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What is the flow of information through the cell?

What is the flow of information through the cell?. Double helix - antiparallel polymers. Major groove Minor groove. 5’ 3’. A. T. G. C. Purine Pyrimidine. 06_12_asymmetrical.jpg. Transcription : dsDNA template Nucleotides (ACGU) make ssRNA Need to separate strands.

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What is the flow of information through the cell?

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  1. What is the flow of information through the cell?

  2. Double helix - antiparallel polymers Major groove Minor groove

  3. 5’ 3’

  4. A T G C Purine Pyrimidine

  5. 06_12_asymmetrical.jpg

  6. Transcription: • dsDNA template • Nucleotides (ACGU) make ssRNA • Need to separate strands. • Nucleotides added to free 3’ OH (5’3’)

  7. Classes of RNA… mRNA rRNA tRNA …also snRNA and microRNA

  8. Prokaryotes untranslated regions 5’ UTR 3’ UTR promoter (not transcribed) coding sequence DNA mRNA RNA Polymerase Ribosome polypeptide

  9. Eukaryotes untranslated regions 5’ URT 3’ UTR promoter (not transcribed) coding sequence DNA pre mRNA mRNA RNA Polymerase Ribosome polypeptide

  10. Transcription start = +1 Consensus sequence = –35; TTGACA, recognized by  Pribnow box = -10, TATAAT; determines +1 Terminator sequence: where polymerase stops Bacterial Promoter Elements

  11. Initiation of transcription in prokaryotes

  12. Initiation of eukaryotic transcription by RNA Pol II (mRNA) TF = transcription factor (compare with prokaryotic sigma factor)

  13. Eukaryotic mRNA: • 5’ cap, • 5’ UTR • coding region • 3’ UTR • 3’ poly-A tail

  14. mRNA processing in Eukaryotes 5’ cap added Remove 3’ end Poly-A tail added Introns removed Exons joined

  15. replication transcription translation DNA RNA Protein Gene cloning - making lots of copies... 1. Make a “library” of small pieces of DNA (2 types) 2. Find the one piece you want 3. Insert it into a “vector” 4. Grow it in a new organism (bacteria, euk. cells) Isolate DNA, fragment with RE Isolate mRNA, convert to cDNA with reverse transcriptase Genomic library cDNA library

  16. Overview of gene expression in eukaryotes 07_37_Protein.produc.jpg

  17. 07_28_ribosome.jpg

  18. Two adapters link an amino acid to a codon 07_26_2_adaptors.jpg

  19. Intiation of translation in Eukaryotes 07_32_initiation.jpg

  20. Intiation of translation in Prokaryotes 07_33_mRNA.encode.jpg

  21. Elongation of proteins 07_30_3_step_cycle.jpg 4 5

  22. 07_34_stop codon.jpg Termination of translation

  23. Frameshift: Adding or removing 1 or 2 nucleotides results in changes the reading frame from that point on. Nonsense: Changing an amino acid codon to a stop codon results in truncated proteins Missense: Changing an amino acid codon to one encoding a different amino acid - effect depends on type of amino acid and where in the protein. Mutations…

  24. 04_03_20 amino acids.jpg

  25. Side chains interact via all of the noncovalent bonds

  26. Primary structure (1°) of a protein: Arabidopsis -glucosidase (single letter codes) MSSLHWFPNIFIVVVVFFSLRSSQVVLEEEESTVVGYGYVVRSVGVDSNRQVLTAKLDLIKPSSVYAPDIKSLNLHVSLETSERLRIRITDSSQQRWEIPETVIPRAGNHSPRRFSTEEDGGNSPENNFLADPSSDLVFTLHNTTPFGFSVSRRSSGDILFDTSPDSSDSNTYFIFKDQFLQLSSALPENRSNLYGIGEHTKRSFRLIPGETMTLWNADTGSENPDVNLYGSHPFYMDVRGSKGNEEAGTTHGVLLLNSNGMDVKYEGHRITYNVIGGVIDLYVFAGPSPEMVMNQYTELIGRPAPMPYWSFGFHQCRYGYKNVSDLEYVVDGYAKAGIPLEVMWTDIDYMDGYKDFTLDPVNFPEDKMQSFVDTLHKNGQKYVLILDPGIGVDSSYGTYNRGMEADVFIKRNGEPYLGEVWPGKVYFPDFLNPAAATFWSNEIKMFQEILPLDGLWIDMNELSNFITSPLSSGSSLDDPPYKINNSGDKRPINNKTVPATSIHFGNISEYDAHNLYGLLEAKATHQAVVDITGKRPFILSRSTFVSSGKYTAHWTGDNAAKWEDLAYSIPGILNFGLFGIPMVGADICGFSHDTTEELCRRWIQLGAFYPFARDHSSLGTARQELYLWDSVASSARKVLGLRMRLLPHLYTLMYEAHVSGNPIARPLFFSFPQDTKTYEIDSQFLIGKSIMVSPALKQGAVAVDAYFPAGNWFDLFNYSFAVGGDSGKHVRLDTPADHVNVHVREGSIVAMQGEALTTRDARKTPYQLLVVASRLENISGELFLDDGENLRMGAGGGNRDWTLVKFRCYVTGKSVVLRSEVVNPEYASKMKWSIGKVTFVGFENVENVKTYEVRTSERLRSPRISLIKTVSDNDDPRFLSVEVSKLSLLVGKKFEMRLRLT

  27. Secondary structure (2°) -helix H-bonds between C=O and N-H of backbone. (No R-groups involved)

  28. Secondary structure -sheet H-bonds between C=O and N-H of backbone. (No R-groups involved)

  29. Tertiary structure - the entire polypeptide -helix -sheet loops and turns disulfide bridge ribonuclease

  30. Quaternary structure - multiple subunits e.g. hemoglobin

  31. lactic (lactate) dehydrogenase immunoglobulin light chain 04_20_protein domains.jpg cytochrome b562

  32. Domains - discrete modules within tertiary structure that fold independently and have a specific function. 4 domains of phospholipase C

  33. Motif - a recurring substructure / barrel e.g. -amylase

  34. Motif - a recurring substructure coiled coil e.g. myosin

  35. How do proteins get to their folded state? unfolded native conformation

  36. Proteins with different functions may have similar shape - members of a family with a common ancestor. 04_21_Serine proteases.jpg

  37. 04_22_protein subunit.jpg

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