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BIOMG 3300
Fall 2012
INSTRUCTIONS TO STUDENTS

You must register if you have not preregistered for this course.



BIOMG 3300 DEADLINE SCHEDULE



Last Name
Group
Number
A-G 1
H-M 2
N-Z 3


Group 1 Group 2 Group 3
Unit 1 W 8/29 W 8/29 W 8/29
2 R 9/6 F 9/7 M 9/10
3 F 9/14 M 9/17 T 9/18
4/5 F 9/21 M 9/24 T 9/25

Thursday 9/27 7:30-9:30 PM, 1st preliminary exam covers Units 1-5


6 R 10/4 F 10/5 W 10/3
7 M 10/15 T 10/16 F 10/12
8 Sun 10/21 M 10/22 F 10/19
9 Sun 10/28 M 10/29 F 10/26

Tuesday 10/30 7:30-9:30 PM, 2nd preliminary exam covers Units 6-9


10 W 11/7 M 11/5 T 11/6
11 T 11/13 Sun 11/11 M 11/12
12 T 11/20 Sun 11/18 M 11/19
13 W 11/28 M 11/26 T 11/27
14 Sun 12/2 R 11/29 F 11/30

To be arranged, 3rd preliminary exam covers Units 10-14

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OVERVIEW OF THE SEMESTER
BIOMG 3300


Dates What Happens

8/22 First class meeting at 4:30 (Baker Lab 200)
Purchase textbook (5
th
ed. Lehninger Principles of Biochemistry, by
Nelson & Cox) from book store
Purchase Study Guide at Kraftees (207 Dryden Road)
(Note: If you are also taking BIOMG 3340, purchase the 3340 course
packet at Kraftees too.)
Start work on units

8/23 Study Center (219 Stimson) opens 11:15 AM.

8/29 Deadline for Unit 1 - No oral quiz required.

9/3 STUDY CENTER CLOSED FOR LABOR DAY HOLIDAY

9/27 Evening Prelim 7:30-9:30 PM
- covering Units 1 through 5 (inclusive)

10/6-10/10 Fall Break. Study Center will close Friday 10/5, 5:00 PM,
reopen Wednesday 10/10, 11:15 AM

10/30 Evening prelim 7:30-9:30 PM
- covering Units 6 through 9 (inclusive)

11/21-11/26 Thanksgiving Recess, Study Center will close Wednesday 11/21,
1:00 PM, reopen Monday 11/26, 11:15 AM

11/29-12/2 Final deadlines

12/3 Study Center open regular hours until 5:00 PM Monday evening. The
Study Center will close for the semester at this time. All quizzes
(written and oral) must be completed at this time to obtain credit.

12/4-12/5 Review sessions will be scheduled

Final Exam date and time to be announced
- covering Units 10 through 14 (inclusive)





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Urgent Announcement

Before arriving to take the Unit 1 quiz, you must do the following:

1) Enroll in the BIOMG 3300-MBG Blackboard website. (See instructions
below.)

Go to:
http://courses.cit.cornell.edu/biobm3300/

Under 'Course Forms, click 'On-line student data sheet/Permission to post
and complete the form. Click the 'Submit this form button.




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After taking BI OMG 3300, students should be able to:

1. Discuss and describe in writing:
The structure and function of biologically important macromolecules
The general catalytic and regulatory mechanisms of enzymes
The energetics, organization, and regulation of metabolic pathways
The mechanisms underlying DNA replication, DNA repair, transcription and
its regulation, and translation (protein synthesis)
The techniques used to study proteins, membranes, and nucleic acids

2. Think analytically and use quantitative reasoning to solve biochemical problems.

3. Formulate conclusions based on the analysis of biochemical experimental results.


I ntroduction

In this course there is no time when the whole class will be together for any further
oral instructions. To avoid mix-ups it is essential that all aspects of the course be
described explicitly in writing. Please read these pages carefully then keep this
document for future reference, especially the semester overview on p. 2 and the
deadline schedule on p. 1.


The Study Center (Phone 255-1984)

The Center is equipped with study tables. Two or more staff persons are on duty at
all times to answer questions and to give quizzes. Access to staff persons is
available on a first-come first-served basis.

The Study Center, Room 219 Stimson Hall, will tentatively be open:

Monday through Thursday 11:15 AM - 5:00 PM, 7:00 PM - 10:00 PM
Friday 11:15 AM - 5:00 PM
Saturday Noon - 3:00 PM
Sunday Noon - 5:00 PM, 7:00 PM - 10:00 PM

If the Study Center hours change due to staffing problems you will be notified by
email and the hours posted on the Blackboard website will be changed to reflect the
new hours.


NOTE: If the University issues an Inclement Weather Notice stating that there will
be a delayed opening or closure, the Study Center will operate/close in accordance to
the University`s directive. You can monitor the University Operating Status through
the Operating Status page at: http://www.cornell.edu/about/status/ -- there is also an
Inclement Weather Phone at 255-3377.


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Recommended Approach to BI OMG 3300

Material for this course is divided into 14 units, described in detail in the Objectives
Notebook available at Kraftees and available in pdf format on the course web site. Most
of the information that you will need to satisfy the objectives can be found in the 5th
edition of Lehninger Principles of Biochemistry (2008) by Nelson & Cox.

Each unit consists of a reading assignment and a list of objectives. You should become
familiar with all the material in the reading assignment. The quizzes and exams will,
however, focus on material detailed in the objectives. We recommend that you approach
each unit in the following manner:

1. Look through the objectives to get an idea of what material we consider most
important.

2. Read the sections of Nelson & Cox listed at the beginning of each unit (or
subunit).

3. Go through the objectives in detail, looking up the answer to each one. We
recommend that you write these answers in a course notebook. You will find
these notes tremendously useful as you review for quizzes and exams. It is an
excellent idea to also write down page references in your notes. This practice
will save you a lot of time when you want to refer to something again.

4. If you have time and interest, go back and review the reading assignment.

5. Ask questions on material that is unclear to you.

6. Take the unit quiz.

Biochemistry is an exciting and rapidly expanding field. In this course we will explore the
structure and function of DNA, RNA, and proteins as well as the chemical reactions that
occur inside the cell. We hope that you will find as much enjoyment in studying
biochemistry as we do in teaching it.

To help you find information efficiently we have cited specific pages in the Study Guide
where you can find facts or concepts. Resist the temptation of skipping the general
reading and going directly to specific objectives. We have made an effort to distill the
most crucial aspects of the subject into the objectives. However, by themselves the
objectives constitute only a narrow and sterile view of Biochemistry. The unit quizzes
and the exams may include concepts that you will get from the general reading, though
these tests do not include details that are not specifically asked for in the objectives.


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Topics Covered in BIOMG 3300

UNIT Title

1A Organic Chemistry Relevant to Biochemistry
1B pH
1C Amino Acids and Peptides

2A Protein Structure
2B Protein Purification and Analysis

3A Myoglobin
3B Hemoglobin
3C Introduction to Enzymes
3D Enzyme Kinetics

4A Enzyme Mechanisms
4B Protein Evolution
4C Control of Enzymatic Activity

5 Membranes and Membrane Proteins

6A DNA Structure
6B DNA Replication

7A RNA Structure and Function
7B RNA Transcription
7C Co-transcriptional and Post-transcriptional Modification of RNA
7D Transcriptional Control of Protein Synthesis in Bacteria

8A The Genetic Code
8B Protein Synthesis

9 Recombinant DNA Methods

10A Bioenergetics
10B Chemistry of Carbohydrates
10C Glycolysis

11A Gluconeogenesis
11B Pyruvate Dehydrogenase and the TCA Cycle

12A The Pentose Phosphate Pathway
12B Oxidative Phosphorylation

13A The Light-dependent Reactions of Photosynthesis
13B The Carbon-assimilation Reactions of Photosynthesis
13C Glycogen Degradation and Synthesis

14A Fatty Acid Degradation
14B Fatty Acid Synthesis
Review of Metabolism

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Written and Oral Quizzes

Upon completion of each unit, you will take a quiz which will usually be both written and
oral. In this quiz you will be responsible for the material outlined in the objectives as
well as for anything in previous units which relates directly to the new material. An
understanding of the material, not just rote memorization is required. If the TA or
instructor is not satisfied with your performance, he or she will ask you to study further
before taking the quiz again. Another test (written or oral) cannot be taken until the
following day. Please attempt to pass all quizzes on your first try. Although we will
allow four quiz retakes per semester, to encourage first time success, we will penalize
your total unit score by 5 points for each time you retake a quiz thereafter.

You are urged to plan your time so that you will complete your units a day or two
before a deadline. Please note that if you plan to take a quiz on the deadline day and do
not pass, you cannot try again until the following day. This means that you will miss
that deadline. The deadline schedule for all units is shown on page 1. If the written
part of the quiz is passed on the deadline day there is no penalty. The oral part must
be passed no later than the second day after the written part (not two days after
the deadline date!). In general it is best to take the oral as soon as possible after the
written quiz, while the material is fresh in your mind.

There are several tests for each unit (e.g. A, B, C, etc.), which are handed out at
random. If you should get test B the first time for a given unit and fail to pass, it is up
to you to remember which test it was and be sure you get version A or C the next time.
You will not get credit for taking the same test a second time.


Review Sessions

Weekly review sessions will be held on Tuesdays and Wednesdays, 3:00-4:30 PM. A
complete list of dates, topics, and locations is available on the course web page.


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Deadline Extensions

You have been assigned, by your last name, to one of three groups of students
(see page 1). You may work as fast as you wish. However, by the specified dates
(shown on p.1) you must have completed the units indicated in order to earn full
credit. It is important that you understand the purpose of these deadlines. They
are absolutely essential to us in terms of the mechanics of the course. More
precisely, they are necessary to even out your workload and to avoid excessive
crowding of the Center toward the end.

Please look at your work schedule for your other courses. You know when you'll
be having prelims and papers due. Try to plan your work in this course with those
things in mind and don't come asking for an extension to bail you out of a
situation that could have been avoided by better planning.

In order to save trouble for all of us, we have the following rule: each student
may have fourteen one-day "self-extensions", to be used whenever needed. A
self-extension can be used to extend either a written or an oral quiz deadline. A
day means any day that the Center is open (including Saturday and Sunday which
each count as separate days). The test must be written within the extension period
- not the next day after it. These self-extensions are meant to be used at any time
when your reason does not qualify for an "emergency" extension. Please do not
use all your self-extensions early in the semester for trivial reasons, because you
may really need them sometime later.

If, however, you need an extension for an extended illness or other uncontrollable
circumstance, submit a written explanation to Shirley Soule (Room 217).

Note that you need to pace yourself as you are only allowed to take a
maximum of one written quiz and one oral quiz per day. This is especially
important to keep in mind as you approach the final deadline at the end of
the semester.


Academic Integrity

"Each student in this course is expected to abide by the Cornell University
Code of Academic Integrity. Any work submitted by a student in this course
for academic credit will be the student's own work."



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Grading

Your grade in the course will be determined as follows:
A. Each of the 13 unit quizzes will be worth 50 points if passed with no
penalty. (25 points for written quiz, 25 points for oral quiz)

Summary of Penalties

4 unit quiz re-takes per semester No penalty
Quiz retakes (if more than 4) 5 pts per retake
Missed written quiz deadline 2 pts/day (10 pt max per unit)
Missed oral quiz deadline 2 pts/day (10 pt max per unit)


B. Your grades on the major exams will be added together and converted to
a scale of 1950 points.

Your final grade, based on a bell shaped curve, will depend mostly on your
performance on the major exams.


Disabilities

We will make appropriate accommodations for students with disabilities. Students with
either an ongoing or short-term disability are encouraged to contact Student Disability
Services (SDS) for a confidential discussion of their needs, and for registration with SDS
to verify eligibility for academic accommodations. Except for unusual circumstances,
please make such requests for accommodation to us during the first three weeks of the
semester so that arrangements can be made. SDS is located in 420 CCC building; phone
number is 254-4545.


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Mental Health

If you are experiencing unusual personal or academic stress at any time during the
semester or need to talk with someone about a personal problem or situation, seek support
as soon as possible. We are available to talk with you about stresses related to your work
in this class. Additionally, we can assist in reaching out to any one of a wide range of
campus resources, including:

Your college`s Academic Advising or Student Services OIIice
Cornell Learning Strategies Center at 255-6310, http://lsc.sas.cornell.edu
Gannett Health Services at 255-5155, www.gannett.cornell.edu
Let`s Talk DropIn Consultation and Support
www.gannett.cornell.edu/Let`sTalk
Peer Support provided by Empathy Assistance and Referral Service at
255-EARS


Incompletes

In accordance with University policy, to be eligible for an incomplete, a student must earn
a passing grade on the first two preliminary exams. In addition, (s)he must have unusual
circumstances beyond his/her control. If during the last part of the course you feel you
can satisfy the above criteria, please submit a written request (with appropriate
documentation) to Jim Blankenship.


Amendments

Although we have outlined dates and procedures as carefully as possible, things do happen
and we have to make changes. Please get in the habit of checking the course web site
regularly. You are responsible for watching these announcements!