Term
| DNA polymerase functions in which part of the central dogma |
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Definition
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Term
| RNA polymerase functions in which part of the central dogma |
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Definition
| transcription of DNA into RNA |
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Term
| ribosomes function in which part of the central dogma |
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Definition
| translation of RNA to polypeptide chain |
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Term
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Definition
| (replication) DNA to RNA via transcription, RNA to protein via translation |
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Term
| General function of DNA polymerase |
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Definition
| replication of DNA: DNA as template to make complementary DNA strand |
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Term
| New strands are always synthesized in what direction |
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Definition
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Term
| Primer for DNA polymerase binds to |
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Definition
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Term
| primer provides a ___ acted on by____ |
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Definition
3' hydroxyl for extension
DNA polymerase |
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Term
| What do proofreading nucleases do |
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Definition
| remove incorrect bases from the growing 3' end |
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Term
| for eukaryotes, DNA is packaged into |
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Definition
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Term
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Definition
| segments of DNA that code for primary sequence of a gene product |
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Term
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Definition
polypeptides
RNA with strucural or catalytic function |
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Term
| eukaryotic genes often have |
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Definition
| intervening sequences of DNA that are not translated |
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Term
| coding regions are called |
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Definition
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Term
non translated regions
(make up majority of DNA) |
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Definition
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Term
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Definition
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Term
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Definition
| messenger RNA - encodes for an aa sequence |
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Term
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Definition
| carries specific aa during protein synthesis |
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Term
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Definition
ribosomal RNA
makes up the large portion of ribsomes |
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Term
| how many subunits are in prokaryotic RNA polymerase |
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Definition
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Term
| how many subunits are there in eukaryotic RNA polymerase |
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Definition
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Term
| what are the 3 required materials for RNA polymerase to function properly |
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Definition
1. template DNA
2. activated precursors (rNTPs)
3. divalent cation cofactor - because eukaryotes use Mg2+ or Mn2+ |
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Term
|
Definition
| divalent cofactor for RNA polymerase |
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Term
| nontemplate strand is synonymous with |
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Definition
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Term
| template strand goes through RNA polymerase in the _____ direction |
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Definition
5'-3'
oriented 3'-5' to new RNA |
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Term
| the coding/non template strand goes through RNA polymerase in the ___ direction |
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Definition
3'-5'
(complementary to template strand) |
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Term
| in transcription, new RNA is synthesized in the ____ direction |
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Definition
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Term
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Definition
| ribo nucleotides enter here to be incorporated into growing RNA |
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Term
| negatively charged amino acid residues (Asp) |
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Definition
| in RNA polymerase active site because they stabilize the metal ion (+0 |
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Term
| incoming NTP is attacked at the ___ by the ____ of the growing RNA chain |
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Definition
alpha phosphate (closest to sugar)
3' hydroxyl
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Term
| what are the 3 phases of RNA synthesis |
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Definition
| initiation elongation and termination |
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Term
| Initiation of RNA synthesis |
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Definition
| transcritpion begins when RNA polymerase binds to the promoter regions of DNA template |
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Term
| responsible for binding - subunit of RNA polymerase in prokaryotes |
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Definition
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Term
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Definition
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Term
| WHEN RNA SYNTH BEGINS, WHAT HAPPENS TO THE PROMOTERo |
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Definition
| it is cleared as the sigma subunit dissociates |
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Term
| define prokaryotic promoter |
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Definition
| two consensus regions upstream (5') side of the transcription start site |
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Term
| what are the two prokaryotic promoters |
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Definition
| the -35 region and the -10 region |
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Term
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Definition
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Term
| eukaryotic polymerase II promoters |
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Definition
| TATA box between positions -100 and -30 relative to transcription start site |
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Term
| upstream of TATA box (eukaryote transcritpion) |
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Definition
| additional promoter regions |
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Term
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Definition
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Term
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Definition
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Term
| Initiation in eukaryotes is more complex than in prokaryotes in that it involves |
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Definition
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Term
|
Definition
| form a transcription complex and recruit RNA polymerase to promoter |
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Term
| transcription initiation complex |
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Definition
| cluster of transcription facots that recruits RNA polymerase to the promoter |
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Term
| examples of transcription factors (members of the transcription initiation complex) |
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Definition
TBP (TATA Binding Protein)
helicase
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Term
| where does Elongation occur |
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Definition
| takes place at a transcription bubble that moves along DNA template |
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Term
| termination in prokaryotes |
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Definition
nascent RNA chain has stop signals that end transcription
RNA hairpin followed by several urcacil residues
^that sequence is recognized by rho protein ATPase |
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Term
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Definition
| terminates prokaryote transcription |
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Term
| eukaryotic termination of trancription |
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Definition
| occurs by unknow mechanism |
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Term
| 2 main ways to regular transcription |
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Definition
1. regulation of polymerase binding and initiation (MOST COMMON)
2. Proteins bind to sites on DNA prior to or near the promoter region |
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Term
| how do you facilitate transcription? |
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Definition
| facilitate binding of RNA polymerase to or near the promoter region |
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Term
| how to inhibit transcription (1 way) |
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Definition
| use a repressor to blcok the sy thesis by reducing affinity for RNA polymerase, or block the promoter regions |
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Term
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Definition
| can regulate transcription in eukaryotes |
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Term
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Definition
| the four letter language of nucleotides (mRNA, tRNA) is translated into the 20 aa language of polypeptides |
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Term
| mRNA is read by ribosomes in the ___ direction |
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Definition
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Term
| where are proteins made/where are ribosomes |
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Definition
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Term
|
Definition
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Term
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Definition
| every 3 NTPs code for an aa |
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Term
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Definition
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Term
| group of proteins that make sure tRNA's are associated witht the CORRECT amino acid |
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Definition
| aminoacyl-tRNA synthetases |
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Term
| read codons in the _____ direction |
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Definition
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Term
| 2 features of the structure of tRNA |
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Definition
1. acceptor stem
2. template recognition site |
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Term
|
Definition
| amino acid attachment side, the 3' end of the tRNA, ends in an A |
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Term
| template recognition site (tRNA) |
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Definition
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Term
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Definition
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Term
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Definition
present in some anticodons on tRNA
capable of forming H-bonds with U, C, and A |
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Term
| inosinate allows tRNAs to |
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Definition
| recognize multiple codons! |
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Term
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Definition
| third base of codons pairs loosely with anticodon |
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Term
| consequence of inosinate's ability to bind with C, U, or A |
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Definition
there are multiple mRNA sequences which correspond to the same aa
same anticodon can go with different codons |
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Term
| aminoacyl-tRNA synthetase |
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Definition
enzyme family that reads genetic code
puts current anticodon with correct aa |
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Term
| what activates the aa to be bound to tRNA |
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Definition
| aminoacyl-tRNA synthetase |
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Term
| how many aminoacyl-tRNA synthetases are there |
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Definition
| at least 20 - at least 1 per amino acid |
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Term
| what are the 2 steps for activating an amino acid (2 steps of aminoacyl tRNA synthetase catalysis) |
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Definition
1. amino acid adenylation
2. formation of aminoacyl-tRNA |
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Term
|
Definition
first step of aminoacyl tRNA synthesis, rxn produces aminoacyl adenylate
an endergonic reaction |
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Term
| how is amino acid adenylation fueled |
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Definition
| ATP - creates activated intermediate |
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Term
| what is the activated intermediat in amino acid adenylation |
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Definition
aminoacyl-AMP
reflecting investment of ATP |
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Term
| formation of aminoacyl-tRNA |
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Definition
aminoacyl-AMP + tRNA reversibly yields aminoacyl-tRNA + AMP
requires input of Energy |
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Term
| standard Gibbs free energy change for amino acid attachment to tRNA |
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Definition
| close to 0 - not spontaneous - requires input of energy |
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Term
| amino acid + ATP reversibly yields |
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Definition
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Term
| aminoacyl-AMP + tRNA reversibly yields |
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Definition
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Term
|
Definition
2Pi
highly exergonic! the driving force behind formation of aminoacyl-tRNA by aminoacyl-tRNA synthetase |
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Term
| overall equation for activating tRNA |
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Definition
| AA+ATP+tRNA --> aminoacyl-tRNA + 2Pi +AMP |
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Term
| the 2 prokaryotic ribosome subunits |
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Definition
|
|
Term
| the 2 eukaryotic ribosome subunits |
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Definition
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Term
| mRNA is translated in ____ direction |
|
Definition
|
|
Term
| proteins are synthesized in the |
|
Definition
| amino to carboxy terminal |
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Term
| three stages of translation |
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Definition
initiation
elongation
termination |
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Term
| in prokaryotes, initiation involves |
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Definition
Shine-Dalgarno sequence
Start codon
initiator tRNA
large 50S subunit joins complex |
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Term
|
Definition
purine (A and G) rich initiator region interacts with 16S rRNA on 30S subunit
connects mRNA bases to small 30S subunit |
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Term
|
Definition
the Inr on mRNA
AUG or GUG or UUG |
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Term
|
Definition
tRNAf
brings N-formylmethionine and base pairs to start codon
SPECIAL |
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Term
| tRNA binding sites on ribosome in prokaryote |
|
Definition
A
P
(on small subunit 30S)
E (on large subunit 50S) |
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Term
|
Definition
a condensation reaction
elimination of H2O |
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Term
|
Definition
next tRNA binds to A site
nucleophilic attack from A to P sites' aminoacyl tRNA's (peptide bond forms)
transpeptidation
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Term
| at the end of elongation round |
|
Definition
deacylated tRNA is displaced to E site and ejected while tRNA carrying growing amino acid chain is transfered to P sire
A site left vacant for incoming tRNA |
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|
Term
termination of translation involves
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|
Definition
stop codon on mRNA
release factors
ribosome dissociation |
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Term
|
Definition
|
|
Term
|
Definition
proteins that recognize stop codons
promots release of completed protein from last tRNA |
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Term
|
Definition
| describes ribosome dissociation at the end of translation |
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Term
|
Definition
| begins before synthesis is completed |
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Term
| energetic cost of protein synthesis |
|
Definition
2 ATP to charge tRNA
1 GTP to make each tRNA anticodon pairing
1 GTP needed in each translocation step
1 GTP in ribosome dissociation |
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|
Term
| the first amino acid in eukaryotic translation |
|
Definition
|
|
Term
| proteins destined to remain in the cytoplasm, nucleus, mitochondria, or chloroplast |
|
Definition
| synthesized in free ribosomes |
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|
Term
| proteins destined to have some contact with the outside world |
|
Definition
| synthesized on rough ER ribosomes |
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