Transcription and the Central Dogma

1. Transcription and the Central Dogma • 1961: DNA is the molecule which stores genetic information, but • DNA is in nucleus, ribosomes (where protein synthesis takes place) are in the cytoplasm. • RNA, a different nucleic acid, is synthesized in the nucleus, and is similar to DNA. • RNA migrates to cytoplasm (where ribosomes are) • Amount of RNA generally proportional to amount of proteins in the cell. • All this suggests role of RNA as messenger.

2. About RNA 1) DNA is double stranded, but RNA is single stranded. However, RNA can base-pair with itself to create double stranded regions. RNA DNA tRNA genetics.gsk.com/graphics/ dna-big.gifhttp://www.fhi-berlin.mpg.de/th/JG/RNA.jpg http://www.santafe.edu/images/rna.gif

3. About RNA-2 2) RNA contains ribose instead of deoxyribose 3) RNA contains uracil instead of thymine. www.layevangelism.com/.../ deoxyribose.htmhttp://www.rothamsted.bbsrc.ac.uk/notebook/courses/guide/images/uracil.gif

4. RNA is similar to DNA • Has sugar-phosphate backbone w/ nitrogenous bases • Has a 5’ to 3’ directionality • When base pairing with itself or other nucleic acids, is antiparallel

5. 3 kinds of RNA mRNA: a copy of the gene; is translated to make protein. tRNA: smallest RNA, does actual decoding. rRNA: 3 sizes that, along with proteins, make up a ribosome. tRNA rRNA http://www.cu.lu/labext/rcms/cppe/traducti/tjpeg/trna.jpeg; Tobin and Duschek, Asking About Life; http://www.tokyo-ed.ac.jp/genet/mutation/nort.gif

6. More kinds of RNA • snRNAs (small nuclear) • Small RNAs (100-200 bases) that attach to proteins to form snRNPs (small nuclear ribonucleoproteins) • snRNPs are components of the spliceosome • Splicesome removes introns from pre-mRNA • snoRNAs • Small nucleolar RNAs, process rRNA • Modify other RNAs; guide RNA of telomerase • Other RNAs, e.g. Xist

7. All RNA comes from the DNA • mRNA, obviously • tRNA, rRNA • Telomerase guide RNA • Xist • antisense-RNA • Thus, we talk about RNA genes, sections of DNA that code for RNAs

8. Using genetic information:the “central dogma” Proteins are needed for cell structures, signaling, and as enzymes to carry out metabolism and regulation of processes. The information in encoded in the DNA; to use it requires transcription followed by translation.

9. Transcription: making mRNA • RNA a polymer assembled from monomers • Ribonucleoside triphosphates: ATP, UTP, GTP,CTP • RNA polymerase • Multi-component enzyme • Needs a template, but NOT a primer • In bacteria, a component (sigma) recognizes the promoter as the place on DNA to start synthesis • Synthesis proceeds 5’ to 3’, just as in DNA • mRNA is complementary and antiparallel to the DNA strand being copied.

10. Transcription-2 • The order of nucleotides in the RNA reflects the order in the DNA • If RNA is complementary to one DNA strand, then it is identical (except for T change to U) to the other DNA strand. Either DNA strand may contain the gene! Transcription just runs the other direction.

11. Different genes on different strands A blow up of a section of DNA in the plant Arabidopsis. Genes above the line are transcribed left to right (on one strand), those below the line are transcribed right to left (on the other strand). http://www.sciencemag.org/feature/data/1051477s1_large.jpeg

12. Sense, antisense Compare the sense strand of the DNA to the mRNA. Note that mRNA synthesis will be 5’ to 3’ and antiparallel. DNA between genes has no sense. http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/S/SenseStrand.gif

13. More about RNA polymerase • In bacteria, components are ββ’α2φσ • RNA polymerase is processive; once enzyme attaches to DNA, it can copy >10,000 nucleotides without falling off. • In eukaryotes, there are 3 RNA polymerases: • One for rRNA • One for tRNAs and some rRNA • One for all mRNAs and some small RNAs (involved in RNA processing)

14. Transcription needs a Promoter A promoter is non-transcribed DNA Prokaryotes Eukaryotes http://opbs.okstate.edu/~petracek/2002%20Gene%20expression/img043.gif

15. The Process of Transcription • Promoter recognition: 2 consensus sequences • The -10 region: TATAAT (10 bases upstream from where transcription actually starts. • The -35 region, farther upstream, also important. • “Consensus” sequence meaning the DNA sequence from many genes averages out to this. • The closer these 2 regions actually are to the consensus sequences, the “stronger” the promoter, meaning the more likely RNA polymerase binding and transcription will occur.

16. Consensus sequence Numbers indicate the percentage of different genes in which that nucleotide appears in that spot in the promoter sequence. http://www.uark.edu/campus-resources/mivey/m4233/promoter.gif

17. The Process of Transcription-2 • After binding to the promoter, polymerase “melts” DNA, lines up first base at the +1 site = Initiation. • RNA synthesis continues (Elongation), only the template strand being transcribed. • Termination: must be a stop sign, right? • In bacteria, hairpin loop followed by run of U’s in the RNA. Of course, the DNA must code for complementary bases and a run of A’s. See next. • Termination factor “rho”. Accessory protein.

18. Termination of Transcription in Bacteria The hairpin loop destabilizes the interactions between the DNA, mRNA, and polymerase; U-A basepairs are very weak, and the complex falls apart. In euks, termination occurs with a processing step. http://www.blc.arizona.edu/marty/411/Modules/Weaver/Chap6/Fig.0649ac.gif

19. About mRNA structure, etc. • Start site of transcription is NOT equal to start site of Translation • First codon read, AUG, is downstream from the first ribonucleotides. +1 is transcription start, not translation start. • AUG marks the beginning of an Open Reading Frame (ORF). • Lifetime of a eukaryotic mRNA is variable • For prokaryotes, mRNA is short lived, fits in with need of microbes to respond quickly to changes in environment.

20. Eukaryotic transcription • Occurs in nucleus, then mRNA goes to cytoplasm • Promoters but also enhancers • Enhancers also segments of DNA • Eukaryotic RNA requires processing • Pre-mRNAs found in nucleus as hnRNA • Heterogeneous nuclear RNA • hnRNPs: heterogeneous nuclear ribonucleoproteins which bind to, process pre-mRNAs

21. Initiation of transcription (euks) • Goldberg-Hogness (TATA) box at -35 • CAAT box at -80 (non specific, but important) • GGCCAATCT consensus sequence • Enhancers • Elements of DNA that promote transcription • Can be upstream, downstream, even in gene

22. Eukaryotic RNA polymerase • A 10 subunit machine • Makes several attempts, abortive transcription • Key: successful synthesis of short DNA-RNA hybrid, stabilizes association of Pol with DNA • Then, processive to a high degree, transcribes until knocked off by termination signal. • Termination not well understood, happens along with polyadenylation (adding poly-A tail, ahead 2)

23. Processing of mRNA • Cap • 7-methyl guanosine is added as a cap, 5’ to 5’ • Cap aids in binding of mRNA to the ribosome • Shine-Delgarno seq. does same in prokaryotes http://www.blc.arizona.edu/Marty/429/Lectures/Figures/CAP.GIF

24. Processing of mRNA-2 • Poly-A tail • In several steps, end of mRNA is cleaved off, and several rounds of AAAAAAA are added • Poly-A tail improves stability of mRNA, resists degradation by nucleases in cell. departments.oxy.edu/.../ processing_of_hnrnas.htm

25. Introns and Exons • Introns are intervening sequences that do not contain information for making the protein. Exons are the coding sequences left behind. http://www.emc.maricopa.edu/faculty/farabee/BIOBK/exintrons.gif

26. Removal of Introns • Three types of intron-removal mechanisms • Spliceosomes: • hnRNA or pre-mRNA (to be processed) • snRNPs: small nuclear ribonucleoproteins • snRNAs: involved structurally and catalytically • In some systems, intron codes for protein that splices out the intron! • In Tetrahymena, intron is self-splicing: ribozyme

27. Splicing of Introns • In most systems, snRNPs cut mRNA, introns come out, and snRNPs help splice exons back together. • Particular sequences in the mRNA mark the beginning, end of exons and introns so snRNPs can do their job. http://www.plantsci.cam.ac.uk/Haseloff/SITEGRAPHICS/splice1.GIF

28. Introns: How were they discovered? RNA-DNA hybrids weren’t colinear- loops of DNA extend out where there is no RNA to base pair with it. RNA = red. • Mutations in introns: don’t have much affect unless: • Mutation is near a splice site • Mutation is in a regulatory region (which could be in an intron) • There is a separate gene within the intron.

29. Why are there introns? • Very ancient? • Located in the same positions in genes common to plants and animals. Maybe bacteria had them once and lost them. • Self-splicing RNAs may be related to RNA as the first nucleic acid, a popular idea in evolution. • Exon-shuffling: a model for gene evolution • Some proteins fold into connected, functional sections called domains; these correspond to exons • Perhaps exons were copied, shuffled to create new genes. Several human genes share exons.

30. Relationship between protein domains and exons http://www.mrc-lmb.cam.ac.uk/genomes/cvogel/SupraDomains/Data_new/sd.figure.supra-domain.jpg