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498 Cards in this Set

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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
elognation phases
1. Bringing each new aminoacylated tRNA into line
2. Forming the new peptide bond to elongate the polypeptide
3. Moving the ribosome to the next codon along th mRNA
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
chaperones
proteins that aid in the proper folding of polypeptides
polycistronic mRNA
An mRNA molecule from which two or more polypeptides are translated; found primarily in prokaryotes
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
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
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
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
redundancy
the feature of the genetic code in which an amino acid corresponds to more than one codon; also called degeneracy
wobble
the acceptable pairing of several possible bases ina an anticodon with the base present in the third position of a codon
polysome
a complex of two or more ribosomes associated with an mRNA molecule and actively engaged in polypeptide synthesis; a polyribosome.
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
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
elognation phases
1. Bringing each new aminoacylated tRNA into line
2. Forming the new peptide bond to elongate the polypeptide
3. Moving the ribosome to the next codon along th mRNA
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
chaperones
proteins that aid in the proper folding of polypeptides
polycistronic mRNA
An mRNA molecule from which two or more polypeptides are translated; found primarily in prokaryotes
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
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
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
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
redundancy
the feature of the genetic code in which an amino acid corresponds to more than one codon; also called degeneracy
wobble
the acceptable pairing of several possible bases ina an anticodon with the base present in the third position of a codon
polysome
a complex of two or more ribosomes associated with an mRNA molecule and actively engaged in polypeptide synthesis; a polyribosome.
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
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