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 Graduate Biochemistry  posted by  duggu   on 12/10/2007  Add Courseware to favorites Add To Favorites  
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Abstract/Syllabus:

Sauer, Bob, Frank Solomon, and Tania Baker, 7.51 Graduate Biochemistry, Fall 2001. (Massachusetts Institute of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed 08 Jul, 2010). License: Creative Commons BY-NC-SA

Molecular dynamics computer simulation of damaged DNA.

Molecular dynamics computer simulation of damaged DNA. (Image courtesy of Lawrence Livermore National Laboratory.)

Course Highlights

This course features a selection of lecture notes.

Course Description

The tools and analytical methods that biochemists use to dissect biological problems. Analysis of the mode of action and structure of regulatory, binding, and catalytic proteins.


*Some translations represent previous versions of courses.

Syllabus

 
 

Lectures

Two sessions / week
2 hours / session

Required Texts

There is no required text. You should have a good undergraduate Biochemistry text (Stryer, Rawn, Voet & Voet, Matthews & van Holde, etc.). In addition, several copies of:

Creighton, T. E. Proteins: Structure and Molecular Properties. 2nd ed. New York, NY: W.H. Freeman and Company, 1992. ISBN: 071677030X.

Fersht, Alan. Enzyme Structure and Mechanism. 2nd ed. New York, NY: W.H. Freeman and Company, 1985. ISBN: 0716716143.

Kyte, Jack. Mechanism in Protein Chemistry. New York, NY: Garland Publishing, 1995. ISBN: 081531700X.

———. Structure in Protein Chemistry. New York, NY: Garland Publishing, 1995. ISBN: 0815317018. 

These will be in the reserve room of the library. These address some of the topics that we will cover and serve as a good alternative source of information. Class material will also be posted on the 7.51 homepage.

Exams and Problem Sets

There will be a quiz, two exams during the semester and a final exam. All exams will be closed book but you may bring one page (8.5 x 11 in.) of notes, equations, etc. to the exam. Problem sets will be given out most weeks. These will not be graded or collected but doing them is important. Answers will be supplied. Collaboration with others is allowed on problem sets.

 

 

Calendar

 
 
Lec # Topics Instructors
1 Reaction models; simple kinetics & equilibria Bob Sauer
2 Analyzing kinetic & equilibria experiments  
3 Free energy, entropy, enthalpy & cycles  
4 Forces, hydrophobic effect, chelate effect  
5 Molecular structure and dynamics  
6 Physical properties of proteins and nucleic acids Tania Baker
7 Principles and practice of protein purification  
8 Principles and practice of protein purification (cont.)  
9 EXAM 1  
10 Domain & subunit organization; molecular weight determination Tania Baker
11 Macromolecular interactions: specificity, affinity and energetics  
12 Macromolecular interactions: specificity, affinity and energetics (cont.)  
13 Enzyme catalysis: kinetics Frank Solomon
14 Mechanism of enzyme catalyzed reactions  
15 inhibition and intermediates  
16 Mechanism of enzyme catalyzed reactions: chemistry  
17 Mechanism of enzyme catalyzed reactions: partitioning & exchange  
18 Mechanism of enzyme catalyzed reactions: binding energy  
19 Specificity of catalysis: energetics and consequences  
20 Specificity of catalysis: energetics and consequences (cont.)  
21 EXAM 2  
22 Coupled vectorial processes: making ATP Frank Solomon
23 Coupled vectorial processes: pumps  
24 Coupled vectorial processes: OxPhos, morphology to enzymology  
25 Coupled vectorial processes: processivity  
26 Coupled vectorial processes: Motors; Polymers – origins & consequences of structural & thermodynamic polarity  
27 Coupled vectorial processes: motors; structural & thermodynamic polarity  
28 Coupled vectorial processes: protein folding  
29 Review Session  
30 FINAL EXAM  



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