BIO 315 Molecular Biology (MB)
Spring 2020
Current Reading Assignments and Problems (CRAaP)
(and Merlyn's advice to Arthur on being sad...)
Exam 1
Bio315 Exam1 Records
Chapter/Pages |
Probs |
PwrPts1 |
HOs1 |
OOPAs1 |
Articles1 |
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3 |
51-55 |
1-6; 8-11; 14 |
Ch3Part1_s20 |
BondPolarity.pdf |
MolBioArticleQuests |
HistoryMolecBio.pdf |
4 |
77-92; 103-104 |
1-4; 7, 8 |
Ch4Prt1_s20 |
TempDepDNA.pdf |
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watsoncrick |
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Labs |
Lab Exercise |
L-HOs1 |
L-articles |
L-PwrPts |
1 |
Introduction to lab and semester project; check-in, |
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2 |
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Old CRAaP!
Slide-Sets (SS), Lab Work (LW) |
Reading Assignments (RAs) | Practice Problems |
Comments, Articles, HandOuts (HOs) |
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MBpp |
CMBB |
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| Course syllabus - all; (SS)chs1_2s13.pptx; ch2MitMeiPrimer.pptx |
ch1( | ch2: 11, 14 | What is Molecular Biology? What is Life? What is the Scientific Method? Don't forget the clickable links to other pages on the WSS- could be worth a couple of MCs or T/F for exam on the syllabus material; Intro to Major Concepts in MB; outline of Course Contents; The Central Dogma (CD) of Molecular Biology; (basically a review of topics covered in BIO215); selected diseases to show the CD and molecular genetics in action. Review of cytogenetics of chromome segreatation and inedpendent assortment to explain essentials of transmission genetics and recombination; human genome and karyotypes. |
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(SS)ch3WeakBondTheoryS13.pptx; (SS)ch3BuffTrisS13.pptx; (SS)ch3BasicThermS13.pptx |
ch3 | MBpp 1-3; 6-10; 11-14; 16-18 | Review of covalent bonding as perspective for Weak Chemical Interactions, especially H-bonds; stereo-chemistry; pH and HH equation; essential thermodynamics; 2 pdf's (HO) | |
| ch2(15-24; 25-34); ch2(35-43) | CMBB 2.1-5; 6-8; 10; 12-15; 17-18; 23 | pH and pKa and HH equation derivation; applied problems | ||
| (SS)ch7PCRs13.pptx | ch7( | Theory and mechanism of PCR; brief history of its discovery; details of PCR reaction as set up and performed in the lab exercises | ||
| ch8(165-173); ch9(211-216) | CMBB ch8 probs 1-7 | Theory and mechanism of PCR, cont'd; application problems | ||
| (SS)ch6DNAstruct(I).pptx | ||||
| Lab Work (LW) | ||||
| LW #1: Orientation - Lab Calculations Problems; Guidelines for laboratory work and safety rules; formal Guide for semester-long Projects | ch1(1-14; review only if needed) | ch1 CMBB review only if needed; ch2 CMBB basic lab solutions; | ||
| LW #2: Primers Exercises: Unique & degenerate primers and primer properties; (SS)PCR.ppt | ch.() | ch(27-35); ch.8(143-150) | CMBB 2.6-2.13; 8.1-8.6 | Unique & Degenerate Primers Exercises, Primer properties, PCR theory, mechanisms, efficiencies, and laboratory practice; annealing temp calculations; design degenerate primers from a.a. seqs |
| LW #3: PCR of Genomic DNA; Degenerate Primers exercise continued |
Start NCBI, ENSEMBL, KEGG exercises on HOXD10; in silico PCR; Eukaryotic Gene Structure exercises, Critical Questions; What is a Homeobox/homeodomain? | |||
LW #4: analysis of primary PCR products; A.G.E.; sizing producs by graphing standards; electrophoresis theory |
ch.6() | ch.8(147-150) | CMBB 8.6, 8.7 | dsDNA Tm & EtOH precipitation. handouts; Gb.b - Gb.water, delta G handout; base-pair speciificty; Temp effect on Spontaneity HO; essential forces for dsDNA stability - thermodynamics |
| LW#5:Chimera Exercise on A, B, Z DNA; Agarose gels of PCR products; HOs on Homeodomains | ch.21(); ch6() | ch.9(224-236) | CMBB 9.19 | EDTA structure-function; HOs (2) on alpha helices in homeodomains; A.G.E theory and standard curves caluclations; HO on DNA conformations (A, B, Z); HOs on base pair (shear, stretch, etc.) and base step co-ordinates (3 translations, 3 rotations); x,y,z co-ordinate frame |
| Summary: chs 2-6; 21 of MBG, selected assignments and readings as shown above... Labs 1-5 plus all associated exercises and readings/problems in CMBB; Chimera only on A, B, Z DNA conformations | ||||
Exam 2
Slide-Sets (SS), Lab Work |
MBp&P |
CCMB |
Practice Problems |
Comments, Articles, HOs |
Labs#5&6: Chimera Exercises cont'd; Lab#7:: Cloning PCR products; Transformations, Colony picking-streaking;; (SS)CloningTheory(I,II).ppt; BtoA_transition.ppt (not propeller twist slides) |
ch.21() | ch.9(186-189) | CCMB 9.1, 9.2 |
Chimera OnePt questions on NAR paper; coordinate system for visualizing base orientations; B-to-A DNA transitions with OnePt and assigned review paper; DNA ligases, mechanisms; Restriction enzyme theory & practivce, biology & biochemistry, reaction mechanisms; Cloning theory & practice; EcoO109I HO for crystal structure of Type II Restriction enzyme |
| Lab#8: Plasmid DNA Isolations; (SS)CloningTheory(I).ppt |
ch.16(), | c | p | HO on plasmid DNA isolations & biochemistry coordinated with lab work; plasmid to vector biology & biochemistry; vector types; alpha complementation biochemistry; lac operon structure, basic function; HO on Lac Operon |
| (SS)Ch8PolMech.ppt | ch8 |
polymerase enzyme mechanisms (DNA or RNA)(ch8); cancer therapuetics paper and associated OnePt; kinetics of DNA pol; | ||
Exam 3
| Slide sets (SS), Lab work | MBGp&p | CCMB | OnePts, problems | Comments, articles, HOs |
| Pedagogical Reminder ----> | w | w | w | Our Focus: structure/mechanism; conceptual pattern leading to function; the molecular function within some discrete process, which is part of an overall biologcial phenomena. The Goal is to explain the biological phenomenon with its underlying processe(s) and mechanism(s) in terms of molecular principles and concetps, which are fundamental to understaning biology. These molecular, fundamental principles exist, and developed from molecular and biochemical experimental data |
| (SS)ch12-13Mechanisms of Transcription and essential splicing reactions; MTE article and associated assignments (see HO) | ch.12( |
w | OnePtAss on MTE; | Eukaryotic transcription molecular mechanism (initiation - elongation); introduction to biochemistry of splicing reactions: capping, transesterifications, polyadenylating; core promoter elements, GTFs; the MTE article and specific methods for discovering and analyzing core elements in promoters |
| (SS)ch16GeneReg.ppt; Prot-DNAmethods.ppt | ch16 | w | w | Gene Regulation in Prokaryotes - (1) Principles of Transcriptional Regulation; (2)lac operon (focus on CAP/reprssor interactions with DNA); (3) Primer extendion, Gel Mobility Shift assays and DNA Footprinting; chromatin immunoppt; (4) Principles of Cooperativity for SSDBP binding to target sites |
| (SS)ch17GeneReg.ppt; Prot_DNAmethods.pptx, slides 1-8 on handout; remaining slides according to the Slide Summary and GAL4 handouts | ch17: | w | w | Gene Regulation in Eukaryotes - (1) General Principles of Gene Regulation in eukaryotes; (2) Two-hybrid assay; (3) DNA-binding domains - Gal4; (4) the Homeodomain, an extended HTH; zinc-fingers, leucine zippers; primer-extension analyses of Met10 DPE |
| (SS)ch19GeneRegDev.ppt | ch19 | w | w | Gene Regulation during Development - Homeobox genes |
| DNAseq2F08.ppt | w | w | w | DNA cycle-sequencing theory: biochemistry & biophysics; slides & handouts |
| Labs#10: Cycle Sequencing Reactions and processing; set up sequencing plate Labs#11&12: automated DNA sequencing in the CEQ 8000; Bioinformatic analyses of sequence data |
w | w | OnePtAss on Cooperativity; p.572-573 Box 16-3 of text | Lab and lecture discussions of Sequencing Theory & Practice: cylce sequencing biochemistry, extension product preparations, capillary electrophoresis, electropherograms of called-bases |