Chapter 15: Genes and Proteins

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⁢𝐴𝑀⁢𝑒⁢𝑡𝑓 ; 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