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7-methylguanosine cap
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modification added to the 5' end of pre-mRNAs to protect mRNA from degradation and assist translation
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aminoacyl tRNA synthetase
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enzyme that “charges” tRNA molecules by catalyzing a bond between the tRNA and a corresponding amino acid
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anticodon
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three-nucleotide sequence in a tRNA molecule that corresponds to an mRNA codon
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CAAT box
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(GGCCAATCT) essential eukaryotic promoter sequence involved in binding transcription factors
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central dogma
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states that genes specify the sequence of mRNAs, which in turn specify the sequence of proteins
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codon
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three consecutive nucleotides in mRNA that specify the insertion of an amino acid or the release of a polypeptide chain during translation
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colinear
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in terms of RNA and protein, three “units” of RNA (nucleotides) specify one “unit” of protein (amino acid) in a consecutive fashion
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consensus
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DNA sequence that is used by many species to perform the same or similar functions
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core enzyme
-
prokaryotic RNA polymerase consisting of
α
,
α
,
β
, and
β
' but missing
σ
; this complex performs elongation
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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
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downstream
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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
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exon
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sequence present in protein-coding mRNA after completion of pre-mRNA splicing
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FACT
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complex that “facilitates chromatin transcription” by disassembling nucleosomes ahead of a transcribing RNA polymerase II and reassembling them after the polymerase passes by
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GC-rich box
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(GGCG) nonessential eukaryotic promoter sequence that binds cellular factors to increase the efficiency of transcription; may be present several times in a promoter
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hairpin
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structure of RNA when it folds back on itself and forms intramolecular hydrogen bonds between complementary nucleotides
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holoenzyme
-
prokaryotic RNA polymerase consisting of
α
,
α
,
β
,
β
', and
σ
; this complex is responsible for transcription initiation
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initiation site
-
nucleotide from which mRNA synthesis proceeds in the 5' to 3' direction; denoted with a “+1”
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initiator tRNA
-
in prokaryotes, called
; in eukaryotes, called tRNA
i
; 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
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intron
-
non–protein-coding intervening sequences that are spliced from mRNA during processing
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Kozak’s rules
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determines the correct initiation AUG in a eukaryotic mRNA; the following consensus sequence must appear around the AUG: 5’-GCC(
purine
)CC
AUG
G
-3’; the bolded bases are most important
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nonsense codon
-
one of the three mRNA codons that specifies termination of translation
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nontemplate strand
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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
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Octamer box
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(ATTTGCAT) nonessential eukaryotic promoter sequence that binds cellular factors to increase the efficiency of transcription; may be present several times in a promoter
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peptidyl transferase
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RNA-based enzyme that is integrated into the 50S ribosomal subunit and catalyzes the formation of peptide bonds
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plasmid
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extrachromosomal, covalently closed, circular DNA molecule that may only contain one or a few genes; common in prokaryotes
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poly-A tail
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modification added to the 3' end of pre-mRNAs to protect mRNA from degradation and assist mRNA export from the nucleus
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polysome
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mRNA molecule simultaneously being translated by many ribosomes all going in the same direction
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preinitiation complex
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cluster of transcription factors and other proteins that recruit RNA polymerase II for transcription of a DNA template
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promoter
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DNA sequence to which RNA polymerase and associated factors bind and initiate transcription
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reading frame
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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
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rho-dependent termination
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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
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rho-independent
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termination sequence-dependent termination of prokaryotic mRNA synthesis; caused by hairpin formation in the mRNA that stalls the polymerase
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RNA editing
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direct alteration of one or more nucleotides in an mRNA that has already been synthesized
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Shine-Dalgarno sequence
-
(AGGAGG); initiates prokaryotic translation by interacting with rRNA molecules comprising the 30S ribosome
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signal sequence
-
short tail of amino acids that directs a protein to a specific cellular compartment
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small nuclear RNA
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molecules synthesized by RNA polymerase III that have a variety of functions, including splicing pre-mRNAs and regulating transcription factors
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splicing
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process of removing introns and reconnecting exons in a pre-mRNA
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start codon
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AUG (or rarely, GUG) on an mRNA from which translation begins; always specifies methionine
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TATA box
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conserved promoter sequence in eukaryotes and prokaryotes that helps to establish the initiation site for transcription
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template strand
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strand of DNA that specifies the complementary mRNA molecule
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transcription bubble
-
region of locally unwound DNA that allows for transcription of mRNA
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upstream
-
nucleotides preceding the initiation site; in general, sequences toward the 5' end relative to a site on the mRNA