1. P2 Discussion 1

2. Revise on Central Dogma 2 http://academic.pgcc.edu/~kroberts/Lecture/Chapter%207/dogma.html

3. Universal Genetic Code (translation) http://plato.stanford.edu/entries/information-biological/GeneticCode.png 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. 4 Physiochemical properties: http://instruct.westvalley.ed 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)

5. 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

6. 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

7. 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

8. 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

9. 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