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7-methylguanosine cap
modification added to the 5' end of pre-mRNAs to protect mRNA from degradation and assist translation
aminoacyl tRNA synthetase
enzyme that “charges” tRNA molecules by catalyzing a bond between the tRNA and a corresponding amino acid
anticodon
three-nucleotide sequence in a tRNA molecule that corresponds to an mRNA codon
CAAT box
(GGCCAATCT) essential eukaryotic promoter sequence involved in binding transcription factors
Central Dogma
states that genes specify the sequence of mRNAs, which in turn specify the sequence of proteins
codon
three consecutive nucleotides in mRNA that specify the insertion of an amino acid or the release of a polypeptide chain during translation
colinear
in terms of RNA and protein, three “units” of RNA (nucleotides) specify one “unit” of protein (amino acid) in a consecutive fashion
consensus
DNA sequence that is used by many species to perform the same or similar functions
core enzyme
prokaryotic RNA polymerase consisting of ααβ, and β' but missing σ; this complex performs elongation
degeneracy
(of the genetic code) describes that a given amino acid can be encoded by more than one nucleotide triplet; the code is degenerate, but not ambiguous
downstream
nucleotides following the initiation site in the direction of mRNA transcription; in general, sequences that are toward the 3' end relative to a site on the mRNA
exon
sequence present in protein-coding mRNA after completion of pre-mRNA splicing
FACT
complex that “facilitates chromatin transcription” by disassembling nucleosomes ahead of a transcribing RNA polymerase II and reassembling them after the polymerase passes by
GC-rich box
(GGCG) nonessential eukaryotic promoter sequence that binds cellular factors to increase the efficiency of transcription; may be present several times in a promoter
hairpin
structure of RNA when it folds back on itself and forms intramolecular hydrogen bonds between complementary nucleotides
holoenzyme
prokaryotic RNA polymerase consisting of ααββ', and σ; this complex is responsible for transcription initiation
initiation site
nucleotide from which mRNA synthesis proceeds in the 5' to 3' direction; denoted with a “+1”
initiator tRNA
in prokaryotes, called tRNAfMet; in eukaryotes, called tRNAi; a tRNA that interacts with a start codon, binds directly to the ribosome P site, and links to a special methionine to begin a polypeptide chain
intron
non–protein-coding intervening sequences that are spliced from mRNA during processing
Kozak’s rules
determines the correct initiation AUG in a eukaryotic mRNA; the following consensus sequence must appear around the AUG: 5’-GCC(purine)CCAUGG-3’; the bolded bases are most important
nonsense codon
one of the three mRNA codons that specifies termination of translation
nontemplate strand
strand of DNA that is not used to transcribe mRNA; this strand is identical to the mRNA except that T nucleotides in the DNA are replaced by U nucleotides in the mRNA
Octamer box
(ATTTGCAT) nonessential eukaryotic promoter sequence that binds cellular factors to increase the efficiency of transcription; may be present several times in a promoter
peptidyl transferase
RNA-based enzyme that is integrated into the 50S ribosomal subunit and catalyzes the formation of peptide bonds
plasmid
extrachromosomal, covalently closed, circular DNA molecule that may only contain one or a few genes; common in prokaryotes
poly-A tail
modification added to the 3' end of pre-mRNAs to protect mRNA from degradation and assist mRNA export from the nucleus
polysome
mRNA molecule simultaneously being translated by many ribosomes all going in the same direction
preinitiation complex
cluster of transcription factors and other proteins that recruit RNA polymerase II for transcription of a DNA template
promoter
DNA sequence to which RNA polymerase and associated factors bind and initiate transcription
reading frame
sequence of triplet codons in mRNA that specify a particular protein; a ribosome shift of one or two nucleotides in either direction completely abolishes synthesis of that protein
Rho-dependent termination
in prokaryotes, termination of transcription by an interaction between RNA polymerase and the rho protein at a run of G nucleotides on the DNA template
Rho-independent
termination sequence-dependent termination of prokaryotic mRNA synthesis; caused by hairpin formation in the mRNA that stalls the polymerase
RNA editing
direct alteration of one or more nucleotides in an mRNA that has already been synthesized
Shine-Dalgarno sequence
(AGGAGG); initiates prokaryotic translation by interacting with rRNA molecules comprising the 30S ribosome
signal sequence
short tail of amino acids that directs a protein to a specific cellular compartment
small nuclear RNA
molecules synthesized by RNA polymerase III that have a variety of functions, including splicing pre-mRNAs and regulating transcription factors
splicing
process of removing introns and reconnecting exons in a pre-mRNA
start codon
AUG (or rarely, GUG) on an mRNA from which translation begins; always specifies methionine
TATA box
conserved promoter sequence in eukaryotes and prokaryotes that helps to establish the initiation site for transcription
template strand
strand of DNA that specifies the complementary mRNA molecule
transcription bubble
region of locally unwound DNA that allows for transcription of mRNA
upstream
nucleotides preceding the initiation site; in general, sequences toward the 5' end relative to a site on the mRNA