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From DNA to Protein

From DNA to Protein. Class 4. From DNA to Protein. From DNA to Protein. Gene. Genome. DNA. Expressed Sequence. Transcriptome. RNA. Protein. Proteome. Transcription. Begins with unwinding of the DNA One DNA strand is used as a template for RNA synthesis

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From DNA to Protein

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  1. From DNA to Protein Class 4 RBIO-0002-U1

  2. From DNA to Protein RBIO-0002-U1

  3. From DNA to Protein Gene Genome DNA Expressed Sequence Transcriptome RNA Protein Proteome RBIO-0002-U1

  4. Transcription • Begins with unwinding of the DNA • One DNA strand is used as a template for RNA synthesis • RNA polymerase synthesizes the transcript • The transcript is complementary to the template • The RNA chain is released from the DNA template and the DNA helix reforms RBIO-0002-U1

  5. RNA polymerase Catalyzes a similar reaction as DNA polymerase, but: • Uses ribonucleotides • Can start a chain without primer • Has a higher error rate than DNA polymerase: 1 in 104 nucleotides vs 1 in 107 nucleotides RBIO-0002-U1

  6. RNA RNA can serve as structural and enzymatic component • mRNA (messenger RNA) specifies the sequence of proteins • tRNA (transfer RNA) forms adaptors between codon and amino acid • rRNA (ribosomal RNA) is part of the ribosome • snRNA (small nuclear RNA) is involved in splicing These are the functions we understand well enough to put in textbooks. http://www.yangene.com/content22_6.htm RBIO-0002-U1

  7. Transcription of a bacterial gene RBIO-0002-U1

  8. DNA Gene OpenReadingFrame DNA Coding Sequence Regulatory elements Termination sites Exon Intron polyA signal Promoter RBIO-0002-U1

  9. Transcriptionfrom DNA to RNA DNA RNA Polymerase + Transcription factors Pre mRNA Cleavage Splicing Polyadenylation (Editing) mRNA AUG AAAAAAAAAAAAA(A)n 3’UTR 5’UTR ORF RBIO-0002-U1

  10. mRNA processing in Eukaryotes • The primary transcript undergoes several processing steps in the nucleus • A 5’ cap is added • Introns (non coding sequences) are removed by splicing • A polyA tail is added to the 3’ end • The mature mRNA is exported to the cytoplasm, where protein synthesis takes place • Only 5% of the transcribed RNA reaches the cytoplasm RBIO-0002-U1

  11. Prokaryotic and Eukaryotic Transcripts RBIO-0002-U1

  12. Splice sites Life is complicated: http://www.swbic.org/education/comp-bio/images/spliceconsensus.gif RBIO-0002-U1

  13. The Splicosome consists of snRNPs and other proteinssnRNRs: small nuclear ribonucleoprotein particles RBIO-0002-U1

  14. Splice Variants RBIO-0002-U1

  15. RBIO-0002-U1

  16. Ensembl Genome browser RBIO-0002-U1

  17. NCBI http://www.ncbi.nlm.nih.gov/ http://www.ncbi.nlm.nih.gov/LocusLink/ RBIO-0002-U1

  18. mRNA export RBIO-0002-U1

  19. RNA stability • The lifetime of a mRNA can vary from minutes to hours • The 3’ UTR is involved in RNA stability • RNA stability allows to regulate the level of protein • Fast degradation of RNAs provides a quick response mechanism RBIO-0002-U1

  20. Expression levels vary RBIO-0002-U1

  21. Road map: From DNA to Protein RBIO-0002-U1

  22. From RNA to Protein:The genetic code • 4 Nucleotides have to code for 20 Amino acids • Triplet code can specify 64 (4 x 4 x 4) amino acids • The genetic code is redundant. Some amino acids are encoded by more than one triplet • A triplet is called codon RBIO-0002-U1

  23. The Genetic Code RBIO-0002-U1

  24. The Genetic Code RBIO-0002-U1

  25. Translation: Reading Frames RBIO-0002-U1

  26. Example: Reading Frames A reading frame uninterrupted by Stop codons is called: Open Reading Frame (ORF) “SequencherTM” RBIO-0002-U1

  27. Transfer RNA (tRNA)recognizes and binds codon on one side, the matching amino acid on the other side RBIO-0002-U1

  28. tRNA and redundancy • Some amino acids are specified by more than on codon • There are more than one tRNA for some amino acids • Some tRNAs tolerate mismatches at position 3 (wobble) RBIO-0002-U1

  29. Adaptors Aminoacyl-tRNA synthetase couples covalently amino acid and corresponding tRNA molecule There are 20 different synthetases, one for each amino acid. They recognize specific nucleotides in anticodon and accepting side RBIO-0002-U1

  30. The Ribosome • Travels along mRNA • “captures” tRNA • Holds tRNA in position • Forms bond • There are millions of ribosomes per cell • Several ribosomes can transcribe a mRNA at the same time • Speed: 2 -20 aa / seconds RBIO-0002-U1

  31. Ribosomes in the cell RBIO-0002-U1

  32. Aminacyl-tRNA Peptidyl-tRNA Exit RBIO-0002-U1

  33. Elongation RBIO-0002-U1

  34. Initiation RBIO-0002-U1

  35. Termination RBIO-0002-U1

  36. RBIO-0002-U1

  37. Websites http://www.blc.arizona.edu/INTERACTIVE/DNA3/proteins.html RBIO-0002-U1

  38. AUG AAAAAAAAAAAAA(A)n Translationfrom RNA to Protein Ribosome Protein M Proteolytic Cleavage Chemical Modification Folding RBIO-0002-U1

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