MBMB 451b

 

Eric C. Niederhoffer, Ph.D.

Associate Professor of Biochemistry and Molecular Biology
Southern Illinois University School of Medicine
Rm 211 Neckers, 453-6467, eniederhoffer@siumed.edu
Copyright 2000, E.C. Niederhoffer. All Rights Reserved.
All trademarks and copyrights are the property of their respective owners.

Peter M. D. Hardwicke, Ph.D.

Professor of Biochemistry and Molecular Biology
Southern Illinois University School of Medicine
Rm 210 Neckers, 453-6469, phardwicke@siumed.edu

Quick Links
 General Information
 Resources
 Grading Policy
 Course Outline
 Lectures (RealAudio)
 Bonus Problems
 Exam #1 Answer Key
 Final Exam Preparation Comments
 Final Exam Answer Key

GENERAL INFORMATION:


MBMB 451b is the second semester of a two-semester biochemistry course for undergraduate and graduate students. We will cover enzymes, carbohydrate metabolism, membranes, lipid metabolism, amino acid metabolism, and nucleotide metabolism. Students should be familiar with analytical, organic, and physical chemistry as well as common mathematical approaches to problem solving. Familiarity with the internet is encouraged and recommended. Class meets on TR from 1-2:15 p.m. in the Life Science III Auditorium.


RESOURCES:


The course will use Biochemistry by Voet and Voet (2nd edition, John Wiley & Sons, Inc., 1995), which is available from the campus bookstore. Appropriate readings are indicated in this handout, but you may wish to include additional materials (the WWW is a good example, check http://www.wiley.com/college/voet586501/bookmarks.html).


Two alternatives or supplements are Fundamentals of Biochemistry by Voet, Voet & Pratt (John Wiley & Sons, Inc., 1999, ISBN 0-471-58650-1), which includes a useful Biochemical Interactions CD-ROM for guided and interactive exercises, and Biochemistry by Garrett & Grisham (2nd edition, Saunders College Publishing, 1999, ISBN 0-03-022318-0).


The
KEGG graphical pathway maps may be of use in learning the material concerning the various metabolic pathways.


You may find it beneficial to practice the problems that are included in the textbook! Remember, it is up to you to develop a comprehensive understanding of all the material that is assigned and presented. Lectures will focus on important concepts and illustrate key points. Select materials may be posted to this course web page. To develop a comprehensive understanding (your key goal), we suggest that you read the material several times, attend class, ask appropriate questions, practice problems from various resources (see On-Line quiz and the sample problems that appear in the course outline), and check this MBMB 451b Web site frequently.


GRADING POLICY:


Your performance in this course will be based on 2 tests and the comprehensive final exam. Each of the two tests and the final exam will consist of a combination of short-answer, multiple-choice, and problem-solving questions. Tests are scheduled for Thursday 9 March and Thursday 4 May 2000. We will use the University's designated final exam day and time (Monday 8 May 2000 from 7:50-9:50 am).


As a general policy, there will be no make-up examinations.

 

Tentative Examination Breakdown and Typical Percentage Ranking
   Tests  2 @ 100 pts = 200 pts  A = 90 to 100%  >360 pts
 B = 80 to 89%  >320 pts
 Final exam  1 @ 200 pts = 200 pts  C = 70 to 79%  >280 pts

 Total potential points = 400 pts
 D = 55 to 69%  >220 pts
 F = less than 55%  <220 pts

 

COURSE OUTLINE:

This section will be presented by Eric C. Niederhoffer (18 January - 9 March 2000)

An On-line Quiz will allow you to assess your learning as you progress through the course material.

Lectures will be made available on-line within a reasonable length of time after the class meeting. In order to listen to the on-line lecture, you will need to have RealAudio installed on the computer. Follow the link to RealAudio and directions supplied by the company. Remember, you can scan through each lecture with RealAudio to the portion you want to listen to.


Lectures (RealAudio)
 Click on lecture to listen  Click on link for full description
 Lecture 1 (1/18/00) 73 min  Introduction to enzymes and rates of enzymatic reactions
 Lecture 2 (1/20/00) 73 min  Rates of enzymatic reactions
 Lecture 3 (1/25/00) 73 min  Rates of enzymatic reactions and enzymatic catalysis
 Lecture 4 (1/27/00) 70 min  Enzymatic catalysis
 Lecture 5 (2/1/00) 70 min  Sugars and polysaccharides
 Lecture 6 (2/3/00) 72 min  Sugars and polysaccharides and introduction to
 metabolism
 Lecture 7 (2/8/00) 74 min  Introduction to metabolism and glycolysis
 Lecture 8 (2/10/00) 76 min  Glycolysis
 Lecture 9 (2/15/00) 73 min  Glycolysis and glycogen metabolism
 Lecture 10 (2/17/00) 71 min  Glycogen metabolism and citric acid cycle
 Lecture 11 (2/22/00) 75 min  Citric acid cycle and electron transport and oxidative
 phosphorylation
 Lecture 12 (2/24/00) 74 min  Electron transport and oxidative phosphorylation
 Lecture 13 (2/29/00) 72 min  Electron transport and oxidative phosphorylation and
 other pathways of carbohydrate metabolism
 Lecture 14 (3/2/00) 75 min  Other pathways of carbohydrate metabolism and
 photosynthesis
 Lecture 15 (3/7/00) 76 min  Photosynthesis

 

Bonus Problems
 BP #1 Enzyme Kinetics  For bonus credit, due in class on 8 February 2000
 
click here for solution (pdf file)
 BP #2 Metabolism  For bonus credit, due in class on 29 February 2000
 
click here for solution

 

Introduction to enzymes (Read pp. 332-344)

Rates of enzymatic reactions (Read pp. 345-370) (PDF file for topic)

Enzymatic catalysis (Read pp. 371-410) (PDF file for topic)

Sugars and polysaccharides (Read pp. 251-276) (PDF file for topic)

Introduction to metabolism (Read pp. 412-442) (PDF file for topic)

Glycolysis (Read pp. 443-483) (PDF file for topic)

Glycogen metabolism (Read pp. 484-512) (PDF file for topic)

Citric acid cycle (Read pp. 538-562) (PDF file for topic)

Electron transport and oxidative phosphorylation (Read pp. 563-598) (PDF file for topic)

Other pathways of carbohydrate metabolism (Read pp. 599-625) (PDF file for topic)

Photosynthesis (Read pp. 626-661) (PDF file for topic)

 

First Examination - Enzymes, sugars and polysaccharides, carbohydrate metabolism and photosynthesis
(Thursday 9 March 2000)

Exam answer key

 Exam #1 3/9/00  answer key (pdf)
 
click here for my comments


SPRING BREAK

 

This section will be presented by Peter Hardwicke (21 March - 4 May 2000)

Lipids and membranes (Read pp. 277-329)

Transport through membranes (Read pp. 513-537)

Lipid metabolism (Read pp. 662-726)

Comparison of triglyceride and carbohydrate as energy stores
Effect of low blood sugar-activation of catabolism
Lipolysis, location in fat (and heart muscle), hormone sensitive lipase mediates the rate limiting step
Distribution of the products of lipolysis, role of serum albumin - use of free fatty acid and glycerol by different tissues
Use of glycerol for gluconeogenesis by liver and kidney
Activation of free fatty acids for metabolism-formation of acyl CoA
b-oxidation of even chain fatty acids in mitochondria, acetyl CoA cannot be directly converted into carbohydrate
b-oxidation of odd chain fatty acids - propionyl CoA, methylmalonyl CoA, succinyl CoA - requirement for vitamin B12
b-oxidation of unsaturated fatty acids
b-oxidation of very long chain fatty acids in peroxisomes
Synthesis of ketone bodies-location in liver and kidney mitochondria
Utilization of ketone bodies by brain and muscles
a- and w-oxidation
Biotin
Accumulation of acetyl CoA in the form of citrate
Regulatory role of acetyl CoA carboxylase, malonyl CoA
Synthesis of palmitate by fatty acid synthase
Elongation of fatty acids
Desaturation of fatty acids
Synthesis of triglyceride
Synthesis of phospholipids - membrane biosynthesis
Synthesis of cholesterol

Amino acid metabolism (Read pp. 727-784, 785-794)

Effect of low blood sugar on protein catabolism - a third store of energy
Transaminases, transfer of most a-amino acid N to a-ketoglutarate to give glutamate, Ser to Thr directly deaminated to pyruvate and a-ketobutyrate, asparaginase and glutaminase
Oxidative deamination of glutamate by glutamate dehydrogenase yields energy/reducing power (NADH/NADPH) plus NH4+
Conversion of NH4+ to urea in liver, the urea cycle, location of enzymes, NH4+ and AspNH2 used to form urea, fumarate, oxaloacetate and a-ketoglutarate link urea formation and the citric acid cycle
Use of carbon skeletons to give energy (and/or glucose in liver and kidney) - ketogenic and glucogenic amino acids
Ala, Ser, Cys, Gly and Thr (glucogenic) give pyruvate
Asp and Asn (glucogenic) give oxaloacetate
Gln, Glu, Pro, Arg and His (glucogenic) give a-ketoglutarate
Leu and Lys (ketogenic) give acetoacetate and/or acetyl CoA
Ile (glucogenic and ketogenic), Val (glucogenic) and Met (glucogenic) give succinyl CoA - requirement for Vit B12
Trp (glucogenic and ketogenic) gives Ala and acetoacetate
Phe and Tyr (glucogenic and ketogenic) give fumarate and acetoacetate, phenylketonuria
Leu, Ile and Val grouped as branched chain amino acids - maple syrup disease
Use of alanine and lactate from muscles for gluconeogenesis in liver (alanine-glucose and Cori cycles)
Utilization of branched chain amino acids in the brain
C1 carriers, tetrahydrofolate, S-adenosylmethionine
Essential and non-essential amino acids

Purine and pyrimidine bases, nucleosides, nucleotides (Read pp. 795-828)

 

Second Examination - Membranes, lipid metabolism, amino acid metabolism, and nucleotide metabolism
(Thursday 4 May 2000)

 

Final Comprehensive Examination
Monday 8 May 2000
7:50 to 9:50 a.m.

Final Exam answer key

 Final exam 5/8/00  answer key (pdf) not posted as yet
 
final exam preparation comments
 (disregard)

Biochemistry and Molecular Biology Resources


For more information or comments about this page contact:
eniederhoffer@siumed.edu