Term
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Definition
Ribonucleic acid. Has a ribose sugar instead of deoxyribose, and uses Uracil instead of Thymine (pyrimidines).
Synthesized as a single strand, but can loop back on itself to form a double helix. |
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Definition
| Viruses that use RNA as their genetic transfer material (e.g., leukemia viruses and HIV). Once in a host cell they must make a DNA copy of their RNA sequence using reverse transcription. |
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Term
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Definition
| Copying of DNA by RNA Polymerase to make RNA strands. |
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Term
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Definition
| Enzymes that transcribe DNA into RNA. There are more RNA polymerases in the cell at any given time than DNA Polymerases. RNA polymerases are faster and less accurate than DNA Polymerases. |
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Term
| Eukaryotic RNA Polymerases |
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Definition
Eukaryotes have 3 different RNA polymerases. RNA Polymerase I and III transcribe non-coding RNAs, and RNA Polymerase II transcribes mRNA. These polymerases are DNA-dependent and reside in the nucleus.
Mitochondrial RNA polymerase is a single unit and is exported to the mitochondria.
At the start of transcription, 20 additional factors are needed in addition to RNA polymerase. |
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Term
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Definition
A site in DNA that signals the start of transcription. RNA polymerases and promoters attach there.
RNA promoters outnumber DNA promoters. |
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Term
| Prokaryotic RNA Polymerases |
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Definition
Only one kind of RNA polymerase is used to transcribe all different kinds of RNA in the cell. This enzyme has 5 subunits, two alpha, one beta, one beta', and one sigma. The alpha, beta, and beta' subunits make up the core. The sigma factor is just needed to gide the enzyme to the correct DNA start site and initiate transcription.
RNA transcription initiation begins when a complex of sigma factors and the large and small units of RNA polymerase assemble at the start site. |
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Term
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Definition
| The DNA strand read for transcription (3' - 5') |
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Term
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Definition
| DNA strand in transcription that is not used as the template but whose sequence matches the RNA product (except with Ts instead of Us). |
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Term
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Definition
| No primer is required for transcription. The first ribonucleoside triphosphate added retains 3 phsophates as transcription continues in a 5' - 3'. Subsequent ribonucleoside triphosphates keep only the phosphate closest to the sugar (alpha phosphate). The other two phosphates are released as orthophosphate. |
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Term
| Prokaryotic Transcription Termination |
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Definition
High levels of the transcript's protein product halt the transcription of that sequence. This may be caused by interactions between RNA polymerase and DNA termination signals. A transcription complex factor, rho (helicase), can inactivate transcription at a C-rich termination site.
Without rho, termination can occur at G:C rich regions followed by A:T regions that form a hairpin structure that slows the elongation process. |
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Term
| RNA Polymerase II Transcription Termination |
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Definition
| A polyadenylated site activates transcription termination. The polymerase will continue on, but the new mRNA is released by an endonuclease associated with the carboxyl end of Polymerase II. The RNA strand still being synthesized s eaten by another exonuclease until it catches up with the polymerase and transcription stops. |
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Term
| RNA Polymerase I and III Transcription Termination |
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Definition
At a DNA site called Sal Box, RNA polymerase I is stopped by transcription factor TTF1.
Polymerase III stops at a run of As in the template with the help of a termination factor. |
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Term
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Definition
| rRNA. The largest component of cellular RNA (80-90%). The different types are named for their sedimentation coefficient (S). They are the structural and functional components of ribosomes. |
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Term
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Definition
Three species:
-16s in the small ribosomal subunit
-23s and 5s in the robosomal large subunit
All three are transcribed from the same gene (polycistronic) |
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Term
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Definition
Synthesized as a precursor 45s unit that is processed to a 28s and 5.8s (large ribosomal subunit) and a 18s (small ribosomal subunit). A separate 5s unit is also included in the large ribosomal subunit, but it is processed separately.
These RNAs are synthesized from highly repeated gene clusters. |
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Term
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Definition
mRNA. The link between gene DNA sequences and their protein products.
Much less plentiful in the cell than rRNA. |
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Term
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Definition
Synthesized at the same time that is is translated.
Can be polycistronic, with the sequences of multiple proteins on one single mRNA strand. |
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Term
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Definition
Monocistronic (one protein per mRNA). Different proteins can come from the same DNA sequence is RNA synthesis is started at different points or if the mRNA is processed differently (alternative splicing).
After transcription eukaryotic mRNA must be processed and transported from the nucleus to the cytoplasm for translation. |
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Term
| Constitutive Transcription |
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Definition
| mRNA sequences that are transcribed constantly, meaning that they are common in the cell. |
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Term
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Definition
| mRNA sequences only transcribed at certain times in the cell cycle or under certain conditions. |
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Term
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Definition
A sequence of polyadenylic acid at the 3' end of an mRNA strand. Added after synthesis, not found in the DNA code.
mRNA is cut 11-30 bases 3' to the AAUAAA site. Polyadenylate polymarase adds adenines to the tail, which can be up to 200 bases long.
30% of mRNAs (including histone mRNAs) are not polyadenylated. |
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Term
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Definition
A 5'-5' pyrophosphate linkage of a 7-methylguanosine to a 2' D-methly guanine or adenine of the mRNA. This cap protects the mRNA and acts as a recognition signal for translational apparatuses.
Methylation of the 5' end of the mRNA may differ, with the first and second or all 3 first nucleotides methylated.
Capping occurs on all mRNA destined for translation, and occurs after initiation of transcription. |
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Term
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Definition
| Sequences of uninterrupted DNA used to code for amino acids in prokaryote structural proteins. A sequence with no introns. |
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Term
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Definition
| hnRNA. Newly transcribed mRNA in eukaryotes that still contains introns. Larger than processed mRNA. hnRNA is capped and tailed before the introns are removed. |
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Term
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Definition
| Process of removing introns from newly transcribed hnRNA molecules, converting them to mRNA. Happens in the nucleus. |
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Term
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Definition
| The process of splicing may be key to the timing of translation of mRNA in the cytoplasm. Introns also might increase recombination within genes as well as between genes without breaking coding sequences. They also might protect genes from toxins and radiation. |
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Term
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Definition
| Modifies gene products by including alternate exons. Can be found in over 40 genes. |
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Term
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Definition
| When the splicing process goes wrong it can cause disease states such as beta thalassemia (from the beta globin gene) and autoimmune conditions from production of antibodies to RNA protein complexes. |
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Term
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Definition
Found in nuclear, mitochondrial, and chloroplast genes.
For their removal from hnRNA, a guanosine triphosphate molecule attacks the 5' phosphate on the 5' end of the intron, leaving a 3' OH (splice donor site) to attack the next 5' end of an exon. A new phosphodiester bond is formed and the old intron sequence is released. |
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Term
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Definition
Found in mitochondrial and chloroplast genes.
The 2' OH group of an adenosine in the intron attacks the 5' phosphate at the splice donor site. Then the 3' OH site of the splice donor site bonds with the splice acceptor site of the next exon, jettisoning the intron as a lariat structure (which has an unusual 2', 3', 5' triply linked nucleotide). |
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Term
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Definition
The RNA chain is broken and reunited.
The intron ends are cleaved by an endonuclease. The exposed ends, a 2' 3' cyclic phosphate and a 5' OH are ligated in a reaction requiring ATP. Some tRNAs undergo further base modification. |
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Term
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Definition
| snRNA. Help with splicing in eukaryotes. RNA Polymerase I or III transcribe snRNAs, which stay in the nucleus. These have a sedimentary range of 6-8s. They serve a structural role in processing mRNA. |
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Term
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Definition
| tRNA. Short, single-stranded. 73-93 bases, 24,000-31,000 mw. Ribosomes translate mRNAs into proteins with the help of tRNAs. Each amino acid has at least 1 tRNA. 8 or more bases in all tRNAs are modified after synthesis (usually methylated). |
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Term
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Definition
Form a cruciform structured via intrastrand hybridization, and make a y-shaped structure via hydrogen bonds.
CCA at the 3' end and a guanylic acid at the 5' end. Amino acids covalently attach to the CCA.
A seven-base TpsiC loop contains sequence 5'-TpsiCG-3'. The 7-base anticodon loop contains a 3 base anticodon that compliments the mRNA.
The D-loop is 8-12 p and is rich in modified nucleotide dihydrouridine. |
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Term
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Definition
| miRNA. 17-27 base long regulatory RNAs formed from endogenous RNA hairpins. Can inhibit translation and control gene expression by pairing with partially complimentary sequences in mRNA. They have other functions, cell development and defense. Production is limited to certain times and stages of the cell cycle, making htem hard to isolate. |
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Term
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Definition
| siRNA. Functional intermediates of RNA interference (RNAi), which protect eukaryotic cells from viral invasions.Transcription of inverted repeats or the activity of RNA-directed RNases leads to the formation of dsRNA species. These are cleaved from dsRNAs over 500 bp in length. Ribonuclease III (Dicer) cuts siRNA and miRNA from dsRNA precursors. |
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Term
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Definition
Tiny non coding RNA (tncRNA), small modulatory RNA (smRNA), small nucleolar RNA (snoRNA), tmRNA, guide RNA, and more.
These molecules affect plasmid replication, bacteriophage development, chromosome structure, and cell development.
Call small RNA (sRNA) in prokaryotes and non coding RNA (ncRNA) in eukaryotes. |
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Term
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Definition
| Located in the nucleolus. Produces 18s, 5.8s, and 28s rRNA. Not alpha-aminitin sensitive. |
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Term
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Definition
| Located in the nucleus. Produces mRNA and snRNA. Inhibited by alpha-aminitin. |
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Term
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Definition
| Found in the nucleus. Produces tRNA and 5s rRNA. Inhibited by high concentrations of alpha-aminitin. |
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Term
| RNA-Dependent RNA Polymerases |
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Definition
| Carried by RNA viruses (e.g., HepC and Dengue Virus) to replicate their genomes.Some lower eukaryotes use them as well, possibly for gene splicing or RNAi. |
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Term
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Definition
| An RNA polymerase that needs no template. It adds adenine nucleotides to the 3' end of the mRNA, creating a polyA tail. |
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Term
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Definition
Degrade RNA. Two different types, exoribonucleases and endoribonucleases.
RNases are extremely stable and degrade every type of RNA. |
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Term
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Definition
Cleave RNA strands. RNA synthesis in mammals is terminated when a cleavage and poladenylation specific factor (CPSF) joins with other factors t form an endoribonuclease that binds to the poly A site. This unit, in addition to RNA polymerase II subunits, cuts the new RNA transcript before the poly A tail is added.
Some RNA endonucleases recognize dsRNA and digest miRNA and siRNA. |
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Term
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Definition
| An endoribonuclease that digests the RNA strand in a DNA-RNA hybrid. |
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Term
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Definition
| Endoribonucleases. RNase I cutes ssRNA, RNase III cuts dsRNA. |
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Term
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Definition
| An endoribonuclease that removes precursor nucleotides from tRNA molecules in a 3'-5'. |
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Term
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Definition
| Endoribonucleases that cut ssRNA at certain sites. This can be used to investigate gene expression and transcription structure. |
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Term
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Definition
Digest ssRNA from either 3' or 5' ends. Include many enzymes: PNPase, RNase PH, RNase II, RNase R, RNase T.
RNase D processes pre-tRNA molecules from the 3'-5'. |
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Term
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Definition
Unwind dsRNA for synthesizing and processing. May work only on RNA or might also process RNA-DNA hybrids or DNA duplexes. Can also remove proteins from RNA-protein compounds.
Also function in RNA turnover and chromatin remodeling. |
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Term
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Definition
| Named for the AA sequence of its conserved region (asp-glu-ala-asp). Not strong helicases. Might be called unwindase or RNA chaperones. Act on the 5' end of mRNA to bind it to the small ribosomal subunit. |
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Term
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Definition
| Named for conserved AA sequence (asp-glue-ala-his). Act like DNA helicases. Act on mRNA and siRNA while splicing occurs. Can also function in ribosome biosynthesis. |
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Term
| Components of Transcription Initiation |
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Definition
-Cis factors
-Trans factors
-Specific transcription factors
-General transcription factors
-RNA polymerase complex |
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Term
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Definition
Factors required for RNA transcription to start.
Cis Factors - DNA sequences that indicate DNA loci wheere RNA synthesis takes place and is controlled.
Trans Factors - Proteins that direct the assembly of the transcription complex at the gene by binding to the cis factor. |
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Term
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Definition
A series of structural genes that are transcribed as one mRNA that is then processed to make several different proteins. Bacteria and viruses use these to coordinate production of enzymes needed all at the same time.
Eukaryotes don't have operons, genes are expressed synchronously via similar cis factors that respond to similar trans factors. |
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Term
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Definition
| The lactose operon, contains three genes that work to metabolize lactose. |
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Term
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Definition
| Codes for beta-galactosidase, an enzyme that hydrolyzes lactose into glucose and galactose. |
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Term
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Definition
| Codes for lactose permease , a transport protein that takes lactose into the cell. |
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Term
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Definition
| Codes for thiogalactoside transacetylate, which transacetylates galactosides. |
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Term
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Definition
| A gene associated with the Lac operon. It codes for a protein repressor that attaches to the operator site 5' to the end of the operon. Together these two regulate the expression of the Lac operon. |
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Term
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Definition
The gene for the repressor protein is 5' to the operon (cis regulatory element). The promoter precedes the operon and is where the RNA polymerase binds to start transcription.
The repressor binds to the operator when lactose isn't present in the cell, preventing transcription. When lactose enters the cell, it binds to the repressor and changes the repressors shape so that it will release the DNA.
This is an example of enzyme induction. |
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Term
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Definition
| A type of negative control used on the arg operon. For this operon to be turned off, a corepressor must bind to the repressor so that it will bind to DNA and stop transcription. |
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Term
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Definition
| Found in the mal operon. The operon is transcribed when an activator binds with RNA polymerase to start transcription. |
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Term
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Definition
Cis factors are generally 4-20 bp and may contain inverted repeats that allow them to form cruciform structures in DNA for proteins to recognize.
Prokaryotes have proximal regulatory elements. Eukaryotes had both proximal elements and distal elements such as enhancers and silencers, which may be 1,000 bp away from the gene. |
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Term
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Definition
Regulation of gene expression without cis elements and transcription factors. Includes histone modification, DNA methylation, ad gene silencing by dsRNA or anti-sense RNA.
Epigenetic means that some phenotypic effects are heritable but not coded for by DNA. |
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Term
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Definition
| Nuclear DNA compacted onto nucleosomes. Relaxed chromosomes found in interphase. |
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Term
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Definition
| A complex of histone proteins with 150 bases of DNA wrapped around it. Histone complexes include two each of H2A, H2B, H3, and H4. |
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Term
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Definition
| Structural proteins that DNA wraps around to make nucleosomes. These proteins can regulate gene expression by allowing trans factors and RNA polymerase to access DNA sequences. Modification of these proteins changes the degree of access to DNA and can also affect the activity of chromatin-associated proteins. These protein interactions can lead to the transition of chromatin from an active to a silent state. |
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Term
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Definition
| Can be modified by methylation, ubiquitination, phosphorylation, and acetylation. These modifications can create docking surfaces for DNA-binding proteins and regulatory proteins. Complexes of these proteins on an enhancer are called an enhanceosomes. |
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Term
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Definition
| More transciptionally active chromatin, usually with acetylated histones and no histone methylation |
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Term
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Definition
Transcriptionally silent, has methylated histones and few acetylated histones. This comes about when localized histones with methyls recruit proteins for DNA methylation and heterochromatin formation, preventing transcription and causing gene silencing. When genes are placed in heterochromatin they become silent (position effect).
This is why the X chromo is inactivated in female embryo development. |
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Term
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Definition
| Type of epigenetic regulation (like histone methylation). Occurs at specific DNA sequences, CpG islands. |
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Term
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Definition
| Cytosine and Guanine rich DNA sequences found around first exons, promoters, and the 3' end of genes. Usually over 200 bp long. Frequent sites of DNA methylation, and aberrant methylation of these genes can cause dysregulation of genes in disease states. |
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Term
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Definition
| Gamete-specific gene silencing via methylation. It selectively methylates homologous genes to ensure balanced gene expression in embryonic development. Happens during gametogenesis and is different in male and female gametes. There is a distinct imprinting of genes from egg formation (oogenesis) and sperm formation (spermatogenesis). |
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Term
| miRNA Gene Expression Regulation |
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Definition
miRNA can bind to the 3' end of mRNA, preventing its translation. The mRNA will eventually degrade.Since miRNA have only partially complimentary sequences to mRNA molecules, on miRNA molecule can bind to multiple different mRNA strands.
miRNA start out as pre-miRNA. RNase III-like endonucleases (dicer and DROSHA) cleave pre-miRNA into hairpins, which are processed down to short ssRNA that imperfectly match the 3' end of the target gene. |
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Term
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Definition
A form of gene silencing found in lower eukaryotes. An enzyme complex, RNA-induced silencing complex (RISC), forms from siRNA and proteins. It uses the siRNA to bind to dsRNA with specific sequences complimentary to the siRNA and degrade them. The siRNA can also bind to complimentary mRNA sequences and degrade them, causing gene silencing.
Good for "knock-out" studies but don't work well in mammalian cell. |
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Term
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Definition
| Pathways that funnel internal and external signals to the nucleus to initiate gene expression or turn it off. |
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