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29 Cards in this Set

  • Front
  • Back

gene expression

the process by which a gene’s information is converted into RNA (transcription) and then, for protein-coding genes, into a polypeptide (translation).

RNA polymerase
the enzyme that transcribes a DNA sequence into an RNA transcript.
promoter
DNA sequences near to (and usually upstream of) a gene’s transcription start site to which RNA polymerase binds directly to initiate transcription
ribosome binding site
region on prokaryotic mRNAs containing both an initiation codon and a Shine-Dalgarno box; ribosomes bind to these elements to start translation of protein-coding sequences on the mRNAs.
Catabolic pathway
a metabolic pathway that breaks down complex molecules to produce smaller molecules (and often, energy). Lactose utilization, which breaks down lactose into glucose and galactose, is an example of a catabolic pathway. (See Fig. 15.2 on p. 517.)
anabolic pathway
a metabolic pathway that synthesizes a complex molecule from simpler ones. The genes of the trp operon encode enzymes that cooperate in the anabolic pathway that leads to the synthesis of the amino acid tryptophan.
transcription factor
a protein that binds DNA sequence-specifically and regulates transcription. In prokaryotes, two types of transcription factors exist: positive regulators activate transcription, and negative regulators (also called repressors) inhibit transcription.
inducible regulation
a mechanism of gene control where transcription occurs only in the presence of a molecule called an inducer. An inducer is a small molecule that binds to a positive regulator, altering the positive regulator’s conformation so that it can bind DNA. Inducible regulation is particularly important for the regulation of catabolic pathways.
repressible regulation
a mechanism of gene control where transcription occurs only in the absence of a corepressor. In prokaryotes, a corepressor is a small molecule that binds to a repressor, thereby altering repressor conformation so that it can bind DNA. Repressible regulation is particularly important for the regulation of anabolic pathways.
induction
the process by which an inducer causes transcription of a gene or a set of genes
operon
a unit of DNA composed of specific structural genes (encoding functional products), plus a promoter and an operator. These elements work in unison to regulate the coordinated response of expression of the structural genes to environmental changes.
allosteric protein
a protein that changes its conformation reversibly when bound to a specific effector molecule
constitutive mutants
cause gene transcription to occur all the time in an unregulated manner; that is, regardless of environmental conditions
effector
a small molecule that binds to an allosteric protein or to an RNA molecule and causes a conformational change. As examples, allolactose (an inducer), cAMP, and tryptophan (a corepressor) are both effectors.
in trans
describes the action of a protein or RNA that can bind to target sites on any DNA or RNA in the cell; a protein or RNA that acts in trans is said to be trans- acting. Molecules that act in trans diffuse throughout the cell to find their target sites.
in c i s
describes the action of a DNA site or a region in an RNA molecule that acts only on the DNA or RNA to which it is connected physically; a DNA site or an RNA that acts in cis is said to be cis-acting.
domain
discrete region of a protein that has a particular function. For example, the lac repressor polypeptide has a domain that binds to the operator, a domain that bindsinducer allolactose, and a domain that allows polypeptides to associate into multimers.
catabolite repression
inhibition of the expression of genes or operons like the lac operon when glucose or another preferred catabolite is present
RNA leader sequence
the 5’ UTR of an mRNA; in prokaryotes, RNA leader sequences can act in cis to regulate transcription elongation or the transcript’s translation.
hairpin loops (stem loops)
structures formed when a single strand of RNA folds back on itself because of complementary base pairing between different regions in the same molecule
attenuation
a type of gene regulation that responds to translation of an ORF in the RNA leader; the RNA leader is called the attenuator. When this ORF is translated efficiently, transcription of a gene or operon terminates in the RNA leader sequence before a complete mRNA transcript is made.
terminator
in prokaryotes, stem-loop structures that cause RNA polymerase to stop downstream transcription. Terminator formation in an RNA leader sequence (such as an attenuator or a riboswitch) can be prevented by formation of a different, competing stem-loop structure called an antiterminator.
riboswitch
an allosteric RNA leader that binds a small molecule effector to control gene expression
RNA thermometer
an allosteric RNA leader that regulates translation in response to temperature through a stem-loop structure whose stability is temperature- dependent.
sRNAs
small RNA molecules that regulate translation in trans by base pairing with sites on mRNAs. This base-pairing of sRNA and mRNA can either hide or expose the ribosome binding site on the mRNA.
antisense RNAs
regulatory RNAs that are complementary in sequence to the mRNAs they regulate because they are transcribed using the opposite strand of DNA as a template. Antisense RNAs can block transcription or translation of their target mRNAs; the target mRNAs are sometimes called sense RNAs.
fusion gene
a gene constructed using recombinant DNA technology that is made up of parts of two or more different genes. For example, a fusion gene may contain the 5’ regulatory region of one gene and the ORF of a different gene.
reporter gene

a fusion gene whose ORF encodes a protein that is easy to detect; expression of that protein “reports” activity of the fusion gene’s promoter and also verifies that the fusion gene transcript was translated. (The term reporter gene also sometimes refers to the ORF of the fusion gene only.)

RNA-Seq (cDNA deep sequencing)

method for analysis of all of the transcripts made in an organism (the transcriptome) under a specific set of conditions. The data are obtained as approximately one billion sequence reads each corresponding to an individual cDNA molecule. With current technology, each read is about 150 nt long.