BIOL-L 211: RNA PROCESSING
33 Cards in this Set
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Messenger RNA (mRNA)
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synthesized from a gene segment of DNA; contains info on primary sequence of aas in a protein to be synthesized; carries code into the cytoplasm where protein synthesis occurs
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Ribosomal RNA (rRNA)
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combines with protein to form a nucleoprotein called a ribosome; serves as the site and carries the enzymes necessary for protein synthesis
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Transfer RNA (tRNA)
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contains about 75 nucleotides, 3 of which are anticodons and one aa; reads the code and carries the aa to be incorporated into the developing protein
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Heteronuclear RNA (hnRNA)
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immediate copy (following transcription) of the coding regions of DNA; very short-lived and quickly processed into mRNA
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small nuclear RNA (snRNA)
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found within the nucleus of eukaryotic cells; involved in RNA splicing, regulating transcription factors, and maintaining telomeres; always associated with specific proteins and complexes that are referred to as small nuclear ribonucleoproteins (snRNPs); rich in uridine
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Catalytic RNA
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perform a variety of functions in the cytoplasm; ribozymes; siRNA/RNAI
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Precursor RNAs (pre-mRNAs)
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need to be modified by RNA processing to make the mature, functional RNA
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3 main benefits of RNA processing
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contribution to regulation of gene activity; diversity- many different RNAs can be produced from 1 gene; quality control-defective mRNAs are detected and degraded
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Ribonucleases
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cleave RNAs into smaller parts
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Exonucleases
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Remove nucleotides from the end of a transcript, most often in the 3'-5' direction
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Endonucleases
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cleave DNA within the strand; some are specific for dsRNA others for ssRNA
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Modification of 5' ends
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Capped with 7-methylguanine nucleotide via a 5'-5' triphosphate linkage; 5' cap then methylated at N7
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Purpose of 5' cap
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needed for efficient elongation and termination of the transcript, for mRNA processing and export from the nucleus, and for directing translation
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Modification of 3' end
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polyadenosine or poly(A) tail of about 200 adenosines; mRNAs have polyadenylation sites where pre-mRNAs are cleaved and poly(A) tail added
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Polyadenylation at 3' end
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initial cleavage then addition of 200 adenosines by poly(A) polymerase
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Purpose of polyadenylation
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needed for efficient transcription termination
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C-terminal domain (CTD) of RNA pol II
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becomes partially phosphorylated on transcription initiation; recruits capping enzyme; elongation further phosphorylates CTD which recruits splicing machinery; leads to recruitment of cleavage and polyadenylation complex
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Sites of transcription, processing, and translation
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Transcription and processing in the nucleus, translation in the cytoplasm
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Exon shuffling
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exons are exchanged and reordered via recombination, allowing evolution of different genes
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Differential removal of introns
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gives different transcripts from the same gene
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Process of joining exons
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Intron is detached from exon 1, exon 1 reacts with exon 2
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Transesterification reaction
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single phosphodiester bond is broken and replaced by another with similar energy; does not require ATP and is easily reversible
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Spliceosome
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removes introns that aren't self-splicing; made of several small nuclear ribonucleoproteins (snRNPs); catalyzes splicing similar to Group II introns
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Group I introns
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found in bacteria, viruses, microeukaryotes, and plants; most are self-splicing
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Group II introns
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in bacteria and in genes in the organelles of plants and fungi; 400-1000 nucleotides long
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Splice sites
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Recognized by spliceosome; defined by short sequence motifs- 5' and 3' splice sites and a branch-point nucleotide within the intron and polypyrimidine region before the 3' splice site
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Degradation of normal RNAs
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Removes RNAs no longer needed
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RNA half-life
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time in which the amount of RNA is reduced by half
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Factors that affect RNA stability
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5' cap protects mRNAs against exonuclease digestion; 5' triphosphate makes bacterial RNAs more stable; 3' stem loop protect bacteria against 3'-5' exonuclease activity; 3' pol(A) tail decreases stability in bacteria and increases stability in eukaryotes
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Bacterial mRNA degradation
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Initiated by endonuclease, usually RNase E; stem loop structures inhibit; 3' poly(A) tracts help
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Degradation of eukaryotic mRNA
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3'poly(A) tails hinder degradation; deadenylase shortens tail; decapping enzymes remove 5' cap; 5'-3' exonucleases degrade RNA or exosome catalyzes exonuclease activity in the 3'-5' direction
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Degredation of foreign or defective RNA
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dsRNA is cleaved into small fragments by Dicer; ds fragments are loaded onto RNA-induced silencing complex (RISC) and 1 strand is released; remaining guide strand directs RISC to complementary full-length RNAs cleaved by Argonaute protein with RISC
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RNA recognition motif
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alpha helices and 4 beta sheets
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BIOL-L 211: DNA REPLICATION