Introduction to Molecular Biology and Genomics

1. Introduction to Molecular Biology and Genomics Sushmita Roy www.biostat.wisc.edu/bmi576/ sroy@biostat.wisc.edu September 5, 2013 BMI/CS 576

2. Key concepts in today’s class • Key molecules • DNA, RNA, proteins • The Central Dogma • transcription, translation, genes, genetic code, codons • Genomics • Genomes • Functional genomics • Biological networks

3. Organization of biological information Ecosystem Lake Monona, Mojave desert, Our guts… Population Central Wisconsin Humans Organism Pine tree, Lizard, Human… Heart, Lungs, Brain… Organ Adipose tissue, Blood, Nerve tissue… Tissue Fat cell, Blood cell, Muscle cell… Cell Organelle Nucleus, Mitochondrion… Molecule DNA, RNA, Protein, Lipids…

4. Deoxyribonucleic acid (DNA) image from the DOE Human Genome Program http://www.ornl.gov/hgmis

5. Nucleotides • DNA is composed of small chemical units called nucleotides • Nucleotide • Nitrogen containing base • 5 carbon sugar • Phosphate group • Four nucleotides make DNA • adenine (A), cytosine (C), guanine (G) and thymine (T) • Each nucleotide differs in the base Phosphate Base Sugar

6. Bases in the nucleotides • Purines (Two rings) • Pyrimidines (one ring) Adenine (A) Guanine (G) Thymine (T) Cytosine (C)

7. Nucleotides are linked to form one strand of DNA O 5’ Base - CH2 O O P O - 1’ Sugar 4’ 2’ 3’ O Base - CH2 O O P 5’ O - 1’ Sugar 4’ 2’ 3’

8. 5’ and 3’ of a DNA molecule • Each strand is made up of linkages between 5’ position (Phosphate) on one nucleotide to the 3’ position of the following nucleotide • At one end, there is a free phosphate group: 5’ end • At the other end, there is a free OH group: 3’ end • Therefore we can talk about the 5’ and the 3’ ends of a DNA strand

9. DNA is a double helical molecule Watson and Crick • In 1953, James Watson and Francis Crick discovered DNA molecule has two strands arranged in a double helix • This was possible through the Xray diffraction data from Maurice Wilkins and Rosalind Frankin Maurice Wilkins Rosalind Frankin http://www.chemheritage.org/discover/online-resources/chemistry-in-history/themes/biomolecules/dna/watson-crick-wilkins-franklin.aspx

10. Watson-Crick Base pairing A always bonds to T Calwaysbonds to G Each strand has a base sequence that is complementary to the sequence on the other strand. If you know the sequence on one strand, you know the sequence on the other strand But the strands are antiparallel and must be read 5’ to 3’.

11. DNA stores the blue print of an organism • The heredity molecule • Has the information needed to make an organism • Double strandedness provides stability, prevents errors in replication • one strand has all the information

12. Chromosomes • All the DNA of an organism is divided up into individual chromosomes • prokaryotes (single-celled organisms lacking nuclei) typically have a single circular chromosome • eukaryotes (organisms with nuclei) have a species-specific number of chromosomes Image from www.genome.gov

13. A eukaryotic cell http://www.genome.gov/Glossary/index.cfm?id=25

14. DNA packaging in Chromatin DNA is very long (3m in humans), cell is very small Chromosome compresses the DNA molecule 50,000 Collection of DNA and proteins is called chromatin.

15. Different organisms have different numbers of chromosomes

16. Genes • genes are the basic units of heredity • a gene is a sequence of bases which specifies a protein or RNA genes • the human genome comprises ~ 25,000 protein-coding genes (still being revised) • One gene can have many functions • One function can require many genes …GTATGTCTAAGCCTGAATTCAGTCTGCTTTAAACGGCTTC…

17. Genomes • Refers to the complete complement of DNA for a given species • the human genome consists of 2X23 chromosomes • every cell (except egg and sperm cells and mature red blood cells) contains the complete genome of an organism

18. Some Greatest Hits

19. Some Genome Sizes

20. Number of sequenced genomes

21. RNA • Ribonucleic acid (RNA) • RNA is like DNA except: • The sugar is ribose (different at the 2’ position) • single stranded • U is used in place of T • a strand of RNA can be thought of as a string composed of the four letters: A, C, G, U

22. RNA molecules have secondary structures that might be important • RNA can double back and form loops • Such structures can be more stable

23. The central dogma of Molecular biology DNA Transcription RNA Translation Proteins

24. Transcription • In eukaryotes: happens inside the nucleus • RNA polymerase is an enzyme that builds an RNA strand from a gene • RNA Pol II is recruited at specific parts of the genome in a condition-specific way. • Transcription factor proteins are assigned the job of Pol II recruitment. • RNA that is transcribed from a protein coding region is called messenger RNA (mRNA)

25. Transcription The RNA string produced is identical to the non-template strand except T is replaced by U.

26. The central dogma of Molecular biology DNA Transcription RNA Translation Proteins

27. Translation • Process of turning mRNA into proteins. • Happens inside the cytoplasm in ribosomes • ribosomesare the machines that synthesize proteins from mRNA • Translation process reads one codon at a time • translation begins with the start codon • translation ends with the stop codon

28. Proteins • Proteins are long strings of composed of amino acids • There are 20 different amino acids known

29. Codons • Each triplet of bases is called a odon • How many codons are possible? • Each codon is responsible for coding a particular amino acid.

30. The Genetic Code: Specifies how mRNA is translated into protein Genetic code is degenerate

31. Codons and Reading Frames 3’ 5’ CUC AGC GUU ACC AU Leu Ser Val Thr C UCA UUA CCA U GCG Ser Ala Leu Pro CU CAG CGU UAC CAU Gln Arg Tyr His

32. Amino Acids

33. Proteins are the workhorses of the cell • structural support • transport of substances • coordination of an organism’s activities • response of cell to chemical stimuli • protection against disease • Catalyzing chemical reactions

34. Proteins are complex molecules • Primary amino acid sequence • Secondary structure • Tertiary structure • Quarternary structure

35. Some well-known proteins Actin: maintenance of cell structure Hemoglobin: carries oxygen Insulin: metabolism of sugar http://en.wikipedia.org/wiki/Hemoglobin http://en.wikipedia.org/wiki/Insulin http://en.wikipedia.org/wiki/Actin

36. Hemoglobin protein HBA1 >gi|224589807:226679-227520 Homo sapiens chromosome 16, GRCh37.p9 Primary Assembly 1 cccacagactcagagagaacccaccatggtgctgtctcctgacgacaagaccaacgtcaa 61 ggccgcctggggtaaggtcggcgcgcacgctggcgagtatggtgcggaggccctggagag 121 gatgttcctgtccttccccaccaccaagacctacttcccgcacttcgacctgagccacgg 181 ctctgcccaggttaagggccacggcaagaaggtggccgacgcgctgaccaacgccgtggc 241 gcacgtggacgacatgcccaacgcgctgtccgccctgagcgacctgcacgcgcacaagct 301 tcgggtggacccggtcaacttcaagctcctaagccactgcctgctggtgaccctggccgc 361 ccacctccccgccgagttcacccctgcggtgcacgcctccctggacaagttcctggcttc 421 tgtgagcaccgtgctgacctccaaataccgttaagctggagcctcggtggccatgcttct 481 tgcccctttgg >sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Homo sapiens GN=HBA1 PE=1 SV=2 MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR Amino acid sequence (142 aa) DNA sequence (491 bp)

37. RNA genes • not all genes encode proteins • for some genes the end product is RNA • ribosomal RNA (rRNA), which includes major constituents of ribosomes • transfer RNAs (tRNAs), which carry amino acids to ribosomes • micro RNAs (miRNAs), which play an important regulatory role in various plants and animals • lincRNAs (long non-coding RNAs), play important regulatory roles.

38. http://www.youtube.com/watch?v=41_Ne5mS2ls A video on transcription and translation

39. Summary • Key concepts in molecular biology • Central Dogma • DNA, RNA, proteins • Chromosomes, Nucleus, Ribosomes • Important processes • Transcription • Translation • Some resources • http://www.genome.gov/Glossary/index.cfm

40. Things we did not talk about • RNA splicing • Alternative splicing • Polyadenylation • Post translational modifications

41. Functional Genomics • Aims to characterize gene, proteins in an organism in an unbiased way using high throughput technologies. • Really focused on “beyond the DNA sequence” • What does a piece of DNA do? • Gene, regulatory element, a mutation • Has generated large collections of “omics” datasets • Gene expression • Protein expression • Metabolite levels

42. Context-specific expression of a cell • The DNA is static • But the set of mRNA per cell type, environment, time-point may be different. • A key process is gene regulation • determines which genes are expressed when Environmental signal

43. Transcriptional gene regulation • Key control process that determines what genes are expressed when • Requires • RNA Polymerase • Transcription factors • Energy http://www.youtube.com/watch?v=WsofH466lqk

44. Structure of genes DNA Gene A Gene B Gene C Non-coding Gene Promoter

45. Transcriptional gene regulation Transcription factor level (trans) P2 P1 HSP12 Transcription factor binding sites (cis) Promoter mRNA levels

46. Transcriptome • The entire set of RNA products in a cell • A cell can decide to make more or less of a particular RNA • Levels change • It’s constituents are context-specific • Context is determined by environment of a cell

47. Transcriptional Regulatory networks • The entire set of interactions between TFs and genes in an organism • The transcriptome is the output of a regulatory network Image courtesy: Dr. Mike Snyder, http://compbio.pbworks.com/w/page/16252928/Transcription%20Regluatory%20Network#1

48. Metabolic networks • Captures metabolism: • A set of chemical processes in cells • Need for sustaining life • Anabolism: production of new cellular material from precursors • Catabolism: breakdown of complex molecules to generate energy • Made up of • Metabolites • Small molecules that are intermediates of metabolism • Sugar • Glycerol • Metabolic enzymes • Metabolic pathway • A set of chemical reactions in a cell

49. The Tri-Carboxylic Acid cycle Metabolites Enzyme Courtesy KEGG Pathways

50. Protein-protein interaction networks Yeast Human Node colors: Red: lethal, green: non-lethal, yellow: slow growth Edge colors: Red: Rualet al., blue: literature Barabasi et al. 2003, Rual et al. 2005