3.5.7: Key Terms

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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 α, α, β, 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 α, α, β, β', 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 $t R N A_{f}^{M e t}$ ; 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

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

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