Biochemistry II
Chemistry 332
(CRN 588)
Class, Test Schedule (Room: PSci 229 - M,W,F 9-9:50 AM) Spring, 2011
Instructor: Dr. Terry L. Helser Office: PS 227 Phone: 607-436-3518 
E-mail To:
Text: Biochemistry, 4th Ed., 2009, Trudy & James R. McKee (Oxford University Press)

Catalog Description: This course is the second part in a two semester biochemistry sequence. It focuses on anabolism and the macromolecular basis of heredity, and thus of life itself.  You will study the structure of proteins and especially nucleic acids, but the major emphasis is on information flow and its regulation from DNA to RNA to protein and beyond.  We will cover microbial genetics, DNA, RNA, and protein synthesis, recombinant DNA, chromatin structure, gene arrangement, the immune system, and more. The course will provide you with the background needed to understand, and participate in, the exciting developments in genetic technology.  Whenever possible topics of current research interest are discussed. (LA) Prerequisite: Introductory Biochemsistry, CHEM 330.

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Month & Days       Study Topic     
Reading Assignment
I. Anabolism Ch. 2, 4
January 19, 21
Introduction, Co-op Class Review
Ch. 12
24, 26, 28
Photosynthesis, Calvin (Dark) Cycle
Ch. 13
31, 2, 4
Amino Acid Biosynthesis
Ch. 14

February 7, 9, 11

Amino Acid Degradation
Ch. 13, p. 392ff
14, 16, 18
Nucleotide Biosynthesis
Exam I (Wednesday, PSci room 229, 9 AM) 
Ch. 15
February 21-25
Spring Break - No Classes

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Month & Days
II. Gene Expression
Reading Assignment 
February 28, 2, 4
 Integration of Metabolism
Ch. 16
March 7, 9, 11
DNA Replication
14, 16, 18
Ch. 17
21, 23, 25
Transcription (RNA Synthesis, Splicing)
Ch. 18
28, 30
Translation (Protein Synthesis)
Ch. 18
April 1
Exam II (Friday, PSci room 229, 9 AM)
4, 6, 8
Control of Gene Expression
Ch. 17, p. 515

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Month & Days
III. Genetic Regulation
Reading Assignment 
April 13, 15
Control of Gene Expression
Ch. 17, p. 515
April 18-25
Spring Break - No Classes
27, 29
May 2, 4, 6
Student Presentations
9, 11
May 16
Final Exam (Wednesday, PSci room 229, 
8-10:30 AM)

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Hourly Exams
2 x 100 pts. = 200 pts.
Scale: 90-100% A
Final Exam
200 pts.
80-89% B
Lab Research Paper
100 pts.
70-79% C
Laboratory Evaluations
200 pts.
60-69% D
Total: 700 pts.
0-59% E

You may earn up to 35 points for extra credit problem sets given throughout the semester. Tests have 10% more points than listed so I can challenge the best.

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Laboratory Schedule (Room: PSci 205 - Monday 2-6 pm) Spring 2011
Required Materials: Graph Ruled Lab Notebook, Safety Goggles

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Month & Days
Laboratory Topic
Evaluation (Due Date)
 January 24
Form Groups, Check In, Plan ??? 
1-Oral Progress Rpt.
1-Prop (1/27)
#1Pipettor Calibration
1-Prop 2 (2/3)
February 7



Report #1 & #2 Photosynthesis

1- Oral Rpt. , 1-Final (2/18)
Spring Break - No Lab
#2 Photosynthesis 
2-Proposal (2/24)

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Month & Days
Laboratory Topic
Evaluation (Due Date)
March 7
Snow Day, lab canceled
2-Proposal (3/4)
#2 Photosynthesis Report #2 & #3 DNA Analysis
2-Oral Rpt., Final 3/25
Report #2 & #3 DNA Analysis
3-Proposal (3/25)
#3 DNA Analysis
3-Proposal (4/1)
April 4
#3 DNA Analysis
3-Oral Rtp.,  

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Month & Days
Laboratory Topic
Evaluation (Due Date)
April 11
#3 DNA P&F Reports & #4 Gene Regulation
4-Final Rpt. (4/15)
April 18 & 25
Break - No Lab
4-Proposal (4/29)
May 2
#4 DNA Analysis
4-Proposal (5/6)
#4 DNA Analysis
(Check Out) Review
4-Oral Rpt., Final 5/14
May 16
Final Exam (Wednesday, PSci room 228,
8-10:30 AM)

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Grading Policies:
Your point total will be divided by the total possible for a % of 200 points. The final report for which you were primary author is worth a maximum of 100 points of your total grade.
Final reports must be typed, spaced >1.5 lines, and signed by all group members. They must contain an objective, introduction, procedure (flow diagram), safety notes, results (an essay w/ tables, plots), and discussion/conclusion sections. The weekly proposals, with objective, equipment and reagents needed, procedure (flow diagram) and safety notes, which proves you are prepared to do each experiment safely, must be accepted by your instructor before you will be allowed to do the lab ( submit on email no later than the Wednesday before the lab). One point /day will be subtracted for reports submitted after due dates.
Oral reports are awarded 100 points, of which 80% is for the group's presentation and 20% for the individual's stage presence, poise and participation. Generally, the score is an average of the peer evaluations from other teams and the instructor's. Copies of the printed grading form are available in the laboratory.
Lab notebooks may be collected at the instructor's whim.
Please note: You are to use your notebook to prepare for each lab with suitable notes on procedures, flow charts, tables for data, etc.; to make notes and take data during the lab; and to do calculations and write your results and conclusions after the lab. Each of these parts will be evaluated.

You must be credited as the major author of at least 1 lab report and score 60% on lab evaluations to pass the course. If you miss more than 1/3 of the labs, you will earn an E for the course, no matter what your test scores total. Plagiarism (see your Handbook ) will not be tolerated. College and departmental policies apply to this course.
Approved clothing and safety goggles must be worn when any experimental work is occurring. Doing unauthorized experiments or procedures is prohibited. If in doubt, ask the instructor. All accidents involving personal injury, however minor, must be reported immediately to the instructor. The instructor has the right to expel anyone from the laboratory without credit for unsafe or offensive behavior or dress. 

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Biochemistry II, Chemistry 332-01 Lab Information

1st Week, Monday lab: 2nd Week:
Week after experiments are done:
Oral (group) report = 100 points
Group's proposal; Emailed by Mon. = 10 points
Final reports = 100 points
Notebook, Quiz = 10 points each
    - 1 point/day late off project total = % of 200 points total
    Final reports earn up to 100 points for the primary author out of the 300 point total for the lab part of the course. S/he must be clearly identified on the first page, and each member must be the primary author on at least one final report. A separate grade may be given for the primary author's work.

If you must miss a class, lab or group meeting, you must inform your group and instructor. Your group should decide how you can repay your responsibilities to the group. Options might be to do extra library research, proposal or report writing, computer searches or whatever the group decides is adequate repayment for the loss of your participation. If the group decides your excuse was not valid, they may consider a loss of credit as appropriate punishment, and should so inform you and the instructor.
Team members who fail to participate adequately with their team may be fired, and justification must be provided to them and the instructor. The member must then find a new team to hire him/her or do the projects on their own, including all reports and proposals.
Penalties, generally -1 point a day for group reports which are late, will be assessed against the primary author of that report, not the rest of the group members, if requested by the group in writing or by email. 
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  Last Modified on 3/9/2011
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