2. Introduction to Molecular Biology
Welcome to Introduction to Bioinformatics Monday, 23 January 2012
Introduction to Molecular Biology
What do we talk about?
Determined by Questionnaires

7. Fraction of participants handing in questionnaires
Fraction of participants active on BioBIKE

8. Your Questions
…how to submit problem sets. Do we type up our responses separately and them to you, submit them on Blackboard, or print and bring them to class?

10. I would like E and F explained better

11. Identify the protein in
Strategies of Life
Study Question 5
Identify the protein in
Study Question 6
Pick out the polymers… which organism specific?
Questionaire II.C
How do lipids self-assemble?

12. Proteins Study Question 8 Why isn't glycogen as varied as protein?
How do genes exert control over cellular processes?
Study Question 12
How does entire the protein determine chymotrypsin function?
Study Question 13
How does glycophorin enter a membrane?
Study Question 14
What kinds of mutations affect protein functions?
Questionaire IV.H
What does all this have to do with bioinformatics?

13. Identify the protein in
Strategies of Life
Study Question 5
Identify the protein in
Study Question 6
Pick out the polymers… which organism specific?
Questionaire II.C
How do lipids self-assemble?

19. Why?

20. Study Question 4 What is an example of a household item that is hydrophobic

28. How do proteins enter membranes? Identify the protein in
Study Question 13
Study Question 5
How do proteins enter membranes?
Identify the protein in

29. I want to have a step by step understanding of how the lipids in soap interact with grime on our bodies and wash away with water.
Study Question 4 What is an example of a household item that is hydrophobic

30. Water
Finger

31. Water
Finger

32. Water
Finger

33. Water
Finger

37. How do genes exert control over cellular processes?
Information
+ Self-assembly
Structure + Function
Protein
DNA
C G A C C A T C G C C T T A G T A C
Study Question 11
How do genes exert control over cellular processes?

38. Study Question 12
If the critical part of an enzyme is its active site, what's the use of the rest of the protein?

39. Study Question 12 Gly-193 His-57 Ser-195 Asp-102
If the critical part of an enzyme is its active site, what's the use of the rest of the protein?
Gly-193
His-57
Ser-195
Asp-102

40. Study Question 12 Gly-193 His-57 Ser-195 Asp-102
If the critical part of an enzyme is its active site, what's the use of the rest of the protein?
Gly-193
His-57
Ser-195
Asp-102

41. Study Question 12 Gly-193 His-57 Ser-195 Asp-102
If the critical part of an enzyme is its active site, what's the use of the rest of the protein?
Gly-193
His-57
Ser-195
Asp-102

42. How does a membrane form?

43. Study Question 13
How did glycophorin A gain its proper position in the red blood cell membrane.

44. How does protein get inside?
Study Question 13
How did glycophorin A gain its proper position in the red blood cell membrane.
How does protein get inside?

45. Study Question 13
How did glycophorin A gain its proper position in the red blood cell membrane.

46. Study Question 13
How did glycophorin A gain its proper position in the red blood cell membrane.

47. Study Question 13
How did glycophorin A gain its proper position in the red blood cell membrane.

48. Study Question 14
What kind of change in the amino acid sequence of a protein might cause it not to work?

49. What does all this have to do with bioinformatics?
Questionnaire IV.H
What does all this have to do with bioinformatics?

50. How do genes exert control over cellular processes?
Information
+ Self-assembly
Structure + Function
Protein
DNA
C G A C C A T C G C C T T A G T A C
Study Question 11
How do genes exert control over cellular processes?

52. What does this have to do with bioinformatics?
Structure
Genomics
TCTACTTATA TTCAATCCAC AGGGCTACAC
AAGAGTCTGT TGAATGAACA CATACATGGT
TTCTGTCTGC TCTGACCTCT GGCAGCTTTC TGGATTTCGG AACTCTAGCC TGCCCCACTC GAACCTTAGT GACTTCTGCT ATACCAAAGT CTCCGTAAAC CTCTAACATG ATGTCAGCAA TGAATAAACT TTGTTAAAGG TACAAATGAA
AAGAGTTTAA AGTTAAAAAC GAATTGCAGT AAACCTGTAT GGTTACATGA ACTGCCTAAA TTATATATTT TAAGAAATTA ATTGCAATTA CCCCAGCTGT CATTAAAAAG AGGCAAATAC GACAGCACTG ACCCTCAAGA AGGCACCGGC GCTGAAATTC CGCTGAGAGC AGAGTGGTAC CCCTGCACCA GGTCTTTCCT GTGGGCACTG ATGAATGACT GAACGAACGA TTGAATGAAA
Metabolomics
What does this have to do with bioinformatics?
Proteomics
Transcriptomics
Systems

53. What is bioinformatics?
TGAGACACATATTTTTGATATTCCAGTTGTTGCAATC
GAATGTAAAACATATTTAGATCTTTAAATGTATGGTAC
ATTCAAGATCCAACCTTCATTCTAGTGTTTAAAGAGAAC
TGATTTGTTTGCAGGGGCAGGAGGCTTTGGTTTAGGTTTTG
AAATGGCAGGCTTCTCTGTACCTTTATCTGTTGAAATTGATACCTGGGCTTGTGATACACTACGCTACAACCGCCCTGATTCAACAGTTATTCAAAATGATATCGGTAACTTTAGTACAGAAAATGACGTTAAGAATATCTGCAACTTTAAACCTGATATTATTATTGGCGGGCCTCCATGCCAGGGATTTAGTATTGCTGGGCCAGCCCAAAAAGATCCTAAAGATCCTAGAAATGG
AATTATCAAACAAATCATATGATCAGAATAATCGCCGTTTAAATCCTCATAAAACT
TTTATTCATCAACTTTGCACAATGGATAAAATTTCTTGAACCTAAAGCGTTTGTCATGGAAAACGTAAAAGGATTGCTATCAAGGAAAAATGCAGAAGGTTTTAAAGTTATAGATA
CTTCTCACTAAATATAAAGATTTTTTAGATCAGCAGCATTATGCAGAAAAATTTGATTCA
AGACGACGGTACTGGTTTAACCAGCCAAATGTTCTTTCTACTACCCACCGTTTGGGCAAAACCT
TTATTAAGAAAACATTTGAAGAACTTGGTTATTTTGTCGAAGTATGGGTTTTAAATGCTGCGGAATATGGCATTCCGCAAATTAGAGAACGTATTTTTATTGTTGGCAATAAAAAAGGTAAAGTACTAGGTATGAGTATTATACCTGCACTAACTTTGTGGGACGCAATATCAGACTTACCAGAACTTAATGCGCGTGAAGGAAGTGAAGAGCAACCCTATCATTTAAAACCTCAAAATACTTATCAGACTTGGGCTAGAAATGGTAGTGCTACGCTTTACAATCATGTTGCAATGGAACATTCTGACCGTTTAGTAGAACGTTTCCGGCATATAAAATGGGGTGAATCCAGTTCGGATGTATCTAAAGAACATGGAGCTAGACGACGTAGTGGTAATGGTGAATTATCAAACAAATCATATGATCAGAATAATCGCCGTTTAAATCCTCATAAACCGTCTCACACTATTGCTGCGTCATTCTATGCTAATTTTGTCCATCCTTTTCAACATCGAAATTTAACAGCCCGTGAAGGAGCTAGAATCCAATCTTTTCCAGATAACTATAGATTTTTTGGAAAAAAAACTGTCGTATCTCATAAACTATTGCATCGAGAAGAAAGATTTGATGAAAAATTTCTTTGTCAATATAATCAAATCGGTAATGCTGTACCCCCTCTTCTCGCTAAAGTAATTGCACATCATCTTCTAGAGAAATTAGAGTTATGCCAACAACTGATAGAAATCCTCTAGTGCATGGATCAAATCTTGAACAAAAAGAGAATCATCGTACAAAATACAGAGATACTGAAAGCAGGACTTTCCTTAGAGAAATCAGAACTGAATATGACAAATGGCATAAAGCAAATATGAACCTGGTTGGACCAAAATCAGAAATTACTGACCAAGATGATTCAATTATTACTCAAAGAGTGGAACTTCTCACTAAATATAAAGATTTTTTAGATCAGCAGCATTATGCAGAAAAATTTGATTCAAGATCCAACCTTCATTCTAGTGTTTTAGAGACCATTTATAAAGTAAATCTTTAGACGACTAGACGACGTAGCATAATACGAGTCATAACGGCATATATGGCAGCCTCACTCATTTCTGGGAGACGCTCATAATCCTTACTGAGACGACGGTACTGGTTTAACCAGCCAAATGTTCTTTCTACTACCCACCGTTTGGGCAAAACCTGAAATTCTTGATTAGTACGCCGGATTACCTCAACATGAGCTTGAATCATCAGCCAAACAGAGAGCGCAAATTTATCACCGTCATAGCCGGAATCAACCCAGATGACTTCAACTTTTTCCAGTAATTCTGGACGCTCTTCTAACAGTTCCATCAAAGTATAGGCGGCAAGTAATCTTTCTCCAGCATTTGCTTCACTTACAACCACTTTTAACAAAAGTCCCAGACTATCAACCAAAGTTTGCCGCTTTCGTCCTTTTACCTTCTTGCCACCATCAAAACCGTACACATCCCCCTTTTTTCAGTCGTTTTTACCGACTGGCTGTCTGCCGCGATCGCCGTGGGTTGAGTTGACTTCCCCATTTTTTGACGAACTTGATCGCGCAAAGTATGATTCATTTCAGTTGAACTAGGAGGAAAATCCCCTGGAAGCATATCCCACTGACAACCTGTTTTCAGATGGTAGTAGATAGCGTTGCATACTTCTCGCATATCAGTTGTTCGGGGATGCCCACCGCATTTAGCGGGTGGAATCAAAGGAGCTAAAATTGCCCATTCTGAGTCATTAAGGTCTGTAGAATAAGACTTTCGTCTCATTGTTTCCTATGTAAATACACTCTACAAACAGTATCTTATCGCTGCCTTTTTATCTTAGCTCTCCTTTAGATTTACTTTATAAATAGCCTCTTAGAAGAATTTCTTTATTATTTATTTAAAGATTTAGTACAAGATTTCGGGCAGAACGCTCTTATTGGTAAGTCACACACGTTCAAAGATATTTTCTTCGTACCACCAAAATATTCTGAAATGCTCAAGCGACCTTATGCGCGAATTGAGAGAAAAGATCATGATTTCGTAATTGGTGCAACTGTTCAAGCATCGCTTGAAGCAGCACCTCCTCCAGAACAAAACCATGCTTGAGGGATCTTCACGCGCAGCAGAGGATTTAAAAGCGAGAAATCCTAACAGTTTATACCTTGTGGTTATGGAATGGATAAAACTGACCAATGATGTAAATTTACGAAAATATAAAGTTGATCAAATTTATGTACTACGTCAGCAAAAAAATACTGATAGAGAGTTTAGGTATGAGTCAACTTACATAAAAAAT
What is bioinformatics?

54. Michael Montague J Craig Venter Institute
Science (17 Dec 2010) 330:1605
IV.G. How a greater ability to predict protein function from its primary structure would change the world we live in
Michael Montague J Craig Venter Institute
Wednesday, January 26, 12:30 (12:15 food)
Engineering West Building, Room 401

55. What at root do enzymes control?
Study Question 1
What at root do enzymes control?

57. What at root do enzymes control?
Study Question 1
What at root do enzymes control?

58. What at root do enzymes control?
Study Question 1
What at root do enzymes control?
Glucose- 6-phosphate
Glucose- 1-phosphate
Glucose-6-phosphate isomerase
Fructose- 6-phosphate

59. What at root do enzymes control?
Study Question 1
What at root do enzymes control?

60. What at root do enzymes control?
Study Question 1
What at root do enzymes control?

61. What at root do enzymes control?
Study Question 1
What at root do enzymes control?

62. What at root do enzymes control?
Study Question 1
What at root do enzymes control?

63. What at root do enzymes control?
Study Question 1
What at root do enzymes control?
Glucose- 6-phosphate
Glucose- 1-phosphate
Glucose-6-phosphate isomerase
Fructose- 6-phosphate

64. How do genes exert control over a cell?
Study Question 2
How do genes exert control over a cell?
mRNA

65. Study Question 6 A. phenylalanine B. protein C. starch
SQ6. Pick out from the list below those compounds that are polymers. Which are identical whether isolated from snails or whales?
A. phenylalanine B. protein C. starch
D. sugar E. acetyl CoA F. actin/myosin
G. nucleoside triphosphates H. hydrophilic compounds

66. Polymers: Organism-specific
Study Question 6
Polymers: Organism-specific
Monomers: Found in all life

67. Polymers: Organism-specific
Study Question 6
Polymers: Organism-specific
Monomers: Found in all life

68. Polymers: Organism-specific
Study Question 6
Polymers: Organism-specific
Monomers: Found in all life

69. Study Question 6 A. phenylalanine B. protein C. starch
SQ6. Pick out from the list below those compounds that are polymers. Which are identical whether isolated from snails or whales?
A. phenylalanine B. protein C. starch
D. sugar E. acetyl CoA F. actin/myosin
G. nucleoside triphosphates H. hydrophilic compounds
glucose
starch

70. Second intercepted message
Study Question 8
SQ8. Glycogen is a linear array of glucose. Why isn't glycogen as varied in its properties as protein?
Intercepted message
Val-Gly-Ser-Val-Cys-Ile-Glu-Ile-Val-Glu-Gly-Asn-Pro-His-Leu-Arg-Ser-Leu-Leu-Gly-Trp-His-Leu-Gln-Gln-Leu-Glu-Tyr-Arg-Val-His-Gln-Ala-Ala-Ser-Ile-Tyr-Gln-Ala-Arg-Glu-Ala-Phe-Leu-Ser-His-Gln-Pro-Thr-...
Second intercepted message
Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-Glc-...

71. Polymers: Organism-specific
Study Question 6
Polymers: Organism-specific
Monomers: Found in all life

72. Polymers: Organism-specific
Study Question 6
Polymers: Organism-specific
Monomers: Found in all life

75. Questionnaire III.D Primary Structure 1. Enumeration
The distinction between primary, secondary, tertiary, and quaternary structures of proteins?
Primary Structure
1. Enumeration
2. Local interaction
3. Distant interaction
4. Interaction between subunits

76. Questionnaire III.D 1. Enumeration Primary Structure
The distinction between primary, secondary, tertiary, and quaternary structures of proteins?
1. Enumeration
Primary Structure
2. Local interaction
Secondary Structure
3. Distant interaction
4. Interaction between subunits

77. Questionnaire III.D 1. Enumeration Primary Structure
The distinction between primary, secondary, tertiary, and quaternary structures of proteins?
1. Enumeration
Primary Structure
2. Local interaction
Secondary Structure
3. Distant interaction
Tertiary Structure
4. Interaction between subunits

78. Questionnaire III.D 1. Enumeration Primary Structure
The distinction between primary, secondary, tertiary, and quaternary structures of proteins?
1. Enumeration
Primary Structure
2. Local interaction
Secondary Structure
3. Distant interaction
Tertiary Structure
4. Interaction between subunits
Quaternary Structure

79. Processing / Translocation
Central Dogma: DNA to RNA to Protein
Replication
Processing / Translocation