BME205: Lecture 2 Bio systems. David Bernick

Transcription

1 BME205: Lecture 2 Bio systems David Bernick

2 Bioinforma;cs Infer pa>erns from life biological sequences structures molecular pathways. Suggest hypotheses from inferred pa>erns Structure and Func;on Novel gain or loss of func;on inter- molecular partners Metabolic pathway Engineering Gene discovery

3 Central Dogma Informa;on flow in biological systems

4 Implica;ons and Extensions of Central Dogma DNA sequence determines structure Structure determines Func;on Func;onal conserva;on > Structural conserva;on > protein sequence conserva;on > DNA sequence conserva;on

5 DNA essen;al concepts W- C base pairing Double stranded An;- parallel orienta;on Coding strand, Template strand 5 and 3 ends Coding Frames

6 Why is Molecular Biology not obvious? How many DNA polymerases are necessary? Living systems are decentralized independent muta;on independent history diverse compe;;ve environments Living systems share both ;me and space Ver;cal inheritance Horizontal inheritance Asexual Gene transfer mediated through Vectors, or inter- species Conjuga;on

7 A Phylogeny 3 super kingdoms LUCA is not known What about Viruses?

8 Core Processes Transcrip;on Promoter regula;on Transla;on Ribosome Binding Shine- Delgarno site 5 cap Internal Ribosome Entry site (IRES) Muta;on DNA replica;on Transposi;on DNA transposons Retro transposons

9 Transcrip;on

10 Nucleo;des Base Nucleoside Nucleo-de RNA DNA Adenine Adenosine Adenosine triphosphate ATP datp Cytosine Cy;dine Cy;dine triphosphate CTP dctp Guanine Guanosine Guanosine triphosphate GTP dgtp Thymine Thymidine Thymidine triphosphate dttp Uracil Uridine Uridine triphosphate UTP

11 Eukaryo;c mrna 5 Cap m7g Introns and splicing Poly- A Tail

12 Prokaryo;c mrna SD Polycistronic 5 PPP- 3 OH Coupled transcrip;on and transla;on

13 A Gene;c code Codons are base- triples 64 possible triples 3 are stop codons 1 (or 3) are start 20 encoded AA Code is redundant Post- transcrip;onal modifica;ons occur

14 Amino acids - - proper;es and symbols Amino acid Alanine A Ala Cysteine C Cys Amino acid Neutral Non-polar Methionine M Met Neutral Non-polar Neutral Slightly Polar Asparagine N Asn Neutral Polar Aspartate D Asp Acidic Polar Proline P Pro Glutamate E Glu Acidic Polar Glutamine Q Gln Neutral Non-polar Neutral Polar Phenylalanine F Phe Neutral Non-polar Arganine R Arg Basic Polar Glycine G Gly Neutral Non-polar Serine S Ser Histidine H His Isoleucine I Ile Lysine K Lys Basic Polar Threonine T Thr Neutral Non-polar Valine V Val Neutral Polar Neutral Polar Neutral Non-polar Basic Polar Tryptophan W Trp Neutral Slightly polar Leucine L Leu Neutral Non-polar Tyrosine Y Tyr Neutral Polar 5/20/2010 David Bernick,

15 Transla;on

16 the pep;de bond 5/20/2010 David Bernick,

17 Pep;des and the pep;de bond N- terminus C- terminus 5/20/2010 David Bernick,

18 pep;de bond distances from Pauling, L x- H ~ 1.05 Å N- Cα ~ 1.45 Å N- C ~ 1.37 Å C- O ~ 1.23Å C- Cα ~ 1.49Å 5/20/2010 David Bernick,

19 primary structure - - 1TIM primary - - sequence >1TIM:A PDBID CHAIN SEQUENCE APRKFFVGGNWKMNGKRKSLGELIHTLDGAKLSADTEVVCGAPSIYLDFARQKLDAK IGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHSERRHVFGESDELIGQKVAH ALAEGLGVIACIGEKLDEREAGITEKVVFQETKAIADNVKDWSKVVLAYEPVWAIGT GKTATPQQAQEVHEKLRGWLKTHVSDAVAVQSRIIYGGSVTGGNCKELASQHDVDGF LVGGASLKPEFVDIINAKH 5/20/2010 David Bernick,

20 secondary structure - 1TIM helix, strand or loop 5/20/2010 David Bernick,

21 ter;ary structure - - 1TIM 5/20/2010 David Bernick,

22 A few notes on Muta;ons Not all muta;ons will be observable Silent (wobble base, similar AA chemistry) Deleterious Single base changes INDELs - Sequence inser;ons and dele;ons Trunca;ons Inversions Duplica;ons chromosomal loss

23 Polymerase Muta;on rates DNA polymerases Taq 1:125,000 Pfu 1:2,300,000 Mitocondrial pol gamma 1:300,000 1:500,000 pol eta 1:18 1/38 Reverse transcriptases (RT) HIV 1:1,700 1:1,8000 RNA Dependent RNA polymerase (RDRP) SIV 1:19,000 Accuscript 1:62,000 flu 1:10,000 Qbeta 1:3,000

24 Sequencer Error rates Sanger sequencing 1:10, / Roche 1:100 Illumina / Solexa 1:100 1:200 ABI / SOLiD 1:75