Calendar for CHE 550, Fall 2009

Please check regularly for updates


27 Aug.

Read Chapter 1

Course syllabus-corrected wrt Final date

Lecture Notes

1 Sept.

Read Chapter 1 & 2

Lecture Notes

3 Sept.

Read Chapter 2 & 3

Lecture Notes

8 Sept.

Read Chapter 3

Lecture Notes

10 Sept.

Start reading Chapter 4

Lecture Notes

15 Sept.

Read Chapter 4

Notes are superceded by those of 17 Sep.

17 Sept.

Read Chapter 5

Lecture Notes

22 Sept.

Read Chapter 6

Lecture Notes

Problems on Chapter 1

Problems on Chapter 2

Problems on Chapter 3

Problems on Chapter 4

Problems on Chapter 5

Guided Tour: last question for Chapter 5

Problems on Chapter 6

24 Sept.

Read Chapter 7

Lecture Notes


29 Sept.

Read Chapter 7

Lecture Notes


1 Oct.

Clarifications for Problem set !! Corrected versions of the problems for chapters 1, 2 and 3 now replace the original versions, so please download again. An expanded version of the guided tour for Chapter 5 also replaces the original version (with more explanation). You need to do this as part of your problems for chapter 5.

Lecture Notes


Updates regarding midterm 1 & Problem set 1:


Problems on Chapters 1-4 are due by noon on Monday Oct 5.

Solutions to Chapters 1-4 are posted outside my office AND you can


My configurations for the peptide in problem 3 of Chapter 3 are here.

I will offer a problem-solving session based on the problems for chapter 4 (problem set AND textbook) from 5-7 pm Monday 5 Oct. in CP137.

Problems for chapters 5 and 6 are due on 20 October (in class).

6 Oct.



8 Oct.

Read Chapter 8

Lecture Notes

Problems on Chapter 7, Due 27 October in class


13 Oct.

Read Chapter 10

Lecture Notes


15 Oct.

Read Chapter 11

Lecture Notes

20 Oct.

Read Chapter 11

Lecture Notes

Problems on Lipids, Due 29 October in class

Problems for chapters 5 & 6 due in class

For Mass Spec problem in Chapter 5 (problem 3) a single value of z explains all the masses observed. The numbers were drawn from a paper, and include a real-world deviation from ideality. Choose the best answer for the numbers given (and note that the answer may not be unique).

22 Oct.

Lecture Notes


27 Oct.

Lecture Notes

Read Chapters 12


29 Oct.

Problems on nucleic acids Chpt 10 & 11, Due 4 November 10 am, in AFM's mailbox

Lecture Notes

Correction to Pblm 4 Chpt 10, pard 'd' should refer to the endonucleases you chose in 'c' (not 'b'). A corrected version is now posted.


3 Nov.

Lecture Notes

Review session from 6:00 to 7:00 pm in CP137


5 Nov.

Midterm II, Best of Luck


10 Nov.

Lecture Notes

Read Chapter 14


12 Nov.

Read Chapter 15 through page 467 & 17

Paper Topics due


Ignore incorrect date on page 4 of syllabus

17 Nov.

Lecture Notes

Read Chapter 13


19 Nov.

Corrected Lecture Notes

Read Chapter 14

Paper Due

Grading Scheme for Paper

Ignore incorrect date on page 4 of syllabus


24 Nov.

Lecture Notes

Read Chapter 15 through page 467 & 17.

Problems on Chpt 12, Due 11 December 12 noon, in AFM's mailbox

special help discussion, 2 pm CP137 Wed 25 Nov.


Thanksgiving, no class


1 Dec.

Lecture Notes

Read Chapter 17

Problems on Chpt 13, Due 11 December 12 noon, in AFM's mailbox


3 Dec.

Lecture Notes, including some hints for the problem set Chpt13 #1

Review Chapters 22 and 23


8 Dec.

Problems on Chpt 14, Bonus points if submitted 14 December at noon, in AFM's mailbox, ON TOP OF EXISTING MAIL

Lecture Notes

Streamlining Q1 of chapter 12 problems Problem set 1: You can write your degenerate primers using the IUPAC notation for degenerate bases, or with degenerate bases grouped in parentheses, or stacked vertically (no need to list them all separately). For part b (as in part c) just choose 5 primers to analyze for secondary structure. The web site listed in the lecture notes provides a schematic output, please copy or snap-shot that and include it in your problem set. Choose the same 5 primers for all three analyses: secondary structure, Tm and Ta.


10 Dec.

REVIEW session, 1 - 3 pm on 14 Dec. in CP137

Lecture Notes


15 Dec., 10:30 am