General Biochemistry

Summer 2016
Class Times - MWF  1:15 to 2:20PM    PG6-116 (Parking Garage-6)  .
Principles of  STUDY
How to Prepare for  Class

Laboratory Link




Office hours

John Makemson



 OE 246/247:  MWF  Mornings after 11AM + Afternoons before 4PM

 Learning Biochemistry

Catalog Description:  Chemistry of proteins, lipids, carbohydrates, and nucleic acids;  principles of enzymology, metabolism and bioenergetics.

Student's Learning Objectives: Students will know the chemical structures and chemistry of biological polymers (proteins, carbohydrates, lipids and nucleic acids) and their monomers (amino acids, sugars, fatty acids and other lipid monomers, and nucleotides) as well as the roles of these biological molecules in living cells.  Students will be able to solve amino acid sequences of protein, nucleotide sequences of nucleic acids from experimental data and how to determine structures of carbohydrates and lipidsStudents will be able analyze enzyme kinetic data as well as the bioenergetics/thermodynamics of biochemical reactions. Students will know the reactions of major metabolic pathways: Central Metabolism (Glycolysis-Gluconeogenesis, Pentosephosphate Patthway, Citric Acid Cycle) and Respiratory Electron Transport System, Glyoxylate Cycle; Beta-oxidation of fatty acids and be able to analyze the regulation of these pathways.  

Lecture Format:  Narrated PowerPoints are in MP4 format that can be viewed on standard and laptop computers as well as tablets.  These were made using the continually updated PowerPoints from the instructor's regular lectures. They usually last less than a full lecture (most are 30-40 min) because there is no interaction with an audience. A few "lectures" go longer than an hour, but each of these are used for two class periods. Each "lecture" is at a private YouTube site and the FIU Media Site. Please use the one that works best for you.  The links to the lectures are below in the schedule.  


THE FLIPPED CLASS:  the lectures here are narrated PowerPoints that you can view at any time you choose before class.   The Power Points used in lecture can also be downloaded to take notes on if you convert them to pdf and print them out.  It is to your distinct advantage to have the lecture pdf printed out so when you are viewing the narrated PowerPoint because you can pause the narrated PowerPoint and take notes on the pdf.  If you went too slow, you can always back the lecture up and get to what you missed.  In other words: YOU HAVE TOTAL CONTROL of the LECTURE.  This makes learning paced to your ability to ACTIVELY LEARN.  PLEASE DO NOT JUST LISTEN, but rather STUDY the LECTURE BEFORE CLASS. Further, you can go to the "lecture" as many times as you like.  Please do the selected End of Chapter problems before class:  in class we will work on problems like these and Case Studies.  Doing them before class will pay off in higher Clicker grades.

ADVANTAGES OF THE FLIPPED CLASS: Because each class is an active learning experience, students have performed much better on the Exams, usually 10 to 20% better than those using traditional lecture format.  This ONLY WORKS for students that STUDY BEFORE CLASS. The payoff is student problem solving and critical thinking skills improve.  This has a distinct advantage when taking admission exams for graduate schools (GRE) and any of those for health professions (MCAT, DAT, etc.).

FREE STUFF: A Biochemistry MOOC (massive on-line open course):  oli.cmu.edu/courses/free-open/biochemistry-course-details. This course was created at Carnegie-Mellon University. It is free and you can use it as an additional resource. It has a slightly different structure, but also has problem sets for each chapter. Further there is a free e-textbook by Kevin Ahern (Oregon State University): BIOCHEMISTRY FREE AND EASY (you can download from various sources, the Kindle version is also free from Amazon, particularly good if you like songs about molecules) and Kevin Aherns lectures are free and on YouTube.

Each Class Time has a Graded Component that REQUIRES you to have a working iClicker for Each Class.  Classroom work counts for 1/3rd of your grade. Last semesters, the i-Clicker-Go app had wi-fi connection problems; the safest is the basic iClicker.  New and Used iClickers are available from the Bookstore. But you might get better deals elsewhere. THE MOST IMPORTANT POINT: Get your iClicker REGISTERED to YOUR NAME as it appears in PantherSoft. If you have a multi-word last name such as "de la Vega", it has to be registered with underlines as "de_la_Vega" which makes it look like one word at the iClicker database. This is the only way it will add your clicker points into the gradebook. We will be testing your iClicker response during the first week with non-graded material.  


Graded iClicker responses begin the 2nd week

Prerequisites :  General Biology - BSC 1010 & BSC 1011 and Organic Chemistry - CHM 2210 & CHM 2211 all with grades of C or Better. 

Text:   Principles of Biochemistry, Lehninger, Sixth Edition (Nov. 2013) -  Available in Three Different Formats:  Hardbound Text 

Loose-leaf Text (10:1-4641-1-1064-6, 13:978-1-461-1) , and e-book.  The latter two cost significantly less than the Hardbound Text.  The loose-leaf form (you don't have to carry the whole thing around each week) was ordered for the Bookstore.  The e-book is at:  http://ebooks.bfwpub.com/lehninger6e or at http://www.Chegg.com (which also has rental books).

New and used copies (of the 6th Edition) of the textbook are available at the FIU Bookstore in the Graham Center. The bookstore sells them at highest possible price. You can save by using the web: new and used are discounted at half.com, abebooks.com, and Amazon. Also check ebay. International editions are at about half the price: check out amazaon.co.uk and others. The international editions are usually paper back, but otherwise are identical to the very costly book in the bookstore (probably ~$280).  Be careful about ordering the text and not the study guide. You do not need the study guide: Answers to all of the End of Chapter Problems are in the end of the text; and Solutions to the End of Chapter Problems are Present as Word or pdf files from this syllabus.

Tentative Syllabus
See Below About Practice Exams


PowerPoint of  "Lecture" Download and Convert to pdf  to Use as Notes When Doing the Narrated Power Point Lecture.

Narrated Power Point "Lecture"


  DO THESE BEFORE CLASS:   End Of Chapter Problems to Solve. Solutions to the Selected EOC Problems are in Word format. Abbreviated Solutions following page 1198 in the textbook: Best Source!   

16 M

Introduction the Flipped Class

YouTube     FIU Media Site


 Introduction to Biochemistry

Ch1               Ch1MS

  1, 3, 5, 8, 11, 12  Ch01SelectedSolutions

20 F

Water, pKa, Buffers  

Ch 2              Ch2MS

  1-5, 8, 11-18, 20, 26    Ch02SelectedSolutions

23 M

Amino Acids and Proteins          

 Ch3a             Ch3aMS

  1-7     Ch03Pt-1Selected Solutions

25 W

Protein Purification

Ch3b             Ch3bMS

 8-11, 13, 15, 16  Ch03Pt-2 Selected Solutions

27 F

Protein Sequencing

Ch3c             Ch3cMS

 18, 19, 21, 22  Ch03Pt-3 Selected Solutions

30 M

Memorial Day Holiday






1 W

EXAM 1   A through F in Pg6-116, G though Z in RDB-1100 (Law College)


 50 points.  Please bring a calculator (non-graphing). This exam integrates material from Chapters 1-3

3 F

Proteins Structure Part 1

Ch 4a           Ch4aMS

  1-4     Ch04 Selected Solutions

6 M

Protein Stucture Part 2

Ch 4b            Ch4bMS


8 W

Protein Function: Binding

Ch 5              Ch5MS

 1, 3, 5-7.      Chapter 5 Selected Solutions

10 F

Enzymes Part 1

Ch 6a            Ch6aMS

 1-6, 9, 11, 13.   Chapter 6 Selected Solutions-Both Classes

13 M

Enzymes Part 2

Ch 6b            Ch6bMS

 12, 19.

15 W


Ch 7               Ch7MS

15, 17- 20, 23, 27    Chapter 7 Selected Solutions

17 F

EXAM 2   A through F in Pg6-116, G though Z in RDB-1100 (Law College)

50 points.  Please bring: No 2. Pencils, Simple Scientific Calculator+ Straight Edge (ruler),  This exam integrates material from Chapters 4, 5, 6 and 7. 

20 M

Nucleic Acids Part 1

Ch 8a             Ch8aMS

1-3, 5     Chapter 8 Selected Solutions-Both Classes

22 W

Nucleic Acids Part 2

Ch 8b             Ch8bMS

 5, 8, 10, 12-15 and another in the Solutions using pBR322.

24 F


Ch 10             Ch10MS

1, 2a, 2c,7-13, and 3 if you can cook.    Chapter 10 Selected Solutions


Membranes Structure

Ch 11a          Ch11aMS

3,5,6     Chapter 11 Selected Solutions


Membranes: Transport

Ch11b          Ch11bMS

10-13, 15, 16, 19, 22





1 F

EXAM 3   A through F in Pg6-116, G though Z in SIPA 125

50 points, integrates material from Chapter 3 and 6 into Chapters 8, 10 and 11.  Be sure to bring your calculator.

4 M

Independence Day HOLIDAY



6 W


Ch 12            Ch12MS

1, 3, 4, 5, 7, 13       Chapter 12 Selected Solutions-Both Classes

8 F


Ch 13            Ch13MS

 6, 9, 12, 14, 19-21, 24-27     Chapter 13 Selected Solutions-Both Classes



Ch 14a          Ch14aMS

1, 2, 4-7, 9, 10, 14, 16      Chapter 14 Selected Solutions-Both Classes


Gluconeogenesis and PPP

Ch 14b          Ch14bMS

21-24, 26, 27

15 F

EXAM 4   A through F in Pg6-116, G though Z in SIPA 125


50 points, bring your calculator. Integrates material from Chapters 12, 13 and 14.


 Citric Acid Cycle

Ch 16           Ch16MS

1-9, 15, 18, 19, 30-32       Chapter 16 Selected Solutions-Both Classes      Last Day to Drop.


Glucose and Glycogen Regulation Part 1

Ch 15a        Ch15aMS

3-5   Chapter 15 Selected Solutions-Both Classes     

22 F

Glucose and Glycogen Regulation Part 2

 Ch 15b       Ch15bMS

6 - 8, 10, 15, 16


Fatty acid oxidation

Ch 17          Ch17MS

  1-4, 9, 10, 13, 16, 26, 28    Chapter 17 Selected Solutions-Both Classes


EXAM 5   A through F in Pg6-116, G though Z in SIPA 125


50 points.  Integrates material from Chapters 15, 16, 17

29 F

Amino acid oxidation and Urea Cycle

Ch18            Ch18MS

1-5, 8, 11  Chapter 18 Selected Solutions




1-5 Chapter 19 Selected Solutions-Part a and b

1 M

Oxidative Phosphorylation Part 1

Ch 19a          Ch19aMS


3 W

Oxidative Phosphorylation Part 2

Ch 19b         Ch19bMS

6, 7, 9-11, 13, 14, 16, 18      Link to Malate-Aspartate Shuttle Study Help

5 F

Final EXAM  A through F in Pg6-116, G though Z in SIPA 125   


Comprehensive.  100 points. American Chemical Society Biochemistry Core Exam is 40 questions.

Course Policies

1. Exams:
There will be six exams over the course of the semester - each worth 50 points plus the cumulative Final Exam (100 points).  There will be multiple choice questions.  There will be different FORMS of the Exam. 

Wearing brimmed hats or baseball caps during exams is not permitted, classroom lighting does not require hats.   Make-Up Exams will be given only to students providing valid documentation of a medical or other serious problem.  NO EXAM IS DROPPED.  All portions of the course are IMPORTANT.  Answers to the exams, grade distribution and Exam Wrapper will be sent by email to each student in a timely fashion after the exams are graded.

2. Preparation for each class: Study the Narrated Power Point well. Make sure you know all the material before class. And, be able to do the selected End of Chapter Problems before class.


3.Each class will have a clicker graded activity = of 5 to 15 points.  Missed class activities can be made up with a written medical, legal or other valid excuse within ONE WEEK of the missed class.

4. Final Grade Calculation

Exams 1 through 6 and Final

400 points

iClicker Points

200+ points


600+ points

Class Clicker Points:  at least 200, the class activities are constantly being improved and changed, the actual number has come to a little more than 200.  But is not the same from semester to semester.  They ALL get counted into your total-final points.

CONVERTING POINTS TO LETTER GRADE OCCURS AT THE END OF THE SEMESTER:  Total points attained on all exams and classes are curved.  If necessary the curve will not allow the lowest C (passing for majors) to go below 50% of the total.

5.  Make-Ups (Classes and Exams), Extra Credit. If you miss a class or exam, please contact the instructor within 24 hours of the exam or class, if possible.  .Missed classes and exams can be made up ONLY if you have a valid written medical or legal excuse.  Make-Up Exams have no multiple choice questions.  If you foresee that an unavoidable prior commitment that will prevent you from attending an exam or class, contact the instructor at least 2 days prior to the scheduled exam time to discuss alternative = taking a make up exam or making up class iClicker questions not more than ONE WEEK from the missed exam or class.

There is NO EXTRA CREDIT, each student's grade comes exclusively from iClicker points, and exam points.

6. Cheating

Students caught cheating during an examination will be ejected from the exam and given an "F" for the course.


The FIU policy on incompletes is: An incomplete grade is a temporary symbol given at the discretion of the instructor for work not completed because of serious interruption not caused by the student's own negligence. An incomplete must be made up as quickly as possible but no later than two semesters or it will automatically default to the grade that the student earned in the course. There is no extension to the two semester deadline. The student must not register again for the course to make up the incomplete.

Incompletes will require written documentation (doctor's note, accident report, etc) of the underlying condition that impedes student progress. A form will need to be signed by the student detailing the procedure and agenda for completing course-work.

Students who receive an incomplete grade and have applied for graduation at the end of that term, must complete the incomplete grade by the end of the fourth week of the following term. Failure to do so will result in a cancellation of graduation. The student will need to reapply for graduation.