods of Denaturation and renaturation
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1. Small DNA fragment mixed with larger DNA fragments, which can help identify specific DNA fragments in a complex mixture.
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2. DNA fragment of one gene can be renatured with other genes of the same genome; is used to identify genes that are smaller, but not identical in sequence and have related functions.
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3. DNA fragment from one species can be renatured with sequences of other species. This allows the isolation of genes that have the same or related functions in multiple species and can be used to study molecular evolution.
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Nucleic acid hybridization
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The process of renaturing DNA strands from two different sources
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probe
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a radioactive DNA and RNA molecule used in DNA-RNA and DNA-DNA hybridization assays
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restriction enzymes
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Also called restriction endonucleases, are able to cleave DNA molecules at the poistions at which particular, short sequences of bases are present.
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restriction site
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the sequence recognized for cleavage by a restriction enzyme
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restriction fragment
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The fragments formed when a large DNA molecule is cut into many restriction fragments of different sizes.
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restriction map
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A diagram of a DNA molecule showing the positions of cleavage by one or more restriction endonucleases
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Southern Blot
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a nucleic acid hybridization method in which, from a gel to a membrane filter and then exposed to radioctive regions locate the homologous DNA fragments on the filter.
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Polymerase chain reaction (PCR)
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repeaated cycles of DNA denaturation, renaturation with primer oligonucleotide sequences, and replication, resulting in exponential growth in the number of copies of the DNA sequence located between the primers.
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dideoxy sequencing method
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procedure for DNA sequencing in which a template strand is replicated from a particular primer sequence and terminated by the incorporation of a nucleotide that contains dideoxyribose instead of deoxyribose; the resulting fragments are separated by size via eletrophoresis.
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dideoxyribose
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a deoxyribose sugar that lacks the 3' hydroxyl group; when incorporated into a polynucleotide chain, it blocks further chain elongation.
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Exonuclease activity
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The ability to break phosphodiester bonds in the sugar-phophate backbones of nucleic acid chains
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cohesive ends
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single-stranded regions at the ends of otherwise double-stranded DNA molecules that are complementary in base sequence
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blunt ends
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ends of a DNA molecule in which all terminal bases are paired; the term usually referes to termini formed by a restriction enzyme that does not produce single-stranded ends.
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mobile DNA
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alternative term for transposable elements
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plasmids
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nonessential DNA molecules that exist inside baterial cells
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conjugation
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a process of DNA transfer in sexual reproduction in certain bateria; in e. coli, the transfer is unidirectional, from donor cell lto recipient cell. Also, a mating between cells of Paramecium
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conjugative plasmids
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a plasmid encoding proteins and other factors that make possible its transmission between cells
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F factor
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a baterial plasmid-often called the fertility factor or sex plasmid-that is capable of transferring itself from a host (f+) cell to a cell not carrying an F factor (F- cell); when an F factor is integrated into the baterial chromosome (in an Hfr cell), the chromosome becomes transferrable to an F- cell during conjugation
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transposon
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a transposable element that contains bacterial genes-i.e. for antibiotic resistance; also used loosely as a synonym for transposable element
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cointegrate
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a DNA molecule, usually circular and formed by recombination, that joins two replicons
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site-specific recombinase
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an enzyme that catalyzes intermolecule cecombination between two duplex DNA molecules at the site of a target sequence that they have in common
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integron
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a DNA element that encodes a site-specific recombinase as well as recognition region that allows other sequences with similar recognitionregions to be incorporated into the integron by recombination
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cassette
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a circular antibiotic-resistance-coding region flanked by a recognition region for an integron
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integrase
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an enzyme that catalyzes a site specific exchange between two DNA sequences
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R Plasmid
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A bacterial plasmid that carries drug resistance genes; commonly used in genetic engineering
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Antibiotic-resistant mutants
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mutants that are able to grow in presence of an antibiotic
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nutritional mutants
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A mutation in a metabolic pathway that creates a need for a substance to be present in the growth medium or that eliminates the ability to utilize a substance present in the growth medium
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prototroph
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microbial strain capable of growth in a defined minimal medium that ideally contains only a carbon source and inorganic compounds. The wildtype genotype is usually regarded as a prototroph
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Auxotroph
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a mutant microorganism that is unable to synthesize a compound required for its growth but is able to grow if the compound is provided
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Carbon-source mutants
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mutants that cannot utilize particular substances as sources of energy or carbon atoms
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nonselective medium
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a medium which all wildtype cells form colonies
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selective medium
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a medium that only allows growth of one type of cell (either wildtype or mutant)
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transformation
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the process of genetic alteration by pure DNA
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cotransformation
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simultaneous transformation of two genetic markers carried on a single DNA fragment in bacteria
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Hfr Cell
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an e coli cell in which an f plasmid is integrated into the chromosome, making possible the transfer of part or all of the chromosome to an F- cell.
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episome
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a genetic element that can exist free in the cell or as a segment of DNA integrated into the chromosome
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selected marker
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a genetic mutation that allows growth in selective medium
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counterselected marker
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a mutation used to prevent growth of a donor cell in an Hfr x F- bacterial mating
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interrupted-mating technique
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in an Hfr x F- cross, a technique by which donor and recipient cells are broken apart at specific times, allowing only a particular length of DNA to be transferred
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time of entry
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in an Hfr x F- bacterial mating, the earliest time that a particular gene in the Hfr parent is transferred to the F- recipient
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F' plasmid
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An F plasmid that contains genes obtained from the bacterial chromosome in a addition to plasmid genes; formed by aberrant excision of an integrated F factor, taking along adjacent bacterial DNA
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partial diploid
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a cell in which a segment of the genome is duplicated, usually in a plasmid
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transduction
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the carrying of genetic information from one bacterium to another by a phage
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transducting phage
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a phage type capable of prducing prticles that contain bacterial DNA (transducing particles)
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generalized transducting phage
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produces particles that may carry any region of the genome
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specialized transducing phage
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produces particles that carry only specific regions of chromosomal DNA;
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cotransduction
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transduction of two or more linked genetic markers by one transducing particle
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frequency of cotransduction
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the proportion of transductants carrying a selected genetic marker that also carry a nonselected genetic marker
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lytic cycle
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the life cycle of a phage, in which progeny phage are produced and the host bacterial cell is lysed.
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plaque
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a clear area in an otherwise turbid layer of bacteria growing on a solid medium, caused by the infectino and killing of the cells by a phage; because each plaque results from the growth of one phage, plaque counting is a way of counting viable phage particles. The term is also used for animal viruses that cause clear areas in layers of animal cells grown in culture
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hotspot
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a site on a DNA molecule for which the rate of mutation is much higher than the rate of mutation on the rest of the molecule.
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lysogenic cycle
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In temperate bacteriophage, the phenomenon in which the DNA of an infecting phage becomes part of the genetic material of the cell
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prophage induction
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activation of a prophage to undergo the lytic cycle
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excisionase
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an enzyme that is needed for prophage excision; works together with an integrase
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phage repressor
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regulatory protein that prevent stranscription of genes in a prophage
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Insertion sequence
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DNA sequence capable of transposition in a prokaryotic genome; such aequences usually code for their own transposase
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Cistron
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DNA sequence specifying a single genetic function as defined by a complementation test; nucleotide sequence coding for a single polypeptide.
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Lysogen
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Clone of bacterial cells that have acquired a prophage
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polypeptide chains
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a polymer of amino acids linmked together by pepptide bonds
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R-group
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refers to the side chain connected to the alpha carbon that differs for each amino acid
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peptide bond
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a polymer of amino acids linked together by peptide bonds
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amino terminus
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the end of a polypetide chain at which the amino acid bears a free amino group
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carboxyl terminus
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the end of a polypeptide chain at which the amino acid has a free carboxyl group
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RNA polymerase holoenzyme
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any of several large protein complexes that inlcudes RNA polymerase aming its constituents
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RNA polymerase I
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used exclusively in producing the transcript that becomes prcessed into ribosomal RNA
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RNA polymerase II
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the workhorse eukaryotic polymerase responsible for transcribing all protein-coding genes as well as the genes for a number of small nuclear RNA's (U1, U2, U3, and so forth) used in RNA processing
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RNA polymerase III
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used in transcribing all transfer RNA genes as well as the 5S component of ribosomal RNA
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Promoter recognition
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The first process of of RNA recognizing which strand of DNA should be transcribed in which the RNA polymerase binds to the promoter
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promoter
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A dna sequence at which RNA polymerase binds and initiates transcription
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consensus sequence
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a generalized base sequence derived from closely related sequences found in many locations in a genome or in many organisms; each position in the sequence consists of the base found in the majority of sequences in that position
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TATA box
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the base sequence 5 prime TAT 3 prime in the DNA of a promoter
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Chain initiation
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The second stage of RNA transcription in which after the initial binding step, the RNA polymerase initiates RNA synthesis at a nearby transcription start site
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Chain Elongation
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the second stage of RNA transcription in which RNA polymerase moves along the DNA template strand, adding nucleotides to the growing RNA chain.
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Chain terminiation
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the forth and final step of RNA transcription in which the RNA polymerase reaches a transcription termination sequence in the DNA and the polymerase enzyme disassociates from the DNA, and the newly synthesized RNA molycule is released.
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primary transcript
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the RNA molecule produced from a DNA template
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messenger RNA
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An RNA molecule transcribed from a DNA sequence and translated into the amino acid sequence of a polypeptide. In eukaryotes, the primary transcript undergoes elaborate processing to become the mRNA
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5' untranslated region
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the initial part of a mRNA which does not code for protein
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open reading frame (ORF)
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in the coding strand of DNA or in mRNA, a region containing a series of codonss uninterrupted by stop codons and therefore capable of coding for a polypeptide chain
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3' untranslated region
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the terminal portion of a messenger RNA, following the stop codon, which does not code for protein
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cap
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a ccomplex structure at the 5' termini of most eukaryotic mRNA molecules, having a 5'-5' linkage instead of the usual 3'-5' linkage
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poly-A tail
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the sequence of adeninees added to the 3' end of many eukaryotic mRNA molecules in processing
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introns
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a noncoding DNA sequence in a gene that is transcribed but is then excised from the primary transcript in froming a mature mRNA molecule; found primarily in eukaryotic cells
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exons
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the sequences in a gene that are retained in the messenger RNA after the introns are removed from the primary transcript.
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RNA splicing
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excision of introns and joining of exons.
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RNA splicing
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excision of introns and joining of exons
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spliceosomes
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an rna protein particle in the nucleus in which hintrons are removed from RNA transcripts
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snRNPs
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any of several classes of small ribonucleoprotein particles involved in RNA splicing
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ribozymes
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an RNA molecule able to catalyze one or more biochemical reactions
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Translation : Messenger rNA
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component of translation - needed to bring the ribosomal subunits together and to provide the coding sequence of bases that determines the amino acid sequence in the resulting polypeptide chain
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Translation : Ribosomes
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component of translation - particles on which protein synthesis takes place. They move along an mRNA molecule and align successive transfer RNA molecules; the amino acids are attached one by one to the growing polypeptide chain by means of peptide bonds. Ribosomes consist of two separate RNA-protein partics, which come together in polypeptide synthesis to form a mature ribosome.
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Translation : transfer RNA
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component of translation - the sequence of amino acids in a polypeptide is determined by the base sequence in the mRNA by means of a set of adapator molecules, the tRNA molecules each which is attached to a particular amino acid. Each set of the mRNA form a codon that binds to a group of 3 adjacent bases in the tRNA, the anticodon, bringing the attached amino acid into line for elngation of the growing polypeptide chain
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Translation : Aminoacyl-tRNA synthetases
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component of translation - Each enzyme in this set of molecules catalyzes the attachment of a particular amino acid to its corresponding tRNA molecule. A tRNA attached to its amino acid is called an aminoacylated tRNA or a charged tRNA
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Translation : initiation, elongation, and termination factors
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polypeptide synthesis can be divided into three stages. Initiation, elongation, and termination. Each stage requires specialized molecules.
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aminoacylated tRNA
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charged tRNA; a tRNA covalentily attached to its amino acid
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initiation (protein synthesis)
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the process by which mRNA binds with ribosomes and other factors and protein synthesis begins
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start codon
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an mRNA codon, usually AUG, at which polypeptide synthesis begins
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E (exit site)
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the tRNA-binding site on the ribosome that binds each uncharged tRNA just prior to its release
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elognation phases
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1. Bringing each new aminoacylated tRNA into line
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2. Forming the new peptide bond to elongate the polypeptide
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3. Moving the ribosome to the next codon along th mRNA
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release phase
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when a stop codon is encountered, the tRNA holding the polypeptide remains in the p site, and a release factor (RF) binds with the ribosome. GTP hydrolysis provides the energy to cleave the polypeptide from the tRNA to wich it is attached, as well as to eject the release factor and dissociate the 80S ribosome from the mRNA
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chaperones
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proteins that aid in the proper folding of polypeptides
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polycistronic mRNA
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An mRNA molecule from which two or more polypeptides are translated; found primarily in prokaryotes
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ribosome-binding site
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the base sequence in a prokaryotic mRNA molecule to which a ribosome can bind to initiate protein synthesis; also called Shine-Dalgarno sequence
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genetic code
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the set of 64 triplets of bases (codons) that correspond to the 20 amino acids in proteins and the signals for the initiation and terminiation of polypeptide synthesis
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reading frame
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the phase in which successive triplets of nucleotides in mRNA form codons; depending on the reading frame, a particular nucleotide in an mRNA could be in the first, second, or third position of a codon. The reading frame actually used is defined by the AUG codon that is selected for chain initiation
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frameshift mutations
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a mutational event caused by the insertion or deletion of one or more nucleotide pairs in a gene, resulting ina shift in the reading frame of all codons following the mutational site
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redundancy
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the feature of the genetic code in which an amino acid corresponds to more than one codon; also called degeneracy
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wobble
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the acceptable pairing of several possible bases ina an anticodon with the base present in the third position of a codon
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polysome
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a complex of two or more ribosomes associated with an mRNA molecule and actively engaged in polypeptide synthesis; a polyribosome.
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Gene regulation
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processes by which gene expression is controlled in response to external or internal signals
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coordinate regulation
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control of synthesis of several proteins by a single regulatory element; in prokaryotes, the proteins are usually translated from a single mRNA molecule
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negative regulation
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regulation of gene expression in which mRNA is not synthesized until a repressor is removed from the DNA of the gene
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repressor
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a protein that binds specifically to a regulatory sequence adjacent to a gene and blocks transciption of the gene
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inducible transcription
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transcription of a gene or a group of genes, only in the presence of an inducer molecule
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inducer
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a small molecule that inactivates a repressor, usually by binding to it and thereby altering the ability of the repressor to bind to an operator.
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repressible transcription
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a regulatory process in which a gene is temporarily rendered unable to be transcribed
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aporepressor
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a protein converted into a repressor by binding with a particular molecule
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co-repressor
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a small molecule that binds with an aporepressor to create a functional repressor molecule
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Beta galactosidase
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an enzyme that cleave lactose into its glucose and galactose constituents; produced by a gene in the lac operon
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lactose premease
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an enzyme responsible for transport of lactose from the environment into bacteria
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constitutive mutant
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a mutant in which synthesis of a particular mRNA molecule and the protein it encodes, takes place at a constant rate independent of the presence or absence of any inducer or repressor molecule
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cis-dominant
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pertaining ot a mutation that affects the expression of only those genes on the same DNA molecule
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operator
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a regulatory region in DNA that intereacts with a specific repressor protein in controlling the transcription of adjacent structural genes
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promoter
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a dna sequence at which rna polymerase binds and initiate transcription
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lactose operon model
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6 steps
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operon
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a collection of adjacent structural genes regulated by an operator and a repressor
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cAMP-CRP
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a regulatory complex consisting of cyclic AMP (cAMP) and the CAP protein; the complex is needed for transcription of certain operons
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attenuation
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transcriptional regulatation that is exerted based on the concentration of charged tryptophan tRNA
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attenuator
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a regulatory base sequence near the beginning of an mRNA molecule at which transcription can be terminated; when an attenuator is present, it precedes the coding sequences
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leader polypeptide
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as short polypeptide encoded in the leader sequence of some operons coding for enzymes in amino acid biosynthesis; translation of the leader polypeptide participates in regulation of the operon through attenuation.
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riboswitch
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a 5' RNA leader sequence that, according to whether it is bound with a small molecule, can adopt either of two configurations, one of which permits transcription and the other of which terminates transcription
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housekeeping genes
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a gene that is experessed at the same level in virtually all cells and whose product participates in basic metabolic processes
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enhancers
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a base sequence in eukaryotes and eukaryotic viruses that increases the rate of transcription of nearby genes; the defining characteristics are that it need not be adjacent to the trancribed gene and that the enhancing activity is independent of orientation with respect to the gene
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silencers
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a nucleotide sequence that binds with certain proteins whose presence prevents gene expression
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transcription complex
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an aggregate of RNA polymerase (consisting of its own subunits) along with other polypeptide subunits that makes transcription possible
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DNA looping
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a mechanism by which enhancers that are distant ifrom the immediate proximity of a promoter can still regulate transcription; the enhancer and promoter, both bound with suitable protein factors, come into indirect physical contact by menas of the looping out of the DNA between them. The physical interactiion simulates transcription
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basal transcription factors
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transcription factors that are associated with transcription of awide variety of genes
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general transcription factors
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a protein molecule needed to bind with a promoter before transcription can proceed; transcription factors are necessary, but not sufficient, for transcription, and they ar e shared among many different promoters
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TATA-box-binding protein (TBP)
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a protein that binds to the TATA motif in the promoter region fo a gene
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TBP-associated factors (TAFs)
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any protein found in close association with TATA binding protein
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Pol II holoenzyme
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a large protein complex containing th etype of RNA polymerase used in transcribing most protein encoding genes
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chromatin-remodeling complexes (CRCs)
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any of a number of complex protein aggregates that reorganizes the nucleosomes of chromatin in prepration for transcription
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epigenetic
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heritable changes in gene expression due to something "in addition to" the DNA sequence, usually either chemical modification of the bases or protein factors bound with the DNA
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DNA methylase
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man enzyme that adds methyl groups to certain bases particularly cytosine
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genomic imprinting
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a process of DNA modifiaction in gametogenesis that affects gene expression in a zygote; one probable mechanism is the methylation of certain bases in the DNA
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RNA interference (RNAi)
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the ability of small fragments of double-stranded RNA to silence gen3es whose transcripts contain homologous sequences
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antisense RNA
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an RNA molecule complementary in nucleotide sequence to all or part of a messenger RNA
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variable antibody regions
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the portion of an immunoglobulin molecule that varies greatly in amino acid sequence among antibodies in the same subclass
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constant antibody regions
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the part of the heavy and light chains of an antibody molecule that has the same amino acid sequence among all antibodies derived from the same heavychain and ligh-chain genes
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variable antibody regions
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the portion of an immunoglobulin molecule that varies greatly in amino acid sequence among antibodies in the same subclass
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joining antibody regions
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any of multiple dna sequences that code for alternative amino acid sequences of an antibody molecule; the J regions of heavy and light chains are different
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v-j joining
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DNA splicing that unites on of the V regions of an antibody light-chain gene with one of the J (joining) regions of the same gene to create a unique antibody sequence
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|
|
constant (C) antibody region
|
the part of the heavy and light chains of an antibody molecule that has the same amino acid sequence among all antibodyies derived from the same heavy chain and light-chain genes.
|
|
|
mating-type interconversion
|
phenomenon in homothallic yeast in which cells switch mating type as a result of the transposition of genetic information from an unexpressed cassette into the active mating-type locus
|
|
|
homothallism
|
the capacity of cells in certain fungi to undergo a conversino in mating type to make possible mating between cells produced by the same parental organism
|
|
|
Positive regulation
|
Mechanism of gene regulation in which an element must be bound to DNA in an active form to allow transcription; contrasts with negative regulation, in which a regulatory element must be removed from DNA
|
|
|
Transcriptional activator protein
|
positive control element that stimulates transcription by binding with particular sites in DNA
|
|
|
Autoregulation
|
Regulation of gene expression by the product of the gene itself
|
|
|
Prader-Willi Syndrome
|
A rare spontaneous deletion inluding chromosme region 15q11 that takes place in the father
|
|
|
Gene regulation
|
processes by which gene expression is controlled in response to external or internal signals
|
|
|
coordinate regulation
|
control of synthesis of several proteins by a single regulatory element; in prokaryotes, the proteins are usually translated from a single mRNA molecule
|
|
|
negative regulation
|
regulation of gene expression in which mRNA is not synthesized until a repressor is removed from the DNA of the gene
|
|
|
repressor
|
a protein that binds specifically to a regulatory sequence adjacent to a gene and blocks transciption of the gene
|
|
|
inducible transcription
|
transcription of a gene or a group of genes, only in the presence of an inducer molecule
|
|
|
inducer
|
a small molecule that inactivates a repressor, usually by binding to it and thereby altering the ability of the repressor to bind to an operator.
|
|
|
repressible transcription
|
a regulatory process in which a gene is temporarily rendered unable to be transcribed
|
|
|
aporepressor
|
a protein converted into a repressor by binding with a particular molecule
|
|
|
co-repressor
|
a small molecule that binds with an aporepressor to create a functional repressor molecule
|
|
|
Beta galactosidase
|
an enzyme that cleave lactose into its glucose and galactose constituents; produced by a gene in the lac operon
|
|
|
lactose premease
|
an enzyme responsible for transport of lactose from the environment into bacteria
|
|
|
constitutive mutant
|
a mutant in which synthesis of a particular mRNA molecule and the protein it encodes, takes place at a constant rate independent of the presence or absence of any inducer or repressor molecule
|
|
|
cis-dominant
|
pertaining ot a mutation that affects the expression of only those genes on the same DNA molecule
|
|
|
operator
|
a regulatory region in DNA that intereacts with a specific repressor protein in controlling the transcription of adjacent structural genes
|
|
|
promoter
|
a dna sequence at which rna polymerase binds and initiate transcription
|
|
|
lactose operon model
|
6 steps
|
|
|
operon
|
a collection of adjacent structural genes regulated by an operator and a repressor
|
|
|
cAMP-CRP
|
a regulatory complex consisting of cyclic AMP (cAMP) and the CAP protein; the complex is needed for transcription of certain operons
|
|
|
attenuation
|
transcriptional regulatation that is exerted based on the concentration of charged tryptophan tRNA
|
|
|
attenuator
|
a regulatory base sequence near the beginning of an mRNA molecule at which transcription can be terminated; when an attenuator is present, it precedes the coding sequences
|
|
|
leader polypeptide
|
as short polypeptide encoded in the leader sequence of some operons coding for enzymes in amino acid biosynthesis; translation of the leader polypeptide participates in regulation of the operon through attenuation.
|
|
|
riboswitch
|
a 5' RNA leader sequence that, according to whether it is bound with a small molecule, can adopt either of two configurations, one of which permits transcription and the other of which terminates transcription
|
|
|
housekeeping genes
|
a gene that is experessed at the same level in virtually all cells and whose product participates in basic metabolic processes
|
|
|
enhancers
|
a base sequence in eukaryotes and eukaryotic viruses that increases the rate of transcription of nearby genes; the defining characteristics are that it need not be adjacent to the trancribed gene and that the enhancing activity is independent of orientation with respect to the gene
|
|
|
silencers
|
a nucleotide sequence that binds with certain proteins whose presence prevents gene expression
|
|
|
transcription complex
|
an aggregate of RNA polymerase (consisting of its own subunits) along with other polypeptide subunits that makes transcription possible
|
|
|
DNA looping
|
a mechanism by which enhancers that are distant ifrom the immediate proximity of a promoter can still regulate transcription; the enhancer and promoter, both bound with suitable protein factors, come into indirect physical contact by menas of the looping out of the DNA between them. The physical interactiion simulates transcription
|
|
|
basal transcription factors
|
transcription factors that are associated with transcription of awide variety of genes
|
|
|
general transcription factors
|
a protein molecule needed to bind with a promoter before transcription can proceed; transcription factors are necessary, but not sufficient, for transcription, and they ar e shared among many different promoters
|
|
|
TATA-box-binding protein (TBP)
|
a protein that binds to the TATA motif in the promoter region fo a gene
|
|
|
TBP-associated factors (TAFs)
|
any protein found in close association with TATA binding protein
|
|
|
Pol II holoenzyme
|
a large protein complex containing th etype of RNA polymerase used in transcribing most protein encoding genes
|
|
|
chromatin-remodeling complexes (CRCs)
|
any of a number of complex protein aggregates that reorganizes the nucleosomes of chromatin in prepration for transcription
|
|
|
epigenetic
|
heritable changes in gene expression due to something "in addition to" the DNA sequence, usually either chemical modification of the bases or protein factors bound with the DNA
|
|
|
DNA methylase
|
man enzyme that adds methyl groups to certain bases particularly cytosine
|
|
|
genomic imprinting
|
a process of DNA modifiaction in gametogenesis that affects gene expression in a zygote; one probable mechanism is the methylation of certain bases in the DNA
|
|
|
RNA interference (RNAi)
|
the ability of small fragments of double-stranded RNA to silence gen3es whose transcripts contain homologous sequences
|
|
|
antisense RNA
|
an RNA molecule complementary in nucleotide sequence to all or part of a messenger RNA
|
|
|
variable antibody regions
|
the portion of an immunoglobulin molecule that varies greatly in amino acid sequence among antibodies in the same subclass
|
|
|
constant antibody regions
|
the part of the heavy and light chains of an antibody molecule that has the same amino acid sequence among all antibodies derived from the same heavychain and ligh-chain genes
|
|
|
variable antibody regions
|
the portion of an immunoglobulin molecule that varies greatly in amino acid sequence among antibodies in the same subclass
|
|
|
joining antibody regions
|
any of multiple dna sequences that code for alternative amino acid sequences of an antibody molecule; the J regions of heavy and light chains are different
|
|
|
v-j joining
|
DNA splicing that unites on of the V regions of an antibody light-chain gene with one of the J (joining) regions of the same gene to create a unique antibody sequence
|
|
|
constant (C) antibody region
|
the part of the heavy and light chains of an antibody molecule that has the same amino acid sequence among all antibodyies derived from the same heavy chain and light-chain genes.
|
|
|
mating-type interconversion
|
phenomenon in homothallic yeast in which cells switch mating type as a result of the transposition of genetic information from an unexpressed cassette into the active mating-type locus
|
|
|
homothallism
|
the capacity of cells in certain fungi to undergo a conversino in mating type to make possible mating between cells produced by the same parental organism
|
|
|
Positive regulation
|
Mechanism of gene regulation in which an element must be bound to DNA in an active form to allow transcription; contrasts with negative regulation, in which a regulatory element must be removed from DNA
|
|
|
Transcriptional activator protein
|
positive control element that stimulates transcription by binding with particular sites in DNA
|
|
|
Autoregulation
|
Regulation of gene expression by the product of the gene itself
|
|
|
Prader-Willi Syndrome
|
A rare spontaneous deletion inluding chromosme region 15q11 that takes place in the father
|
|
|
C-value paradox
|
among eukaryotes, there is no consistent relationship between the dna content of the haploid genome and the metabolic developmental, or behavioral complexity of the organism
|
|
|
purines
|
double ring structured bases (Adenine and Guanine)
|
|
|
pyrimidines
|
single ring-ring structures bases (Thymine and Cytosine)
|
|
|
nucleoside
|
a base chemically linked to one molecule of sugar deoxydribose
|
|
|
nucleotide
|
phosphate group attached to a sugar molecule attached to the base
|
|
|
polynucleotide chain
|
phosphate attached to the 5' carbon of one sugar linked to the hydroxyl group attached to the 3' carbon of the next sugar in line (ncleotides joined together)
|
|
|
phosphodiester bonds
|
chemical bonds that bond the sugar components of the adjacent nucleotides that are linked through the phosphate groups
|
|
|
5' end
|
the end that terminates in a phosphate
|
|
|
3' end
|
the end that terminates in a hydroxyl
|
|
|
hydrogen bond
|
a weak bond in which two negatively charged atoms share a hydrogen atom
|
|
|
antiparallel
|
the orientation of the two strands of double stranded nucleic acid molecules;; (the 5' to 3' orientation)
|
|
|
daughter strand
|
the newly replicated complimentrary strand
|
|
|
parental strand
|
the strand being replicated
|
|
|
template
|
a strand of nucleic acid whose base sequence is copied in a polymerization reaction to produce either a complementrary DNA or an RNA strand
|
|
|
semiconservative replication
|
the usual form of replication in which one strand of dna serves as a template for another
|
|
|
Mathew Meselson and Franklin Stahl in 1958
|
the expiriment that showed DNA replication was semiconservative by using bacteria in a heavy N-containing medium and replicating their DNA several generations.
|
|
|
theta replication
|
bidirectional replicaion of a circular dna molecule, starting from a single origin of replication
|
|
|
replication origin
|
the position long a molecule at which DNA replication begins
|
|
|
replication fork
|
the region on dna molecule where the parental strands are separating and new strands are being sythesized
|
|
|
initiation
|
the process of generaing a new replication fork
|
|
|
rolling-circle replication
|
a mode of replication in which a circular parent molecule produces a linear branch of newly formed dna
|
|
|
helicase
|
protein that hydrolyzes ATP to drive the unwinding reaction
|
|
|
single stranded DNA binding protein (SSB)
|
binds single-stranded DNA tightly and cooperatively and it has an affinity for single stranded DNA at least 1000-fold greater than that for double stranded DNA
|
|
|
gyrase
|
a type of topoisomerase II that cleaves and rejoins both strands of a DNA duplex to relieve torsional stress
|
|
|
ribose
|
identical to deoxyribose of DNA except for the presence of an -OH group on the 2' carbon atom
|
|
|
RNA polymerase
|
An enzyme that makes RNA by copying the base sequence of a DNA strand
|
|
|
primer
|
in nucleic acids, a short RNA or single-stranded DNA segment that functions as a growing point in polymerization
|
|
|
primosome
|
the enzyme complex that forms the RNA primer for DNA replication. Multienzyme complex composed of 15 to 20 polypeptide chains
|
|
|
DNA polymerase
|
the enzyme that forms the sugar-phosphate bond between adjacent nucleotides in a new DNA acid chain.
|
|
|
editing function or proofreading function
|
The activity of DNA polymerases that removes incorrectly incorporated nucleotides
|
|
|
precursor fragments (okazaki fragment)
|
any of the short strands of DNA produced during discontinuous replication of the lagging strand
|
|
|
leading strand
|
DNA strand whose complement is synthesized as a continuous unit
|
|
|
lagging strand
|
the DNA strand whose complement is synthesized in short fragments that are ultimately joined together
|
|
|
DNA ligase
|
an enzyme that catalyzes formation of a covalent bond between adjacent 5' P and 3' OH termini in broken polynucleotide strand of double-stranded DNA
|
|
|
Denaturation
|
Separation of DNA strands (i.e. heating them up)
|
|
|
Renaturation
|
DNA strands coming together (i.e. when the heat is lowered in a solution)
|
|
|
3 uses and methods of Denaturation and renaturation
|
1. Small DNA fragment mixed with larger DNA fragments, which can help identify specific DNA fragments in a complex mixture.
|
|
|
|
2. DNA fragment of one gene can be renatured with other genes of the same genome; is used to identify genes that are smaller, but not identical in sequence and have related functions.
|
|
|
|
3. DNA fragment from one species can be renatured with sequences of other species. This allows the isolation of genes that have the same or related functions in multiple species and can be used to study molecular evolution.
|
|
|
Nucleic acid hybridization
|
The process of renaturing DNA strands from two different sources
|
|
|
probe
|
a radioactive DNA and RNA molecule used in DNA-RNA and DNA-DNA hybridization assays
|
|
|
restriction enzymes
|
Also called restriction endonucleases, are able to cleave DNA molecules at the poistions at which particular, short sequences of bases are present.
|
|
|
restriction site
|
the sequence recognized for cleavage by a restriction enzyme
|
|
|
restriction fragment
|
The fragments formed when a large DNA molecule is cut into many restriction fragments of different sizes.
|
|
|
restriction map
|
A diagram of a DNA molecule showing the positions of cleavage by one or more restriction endonucleases
|
|
|
Southern Blot
|
a nucleic acid hybridization method in which, from a gel to a membrane filter and then exposed to radioctive regions locate the homologous DNA fragments on the filter.
|
|
|
Polymerase chain reaction (PCR)
|
repeaated cycles of DNA denaturation, renaturation with primer oligonucleotide sequences, and replication, resulting in exponential growth in the number of copies of the DNA sequence located between the primers.
|
|
|
dideoxy sequencing method
|
procedure for DNA sequencing in which a template strand is replicated from a particular primer sequence and terminated by the incorporation of a nucleotide that contains dideoxyribose instead of deoxyribose; the resulting fragments are separated by size via eletrophoresis.
|
|
|
dideoxyribose
|
a deoxyribose sugar that lacks the 3' hydroxyl group; when incorporated into a polynucleotide chain, it blocks further chain elongation.
|
|
|
Exonuclease activity
|
The ability to break phosphodiester bonds in the sugar-phophate backbones of nucleic acid chains
|
|
|
cohesive ends
|
single-stranded regions at the ends of otherwise double-stranded DNA molecules that are complementary in base sequence
|
|
|
blunt ends
|
ends of a DNA molecule in which all terminal bases are paired; the term usually referes to termini formed by a restriction enzyme that does not produce single-stranded ends.
|
|
|
mobile DNA
|
alternative term for transposable elements
|
|
|
plasmids
|
nonessential DNA molecules that exist inside baterial cells
|
|
|
conjugation
|
a process of DNA transfer in sexual reproduction in certain bateria; in e. coli, the transfer is unidirectional, from donor cell lto recipient cell. Also, a mating between cells of Paramecium
|
|
|
conjugative plasmids
|
a plasmid encoding proteins and other factors that make possible its transmission between cells
|
|
|
F factor
|
a baterial plasmid-often called the fertility factor or sex plasmid-that is capable of transferring itself from a host (f+) cell to a cell not carrying an F factor (F- cell); when an F factor is integrated into the baterial chromosome (in an Hfr cell), the chromosome becomes transferrable to an F- cell during conjugation
|
|
|
transposon
|
a transposable element that contains bacterial genes-i.e. for antibiotic resistance; also used loosely as a synonym for transposable element
|
|
|
cointegrate
|
a DNA molecule, usually circular and formed by recombination, that joins two replicons
|
|
|
site-specific recombinase
|
an enzyme that catalyzes intermolecule cecombination between two duplex DNA molecules at the site of a target sequence that they have in common
|
|
|
integron
|
a DNA element that encodes a site-specific recombinase as well as recognition region that allows other sequences with similar recognitionregions to be incorporated into the integron by recombination
|
|
|
cassette
|
a circular antibiotic-resistance-coding region flanked by a recognition region for an integron
|
|
|
integrase
|
an enzyme that catalyzes a site specific exchange between two DNA sequences
|
|
|
R Plasmid
|
A bacterial plasmid that carries drug resistance genes; commonly used in genetic engineering
|
|
|
Antibiotic-resistant mutants
|
mutants that are able to grow in presence of an antibiotic
|
|
|
nutritional mutants
|
A mutation in a metabolic pathway that creates a need for a substance to be present in the growth medium or that eliminates the ability to utilize a substance present in the growth medium
|
|
|
prototroph
|
microbial strain capable of growth in a defined minimal medium that ideally contains only a carbon source and inorganic compounds. The wildtype genotype is usually regarded as a prototroph
|
|
|
Auxotroph
|
a mutant microorganism that is unable to synthesize a compound required for its growth but is able to grow if the compound is provided
|
|
|
Carbon-source mutants
|
mutants that cannot utilize particular substances as sources of energy or carbon atoms
|
|
|
nonselective medium
|
a medium which all wildtype cells form colonies
|
|
|
selective medium
|
a medium that only allows growth of one type of cell (either wildtype or mutant)
|
|
|
transformation
|
the process of genetic alteration by pure DNA
|
|
|
cotransformation
|
simultaneous transformation of two genetic markers carried on a single DNA fragment in bacteria
|
|
|
Hfr Cell
|
an e coli cell in which an f plasmid is integrated into the chromosome, making possible the transfer of part or all of the chromosome to an F- cell.
|
|
|
episome
|
a genetic element that can exist free in the cell or as a segment of DNA integrated into the chromosome
|
|
|
selected marker
|
a genetic mutation that allows growth in selective medium
|
|
|
counterselected marker
|
a mutation used to prevent growth of a donor cell in an Hfr x F- bacterial mating
|
|
|
interrupted-mating technique
|
in an Hfr x F- cross, a technique by which donor and recipient cells are broken apart at specific times, allowing only a particular length of DNA to be transferred
|
|
|
time of entry
|
in an Hfr x F- bacterial mating, the earliest time that a particular gene in the Hfr parent is transferred to the F- recipient
|
|
|
F' plasmid
|
An F plasmid that contains genes obtained from the bacterial chromosome in a addition to plasmid genes; formed by aberrant excision of an integrated F factor, taking along adjacent bacterial DNA
|
|
|
partial diploid
|
a cell in which a segment of the genome is duplicated, usually in a plasmid
|
|
|
transduction
|
the carrying of genetic information from one bacterium to another by a phage
|
|
|
transducting phage
|
a phage type capable of prducing prticles that contain bacterial DNA (transducing particles)
|
|
|
generalized transducting phage
|
produces particles that may carry any region of the genome
|
|
|
specialized transducing phage
|
produces particles that carry only specific regions of chromosomal DNA;
|
|
|
cotransduction
|
transduction of two or more linked genetic markers by one transducing particle
|
|
|
frequency of cotransduction
|
the proportion of transductants carrying a selected genetic marker that also carry a nonselected genetic marker
|
|
|
lytic cycle
|
the life cycle of a phage, in which progeny phage are produced and the host bacterial cell is lysed.
|
|
|
plaque
|
a clear area in an otherwise turbid layer of bacteria growing on a solid medium, caused by the infectino and killing of the cells by a phage; because each plaque results from the growth of one phage, plaque counting is a way of counting viable phage particles. The term is also used for animal viruses that cause clear areas in layers of animal cells grown in culture
|
|
|
hotspot
|
a site on a DNA molecule for which the rate of mutation is much higher than the rate of mutation on the rest of the molecule.
|
|
|
lysogenic cycle
|
In temperate bacteriophage, the phenomenon in which the DNA of an infecting phage becomes part of the genetic material of the cell
|
|
|
prophage induction
|
activation of a prophage to undergo the lytic cycle
|
|
|
excisionase
|
an enzyme that is needed for prophage excision; works together with an integrase
|
|
|
phage repressor
|
regulatory protein that prevent stranscription of genes in a prophage
|
|
|
Insertion sequence
|
DNA sequence capable of transposition in a prokaryotic genome; such aequences usually code for their own transposase
|
|
|
Cistron
|
DNA sequence specifying a single genetic function as defined by a complementation test; nucleotide sequence coding for a single polypeptide.
|
|
|
Lysogen
|
Clone of bacterial cells that have acquired a prophage
|
|
|
polypeptide chains
|
a polymer of amino acids linmked together by pepptide bonds
|
|
|
R-group
|
refers to the side chain connected to the alpha carbon that differs for each amino acid
|
|
|
peptide bond
|
a polymer of amino acids linked together by peptide bonds
|
|
|
amino terminus
|
the end of a polypetide chain at which the amino acid bears a free amino group
|
|
|
carboxyl terminus
|
the end of a polypeptide chain at which the amino acid has a free carboxyl group
|
|
|
RNA polymerase holoenzyme
|
any of several large protein complexes that inlcudes RNA polymerase aming its constituents
|
|
|
RNA polymerase I
|
used exclusively in producing the transcript that becomes prcessed into ribosomal RNA
|
|
|
RNA polymerase II
|
the workhorse eukaryotic polymerase responsible for transcribing all protein-coding genes as well as the genes for a number of small nuclear RNA's (U1, U2, U3, and so forth) used in RNA processing
|
|
|
RNA polymerase III
|
used in transcribing all transfer RNA genes as well as the 5S component of ribosomal RNA
|
|
|
Promoter recognition
|
The first process of of RNA recognizing which strand of DNA should be transcribed in which the RNA polymerase binds to the promoter
|
|
|
promoter
|
A dna sequence at which RNA polymerase binds and initiates transcription
|
|
|
consensus sequence
|
a generalized base sequence derived from closely related sequences found in many locations in a genome or in many organisms; each position in the sequence consists of the base found in the majority of sequences in that position
|
|
|
TATA box
|
the base sequence 5 prime TAT 3 prime in the DNA of a promoter
|
|
|
Chain initiation
|
The second stage of RNA transcription in which after the initial binding step, the RNA polymerase initiates RNA synthesis at a nearby transcription start site
|
|
|
Chain Elongation
|
the second stage of RNA transcription in which RNA polymerase moves along the DNA template strand, adding nucleotides to the growing RNA chain.
|
|
|
Chain terminiation
|
the forth and final step of RNA transcription in which the RNA polymerase reaches a transcription termination sequence in the DNA and the polymerase enzyme disassociates from the DNA, and the newly synthesized RNA molycule is released.
|
|
|
primary transcript
|
the RNA molecule produced from a DNA template
|
|
|
messenger RNA
|
An RNA molecule transcribed from a DNA sequence and translated into the amino acid sequence of a polypeptide. In eukaryotes, the primary transcript undergoes elaborate processing to become the mRNA
|
|
|
5' untranslated region
|
the initial part of a mRNA which does not code for protein
|
|
|
open reading frame (ORF)
|
in the coding strand of DNA or in mRNA, a region containing a series of codonss uninterrupted by stop codons and therefore capable of coding for a polypeptide chain
|
|
|
3' untranslated region
|
the terminal portion of a messenger RNA, following the stop codon, which does not code for protein
|
|
|
cap
|
a ccomplex structure at the 5' termini of most eukaryotic mRNA molecules, having a 5'-5' linkage instead of the usual 3'-5' linkage
|
|
|
poly-A tail
|
the sequence of adeninees added to the 3' end of many eukaryotic mRNA molecules in processing
|
|
|
introns
|
a noncoding DNA sequence in a gene that is transcribed but is then excised from the primary transcript in froming a mature mRNA molecule; found primarily in eukaryotic cells
|
|
|
exons
|
the sequences in a gene that are retained in the messenger RNA after the introns are removed from the primary transcript.
|
|
|
RNA splicing
|
excision of introns and joining of exons.
|
|
|
RNA splicing
|
excision of introns and joining of exons
|
|
|
spliceosomes
|
an rna protein particle in the nucleus in which hintrons are removed from RNA transcripts
|
|
|
snRNPs
|
any of several classes of small ribonucleoprotein particles involved in RNA splicing
|
|
|
ribozymes
|
an RNA molecule able to catalyze one or more biochemical reactions
|
|
|
Translation : Messenger rNA
|
component of translation - needed to bring the ribosomal subunits together and to provide the coding sequence of bases that determines the amino acid sequence in the resulting polypeptide chain
|
|
|
Translation : Ribosomes
|
component of translation - particles on which protein synthesis takes place. They move along an mRNA molecule and align successive transfer RNA molecules; the amino acids are attached one by one to the growing polypeptide chain by means of peptide bonds. Ribosomes consist of two separate RNA-protein partics, which come together in polypeptide synthesis to form a mature ribosome.
|
|
|
Translation : transfer RNA
|
component of translation - the sequence of amino acids in a polypeptide is determined by the base sequence in the mRNA by means of a set of adapator molecules, the tRNA molecules each which is attached to a particular amino acid. Each set of the mRNA form a codon that binds to a group of 3 adjacent bases in the tRNA, the anticodon, bringing the attached amino acid into line for elngation of the growing polypeptide chain
|
|
|
Translation : Aminoacyl-tRNA synthetases
|
component of translation - Each enzyme in this set of molecules catalyzes the attachment of a particular amino acid to its corresponding tRNA molecule. A tRNA attached to its amino acid is called an aminoacylated tRNA or a charged tRNA
|
|
|
Translation : initiation, elongation, and termination factors
|
polypeptide synthesis can be divided into three stages. Initiation, elongation, and termination. Each stage requires specialized molecules.
|
|
|
aminoacylated tRNA
|
charged tRNA; a tRNA covalentily attached to its amino acid
|
|
|
initiation (protein synthesis)
|
the process by which mRNA binds with ribosomes and other factors and protein synthesis begins
|
|
|
start codon
|
an mRNA codon, usually AUG, at which polypeptide synthesis begins
|
|
|
E (exit site)
|
the tRNA-binding site on the ribosome that binds each uncharged tRNA just prior to its release
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elognation phases
|
1. Bringing each new aminoacylated tRNA into line
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2. Forming the new peptide bond to elongate the polypeptide
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3. Moving the ribosome to the next codon along th mRNA
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release phase
|
when a stop codon is encountered, the tRNA holding the polypeptide remains in the p site, and a release factor (RF) binds with the ribosome. GTP hydrolysis provides the energy to cleave the polypeptide from the tRNA to wich it is attached, as well as to eject the release factor and dissociate the 80S ribosome from the mRNA
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chaperones
|
proteins that aid in the proper folding of polypeptides
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polycistronic mRNA
|
An mRNA molecule from which two or more polypeptides are translated; found primarily in prokaryotes
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ribosome-binding site
|
the base sequence in a prokaryotic mRNA molecule to which a ribosome can bind to initiate protein synthesis; also called Shine-Dalgarno sequence
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genetic code
|
the set of 64 triplets of bases (codons) that correspond to the 20 amino acids in proteins and the signals for the initiation and terminiation of polypeptide synthesis
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reading frame
|
the phase in which successive triplets of nucleotides in mRNA form codons; depending on the reading frame, a particular nucleotide in an mRNA could be in the first, second, or third position of a codon. The reading frame actually used is defined by the AUG codon that is selected for chain initiation
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frameshift mutations
|
a mutational event caused by the insertion or deletion of one or more nucleotide pairs in a gene, resulting ina shift in the reading frame of all codons following the mutational site
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redundancy
|
the feature of the genetic code in which an amino acid corresponds to more than one codon; also called degeneracy
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wobble
|
the acceptable pairing of several possible bases ina an anticodon with the base present in the third position of a codon
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polysome
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a complex of two or more ribosomes associated with an mRNA molecule and actively engaged in polypeptide synthesis; a polyribosome.
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Gene regulation
|
processes by which gene expression is controlled in response to external or internal signals
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coordinate regulation
|
control of synthesis of several proteins by a single regulatory element; in prokaryotes, the proteins are usually translated from a single mRNA molecule
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negative regulation
|
regulation of gene expression in which mRNA is not synthesized until a repressor is removed from the DNA of the gene
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repressor
|
a protein that binds specifically to a regulatory sequence adjacent to a gene and blocks transciption of the gene
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|
inducible transcription
|
transcription of a gene or a group of genes, only in the presence of an inducer molecule
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|
inducer
|
a small molecule that inactivates a repressor, usually by binding to it and thereby altering the ability of the repressor to bind to an operator.
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repressible transcription
|
a regulatory process in which a gene is temporarily rendered unable to be transcribed
|
|
|
aporepressor
|
a protein converted into a repressor by binding with a particular molecule
|
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co-repressor
|
a small molecule that binds with an aporepressor to create a functional repressor molecule
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|
Beta galactosidase
|
an enzyme that cleave lactose into its glucose and galactose constituents; produced by a gene in the lac operon
|
|
|
lactose premease
|
an enzyme responsible for transport of lactose from the environment into bacteria
|
|
|
constitutive mutant
|
a mutant in which synthesis of a particular mRNA molecule and the protein it encodes, takes place at a constant rate independent of the presence or absence of any inducer or repressor molecule
|
|
|
cis-dominant
|
pertaining ot a mutation that affects the expression of only those genes on the same DNA molecule
|
|
|
operator
|
a regulatory region in DNA that intereacts with a specific repressor protein in controlling the transcription of adjacent structural genes
|
|
|
promoter
|
a dna sequence at which rna polymerase binds and initiate transcription
|
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|
lactose operon model
|
6 steps
|
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|
operon
|
a collection of adjacent structural genes regulated by an operator and a repressor
|
|
|
cAMP-CRP
|
a regulatory complex consisting of cyclic AMP (cAMP) and the CAP protein; the complex is needed for transcription of certain operons
|
|
|
attenuation
|
transcriptional regulatation that is exerted based on the concentration of charged tryptophan tRNA
|
|
|
attenuator
|
a regulatory base sequence near the beginning of an mRNA molecule at which transcription can be terminated; when an attenuator is present, it precedes the coding sequences
|
|
|
leader polypeptide
|
as short polypeptide encoded in the leader sequence of some operons coding for enzymes in amino acid biosynthesis; translation of the leader polypeptide participates in regulation of the operon through attenuation.
|
|
|
riboswitch
|
a 5' RNA leader sequence that, according to whether it is bound with a small molecule, can adopt either of two configurations, one of which permits transcription and the other of which terminates transcription
|
|
|
housekeeping genes
|
a gene that is experessed at the same level in virtually all cells and whose product participates in basic metabolic processes
|
|
|
enhancers
|
a base sequence in eukaryotes and eukaryotic viruses that increases the rate of transcription of nearby genes; the defining characteristics are that it need not be adjacent to the trancribed gene and that the enhancing activity is independent of orientation with respect to the gene
|
|
|
silencers
|
a nucleotide sequence that binds with certain proteins whose presence prevents gene expression
|
|
|
transcription complex
|
an aggregate of RNA polymerase (consisting of its own subunits) along with other polypeptide subunits that makes transcription possible
|
|
|
DNA looping
|
a mechanism by which enhancers that are distant ifrom the immediate proximity of a promoter can still regulate transcription; the enhancer and promoter, both bound with suitable protein factors, come into indirect physical contact by menas of the looping out of the DNA between them. The physical interactiion simulates transcription
|
|
|
basal transcription factors
|
transcription factors that are associated with transcription of awide variety of genes
|
|
|
general transcription factors
|
a protein molecule needed to bind with a promoter before transcription can proceed; transcription factors are necessary, but not sufficient, for transcription, and they ar e shared among many different promoters
|
|
|
TATA-box-binding protein (TBP)
|
a protein that binds to the TATA motif in the promoter region fo a gene
|
|
|
TBP-associated factors (TAFs)
|
any protein found in close association with TATA binding protein
|
|
|
Pol II holoenzyme
|
a large protein complex containing th etype of RNA polymerase used in transcribing most protein encoding genes
|
|
|
chromatin-remodeling complexes (CRCs)
|
any of a number of complex protein aggregates that reorganizes the nucleosomes of chromatin in prepration for transcription
|
|
|
epigenetic
|
heritable changes in gene expression due to something "in addition to" the DNA sequence, usually either chemical modification of the bases or protein factors bound with the DNA
|
|
|
DNA methylase
|
man enzyme that adds methyl groups to certain bases particularly cytosine
|
|
|
genomic imprinting
|
a process of DNA modifiaction in gametogenesis that affects gene expression in a zygote; one probable mechanism is the methylation of certain bases in the DNA
|
|
|
RNA interference (RNAi)
|
the ability of small fragments of double-stranded RNA to silence gen3es whose transcripts contain homologous sequences
|
|
|
antisense RNA
|
an RNA molecule complementary in nucleotide sequence to all or part of a messenger RNA
|
|
|
variable antibody regions
|
the portion of an immunoglobulin molecule that varies greatly in amino acid sequence among antibodies in the same subclass
|
|
|
constant antibody regions
|
the part of the heavy and light chains of an antibody molecule that has the same amino acid sequence among all antibodies derived from the same heavychain and ligh-chain genes
|
|
|
variable antibody regions
|
the portion of an immunoglobulin molecule that varies greatly in amino acid sequence among antibodies in the same subclass
|
|
|
joining antibody regions
|
any of multiple dna sequences that code for alternative amino acid sequences of an antibody molecule; the J regions of heavy and light chains are different
|
|
|
v-j joining
|
DNA splicing that unites on of the V regions of an antibody light-chain gene with one of the J (joining) regions of the same gene to create a unique antibody sequence
|
|
|
constant (C) antibody region
|
the part of the heavy and light chains of an antibody molecule that has the same amino acid sequence among all antibodyies derived from the same heavy chain and light-chain genes.
|
|
|
mating-type interconversion
|
phenomenon in homothallic yeast in which cells switch mating type as a result of the transposition of genetic information from an unexpressed cassette into the active mating-type locus
|
|
|
homothallism
|
the capacity of cells in certain fungi to undergo a conversino in mating type to make possible mating between cells produced by the same parental organism
|
|
|
Positive regulation
|
Mechanism of gene regulation in which an element must be bound to DNA in an active form to allow transcription; contrasts with negative regulation, in which a regulatory element must be removed from DNA
|
|
|
Transcriptional activator protein
|
positive control element that stimulates transcription by binding with particular sites in DNA
|
|
|
Autoregulation
|
Regulation of gene expression by the product of the gene itself
|
|
|
Prader-Willi Syndrome
|
A rare spontaneous deletion inluding chromosme region 15q11 that takes place in the father
|
|
|
Gene regulation
|
processes by which gene expression is controlled in response to external or internal signals
|
|
|
coordinate regulation
|
control of synthesis of several proteins by a single regulatory element; in prokaryotes, the proteins are usually translated from a single mRNA molecule
|
|
|
negative regulation
|
regulation of gene expression in which mRNA is not synthesized until a repressor is removed from the DNA of the gene
|
|
|
repressor
|
a protein that binds specifically to a regulatory sequence adjacent to a gene and blocks transciption of the gene
|
|
|
inducible transcription
|
transcription of a gene or a group of genes, only in the presence of an inducer molecule
|
|
|
inducer
|
a small molecule that inactivates a repressor, usually by binding to it and thereby altering the ability of the repressor to bind to an operator.
|
|
|
repressible transcription
|
a regulatory process in which a gene is temporarily rendered unable to be transcribed
|
|
|
aporepressor
|
a protein converted into a repressor by binding with a particular molecule
|
|
|
co-repressor
|
a small molecule that binds with an aporepressor to create a functional repressor molecule
|
|
|
Beta galactosidase
|
an enzyme that cleave lactose into its glucose and galactose constituents; produced by a gene in the lac operon
|
|
|
lactose premease
|
an enzyme responsible for transport of lactose from the environment into bacteria
|
|
|
constitutive mutant
|
a mutant in which synthesis of a particular mRNA molecule and the protein it encodes, takes place at a constant rate independent of the presence or absence of any inducer or repressor molecule
|
|
|
cis-dominant
|
pertaining ot a mutation that affects the expression of only those genes on the same DNA molecule
|
|
|
operator
|
a regulatory region in DNA that intereacts with a specific repressor protein in controlling the transcription of adjacent structural genes
|
|
|
promoter
|
a dna sequence at which rna polymerase binds and initiate transcription
|
|
|
lactose operon model
|
6 steps
|
|
|
operon
|
a collection of adjacent structural genes regulated by an operator and a repressor
|
|
|
cAMP-CRP
|
a regulatory complex consisting of cyclic AMP (cAMP) and the CAP protein; the complex is needed for transcription of certain operons
|
|
|
attenuation
|
transcriptional regulatation that is exerted based on the concentration of charged tryptophan tRNA
|
|
|
attenuator
|
a regulatory base sequence near the beginning of an mRNA molecule at which transcription can be terminated; when an attenuator is present, it precedes the coding sequences
|
|
|
leader polypeptide
|
as short polypeptide encoded in the leader sequence of some operons coding for enzymes in amino acid biosynthesis; translation of the leader polypeptide participates in regulation of the operon through attenuation.
|
|
|
riboswitch
|
a 5' RNA leader sequence that, according to whether it is bound with a small molecule, can adopt either of two configurations, one of which permits transcription and the other of which terminates transcription
|
|
|
housekeeping genes
|
a gene that is experessed at the same level in virtually all cells and whose product participates in basic metabolic processes
|
|
|
enhancers
|
a base sequence in eukaryotes and eukaryotic viruses that increases the rate of transcription of nearby genes; the defining characteristics are that it need not be adjacent to the trancribed gene and that the enhancing activity is independent of orientation with respect to the gene
|
|
|
silencers
|
a nucleotide sequence that binds with certain proteins whose presence prevents gene expression
|
|
|
transcription complex
|
an aggregate of RNA polymerase (consisting of its own subunits) along with other polypeptide subunits that makes transcription possible
|
|
|
DNA looping
|
a mechanism by which enhancers that are distant ifrom the immediate proximity of a promoter can still regulate transcription; the enhancer and promoter, both bound with suitable protein factors, come into indirect physical contact by menas of the looping out of the DNA between them. The physical interactiion simulates transcription
|
|
|
basal transcription factors
|
transcription factors that are associated with transcription of awide variety of genes
|
|
|
general transcription factors
|
a protein molecule needed to bind with a promoter before transcription can proceed; transcription factors are necessary, but not sufficient, for transcription, and they ar e shared among many different promoters
|
|
|
TATA-box-binding protein (TBP)
|
a protein that binds to the TATA motif in the promoter region fo a gene
|
|
|
TBP-associated factors (TAFs)
|
any protein found in close association with TATA binding protein
|
|
|
Pol II holoenzyme
|
a large protein complex containing th etype of RNA polymerase used in transcribing most protein encoding genes
|
|
|
chromatin-remodeling complexes (CRCs)
|
any of a number of complex protein aggregates that reorganizes the nucleosomes of chromatin in prepration for transcription
|
|
|
epigenetic
|
heritable changes in gene expression due to something "in addition to" the DNA sequence, usually either chemical modification of the bases or protein factors bound with the DNA
|
|
|
DNA methylase
|
man enzyme that adds methyl groups to certain bases particularly cytosine
|
|
|
genomic imprinting
|
a process of DNA modifiaction in gametogenesis that affects gene expression in a zygote; one probable mechanism is the methylation of certain bases in the DNA
|
|
|
RNA interference (RNAi)
|
the ability of small fragments of double-stranded RNA to silence gen3es whose transcripts contain homologous sequences
|
|
|
antisense RNA
|
an RNA molecule complementary in nucleotide sequence to all or part of a messenger RNA
|
|
|
variable antibody regions
|
the portion of an immunoglobulin molecule that varies greatly in amino acid sequence among antibodies in the same subclass
|
|
|
constant antibody regions
|
the part of the heavy and light chains of an antibody molecule that has the same amino acid sequence among all antibodies derived from the same heavychain and ligh-chain genes
|
|
|
variable antibody regions
|
the portion of an immunoglobulin molecule that varies greatly in amino acid sequence among antibodies in the same subclass
|
|
|
joining antibody regions
|
any of multiple dna sequences that code for alternative amino acid sequences of an antibody molecule; the J regions of heavy and light chains are different
|
|
|
v-j joining
|
DNA splicing that unites on of the V regions of an antibody light-chain gene with one of the J (joining) regions of the same gene to create a unique antibody sequence
|
|
|
constant (C) antibody region
|
the part of the heavy and light chains of an antibody molecule that has the same amino acid sequence among all antibodyies derived from the same heavy chain and light-chain genes.
|
|
|
mating-type interconversion
|
phenomenon in homothallic yeast in which cells switch mating type as a result of the transposition of genetic information from an unexpressed cassette into the active mating-type locus
|
|
|
homothallism
|
the capacity of cells in certain fungi to undergo a conversino in mating type to make possible mating between cells produced by the same parental organism
|
|
|
Positive regulation
|
Mechanism of gene regulation in which an element must be bound to DNA in an active form to allow transcription; contrasts with negative regulation, in which a regulatory element must be removed from DNA
|
|
|
Transcriptional activator protein
|
positive control element that stimulates transcription by binding with particular sites in DNA
|
|
|
Autoregulation
|
Regulation of gene expression by the product of the gene itself
|
|
|
Prader-Willi Syndrome
|
A rare spontaneous deletion inluding chromosme region 15q11 that takes place in the father
|
