BIOL 4843 1st EditionExam # 3 Study Guide Chapters: 16 - 20Chapter 16: RNA ProcessingDescribe transcription in bacteria.- very little posttranslational processing of bacterial mRNAs- transcription and translation are coupledDescribe transcription in eukaryotes.- not coupled- mRNAs are modified in the nucleus What are three different ways mRNA is processed in eukaryotes?1. 5’ cap (capping)2. 3’ poly A tail (polyadenylation)3. splicing → exons and introns- transported to cytoplasm (translation)What is the function of the 5’ cap (m7G) of eukaryotic mRNAs?- its function is protection; acts like a “handle”- if not capped, mRNA is degraded- if capped, it is not degraded and goes to downstream processesWhat does the capping enzyme do?- associates with CTD tail- only messenger RNA is cappedWhat does the cap-binding complex do? What process is it important for?- it binds cap- important for translation (initiation)These notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.Why is the 3’ poly A tail important?- associated with CTD tail- mRNA: poly A tail- polyadenylation factors recognize the signal- binding initiates cleavageWhat does polyadenylation polymerase (PAP) do?- adds A tail without a templateWhat does poly A binding protein (PABP) do?- binds poly A tail (for protection)When does regulation of mRNA processing occur?- during synthesisWhat happens during splicing of pre-mRNA?- all happening as mRNA is synthesized- exon is the coding part that is kept- intron is the noncoding part that is tossed- single-stranded- splicing is ordered breaking and joining of specific regions of this messageDescribe alternative splicing.- remember one gene is > 1 polypeptide- 2 different transcripts from a single gene- cis-splicing: all exons are from the same mRNA- alternative poly A sites- splicing and different poly A sites- calcitonin and CGRP: different hormones/effect- posttranslational hormonesWhat are spliceosomes?- RNA + protein- catalyze most mRNA splicing in eukaryotes- 5 snRNPs- comprised of 1 snRNA (functional RNA) + smproteins (core) + other proteins specific to each snRNPName some important regions of the pre-MRNA.- pre-mRNA is mRNA before splicing- 2’ OH attacks 5’ splice site- 2 site-specific phosphodiester bond cleavage reactions + ligation- snRNA recognize splice siteWhat happens during the splicing process?- sequential use of snRNPs- snRNAs recognize splice sites- snRNPs catalyze splicing, phosphodiester bond cleavage, and ligation- remove intron lariatWhat are self-splicing introns?- don’t require proteins for splicing RNA, acting as an enzyme- group 1 and 2 (chemistry is like spliceosome 2’ OH)- some bacteria and bacterial viruses have self-splicing intronsGive an example of group 1 self-splicing introns.- exogenous guanosine- 3’ OH attack- cut on either side of the intron (specific) (RNA)- ligation- linear intron release + fused exonsDescribe group 2 self-splicing introns.- 2’ OH + 5’ splice site- chemistry is similar to spliceosomes but is RNA-catalyzing- fused exons and introns (lariat)What happens during trans-splicing?- leads to 2 different messages- first described in nematodes (eukaryotes)- much more rare than cis-splicingWhat is RNA editing?- chemical modification of RNA post-transcriptionally- can create mRNAs not encoded in the DNAName and describe 3 types of RNA editing.1. insertions2. deletionsa. guide RNA + editosome protein complex uses guide RNA to insert and/or delete nucleotidesb. modified mRNA so it no longer reflects what is encoded to the DNA3. substitutionsa. deamination of Ab. converts A to I → can base pair with C, U, and AWhat is the role of Ca+2 channels?- in bacteria and eukaryotes- C → U- form of LDL (cholesterol)- get a truncated form of protein, involved in fat absorptionHow is RNA transported out of and into the nucleus?- karyopherins: exportins, importins- GTP + RNA + protein + nuclear poreHow is mRNA transport coupled with splicing?- after splicing, exon junction complex is placed on the message- exon-exon splices- EJC ensures that message associates with exportins- EJC is removed in the cytoplasmLocalization of mRNAs in the cytoplasm.- certain cells’ (oocytes) mRNAs are localized to certain regions prior to translation- production of protein is in the correct spotHow is mRNA degraded?- this is typically short lived1. cell removes 5’ cap and tail2. then you have exosome → complex of ribonucleasesDescribe bacterial mRNA.- do not have cap and tail- have ribonucleases that are endo and exoHow is the amount of a particular transcript is governed?- by amount made and amount degraded; rates of synthesis and degradationHow is tRNA processed?- similar in eukaryotes and bacteria- end trimming 5’ (RNaseP) and 3’ (RNaseD)- splicing (sometimes occurs in eukaryotes)- CCA 3’ end, amino acids will be attached- sometimes chemical modificationHow is rRNA processed?- bacteria and eukaryotes- transcribed together, pre-RNA- nuclease separate and trim- snoRNPs: RNA and proteinHow are other RNAs processed?- these include small regulatory RNAs, such as miRNAs- large transcript interacts with proteins- involved in gene expressionWhat are ribozymes?- RNA enzyme- example: RNaseP (tRNA processing, ribosome)________________________________________________________________Chapter 17: The Genetic CodeWhat is the genetic code?- a set of rules about how genetic information is translated to amino acids (proteins)- the table of amino acids is nearly universal- codons 5’ → 3’- used mathematics to figure out that 3 nucleotides make up 1 amino acidWhat is the adaptor hypothesis?- Crick came up with this in 1955- adaptor recognizes the codons in mRNA and carries the corresponding amino acid- adaptors “line up” on mRNA aligning the amino acidWhat is the structure of tRNAs?- similar structure of “arms”- amino acid arm and anticodon arm are most important- aminoacyl tRNA synthetases- CCA-3’ amino acid- amino acid + tRNA = aminoacylated tRNA or charged tRNAHow do codons and anticodons pair with each other?- 5’ → 3’ - 1, 2, 3 and 3, 2, 1- anticodon 3 pairs with codon 1Describe the genetic code. Why is is called degenerate?- single amino acid is encoded with more than 1 codon- 20 common amino acids- 61 codons for amino acids- most cells have less than 61 tRNAs- 3 codons for stops- tRNAs can recognize more than 1 codon- How?