General Biochemistry

Spring  -  2014
Class Times - MWF  2:00-2:50 AM    RDB 1100 (Law School)
  Class Links (below) are to pdf Handouts.
Principles of  STUDY

Laboratory Link
Instructor Email Phone Office hours
John Makemson
 OE 246/247:  MTWF  Mornings 9-10AM + Afternoons before 4PM

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

The Professor'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 bioenergetics/thermodynamics of biochemical reactions.  Students will know the reactions of major metabolic pathways (Central Metabolism: Glycolysis-Gluconeogenesis, Pentosephosphate Patthway, Citric Acid Cycle, Respiratory Electron Transport System, Glyoxylate Cycle; Beta-oxidation) and be able to analyze the regulation of these pathways.  

Lecture (Narrated PowerPoint) 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.  In making these MP4's I used no script, they are produced extemporaneously as I would have done in a traditional lecture: they do not have a mechanical script driven voice, but rather mine which is not totally perfect.  They usually last less than a full lecture 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.  

CLASS is for Exercising Your Knowledge.  CLASS IS NOT TO LEARN NEW MATERIAL.  You must come fully prepared having studied the Lectures at home, in the Library or where ever you can do this productively.  You learn the new material BEFORE class.

ADVANTAGES of the FLIPPED CLASS:  the lectures here are   narrated PowerPoints that you can view at times you choose.  BUT, this has to happen BEFORE Class Time.  The Power Points used in lecture can also be downloaded to take notes on if you convert them to pdf.  It is to your distinct advantage to have the 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 far, you can always back the lecture up and get to what you missed.  In other words: YOU HAVE TOTAL CONTROL of the LECTURE.  All this makes learning paced to your ability to keep up and ACTIVELY LEARN.  End of chapter problems need to be done before class:  the class will work on problems like these, but not the exact ones you will practice before class.

A Biochemistry MOOC:  oli.cmu.edu/courses/free-open/biochemistry-course-details   This course was created at Carnegie-Mellon University (the author this summer is moving to Stanford, so it may pop up there).  MOOC: massive online open course.  It is free and you can use it as a resource.  It has a slightly different structure, but has problem sets for each chapter.

Each Class Time has a Graded Component that REQUIRES you to have a working iClicker or iClicker-Go app on your smartphone or tablet for Each Class.   Classroom work counts for 33% of your grade.  Last semesters, the i-Clicker-Go app had wi-fi connection problems; the safest is the basic iClicker.

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. 2012) -  Should Be 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.   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 ~$210).  Be careful about ordering the text and not the study guide.   NOTE:  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 pdf files from this syllabus.

Tentative Syllabus (Likely to Change During the Semester)
See Below About Practice Exams

PowerPoint of  "Lecture" to Use as NotesWhen Doing the Narrated Power Point Lecture
Narrated Power Point "Lecture"
  DO THESE BEFORE CLASS:  End Of Chapter Problems to Solve
(Published Solutions are included)
 and all the short solutions with answers are in Abbreviated
Solutions following page 1198 in the textbook: Best Source!   
6 M Introduction the Flipped Class
YouTube     FIU Media Site

8W  Introduction to Biochemistry
Ch1               Ch1MS   1, 3, 5, 8, 11, 12  Chapter 1 Problem Solutions
10 F
Water, pKa, Buffers  
Ch 2              Ch2MS
  1-5, 8, 11-26     Chapter 2 Problem Solutions
 13 M
Amino Acids and Proteins            ClassGrades
 Ch3a             Ch3aMS
  1-7      Chapter 3 Problem  Solutions  
 15 W
Protein Purification    
Ch3b             Ch3bMS
  8-11, 13, 15, 16
17 F
Protein Sequencing
Ch3c             Ch3cMS
 18, 19, 21, 22
Martin Luther King, Jr. Day

22 W EXAM 1

 50 points.  Please bring a calculator (non-graphing). This exam integrates material from Chapters 1-3
24 F
Proteins Structure Part 1
Ch 4a           Ch4aMS
  1-4     Chapter 4 Problem Solutions
 27 M Protein Stucture Part 2
Ch 4b            Ch4bMS
Protein Function: Binding
Ch 5              Ch5MS
 1, 3, 5-7.      Chapter 5 Problem Solutions
31 F
Enzymes Part 1
Ch 6a            Ch6aMS
 1-6, 11, 13.   Chapter 6 Problem Solutions 

3 M
Enzymes Part 2
Ch 6b            Ch6bMS
 12, 18, 19.
5 W
Ch 7               Ch7MS
15, 17- 20, 23, 27    Chapter 7 Problem Solutions
7 F
 EXAM 2  

50 points.  Please bring: No 2. Pencils, Simple Scientific Calculator+ Straight Edge (ruler),  This exam integrates material from Chapters 4, 5, 6 and 7. 
10 M
Nucleic Acids Part 1
Ch 8a             Ch8aMS
1-3, 5, 8, 10     Chapter 8 Problem Solutions
12 W
Nucleic Acids Part 2
Ch 8b             Ch8bMS
14 F
Ch 10             Ch10MS
1, 2a, 2c,7-13, and 3 if you can cook.    Chapter 10 Problem Solutions
17 M
Membranes Structure
Ch 11a          Ch11aMS
3,5,6     Chapter 11 Problem Solutions
19 W
Membranes: Transport
Ch11b          Ch11bMS
10-13, 15, 16, 19, 22
21 F
More membrane in class work

Bring a straight edge.  
24 M

50 points, integrates material from Chapter 3 and 6 into Chapters 8, 10 and 11.  Be sure to bring your calculator.
26 W
Ch 12            Ch12MS
1,4, 5, 7, 13       Chapter 12 Problem Solutions
28 F
Biosignaling, continued


3 M
Ch 13            Ch13MS
 6, 9, 12, 14, 19-21, 24-26     Chapter 13 Problem Solutions
 5 W
Bionenergetics, con't

 7 F
Ch 14a          Ch14aMS
1, 2, 4-7, 9, 10, 14, 16      Chapter 14 Problem Solutions
A Really Great Time to Review Amino
Acid, Nucelotide, Sugar and Lipid
And to review pKa, Enzyme Kinetics, and Thermodynamics.
 17 M
Gluconeogenesis and PPP
Ch 14b       Ch14bMS
21-24, 26, 27
 19 W
More Problems/Case Studies

21 F

50 points, bring your calculator. Integrates material from Chapters 12, 13 and 14.
 24 M
 Citric Acid Cycle
Ch 16           Ch16MS
1-9, 16, 18, 19, 30, 31, 32       Chapter 16 Problem Solutions
26 W
Citric Acid Cycle continued

28 F
Glucose and Glycogen Regulation Part 1
Ch 1            Ch15aMS
3-5      Chapter 15 Problem Solutions     
  31 M
Glucose and Glycogen Regulation Part 2
 Ch 15b       Ch15bMS
6 - 8m 10, 15

 2 W
Fatty acid oxidation
Ch 17          Ch17MS
  1-4, 9, 10, 13, 16, 26, 28    Chapter 17 Problem Solutions
 4 F
Blood Cholesterol, Ch 17 continued

 7 M

50 points.  Integrates material from Chapters 15, 16, 17
 9 W
Amino acid oxidation and Urea Cycle
Ch18            Ch18MS
 1-5, 8, 11           Chapter 18 Problem Solutions
11 F
Oxidative Phosphorylation Part 1
Ch 19a          Ch19aMS
1-5        Chapter 19 Problem Solutions
14 M
Oxidative Phosphorylation Part 2
Ch 19b         Ch19bMS
6, 7, 9-11, 13, 14, 16, 18      Link to Malate-Aspartate Shuttle Study Help
16 W
Ch 19c          Ch19cMS
27, 28, 30, 31, 35, 37, 39, 41
18 F

50 points.  Integrates material from Chapters 18, 19 and 20

Final EXAM   TBA
Comprehensive.  100 points.  After: the graded Exam can be picked up from OE 246.  There will be a key and grade distribution on the bulletin board.
Course Policies
1. Exams:
There will be several exams over the course of the semester - each worth 50 points. The Final Exam (100 points) will be cumulative. 

The EXAMS ANSWERS requiring a written answer will be chemical structures to construct or problems to solve.  There will be multilple choice questions.  There will be different FORMS of the Exam.  Each exam will contain a structures set of the common monomers (WITHOUT THEIR NAMES) relevant to that particular exam. 

    Wearing brimed 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 extremely IMPORTANT.  Answers to the exams will be posted on the course website in a timely fashion.

2.Each class will have a graded activity = of 2 to 15 points.  Missed class activities can not be made up with out a medical, legal or other valid excuse.
3. Final Grade:  Exams 1-6 + Final Exam = 400 points
                          Class iClicker Grade      = 200 points
                              Total Possible Points = 600 points

CONVERTING POINTS TO LETTER GRADE:  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.

4.  Make-Ups (Classes and Exams)

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 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.

5. Cheating

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

6. Incompletes for the course

The FIU policy on incompletes is as follows: 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.