Gene Expression and Regulation Flashcards
What is an activator?
a protein (transcription factor) that increases gene transcription of a gene or set of genes. Mostactivatorsare DNA-binding proteins that bind to enhancers or promoter-proximal elements.
What is alternative RNA splicing?
production of different RNAs from the same gene by splicing the transcript in different ways
What is aminoacyl-tRNA synthetase?
enzyme that attaches the correct amino acid to a tRNA molecule to form an aminoacyl-tRNA
What is an anticodon?
sequence of three nucleotides in a transfer RNA molecule that is complementary to a three-nucleotide codon in a messenger RNA molecule
What is attenuation?
a proposed mechanism of control in some bacterial operons which results in premature termination of transcription and is based on the fact that, in bacteria, transcription and translation proceed simultaneously
What is a bacterial operon?
anoperonis a functioning unit of genomic DNA containing a cluster ofgenesunder the control of a singlepromoter. The genes aretranscribedtogether into anmRNAstrand and eithertranslatedtogether in the cytoplasm, or undergotrans-splicingto createmonocistronicmRNAs that are translated separately, i.e. several strands of mRNA that each encode a single gene product. The result of this is that the genes contained in the operon are eitherexpressedtogether or not at all.
What is a β-interferon enhanceosome?
a higher-orderprotein complex assembled at theenhancer and regulates expression of a targetgene
What is capping?
the modification (capping) of the 5’ end of eukaryotic mRNAs. This modification occurs after the beginning of transcription in the nucleus, and consists of adding a guanosine nucleotide to the 5’-end of mRNAs and then, methylating the guanosine. Capping protects mRNAs at their termini against attack by phosphatases and other nucleases and promotes mRNA function at the level of initiation of translation.
What is cell memory?
retention by cells and their descendants of persistently altered patterns of gene expression, without any change in DNA sequence (epigenomic inheritance)
What are CG islands?
region of DNA is vertebrate genomes with a greater than average density of CG sequences; these regions generally remain unmethylated
What is chromatin remodelling?
the dynamic modification of chromatinarchitecture to allow access of condensed genomicDNAto the regulatory transcription machinery proteins, and thereby controlgene expression.
What are cis-regulatory sequences?
DNA sequences to which transcription regulators bind to control the rate of gene transcription. In nearly all cases, these sequences must be on the same chromosome (cis) to the genes they control
What are co-repressors?
a substance that inhibits the expression ofgenes. In prokaryotes, corepressors are small molecules whereas in eukaryotes, corepressors are proteins
What is a codon?
sequence of three nucleotides in a DNA or mRNA molecule that represents the instruction for incorporation of a specific amino acid into a growing polypeptide chain
What is a consensus nucleotide sequence?
a summary or “average” of a large number of individual nucleotide sequences derived by comparing many sequences with the same basic function and tallying up the most common nucleotides found at each position
What is CRISPR?
a defence mechanism in bacteria using small noncoding RNA molecules (crRNAs) to seek out and destroy invading viral genomes through complementary base-pairing and targeted nuclease digestion
What is crRNA?
small noncoding RNAs (around 30 nucleotides) that are the effected of CRISPR-mediated immunity in bacteria
What is DNA methylation?
addition of methyl groups to DNA. Exstensive methylation of the cytosine base in CG sequences is used in plants and animals to help keep genes in an inactive state
What is DNA supercoiling?
a conformation with loops or coils that DNA adopts in response to superhelical tension; conversely, creating carious loops or coils in the helix can create such tension
What is epigenetic inheritance?
inheritance of phenotypuc changes in a cell or organism that do not result from changes in the nucleotide sequence of DNA. Can be due to positive feedback loops of transcriptions regulators or to heritable modifications in chromatin such as DNA methylation or histone modifications
What is an exon?
A segment of a eukaryotic gene that consists of a sequence of nucleotides that will be represented in mRNA or in a final transfer, ribosomal, or other mature RNA molecule. In protein-coding genes, exons encode the amino acids in the protein. An exon is usually adjacent to a noncoding DNA segment called and intron
What is an exosome?
large protein complex with an interior rich in 3’-to-5’ RNA exonucleases; degrades RNA molecules to produce ribonucleotides
What is feedback inhibition?
the process in which a product of a reaction feeds back to inhibit a previous reaction in the same pathway
What is a gene?
region of DNA that is transcribed as a single unit and carries information fir a discrete hereditary characterisitic, usually corresponding to (1) a single protein (or set of related proteins generated by variant post-transcriptional processing), or (2) a single RNA (or set of closely related RNAs)
What is a gene control region?
the set of linked DNA sequences regulating expresision of a particular gene. Includes promtoer and cis-regulatory sequences required to initate transcription of the gene and control the rate of transcripton
What are general transcription factors?
any of the proteins whose assembly at all promoters of a given type is required for the binding and activation of RNA polymerase and the initiation of transcription
What is genomic imprinting?
phenomenon in which a gene is either expressed or not expressed in the offspring depending on which parent it is inherited from
What does homologous mean?
genes that are similar as a result of a shared evolutionary origin
What is an inducer?
a molecule that regulatesgeneexpression. An inducercan bind to protein repressors or activators.Inducersfunction by disabling repressors. Thegeneis expressed because aninducerbinds to the repressor
What is an intercistronic region?
Any of the DNA in between gene-coding DNA, including untranslated regions, 5’ and 3’ flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.
What is an internal ribosome entry site?
specific site in a eukaryotic mRNA, other than at the 5’ end, at which translation ban be initated
What is an intrinsic terminator?
a section ofnucleic acid sequence that marks the end of ageneoroperonin genomicDNA duringtranscription. This type of terminator requires the formation of aself-annealinghairpinstructure on the elongating transcript, which results in the disruption of themRNA-DNA-RNA polymerase ternary complex
What are introns?
Noncoding region of a eukaryotic gene that is transcribed into an RNA molecule but is then excised by RNA splicing during production of the mRNA or other functional RNA
What is a lac operon?
anoperonrequired for the transport and metabolism oflactosein Escherichia coli and many other enteric bacteria
What is a lac repressor?
acts as a lactose sensor. It normally blocks transcription of the operon, but stops acting as a repressor when lactose is present. Thelacrepressor senses lactose indirectly, through its isomerallolactose.
What is lncRNA?
long non-coding RNA: a large and diverse class of transcribed RNA molecules with a length of more than 200 nucleotides that do not encode proteins
What are master transcription regulators?
a transcription regulator specifically required for formtaion of a particular cell type. Artificial expression of master transcription regulatorys (alone or in combination with others) will often convert one cell type onto another
What is miRNA?
microRNA: a small non-coding RNA molecule (containing about 22 nucleotides) found in plants, animals and some viruses, that functions in RNA silencing and post-transcriptional regulation of gene expression
What is a mitotic chromosome?
highly condensed duplicated chromosome as seen at mitosis, consisting of two sister chromatids held together at the centromeres
What is monoallelic gene expression?
expression of only one of the two copies of a gene in a diploid genome, occurring, for example, as a result of imprinting or X-chromosome inactivation
What does monocistronic mean?
a type of messenger RNA that can encode only one polypeptide per RNA molecule. In eukaryotic cells virtually all messenger RNAs aremonocistronic
What is mRNA?
messenger RNA: RNA molecule that specifies the amino acid sequence of a protein. Produced in eukaryotes by processing of an RNA molecule made by RNA polymerase as a complimentary copy of DNA. It is translated into protein in a process catalysed by ribosomes
What is mRNA degradation control?
regulation by a cell of gene expression by selectively preserving or destroying certain mRNA molecules in the cytoplasm
What is negative regulation?
when the regulatory protein is a repressor. It binds to the operon and inhibits transcription. Like a switch, the regulatory protein turnsgene expressionoff.
What is noncoding RNAs?
an RNA molecule that is the final product of a gene and does not code for protein. These RNAs serve as enzymatic, structural, and regulatory components for a wide variety of processes in the cell
What are nuclear pore complexes?
large multiprotein structure forming an aqueous channel (the nuclear pore) though the nuclear envelope that allows selected molecules to move between nucleus and cytoplasm
What is an operator site?
a segment ofDNAto which a transcription factor binds to regulategeneexpression by repressing it
What does polycistronic mean?
Describing a type of messenger RNA that can encode more than one polypeptide separately within the same RNA molecule. Bacterial messenger RNA is generallypolycistronic
What is positive regulation?
Inpositive regulationa transcription factor is required to bind at the promoter in order to enable RNA polymerase to initiate transcription.
What are post-transcriptional controls?
any control on gene expression that is exerted at a stage after transcription has begun
What is a promoter?
nucleotide sequence in DNA to which RNA polymerase binds to begin trascription
What are promoter proximal elements?
Any regulatory sequence in eukaryotic DNA that is located close to (within 200 base pairs) apromoterand binds a specific protein thereby modulating transcription of the associated protein coding gene
What is protein activity control?
the selective activation, inactivation, degradation, or compartmentalisation of a specific proteins after they have been made. One of the means by which a cell controls which proteins are active at a given time or location in the cell
What is a pseudogene?
nucleotide sequence of DNA that has accumulated multiple mutations that have rendered an ancestral gene inactive and nonfunctional
What is purifying selection?
natural selection operating in a population to slow genome hanges and reduce divergence by eliminating individuals carrying deleterious mutations
What are reading frames?
a way of dividing the sequence of nucleotides in a nucleic acid (DNAor RNA) molecule into a set of consecutive, non-overlapping triplets.
What is regulated nuclear transport?
mechanisms controlling the export of mRNAs from the nucleus to the cytosol that can be used to regulate gene expression. Also includes the selective import of proteins and RNA molecules into the nucleus
What is a repressor?
a DNA- or RNA-binding protein that inhibits the expression of one or more genes by binding to the operator or associated silencers.
What is a Rho dependent terminator?
a section of nucleic acid sequence that marks the end of ageneor operon in genomicDNA during transcription.
Rho-dependent transcription terminators require a protein calledRho factor, which exhibits RNAhelicaseactivity, to disrupt the mRNA-DNA-RNA polymerase transcriptional complex.
What is a ribozyme?
An RNA molecule with catalytic activity
What is RNA editing?
type of RNA processing that alters the nucleotide sequence of an RNA transcript after it is synthesised by inserting, deleting, or latering indiviual nucleotides
What is RNA interference?
as originally described, mechanism by which an experimentally introduced double-stranded RNA induces sequence-specific destruction of complimentary mRNAs. The term RNAi is often used to include the inhinition of gene expression by microRNAs (miRNAs) and piwiRNAs (piRNAs), which are encoded in the cell’s own genome
What is RNA polymerase?
enzyme that ctalyses the synthesis of an RNA molecule on a DNA template from ribonucleoside triphosphate precursors
What is RNA polymerase I?
in higher eukaryotes, thepolymerase that only transcribes ribosomalRNA(but not 5S rRNA, which is synthesized byRNA polymerase III), a type ofRNAthat accounts for over 50% of the totalRNA synthesized in a cell.
What is RNA polymerase II?
a protein-protein complex. It is one of the three RNAP enzymes found in the nucleus of eukaryotic cells. It catalyzes the transcription of DNAto synthesize precursors ofmRNAand most snRNA and microRNA.
What is RNA polymerase III?
an enzyme found in eukaryotes that transcribesDNAto synthesize ribosomal 5S rRNA, tRNA and other small RNAs. Thegenestranscribed byRNA Pol IIIfall in the category of “housekeeping”geneswhose expression is required in all cell types and most environmental conditions.
What is RNA processing control?
Regulation by a cell of gene expression by controlling the processing of RNA transcripts, which includes their splicing
What is RNA splicing?
process in which intron sequences are excised from RNA transcripts. A major process in the nucleus of eukaryotic cells leading to formation of mRNAs
What is RNA transport and localisation control?
regulation by a cell of gene expression by selecting which completed mRNAs are exported from the nucleus to the cytosol and determining where in the cytosol they are localised
What is the RNA world?
hypothesis that early life on Earth was based primarily on RNA molecules that both stored genetic information and catalysed biochemical reactions
What is rRNA?
ibosomal RNA: any one of a number of specific RNA molecules that form part of the structure of a ribosome and participate in the synthesis of proteins. Oftern distinguished by their sedimentation coefficient
What are RNA genes?
gene that specifies a ribosomal RNA
What is a sigmal factor?
a protein needed only for initiation of RNA synthesis. It is a bacterial transcription initiationfactorthat enables specific binding of RNA polymerase togenepromoters
What is siRNA?
small interfering RNA: short (21-26 nucleotide) double-stranded RNAs that inhibit gene expression by directing destruction of complementary mRNAs. Production of siRNAs is usually triggered by exogenously introduced double-stranded RNA
What are small nuclear ribonucleoprotein (snRNPs)?
RNA-protein complexes that combine with unmodifiedpre-mRNAand various other proteins to form aspliceosome, a large RNA-protein molecular complex upon whichsplicingofpre-mRNA occurs
What is snRNP U1?
the initiator of spliceosomal activity in the cell by base pairing with the hnRNA
What is snoRNA?
small nucleolar RNA: small RNAs found in the nucleolus, with various functions, including guiding the modifications of precursoe rRNA
What is snRNA?
small nuclear RNA: small RNA molecules that are complexed with proteins to form the ribonucleoprotein particles (snRNPs) involved in RNA splicing
What are spliceosomes?
large assembly of RNA and pritein molecules that performed pre-mRNA splicing in eularyotic cells
What is a start codon?
AUG (seegeneticcode), which codes for the amino acid methionine
What is SWI-SNF?
anucleosome remodeling complex found in botheukaryotesandprokaryotes. In simpler terms, it is a group ofproteinsthat associate to remodel the way DNA is packaged.
What is a TATA box?
sequence in the promoter region of many eukaryotic genes that binds a general transcription factor (TFIID) and hence specifies the position at which transcription is initiated
What is a terminator?
signal in bacterial DNA that halts transcription; in eukaryotes, transcritpion terminates after cleavage and polyadenylation of the newly synthesised RNA
What is transcription?
copying one strand of DNA into a complementary RNA sequene by the enzyme RNA polymerase
What are transcription factors?
proteins involved in the process of converting, or transcribing, DNA into RNA. Transcription factorsinclude a wide number of proteins, excluding RNA polymerase, that initiate and regulate thetranscriptionof genes
What are transcription regulators?
general name for nay protein that binds to a specific DNA sequence (known as cis-regulatory sequence) to influence the transcription of a gene
What are transcriptional activator proteins?
aprotein(transcriptionfactor) that increasesgene transcriptionof ageneor set ofgenes. Most activatorsareDNA-bindingproteinsthat bind to enhancers or promoter-proximal elements
What is transcriptional control?
regulation by a cell of gene expression by controlling when and how often a given gene is transcribed
What are transcriptional repressor proteins?
Aproteinin which its binding to the operator inhibits thetranscriptionof one or moregenes
What is translation?
Process by which the sequence of nucleotides in an mRNA molecule directs the incorporation of amino acids into protein. Occurs on a ribosome
What is translational control?
regulation by a cell of gene expression by selecting which mRNAs in the cytoplasm are translated by ribosomes
What is tRNA?
set of small RNA molecules used in protein synthesis as an interface (adapter) between mRNA and amino acids. Each type of tRNA molecule is covalently linked to a particular amino acid
What is a trp operon?
anoperon—a group of genes that is used, or transcribed, together—that codes for the components for production oftryptophan. Thetrp operonis present in many bacteria, but was first characterized in Escherichia coli
What is a trp repressor?
a transcription factor involved in controlling amino acid metabolism. It has been best studied in Escherichia coli, where it is a dimeric protein that regulates transcription of the 5genesin thetryptophanoperon
What are upstream activation sequences?
Abinding sitefortranscriptionfactors, generally part of apromoterregion. A UAS may be foundupstreamof the TATAsequence(if there is one), and its function is (like anenhancer) to increasetranscription. Unlike anenhancer, it can not be positioned just anywhere or in any orientation.
What is the wobble position?
the third position in the codon that,
due to the degeneracy of the genetic code, is less discriminatory for the amino acid than the other two bases
What is X-inactivation?
inactivation of one copy of the X chromosome in the somatic cells of female mammals
What determines the structure of RNA?
The intramolecular base pairing between nucleotides of the single strand
True or False: The coding strand of the DNA is the template for transcription
False - The template strand is the template, the coding strand has the same sequence as the transcribed RNA
True or False: Transcription and translation occur at the same time in prokaryotes
True - They both occur in the cytoplasm as prokaryotes do not have a nucleus
True or False: prokaryotes only have one type of RNA polymerase
True - Prokaryotes have one, eukaryotes have three
What does the +1 site denote?
The first DNA base to be transcribed. Also known as the initiation site
True or False: the transcription site +1 is downstream of the start codon
False - it is usually well upstream
Where are the promoters found for E. coli?
-35 and -10 regions upstream of the gene
What does the RNA polymerase holoezyme consist of?
Core enzyme plus sigma-factor
What does the sigma-factor do?
Binds to the two promoters and positions the RNA polymerase
How is transcription regulated in prokaryotes?
Activators
Repressors
Attenuation
True or False: there is only one type of sigma factor
False - each different promoter has a specific sigma-factor
How do intrinsic terminators work?
Intrinsic terminators consist of a GC-rich inverse repeat sequence followed by a string of Us. This causes a hairpin loop that blocks the polymerase and the weak A-U bonds cause the RNA to fall off
How does Rho-dependent termination work?
A Rho factor binds to the RNA, and as DNA polymerases moves further along the DNA, the Rho factor moves along the newly synthesised RNA strand trying to catch up. When RNA polymerase reaches the terminator sequence it stops, and Rho catches up. Rho then unwinds the DNA-RNA transcription bubble resulting in the release of the RNA and enzymes
Where does transcription and translation occur in eukaryotes?
Transcription occurs in the nucleus, translation occurs in the cytoplasm
True or False: Prokaryotic RNA undergoes splicing
False - Only eukaryotic RNA does
How is pre-mRNA processed before it is translated?
- Addition of a 7-methylguanosine cap at the 5’ end
- Addition of a poly-A tail
- Splicing to remove introns
True or False: Polycistronic mRNA has both non-translated and translated regions
True
True or False: Each coding region of polycistronic mRNA has its own initiation and termination signals
True
Which polymerase transcribes rRNA genes (except for 5S RNA) in eukaryotes?
RNA Polymerase I
Which polymerase produces mRNA and some snRNA genes in eukaryotes?
RNA Polymerase II
Which polymerase transcribed most small RNA genes (tRNA, some snRNA and the 5S rRNA) in eukaryotes?
RNA Polymerase III
What is the eukaryote equivalent of a sigma-factor?
Transcription factors
True or False: RNA polymerase binds directly to the DNA to initiate transcription
False - RNA polymerase binds to the transcription factors that are bound to the promoter sequences
What does eukaryotic RNAP II require for its activity?
An activator, mediator and chromatic modifying proteins
How is it that some activator proteins can act from a distance of several thousand nucleotides away?
The DNA is flexible and can bend and form loops
What is the CTD?
Found on the beta-subunit of RNAP II near the site where newly synthesised RNA emerges, CTD ochestrates the processing of mRNA, particularly the capping of the 5’ end
Which heavily conserved sequences are crucial for intron splicing?
- GU at 5’ and AG at 3’
- Branch point A 15-45bp upstream of splice site
- Poly-pyrimidine tract upstream of splice site
Which small nuclear ribonucleoproteins make up the spliceosome?
U1, U2, U4, U5 and U6
How is the spliceosome assembled?
U1 forms base pairs with GU at the 5’ splice function. U2 recognises the branch-point site A. The U4-U5-U6 complex joins the spliceosome. The complex bends the RNA, attaching one end of the intron to the branch point creating a loop. The other end of the intron is cleaved, and the two exons are joined together.
What is the difference between intercistronic regions and introns?
An intercistronic region separates the RNA coding region for one proteins from the coding region of another so it is in between genes.
Introns split coding regions of genes in two so it is inside the gene.
What is the catalyst in splicing?
snRNA acts as a ribozyme, which is a RNA molecule that functions as an enzyme
What is the default state of transcription for prokaryotes?
On
What is the default state of transcription for eukaryotes?
Off
What is negative regulation?
When a regulatory protein (repressor) binds to the operator site and blocks RNA polymerase
How is repression relieved?
An inducer molecule attaches to the repressor causing it to be released from the operator site
What is positive regulation?
When a regulatory protein (activator) binds to the operator site promoting the attachment of RNA polymerase to the DNA
In what conditions does a activator bind to DNA?
Activators can only bind to DNA in the presence of an inducer molecule
What type of regulation is the lac operon an example of?
Positive - when AMP (inducer) levels are high, signalling low levels of glucose causing more enzyme to be made
Negative - when lactose levels are low so no enzyme is produced
What is feedback inhibition?
Where the product of a pathway inhibits the activity of an enzyme earlier in the pathway
What is feedback repression?
Where the product of a pathway interacts with a regulatory protein (i.e repressor) to stop transcription of genes encoding enzymes in the pathway
What regulation mechanism does the trp operon use?
Repression and attenuation
