BIOL-L 211 : EXAM 2
71 Cards in this Set
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Purine
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Adenine, Guanine
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Pyrimadine
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Cysteine, Thymine
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Stem-loop structure
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RNA - short stretches of complementary sequences that base pair (aka hairpin - bases aren't paired)
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Internal loops
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RNA - unpaired nucleotides on either side of the stem (think introverts don't have a match)
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Bulge
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RNA - unpaired nucleotide on one side
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Junctions
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RNA - site where three or four stems branch off (jungle has tree with stems)
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rRNA
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RNA that forms the structure of ribosomes, recognizes messages, and assembles proteins
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tRNA
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RNA that activates amino acids and reads the mRNA message
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mRNA
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RNA that carries the message from DNA
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Primer
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REPLICATION - can be DNA or RNA and removed at the end of replication; DNA polymerase requires a starting point
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Holoenzyme
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REPLICATION - Links 4 enzymes (3 DNA Polymerases and 1 sliding clamp loader)
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Replisome
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REPLICATION - all the proteins acting at the replication fork
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RNase H
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TERMINATION OF REPLICATION - endonuclease that removes the RNA primer
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Promoter
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DNA sequence that indicates where to start TRANSCRIPTION (-35 & -10)
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Consensus sequence
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The average of all recognized promoter sequences
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Sigma factor
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PROKARYOTIC TRANSCRIPTION - proteins that bind to specific promoter sequences and instruct RNA polymerase where to begin transcription
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Pre-initiation Complex
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TRANSCRIPTION - (Pol II + 6 general transcription factors + addition proteins bound at the promoter) help position Pol II over the transcriptional start site and separate DNA strands at promoter
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Abortive synthesis
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TRANSCRIPTION - RNA polymerase produces and release numerous short transcripts to generate energy for promoter escape
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Scrunching
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TRANSCRIPTION - ABORTIVE SYNTH - RNAP remains stationary and is bound to the promoter as it pulls DNA into itself
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Step Mechanism
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TRANSCRIPTION - ELONGATION - advances one base pair for every nucleotide that is added to the transcript
*size of transcription bubble remains constant
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Pyrophosphorolytic editing
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TRANSCRIPTION - Proofreading - removes incorrectly inserted ribonucleotides by adding beta and gamma phosphates reverse of synthesis and inserts correct ribonucleotide
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Hydrolytic editing
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TRANSCRIPTION - Proofreading - RNAP backtracks one or more nucleotides, cleaves RNA, removes sequence
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Repressor
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TRANSCRIPTIONAL REGULATION - PROK - bind to an operator sequence that blocks RNAP from binding to promoter by overlapping the promoter
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Rho-independent termination
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TRANSCRIPTION - PROK TERMINATION - requires C-G rich stem loop structure. The stable stem loop is followed by many U's, which knocks RNA polymerase off and halts transcript
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Rho-dependent termination
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TRANSCRIPTION - PROK TERMINATION - requires protein Rho. Rho binds to Rut site on mRNA and causes unwinding of RNA/DNA hybrid -> RNAP dissociates
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Transcriptional fusion
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TRANSCRIPTION - When you place the promoter for gene in front of other genes
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TFIID
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TRANSCRIPTION - EUK PREINITIATION - transcriptional factor containing TATA binding protein (TBP); holds promoter in place
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TBP
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TRANSCRIPTION - EUK PREINITIATION - binds the TATA box in core promoter
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TFIIA
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TRANCRIPTION - EUK PREINITIATION - helps TBP bind the TATA box
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TFIIB
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TRANSCRIPTION - EUK PREINITIATION - binds the TFIIB recognition element (BRE) in core promoter
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TFIIE
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TFIIE TRANSCRIPTION - EUK PREINITIATION - joins the complex, recruits TFIIH
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TFIIH
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TRANSCRIPTION - EUK PREINITIATION - mediates promoter melting by ATP hydrolysis; binds downstream of promoter
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Activators
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TRANSCRIPTION - EUK PREINITIATION - bind enhancers upstream of promoter; helps recruite Pol II to promoter
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Phosphorylation of Pol II
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TRANSCRIPTION - EUK PROMOTER ESCAPE - large subunit of Pol II has carboxyl termial domain (CTD) "tail"
-when recruited to promoter, mostly unphosphorylated
-then phosphorylated by TFIIH
-the phosphorylation of the tail helps Pol II "escape" the general transcription factors
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FACT
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TRANSCRIPTION - EUK ELONGATION - SSRP1 binds H3 and H4 tetramer
-Spt16 binds and removes H2A and H2B dimer
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Formation of 5' Cap
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TRANSCRIPTION - EUK ELONGATION - a methylated guanine is added to the 5' end of RNA
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Polyadenylation of 3' tail
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TRANSCRIPTION - EUK ELONGATION - poly-A signal sequence gets transcribed, causes polyadenylation enzymes to transfer from CTD tail to RNA causes CstF and CPSF to transfer as well
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CstF
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TRANSCRIPTION - EUK ELONGATION - binds to mRNA at poly-A signal and recruits PAP
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CPSF
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TRANSCRIPTION - EUK ELONGATION - binds to mRNA at poly-A signal and recruits PAP
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PAP
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TRANSCRIPTION- EUK ELONGATION - binds to 3' end of mRNA and adds a string of A's to end
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Torpedo model
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TRANSCRIPTION - EUK TERMINATION - the RNase that degrades the smaller piece of RNA is Rat1 (5'-3') until it reaches Pol II.
-Pol II dissociates and transcript terminates
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Allosteric model
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TRANSCRIPTION - EUK TERMINATION - once poly-A signal is transcribed, processivity decreases and Pol II dissociates
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Histone Acetyltransferases (HATs)
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TRANSCRIPTIONAL REGULATION - NUCLEOSOME MODIFIERS - adds acetyl group to make more negative and LOOSEN chromatin
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Histone Deacytltransferases (HDACs)
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TRANSCRIPTIONAL REGULATION - NUCLEOSOME MODIFIERS - removes acetyl group to tighten chromatin
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Chromatin-remodeling complex
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TRANSCRIPTIONAL REGULATION - NUCLEOSOME MODIFIERS - don't change histone charge alter the structure of DNA bound to histone core
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Repressor (EUK)
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TRANSCRIPTIONAL REGULATION - EUK - DO NOT bind a site overlapping the promoter, but overlap the activator site
-recruits histone modifiers
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Polysome
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TRANSLATION - increases the amount of protein produced prior to mRNA degradation
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Ribosomal binding sites
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TRANSLATION - PROK - consensus sequence
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fMet
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TRANSLATION - PROK - initiator tRNA
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IF1
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TRANSLATION - PROK INITIATION - binds A
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IF3
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TRANSLATION - PROK INITIATION - binds E
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IF2
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TRANSLATION - PROK INITIATION - binds IF1, will contact initiator and help bind the small subunit
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eIF4E
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TRANSLATION - EUK INITIATION - binds the 5' cap, other initiation factors recruited
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A site
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A site TRANSLATION - polypeptide chain grows in A site
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P site
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TRANSLATION - initiator tRNA binds to the P site
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E site
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TRANSLATION - uncharged tRNA are ejected from the ribosome
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eIF4G
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TRANSLATION - EUK INITIATION - helps eIF4E bind 5' cap
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EF-Tu-GTP
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TRANSLATION - EUK ELONGATION - binds charged tRNA and prevents tRNA from making peptide bonds too early
-brings tRNA to A site
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EF-G
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TRANSLATION - EUK ELONGATION - promotes translocation, helps shift out of hybrid state
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Class I release factors
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TRANSLATION - TERMINATION - binds to the stop codon
**prokaryotes: different RFs recognize 3 stop codons
**eukaryotes: one RF recognizes all stop codons
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Class II release factors
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TRANSLATION - TERMINATION - cause class I to dissociate, exchanges GDP for GTP, to dissociate GTP hydrolyzes to GDP
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Ribosome Recycling
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TRANSLATION - TERMINATION - removal of tRNAs and mRNAs from ribosome
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Ribosome Recycling Factor (RRF)
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TRANSLATION - TERMINATION - inserts in A site, which contains stop codon
-bound by EF-G
-moves from A site to P site and stimulates the release of tRNAs in P and E site
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EJC
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TRANSLATION - TERMINATION - serve as "guide posts" for advancing ribosome
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EMSA
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In vitro method to detect protein-DNA interactions
-Generate radioactively labeled dsDNA containing a potential DNA-binding site (DNA probe)
-Purify the protein of interest
-Mix and do gel electrophoresis
-DNA:protein complex shifts up because it is bigger and takes more time to go th…
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DNase Footprinting Assay
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In vitro method to tell WHERE the proteins bind.
-Generate DNA probe
-Purify protein of interest
-Digest with DNase (endonuclease)
-DNA binding proteins provide protection from cleavage (DNase cannot access)
-Electrophoresis
-"Foot print" is an absence of the site of protein binding…
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ChIP
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Used to detect genome-wide protein-DNA interactions in vivo.
-Add formaldehyde to living cells to cross link proteins to DNA
-Lyse cell
-Shear DNA into small fragments
-Antibodies specific to protein of interest attached to beads in the column
-Remove proteins, left with just DNA
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Restriction endonucleases
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MOLECULAR CLONING - digest DNA at restriction sites
-Used in research labs to cut DNA into smaller pieces **creates the sticky ends
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Plasmid vector
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MOLECULAR CLONING - contains: -replication origin, which allows plasmid to replicate independently from chromosome
-Genes encoding resistance to antibiotics
-One or more where restriction endonucleases will cleave (cluster = MCS, multiple cloning site)
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Insert
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MOLECULAR CLONING - fragment of DNA to be cloned into the vector
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Cloning Process
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-Amplify the fragment of DNA using PCR
-Digest plasmid vector and insert with same endonucleases (produce compatible sticky ends)
-Once digested, introduce insert to plasmid vector and sticky ends will join and anneal
-Introduce to E. coli (transformation)
-Plasmid replicates independ…
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BIOL-L 211: DNA REPLICATION