P2 Discussion 1. Revise on Central Dogma 2

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Presentation transcript:

P2 Discussion 1

Revise on Central Dogma 2

Universal Genetic Code (translation) Name3 Letter1 Letter AlanineAlaA CysteineCysC Aspartic AcidAspD Glutamic AcidGluE PhenylalaninePheF GlycineGlyG HistidineHisH IsoleucineIleI LysineLysK LeucineLeuL MethionineMetM AsparagineAsnN ProlineProP GlutamineGlnQ ArginineArgR SerineSerS ThreonineThrT ValineValV TyrosineTyrY TryptophanTrpW 64 genetic codes  20 amino acids

4 Physiochemical properties: u/svensson/Cells/07molecu les.htm R: variable side chain: strongly influences the property of amino acids. Each amino acid: different chemical properties (large vs small, hydrophobic vs hydrophilic)

Discussion: six-frame translation 5 Emboss six-pack:  in-silico translate p53 mRNA sequence in 6-frames In-vivo Translation:  Begins with start codon & ends at stop codon  Introns & UTRs are not translated (spliced) In-silico Translation:  6 reading frames (3 forward & 3 reverse strand)  Look for stop codons for each reading frame  Output translations from all open reading frames enclosed by stop codons  Translate entire sequence including introns & UTRs

Open Reading Frame (ORF) A fragment of DNA sequence that has the potential to encode a peptide or protein A stretch of triplet codons that encode amino acids with an initiator codon (ATG) at one end and a stop codon (TAA, TAG or TGA) at the other Computational translation (in-silico) (e.g., six-pack)  Output ORFs: enclosed by stop codons  Not necessarily begin with a start codon  Translate according to the 6-reading frames  Theoretical prediction

ACU UAG CUA CGA UCG ACA UCG CUG U Reading Frame 1 7 In-silico 6-frame Translation 5’-ACAGCGATGTCGATCGTAGCTAAGT-3’ Forward DNA 3’-UGUCGCUACAGCUAGCAUCGAUUCA-5’ mRNA1(forward DNA) 5’-ACAGCGAUGUCGAUCGUAGCUAAGU-3’ mRNA2(complement DNA) Transcription 5’-ACUUAGCUACGAUCGACAUCGCUGU-3’ mRNA1(forward DNA) Translation A CUU AGC UAC GAU CGA CAU CGC UGU Reading Frame 2 AC UUA GCU ACG AUC GAC AUC GCU GU Reading Frame 3 Frame1: CDAKLQMLDSGRHKS*KSLDFDFKHY*GTWQVN In-silico ORF1: CDAKLQMLDSGRHKS In-silico ORF2: KSLDFDFKHY In-silico ORF3: GTWQVN In-vivo Translation: start M, end at first * 3’-TGTCGCTACAGCTAGCATCGATTCA-5’ Complement Reverse strand: Reading Frame 4,5,6

Naming of Frames – Caution! There is still no standard (different groups call them differently) –1, 2, 3, 4, 5, 6 –+1, +2, +3, -1, -2, -3 –1, 2, 3, 1’, 2’, 3’ Be careful when cross-referencing frame names between two or more programs –know which frames the numbers are really referring to

Translation tool: Wemboss sixpack Outseq: lists all the ORFs obtained from the six translation frames. Outfile: shows users the input sequence, its complementary strand, and all the open reading frames (ORFs) in the six translation frames