Biology 15

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

CAAT box

(GGCCAATCT) essential eukaryotic promoter sequence involved in binding transcription factors

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

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

start codon

AUG (or rarely, GUG) on an mRNA from which translation begins; always specifies methionine

consensus

DNA sequence that is used by many species to perform the same or similar functions

promoter

DNA sequence to which RNA polymerase and associated factors bind and initiate transcription

peptidyl transferase

RNA-based enzyme that is integrated into the 50S ribosomal subunit and catalyzes the formation of peptide bonds

initiator tRNA

in prokaryotes, called tRNAMetftRNAfMet; 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

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

colinear

in terms of RNA and protein, three "units" of RNA (nucleotides) specify one "unit" of protein (amino acid) in a consecutive fashion

polysome

mRNA molecule simultaneously being translated by many ribosomes all going in the same direction

poly-A tail

modification added to the 3' end of pre-mRNAs to protect mRNA from degradation and assist mRNA export from the nucleus

7-methylguanosine cap

modification added to the 5' end of pre-mRNAs to protect mRNA from degradation and assist translation

small nuclear RNA

molecules synthesized by RNA polymerase III that have a variety of functions, including splicing pre-mRNAs and regulating transcription factors

intron

non-protein-coding intervening sequences that are spliced from mRNA during processing

initiation site

nucleotide from which mRNA synthesis proceeds in the 5' to 3' direction; denoted with a "+1"

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

upstream

nucleotides preceding the initiation site; in general, sequences toward the 5' end relative to a site on the mRNA

nonsense codon

one of the three mRNA codons that specifies termination of translation

splicing

process of removing introns and reconnecting exons in a pre-mRNA

core enzyme

prokaryotic RNA polymerase consisting of α, α, β, and β' but missing σ; this complex performs elongation

holoenzyme

prokaryotic RNA polymerase consisting of α, α, β, β', and σ; this complex is responsible for transcription initiation

transcription bubble

region of locally unwound DNA that allows for transcription of mRNA

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

exon

sequence present in protein-coding mRNA after completion of pre-mRNA splicing

signal sequence

short tail of amino acids that directs a protein to a specific cellular compartment

central dogma

states that genes specify the sequence of mRNAs, which in turn specify the sequence of proteins

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

template strand

strand of DNA that specifies the complementary mRNA molecule

hairpin

structure of RNA when it folds back on itself and forms intramolecular hydrogen bonds between complementary nucleotides

rho-independent

termination sequence-dependent termination of prokaryotic mRNA synthesis; caused by hairpin formation in the mRNA that stalls the polymerase

Eukaryotic pre-mRNAs are modified with a 5' methylguanosine cap and a poly-A tail. These structures protect the mature mRNA from degradation and help export it from the nucleus. Pre-mRNAs also undergo splicing, in which introns are removed and exons are reconnected with single-nucleotide accuracy. Only finished mRNAs that have undergone 5' capping, 3' polyadenylation, and intron splicing are exported from the nucleus to the cytoplasm. Pre-rRNAs and pre-tRNAs may be processed by intramolecular cleavage, splicing, methylation, and chemical conversion of nucleotides. Rarely, RNA editing is also performed to insert missing bases after an mRNA has been synthesized.

Eukaryotic pre-mRNAs are modified with a 5' methylguanosine cap and a poly-A tail. These structures protect the mature mRNA from degradation and help export it from the nucleus. Pre-mRNAs also undergo splicing, in which introns are removed and exons are reconnected with single-nucleotide accuracy. Only finished mRNAs that have undergone 5' capping, 3' polyadenylation, and intron splicing are exported from the nucleus to the cytoplasm. Pre-rRNAs and pre-tRNAs may be processed by intramolecular cleavage, splicing, methylation, and chemical conversion of nucleotides. Rarely, RNA editing is also performed to insert missing bases after an mRNA has been synthesized.

In prokaryotes, mRNA synthesis is initiated at a promoter sequence on the DNA template comprising two consensus sequences that recruit RNA polymerase. The prokaryotic polymerase consists of a core enzyme of four protein subunits and a σ protein that assists only with initiation. Elongation synthesizes mRNA in the 5' to 3' direction at a rate of 40 nucleotides per second. Termination liberates the mRNA and occurs either by rho protein interaction or by the formation of an mRNA hairpin.

In prokaryotes, mRNA synthesis is initiated at a promoter sequence on the DNA template comprising two consensus sequences that recruit RNA polymerase. The prokaryotic polymerase consists of a core enzyme of four protein subunits and a σ protein that assists only with initiation. Elongation synthesizes mRNA in the 5' to 3' direction at a rate of 40 nucleotides per second. Termination liberates the mRNA and occurs either by rho protein interaction or by the formation of an mRNA hairpin.

TATA box

conserved promoter sequence in eukaryotes and prokaryotes that helps to establish the initiation site for transcription

The genetic code refers to the DNA alphabet (A, T, C, G), the RNA alphabet (A, U, C, G), and the polypeptide alphabet (20 amino acids). The central dogma describes the flow of genetic information in the cell from genes to mRNA to proteins. Genes are used to make mRNA by the process of transcription; mRNA is used to synthesize proteins by the process of translation. The genetic code is degenerate because 64 triplet codons in mRNA specify only 20 amino acids and three nonsense codons. Most amino acids have several similar codons. Almost every species on the planet uses the same genetic code.

The genetic code refers to the DNA alphabet (A, T, C, G), the RNA alphabet (A, U, C, G), and the polypeptide alphabet (20 amino acids). The central dogma describes the flow of genetic information in the cell from genes to mRNA to proteins. Genes are used to make mRNA by the process of transcription; mRNA is used to synthesize proteins by the process of translation. The genetic code is degenerate because 64 triplet codons in mRNA specify only 20 amino acids and three nonsense codons. Most amino acids have several similar codons. Almost every species on the planet uses the same genetic code.

The players in translation include the mRNA template, ribosomes, tRNAs, and various enzymatic factors. The small ribosomal subunit binds to the mRNA template either at the Shine-Dalgarno sequence (prokaryotes) or the 5' cap (eukaryotes). Translation begins at the initiating AUG on the mRNA, specifying methionine. The formation of peptide bonds occurs between sequential amino acids matched to the mRNA template by their tRNAs according to the genetic code. Charged tRNAs enter the ribosomal A site, and their amino acid bonds with the amino acid at the P site. The entire mRNA is translated in three-nucleotide "steps" of the ribosome. When a nonsense codon is encountered, a release factor binds and dissociates the components and frees the new protein. Folding of the protein occurs during and after translation.

The players in translation include the mRNA template, ribosomes, tRNAs, and various enzymatic factors. The small ribosomal subunit binds to the mRNA template either at the Shine-Dalgarno sequence (prokaryotes) or the 5' cap (eukaryotes). Translation begins at the initiating AUG on the mRNA, specifying methionine. The formation of peptide bonds occurs between sequential amino acids matched to the mRNA template by their tRNAs according to the genetic code. Charged tRNAs enter the ribosomal A site, and their amino acid bonds with the amino acid at the P site. The entire mRNA is translated in three-nucleotide "steps" of the ribosome. When a nonsense codon is encountered, a release factor binds and dissociates the components and frees the new protein. Folding of the protein occurs during and after translation.

Transcription in eukaryotes involves one of three types of polymerases, depending on the gene being transcribed. RNA polymerase II transcribes all of the protein-coding genes, whereas RNA polymerase I transcribes the tandemly duplicated rRNA genes, and RNA polymerase III transcribes various small RNAs, like the 5S rRNA, tRNA, and small nuclear RNA genes. The initiation of transcription in eukaryotes involves the binding of several transcription factors to complex promoter sequences that are usually located upstream of the gene being copied. The mRNA is synthesized in the 5' to 3' direction, and the FACT complex moves and reassembles nucleosomes as the polymerase passes by. Whereas RNA polymerases I and III terminate transcription by protein- or RNA hairpin-dependent methods, RNA polymerase II transcribes for 1,000 or more nucleotides beyond the gene template and cleaves the excess during pre-mRNA processing.

Transcription in eukaryotes involves one of three types of polymerases, depending on the gene being transcribed. RNA polymerase II transcribes all of the protein-coding genes, whereas RNA polymerase I transcribes the tandemly duplicated rRNA genes, and RNA polymerase III transcribes various small RNAs, like the 5S rRNA, tRNA, and small nuclear RNA genes. The initiation of transcription in eukaryotes involves the binding of several transcription factors to complex promoter sequences that are usually located upstream of the gene being copied. The mRNA is synthesized in the 5' to 3' direction, and the FACT complex moves and reassembles nucleosomes as the polymerase passes by. Whereas RNA polymerases I and III terminate transcription by protein- or RNA hairpin-dependent methods, RNA polymerase II transcribes for 1,000 or more nucleotides beyond the gene template and cleaves the excess during pre-mRNA 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

RNA editing

direct alteration of one or more nucleotides in an mRNA that has already been synthesized

aminoacyl tRNA synthetase

enzyme that "charges" tRNA molecules by catalyzing a bond between the tRNA and a corresponding amino acid

plasmid

extrachromosomal, covalently closed, circular DNA molecule that may only contain one or a few genes; common in prokaryotes

preinitiation complex

cluster of transcription factors and other proteins that recruit RNA polymerase II for transcription of a DNA template

FACT

complex that "facilitates chromatin transcription" by disassembling nucleosomes ahead of a transcribing RNA polymerase II and reassembling them after the polymerase passes by

codon

three consecutive nucleotides in mRNA that specify the insertion of an amino acid or the release of a polypeptide chain during translation

anticodon

three-nucleotide sequence in a tRNA molecule that corresponds to an mRNA codon