Lecture Notes: Introduction to Bioinformatics and Bioinformatics Tools - Prof. Giri Narasi, Study notes of Computer Science

Download Lecture Notes: Introduction to Bioinformatics and Bioinformatics Tools - Prof. Giri Narasi and more Study notes Computer Science in PDF only on Docsity! 1/13/05 CAP5510/CGS5166 (Lec 2) 1 CAP 5510: Introduction to Bioinformatics CGS 5166: Bioinformatics Tools Giri Narasimhan ECS 389; Phone: x3748 giri@cs.fiu.edu www.cs.fiu.edu/~giri/teach/5166S05.html 1/13/05 CAP5510/CGS5166 (Lec 2) 2 Course Homepage www.cs.fiu.edu/~giri/teach/5166S05.html • Lecture notes, required reading material, homework, announcements, etc. 1/13/05 CAP5510/CGS5166 (Lec 2) 5 The Players DNA String with alphabet {A, C, G, T} Nucleotides/Bases RNA String with alphabet {A, C, G, U} Bases Protein String with 20-letter alphabet Amino acids/Residues Central Dogma • DNA acts as a template to replicate itself. • DNA is transcribed into RNA. • RNA is translated into Protein. DNA RNA Protein Transcription TranslationReplication 1/13/05 CAP5510/CGS5166 (Lec 2) 6 1/13/05 Basic Genetic Processes DNA replication DNA repair genetic recombination 3 5° DNA transcription (RNA synthesis) RNA 5! 3 ee eos | protein synthesis PI HNO OOS COOH amino acids Figure 6-1 The basic genetic processes. The processes shown here are thought to occur in all present- day cells. Very early in the evolution of life, however, much simpler cells probably existed that lacked both DNA and proteins (see Figure 1-11). Note that a sequence of three nucleotides (a codon) in an RNA molecule codes for a specific amino acid in a protein. CAP5510/CGS5166 (Lec 2) 1/13/05 DNA Molecule 5 a 2 : C o.44nm = -2. (aA) S.4nm (4A) 10 1/13/05 CAP5510/CGS5166 (Lec 2) 11 DNA Complementary Bases 1/13/05 amino acid [3 letter code [1 letter code alanine Ala A arginine ATE R aspartic acid Asp D asparginine Asn N cysteine Cys C glutamic acid Glu E glutamine Gln Q glycine Gly G histine His H isoleucine Tle I leucine Leu L lysine Lys K methionine Met M phenylalanine Phe F proline Pro P serine Ser 5 threonine Thr iT, tryptophan Tip Ww tyrosine Tyr Y¥ valine ‘Val ¥ Table 11: Amine acid abbreviations CAPS5510/CGS5166 (Lec 2) 12 1/13/05 Nucleatides pbiriry ~~ =< Ant a we ut | : - CAPS5510/CGS5166 (Lec 2) re Protein 15 The Genetic Code 1/13/05 C— oS i * Uc A anticodon AUG 5 A G U codon UAC mRNA 3 eee eg @ pg we 2nd base in codon Phe | Ser Tyr Cys U U Phe | Ser Tyr Cys Cc 9 5 Leu | Ser | STOP| stop | A 2 3 Leu | Ser | STOP] Trp G a o Leu | Pro His Arg U = = Cc Leu | Pro His Arg c 5 2 Leu | Pro Gln Arg A 9 g Leu | Pro Gln Ary G £ * lle | Thr | Asn | Ser U 3 = A We | Thr | Asn Ser c We | Thre | Lys | Arg A Met | Thr | Lys Arg G Val Ala | Asp Gly U G Val Ala Asp Gly c Val | Ala | Glu Gly A Val | Ala | Glu | Gly G © The Genetic Code 1/13/05 Tm Gf thee subunit Figure 4.21 Schomutic diag structure of hinmagdlutinin trom influenss virus. ‘The structute compriues about S80 amine acits-arrunyed in two ct » teed) anal ie). Te far halt ad eae hus a lighter nein the-clagram, The su very S wilt & ong stemlike regions Erxilt gy dues from beth Chins and includes ane ef the longest a titles knwwr lia obubar structine, about 7A borg! The ferment bry tested fram H Dan Wiley, Harvard University) 5510/CGS5166 (Lec 2) 17 1/13/05 CAP5510/CGS5166 (Lec 2) 20 Transcription Regulation Exon 1 Exon 2 Tr an sc rip tio n St art po int Gene Intron Gene-Specific TF Binding Sites TATA BoxCAT Box Basal TF Binding Sites TATAATCCAAT coding region promoter region enhancer DNA Transcription g Chromosomal DNA intron 1 intron 2 Transcription (RNA synthesis) exon Wyo Yj exon 3 Nuclear ANA YU WL 4 RNA Splicing exon exon 2 exon 3 Messen ger RNA RNA synthesis and processing 1/13/05 . , 21 start of transcription TATA box f Transcription “ f a) =) ele e TEND Initiation IBb OQ Be TFB cp TRAUF other factors TRUE RANA polwmnerase Il TFHH 1D) i ATP 1E) 1/13/05 CAP551¢ CTP, GTP 22 1/13/05 CAP5510/CGS5166 (Lec 2) 25 Transcription Factors • The general transcription factors have been highly conserved in evolution; some of those from human cells can be replaced in biochemical experiments by the corresponding factors from simple yeasts. Protein Synthesis 1. Transcription i e amino acids rRNA Fa 80 _ yy ~Anticoden ae Bootes / 1/13/05 ; . Protein synthesis 26 1/13/05 CAP5510/CGS5166 (Lec 2) 27 Protein Synthesis: Incorporation of amino acid into protein