Biology 111
Molecules, Genes, and Cells

Fall 2015, Davidson College
MWF 9:30-10:20 in Chambers 3106
Lab Mon 1:30 PM or Tues 8:15 AM in Watson 147
Dr. Karen Hales
Dana 201A, x2324

class schedule
Jump to Aug, Sep, Oct, Nov, Dec

Science news web sites:
Science Daily
Scientific American
New Scientist
New York Times Science Times

lab schedule

Learning objectives: Cellular and molecular biology is a vast discipline that encompasses a number of sub-fields, each of which is growing extremely rapidly. Instead of aiming to learn every detail, students will, by the end of this course, be able to do the following:

Textbooks and other resources:
Life: the Science of Biology, 9th edition, by Sadava, Heller, Orians, Purves, and Hillis (we are deliberately using the 9th edition which is not the latest)
Study Guide and Lab Manual by Campbell, Lom, Hales, Bernd, Sarafova, and Wessner, Fall 2015 version (previous versions will not work!!)
A Short Guide to Writing About Biology, 8th edition, by Jan Pechenik.
Additional handouts and web reading to be announced.

Office hours
Mondays 11 AM-12 PM and Wednesdays 12:50-1:50, as well as Tuesday Common Hours when I don't have other meetings. Sign up for appointments at this web page. You will be able to access the page after I activate the invitation to the class. I'll update the page with new dates and times as the semester progresses; I may vary time slots according to demand. Claim a few consecutive slots if you need more time. I can meet with you at other times if necessary--stop by if my door is open, or email to make an appointment (list three possible dates/time ranges).

Email: You are responsible for all information I send by email, so check your messages each day.

Grading: Your final grade for the course will be calculated as follows:

Three reviews
Daily quizzes and assignments
Lab reports, both written and oral (details)
Final exam
Participation and daily preparation, both lecture and lab
36% (12% each)
9%
25%
20%
10%

%
94-100
90-93.9
87-89.9
83-86.9
80-82.9
77-79.9
73-76.9
70-72.9
66-69.9
60-65.9
0-59.9
Final grade
A
A-
B+
B
B-
C+
C
C-
D+
D
F

Attendance and participation

In class I do not record attendance. However, if you are not there to participate, your participation grade is affected. Laboratory sessions are mandatory. An unexcused absence from lab will result in a full letter grade deduction from your course grade.

Honor Code
You are to affirm your respect for and compliance with the Davidson Honor Code on every assignment. The full Honor Pledge reads as follows: "On my honor I have neither given nor received unauthorized information regarding this work, I have followed and will continue to observe all regulations regarding it, and I am unaware of any violation of the Honor Code by others." Plagiarism is an Honor Code violation and is defined as representing another person's words and ideas as one's own. Please carefully read the Davidson Department of Biology statement on plagiarism for comprehensive information on what constitutes plagiarism and how to avoid it.

Classroom etiquette and use of electronic devices
Do not leave the classroom in the middle of class unless it is a true emergency (in lab it's fine to step out briefly at appropriate stopping points). Set cell phones to silent/no vibration so that they do not disturb/distract you or others. Take handwritten notes unless you have received my permission to use a laptop. Laptops, tablets, and cell phones must be closed or face down on your desk unless I have assigned you to investigate something on the internet during class.

Policy on recording of class
Davidson College policy prohibits audio and video recording of classes by students without permission of the instructor. I will consider permission requests on a case-by-case basis. For students with a disability, permission will always be granted when the accommodations authorized by the Dean of Students Office include recording. Authorized recordings are for the sole use of the individual student and may not be reproduced, sold, posted online, or otherwise distributed.

Disabilities
I will do my best to provide accommodations for students with learning or physical disabilities. If you have a learning disability documented by Davidson College, please let me know during the first week of class so that arrangements can be made. I encourage students with other disabilities to self-identify (confidentiality guaranteed) so that we may explore ways to enhance your learning.

Class materials
PowerPoint files used in class will be posted online by the previous evening. I use PowerPoint only to provide illustrations and outline topics; viewing a PowerPoint file does **not** substitute for attending class. Click the link from the schedule below to download; log in with email credentials. To print, please first set options to include multiple slides per page.

Assignments
Assignments on the syllabus relate to the topic of that day--you must read/listen/view and take notes on material before coming to class, and be ready to answer questions.

Quizzes
There will be regular short written quizzes that cover the previous day's material along with the material assigned for that day. Your two lowest quiz scores will be dropped.

Reviews
There will be three in-class reviews during the semester. The final exam will be administered through the self-scheduled exam system.

Penalty for late assignments
Ten percent per day or part thereof. The full ten percent penalty applies starting at the beginning of each day that the assignment is late; for example, an assignment that is one hour late will have a ten percent penalty applied.

Math, Science, and Economics Center
The MSEC offers free assistance to students in all areas of quantitative and scientific reasoning, with a focus on the introductory courses. Trained and highly qualified peers hold one-on-one and small-group tutoring sessions on a drop-in basis or by appointment, as well as timely recap sessions ahead of scheduled reviews. Emphasis is placed on thinking critically, understanding concepts, making connections, and communicating effectively, not just getting correct answers.  In addition, students can start or join a study group and use the Center as a group or individual study space.  The MSEC is located in the Center for Teaching and Learning in the library.  See the website for hours or contact Dr. Mark Barsoum (mabarsoum or 704-894-2796).

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Class schedule

Date

Topic
Links will become active by the evening before each class.

Click lecture title to download powerpoint file for printing. Use email credentials to log in. You may need to type davidson\username. Please conserve paper by printing double sided, with multiple slides per page.

Assignments
Page numbers refer to the Study Guide (SG) unless otherwise noted. SG assignments normally end with the study questions on the appropriate page.  Assignments accompany the indicated day's lecture. Additional reading TBA.
Web links in Study Guide reading
Web links embedded in the SG reading will also be listed here for convenience
M 8/24

Intro to the course; cells; thinking like a biologist

Read the whole syllabus. You are responsible for knowing all the information/requirements detailed therein.

 
Special assignment to be fulfilled by the afternoon of Thursday September 3rd: everyone must come see me in my office for a least a few minutes. If you want, you may come by in pairs or groups of three, but no more than that. It's best to make an appointment ahead of time, but you are welcome to drop by any time I am in the office. This visit will be worth 3 points on the first review. A visit must take place for me to record your grade on the first review. The purpose is to familiarize you with the location of my office and to help me get to know you.
W 8/26 Beginning of Unit 1: Cellular communication
Unit 1 introduction: Your body's cellular and molecular response to fear. What role does the liver play?
1-5
Note that all Study Guide readings will refer you to more extensive readings in the textbook as well as web reading!
Animated Tutorial 3.1 • Macromolecules
Cancer quest carbohydrates
Cancer quest proteins
F 8/28 How does your liver "know" when you're scared?
5-7
Lipids section of CancerQuest    
Crystal model of a lipid bilayer

Fluid model of a lipid bilayer
Combinations… section of CancerQuest    
M 8/31 Connecting epinephrine to glucose release in the liver: enzyme cascades and second messengers  7-12 Animated Tutorial 7.1 • Signal Transduction
W 9/2
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Why does your heart pound harder when you're scared?
12-18
Animated Tutorial 6.1 • Passive Transport
How the Calcium Pump Fills the SER
Animated Tutorial 5.2 • Eukaryotic Cell Tour
Cell Structure section of CancerQuest    
Immunofluorescence Labeling of ER
Virtual Cell
F 9/4

How does your heart muscle contract?

18-20
Also study this infographic
Animated Tutorial 48.1 • Molecular Mechanisms...
M 9/7 How does your brain tell your legs to run away? 20-29
Also read this article about animals resistant to snake venom
Animated Tutorial 6.2 • Active Transport
Animated Tutorial 45.1 • Resting Membrane...
Animated Tutorial 45.2 • The Action Potential 
Movie of Calcium Influx into a Neuron 
W 9/9 Another example of cellular communication-- how does an egg know when it's been fertilized?
29-35
Sea urchin sperm competing to fertilize
Mechanism for IP3 production and Ca2+ ion wave   
Movie of Calcium During Fertilization  
    ([Ca++]i indicated by white in right panel)

Movie of Sea Urchin Fertilization
Movie of IP3 injection
Anim. Tutorial 43.1 Fertilization in the Sea Urchin
F 9/11
Cellular communication in bacteria
(End of Unit 1)
Watch the first ~18 minutes of Part 1 of this lecture by Bonnie Bassler and write a paragraph summarizing what you learned. Don't worry if you don't understand all the terminology--just do your best. Note that you can also get this video free through iTunes.

M 9/14 Review #1

W 9/16 Beginning of Unit 2: Genetics
Unit 2 introduction: Three genetic disorders
Dominance and recessiveness at the molecular level
Chromosomes and genes
39-42
Cystic Fibrosis web site
Sickle Cell web site
Huntington's web site
F 9/18 DNA structure, DNA replication
42-43 Animated tutorial 13.1 DNA replication I
Animated tutorial 13.3 DNA replication II
M 9/21 DNA packaging in chromosomes; mitosis
DNA sequencing
43
Cartoon of mitosis
Movie of mitosis
Animated tutorial 11.1 Mitosis
W 9/23 RNA structure
The steps of gene expression: transcription and RNA processing; the genetic code
44-45
Animated Tutorial 14.1 Transcription  
Animated Tutorial 14.3 RNA splicing
F 9/25 The steps of gene expression: translation and beyond
The genetic code; mutations and diseases
 45-48

also see an extra translation animation here

Animated Tutorial 14.4 • Protein Synthesis
M 9/28 Meiosis and inheritance; Mendel and his monohybrid crosses
48-50
Animated Tutorial 11.2 • Meiosis
Movie of Meiosis    
Side-by-Side Animations of Mitosis & Meiosis
W 9/30 Analyzing patterns of inheritance
51-54
SRY paper
F 10/2
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Finding the sickle cell anemia gene, then dihybrid crosses 54-58 Reflections on living with Sickle Cell
Sickle Cell Disease
M 10/5 Finding the HD gene:
Dihybrid crosses, linkage, and gene mapping
58-61  
W 10/7
Recombination & mapping the HD gene via linkage to molecular markers 61-70 What is a Short Tandem Repeat Polymorphism?
Visualizing SNPs: Restriction Fragment Length Polymorphism
F 10/9 Mapping HD via linkage, continued.
61-70 again
70-73
HD online exercise: instructions and genome browser
M 10/12
FALL BREAK
 
W 10/14 Side topic: DNA fingerprinting
  73-74 CODIS STR DNA loci
F 10/16 NO CLASS
Optional web listening:
My So-Called Lungs
Remembering Laura Rothenberg
Genetic Testing, Part 2: Reading Genes for Disease--One Couple's Decision Against Testing for Cystic Fibrosis
M 10/19

Finding the CF gene
Confirming you've found the right gene; analyzing the defect at the molecular level

74-80
CF online exercise
In situ methodology
Immunofluorescence methodology
W 10/21 Finding genes associated with disease: modern methods: exome sequencing to find cystic fibrosis gene modifiers 80-81
Exome sequencing of extreme phenotypes...
(Just read the abstract)

New initiative will sequence 10,000 whole genomes….
100,000 Genomes Project leads to first rare disease diagnoses
Optional:
One of a Kind (New Yorker article)
F 10/23 Review #2
 
M 10/26

Viral genetics; HIV, influenza, AAV

127-138
Life Cycle of HIV
Anim. Tutorial 42.3 • Humoral Immune...
Anim. Tutorial 42.4 • Cellular Immune..
Cytotoxic T-cell Killing Its Target
Life Cycle of HIV - Reverse Transcriptase
Life Cycle of HIV - Viral Protease  
Treatments for HIV
W 10/28 More on HIV, influenza, AAV 138-146

extra animations:
AZT blocks reverse transcriptase

Protease inhibitors
ELISA for HIV
Transcription mediated amplification
F 10/30 Gene therapy and other treatments
81-83 Surfing and CF
M 11/2
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Genetic engineering of other organisms
(End of Unit 2)
146-151
Methodology for Making Transgenic Mice
A Portable Gene Gun    
Not all GMOs are created equally
W 11/4 Beginning of Unit 3: Bioenergetics
Unit 3 intro: bioenergetics and energy conversions
Reactions of photosynthesis: why was paraquat sprayed on Mexican marijuana?
84-93
F 11/6 Energy conversions in chemical reactions; role of enzymes; more on light reactions of photosynthesis 93-94
Animated Tutorial 10.2 Photophosphorylation
Animation of Photosynthesis        
Diagram of NADP+ conversion to NADPH  
M 11/9 More on light reactions of photosynthesis
no powerpoint today!
extra animation of photosynthesis light reactions  
W 11/11
Finishing photosynthesis: synthesizing food via the Calvin Benson cycle
94-98
 Animated Tutorial 10.3 Tracing the pathway...
F 11/13 Releasing energy from food: glycolysis, pyruvate oxidation, and the Krebs cycle; also fermentation 98-103  
M 11/16 Releasing energy from food, continued. Why is cyanide a good poison?
104-107
 Animated Tutorial 9.1 Electron transport..
W 11/18 Why update vaccinations after a flood? Anaerobic metabolism: bacteria that cause tetanus and botulism
107-110
 
F 11/20 Nitrogen metabolism: why is tofu a good source of protein?
(End of Unit 3)
110-112
M 11/23 Review #3


W 11/25

THANKSGIVING BREAK



F 11/27 THANKSGIVING BREAK
 
M 11/30 Integrating signaling, genetics, and metabolism: Cancer  113-121

What is Cancer from NCI
Cancer Biology Videos
Hallmarks of Cancer

W 12/2
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Integrating signaling, genetics, and metabolism: Cancer 121-126
MAPK Signal Transduction     
Cancer Biology Videos
Hallmarks of Cancer
F 12/4 Integrating signaling, genetics, and metabolism: Cancer Article: Cancer Driving Mutations Common in Normal Skin Cells

More TBA
 
M 12/7
Hints for final exam; course evaluations

W 12/9
Optional question and answer session. 

12/7-12/17 Self-scheduled final exam

 

   

   

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Laboratory schedule

Date
Topic
Reading
Page numbers refer to the Lab Manual unless otherwise noted. In the Lab Manual, you will also be referred to particular textbook pages.
Aug 24-25

Preliminaries: Introduction to lab. Lab safety. How to measure very small volumes with a pipetman.

Main activity: Introduction to spectrophotometry

1-16
Aug 31-Sep 1

IDH enzyme activity

After experiments are done: TOSLS assessment tool
BRING A LAPTOP/TABLET if you have one.

 17-35
Sep 7-8 Parameters that affect IDH activity: independent experiments

36-43

Also, in Pechenik, read "Introduction and General Rules"

Sep 14-15

Introduction to data presentation

For reference: sample lab report 1, sample lab report 2 (PDF files).


44-48, also Appendices B and C

Read the Pechenik chapter entitled "Preparing Oral Presentations"

Read the Pechenik chapter entitled "Writing Laboratory and other Research Reports"

Read the Biology Department statement on plagiarism

Sep 21-22

Group oral presentations on IDH lab results.
Written report on the IDH experiments due at lab time.


Sep 28-29 What is your genotype? A PCR answer.
PCR animations are here and here.
49-51 through "D1S80 factoids"
also p. 52 "How to calculate..."

Movie of PCR method
Polymerase Chain Reaction
Gel electrophoresis
Oct 5-6 PCR results
51-54

Read the abstract and introduction of this paper (the whole first page and first bit of second page)
We will explore parts of the paper together
Oct 12-13 NO LAB: FALL BREAK
Oct 19-20 Using microscopes; introduction to Chlamydomonas
56-top of 62

Read the abstracts of the following two papers:
Pederson et al., 2005 (click on PDF download)
Bujakowska et al., 2015
We will explore parts of the papers together.
Oct 26-27 Chlamydomonas flagellar regeneration
62-70
Nov 2-3 Varying parameters affecting Chlamydomonas flagellar regeneration: independent experiments
71-73
Nov 9-10 A beginner's guide to statistics and graphing  

74-78

Skim the Pechenik chapter entitled "Reading and Writing about Statistical Analyses," focusing on the information related to the lab manual material.

Nov 16-17 Group oral presentations on Chlamydomonas lab results.
Written lab report on the Chlamydomonas experiments due at lab time.

Nov 23-24 Exploring the research literature on cancer and IDH: connections to cell signaling, genetics, and metabolism

Go to this page to guide your explorations

Nov 30-Dec 1 Exploring the research literature on cancer and IDH: connections to cell signaling, genetics, and metabolism, part II

Dec 7-8

IDH/cancer writing assignment due by email at the beginning of your assigned lab time**. We are not actually meeting this week.

**The file attached to your email MUST have a title that begins with your LAST name. Three point penalty for not following this instruction.


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More information on laboratory write-ups and presentations

Written lab reports:
You will be writing a group report for the first lab report assignment. For that report, a different person within your lab group should be in charge of each of the major sections (introduction, materials and methods, results, discussion). Your steps are as follows:
1. Each group member completes a first draft of a particular section.
2. A different group member provides detailed editing feedback for the section. Editing involves more than fixing typos; rework the order of ideas, the language, and the logic to achieve maximal precision, completeness, and clarity.
3. Everyone in the group reads through the whole report and provides further feedback to tie the work together.
4. Everyone works together to construct the title, abstract, references, and chart indicating who who was the primary author and who was the primary editor of each section.
5. Signing the pledge on your lab report signifies (among other things) that everyone in the group has contributed his or her fair share of the work.

You will write an individual report for the second lab report assignment.

See the appropriate appendix in your Study Guide & Lab Manual, as well as the appropriate Pechenik chapter, for instructions on the organization and content of your lab reports. Pay special notice to this additional requirement regarding the reference section: you should cite the lab manual, AND you must find at least three additional relevant sources, two of which must be peer reviewed. Proper formatting of citations is described at the Biology Department statement on plagiarism. Correct spelling, grammar, and syntax are essential. It is in your best interest to focus my attention on the meat of your report instead of on messy mechanics.

Third lab writing assignment: At the end of the semester you will write an individual analysis responding to our explorations in the literature of IDH and cancer mechanisms.

Oral presentations:
Oral presentations will accompany the two lab reports. Each group will have 15 minutes for their oral presentation, with a few additional minutes for questions afterwards. You will have access to all the audiovisual equipment in the lab, including the computer and document camera. Each presentation should be divided into four sections: Introduction, Materials and Methods, Results, and Discussion. Each member of your lab group must speak, with everyone contributing roughly equally. See the appropriate appendix in your Study Guide & Lab Manual for what kinds of information to put into each section.Your classmates will critique your presentations, but their comments will not determine your grade.

Grading rubric for oral presentations:
Organization 5 pts
Clarity 5 pts
Accuracy 5 pts
Introduction 5 pts
Materials and Methods 5 pts
Results 5 pts
Discussion 5 pts
Answering questions at the end 5 pts

Grading rubric for 1st/2nd written lab reports:
Title/authors/affiliation 2/3 pts (2 pts on the first report, 3 on the second)
Abstract 4/5 pts
Introduction 7/11 pts
Methods 5/8 pts
Results 7/10pts
Discussion/conclusions/future directions 7/11 pts
References and acknowledgments 3/4 pts
Quality/organization of writing 5/8 pts

The lab grades are apportioned as follows:


IDH lab report
Chlamydomonas lab report
IDH and cancer assignment
Total lab grade
oral component
4%
4%
(none)
25% of course grade
written component
4%
6%
7%

 



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Copyright 2015 Department of Biology, Davidson College, Davidson NC 28035
last modified May 2015