Syllabus
Fall Semester 2017
August
15, 2017
(Latest update overrides all previous versions, electronic
and print.)
MWF
10:10 AM-11:00 AM (Period 3)
SMA 215
Dr.
Wade Powell
FSH 202, (740) 427-5396
powellw[a]kenyon.edu
Office hours:
M,T,R,F: 1:30 - 3:00 PM
(and by appointment; sorry, never on Wednesdays)
Introduction:
The molecular and genomic basis of life is at the heart of modern
biology. In BIOL 263, we will learn techniques and explore research
questions at the forefront of molecular biology, focusing on the
mechanisms by which the information of the genome is expressed to
form the functional molecules of living cells and organisms. The
processes of DNA replication, recombination and repair,
transcription of RNA from DNA templates, and translation of RNA into
protein are discussed in the context of current research, frequently
using primary literature. The function of genes and regulation and
measurement of gene expression are treated in depth. Students
analyze and publish interactive tutorials on the structure and
function of key macromolecules. This intermediate-level course
presumes a strong background in the basics of protein
structure/function, central dogma processes, fundamental molecular
techniques for manipulating nucleic acids and proteins, and general
chemistry.
Required prerequisites: BIOL 115, 116; one year of chemistry
(Intro or Honors Intro); or permission of the
instructor.
Recommended prerequisite or co-requisite: CHEM 231 and 232 (Organic
Chemistry).
Reading Materials and Resources:
All reading assignments must be completed before class on the date indicated on syllabus.
Assignments and Grades: Your letter grade is assigned at the end of the course based on performance in the following areas:
Course Schedule
Day
|
Date
|
Topic;
interesting links
|
Primary
Reading Assignment
|
Supporting
Reading
|
Part
I: Molecular Interactions
|
||||
F |
Aug
26
5 |
Course
Introduction. Nucleic acid and nucleotide structure. |
DNA intro; B-DNA; A-DNA | |
M |
Aug
28
|
Amino acid structure. Weak bonds in macromolecules. | Watson Ch 3, pp. 55-63; Ch. 6, pp. 121-122 + Fig. 6-2. | Weak bonds. Amino Acids; CAP; Ident |
W |
Aug
30
|
Advanced DNA structure: Base Tautomers, Supercoiling | Watson Ch 4. | Adv DNA; Z-DNA ; Triplex; Quad; base tautomers; supercoiling; Topoisomerase |
F |
Sept
1
|
Protein
Structure: Helices, strands, sheets, interactions
between aa residues |
Ch 6, pp. 121-129. |
AA2
in proteins. Ch. 6, pp. 130-144. |
M |
Sept
4
|
Methods for Solving Macromolecular Structures. Intro to pdb and JMOL |
Protein Purification: Ch. 7, pp. 148-149. Ch 4, p. 88. basic X-ray; another explanation (pdf). |
Protein
purification by liquid chromatography Critical Thinking: |
W |
Sept
6
|
Structure of a DNA binding protein, ADAR1
|
Schwartz
99; |
The famous Gillen guide to reading journal articles. Vocab; |
Part
II: Gene Expression
|
||||
F |
Sept
8
|
Transcription
initiation, elongation, termination |
Watson Ch 13, pp. 429-447. | Structures: RNAP open complex; RnaPol-Euk; movies! |
M |
Sept
11
|
Transcription
Research: RNA polymerase "scrunching" |
Watson Ch. 13, pp. 441-442 |
Background: Single-molecule techniques explained. DNA footprinting: Watson Ch. 7, pp. 184-185. |
W |
Sept
13
|
Bacterial Gene Regulation at level of transcription initiation. |
Watson Ch 18, pp. 615-636 | CAP-CTD;
Lac
repressor; Benoff Cooperative binding |
R |
Sept 14 |
Chemistry/BMB Seminar: Susan Schroeder, Dept. of Chemistry and Biochemistry, University of Oklahoma |
Exploring RNA structure,
function, and energetics |
|
F |
Sept
15
|
Bacterial
gene regulation, cont'd; Regulation of events after initiation: Riboswitches, attenuation |
Watson
Ch. 20, pp. 703-708; |
-Soukup
2004 review -Breaker Lab Riboswitch site (Yale) &movie -riboswitch methods/data |
M |
Sept
18
|
Unique
mechanism of attenuation in Bacillus. |
Paper:
Antson 99 |
|
W |
Sept
20
|
Catch-up
|
|
|
R |
Sept 21 |
Biology/BMB Seminar: Arianna Smith Dept. of Obstetrics, Gynecology, and Reproductive Biology, Michigan State University and Biology Department, Kenyon College |
Exploring the Role of Prenatal Maternal Stress on Allergic Asthma Development in Offspring | |
F |
Sept
22
|
Exam I (in class). | score distribution | |
M |
Sept
25
|
Eukaryotic
Basal Transcription Factors. DAB
Pol II; TBP; TAF;
solving
the structure of RNA pol II. |
Watson
Ch. 13 pp.448-464 |
gel
shifts: Watson Ch. 7, pp. 183-184 chromatography: Ch. 7, pp. 173-177. |
W |
Sept
27
|
Eukaryotic Transcription, cont'd. | ||
F |
Sept
29
|
Eukaryotic
Transcription Research: GTFs and promoter
clearance |
Pal et al. 2005 | |
M | Oct
2
|
Eukaryotic Transcriptional Regulation | Watson Ch, 19, pp. 657-665 + 669-686 | |
W |
Oct
4
|
Nucleosomes & Transcriptional regulation; Histone Code. Nucleosome tutorial | Watson
Ch. 8 pp. 219-255; Ch. 19 pp. 665-669; Ch. 7, pp. 185-187. Histone binding sites: Nature N&V 2006 |
|
F |
Oct
6
|
October Reading Days; No Class | ||
M |
Oct
9
|
Research in Eukaryotic Transcriptional Regulation: Chromatin Immunoprecipitation; Histone acetyltransferase recruitment
|
Sharma
2002 See moodle for guided meditation assignment. |
ChIP:Watson Ch. 21, pp. 751-752; 778-780. cross-link chemistry PCR: Watson Ch. 21, pp. 751-752 Remember PCR? |
W |
Oct
11
|
Due date: Molecular Tutorial Proposal | (instructions and electronic submission page on moodle) | |
R |
Oct
12 |
Biology/BMB
Seminar: Heidi Andersen, MD Pediatric Infectious Disease, Cincinnati Children's Hospital |
Metagneomic
shotgun sequencing for detection of colonization,
transmission, and invasion with multidrug resistant pathogens
in high risk children |
4:00 PM, HIG AUD |
F |
Oct
13
|
Watson Ch. 14: pp. 467-477, 480-487, 491-496. | Family
Weekend; Summer Science Posters |
|
M |
Oct
16
|
Splicing conclusion; Peptide bond formation; ribosome size | Watson Ch. 15, pp. 509-535. | |
W |
Oct
18
|
Translation basics; initiation. Initiation. PDB; ribosome structural primer | ||
F |
Oct
20
|
Translation elongation, termination. | Watson Ch. 15. pp. 535-549. | |
M |
Oct
23
|
Translation Research: Ribosome hybrid state | Dorner et al. 2006 | Watson Ch. 15: pp. 552-553 |
T |
Oct
24 |
Chemistry/BMB
Seminar: Chris Neale, Center for Nonlinear Studies, Los Alamos National Laboratory |
Structure/function
of G-protein coupled-receptors |
|
W |
Oct
25
|
RNA
Interference Animation from Nature Reviews Genetics . |
Wilson
and Doudna 2013 (RNAi review
paper) Watson Ch. 20, pp. 710-727. |
|
F |
Oct
27
|
Exam II (points to ponder) | ||
M |
Oct
30
|
DNA Replication; Beta ring; DNA Rep; Replisome | Watson Ch. 9, pp. 257-287 | |
Part
III: DNA Replication, Repair, Recombination
|
||||
W |
Nov
1
|
DNA
Replication, cont'd.; Web Project Workshop, 7-10 PM |
Watson Ch. 9, pp. 288-296 | |
R | Nov 2 | Biology/BMB
Seminar: Ann Miller, Dept. of Molecular, Cellular, and Developmental Biology, University of Michigan Web Project Workshop, 7-10 PM |
Regulation
and localization of RhoA GTPase in cytokinesis |
|
F |
Nov
3
|
Telomerase and telomeres. Telomerase structure. Telomeres 12-mer; 22-mer; Ten1, Stn1 |
Watson
Ch. 9 p. 302-310. Blackburn 2000 review |
|
S | Nov 5 |
Web Project Workshop, 4-6 PM | ||
M |
Nov
6
|
Replication
Paper--Single-molecules replisome study: Are leading and
lagging strad polymerases really coordinated? |
Graham
et al. 2017 Guided meditation on moodle due at beginning of class |
Don't ignore the supplemental information figures! |
W |
Nov
8
|
DNA
Sequencing, RNAseq |
Watson Ch. 2, p. 40-41; Ch. 8, p. 199-208; Ch. 7, p. 158-171. | cycle; pyrosequencing (454); illumina video; another illumina video; cheap genomes |
R |
Nov
9
|
Web Project Workshop, 7-10 PM | ||
F |
Nov
10
|
Research:
ChiPseq Estrogen Receptor Binding throughout the Genome |
Hurtado, et al. 2011. | Integrates: Eukaryotic transcription factors, enhancer elements ChIP, NextGen sequencing, PCR, westerns, siRNAs, cell cycle, cancer |
M |
Nov
13
|
|
Watson
Ch. 10 |
|
W |
Nov
15
|
Homologous Recombination; | Watson Ch. 11: pp. 341-368 and 371-375 | Experiments; RuvA; PNAS; Tn; |
F |
Nov
17
|
Knockout mice in molecular biology Knockout mice, cont'd
|
H19 Gene; Generation of Transgenic animals; MIT core facility |
|
Nov. 20 - Nov 24: Thanksgiving Break | ||||
M |
Nov
27
|
CRISPR Genome Editing | ||
W |
Nov
29
|
Catch-up | |
|
F |
Dec
1
|
Exam III | ||
M |
Dec
4
|
In-class pdb time | ||
W |
Dec
16
|
Student Project Presentations | . | Completed JMol Tutorial |
F |
Dec
8
|
Student Project Presentations |
. |
|
R |
Dec
14
|
Revised Molecular Tutorials Due (corresponds with end of scheduled exam period) | No Broken Links | 9:30 PM |
|
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