Introduction to Bioinformatics

1. Introduction to Bioinformatics Molecular Biology Primer

2. Genetic Material • DNA (deoxyribonucleic acid) is the genetic material • Information stored in DNA • the basis of inheritance • distinguishes living things from nonliving things • Genes • various units that govern living thing’s characteristics at the genetic level

3. Nucleotides • Genes themselves contain their information as a specific sequence of nucleotides found in DNA molecules • Only four different bases in DNA molecules • Guanine (G) • Adenine (A) • Thymine (T) • Cytosine (C) • Each base is attached to a phosphate group and a deoxyribose sugar to form a nucleotide. • The only thing that makes one nucleotide different from another is which nitrogenous base it contains Base P Sugar

4. Purine: Pyrimidine: Nucleoside

5. Nucleotides • Complicated genes can be many thousands of nucleotides long • All of an organism’s genetic instructions, its genome, can be maintained in millions or even billions of nucleotides

6. Orientation • Strings of nucleotides can be attached to each other to make long polynucleotide chains • 5’ (5 prime) end • The end of a string of nucleotides with a 5' carbon not attached to another nucleotide • 3’ (3 prime) end • The other end of the molecule with an unattached 3' carbon

7. 5’ 1’ 4’ 2’ 3’

8. Base Pairing • Structure of DNA • Double helix • Seminal paper by Watson and Crick in 1953 • Rosalind Franklin’s contribution • Information content on one of those strands essentially redundant with the information on the other • Not exactly the same—it is complementary • Base pair • G paired with C (G  C) • A paired with T (A = T)

10. Base Pairing • Reverse complements • 5' end of one strand corresponding to the 3' end of its complementary strand and vice versa • Example • one strand: 5'-GTATCC-3' the other strand: 3'-CATAGG-5'  5'-GGATAC-3' • Upstream: Sequence features that are 5' to a particular reference point • Downstream: Sequence features that are 3' to a particular reference point 5' 3' Upstream Downstream

11. DNA Structure

12. DNA Structure

13. Chromosome • Threadlike "packages" of genes and other DNA in the nucleus of a cell

15. Chromosome • Different kinds of organisms have different numbers of chromosomes • Humans • 23 pairs • 46 in all

16. Central Dogma of Molecular Biology • DNA: information storage • Protein: function unit, such as enzyme • Gene: instructions needed to make protein • Central dogma

17. Central Dogma of Molecular Biology • Central dogma reverse transcription (reverse transcriptase) replication (DNA polymerase) • DNA obtained from reverse transcription is called complementary DNA (cDNA) • Difference between DNA and cDNA will be discussed later

18. Base Base P P Sugar Sugar Central Dogma of Molecular Biology • RNA (ribonucleic acid) • Single-stranded polynucleotide • Bases • A • G • C • U (uracil), instead of T • Transcription (simplified …) • A  A, G G, C  C, T  U DNA H RNA OH

21. DNA Replication (DNA  DNA)

22. DNA Replication (DNA  DNA)

23. DNA Replication Animation Courtesy of Rob Rutherford, St. Olaf University

24. Transcription (DNA  RNA) • Messenger RNA (mRNA) • carries information to be translated • Ribosomal RNA (rRNA) • the working “spine” of the ribosome • Transfer RNA (tRNA) • the “decoder keys” that will translate nucleic acids to amino acids

25. Transcription Animation Courtesy of Rob Rutherford, St. Olaf University

26. Peptides and Proteins • mRNA  Sequence of amino acids connected by peptide bond • Amino acid sequence • Peptide: < 30 – 50 amino acids • Protein: longer peptide

29. Genetic Code – Codon Codon: 3-base RNA sequence Stop codons Start codon

30. List of Amino Acids Amino acid Symbol Codon A Alanine Ala GC* C Cysteine Cys UGU, UGC D Aspartic Acid Asp GAU, GAC E Glutamic Acid Glu GAA, GAG F Phenylalanine Phe UUU, UUC G Glycine Gly GG* H Histidine His CAU, CAC I Isoleucine Ile AUU, AUC, AUA K Lysine Lys AAA, AAG L Leucine Leu UUA, UUG, CU*

31. List of Amino Acids Amino acid Symbol Codon M Methionine Met AUG N Asparagine Asn AAU, AAC P Proline Pro CC* Q Glutamine Gln CAA, CAG R Arginine Arg CG*, AGA, AGG S Serine Ser UC*, AGU, AGC T Threonine Thr AC* V Valine Val GU* W Tryptophan Trp UGG Y Tyrosine Tyr UAU, UAC 20 letters, no B J O U X Z

32. Codon and Reading Frame • 4 AA letters  43 = 64 triplet possibilities • 20 (< 64) known amino acids • Wobbling 3rd base • Redundant  Resistant to mutation • Reading frame: linear sequence of codons in a gene • Open Reading Frame (ORF), definition varies: • a reading frame that begins with a start codon and end at a stop codon • a series of codons in a DNA sequence uninterrupted by the presence of a stop codon  a potential protein-coding region of DNA sequence

33. Open Reading Frame • Given a nucleotide sequence • How many reading frames? __ • __ forward and __ backward • Example: Given a DNA sequence, 5’-ATGACCGTGGGCTCTTAA-3’ • ATG ACC GTG GGC TCT TAA  M T V G S * • TGA CCG TGG GCT CTT AA  * P W A L • GAC CGT GGG CTC TTA A  D R G L L • Figure out the three backward reading frames • In random sequence, a stop codon will follow a Met in ~20 AAs • Substantially longer ORFs are often genes or parts of them

34. Translation (RNA  Protein)

35. Translation Animation Courtesy of Rob Rutherford, St. Olaf University

36. Gene Expression • Gene expression • Process of using the information stored in DNA to make an RNA molecule and then a corresponding protein • Cells controlling gene expression by • reliably distinguishing between those parts of an organism’s genome that correspond to the beginnings of genes and those that do not • determining which genes code for proteins that are needed at any particular time.

37. Promoter • The probability (P) that a string of nucleotides will occur by chance alone if all nucleotides are present at the same frequency P = (1/4)n, where n is the string’s length • Promoter sequences • Sequences recognized by RNA polymerases as being associated with a gene • Example • Prokaryotic RNA polymerases scan along DNA looking for a specific set of approximately 13 nucleotides marking the beginning of genes • 1 nucleotide that serves as a transcriptional start site • 6 that are 10 nucleotides 5' to the start site, and • 6 more that are 35 nucleotides 5' to the start site • What is the frequency for the sequence to occur?

38. Gene Regulation • Regulatory proteins • Capable of binding to a cell’s DNA near the promoter of the genes • Control gene expression in some circumstances but not in others • Positive regulation • binding of regulatory proteins makes it easier for an RNA polymerase to initiate transcription • Negative regulation • binding of the regulatory proteins prevents transcription from occurring

39. Promoter and Regulatory Example • Low tryptophan concentration •  RNA polymerase binds to promoter • genes transcribed • High tryptophan concentration •  repressor protein becomes active and binds to operator •  blocks the binding of RNA polymerase to the promoter • Tryptophan concentration drops •  repressor releases its tryptophan and is released from DNA •  polymerase again transcribes genes

40. Gene Structure

41. Exons and Introns

42. Exons and Introns Example

43. Protein Structure and Function • Genes encode the recipes for proteins

44. Protein Structure and Function • Proteins are amino acid polymers

45. Proteins: Molecular Machines • Proteins in your muscles allows you to move:myosinandactin

46. Proteins: Molecular Machines • Digestion, catalysis (enzymes) • Structure (collagen)

47. Proteins: Molecular Machines • Signaling(hormones, kinases) • Transport(energy, oxygen)

48. Protein Structures

49. Information Flow in Nucleated Cell

50. Wild-type hemoglobin DNA 3’----CTT----5’ mRNA 5’----GAA----3’ Normal hemoglobin ------[Glu]------ Mutant hemoglobin DNA 3’----CAT----5’ mRNA 5’----GUA----3’ Mutant hemoglobin ------[Val]------ Point Mutation Example: Sickle-cell Disease