Doug Raiford Lesson 2

 Material of life  Heritable traits  The job of DNA is to produce proteins  Involved in virtually every chemical reaction ▪ Enzymes catalyze reactions  Structure ▪ muscle, cellulose, etc.  Every cell has the same DNA  Yet not all cells perform same job 2Background

 Double stranded  Sequence of nucleotides  Named for their nitrogenous bases ▪ Adenine ▪ Guanine ▪ Cytosine ▪ Thymine  Strands are complementary  Gs with Cs, As with Ts  Called base-pairs 3Background

 Article: molecular structure of nucleic acids  Published in Nature in April of 1953  a50/watsoncrick.pdf a50/watsoncrick.pdf  One page  Possibly the most famous passage in all of science “It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.” 4Background

 Carbons numbered  Synthesis 5’ to 3’  Strands are antiparallel  Reverse complement Deoxyribonucleic acid 5Background

 Can be represented as a string of characters 1 aataaatact tacaggtatt ccacctgaaa ctctttctat gaatgacttt caagtctata 61 tcctatattt atcctcaata aaatatgcac aatagatctc tactgagaaa actttatatt 121 ttagaagcaa ttcatctccc ttttaaaata caaacttgca taggattgcc ataaattaat 181 gcacctaaaa ttaagtcgtt tctatgaaat ttattttagg tgtgaaatta tatattaggt 241 gtacaattag ccataccatt ccgacaatat cgacatagga atattgagta gaacaagatg 301 taccattatt agcttctggg ttggcataag ggaatacagg caaagactta aacctattcg 361 gactctgtag agctggctca atattcaaaa gaataatgtc cctcgataca agcatcagaa 421 tagagatcgc gctctttaca cctattaaat acatcatcta aaacaactgc atattgttct 481 atgctcaagc tgtaagcatc aatatctagg caagctcatt gactaaaaca gtctctatcg 541 aaatgttcca gctcaattca aggtcgagat agtacaccta ttaaattaat ttcataccta 601 taaattcgag attcccagta gtctattggt gactacatca atcgggcaac accaccatgg 6Background

 DNA strand: chromosome  Genome: all chromosomes combined 7Background

 Gene is a sub-region of DNA  As mentioned: job of a gene is to produce protein  Each gene is associated with a particular protein 8Background

 Two step process  Transcription  Translation  Central dogma DNA  RNA  Protein transcriptiontranslation 9Background

 RNA polymerase  Protein complex  Free-floating nucleotides stitches together  Result is single strand of RNA  Messenger RNA  mRNA  Exact copy  Hence transcription 10Background

 Strand of amino acids  20 common aa’s  Folds into shape  Shape dictates function 11Background

 mRNA: 4 nucleotide alphabet  Protein: 20 amino acid alphabet  How translate?  Triplet nucleotides “code” for amino acid  Codon atg  Methionine 12Background

 64 combinations of 3 nucleotides  But only 20 amino acids  Some amino acids are coded for by multiple codons CTA CTC CTG CTT TTA TTG Leucine 13Background

 Ribosome  Protein and RNA complex  AAs delivered by Transfer RNA (tRNA) 14Background

 Translation Translation  DNA Replication DNA Replication 15Background

 Central dogma DNA  RNA  Protein transcriptiontranslation RNA Polymerase Free-floating nt’s Ribosome tRNAs 16Background

 Use the cell’s own machinery for replicating DNA  Polymerase chain reaction (PCR)  Free-floating nucleotides  DNA Polymerase  Amplifies a single or small number of strands into millions 17Background

 Instead of free floating ATP, CTP, TTP, and GTP  Small percentage is dideoxy variant  Stops transcription if encounters one of these  All fragments end with A, C, T, or G depending on test tube 18Background

 Dye-labeled chain terminators: can do all in one chamber  Capillary electrophoresis instead of gel 19Background

 Sequence termination techniques  Only base-pairs at a time  Very time consuming and labor intensive Slow: human genome would take 8,000 years 20Background

 Breakup into random sized fragments  Determine sequences of fragments  Reassemble algorithmically  High-throughput Look for regions of overlap 21Background

 How the polymerase knows where to attach  The term expression: phenotypical expression  Now equated to protein production rate Promoter RegionCoding regionTerminator Region RNA polymerase Start Codon ‘ATG’ = Methionine Stop Codon: non coding ‘TAA’, ‘TAG’, or ‘TGA’ 22Background

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