P2 Discussion 1. Revise on Central Dogma 2 kroberts/Lecture/Chapter%207/dogma.html.
-
Upload
derick-payne -
Category
Documents
-
view
230 -
download
3
Transcript of P2 Discussion 1. Revise on Central Dogma 2 kroberts/Lecture/Chapter%207/dogma.html.
![Page 1: P2 Discussion 1. Revise on Central Dogma 2 kroberts/Lecture/Chapter%207/dogma.html.](https://reader036.fdocuments.in/reader036/viewer/2022062407/56649e2b5503460f94b19dbb/html5/thumbnails/1.jpg)
P2 Discussion
1
![Page 2: P2 Discussion 1. Revise on Central Dogma 2 kroberts/Lecture/Chapter%207/dogma.html.](https://reader036.fdocuments.in/reader036/viewer/2022062407/56649e2b5503460f94b19dbb/html5/thumbnails/2.jpg)
Revise on Central Dogma
2
http://academic.pgcc.edu/~kroberts/Lecture/Chapter%207/dogma.html
![Page 3: P2 Discussion 1. Revise on Central Dogma 2 kroberts/Lecture/Chapter%207/dogma.html.](https://reader036.fdocuments.in/reader036/viewer/2022062407/56649e2b5503460f94b19dbb/html5/thumbnails/3.jpg)
Universal Genetic Code (translation)
http://plato.stanford.edu/entries/information-biological/GeneticCode.png
Name 3 Letter 1 Letter Alanine Ala A Cysteine Cys C Aspartic Acid Asp D Glutamic Acid Glu E Phenylalanine Phe F Glycine Gly G Histidine His H Isoleucine Ile I Lysine Lys K Leucine Leu L Methionine Met M Asparagine Asn N Proline Pro P Glutamine Gln Q Arginine Arg R Serine Ser S Threonine Thr T Valine Val V Tyrosine Tyr YTryptophan Trp W
64 genetic codes 20 amino acids
![Page 4: P2 Discussion 1. Revise on Central Dogma 2 kroberts/Lecture/Chapter%207/dogma.html.](https://reader036.fdocuments.in/reader036/viewer/2022062407/56649e2b5503460f94b19dbb/html5/thumbnails/4.jpg)
4
Physiochemical properties:http://instruct.westvalley.edu/svensson/Cells/07molecules.htm
• R: variable side chain: strongly influences the property of amino acids.
• Each amino acid: different chemical properties (large vs small, hydrophobic vs hydrophilic)
![Page 5: P2 Discussion 1. Revise on Central Dogma 2 kroberts/Lecture/Chapter%207/dogma.html.](https://reader036.fdocuments.in/reader036/viewer/2022062407/56649e2b5503460f94b19dbb/html5/thumbnails/5.jpg)
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 codonIntrons & UTRs are not translated (spliced)
In-silico Translation:6 reading frames (3 forward & 3 reverse strand)Look for stop codons for each reading frameOutput translations from all open reading frames enclosed by stop codonsTranslate entire sequence including introns & UTRs
![Page 6: P2 Discussion 1. Revise on Central Dogma 2 kroberts/Lecture/Chapter%207/dogma.html.](https://reader036.fdocuments.in/reader036/viewer/2022062407/56649e2b5503460f94b19dbb/html5/thumbnails/6.jpg)
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
![Page 7: P2 Discussion 1. Revise on Central Dogma 2 kroberts/Lecture/Chapter%207/dogma.html.](https://reader036.fdocuments.in/reader036/viewer/2022062407/56649e2b5503460f94b19dbb/html5/thumbnails/7.jpg)
ACU UAG CUA CGA UCG ACA UCG CUG U Reading Frame 1
7
In-silico 6-frame Translation5’-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: CDAKLQMLDSGRHKSIn-silico ORF2: KSLDFDFKHYIn-silico ORF3: GTWQVN
In-vivo Translation: start M, end at first *
3’-TGTCGCTACAGCTAGCATCGATTCA-5’ Complement
Reverse strand: Reading Frame 4,5,6
![Page 8: P2 Discussion 1. Revise on Central Dogma 2 kroberts/Lecture/Chapter%207/dogma.html.](https://reader036.fdocuments.in/reader036/viewer/2022062407/56649e2b5503460f94b19dbb/html5/thumbnails/8.jpg)
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
![Page 9: P2 Discussion 1. Revise on Central Dogma 2 kroberts/Lecture/Chapter%207/dogma.html.](https://reader036.fdocuments.in/reader036/viewer/2022062407/56649e2b5503460f94b19dbb/html5/thumbnails/9.jpg)
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