Term
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Definition
| occasionally 2 exons from different transcripts join together, common in worms and protists, same chemistry as nuclear introns but 2 transcripts |
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Term
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Definition
| sequence on some eukaryotic RNAs altered, one type occurs in mitochondria of trypanosomes, U resides either inserted or deleted |
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Term
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Definition
| catalyzes editing, insert Us via enzyme called TUTase, uses small guide RNAs partially complementary to RNA |
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Term
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Definition
-Anchor complementary to target TNA
-Middle containing editing info
-3' oligo U stretch |
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Term
| Adenosine Deaminase Acting on RNA (ADAR) |
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Definition
| catalyzes the conversion of adenine to inosine, causes one codon to be translated differently, recognizes dsRNA, occurs before splicing |
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Term
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Definition
| convert cytosine to uracil, can be used to produce different gene products in different tissues |
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Term
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Definition
| several proteins bind to exon-exon junctions as consequence of splicing, go with mRNA into the cytoplasm where they are removed by the first round of translation |
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Term
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Definition
| catalyzed by ribonucleases is the complete hydrolysis of RNA into nucleotides, varies greatly from gene to gene |
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Term
| Nonsense mediated mRNA decay |
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Definition
| mammals rely on exon junction complexes formed during splicing, first round of translation displaces them, if ribosome is released too soon and these proteins aren't all displaced it will trigger decay |
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Term
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Definition
| acts on mRNAs that don't have a stop codon, ribosome translates into poly A tail, AAA id codon for lysine, ribosomes stall out when comes to end of tail, both mRNA and protein degraded |
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Term
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Definition
| processes the 5'end of tRNAs, RNA component of the enzyme essential for activity, protein component is not essential |
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Term
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Definition
| processed by several different endonucleases including RNaseD, some eukaryotes tRNAs also have intron that must be removed |
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Term
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Definition
| added by enzyme called tRNA nucletidyltransferase, binds three nucleotides separately to make CCA sequence doesn't require template, many bases of tRNA are then methylated |
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Term
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Definition
| in eukaryotes three of the rRNAs are cleaved from a larger transcript made by RNA pol I, these are processed in part by snorRNPs in the nucleolus |
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Term
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Definition
| process by which information contained in the mRNA is converted to an actual protein product, highly conserved in all organisms |
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Term
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Definition
| protein encoding region of mRNA consists of ordered series of 3 base units called codons |
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Term
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Definition
| hypothesized the existence of adaptor molecule, proposed this molecule would recognize code words or codons on RNA, each adaptor molecule would carry an amino acid |
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Term
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Definition
| tRNAs linked to an amino acid, produced by enzymes called aminoacyl-tRNA synthases |
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Term
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Definition
| serve as adaptor molecules, small between 75-95 bases in length, all end with the bases CCA-3', have several unusual bases |
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Term
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Definition
acceptor arm where the amino acid linked, pseudo uridine loop, D loop because of dihydrouridine, anticodon loop, variable loop
-base pairing between codon and anticodon antiparallel |
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Term
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Definition
degenerate, 64 possible codons, only 20 amino acids, 61 codons used for amino acids, 3 stop codons
-differences in codons often at third base
-codon families have 4 codons that code for the same amino acid |
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Term
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Definition
| there are 61 codons for amino acids, cells usually have only 32 tRNAs, some non-regular base pairing is tolerated at the 3 position of a codon-anticodon pairing |
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Term
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Definition
| the base that pair irregularly in the pairing (usually third base in codon) |
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Term
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Definition
| the 5' base of the anticodon |
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Term
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Definition
| very flexible Wobble base, can base pair with several bases |
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Term
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Definition
| region that could potentially code for a protein, bound by start codon and stop codon, typically long sequence with no stop codons |
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Term
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Definition
| allows us to absorb many mutations, allows for silent mutations within genes |
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Term
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Definition
| in bacteria AUG is the most common but GUG and UUG are sometimes used, in eukaryotes only AUG is used, specifies the first amino acid in the protein and sets the reading frame |
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Term
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Definition
| UAG, UGA, and UAA define the end of a reading frame |
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Term
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Definition
| produce premature stop codons, results in incomplete protein |
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Term
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Definition
| correct nonsense mutations, mutations in tRNA that will respond to a stop codon, suppressor tRNAs |
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Term
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Definition
| must not be too efficient or they would suppress too many stop codons, accomplished by having multiple genes for the same tRNAs |
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Term
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Definition
| non overlapping, established by examining mutations, one base change would change amino acid in code that didn't overlap but two or three in a code that did overlap, no gaps in code |
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Term
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Definition
| showed that there were no gaps in the code, Crick showed this |
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Term
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Definition
| not all codons for same amino acid used equally, often reflects amount of tRNA population in cells |
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Term
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Definition
70S in E. Coli made up of two subunits (30S and 50S) made of several rRNAs and proteins (r-proteins)
-formed under right conditions
-eukaryotic slightly larger but pretty much the same |
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Term
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Definition
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Term
| 2 Steps linking tRNAs to amino acids |
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Definition
Step 1: adenylylation,amino acid activated using energy from ATP, facilitates formation of peptide bond, product is an amino-acyl AMP
Step 2: energy used to transfers amino acid to tRNA, tRNA charging step, amino acid transferred to either 2' or 3'OH of the A on the tRNA depending on class of synthetase |
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Term
| Amino Acyl tRNA Synthestases |
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Definition
| must recognize the correct set of tRNAs, must charge them with the correct amino acid, sometimes referred to as the second genetic code |
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Term
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Definition
| tend to look at bases concentrated in the acceptor arm and anticodon arm, 10 or more nucleotides may be involved, also sometimes the anticodon examined |
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Term
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Definition
| 3 stages (initiation, elongation, termination), process of interpreting and carrying out the code using tRNA |
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Term
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Definition
-ribosome must be recruited to mRNA
-ribosome must be positioned over start codon
-large ribosomal subunit must be recruited
This is the most regulated part of translation |
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Term
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Definition
prokaryotes there are 3 types:
IF1
IF2
IF3
(In eukaryotes at least 12 types) |
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Term
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Definition
| some organisms referred to as Shine-Dalgarno sequence (4-9bp, 8-13bp upstream of AUG start codon), attract mRNA, position the ribosome, good ones give a lot of translation |
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Term
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Definition
| increase efficiency in eukaryotes binding of the ribosome |
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Term
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Definition
| all code for methionine, all cells have at least 2 tRNAs that respond to AUG, only one responds to initiating AUG in the middle of the reading frame |
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Term
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Definition
-Bacteria use initiator tRNA that carries N-formyl methionine
-Eukaryotes use special tRNA for initiation but not N-formyl methionine |
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Term
| Initiation in Bacteria Step 1 |
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Definition
| 30S subunit binds initiation factors IF1 and IF3, blocks partial A site and makes sure no tRNA binds, small subunit binds mRNA on ribosome binding site and positions start codon next to P site, only place tRNA can bind |
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Term
| Initiation in Bacteria Step 2 |
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Definition
| complex joined by GTP bound IF2 and the initiator tRNA, pairs with start codon at P site |
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Term
| Initiation in Bacteria Step 3 |
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Definition
| IF3 released, 50S subunit joins, GTP hydrolyzed, IF2 and IF1 released, forms the 70S initiation complex, initiator tRNA is at P site |
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Term
| Eukaryotic Ribosomal Subunits |
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Definition
kept separate by eIF3 and eIF1A which are functional homologs to IF1 and IF3
-eIF3 prevents large subunit joining early
-eIF1A blocks partial A site
-eIF1 binds to the E site |
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Term
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Definition
| GTP and initiator tRNA join, two other proteins eIF5 and eIF5B also join forming the 43S initiation complex |
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Term
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Definition
mediates as eIF4E binds the cap on the mRNA
-eIF4A is an ATPase and helicase
-eIF4G bridges the mRNA to the ribosome complex and binds the poly A tail
This complex scans for the start codon |
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Term
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Definition
| helps displace the eIF1, eIF1A, eIF2, and eIF3 once the start codon has been found |
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Term
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Definition
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Term
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Definition
| three proteins help in this process, 2 use the energy of GTP, with the addition of each amino acid the correct charge (aminoacyl) tRNA must be loaded onto the A site |
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Term
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Definition
| binds the charged tRNAs 3'end masking the amino acid, can only bind tRNA when it is associated with a GTP, only hydrolyzes GTP when bound to ribosome and releases tRNA, only hydrolyzes GTP after correct binding has been made |
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Term
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Definition
| about 10-3 and 10-4, basis for selection is the correct base pairing between tRNA and codon displayed at the A site, 3 mechanisms assure accuracy |
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Term
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Definition
| only works well when the tRNA is correctly placed |
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Term
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Definition
| tRNAs must be rotated to allow for peptide bond formation, incorrectly paired tRNAs can't do this |
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Term
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Definition
| catalyzed by the 23SrRNA of the large subunit, proteins associated help the reaction to happen but aren't catalytic agents, the ribosome acts as a ribozyme, a 2'OH group on the 3' A in the P site tRNA may also be important |
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Term
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Definition
| once peptidyl transferase has occurred the tRNA at the P site is empty, growing chain is now linked to tRNA at the A site, P site tRNA moves to E site and A site tRNA moves to P site, A site is empty again, mRNA moves three bases |
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Term
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Definition
| translocation requires energy provided by hydrolysis of GTP, binds ribosome when associated with a GTP, peptidyl transferase and the shift uncover a binding site for EFG, similar in structure to a charged tRNA, after GTP hydrolysis EF-G brings about a translocation of the A site tRNA |
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Term
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Definition
| process starts with one of the stop codons ends up at the A site, not recognized by tRNAs, stop codons recognized by release factors |
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Term
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Definition
recognize stop codons and trigger hydrolysis of the peptide chain from the tRNA at the P site, prokaryotes have 2:
RF1- recognizes UAG
RF2- recognizes UGA
UAA recognized by both
(eRF1 in eukaryotes recognizes all three) |
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Term
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Definition
| stimulate the disassociation of class one factors from the ribosome after the release of the polypeptide chain, both prokaryotes and eukaryotes have a single (RF3 and eRF3), regulated by GTP binding hydrolysis |
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Term
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Definition
removed from mRNA by ribosome recycling factor (RRF), recruits EF-G to release the uncharged tRNAs from P and E sites, subunits dissociated and IFs bind small subunits
-Eukaryotes do not have RRF |
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Term
|
Definition
many inhibit protein synthesis by targeting differences between eukaryotic and bacterial systems
-puromycin
-tetracyclin
-cyclohexamide (eukaryotes only) |
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Term
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Definition
| can occur when transcription end prematurely, ribosome will reach end of mRNA and stop, recognized by small RNA called tmRNA |
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Term
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Definition
| looks like tRNA charged with alanine and mRNA molecule, binds to A site of stalled ribosome part of molecule acts like mRNA, this codes for 9 amino acids served as a signal to destroy this protein |
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Term
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Definition
| occurs in eukaryotes, happens when there is no stop codon in mRNA, mediated by protein called Ski7 which is related to eRF3 |
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Term
| Nonsense Mediated mRNA Decay |
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Definition
| mammals rely on exon junction complexes formed during splicing, first round translation displaces them, ribosome is released too soon and these trigger decay |
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Term
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Definition
| central problem in biology (not all genes are expressed, making of RNAs and proteins takes a lot of energy) |
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Term
| Regulation of Transcription |
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Definition
| probably the best and most common, typically involves how the RNA polymerase interacts with promoters, most basic type of control is the strength of the promoter and how well the RNA polymerase sees the promoter |
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Term
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Definition
| aren’t regulated, their expression is constant and governed only by the promoter strength |
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Term
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Definition
| genes that code for the products the cell needs all the time |
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Term
| Regulated Gene Expression |
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Definition
| amount of the gene product rises and falls with the cells needs |
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Term
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Definition
| control expression of other genes, there are 2 types (repressors and activators) |
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Term
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Definition
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Term
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Definition
| help with recruiting the RNA polymerase to the promoter, may aid in either forming an open or closed promoter complex |
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Term
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Definition
| both activators and repressors are sometimes referred to, typically recognize specific sequences at or near genes they control, DNA binding proteins |
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Term
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Definition
| when binding of an activator protein enhances gene expression |
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Term
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Definition
| repressor protein wil inhibit gene expression |
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Term
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Definition
| called enhancers, can result in either activation or repression |
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Term
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Definition
| bridge activators and RNA polymerase but do not bind DNA directly, may be mediators |
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Term
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Definition
| repression can also be mediated by proteins that bind activator proteins and prevent their action on RNA polymerase |
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Term
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Definition
| prevent activators from interacting with the wrong promoter |
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Term
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Definition
| many genes are regulated by more than one regulatory protein, one system is often pathway specific while the other is more general |
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Term
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Definition
| molecular signal regulates activator or repressor function |
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Term
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Definition
| in bacteria genes with related function will be clustered together to be coordinately controlled, will produce polycistronic messages |
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Term
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Definition
| common in bacteria, one promoter will control transcription of several genes, one mRNA will contain several open reading frames, rare in eukaryotes |
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Term
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Definition
| group of operons that are controlled together, results in global regulation |
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Term
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Definition
| usually use a lot more regulators and regulatory sites than bacteria, more complex organisms have more regulatory sites |
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Term
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Definition
| happens when specific combination of regulators unlock each particular gene |
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Term
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Definition
-Eukaryotes mostly positive because genes tend to normally be repressed by nucleosomes, promoters need to be revealed
-Bacteria most regulation is negative because promoters always free and may need to be hidden by repressors |
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Term
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Definition
| usually DNA contacted through certain amino acids of an alpha helix, usually read DNA sequence along the major grove |
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Term
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Definition
| usually short inverted repeats (symmetrical), DNA binding proteins dimmers |
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Term
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Definition
| common in bacterial regulators, two short alpha helices connected by a B turn, not stable so usually part of larger DNA binding domain |
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Term
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Definition
| conserved 60 amino acid sequence, control developmental functions in fruit flies, found in lots of higher organisms including humans, has a helix-turn-helic motif as part of its structure |
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Term
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Definition
| dimerization domain that positions two recognition helices, contains hydrophobic amino acids like leucine which are used as a surface for dimerization |
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Term
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Definition
| combine leucine zippers with basic residues at the end of the alpha helix that make up recognition helices, bZIP proteins tend to bind like tongs |
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Term
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Definition
| about 30 amino acids that form a loop held together at the base by a Zn ion, Z coordinated by either 4 Cys or 2 Cys and 2His, this presents a recognition helix to the DNA, usually DNA binding protein will have several of these |
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Term
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Definition
| domains are somewhat unstructured, often have many acidic residues |
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Term
| Protein Fusion Experiments |
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Definition
| demonstrated that DNA binding and activation domains were functionally separate, eukaryotes activation domain was fused with DNA binding domain from a bacterial repressor, as long as the repressor DNA binding site was present the activator worked |
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Term
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Definition
| one of best models of gene regulation in bacteria |
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Term
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Definition
| discovered one enzyme involved in lactose metabolism in E. coli inducible, called B galactosidase, mutants unable to grow as a carbon source (lacZ gene) and others couldn't transport lactose into cell (lacY gene- codes for protein to bring lactose into cell), performed merodiploid analysis |
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Term
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Definition
| transcribed as single unit, polycistronic RNA (contains three ribosomal binding sites) |
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Term
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Definition
| mutants produced all three gene products all the time, Jacob and Monod isolated these mutants then performed merodiploid analysis |
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Term
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Definition
| partially diploid, constructed with respect to the lac operon revealed there were 2 types of constitutive mutants for the lac operon |
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Term
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Definition
| mutation, can be compliments or rescued by merodiploid, mutations are recessive, defined a gene of the lactose operon, gene was regulatory and product repressed the expression of structural genes in the absence of lactose |
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Term
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Definition
| occurs when normal gene product can mask the presence of a defective one |
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Term
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Definition
| defined cis acting site, could not rescued or complemented in a merodiploid, sequences that functioned only as DNA sequences, never transcribed or translated, for lactose operon mutations defined a region where the lacI gene product would bind to the DNA and repress transcription |
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Term
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Definition
| control involved two main elements (protein repressor coded for by lacI and DNA sequence called an operator site) |
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Term
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Definition
| repsonds to the presence or absence of lactose, gene is not part of the operon, binds to the operator site in the absence of lactose and blocks transcription |
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Term
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Definition
| acts as inducer, will bind the repressor and cause it to lose affinity for DNA, operon may become active |
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Term
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Definition
| E. coli's preferred energy source, cell isn't interesting in metabolizing other carbon sources if glucose is present |
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Term
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Definition
| limits expression of genes for alternative carbon sources is glucose is present |
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Term
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Definition
| effect of glucose mediated by cAMP and protein called CRP (CAP), when glucose absent the cAMP-CRP complex binds to site near many promoters and stimulates transcription |
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Term
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Definition
| positive regulator, has little effect when the lactose repressor is bound |
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Term
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Definition
| poor promoter unless CRP present |
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Term
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Definition
| codes for 5 genes that encode enzymes to make amino acid tryptophan, genes expressed only when tryptophan is limiting, E. coli can make all of its own amino acids |
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Term
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Definition
| controls transcription of the operon, when tryptophan present it causes the repressor to be active and bind an operator site near the promoter, here tryptophan is limiting, E. coli can make all of its own amino acids |
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Term
| Transcriptional Attenuation |
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Definition
| second mechanism regulates gene expression over 700 fold range, repressor only regulates over a 70 fold range |
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Term
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Definition
key is leader sequence of the trp RNA, region has 2 unusual features
-Leader peptide
-Rho independent terminator |
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Term
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Definition
base pair with each other to form Rho independent terminator (GC rich stem loop and Run of Us), transcription will end before reaching the structural genes of the operon
-region 3 will pair with 2 if no trp RNAs and transcription will continue |
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Term
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Definition
| translated effectively then terminator forms, has two back to back trp codon, if ribosome can't translate because no trp RNAs then region 2 will pair with region 3 |
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Term
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Definition
| early on hypothesized the RNAs could be regulatory factors however all firs regulators were proteins, 1990s several developments showed role of RNAs in regulation |
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Term
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Definition
| cis acting RNA regulatory elements, RNAs will assume different shaped that will regulate gene expression, typically respond to small molecules, located within 5' un-translated region of the genes they control, made up of two parts (aptamer and expression platform) |
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Term
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Definition
| binds small molecules and undergoes a conformational change, will cause a change in the expression platform |
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