Chapter 14 RNA Molecules and RNA Processing

alternative processing pathways

One of several pathways by which a single pre-mRNA can be processed in different ways to produce alternative types of mRNA.

RNA editing

Alters nucleotide sequence of mRNA; Process in which the protein-coding sequence of an mRNA is altered after transcription. The amino acids specified by the altered mRNA are different from those predicted from the nucleotide sequence of the gene encoding the protein.

3' splice site

The 3′ end of an intron where cleavage takes place in RNA splicing.

5' splice site

The 5′ end of an intron where cleavage takes place in RNA splicing.

transfer RNA (tRNA)

serves as a link between the genetic code in mRNA and the amino acids that make up a protein. Each tRNA attaches to a particular amino acid and carries it to the ribosome, where the tRNA adds its amino acid to the growing polypeptide chain at the position specified by the genetic instructions in the mRNA.

tRNA processing

processing may include cleavage, splicing, base addition, and base modification; processing differs between eukaryotes and prokaryotes but occurs in both

ribosome

protein + rRNA consists of two subunits, a large ribosomal subunit and a small ribosomal subunit, each of which consists of one or more pieces of RNA and a number of proteins. Measured in Svedberg Units (S)--Not additive

splicing

(1) the 5′ end of the intron is cleaved and attached to the branch point to form a lariat and (2) the 3′ end of the intron is cleaved and the ends of the two exons are spliced together.

snRNPs =

1 snRNA + proteins

the structure of mRNA

5' UTR, Protein Coding Region, 3' UTR The 5′ and 3′ untranslated regions do not encode any amino acids of a protein, but contain information that is important in translation, RNA stability, and regulation of gene expression.

colinear

Concept that there is a direct correspondence between the nucleotide sequence of a gene and the continuous sequence of amino acids in a protein.

exon

Coding region of a split gene (a gene that is interrupted by introns). After processing, the exons remain in messenger RNA.

Shine-Dalgarno Sequence

Consensus sequence found in the bacterial 5′ untranslated region of mRNA; contains the ribosome-binding site. it is found approximately seven nucleotides upstream of the first codon translated into an amino acid (called the start codon). During translation, the Shine-Dalgarno sequence is complementary to and pairs with sequences found in one of the RNA molecules that make up the ribosome. Eukaryotic mRNA has no equivalent consensus sequence in its 5′ untranslated region.

Addition of the 5' cap

Facilitates binding of ribosome to 5′ end of mRNA, increases mRNA stability, enhances RNA splicing. The initial step is carried out by an enzyme that associates with RNA polymerase II.

3′ cleavage and addition of poly(A) tail

Increases stability of mRNA, facilitates binding of ribosome to mRNA; pre-mRNA is cleaved, at a position 11-30 nucleotides downstream of the consensus sequence, in the 3' UTR; the addition of adenine nucleotides (polyadenylaion) takes place at the 3' end of the pre-mRNA, generating the poly-A tail.

intron

Intervening sequence in a split gene; removed from the RNA after transcription.

spliceosome

Large complex consisting of several RNAs and many proteins that splices protein-encoding pre-mRNA; contains five small ribonucleoprotein particles (U1, U2, U4, U5, and U6). Composed of five snRNPs (U1, U2, U4, U5, and U6), and some proteins not associated with an snRNA.

lariet

Looplike structure created in the splicing of nuclear pre-mRNA in which the 5′ end of an intron is attached to a branch point in pre-mRNA.

5' cap

Modified 5′ end of eukaryotic mRNA, consisting of an extra nucleotide (methylated) and methylation of the 2′ position of the ribose sugar in one or more subsequent nucleotides; plays a role in the binding of the ribosome to mRNA and affects mRNA stability and the removal of introns.

alternative splicing

Process by which a single pre-mRNA can be spliced in more than one way to produce different types of mRNA.

RNA Splicing

Process by which introns are removed and exons are joined together. Removes noncoding introns from pre-mRNA, facilitates export of mRNA to cytoplasm, allows for multiple proteins to be produced through alternative splicing

RNA interference (RNAi)

Process in which cleavage of double-stranded RNA produces small interfering RNAs (siRNAs) that bind to mRNAs containing complementary sequences and bring about their cleavage and degradation. Uses dicer to cut double stranded RNA to produce micoRNA and siRNA (small interfereing RNAs) Purpose? defense mechanism against viruses regulation of gene expression

guide RNA

RNA molecule that serves as a template for an alteration made in mRNA during RNA editing. After the mRNA is anchored to the gRNA, the mRNA undergoes cleavage and nucleotides are added, deleted, or altered according to the template provided by gRNA.

modified base

Rare base found in some RNA molecules. Such bases are modified forms of the standard bases (adenine, guanine, cytosine, and uracil). Created by tRNA modifying bases

multiple 3' cleavage sites

Refers to the presence of more than one 3′ cleavage site on a single pre-mRNA, which allows cleavage and polyadenylation to take place at different sites, producing mRNAs of different lengths.

cloverleaf structure

Secondary structure common to all tRNAs. anticodon lies at base of structure on the anticodon arm

3' Untranslated Regin (3' UTR)

Sequence of nucleotides at the 3′ end of mRNA; does not encode the amino acids of a protein but affects both the stability of the mRNA and its translation.

5' Untranslated Region (5' UTR)

Sequence of nucleotides at the 5′ end of mRNA; does not encode the amino acids of a protein.

codon

Sequence of three nucleotides that encodes one amino acid in a protein.

poly-A Tail

String of adenine nucleotides added to the 3′ end of a eukaryotic mRNA after transcription. stability; The poly(A) tail also facilitates attachment of the ribosome to the mRNA and plays a role in export of the mRNA into the cytoplasm.

protein-coding region

The part of mRNA consisting of the nucleotides that specify the amino acid sequence of a protein.

trans-splicing

The process of splicing together exons from two or more pre-mRNAs. exons from different pre-mRNAs spliced together

in eukaryotic cells

Transcription takes place in the nucleus, whereas translation takes place in the cytoplasm; this separation provides an opportunity for eukaryotic RNA to be modified before it is translated. Indeed, eukaryotic mRNA is extensively altered after transcription. Changes are made to the 5′ end, the 3′ end, and the protein-coding section of the RNA molecule

What evidence indicated that eukaryotic genes are not colinear with their proteins?

When a continuous sequence of nucleotides in DNA encodes a continuous sequence of amino acids in a protein, the two are said to be colinear. In eukaryotes, not all genes are colinear with the proteins that they encode.

calcitonin

alternative splicing AND multiple 3' cleavage sites In thyroid cells, cleavage and polyadenylation take place at the end of exon 4, producing an mRNA that contains exons 1, 2, 3, and 4. Translation produces the hormone calcitonin. In brain cells, 3' cleavage takes place at the end of exon 6. During splicing, exon 4 is elminiated with the five introns, producing an mRNA that contains 1, 2, 3, 5, and 6. Translation yields calcitonin-gene-related peptide (CGRP).

microRNAs

cleaved from single-stranded RNA precursor; transcription through an inverted repeat in the DNA produces a primary miRNA (pri-miRNA). The pri-miRNA is cleaved to produce a short RNA with a hairpin. Dicer removes the terminal loop of the hairpin. One strand of miRNA combines with proteins to form an RNA-inducing silencing complex (RISC) which pairs with an mRNA and inhibits translation Degradation of mRNA, inhibition of transcription, chromatin modification

siRNAs (small interfering)

double stranded RNA may arise from RNA viruses or long hairpins. Double stranded RNA is cleaved by Dicer to produce siRNAs. An siRNA combines with proteins to form RISC which pairs with and cleaves mRNA, leading to degradation. Degradation of mRNA, inhibition of translation, chromatin modification

mRNA

functions as the template for protein synthesis; it carries genetic information from DNA to a ribosome and helps to assemble amino acids in their correct order. In bacteria, mRNA is transcribed directly from DNA but, in eukaryotes, a pre-mRNA (also called the primary transcript) is first transcribed from DNA and then processed to yield the mature mRNA.

rRNA processing

methylation and cleavage In Eukaryotes, methylation aided by snoRNA (Small nucleolar RNAs) help to cleave and modify eukaryotic rRNAs and assemble the processed rRNAs into mature ribosomes.

polyadenylation

the addition of 50-250 adenine nucleotides to the 3' end; (after transcription) not encoded;

In bacterial cells

transcription and translation take place simultaneously; while the 3′ end of an mRNA is undergoing transcription, ribosomes attach to the Shine-Dalgarno sequence near the 5′ end and begin translation. Because transcription and translation are coupled, bacterial mRNA has little opportunity to be modified before protein synthesis.