1. BIO513: Lecture 1

2. Central dogma “The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred back from protein to either protein or nucleic acid.” -Francis Crick

3. The Alphabet of DNA DNA consists of a 4 letter alphabet, arranged in complementary pairs on a sugar/phosphate backbone –A (adenine, a purine) –C (cytosine, a pyrimidine) –G (guanine, a purine) –T (thymine, a pyrimidine)

4. Bonds There are strict rules for the complementary strands (with nucleotides linked by a hydrogen bond). A – T C – G G – C T – A

5. DNA double helix http://academic.brooklyn.cuny.edu

6. Gene and Genomics A gene is the basic unit of heredity in a living organism. All living things depend on genes. Genes hold the information to build and maintain their cells and pass genetic traits to offspring. The genome of an organism is its hereditary information encoded in DNA

7. SpeciesGenome size (Mb)Number of genes Mycoplasma genitalium0.58500 Streptococcus pneumoniae2.22300 Escherichia coli4.64400 Saccharomyces cerevisiae125800 Arabidopsis thaliana12525,500 Caenorhabditis elegans9719,000 Sea urchin81423,300 Drosophila melanogaster18013,700 Mus musculus2500~21,000 Homo sapiens290020-25,000 Oryza sativa46645-55,000

8. RNA RNA is very similar to DNA RNA is usually single-stranded, while DNA is usually double-stranded RNA nucleotides contain ribose while DNA contains deoxyribose. and RNA has the base uracil rather than thymine that is present in DNA.

9. RNA structure

10. Transcription: from DNA to RNA A C G T DNA RNA U G C A

11. TATA activator TFIID Steps of gene transcription Pol II

12. TATA Steps of gene transcription activator TFIID Pol II

13. TATA Steps of gene transcription Pol II

14. Transcription factors recognizes specific sequences AGCTGGTgene 1 AGCTGGTgene 2 AGCTGGT gene 3 CGCTGGT gene 4 CGCTGGT gene 5 CGCTGGT gene 6 GGCTGGT gene 7 GGCTGGT gene 8 GGCTGGT gene 9 TGCTGGT gene 10 TGCTGGT gene 11 TGCTGGT gene 12....... Motif logo

15. Protein Proteins are made of amino acids arranged in a linear chain and joined together by peptide bonds. Proteins are used to execute almost all cell functions (signaling, enzyme, structure, regulation, etc.) The biological functions of a protein is defined by its structure and ability to bind.

16. Translation mRNA is used as the template for protein synthesis. Proteins are made in the cytoplasm (outside of the nucleus). Translation starts from the AUG (START) codon.

17. UCAG UPheSerTyrCysU PheSerTyrCysC LeuSerSTOP A LeuSerSTOPTrpG CLeuProHisArgU LeuProHisArgC LeuProGlnArgA LeuProGlnArgG AIleThrAsnSerU IleThrAsnSerC IleThrLysArgA MetThrLysArgG GValAlaAspGlyU ValAlaAspGlyC ValAlaGluGlyA ValAlaGluGlyG Genetic Code: Three nucleotides (CODON) determine a amino acid. 64 possible codons correspond to 20 amino acids. Example: AAA, AAG - Lysine

18. Topics of reading 1.Genome sequencing technologies and their impact on public health approaches 2.Analysis of gene expression 3.Transcription factor regulation and motif finding 4.Epigenetics and its role in transcription regulation, development, and diseases. 5.Network structure analysis 6.Tools and paradigms for network analysis 7.Role of networks in offering systems level insights in interpretation of disease 8.Genetic variation within human population 9.Genome diversity in microbial pathogens

19. Genome sequencing technologies and their impact on public health approaches What is “next-generation” sequencing? How do you search for a short DNA sequence fragment in a genome or large database?

20. Genome sequencing technologies and their impact on public health approaches What is “next-generation” sequencing? How do you search for a short DNA sequence fragment in a genome or large database? Mardis 2008

21. Genome sequencing technologies and their impact on public health approaches What is “next-generation” sequencing? How do you search for a short DNA sequence fragment in a genome or large database? Mardis 2008 Trapnell et al. 2009

22. Analysis of gene expression Which genes are expressed in a given cell type under a specific environmental condition? What do these expressed genes do? What genes are expressed differently between disease and normal tissues?

23. Analysis of gene expression Hughes et al. 2000 Which genes are expressed in a given cell type under a specific environmental condition? What do these expressed genes do? What genes are expressed differently between disease and normal tissues?

24. Transcription factor regulation and motif finding How are gene expression levels regulated? To what extent is the gene expression pattern encoded in the genome?

25. Transcription factor regulation and motif finding How are gene expression levels regulated? To what extent is the gene expression pattern encoded in the genome?

26. Epigenetics and its role in transcription regulation Why are different sets of genes expressed in different cell-types? How is tissue-specific regulatory information inherited?

27. Epigenetics and its role in transcription regulation Why are different sets of genes expressed in different cell-types? How is tissue-specific regulatory information inherited? Mikkelsen 2007

28. Tools and paradigms for network analysis How do the all the genes/proteins inside a cell interact with each other? How can we reconstruct a biological network from experimental data?

29. Tools and paradigms for network analysis How do the all the genes/proteins inside a cell interact with each other? How can we reconstruct a biological network from experimental data? Friedman 2004

30. Network structure analysis Is a biological network made of modules? How does a biological network differ from a random network? Does biological networks change during development and evolution?

31. Network structure analysis Is a biological network made of modules? How does a biological network differ from a random network? Does biological networks change during development and evolution? Milo et al. 2002Kim et al. 2008

32. Network interpretation of diseases What does network analysis tell us about diseases?

33. Network interpretation of diseases What does network analysis tell us about diseases? Segal et al. 2004

34. Genetic variation within human population How similar are the genome sequences of two random individuals? How much variation of gene expression can be linked to genetic differences?

35. Genetic variation within human population How similar are the genome sequences of two random individuals? How much variation of gene expression can be linked to genetic differences? Altschuler et al. 2008

36. Genome diversity in microbial pathogens How many microorganisms are there living inside a human being? How do these microorganisms contribute to normal physiology and diseases?

37. Genome diversity in microbial pathogens How many microorganisms are there living inside a human being? How do these microorganisms contribute to normal physiology and diseases? Turnbaugh et al. 2007