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Biochemistry Calendar

CHY461/561 Fall 2007

Subject to revision. Last revised 2007/10/23.

Unless stated otherwise, chapter assignments are from
Horton, et al., Principles of Biochemistry,
Fourth edition, Pearson/Prentice Hall, 2006

Consult Biochemistry Topics for specific assignments.

Date
Monday
Wednesday
Friday
Week of
9/3

NO CLASS

Introduction

Rhodes, Chapter Zero: Reviewing your chemistry in a metabolic context.

Click HERE to download Chapter Zero (PDF file: Adobe Reader or Apple Preview needed to view.)

Week of
9/10

Quiz on Chapter Zero
Consists of five short-answer questions based on the questions asked in this chapter.

Chapter 1: biomolecules, energy

Chapter 1: cells

Chapter 2: water, pH

Chapter 2: buffers, ionization states of biomolecules

Quiz: See Learning Strategy for this chapter.
Week of
9/17

Chapter 3: amino acids, composition of proteins

Quiz: See Learning Strategy for this chapter. This is the most important quiz in the course.

CHALLENGE: Can you sketch a mechanism for oxidation of thiols to disulfides by oxygen
(O2)?

Chapter 3: purifying and characterizing proteins

For an example of a published protein purification, click HERE (2.5 Mb file).

Chapter 3: sequencing proteins

Sequencing Problem for Discussion

CHALLENGE: Can you sketch mechanisms for
1) Edman cleavage?
2) Cyanogen bromide cleavage?
3) Disulfide reduction?
Week of
9/24

Chapter 3. sequence comparison and the meaning of sequence

If you want to learn more about sequence comparison, take the Bioinformatics Tutorial (not required--will be covered in depth during second semester).

Loose ends; preparation for Exam I

Exam I: Rhodes, Chapter Zero; Horton, Chapters 1-3; plus Protein Purification Paper(purification procedures only).

Exams are at normal class place and time.

Click HERE to download a key and grade chart for Exam I (will appear after exam).

Week of
10/1

Chapter 4: protein structure, common structural elements and motifs

Chapter 4: examples of protein function

 

MEET IN COMPUTER CLASSROOM, Luther Bonney 202
Hands-on Workshop with DeepView.

Come early, if you like. We have the computer classroom from 10:00 until 11:30 AM.

Please look over Deep View Tutorial before class.

Workshop Outline
Week of
10/8

NO CLASS

Chapter 4: more about oxygen transport; how molecular models explain oxygen binding, cooperativity, and the effects of pH and BPG.

Supplemental Problems on oxygen transport.

 

Quiz: See Learning Strategy for Protein Function.

Chapter 4: where protein models come from (see links to readings below). Using the Protein Data Bank.

BEFORE THIS CLASS, PLEASE
1. STUDY READINGS (below), and
2. TAKE (at least) THE FIRST TWO TUTORIALS UNDER "Site Tutorials" at the Protein Data Bank.

Click
HERE for the reading and
HERE for an additional figure used in class.

More About Fourier Transforms
Week of
10/15

Chapter 5: enzyme kinetics

Quiz: See Learning Strategy for this chapter

Solutions to Supplemental Problems on oxygen transport are available. Ask your instructor.

Chapter 5: enzyme inhibition and regulation

 

Chapter 6: principles of enzyme catalysis, with examples

DeepView Project due before beginning of class.

See this Kinetics Problem for Discussion
OPTIONAL: You can hand in solution to kinetics questions #1 and #2 as a free 10-point quiz (can help quiz average, can't hurt it.) Accepted today only.
NEW: Can you figure out how to solve these problems using this Nonlinear Least Squares Curve Fitter?

Appearing this weekend: Solutions to Kinetics Problem. Send me email if I forget (ugh—for me, forget is the f-word).
Week of
10/22

Chapter 6: more examples of enzyme mechanisms

loose ends and review for exam

Exam II: Horton, Chapters 4-6 and Protein Data Bank

Exams are at normal class place and time.

Click HERE to download a key and grade chart for Exam II (will appear after exam).
Week of
10/29

Chapter 7: coenzymes, vitamins

Quiz: See Learning Strategy on Coenzymes.

 

 
Week of
11/5

Chapter 8: carbohydrates

Quiz: See Learning Strategy for Carbohydrates.

Chapter 9: lipids, membranes

Quiz: See Learning Strategy for Lipids.

transmembrane transport

More detailed model of the Na+/K+ pump (Horton Fig 9.35) HERE.

supplemental problems on transmembrane transport

Week of
11/12

signal sransduction; intro to Chapter 10

Chapter 10: intro. to metabolism

Solutions to supplemental problems on transmembrane transport will appear here.

 
Week of
11/19

Exam III

Exams are at normal class place and time.

Click HERE to download a key and grade chart for Exam III (will appear after exam).

NO CLASS

NO CLASS

Week of
11/26

Chapter 11: glycolysis

Quiz: See Learning Strategy for Glycolysis.

HERE is a one-page glycolysis overview figure that I will use in class.

 

 
Week of
12/3

SNOWED OUT (or snowed in)

Chapter 13: citric-acid cycle
(saving Chapter 12 for next semester)

Quiz: See Learning Strategy for Citric-Acid Cycle.

HERE is a one-page citrate-cycle overview figure that I will use in class.

 
Week of
12/10

Chapter 14: electron transport & oxidative phosphorylation

Quiz: See Learning Strategy for ET&OP.

 

Finish Ch. 14 and Review

Preview of Biochemistry II

Week of
12/17

 

Final Exam: Wednesday December 19, 10:45 AM - 12:45 PM, Room 503 Luther Bonney (This is normally our Monday room.)

Click HERE to download a key and grade chart for Final Exam (will appear after exam).

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