12. Gene Transcription and RNA Modification Flashcards
the process of synthesizing RNA from a DNA template.
Transcription
a segment of DNA that contains the information to make a functional product, either RNA or a polypeptide.
Gene
genes that produce mRNA and encode polypeptides
Protein-Coding (Structural) Genes
a type of RNA that is transcribed from a protein-encoding gene and contains the information for the synthesis of a polypeptide.
Messenger RNA (mRNA)
the process in which the sequence of codons within mRNA provides the information to synthesize the sequence of amino acids that constitute a polypeptide.
Translation
the idea that the usual flow of genetic information is from DNA to RNA to polypeptide (protein). In addition, DNA replication serves to copy the information so that it can be transmitted from cell to cell and from parent to offspring.
Central Dogma of Genetic
the process by which the information within a gene is accessed, first to synthesize RNA and polypeptides, and eventually to affect the phenotype of the organism.
Gene Expression
a sequence within a gene that initiates (i.e., promotes) transcription.
Promoter
a sequence within a gene that signals the end of transcription.
Terminator
a strand of DNA that is used to synthesize a complementary strand of DNA or RNA.
Template Strand
a strand of DNA that is not used as a template during transcription.
Nontemplate Strand
the strand in DNA that is not used as a template for mRNA synthesis.
Coding (Sense) Strand
a category of proteins that influence the ability of RNA polymerase to transcribe DNA into RNA.
Transcription Factors
a segment of DNA that is recognized by a regulatory transcription factor. The binding of the transcription factor affects the rate of transcription.
Regulatory Sequence (Element)
a short sequence in bacterial mRNA that binds to a ribosome and initiates translation.
Ribosome-Binding Site (Shine-Dalgarno Sequence)
a sequence of three nucleotides in mRNA that functions in translation.
Codon
a three-base sequence in mRNA that initiates translation. It is usually 5′-AUG-3′ and encodes methionine.
Start Codon
a three-base sequence in mRNA that signals the end of translation of a polypeptide. The three are 5′–UAA–3′, 5′–UAG–3′, and 5′–UGA–3′.
Stop Codon
(1) in transcription, the stage that involves the initial binding of RNA polymerase to the promoter in order to begin RNA synthesis; (2) in translation, the formation of a complex between mRNA, the initiator tRNA, and the ribosomal subunits.
Initiation
(1) in transcription, the release of the newly made RNA transcript and RNA polymerase from the DNA; (2) in translation, the release of the polypeptide and the last tRNA and the disassembly of the ribosomal subunits and mRNA.
Termination
an enzyme that synthesizes a strand of RNA using a DNA strand as a template.
RNA Polymerase
the region of separation of two DNA strands produced by RNA polymerase during transcription.
Open Complex
the site in a gene where transcription begins.
Transcriptional Start Site
the TATAAT sequence that is often found at the −10 site of a bacterial promoter.
Pribnow Box
the most commonly occurring bases within a specific type of sequence.
Consensus Sequence
an enzyme composed of subunits that are needed for catalytic activity, as in the core enzyme of RNA polymerase.
Core Enzyme
a transcription factor that recognizes bacterial promoter sequences and facilitates the binding of RNA polymerase to the promoter.
Sigma (σ) Factor
an enzyme containing all of the functional subunits, such as the RNA polymerase holoenzyme that has σ factor along with the core enzyme.
Holoenzyme
a structure found in transcription factor proteins that promotes binding to the major groove of DNA.
Helix-Turn-Helix Motif
the complex between transcription factors, RNA polymerase, and a promoter before the DNA has denatured to form an open complex.
Closed Complex
transcriptional termination that requires the participation of the ρ (rho) protein.
ρ-Dependent Termination
transcription termination that does not require the ρ (rho) protein
ρ-Independent (Intrinsic) termination
a relatively short DNA sequence that is necessary for transcription to take place. It provides the binding site for general transcription factors and RNA polymerase.
Core Promoter
a sequence found within eukaryotic core promoters that determines the starting site for transcription. The TATA box is recognized by a TATA-binding protein, which is a component of TFIID.
TATA Box
in eukaryotes, a low level of transcription produced by the core promoter. The binding of transcription factors to enhancer elements may increase transcription above the basal level.
Basal Transcription
a DNA sequence that functions as a regulatory element in eukaryotes. The binding of a regulatory transcription factor to an enhancer increases the rate of transcription.
Enhancer
a DNA sequence that functions as a regulatory element in eukaryotes. The binding of a regulatory transcription factor to a silencer decreases the rate of transcription.
Silencer
a sequence of DNA, such as a regulatory element, that exerts a cis-effect.
Cis-Acting Element
a regulatory protein that binds to a regulatory element in DNA and exerts a trans-effect.
Trans-Acting Element
one of several proteins that are necessary to initiate basal transcription at the core promoter.
General Transcription Factor (GTF)
a closed complex formed by the assembly of RNA polymerase II and general transcription factors at the core promoter, which initiates transcription.
Preinitiation Complex
the minimum components that are needed to transcribe a eukaryotic gene; these include TFIID, TFIIB, TFIIF, TFIIE, TFIIH, RNA polymerase II, and a DNA sequence containing a TATA box and transcriptional start site.
Basal Transcription Apparatus
a large protein complex that interacts with RNA polymerase II and various regulatory transcription factors. Depending on its interactions with regulatory transcription factors, mediator may stimulate or inhibit RNA polymerase II.
Mediator
the correspondence between the sequence of codons in the DNA coding strand and the amino acid sequence of a polypeptide.
Colinearity
a region of an RNA molecule that remains after splicing has removed the introns. In mRNA, the coding sequence of a polypeptide is contained within the exons.
Exon
A segment of RNA that is removed during RNA splicing.
Intervening Sequence (Intron)
in eukaryotes, a long transcript corresponding to the entire sequence of a protein-encoding gene, which is produced within the nucleus during transcription. This pre-mRNA is usually altered by splicing and other modifications before it exits the nucleus.
pre-mRNA
the process in which pieces of RNA are removed and the remaining pieces are covalently attached to each other.
RNA Splicing
an organelle within the nucleus of eukaryotic cells where the assembly of ribosomal subunits occurs.
Nucleolus
an enzyme that digests an RNA or DNA strand from the end.
Exonuclease
an enzyme that can cleave a bond between adjacent nucleotides within a DNA or RNA strand.
Endonuclease
a type of intron found in self-splicing RNA that uses free guanosine in its splicing mechanism.
Group I Intron
a type of intron found in self-splicing RNA that uses an adenine nucleotide within the intron itself in its splicing mechanism.
Group II Intron
RNA splicing mechanism that occurs without the aid of any other catalyst.
Self-Splicing
a protein that enhances the rate of self-splicing of group I and II introns.
Maturase
a multisubunit complex that plays a key role in the splicing of eukaryotic pre-mRNAs.
Spliceosome
a subunit of a spliceosome that consists of small nuclear RNA and a set of proteins.
snRNP
a catalytically active RNA that uses one or more metal ions in its catalytic action.
Metalloribozyme
the phenomenon that a pre-mRNA can be spliced in more than one way.
Alternative Splicing
an exon that is always found in mature mRNAs following splicing.
Constitutive Exon
an exon that is not always found in mature mRNAs. It is only found in certain types of alternatively spliced mRNAs.
Alternative Exon
a protein that regulates the choice of splice sites in the process of RNA splicing.
Splicing Factor
a type of splicing factor.
SR Protein
the splicing out of an exon from a pre-mRNA so that it is not included in the mature mRNA.
Exon Skipping
the covalent attachment of a 7-methylguanosine to the 5′ end of mRNA in eukaryotes.
Capping
the string of adenine nucleotides at the 3′ end of eukaryotic mRNAs.
polyA Tail
the process of attaching a string of adenine nucleotides to the 3′ end of eukaryotic mRNAs.
Polydenylation
the process in which a change is made in the nucleotide sequence of an RNA molecule that involves additions or deletions of particular bases or conversion of one type of base to a different type.
RNA Editing
