Introduction to Biochemistry Chem-527 (Spring 2009)

 

http://www.udel.edu/chem/thorpe/Chem527/links527.html

 

Instructor:                         Colin Thorpe

                                   

                                    204 Drake Hall

                                    Phone: 831-2689

                                    EMail: cthorpe@udel.edu

 

Office Hours:         Tuesday 3-4 PM

                                       Thursday 6- 7 PM

 

Lectures and out-of-class exams for sections 01o and 011 (taken from the catalog):         

             

CHEM-527 INTRODUCTORY BIOCHEMISTRY  3cr

      010          (LEC)     TuTh           9:30a-10:45a BRL-207                 

              (LEC)               Sa                 9:00a-11:00a                      3/14     

              (LEC)               Sa                 9:00a-11:00a                      4/25     

CHEM 527 SECTIONS 010 AND 011 WILL BE EXAMINED ON COMMON DATES: SATURDAYS, MAR. 14 AND APR. 25 FROM 9:00 AM -11:00 AM.  NO EXCEPTIONS WILL BE MADE.

 

      011          (LEC)     TuTh           4:30p-5:45p    BRL-101                 

              (LEC)               Sa                 9:00a-11:00a                      3/14     

              (LEC)               Sa                 9:00a-11:00a                      4/25     

CHEM 527 SECTIONS 010 AND 011 WILL BE EXAMINED ON COMMON DATES: SATURDAYS, MAR. 14 AND APR. 25 FROM 9:00 AM -11:00 AM.  NO EXCEPTIONS WILL BE MADE.

 

Examination               Date                                              % of Grade

 

Exam 1                     Saturday, March 14                                     30

 

Exam 2                     Saturday, April  25                                       30

 

Final Exam                        Final’s Week                                                  40

 

 

There will be no make-up examinations.  Medical excuses require a note from your doctor (for excused absences on Exams 1 and 2, your score on the final will be prorated to cover that 30% of your grade).    

     

Text:             Lehninger Principles of Biochemistry 5th Edition (Nelson, D.L. and Cox, M.M.).  Worth Publishers.  (Reading assignments also specified for the 4th edition.)

 

Visit the publisher’s web site at: www:worthpublishers.com/lehninger

 for useful information and links

A tentative outline of major topics is listed here.  Please note that we cannot cover the whole of the book.  I will direct you to what I think is important as we progress.  In the past my tests usually come from, or are inspired by, material covered in class.  I anticipate that coming to class will be advantageous.

 

Tentative reading order

 

Chapters 1:                An introduction to molecular logic, cells and biomolecules (a review of some basic chemical concepts). This is a support chapters for background and/or review.

Chapter  2:                Water

Chapters 3-5:            Amino acids through protein structure and function

Chapter  6:                Enzymes

Chapter  7:                 Carbohydrates

Chapters 10-11         Lipids and Membranes

Chapter 13 + Part II  Bioenergetics

Chapter 14/15          Glycolysis

Chapter 16                 Citric acid cycle

Chapter 17                 Fatty acid oxidation

Chapter 19                 Oxidative phosphorylation

Chapters 20-22        Some topics in biosynthesis

Chapter 24 + 8          Genes and Chromosomes

Chapters 9                 Topics in information pathways and recombinant DNA technology                

 

Grading:                  The distribution of grades averaged over the last few years:

(A/A-) totalled 24%; (all B grades) 34%; (all Cs) 36%; (all Ds and Fs) 6%.   The average grade on the three exams was 59% (highest avg. grade was 95%).  Please consider these statistics in judging your prospects.  A part of each exam tests the application of concepts we cover in the course to material you may never have encountered.  The course is graded on the curve and, given a comparable class, we expect a similar distribution of grades.  To give you an idea what to expect a sample of exams will be included on the Website.  Note that metabolic charts will be included where appropriate.  Please also note that biochemistry is “CHEMISTRY brought to life” and there are chemistry prerequisites for this course.

 

Extra stuff:            I will regularly post a brief synopsis on the Webpage together with readings and announcements and extra material as appropriate.

 

 

Finally:                    Good luck.

 

 

ANNOUNCEMENTS

 

·        Office Hours:         Tuesday 3-4 PM

       Thursday 6- 7 PM

 

·        Wrong exam key PDFs replaced – hopefully

 

 

EXAM PDFs

 

Green highlighted entries are some old exams.  Red .. are the keys.  Please don’t peek at the keys until you need to!  Here are some of the types of questions you may encounter.

 

FIRST CHEM527 EXAM 2006F                PDFs\exam1_chem527_06F.pdf

 

FIRST CHEM527 EXAM 2006F                    PDFs\Chem527E1keyF06.pdf   

 

SECOND CHEM527 EXAM 2006F            PDFs\CHEM 527 Exam 2 F02.pdf

SECOND CHEM527 EXAM 2006F           PDFs\CHEM 527 Second Ex_Key F06.pdf

 

FINAL CHEM527 EXAM 2006F               PDFs\chem527_Final_ex_F2006.pdf

FINAL CHEM527 EXAM 2006F               PDFs\CHEM527_06F_FinalKEY.pdf

 

 

FIRST CHEM527 (CT) EXAM 2004        PDFs\1stFall2004.pdf

FIRST CHEM527 (CT) EXAM 2004       PDFs\CHEM 527 First Exam F04.pdf        

 

SECOND CHEM527 (CT) EXAM 2004      PDFs\2ndFall2004.pdf

SECOND CHEM527 (CT) EXAM 2004      PDFs\CHEM 527 Second Ex_Key F04.pdf

 

FINAL CHEM527 (CT) EXAM 2004          PDFs\FinalFall2004.pdf

FINAL CHEM527 (CT) EXAM 2004           PDFs\CHEM 527 Final Exam F04.pdf

 

 

FIRST CHEM527 (CT) EXAM 2002         PDFs\CHEM 527 Exam 1 F02.pdf            

FIRST CHEM527 (CT) EXAM       PDFs\CHEM 527 Exam 1 Key F02.pdf

 

SECOND CHEM527 (CT) EXAM 2002    PDFs\CHEM 527 Exam 2 F02.pdf  

SECOND CHEM527 (CT) EXAM 2002    PDFs\CHEM 527 Exam 2 Key F02.pdf     

 

FINAL CHEM527 (CT) EXAM 2002       PDFs\CHEM 527 Final F02.pdf  

FINAL CHEM527 (CT) EXAM 2002         PDFs\CHEM 527 Final Key F02.pdf      

 

 

 

 

Please note, as we have said already,  that there are chemistry pre-requisites for this course – so dust off that introductory text and remind yourself how to do basic stuff such as moles/molar/C1*V1 etc / logs / pH / stoichiometry / equilibria / kinetics / basic organic / curved arrows / bonding and etc. 

 

Biochemistry is bioCHEMISTRY.  A description of the Krebs cycle as a parade of chemical names is not the style of this course

 

< << < << > >> > >>

 

BRIEF SYNOPSIS OF MATERIAL COVERED IN LECTURE  

 

 

 

>>> Reading advisory: (for those who have the fourth edition of Lehninger (L) I will include suggested pages for both L(IV) and L(V)

 

(L)V  Chapter 2  and Chapter 3 (pp. 71-85;  

or (L)IV  Chapter 2 and Chapter 3 (pp. 75-88) .    (The subsequent sections in Chapter 3  … on protein purification … will be covered a little later   Don't need them just now.

 

Please note: Chapter 1 is not specifically covered – just useful background/synopsis and review from earlier classes.

 

<<<>>> 

 

General introduction to the course.  Attention will be drawn to the typical grade distribution in CHEM527 taught by CT.  Please take a look at the sample exams (above) to judge the style of exams and your prospects in the course.

 

We started with water (again). Concepts polarized bond, dipole, H-bond, electrostatic bond, strength of typical covalent bond and "typical" H-bond, solvation, hydrophilic, hydrophobic, clathrates, amphipathic, surfactants, soaps, micelles, bilayers, biological membranes, monolayers, a molecular explanation of surface tension, the importance of surfactants in physiology (without surfactants breathing would be very difficult). 

 

Then we started with equilibria (again) ionization of water [remember - we need to assume basic familiarity with prerequisite materials – here equilibria such as  A ↔ B  +  C)]

 

We reminded you about: ion product of water and strong and weak acids/bases

 

 

We covered the Henderson Hasselbalch equation, titrations of a weak acid by a strong base, pH/titration curves, buffers, the components of the buffering capacity of biological fluids, the need for pH control, and the general effect of pH on the absorption of drugs with titrating groups.

 

>>> Problems Water – titrations and buffers

 

First exam 2006F:               questions:  1a, b, c, e; q. 6

Final exam 2006F:              questions: 8; 9c

 First exam 2004:                 questions: 1a, b, c, d, e.

Final exam 2004:                 questions: 8 a, b, e.

 First exam 2002                  questions: 1 a, b, c, d, e, f

Final exam 2002                  questions: 12 a, b

 

 

Started "amino acids, peptides and proteins" section. 

 

Here>>>>   We will resume next week and probably take about 2-3 lectures over the following parts of the book.

 

READING:     L(V) 92-106  and for the next part dealing with 3D structure of proteins  pp. 113-148        

                        L(V 96-111 and for the next part dealing with 3D structure of proteins  pp. 116-153

 

 

 

 

 <<<<>>>>

Biochemistry is “chemistry brought to life”