Introduction to Cell and Molecular Biology Biology 111 - Spring 2012 Instructor - John S. Peters, Ph.D. Office - Rm. 207 RHSC Contact: petersj@cofc.edu; 953-1422 Office Hours: Mon. & Wed. 1:30-3:00 PM or by appointment Biology Department Course Announcements Excused Absences Information Be sure to REFRESH your browser each time you visit this course page!  Supplemental Instruction SI Leader - London Penland Sun 4 PM & Tues 8 PM - 317 RHSC; Thurs 8 PM -  239 RHSC Coming up! - Tuesday & Thursday - Review for the Friday Progress report! General Course Information Problems & Case Studies Working in Teams Lecture Notes Research and Writing Resources Assignments & Readings Study Guides & Tutorials Center for Student Learning Cool Links                                              Biology in the News: Are we Alone in the Universe? View that Mars is Lifeless is Challenged Flowing Water on Mars Mars Rover Discovery Mitochondria, Metabolism & Athletic Performance Beer and Athletic Recovery Genetics NY Preschool Starts Genetic Testing - At the Porsafillo Preschool Academy, there are 32 spots but more than 12,000 applications.  Beginning next year, all applicants must now submit a DNA analysis of their children.  The school "is looking for genetic markers that indicate future excellence — things like intelligence, confidence and other leadership traits." - Posted April 1, 2012 - Listen CAREFULLY to the podcast of the report! : )                               Podcasts/Videos, Events & Opportunities: Amazing Ant Hills - many species of ants, like termites are eusocial and live in complex societies in "homes" that they cooperate to build.  Have a look at one of these amazing ant homes! Animal Minds - more about the grateful whale on NPR's Radiolab Darwin Week at the College of Charleston - note that one of the presentations in directly related to the extraterrestrial life problem we are working on! Palmetto Research Academy - Perhaps our Life in the Universe problem stimulated an interest in this area of science.  If so consider a summer program with NASA!  Research, opportunities to travel to NASA sites, paid internships! NPR Sciencey BLOG - Lord Save Me From the Krebs Cycle! - scroll down and watch the music video.  Do you understand it? Course Information The What and Why of the Class Course Policies Course Learning Goals & Objectives Class Schedule - updated 4-9-12 How your grade will be determined in this class Guidelines for submitting assignments to Dropbox Problems and Case Studies (some links are password protected) Are We Alone in the Universe - The Search for Life on Other Planets Part 1 - Nanobes Mars Labeled Release Experiment - 2 perspectives - Please read these articles for class on 2/1/12 Levin, G (2007). Possible evidence for panspermia: the labeled release experiment.  International J. of Astrobiology, (6(2):95-108. Klein, H. (1998).  Did Viking Discover Life on Mars?  Origins of Life and Evolution of the Biosphere 29: 625-631. Mitochondria, Metabolism, and Athletic Performance (MMAP) Part 1 - Blood Boosting in Sports - note the due date for your individual learning issues on the class schedule Part 2 - What blood boosting practices should be legal in sports? Policy Statement Assignment - see class schedule for due date Sometimes it is All in the Genes Part 1 Part 2 Part 3 - The questions for each of the genetic disorders listed at the end of Part 3 should be answered in preparation for a RAT the day they are due (consult the class schedule for due date).  - Learning issues are due Monday 4/16 Part 4- Learning issues are due Monday 4/16.  Have a look at the assignment below before you develop your learning issues! Gene Therapy Genetic Counselor Letter Assignment - this is now an optional assignment.  See note posted in the announcements section at the top of the web page. Gene Therapy Letter Learning Issues - Assignment is NOW due by the end of the day on Tuesday, April 24. Exploring the Molecular Biology and Evolutionary Genetics of Sickle Cell Anemia Part 1 - Meeting the Family Affected by Sickle Cell Anemia Part 2 - Nature of the Sickle Cell Mutation Part 3 - A Best Guess? Part 4 - The Results are In! Part 5 - Do this part of the problem for class on 4/13 in preparation for a mini-RAT.   Working in Teams Since we will be working in permanent teams throughout this course, it will be necessary that you periodically evaluate the contribution of your teammates to the team effort.  Complete the on-line peer evaluation form after we have finished each problem or case study.  Please read the instructions before you complete this form. Lecture Notes (password protected) You will need Adobe Reader on your computer to download the class notes!  Class notes will be posted at least 24 hours in advance of class, so it is your responsibility to print the notes and bring them with you to class.  Termite Trails Discussion - for class on 1/18/12-1/20/12 Cellular Respiration - for class 2/15 & 2/17 - I passed these out in class on 2/15, if you were not there, print these and bring them to class as I will not provide a copy during class. Hemoglobin - for class on 2/22- I passed these out in class on 2/20, if you were not there, print these and bring them to class as I will not provide a copy during class. Genes, Alleles,DNA, Mutations & Inheritance - Notes for class starting on 3-23-12 Please print and bring to class with you if you want! I WILL NOT PROVIDE COPIES OF THESE IN CLASS!   Research and Writing Resources The most important things to consider when writing for this course Grading Feedback Symbols for writing assignments in this course - These symbols reflect common problems I have found with students' writing in the past.  Have a look at them, and what they mean, so that you don't make these same mistakes! Assessing Writing for Logical Fallacies: common logical fallacies that you may encounter in your own writing or the writing of others. The web site provides definitions, examples, and tips on avoiding these fallacies. From the University of North Carolina Writing Center. CofC Library - Research Guides for Biology APA Citation Style Guide Citation Style Guides from Duke University Library Hamilton University's Writing Center - Tips for effective writing and other writing resources CofC Writing Lab Writing Scientific Abstracts Download Adobe (pdf files) reader to your personal computer to get many of the resources posted on this page. Assignments & Readings Class Passport - Due 1/11/12 in class; 10 points Termite Trails Revision - Due 1/27 to your Dropbox folder, 20 points Student Instructions Team Lab Notebook - This is a MS Word file.  You can upload it to your computer, complete it, and save the completed file to your shared Dropbox folder.   Consult the Dropbox guidelines before you upload this to your shared Dropbox folder! Life Table - Due 1/20/12 Start in Chapter 1 to complete this table.  But you will need to generally explore other relevant chapters in the text as you define and provide examples & evidence in the table.  I do not expect you to completely read these later chapters; instead skim them to find what the table directs you to find.  Part of the reason for this assignment is to get you used to looking for information you need in this very large text! Complete this assignment on a computer in a word processor like MS Word.  If you are using a word processor other than MS Word, please save your file as a Word 97-2003 document.  Submit this assignment to your shared Dropbox folder before class on 1/20/12. Chapter 2 Reading Companion - complete this as you read chapter 2 (sections 1 & 2) in your textbook. Due 1/25 to your Dropbox folder.  Also print and bring a hard-copy to class. Concept Map PowerPoint Slide - do your concept map for question #1 in the reading companion in PowerPoint, save the slide as an jpeg image file and insert it into your Reading Companion document. Mars Labeled Release Experiment - 2 perspectives - Please read these articles for class on 2/1/12 Levin, G (2007). Possible evidence for panspermia: the labeled release experiment.  International J. of Astrobiology, (6(2):95-108. Klein, H. (1998).  Did Viking Discover Life on Mars?  Origins of Life and Evolution of the Biosphere 29: 625-631. Mitochondria, Metabolism & Athletic Performance - Blood Boosting in Sports Here are the two graphs we worked on in class on Monday (2/13) after our Voyage to the Center of a Mitochondrion.  The HOMEWORK (due Wed. in class 2/15) is on the second page. Blood Boosting Learning Issues Research Assignment - NOW Due 2/24/12.  Submit to your Dropbox folder prior to class that day, and be sure to bring a hard or electronic copy to class the day it is due.  If you missed class on Monday, it is your responsibility to find out from your teammates, which set of learning issues were assigned to you.  You will only receive 1/2 credit for this assignment if you miss class the day it is due for an UNEXCUSED reason! Policy Statement Assignment - see class schedule for due date The Genetic Wheel of Fortune - you will need to consult with your family members (Mom, Dad, Siblings) to complete this!   Pedigree Evaluation Homework - Due Friday, 4/6/2012.  Submit to one team member's Dropbox folder according to the naming guidelines posted in the assignment. Gene Therapy Genetic Counselor Letter Assignment - this is now an optional assignment.  See note posted in the announcements section at the top of the web page. Gene Therapy Letter Learning Issues - Assignment is NOW due by the end of the day on Tuesday, April 24. Study Guides, Tutorials and Textbook Reading Companions Interactive PowerPoint Tutorials -*All interactive tutorials are PowerPoint shows and require access to MS PowerPoint (PC or Mac version).  I would suggest you review tutorials before you begin reading the relevant chapter(s) and then after you read each chapter, return to the corresponding section in the tutorial and try and answer the questions.  If you are having trouble viewing these tutorial email me (petersj@cofc.edu) immediately. Organic Molecules Cellular Respiration Tutorial Photosynthesis Tutorial Learning to Use the CO2 Sensors & LabQuest Unit Tutorial - please review this before class on Monday, 3/12.  I will not show you how to use this equipment during class! Calculation Photosynthetic Productivity Tutorial - You will need your light and dark slopes from class on Monday to complete this tutorial.   Mutations Tutorial - This tutorial should be reviewed for class on Wed. (4/2).  It covers transcription, translation and how mutations affect the polypeptide products of genes. Reading Companions Chapter 2 Reading Companion - complete this as you read chapter 2 (sections 1 & 2) in your textbook. Due 1/25 to your Dropbox folder.  Also print and bring a hard-copy to class. Concept Map PowerPoint Slide - do your concept map for question #1 in the reading companion in PowerPoint, save the slide as an jpeg image file and insert it into your Reading Companion document. Help with Bonds and Molecules Key Concepts Study Guides Progress Report #1 Study Guide Progress Report #2 Study Guide Progress Report #3 Study Guide Final Progress Report - Key Concepts Other Study Resources Condensation Rummy Deck -  Feel free to print these PowerPoint Slides, cut them out into "playing card" and practice identifying and categorizing the monomers into polymers.  London will be working on this in SI on Sunday!

The Biology Place - This is the Web page associated with your text book!  This is a fantastic page choke full of materials to help you in this class!  You should be visiting this page often!!  You will need a user ID and password to visit this page.  You should be able to get these from your textbook, if not, come and see me!

Nature Science Updates
This site from Nature has current and archived articles from one of the premier international scientific magazines.  This site will provide you with excellent sources for class projects.

Scientific American - Past issues, explorations, exhibits, feature articles and much more!

UC Berkeley - Museum of Paleontology - A wonderful interactive page exploring the history of life on earth.  You MUST visit this page!

CNN.com  Health - Current news on important health related issues!

Access Excellence Science Updates - Current and past biological (mostly genetic) news.

The Virtual Lab Bench

The Biology Project – Studying Cells Tutorial
This site reviews the scientific method and introduces you to the cell as the fundamental unit of life.  You will explore the activity of science, the concept of testing what we believe to be true, and the ever-changing nature of science.  To understand life in a useful and meaningful way, you have to understand the cell.  The site will show how an experimental approach has allowed great progress in understanding the lives of cells.

Chemistry

CHEMystery – An Interactive Guide to Chemistry
CHEMystery, a virtual chemistry textbook, provides an interactive guide for high school chemistry students, but college students might find it a helpful review.  In addition, CHEMystery allows you to further expand your chemistry knowledge by letting you interact with other Internet resources on the World Wide Web.

Chemicool
This site provides and interactive periodic table.  Click on an element and receive information on the element.

Radiocarbon Dating - The Shroud of Turin
Click on the Shroud itself to get to the main menu.  Go to the "Late Breaking News" in the menu and look over the papers concerning radiocarbon dating of the Shroud.

RadioCarbon Web Page
Gives some great applications of radiocarbon dating along with an easy to understand summary of the process.

Water, pH, Organic Chemistry

MathMol Library
The MathMol library contains 3-D structures for many molecules discussed in introductory biology and chemistry textbooks.

US Geological Survey – Water Resources of the United States
This page contains information about the nation’s water resources.

The Biology Project – Macromolecules
Learn about structures and properties of sugars, lipids, amino acids, and nucleotides, as well as macromolecules including proteins, nucleic acids and polysaccharides.

The Biology Project - Acids and Bases
In this site, learn about the solvent properties of water, pH, pKa and buffering capacity.

The Biology Project - Clinical Correlates of pH Levels
In Clinical Correlates section of the Biology Project, learn how metabolic acidosis or alkalosis can arise and how these conditions shift the bicarbonate equilibrium.  The body's compensatory mechanisms and treatment options are also discussed.

Introduction to Metabolism

The Biology Project – Energy, Enzymes and Catalysis
Familiarize yourself with some essential principles about enzymes, catalysis, and energy that are central to a subsequent study of metabolic pathways.

The Biology Project - Using Computers to Study Molecular Structure
The main objective of this site is to enhance your study of the properties and structures of biological molecules with modern computer graphics.  Rather than passively viewing illustrations of molecular structure as they occur in your textbook,  you'll have the opportunity to actively view, manipulate, rotate, and even create colorful, 3D models of molecular structure.

The Cell

Washington State University – Microbiology Internet Textbook – Prokaryotic and Eukaryotic Cells
This is an Internet textbook created for an introductory microbiology course at WSU.  Chapter 2 deals with the biology of prokaryotes and eukaryotes.  This is an excellent supplement to your course textbook and class notes.

CELLS Alive!
This is a commercial web site that has free pictures and videos of various types of cells and cell processes. For further information, refer to chapter 4 in your textbook.

Cell Biology Topics
This group of web pages provides basic information about cell biology topics. Many of the photos are taken from texts used by our students. These are used as supplemental handouts and guides for the discussions in our lectures.  Most of these topics focus on structure/function correlations. They are not intended to be comprehensive. Some topics, like those focusing on mitochondria, will correlate with biochemistry and physiology lectures that expand students' understanding of that organelle system.

Cell Membranes
This site provides a comprehensive review of membrane structure, function and electron micrographs of membranes.

Lab Books – Diffusion, Osmosis and the Nernst Equation
This site explains the processes of diffusion and osmosis.  It has great animations that allow you to see the affects of concentration on movement of molecules across membranes.

Cellular Respiration

Develop a basic understanding of some of the fundamental concepts of metabolism including: Glycolysis, affect of pH on Mitochondria, lactic acid production, the Electron Transport Chain, acidity during electron transport , fermentation, storing usable energy , metabolism during a heart attack, ATP Production and ATP synthase.

Why Study Photosynthesis
This site by Devens Gust, Ph.D., Professor of Chemistry and Biochemistry at Arizona State University, considers the importance of photosynthesis by discussing the relationship between photosynthesis, food, energy, the environment, agriculture, medicine, fibers and materials.

An Introduction to Photosynthesis and Its Applications
This site by Wim Vermaas, Professor of Plant Biology at Arizona State University, presents the basic concepts of  photosynthesis and its applications. He covers such topics as: increasing levels of carbon dioxide, the diversity of photosynthetic organisms, and evolution.  This article appeared in condensed form in the magazine "The World and I" (March 1998 issue, pages 158-165).

The Biology Project – Photosynthesis I
The Photosynthesis I site discusses how light energy is converted into different forms of chemical energy during photosynthesis.  Review the equations for the light reactions of photosynthesis, study the pathway for electron transport during cyclic and non-cyclic photophosphorylation, and explore the mechanism for coupling electron transport to ATP synthesis.

The Biology Project – Photosynthesis II
The Photosynthesis II site reviews the location and overall reactions of carbohydrate biosynthesis during photosynthesis, including RUBISCO, the difference between C3 and C4 plant leaf anatomy, and pathways for carbohydrate biosynthesis.

Virtual Photosynthesis Experiments
An interactive site at ASUPC with on-line virtual experiments that show you some of the ways scientists can study photosynthesis.

The Cell Cycle/Mitosis

The Biology Project -The Cell Cycle and Mitosis Tutorial
The Cell Cycle page is a well conceived that explains clearly with graphics and animation.  You can take a small interactive test at the end to see how well you understand the cell cycle and mitosis.  F

The Biology Project -Online Onion Root Tips
The Onion Root Tip page lets you score the number of onion root tip cells in various stages of the cell cycle and then calculate the time cells spend in each phase of the cycle.

BIOLOGY 102L Laboratory Review
This site from the University if North Dakota provides a practice test, which will give you a general idea of the types of questions you might expect to see on a laboratory exam covering mitosis.  It also has practice tests for many other areas of a general biology lab.

Meiosis and the Sexual Life Cycle

DNA From the Beginning
This excellent site provides information on the discoveries of Mendel.  It contains information about Mendel, movie clips, simulations of Mendel’s experiments etc….  You can log on initially as a guest, but you must subscribe eventually.

MendelWeb
MendelWeb is an educational resource for teachers and students interested in the origins of classical genetics, introductory data analysis, elementary plant science, and the history and literature of science.  Constructed around Gregor Mendel's 1865 paper "Versuche über Pflanzen-Hybriden" and a revised version of the English translation by C.T. Druery and William Bateson, "Experiments in Plant Hybridization",  MendelWeb is offered as a public sourcebook and collaborative environment compatible with a variety of guided and independent study.

The Biology Project – Mendelian Genetics
This site contains problem sets and tutorials on monohybrid crosses, dihybrid cross, and sex-linked inheritance.

OMIM, Online Mendelian Inheritance in Man. This database is a catalog of human genes and genetic disorders.

Blazing the Genetic Trail
A whole host of articles published on-line by the Howard Hughes Medical Institute on human genetics.

The Biology Project - Human Biology
The Human Biology section of the Biology Project contains problem sets and tutorials on DNA forensics, immunology, karyotyping, reproduction, genetics, and AIDS.

The Virtual Fly Lab
Virtual FlyLab allows you play the role of a research geneticist.  It is an educational application for learning the principles of genetic inheritance.  You design matings between female and male fruit flies carrying one or more genetic mutations.  The Virtual FlyLab will apply the correct rules of genetic inheritance to these mutations to obtain the offspring.  It is your job to determine these rules based on the "experimental" results.

Genetic Diseases
A list of links to information about common genetic disorder.

The Biology Project
This Biology Project site contains tutorials and problem sets on the molecular genetics of prokaryotes,  nucleic acids (base pairing, replication and translation),  recombinant DNA technology, and eukaryotic gene expression.

DNA Workshop
An interactive workshop that show DNA replication and translation.

Comments, suggestions, or requests to petersj@cofc.edu. Last updated 12 Aug 2009.  College of Charleston.