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BIOL-L 211 : EXAM 2
Purine |
Adenine, Guanine |
Pyrimadine |
Cysteine, Thymine |
Stem-loop structure |
RNA - short stretches of complementary sequences that base pair (aka hairpin - bases aren't paired) |
Internal loops |
RNA - unpaired nucleotides on either side of the stem (think introverts don't have a match) |
Bulge |
RNA - unpaired nucleotide on one side |
Junctions |
RNA - site where three or four stems branch off (jungle has tree with stems) |
rRNA |
RNA that forms the structure of ribosomes, recognizes messages, and assembles proteins |
tRNA |
RNA that activates amino acids and reads the mRNA message |
mRNA |
RNA that carries the message from DNA |
Primer |
REPLICATION - can be DNA or RNA and removed at the end of replication; DNA polymerase requires a starting point |
Holoenzyme |
REPLICATION - Links 4 enzymes (3 DNA Polymerases and 1 sliding clamp loader) |
Replisome |
REPLICATION - all the proteins acting at the replication fork |
RNase H |
TERMINATION OF REPLICATION - endonuclease that removes the RNA primer |
Promoter |
DNA sequence that indicates where to start TRANSCRIPTION (-35 & -10) |
Consensus sequence |
The average of all recognized promoter sequences |
Sigma factor |
PROKARYOTIC TRANSCRIPTION - proteins that bind to specific promoter sequences and instruct RNA polymerase where to begin transcription |
Pre-initiation Complex |
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 |
Abortive synthesis |
TRANSCRIPTION - RNA polymerase produces and release numerous short transcripts to generate energy for promoter escape |
Scrunching |
TRANSCRIPTION - ABORTIVE SYNTH - RNAP remains stationary and is bound to the promoter as it pulls DNA into itself |
Step Mechanism |
TRANSCRIPTION - ELONGATION - advances one base pair for every nucleotide that is added to the transcript
*size of transcription bubble remains constant |
Pyrophosphorolytic editing |
TRANSCRIPTION - Proofreading - removes incorrectly inserted ribonucleotides by adding beta and gamma phosphates reverse of synthesis and inserts correct ribonucleotide |
Hydrolytic editing |
TRANSCRIPTION - Proofreading - RNAP backtracks one or more nucleotides, cleaves RNA, removes sequence |
Repressor |
TRANSCRIPTIONAL REGULATION - PROK - bind to an operator sequence that blocks RNAP from binding to promoter by overlapping the promoter |
Rho-independent termination |
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 |
Rho-dependent termination |
TRANSCRIPTION - PROK TERMINATION - requires protein Rho. Rho binds to Rut site on mRNA and causes unwinding of RNA/DNA hybrid -> RNAP dissociates |
Transcriptional fusion |
TRANSCRIPTION - When you place the promoter for gene in front of other genes |
TFIID |
TRANSCRIPTION - EUK PREINITIATION - transcriptional factor containing TATA binding protein (TBP); holds promoter in place |
TBP |
TRANSCRIPTION - EUK PREINITIATION - binds the TATA box in core promoter |
TFIIA |
TRANCRIPTION - EUK PREINITIATION - helps TBP bind the TATA box |
TFIIB |
TRANSCRIPTION - EUK PREINITIATION - binds the TFIIB recognition element (BRE) in core promoter |
TFIIE |
TFIIE TRANSCRIPTION - EUK PREINITIATION - joins the complex, recruits TFIIH |
TFIIH |
TRANSCRIPTION - EUK PREINITIATION - mediates promoter melting by ATP hydrolysis; binds downstream of promoter |
Activators |
TRANSCRIPTION - EUK PREINITIATION - bind enhancers upstream of promoter; helps recruite Pol II to promoter |
Phosphorylation of Pol II |
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 |
FACT |
TRANSCRIPTION - EUK ELONGATION - SSRP1 binds H3 and H4 tetramer
-Spt16 binds and removes H2A and H2B dimer |
Formation of 5' Cap |
TRANSCRIPTION - EUK ELONGATION - a methylated guanine is added to the 5' end of RNA |
Polyadenylation of 3' tail |
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 |
CstF |
TRANSCRIPTION - EUK ELONGATION - binds to mRNA at poly-A signal and recruits PAP |
CPSF |
TRANSCRIPTION - EUK ELONGATION - binds to mRNA at poly-A signal and recruits PAP |
PAP |
TRANSCRIPTION- EUK ELONGATION - binds to 3' end of mRNA and adds a string of A's to end |
Torpedo model |
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 |
Allosteric model |
TRANSCRIPTION - EUK TERMINATION - once poly-A signal is transcribed, processivity decreases and Pol II dissociates |
Histone Acetyltransferases (HATs) |
TRANSCRIPTIONAL REGULATION - NUCLEOSOME MODIFIERS - adds acetyl group to make more negative and LOOSEN chromatin |
Histone Deacytltransferases (HDACs) |
TRANSCRIPTIONAL REGULATION - NUCLEOSOME MODIFIERS - removes acetyl group to tighten chromatin |
Chromatin-remodeling complex |
TRANSCRIPTIONAL REGULATION - NUCLEOSOME MODIFIERS - don't change histone charge alter the structure of DNA bound to histone core |
Repressor (EUK) |
TRANSCRIPTIONAL REGULATION - EUK - DO NOT bind a site overlapping the promoter, but overlap the activator site
-recruits histone modifiers |
Polysome |
TRANSLATION - increases the amount of protein produced prior to mRNA degradation |
Ribosomal binding sites |
TRANSLATION - PROK - consensus sequence |
fMet |
TRANSLATION - PROK - initiator tRNA |
IF1 |
TRANSLATION - PROK INITIATION - binds A |
IF3 |
TRANSLATION - PROK INITIATION - binds E |
IF2 |
TRANSLATION - PROK INITIATION - binds IF1, will contact initiator and help bind the small subunit |
eIF4E |
TRANSLATION - EUK INITIATION - binds the 5' cap, other initiation factors recruited |
A site |
A site TRANSLATION - polypeptide chain grows in A site |
P site |
TRANSLATION - initiator tRNA binds to the P site |
E site |
TRANSLATION - uncharged tRNA are ejected from the ribosome |
eIF4G |
TRANSLATION - EUK INITIATION - helps eIF4E bind 5' cap |
EF-Tu-GTP |
TRANSLATION - EUK ELONGATION - binds charged tRNA and prevents tRNA from making peptide bonds too early
-brings tRNA to A site |
EF-G |
TRANSLATION - EUK ELONGATION - promotes translocation, helps shift out of hybrid state |
Class I release factors |
TRANSLATION - TERMINATION - binds to the stop codon
**prokaryotes: different RFs recognize 3 stop codons
**eukaryotes: one RF recognizes all stop codons |
Class II release factors |
TRANSLATION - TERMINATION - cause class I to dissociate, exchanges GDP for GTP, to dissociate GTP hydrolyzes to GDP |
Ribosome Recycling |
TRANSLATION - TERMINATION - removal of tRNAs and mRNAs from ribosome |
Ribosome Recycling Factor (RRF) |
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 |
EJC |
TRANSLATION - TERMINATION - serve as "guide posts" for advancing ribosome |
EMSA |
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 through the gel |
DNase Footprinting Assay |
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
-Use chain-terminating gel to find sequence **3' H instead of 3' OH |
ChIP |
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 |
Restriction endonucleases |
MOLECULAR CLONING - digest DNA at restriction sites
-Used in research labs to cut DNA into smaller pieces **creates the sticky ends |
Plasmid vector |
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) |
Insert |
MOLECULAR CLONING - fragment of DNA to be cloned into the vector |
Cloning Process |
-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 independently because it has its own origin of replication
-Grow bacteria in liquid culture
-Plate bacteria with antibiotics
-Bacterial cells without the plasmid die |