Biochemistry II
Chemistry 332
(CRN 189)
 
Class, Test Schedule (Room: PSci 229 - M,W,F 12 Noon) Spring, 2008
Instructor: Dr. Terry L. Helser Office: PS 227 Phone: 607-436-3518 
E-mail To: HELSERTL@oneonta.edu.
Text: Biochemistry, 5th Ed., 2006, M. Campbell & S. Farrell (Thomson Brooks/Cole Publishers) 

Catalog Description: This course is the second part in a two semester biochemistry sequence. It focuses on 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 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 interest are discussed. (LA) Prerequisite: CHEM 330.

Click on the highlighted text to move directly to sections 1 , 2 or 3 of the class schedule, to the grade scale , or to the bottom of the page for addresses and other options. You also can move to the lab schedule , the lab grading information, and the general information on lab operation. Study guides are linked to the reading assignments.
 
Month & Days       Study Topic     
Reading Assignment
I. Anabolism Ch. 2, 5
January 16,18
Introduction, Co-op Class Review
Ch. 19
21,23,25
Photosynthesis
 Ch. 20
28,30, February 1
Calvin (Dark) Cycle
Ch. 24
4,6,8
Amino Acid Biosynthesis
 Ch. 25
11,13,15
Nucleotide Biosynthesis
 Ch. 30
February 18-22
Spring Break - No Classes 
  
25,29
Integration of Metabolism
Ch. 27
27
Exam I (Wednesday, PSci room 229, 12 Noon) 

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Month & Days
II. Gene Expression
Reading Assignment 
March 3,5,7
DNA Replication
  
10,12,14
Mutations
 Ch. 27
17,19,21
Transcription (RNA Synthesis, Splicing)
Ch. 28
March 24-28
Spring Break - No Classes
 Ch. 29
19,21,23
Translation (Protein Synthesis)
 
31, April 2,4
Translation Continued
 
April 7,9
Selected Topics
 
April 11
Exam II (Friday, PSci room 229, 12 Noon)

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Month & Days
III. Genetic Regulation
Reading Assignment 
April 14,16,18
Control of Gene Expression
 Ch. 31
21,23,25
Senses
Ch. 32
28,30, May 2
Immunity, Motors
Ch. 33, 34
5 (7 study day)
Review
  
May 9
Final Exam (Friday, PSci room 229, 
2-4:30 PM)

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Grading
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 2008
Required Materials: Graph Ruled Lab Notebook, Safety Goggles

You can go to the second or third part of the lab schedule, lab grading procedures or general information on lab time management from here.

 
Month & Days
Laboratory Topic
Evaluation (Due Date)
 January 21
Form Groups, Check In, Plan ??? 
1-Oral Progress Rpt.
1-Prop (1/24)
 
28
#1Pipettor Calibration
1-Prop (2/7)
February 4

#1Pipettor Calibration 

 
11

Report #1 & #2 Photosynthesis
1- Oral Rpt. , Final (2/14)
 
18
Spring Break - No Lab
2-Proposal (2/21)
25
#2 Photosynthesis 
  

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Month & Days
Laboratory Topic
Evaluation (Due Date)
March 3
Reports #2 & #3 DNA Preparation
10
 
#3 DNA Preparation
2-Oral Rpt., Final 3/14
3-Proposal (3/14)
17
#3 DNA Fingerprinting
 3-Proposal (3/21)
24
 
Break - No Lab
 
 
 
31
#3 DNA P&F,
#4 Gene Regulation
 3-Oral Rtp., Final Rpt. (3/28),
 

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Month & Days
Laboratory Topic
Evaluation (Due Date)
April 7
April 14
#4 Gene Regulation
4-Proposal (4/11) 
21
#4 Gene Regulation
 4-Proposal (4/18)
28
#4 Gene Regulation
4-Oral Rpt., Final 5/2
May 5
(Check Out) Review
May 9
Final Exam (Friday, PSci room 229,
2-4:30 PM)

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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.

Attendance:
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.
Safety:
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:
Grading:
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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If you have questions or comments, write the:

  Author of this page: Terry Helser - helsertl@oneonta.edu
  Web Coordinator: Philip S. Bidwell - bidwelps@oneonta.edu
Or return to the SUNY @ Oneonta Home Page to see where we live and work.
  Last Modified on 1/7/2008
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