1. Introduction to Molecular Biology, Genetics and Genomics References: www.biostat.wisc.edu/ Lecture 1

2. Overview  Molecular biology crash course:  The different parts of a cell  DNA, RNA, chromosomes, nucleus, cytoplasm  Bio-chemical entities of a cell: mRNA, proteins  genes, heredity, transcription, translation, gene regulation, gene expression, alternative splicing

3. Life  Two categories:  Prokaryotes (e.g. bacteria)  Unicellular  No nucleus  Eukaryotes (e.g. fungi, plant, animal)  Unicellular or multicellular  Has nucleus

4. Prokaryote vs. Eukaryote  Eukaryote has many membrane-bounded compartment inside the cell  Different biological processes occur at different cellular location

5. Organization of biological information Organism Tissue Chromosome Cell http://publications.nigms.nih.gov/thenewgenetics/chapter1.html

6. Chemical contents of cell  Water  Macromolecules (polymers) - “strings” made by linking monomers from a specified set (alphabet)  Protein  DNA  RNA ……  Small molecules  Sugar  Ions (Na +, Ka +, Ca 2+, Cl -,…)  Hormone ……

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

8. image from the DOE Human Genome Program http://www.ornl.gov/hgmis

9. DNA  Short for Deoxyribonucleic acid  composed of small chemical units called nucleotides (or bases)  adenine (A), cytosine (C), guanine (G) and thymine (T)  ATGC is the alphabet  DNA is double stranded: made up two twisting strands  Each strand of DNA is a string composed of the four letters: A, C, G, T

10. Nucleotides  A nucleotide has 3 components  Sugar ring (ribose in RNA, deoxyribose in DNA)  Phosphoric acid  Nitrogen base  Adenine (A)  Guanine (G)  Cytosine (C)  Thymine (T) or Uracil (U)

11. Polymerization: Nucleotides => nucleic acids Phosphate Sugar Nitrogen Base Phosphate Sugar Nitrogen Base Phosphate Sugar Nitrogen Base

12. G A G T C A G C 5’-AGCGACTG-3’ AGCGACTG Phosphate Sugar Base 1 2 3 4 5 Often recorded from 5’ to 3’, which is the direction of many biological processes. e.g. DNA replication, transcription, etc. 5’ 3’ DNA Free phosphate 5 prime 3 prime

13. DNA is a double helical molecule  DNA molecules consist of two strands arranged in a double helix  DNA is made up of nucleotides Double-helical structure is needed for the DNA molecule to store and pass with great precision James Watson, Francis Crick, Maurice Wilkins and Rosalind Franklin

14. Watson-Crick Base Pairs A always bonds to T C alwaysbonds to G This is called base pairing. A and G are double ringed structures called purines. C and T single ringed structures called pyrimidines

15. 5’ and 3’ of a DNA molecule The backbone of this molecule has alternating carbon and phosphate molecules  each strand of DNA has a “direction”  at one end, the terminal carbon atom in the backbone is the 5’ carbon atom of the terminal sugar  at the other end, the terminal carbon atom is the 3’ carbon atom of the terminal sugar  therefore we can talk about the 5’ and the 3’ ends of a DNA strand

16. DNA double helix G-C pair is stronger than A-T pair

17. DNA stores the blue print of an organism  The heredity molecule  Has the information needed to make an organism  Base pairing enables self-replication:  one strand has all the information

18. 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

19. Different organisms have different numbers of chromosomes Organism# of chromosomes Yeast32 Human46 Fly8 Mouse40 Arabidopsis10 Worm12

20. Human Chromosomes

21. 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 …GTATGTCTAAGCCTGAATTCAGTCTGCTTTAAACG GCTTC…

22. Structure of genes DNA GeneNon-codingPromoter Gene A Gene BGene C

23. 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

24. Some Greatest Hits

25. Some Genome Sizes

26. Number of sequenced genomes

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

28. RNA  RNA is like DNA except:  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

29. 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 gene is called messenger RNA (mRNA)

30. Transcription: Process of turning DNA into RNA mRNA

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

32.  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

33. Translation happens in ribosomes

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

35. The Genetic Code

36. Proteins  Protein is the actual “worker” for almost all processes in the cell  Proteins are long strings ofcomposed of amino acids  There are 20 different amino acids known  The structure of a protein is intimately connected to its function

37. Protein: a polymer of amino acids

38. Amino Acids

39. Proteins are the workhorses of the cell  structural support  storage of amino acids  transport of other substances  coordination of an organism’s activities  response of cell to chemical stimuli  movement  protection against disease  selective acceleration of chemical reactions

40. Proteins are complex molecules  Primary amino acid sequence  Secondary structure  Tertiary structure  Quaternary structure

41. Some well-known proteins Hemoglobin: carries oxygen Insulin: metabolism of sugar Actin: maintenance of cell structure

42. Hemoglobin protein HBA1 >gi|224589807:226679-227520 Homo sapiens chromosome 16, GRCh37.p9 Primary Assembly 1 CCCACAGACTCAGAGAGAACCCACCATGGTGCTG TCTCCTGACGACAAGACCAACGTCAA 61 GGCCGCCTGGGGTAAGGTCGGCGCGCACGCTGG CGAGTATGGTGCGGAGGCCCTGGAGAG 121 GATGTTCCTGTCCTTCCCCACCACCAAGACCTACT TCCCGCACTTCGACCTGAGCCACGG 181 CTCTGCCCAGGTTAAGGGCCACGGCAAGAAGGTG GCCGACGCGCTGACCAACGCCGTGGC 241 GCACGTGGACGACATGCCCAACGCGCTGTCCGCC CTGAGCGACCTGCACGCGCACAAGCT 301 TCGGGTGGACCCGGTCAACTTCAAGCTCCTAAGC CACTGCCTGCTGGTGACCCTGGCCGC 361 CCACCTCCCCGCCGAGTTCACCCCTGCGGTGCAC GCCTCCCTGGACAAGTTCCTGGCTTC 421 TGTGAGCACCGTGCTGACCTCCAAATACCGTTAA GCTGGAGCCTCGGTGGCCATGCTTCT 481 TGCCCCTTTGG DNA sequence (491 bp) >sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Homo sapiens GN=HBA1 PE=1 SV=2 MVLSPADKTNVKAAWGKVGAHAGEYGAEAL ERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKV ADALTNAVAHVDDMPNALSALSDLHAHKLRV DPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLD KFLASVSTVLTSKYR Amino acid sequence (142 aa)Protein 3d structure

43. Examples of proteins

44. RNA Processing in Eukaryotes  eukaryotes are organisms that have enclosed nuclei in their cells  in many eukaryotes,RNAs consist of alternating exon/intron segments  exons are the coding parts  introns are spliced out before translation

45. RNA Splicing

46. 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.

47. Central Dogma revisited DNA RNA Proteins Transcription Translation ncRNA, miRNA, rRNAs Non-coding RNA processing

48. Summary  Key concepts in molecular biology  Central Dogma  DNA, RNA, proteins  Chromosomes, Nucleus, Ribosomes  Important processes  Transcription  Translation  RNA splicing