Lecture # 1: Molecular and Cellular Biology Overview  http:// www.youtube.com/watch?v =FZtRn1fst-g
WELCOME!
instructor Mark E Minie PhD [email_address]
Class mechanics…
The wiki… http:// uweobasicbiomolcelli.wikispaces.com /
<ul><li>Grading Policies: </li></ul><ul><li>25% Attendance & Engagement  </li></ul><ul><li>25% Self Assessment Exams (simp...
A word about PMIDs and  UW restricted resources…
Tonight’s timeline: 5:30 PM-6:30 PM: Shannon Kuyper Orientation 6:30 PM-6:45 PM: Break 6:45 PM-7:45 PM: Lecture # 1 7:45 P...
<ul><ul><li>Tonight’s take-homes: </li></ul></ul><ul><li>The basic unit of life on Earth is the cell </li></ul><ul><li>All...
What is life?: Dictionary.com  Unabridged (v 1.1)  -  Cite This Source  -  Share This   life            laɪf/  Pronunciati...
<ul><ul><li>Problems? </li></ul></ul>
<ul><ul><ul><li>Viruses?  </li></ul></ul></ul><ul><ul><ul><li>Mimivirus and the “sputnik” virophage… </li></ul></ul></ul><...
<ul><ul><ul><li>Prions? </li></ul></ul></ul><ul><ul><ul><li>self-replicating proteins… </li></ul></ul></ul><ul><ul><ul><li...
<ul><ul><ul><li>Non-replicating organisms? </li></ul></ul></ul><ul><ul><ul><li>The Hayflick Limit… </li></ul></ul></ul>Hay...
<ul><ul><ul><ul><li>Computer programs, viruses, worms etc… </li></ul></ul></ul></ul>http:// en.wikipedia.org/wiki/Spore_(g...
<ul><ul><ul><li>Many other examples? </li></ul></ul></ul><ul><ul><ul><li>Self-replicating DNA nanomachines/DNAzymes  </li>...
Are aliens among us?  PMID: 18237098
<ul><ul><li>For our purposes: </li></ul></ul><ul><ul><ul><li>CHONPS+”minor contaminants” based… </li></ul></ul></ul><ul><u...
<ul><ul><li>KEY CONCEPT I: </li></ul></ul><ul><ul><ul><li>The basic unit of life on Earth is the cell </li></ul></ul></ul>
There are two different types of cells on Earth*… *Really three, but we won’t be talking about the Archaea today :)  Proka...
And they are simultaneously the same  but very different in structure, function,  composition, behavior, etc...
Prokaryotic cell structure
Eukaryotic animal cell structure
Eukaryotic plant cell structure
Size-eukaryotes are generally bigger than prokaryotes
prokaryotes & eukaryotes have different  genetic structures  as well…
<ul><ul><li>KEY CONCEPT II: </li></ul></ul><ul><ul><ul><li>All organisms on earth are related by evolution from a common a...
THE TREE OF LIFE Fun with genealogy.  PMID: 9398070
<ul><li>Most of modern cell and molecular biology has been  </li></ul><ul><li>derived from the study of about 8 “model” or...
<ul><ul><li>KEY CONCEPT III: </li></ul></ul><ul><ul><li>The properties and behaviors of cells can be understood in terms o...
Molecular motors http:// www.youtube.com/watch?v =InIha7bCTjM&feature=related
<ul><ul><li>KEY CONCEPT IV: </li></ul></ul><ul><ul><ul><li>The “Central Dogma” of molecular biology… </li></ul></ul></ul><...
The central dogma of molecular biology
The sequences of these biomolecules are digital in nature… and thus lend themselves to digital analysis with computers… DN...
<ul><ul><li>KEY CONCEPT V: </li></ul></ul><ul><ul><ul><li>The digital nature of DNA, RNA and Protein sequences makes it po...
http:// www.ncbi.nlm.nih.gov/sites/gquery A key bioinformatics resource—ENTREZ  The National Center for Biotechnology Info...
<ul><ul><li>KEY CONCEPT VI: </li></ul></ul><ul><ul><ul><li>The key players in the central dogma are  “informational macrom...
deoxyribonucleotide sequences self-organize  into a double helix, amino acid sequences self-organize into various peptide ...
and it is this informational and self-organizing chemical  nature that forms the basis for all structural and behavioral a...
and is the basis for our current concepts of the origin of cellular life on Earth…
“ Classic” Miller-Urey Experiment
<ul><li>“ Genes first”-the RNA world model for the origin of life… </li></ul><ul><li>Metabolism first… </li></ul><ul><li>E...
Metabolome The sum total of the chemical  reactions and pathways in a given organism
<ul><ul><li>KEY CONCEPT VII: </li></ul></ul><ul><ul><ul><li>Cells function  via  metabolic pathways and processes </li></u...
A “simple” metabolic pathway…GLYCOLYSIS http:// www.biocarta.com/pathfiles/h_glycolysisPathway.asp
http:// www.expasy.ch /tools/pathways/ Metabolic pathways and cellular processes THE BIG PICTURE
These cellular processes and metabolic pathways are  mediated by proteins, carbohydrates, lipids, DNA, RNA and other molec...
http:// www.biocyc.org / Computer generated models of metabolic pathways…
<ul><ul><li>KEY CONCEPT VIII: </li></ul></ul><ul><ul><ul><li>Biology is currently undergoing  </li></ul></ul></ul><ul><ul>...
Vast amounts of data at every level, with the blurring barriers between biology and information technology  DNA Sequence D...
http:// www.youtube.com/watch?v =5ukPD4G5eSw  The inner complexity of a cell (eukaryote)…
Open discussion and Q&A
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Lecture 1 Molecular And Cellular Biology Overview

  1. 1. Lecture # 1: Molecular and Cellular Biology Overview http:// www.youtube.com/watch?v =FZtRn1fst-g
  2. 2. WELCOME!
  3. 3. instructor Mark E Minie PhD [email_address]
  4. 4. Class mechanics…
  5. 5. The wiki… http:// uweobasicbiomolcelli.wikispaces.com /
  6. 6. <ul><li>Grading Policies: </li></ul><ul><li>25% Attendance & Engagement </li></ul><ul><li>25% Self Assessment Exams (simply taking) </li></ul><ul><li>25% Mid-Term Exam </li></ul><ul><li>25% Final Exam </li></ul>
  7. 7. A word about PMIDs and UW restricted resources…
  8. 8. Tonight’s timeline: 5:30 PM-6:30 PM: Shannon Kuyper Orientation 6:30 PM-6:45 PM: Break 6:45 PM-7:45 PM: Lecture # 1 7:45 PM-8:00 PM: General discussion and Q&A
  9. 9. <ul><ul><li>Tonight’s take-homes: </li></ul></ul><ul><li>The basic unit of life on Earth is the cell </li></ul><ul><li>All organisms on earth are related by evolution </li></ul><ul><li>from a common ancestor which existed on Earth </li></ul><ul><li>about 4.0-3.5 billion years ago… </li></ul><ul><li>III. The properties and behaviors of cells can be understood </li></ul><ul><li>in terms of chemistry… </li></ul><ul><li>The “Central Dogma” of molecular biology…DNA>RNA>PROTEIN </li></ul><ul><li>The digital nature of DNA, RNA and Protein sequences makes it </li></ul><ul><ul><li>possible to study and simulate the structures and functions of these critical </li></ul></ul><ul><ul><li>biological macromolecules using the new science of Bioinformatics </li></ul></ul><ul><li>VI. The key players in the central dogma are “informational macromolecules”, </li></ul><ul><ul><li>and are “self-organizing”… </li></ul></ul><ul><li>VII. Cells function via metabolic pathways and processes </li></ul><ul><li>VIII. Biology is currently undergoing rapid and radical change… </li></ul>
  10. 10. What is life?: Dictionary.com Unabridged (v 1.1) - Cite This Source - Share This life       laɪf/ Pronunciation Key - Show Spelled Pronunciation [lahyf] Pronunciation Key - Show IPA Pronunciation noun, plural lives       laɪvz/ Pronunciation Key - Show Spelled Pronunciation [lahyvz] Pronunciation Key - Show IPA Pronunciation , adjective – noun 1.the condition that distinguishes organisms from inorganic objects and dead organisms, being manifested by growth through metabolism, reproduction, and the power of adaptation to environment through changes originating internally. 2.the sum of the distinguishing phenomena of organisms, esp. metabolism, growth, reproduction, and adaptation to environment.
  11. 11. <ul><ul><li>Problems? </li></ul></ul>
  12. 12. <ul><ul><ul><li>Viruses? </li></ul></ul></ul><ul><ul><ul><li>Mimivirus and the “sputnik” virophage… </li></ul></ul></ul><ul><ul><ul><li>http:// en.wikipedia.org/wiki/Mimivirus </li></ul></ul></ul><ul><ul><ul><li>The virophage as a unique parasite of the giant mimivirus. PMID: 18690211 </li></ul></ul></ul>
  13. 13. <ul><ul><ul><li>Prions? </li></ul></ul></ul><ul><ul><ul><li>self-replicating proteins… </li></ul></ul></ul><ul><ul><ul><li>http:// en.wikipedia.org/wiki/Prions </li></ul></ul></ul>The expanding universe of prion diseases. PMID: 16609731
  14. 14. <ul><ul><ul><li>Non-replicating organisms? </li></ul></ul></ul><ul><ul><ul><li>The Hayflick Limit… </li></ul></ul></ul>Hayflick, his limit, and cellular ageing. PMID: 11413492
  15. 15. <ul><ul><ul><ul><li>Computer programs, viruses, worms etc… </li></ul></ul></ul></ul>http:// en.wikipedia.org/wiki/Spore_(game )
  16. 16. <ul><ul><ul><li>Many other examples? </li></ul></ul></ul><ul><ul><ul><li>Self-replicating DNA nanomachines/DNAzymes </li></ul></ul></ul>A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron. PMID: 14961116 Functional DNA nanotechnology: emerging applications of DNAzymes and aptamers. PMID: 17056247
  17. 17. Are aliens among us? PMID: 18237098
  18. 18. <ul><ul><li>For our purposes: </li></ul></ul><ul><ul><ul><li>CHONPS+”minor contaminants” based… </li></ul></ul></ul><ul><ul><ul><li>H 2 O solvent </li></ul></ul></ul><ul><ul><ul><li>self-contained </li></ul></ul></ul><ul><ul><ul><li>self-replicating </li></ul></ul></ul><ul><ul><ul><li>DNA/RNA/PROTEIN/LIPID/CARBOHYDRATE </li></ul></ul></ul><ul><ul><ul><li>components (“PARTS”) </li></ul></ul></ul><ul><ul><ul><li>Adaptive short-term </li></ul></ul></ul><ul><ul><ul><li>Adaptive long-term </li></ul></ul></ul>
  19. 19. <ul><ul><li>KEY CONCEPT I: </li></ul></ul><ul><ul><ul><li>The basic unit of life on Earth is the cell </li></ul></ul></ul>
  20. 20. There are two different types of cells on Earth*… *Really three, but we won’t be talking about the Archaea today :) Prokaryote Eukaryote plant animal
  21. 21. And they are simultaneously the same but very different in structure, function, composition, behavior, etc...
  22. 22. Prokaryotic cell structure
  23. 23. Eukaryotic animal cell structure
  24. 24. Eukaryotic plant cell structure
  25. 25. Size-eukaryotes are generally bigger than prokaryotes
  26. 26. prokaryotes & eukaryotes have different genetic structures as well…
  27. 27. <ul><ul><li>KEY CONCEPT II: </li></ul></ul><ul><ul><ul><li>All organisms on earth are related by evolution from a common ancestor which existed on Earth about </li></ul></ul></ul><ul><ul><ul><li>4.0-3.5 billion years ago… </li></ul></ul></ul>
  28. 28. THE TREE OF LIFE Fun with genealogy. PMID: 9398070
  29. 29. <ul><li>Most of modern cell and molecular biology has been </li></ul><ul><li>derived from the study of about 8 “model” organisms: </li></ul><ul><ul><li>e. coli </li></ul></ul><ul><ul><li>yeast </li></ul></ul><ul><ul><li>c. elegans (nematode) </li></ul></ul><ul><ul><li>Drosophila (Fruit Fly) </li></ul></ul><ul><ul><li>Arabidopsis </li></ul></ul><ul><ul><li>Mouse </li></ul></ul><ul><ul><li>Rat </li></ul></ul><ul><ul><li>Human </li></ul></ul><ul><li>Based on the principle of conservation through evolution, </li></ul><ul><li>the lessons learned from these “models” are assumed to </li></ul><ul><li>be applicable to all terrestrial cells and organisms…there </li></ul><ul><li>are exceptions however…more on this later…much later… </li></ul>Model systems
  30. 30. <ul><ul><li>KEY CONCEPT III: </li></ul></ul><ul><ul><li>The properties and behaviors of cells can be understood in terms of chemistry… </li></ul></ul>
  31. 31. Molecular motors http:// www.youtube.com/watch?v =InIha7bCTjM&feature=related
  32. 32. <ul><ul><li>KEY CONCEPT IV: </li></ul></ul><ul><ul><ul><li>The “Central Dogma” of molecular biology… </li></ul></ul></ul><ul><ul><ul><ul><ul><li>DNA>RNA>PROTEIN </li></ul></ul></ul></ul></ul>
  33. 33. The central dogma of molecular biology
  34. 34. The sequences of these biomolecules are digital in nature… and thus lend themselves to digital analysis with computers… DNA Protein … arrsrarklqrmkql … … tggagatgacgtca … … 0111000101011111 … … 010110101110000 … RNA … uggagaugacguca … … 0111000101011111 …
  35. 35. <ul><ul><li>KEY CONCEPT V: </li></ul></ul><ul><ul><ul><li>The digital nature of DNA, RNA and Protein sequences makes it possible to study and simulate the structures </li></ul></ul></ul><ul><ul><ul><li>and functions of these critical biological macromolecules… </li></ul></ul></ul><ul><ul><ul><li>using the new science of Bioinformatics </li></ul></ul></ul>
  36. 36. http:// www.ncbi.nlm.nih.gov/sites/gquery A key bioinformatics resource—ENTREZ The National Center for Biotechnology Information (NCBI)
  37. 37. <ul><ul><li>KEY CONCEPT VI: </li></ul></ul><ul><ul><ul><li>The key players in the central dogma are “informational macromolecules”, and are “self-organizing”… </li></ul></ul></ul>
  38. 38. deoxyribonucleotide sequences self-organize into a double helix, amino acid sequences self-organize into various peptide structural motifs…
  39. 39. and it is this informational and self-organizing chemical nature that forms the basis for all structural and behavioral activities of cells…
  40. 40. and is the basis for our current concepts of the origin of cellular life on Earth…
  41. 41. “ Classic” Miller-Urey Experiment
  42. 42. <ul><li>“ Genes first”-the RNA world model for the origin of life… </li></ul><ul><li>Metabolism first… </li></ul><ul><li>Evolution by fusing independent “life-like” components </li></ul><ul><li>into a cell? (viruses?) </li></ul><ul><li>Hot vents? </li></ul><ul><li>Comets? </li></ul><ul><li>Panspermia? </li></ul><ul><li>Novel mechanisms? </li></ul>
  43. 43. Metabolome The sum total of the chemical reactions and pathways in a given organism
  44. 44. <ul><ul><li>KEY CONCEPT VII: </li></ul></ul><ul><ul><ul><li>Cells function via metabolic pathways and processes </li></ul></ul></ul>
  45. 45. A “simple” metabolic pathway…GLYCOLYSIS http:// www.biocarta.com/pathfiles/h_glycolysisPathway.asp
  46. 46. http:// www.expasy.ch /tools/pathways/ Metabolic pathways and cellular processes THE BIG PICTURE
  47. 47. These cellular processes and metabolic pathways are mediated by proteins, carbohydrates, lipids, DNA, RNA and other molecular entities and function in “ real time”—they are only indirectly regulated and controlled by the cellular gene structure…
  48. 48. http:// www.biocyc.org / Computer generated models of metabolic pathways…
  49. 49. <ul><ul><li>KEY CONCEPT VIII: </li></ul></ul><ul><ul><ul><li>Biology is currently undergoing </li></ul></ul></ul><ul><ul><ul><li>rapid and radical change… </li></ul></ul></ul>
  50. 50. Vast amounts of data at every level, with the blurring barriers between biology and information technology DNA Sequence Data RNA Expression Data Protein Structure Data
  51. 51. http:// www.youtube.com/watch?v =5ukPD4G5eSw The inner complexity of a cell (eukaryote)…
  52. 52. Open discussion and Q&A

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