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BEGR 424/Bio 324 Molecular Biology William Terzaghi Spring, 2013

BEGR 424/Bio 324 Molecular Biology William Terzaghi Spring, 2013. BEGR424/BIO 324 - Resource and Policy Information Instructor: Dr. William Terzaghi Office: SLC 363 Office hours: MWF 10:00-12:00, or by appointment Phone: (570) 408-4762 Email: terzaghi@wilkes.edu.

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BEGR 424/Bio 324 Molecular Biology William Terzaghi Spring, 2013

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  1. BEGR 424/Bio 324 Molecular Biology William Terzaghi Spring, 2013

  2. BEGR424/BIO 324 - Resource and Policy Information Instructor: Dr. William Terzaghi Office: SLC 363 Office hours: MWF 10:00-12:00, or by appointment Phone: (570) 408-4762 Email: terzaghi@wilkes.edu

  3. BEGR424/BIO 324 - Resource and Policy Information Instructor: Dr. William Terzaghi Office: SLC 363 Office hours: MWF 10:00-12:00, or by appointment Phone: (570) 408-4762 Email: terzaghi@wilkes.edu Course webpage: http://staffweb.wilkes.edu/william.terzaghi/BIO324.html

  4. General considerations What do you hope to learn?

  5. General considerations • What do you hope to learn? • Graduate courses • learning about current literature

  6. General considerations • What do you hope to learn? • Graduate courses • learning about current literature • Learning how to give presentations

  7. General considerations • What do you hope to learn? • Graduate courses • learning about current literature • Learning current techniques

  8. General considerations • What do you hope to learn? • Graduate courses • learning about current literature • Learning current techniques • Using them!

  9. Plan A • Provide a genuine experience in using cell and molecular biology to learn about a fundamental problem in biology. • Rather than following a set series of lectures, study a problem and see where it leads us. • Lectures & presentations will relate to current status • Some class time will be spent in lab & vice-versa • we may need to come in at other times as well

  10. Plan A Pick a problem Design some experiments

  11. Plan A Pick a problem Design some experiments See where they lead us

  12. Plan A Pick a problem Design some experiments See where they lead us Grading? Combination of papers and presentations

  13. Plan A • Grading? • Combination of papers and presentations • First presentation:10 points • Research presentation: 10 points • Final presentation: 15 points • Assignments: 5 points each • Poster: 10 points • Intermediate report 10 points • Final report: 30 points

  14. Plan A Topics? Bypassing Calvin cycle Making vectors for Dr. Harms Making vectors for Dr. Lucent Cloning & sequencing antisense RNA Studying ncRNA Something else?

  15. Plan A Assignments? identify a gene and design primers presentation on new sequencing tech designing a protocol to verify your clone presentations on gene regulation presentation on applying mol bio Other work draft of report on cloning & sequencing poster for symposium final gene report draft of formal report formal report

  16. Plan B • Standard lecture course, except: • Last lectures will be chosen by you -> electives

  17. Plan B • Standard lecture course, except: • Last lectures will be chosen by you -> electives • Last 4 labs will be an independent research project

  18. Plan B • Standard lecture course, except: • Last lectures will be chosen by you -> electives • Last 4 labs will be an independent research project • 20% of grade will be “elective” • Paper • Talk • Research proposal • Poster • Exam

  19. Plan B schedule- Spring 2013 • Date TOPIC • JAN 14 General Introduction • 16 Genome organization • 18 Cloning & libraries: why and how • 21 DNA fingerprinting • 23 DNA sequencing • 25 Genome projects • 28 Studying proteins • 30 Meiosis & recombination • FEB 1 Recombination • 4 Cell cycle • 6 Mitosis • 8 Exam 1 • 11 DNA replication • 13 Transcription 1 • 15 Transcription 2 • 18 Transcription 3

  20. 20 mRNA processing 22 Post-transcriptional regulation 25 Protein degradation 27 Epigenetics MAR 1 Small RNA 4 Spring Recess 6 Spring Recess 8Spring Recess 11 RNomics 13 Proteomics 15 Exam 2 18 Protein synthesis 1 20Protein synthesis 2 22Membrane structure/Protein targeting 1 25 Protein targeting 2 27 Organelle genomes 29 Easter Apr 1 Easter

  21. APR 3 Mitochondrial genomes and RNA editing 5 Nuclear:cytoplasmic genome interactions 8 Elective 10 Elective 12 Elective 15 Elective 17 Elective 19 Elective 22 Elective 24 Elective 26 Elective 29Exam 3 May 1 Elective Last Class! ??? Final examination

  22. Lab Schedule • Date TOPIC • Jan 16 DNA extraction and analysis • 23 BLAST, etc, primer design • 30 PCR • Feb 6 RNA extraction and analysis • 13 RT-PCR • 20 qRT-PCR • 27 cloning PCR fragments • Mar 6Spring Recess • 13 DNA sequencing • 20 Induced gene expression • 27 Northern analysis • Apr3 Independent project • 10 Independent project • 17 Independent project • 24 Independent project

  23. Genome Projects Studying structure & function of genomes

  24. Genome Projects • Studying structure & function of genomes • Sequence first

  25. Genome Projects • Studying structure & function of genomes • Sequence first • Then location and function of every part

  26. Genome Projects • How much DNA is there? • SV40 has 5000 base pairs • E. coli has 5 x 106 • Yeast has 2 x 107 • Arabidopsishas 108 • Ricehas 5 x 108 • Humans have 3 x 109 • Soybeans have 3 x 109 • Toads have 3 x 109 • Salamanders have 8 x 1010 • Lilies have 1011

  27. Genome Projects • C-value paradox: DNA content/haploid genome varies widely

  28. Genome Projects • C-value paradox: DNA content/haploid genome varies widely • Some phyla show little variation: • birds all have ~109bp

  29. Genome Projects • C-value paradox: DNA content/haploid genome varies widely • Some phyla show little variation: • birds all have ~109bp • mammals all have ~ 3 x 109 bp

  30. Genome Projects • C-value paradox: DNA content/haploid genome varies widely • Some phyla show little variation: • birds all have ~109bp • mammals all have ~ 3 x 109 bp • Other phyla are all over: • insects and amphibians vary 100 x

  31. Genome Projects • C-value paradox: DNA content/haploid genome varies widely • Some phyla show little variation: • birds all have ~109bp • mammals all have ~ 3 x 109 bp • Other phyla are all over: • insects and amphibians vary 100 x • flowering plants vary 1000x

  32. C-value paradox • One cause = variations in chromosome numbers and ploidy • 2C chromosome numbers vary widely • Haplopappus has 2

  33. C-value paradox • One cause = variations in chromosome numbers and ploidy • 2C chromosome numbers vary widely • Haplopappus has 2 • Arabidopsis has 10

  34. C-value paradox • One cause = variations in chromosome numbers and ploidy • 2C chromosome numbers vary widely • Haplopappus has 2 • Arabidopsis has 10 • Rice has 24 • Humans have 46 • Tobacco (hexaploid) has 72 • Kiwifruit (octaploid) have 196

  35. C-value paradox Chromosome numbers vary So does chromosome size! Reason = variation in amounts of repetitive DNA

  36. C-value paradox Chromosome numbers vary So does chromosome size! Reason = variation in amounts of repetitive DNA first demonstrated using Cot curves

  37. Cot curves • denature (melt) DNA by heating

  38. Cot curves • denature (melt) DNA by heating • dissociates into two single strands

  39. Cot curves • denature (melt) DNA by heating • Cool DNA

  40. Cot curves • denature (melt) DNA by heating • Cool DNA:complementary strands find each other &anneal

  41. Cot curves • denature (melt) DNA by heating • Cool DNA:complementary strands find each other &anneal • hybridize

  42. Cot curves • denature (melt) DNA by heating • Cool DNA:complementary strands find each other &anneal • Hybridize: don't have to be the same strands

  43. Cot curves • denature (melt) DNA by heating • Cool DNA:complementary strands find each other &anneal • Hybridize: don't have to be the same strands • Rate depends on [complementary strands]

  44. Cot curves • 1) denature DNA • 2) cool DNA • 3) at intervals measure • [single-stranded DNA]

  45. Cot curves viruses & bacteria show simple curves Cot is inversely proportional to genome size

  46. Cot curves eucaryotes show 3 step curves Step 1 renatures rapidly: “highly repetitive”

  47. Cot curves eucaryotes show 3 step curves Step 1 renatures rapidly: “highly repetitive” Step 2 is intermediate: “moderately repetitive”

  48. Cot curves eucaryotes show 3 step curves Step 1 renatures rapidly: “highly repetitive” Step 2 is intermediate: “moderately repetitive” Step 3 is ”unique"

  49. Molecular cloning To identify the types of DNA sequences found within each class they must be cloned

  50. Molecular cloning • To identify the types of DNA sequences found within each class they must be cloned • Force host to make millions of copies of a specific sequence

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