Physiological Chemistry Lecture

Caren Seagraves
617-287-6133
E-Mail: centercls@gmail.com
Office: S-130
Office hours: Mon. 1-2, Thurs. 10-12 and 1-2.

This page gives resources that relate directly to the lecture. Keep in mind that CHEM 130 has 3 components: Lecture, Lab, and Discussion. You must take each part in order to receive credit for Chem 130. This website only has material that relates to the lecture. Information relating to laboratory can be found here.

***Exam 3 has been moved to April 17!***

General Class Information | Powerpoints | Homework & Practice | Keypoints for Exams | Textbook Powerpoints

Announcements

Here is the link to the modified Keypoints and Mainpoints lists that should be used to study for the final. Final Keypoints/Mainpoints

I have prepared a worksheet and answer sheet that will give you an idea of the type of numeric questions that you can expect on the final exam.

This is a link to a .pdf file that has the glycolysis diagram that you will be given on the exam. Please take the time to study it by comparing it with your notes and the textbook. Test Diagram

I have also prepared a page “How to Answer Open Response Questions”, that shows how to answer open response questions. Please take the time to look at this, and its companion “How Not to Answer Open Response Questions” .

This the new class web page. If you need something from the old page that you can’t find here, here is a link to the old one. I will no longer update the old page.

General Class Information

Course Syllabus

Course Schedule

pdf file of the periodic table

Powerpoints from Lecture

These are the powerpoints that will be and have been used in lecture. When you are going over the powerpoints before be sure to make notes of your questions so that you can be sure they are addressed in lecture. I plan on adding new powerpoints over the weekends or on Friday afternoon. In most cases I should have the week's powerpoints up before the week begins. In some cases there will be differences between the powerpoint presentations I have posted before lecture and those that I use in lecture. These powerpoints give a framework for what goes on in lecture but they are not a substitute for attending lecture, most lectures will contain examples that are not in these powerpoints. If you miss class you must get notes from a classmate and go over the material that you missed with them.

DATE ADDED	POWERPOINT SLIDES FROM LECTURE	ADDITIONAL ONLINE READING
JAN 26	Course Overview
JAN 26	Introduction to Chemistry	Google Books Description of Matter Classification Don't worry about the different types or heterogeneous mixtures. ChemProfesssor Classification of Matter This is another description of the classification of matter, it has many examples and is clearly worded. Identification of Mixtures and Pure Substances Flow Chart Separation Of Mixtures - From Discussion
JAN 30	Numbers and Units	Google Video of a lecture on significant figures. I think this is a very clear lecture and I would like to know what you think. Factor Product Video This is a video lecture about factor product method. It is a god resource and I highly recommend it to anyone who is feeling unsure about the mathematics in this course. Factor-Product is also called Dimensional Analysis. Introduction to the Factor-Product Method This introduction ends with an example that uses more chemistry than you may know right now, but the method is clear even if the reasons are not.
FEB 2	Scientific Notation and Atomic Structure
FEB 4	Periodic Trends Lecture
FEB 6	Atomic Structure And Periodic Trends I	Intro to Atomic Structure I First, do not hate me for including a site that is aimed at kids. Just keep this bookmark so that you can use this site with your own children. This site has many very good introductions to topics and I know profs who, wrongly, will copy the text from this site and hand it out to student because they don't want their students to be offended that it is meant for kids. I can't see doing this. Intro to Atomic Structure II This site covers all of the material about basic atomic structure that we will consider in this course. (We will return to atomic structure but at a bit more complex level.) You should be able to do the quiz at the end of this reference. Summary of Atomic Structure The basics of atomic structure on one sheet. Atomic Structure Video
FEB 9	Atomic Structure And Periodic Trends II	Introduction to Atomic Orbitals This is a reference that covers material in the "Atomic Structure and Periodic Trends" Lecture. Unless you know this stuff very well make the time to read this. Interactive display gives the occupation of orbital shells and subshells, You may use this page to teach yourself about how electron orbitals are filled. Trends of the Periodic Table This site gives a clear description of periodic trends. It does not relate everything back to the changes seen in atomic radii as we have done in lecture but it is written clearly and reinforces the ideas we went over in lecture. It also includes electronegativity and melting point as part of periodic trends. Electronegativities are similar to electron affinity. Melting point is the temperature at which a solid becomes a liquid." Periodic Properties of the Elements: Trends in the Periodic Table This reference describes trends we observed in the periodic table.
FEB 9	Radii and Reactivity
FEB 11	Chemical Formulas and Equations	Interpreting Formulas Quiz This is a short but excellent quiz. Rules for Balancing Chemical Equations
FEB 13	Ions, Noble Gases, Salts, and Covalent Bonds	An Interactive Slide Show on Ionic Bonds This interactive slide show does a good job explaining what ionic compounds are and how they are formed. Its images and wordings are clear and make watching this worthwhile. It does not consider whys other than to say that metals generally lose electrons while nonmetals gain. Description of Ionic and Covalent Bonds This is pretty reasonable site describing ionic and covalent bonds. Keep in mind that animations are cartoons. They are meant to illustrate of was of thinking about the bonds but they are not meant to represent what is going on. Just as the chemical symbols with the dots around them are a very nice way to keep count of electrons they do give a picture of what a molecule looks like.
FEB 18	Molecular Geometry and Dipole Moments	Dot Structure Tutorial Lewis Dot Structures I A good Discussion of Lewis Dot structures. Lewis Dot Structures II This is a less wordy description of Lewis dot structures. Many of you may find that you prefer the instruction for drawing Lewis Dot structures that is provided at this site VSEPR I This site has a pretty reasonable description of the VSEPR Model of predicting molecular geometry. This is the method we have been using but we are only considering a central atom with 3 objects (atoms or lone pairs), or 4 (atoms or lone pairs) around. More are considered here but the description is the same. VSEPR II This is a description of VSEPR that is short on words but still has enough information.
FEB 23	Moles and Concentrations	What is a mole? Discusses Moles as a unit of measure, and explains why having this unit is useful. Note that when she describes a mole as a unit of measure, it is different from what I presented in lecture. In lecture I presented a mole as a counting unit, like a dozen, or a gross. Calculating Molar Masses Clear instructions on how to calculate molar masses of molecules. There is a mistake in this write up though, when they gave the molecular mass of water at the end they used an "8" when they should have used an "18". Calculating Amounts of Reactants and Products This is a video that describes the sort of calculation that we did in lecture on Monday 2/23. The video is clear, and it is useful, in part because it combines the 3 steps that we did in class into 1 step and many of you may prefer this method, to using separate steps.
FEB 25	Solutions and Concentrations	Introduction to Molarity An introduction to Molarity with example problems Description of Concentrations by Percents, ppm, and ppb. This is a brief description of concentration by percents, ppm and ppb. There are several worked example problems.
FEB	Dilutions
FEB 27	Background for Protein Chemistry	Bond and Molecular Polarity This site discusses charge separation in ionic and covalent bonds. It has simple animations and can take a few seconds to load. Don't assume it is a broken link until your browser says so. Intermolecular Forces This site discusses the forces that hold molecules together as solids and liquid, electrostatic forces, dipole-dipole forces, hydrogen bonding, and London Forces.
March 4	Acids and Bases	Acids and Bases This is a clear description of acids and bases. Conjugate Acid Base Pairs The Nature of Bases Read up to “Explaining Differences in Base Strengths.
March 23	Thermodynamics	Chapter 7, without the section on equilibrium constants and LeChatelier’s Principle
March 27	Amino Acids and Proteins	Chapter 18 sections 18.1-18.8
March 30	Amino Acids and Proteins Pt.2	Chapter 18, all sections
April 1	Enzymes	Chapter 19, up to the section on vitamins
April 3	Vitamins	Chapter 19, complete chapter
April 6 and April 9	Generation of Biochemical Energy	Chapter 21, complete chapter
April 9	Carbohydrates	Chapter 22 Reading Assignment
April 20	Carbohydrate Metabolism No Powerpoints Carbohydrate Metabolism Mainpoints	Chapter 23 Complete Chapter Glycolysis Animation Extra and Advanced Reading on Glucose Metabolism (This is only if you are interested and you have the time to read this. It does not reflect what you need to know in this class.)
April 23	Lipids Introduction to Lipids Mainpoints	Chapter 24 Complete Chapter
May 6	Lipids Digestion and Transportation Lipids Digestion and Transportation Mainpoints	Chapter 25, through 25.2, including the Application “Lipids and Atherosclerosis”

Homework Assignments

These are grouped according to the content not the dates of the assignment. The assignment titles match what is on the powerpoint titles, but the powerpoints do not necessarily contain all of the information that you will need to do the assignments. You will need to check with other resources, the text, other handouts, lecture notes, and/or come to office hours or make an appointment. Do not let yourself fall behind, or decide that you can put off understanding the ones that seem hard until the exam.

The answer to many of the homework problems are posted across from my office, which is room 130, floor 1 of the science building. There are example answers to almost every type of problem you will see, use these answers to develop strategies for the problems that don't have answers. If you can't figure a problem out after trying for 20 minutes get help from me or a friend.

Date Posted	Written Homework Assignments	Additional Online Practice
	Mixtures and Pure Substances	Classification of Matter Summary and Practice Problems
	Measurements and Significant figures	An interactive problem set that lets you practice recognizing the number of significant figures in a number. An Excellent Significant Figure Online Quiz Generator It has very clear explainations of the answers. You finish a whole page of problems before checking your answers, though. Rounding Practice I A rounding that is very basic, but it would be a good place to start if you have not rounded numbers for a while. It only practice rounding, it does not teach the whys at all. Rounding Practice II This is excellent rounding practice and at the level required for this class. In these you consider significant figures as well as rounding.
	Scientific Notation and Unit Conversions	Unit Conversion Practice I When calculating the volumes, convert the units for each side before calculating the volume. Problems 5, 8, 7,9 have the wrong number of Significant Figures Unit Conversion Practice II Use a table to identify the SI prefixes and their relative sizes. Unit Conversion Practice III In the question when they ask about 430 mmHg they cannot be sure that there are 2 significant figures. Do not worry about the question about specific gravity
	Basic Atomic Structure and the Periodic Table
	Electron Configuration Homework This assignment is from a website, but print it out and do it as a written homework assignment. Though I did not write if it reflects what you are expected to know. You will not be able to access the answer but a key will be availale on the bulletin board.	Atomic Orbital Diagram Practice Place electrons in atomic orbital diagrams. The script gives an immediate response with hints to solve the problem. You will need a periodic table to do these problems. Principles of Quantum Mechanic Quiz Select the quiz "Atomic Theory III: The Quantum Mechanical Model." Electron Configuration Quiz Select the quiz "Electron Configurations." There are many other quizzes on this subject but this is the only one that relates to material in this course.
	Atomic Radii and Periodic Trends This is a quiz that I reformated and edited to reflect what we have done in class. This problem set is from the chemcool website
	Names and Formulas of Ionic Compounds Answer Key
	Balancing Equations Practice This assignment is from a website, but print it out and do it as a written homework assignment. Though I did not write if it reflects what you are expected to know. The answer key for these problems is in the same .pdf file.	Chembalancer I This is a good balancing equation practice. On my browser the page looks a bit odd but all of the information is there. Once you have filled the boxes in with the coefficients you pressed the "Balanced" button in the green box to check your answer. Chembalancer II This is a chance for balancing chemical equations it is a step harder than chembalancer I Balancing Practice with Hints This online practice site has hints to help if you get stuck balancing problems. This is a nice feature plus it lets you chose how many problems you want to do before checking your answers.
	Lewis Dot Structure Problem Set There is a written tutorial in the Reference section that supports this problem set.	Lewis Dot Structure VESPER Practice Practice drawing Lewis dot structures and identifying objects around the central atom. Online VSEPR and Intermolecular Forces Quiz This is a pretty good online VSEPR Quiz. I have only done the Level 1. If your computer does not show the formulas just enter the molecules name in google, and it will be easy to find out what the formula is. There is a chance to answer 3 questions about each molecule. Its geomentry, by which they mean the shape of the molecule when all of the objects around it are considered. The shape of the molecule, by which they mean the shape formed when only atoms are considered. Finally when C is selected the quiz asks about the kind of forces that may act between molecules of this type. This is something that we will get to on Monday Feb. 23.
	Reactants & Products	Calculating Amounts of Reactants and Products I This is a short problem set that follows a video on this subject. I highly recommend doing this quiz. Calculating Amounts of Reactants and Products II Here is a quiz that provides a chance to practice using the number of moles of either products and a balanced chemical equation to determine the amount of another element or compound that is part of the equation. These questions are at the level that we did in class and in Discussion section. In the instructions for this quiz it indicates that calculators should not be used. This prejudice against calculators belongs to the person who made this quiz, not me. Use a calculator. Calculating Amounts of Reactants and Products III This is an online quiz that covers what we did in class on 2/23, but in a way that requires a good understanding of the concepts involved. Do this quiz after you feel comfortable with calculating molecular molar masses. The last question is about limiting reagents. We will not be covering limiting regents in depth so just skip this one.
	Molarity Calculations Go to Calculate Molarity - Interesting Substances. This is a 3 problem online quiz. Unlike the quizzes that are below and meant for practice these problems are homework problems and a key for them will be posted across from my office. This program generates more than 3 questions if you return to it repeatedly. If you get it after 3 questions you are done otherwise try a few more. Answer Key	Molarity I A quiz in which you do basic calculations relating, # of moles, volume and molarity. Molarity II A quiz composed of molarity word problems. In some of these problems you need to bring what we did in lecture on 2/23 together with molarity problems You will need to do problems at this level for this class. #5 answer key
	Percents, ppm and ppb Problem Set These are homework problems that are typical calculations. The numeric answers are given at the end of this problem set.	Concentration Calculations Practice These are fairly straight forward concentration calculations. The numeric answers to these problems are given on the last page of this handout.
	Acids & Bases Homework1 Acids & Bases Homework1 Answer Key ----------------------------------- Acids & Bases Homework 2 (Multiple Choice Answer Key)	Multiple Choice Acid Base Review Quiz Use these questions to help you review lecture and to direct you to what subjects you need to review. Multiple Choice Acid Base Review Quiz II Use these questions to help you review lecture and to direct you to what subjects you need to review. Ignore # 14. It does not make sense.
	ThermodynamicsReview
April 3	Proteins
April 6	Enzyme Book Problems
April 10	Generation of Biochemical Energy Homework and Reveiw
April 10	Carbohydrates Book Problems
April 20	Cabohydrate Metabolism Book Problems
April 23	Lipids Book Problems

Keypoints & Answer Keys for Exams & Quizzes

Quiz/Exam #	Keypoints	Answer Keys
Quiz 1
Exam 1	Keypoints Classification of Matter Keypoints Units and Numbers Keypoints Basic Atomic Structure Keypoints Periodic Table Groups and Reactivities Atomic Orbitals and Periodic Trends Keypoints Chemical Formulas and Equations Keypoints Noble Gas Configurations, Ions, and Covalent Bonds	This handout links the questions in Exam 1 to the corresponding Keypoints. It is not really an answer key but this seemed to be the best place for it.
Quiz 2		Quiz 2 Answer Key
Exam 2	Keypoints on Lewis Dot Structures and VSEPR Keypoints Stoichiometry KeypointsProblems Partial Problem Key	Exam 2 Answer Key This answer key gives the answers for all of the questions and links to resources available through this website that will help you understand the material, and get the practice that you need in order to solve the problems on the Exam. I have given detailed examples of how to solve the longer problems on the exam. The links offer many chances to solving similar problems. Practicing how to do these problems is the key to being able to recognize them and solve them readily, which is what you need to be able to do on an exam.
Quiz 3	Quiz Announcement Sheet	Quiz 3 Answer Key
Exam 3	Keypoints Amino Acids and Proteins Enzymes and Vitamins Generation of Biochemical Energy Carbohydrates
Final	Keypoints/Mainpoints

Textbook Powerpoints

These are links to powerpoint slides for the text Fundamentals of General, Organic, and Biological Chemistry. Most of the information has not been covered in lecture because the text is meant for a yearlong course. This can lead to confusion, which is why the first part of the text has not traditionally been the required text for this course. If you use these powerpoints to study use the Keypoint lists to focus on the topics that are covered in this course. You will still need the powerpoints that I have prepared as well as the websites that I have given links to.

Chapter 1

Chapter 2

Chapter 3

Chapter 4

Chapter 5

Chapter 6

Chapter 7

Chapter 8

Chapter 9

Chapter 10