Download BISC 330L – Biochemistry Lab Syllabus

BISC 330 Biochemistry - Spring 2009
Lecture Syllabus
Topics: Biochemical bonds and reactions. Interactions with water molecules.
Structure/function of DNA, RNA, proteins, lipids and carbohydrates. Enzyme kinetics
and mechanisms. Enzyme cofactors and vitamins. Enzyme regulatory strategies. Cell
structure, membranes and organelles. Protein biosynthesis and targeting to membranes
and organelles. Glucose and O2 production by photosynthesis in plant chloroplasts.
Glucose oxidation and ATP production: glycolysis, citric acid cycle & oxidative
phosphorylation. Ribose biosynthesis from glucose by pentose phosphate pathway.
Professors:
Dr. John Petruska , tel: (213) 740-5189, email: [email protected]
Office: MCB (RRI) 119B, Off. Hours RRI 121: Tu Th 11 am - 1 pm.
Dr. Steven Goodman, tel: (213) 740-3867, email: [email protected]
Office: DEN 4108, Office Hours: TBA
Text: Berg, Tymocko & Stryer, BIOCHEMISTRY (6th ed. 2007)
Lecturer, Date
Subject
Chap.
Biochemical bonds and reactions
1.1-1.3
14
Water, pH and acid/base equilibria
1.3
16
DNA discovery & genomic revolution
1.4
19
No Lecture - Martin Luther King Day
21
Amino acid structures & properties
2.1
23
Primary structure of proteins
2.2
26
Secondary structure
2.3
28
Tertiary & quaternary structures
2.4-2.6
30
Protein purification methods
3.1
2
Amino acid analysis & sequencing
3.2
4
Protein structure determination
3.3-3.6
JP, Jan 12
Feb
JP, Feb 6
MIDTERM EXAM #1 ( 175 points)
1
JP, Feb 9
11
DNA & RNA structure & purification
DNA replication & gene expression
4.1,4.2
4.3-4.6
13
Intro. to thermodynamics & kinetics
8.1-8.3
16
No Lecture - Presidents Day
18
Enzyme kinetics: M-M model
8.4
20
Enzyme kinetics with inhibitors
8.5
23
Enzyme catalytic strategies
9.1-9.4
25
Enzyme regulatory strategies
10.1--10.4
27
Carbohydrate structures
11.1-11.4
Fatty acids, lipids & membranes
12.1-12.5
Coenzymes & vitamins
15.1-15.4
Mar 2
4
JP, Mar 6
9
11
13
16-20
MIDTERM EXAM #2 ( 175 points)
Cell structure & organelles: nucleus,
mitochondria & chloroplasts
Cell membranes & vesicles, RER, Golgi,
lysosomes, micro-tubules & -filaments.
Protein targeting to membranes
12.6
18.1,19.1
11.3, 30.6
34.2, 34.3
30.5, 30.6
NO LECTURES- SPRING BREAK
23
PS I,II & Cyt bf action: pump H+, store H-
19.3
25
ATP synthesis using H+ current
19.4
27
Glucose synth. using ATP & H- in NADPH
20.1,20.2
30
Ribose synthesis by Pentose Phos. Pway
20.3
JP, Apr 1
MIDTERM EXAM #3 ( 175 points)
2
SG, Apr. 3
Glycolysis: Glucose -> 2 Pyruvate
16
6
Citric Acid Cycle: Entry of pyruvate
17
8
CA Cycle: Enzymatic reactions & shunts
17
10
CA Cycle: Links to AA ,FA & heme synth.
17
13
CA Cycle: Net reaction and energetics
17
15
CA Cycle: Regulation & biosynthetic roles
17
CA Cycle: Link to memb. respiratory chain
17,18
20
Respiratory chain electron transport enz.
18
22
Respiratory chain proton pumps
18
24
Oxidative phosphorylation & ATP synthesis
18
27
ATP synthase: Molecular motor
18
29
Mitochondrial DNA and human evolution
18
1
Mitochondrial DNA and human diseases
18
JP, Apr.17
May
JP & SG,
May 6 or 8
FINAL EXAM (175 points)
Statement on Academic Integrity
USC seeks to maintain an optimal learning environment. General principles of academic
honesty include the concept of respect for the intellectual property of others, the
expectation that individual work will be submitted unless otherwise allowed by an
instructor, and the obligations both to protect one’s own academic work from misuse by
others as well as to avoid using another’s work as one’s own. All students are expected to
understand and abide by these principles. Scampus, the Student Guidebook, contains the
Student Conduct Code in Section 11.00, while the recommended sanctions are located in
Appendix A: http://www.usc.edu/dept/publications/SCAMPUS/gov/. Students will be
referred to the Office of Student Judicial Affairs and Community Standards for further
review, should there be any suspicion of academic dishonesty. The Review process can
be found at: http://www.usc.edu/student-affairs/SJACS/.
Statement for Students with Disabilities
Any student requesting academic accommodations based on a disability is required to
register with Disability Services and Programs (DSP) each semester. A letter of
verification for approved accommodations can be obtained from DSP. Please be sure the
letter is delivered to me (or to TA) as early in the semester as possible. DSP is located in
STU 301 and is open 8:30 a.m.–5:00 p.m., Monday through Friday. The phone number
for DSP is (213) 740-0776.
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BISC 330L – Biochemistry Lab Syllabus
Spring Semester, 2009
Laboratory Schedule
Week
1
Week
Experiments, Exam, or Assignment
Beginning
Jan 12
First week of class, no labs
2
Jan 19
Mandatory Lab Orientation and Check-in
3
Jan 26
Lab 1: Spectrophotometric Quantification
4
Feb 2
Lab 2: Measurement of Cholesterol in Biological Samples
(Lecture midterm 1, Feb. 6)
5
Feb 9
Lab 3: Affinity Chromatography (Lab Report #1)
6
Feb 16
President’s Day Weekend, no labs
7
Feb 23
Lab 4: -Galactosidase, Session 1 - Standard Dilutions and (NH4)2SO4 Precipitation
(Lab Report #1 due)
8
Mar 2
Lab 5: -Galactosidase, Session 2 - DEAE Ion-Exchange Chromatography
(Lecture midterm 2, Mar. 6)
9
Mar 9
Lab 6: -Galactosidase, Session 3 - Michaelis-Menten Enzyme Kinetics
10
Mar 16
Spring Recess, no labs
11
Mar 23
Lab 7: Photosynthesis (Lab report #2)
12
Mar 30
Lab 8: Cell Compartments, Session 1 - Separation of Intracellular Compartments
(Lecture midterm 3, Apr. 1)
13
Apr 6
Lab 9: Cell Compartments, Session 2 - Identification of Pathway-specific Enzymes
(Lab report #2 due)
Apr. 10th: Last day to drop class with “W”
14
Apr 13
Group Presentation
15
Apr 20
Lab Exam Review
16
Apr 27
Comprehensive Lab Exam
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Laboratory Director:
Pamela Lum, Ph.D.
Office: ZHS 353
Tel: (213) 740-6079
e-mail: [email protected]
Lecture Information and Policies:
See separate lecture syllabus provided by Prof. Petruska.
Online Course Materials:
Supplemental course materials will be posted on the Blackboard website.
Your USC e-mail user name and password allow you access of the secure
site: https://blackboard.usc.edu.
Grading:
Final Grades will be given out of 1000 points total for the course: 700
points from lecture and 300 points from laboratory.
Required Laboratory Supplies:
1. BISC 330 Lab Manual, available at the USC bookstore (required)
2. Lab notebook with carbon- or carbon-less duplicate pages (required)
3. Very fine-point permanent marker (required)
4. Lab coat or apron (optional)
Laboratory Guidelines
1. MANDATORY ATTENDANCE OF LABORATORY SESSION.
You are required to attend the weekly laboratory session in your
registered section. You are also to remain for the entire lab session or
until excused by your TA. Do not schedule any appointments during
your regular lab periods. Students who are within 5 points of a grade
borderline at the end of the semester will be considered for an
upgrade based on the following criteria: class participation,
attendance, participation in reviews, coming to office hours, and
subjective evaluation by the TA, Lab Director, and faculty.
Policy on lab make-up or substitution:
If you missed your regular lab due to a serious illness or emergency
which prevents you from attending school, you may attend another open
lab within the same week. No make-up lab is allowed once the week is
over. Please send an e-mail request to the administrative TA within 24
hours to acquire approval. Proof is required.
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If you need to make a lab substitution due to university sponsored
events (e.g. athletic events, class fieldtrips) or religious holidays, send an
e-mail request to the administrative TA at least 48 hours in advance to
acquire approval. Proof is required.
If you are approved for lab make-up or substitution, it is your
responsibility to make sure your quiz and lab write-up scores are
properly recorded.
2. LABORATORY POINT DISTRIBUTION
The laboratory session will count for 30% of your final grade (300 points).
The points are distributed as follows:
Lab Quizzes
Post Lab Reports
Lab Reports
Group Presentation
Lab Exam
45 points
90 points
50 points (25 points each)
40 points
75 points
Lab Quizzes: Each student will take a quiz during the FIRST 5 MINUTES
of each lab session. Each quiz is worth 5 points. There is no make-up for
the quiz. To prepare, make sure your read the lab manual before coming
to lab, know the purpose of the lab, and have a generalized idea of the
procedures to be used in the exercise.
Post Lab Reports: For each experiment there will be one lab write-up
worth 10 points. See Lab Write-up Guideline in the Laboratory Manual
for details. For each day the write-up is handed in later, you will receive
20% deduction.
Lab Reports: Lab report is due 2 weeks after the lab exercise at the
beginning of your lab session. Specific requirements for the lab report
will be provided before you perform the experiment. For each day the lab
report is handed in late, you will receive 20% deduction.
Group Presentation: Detailed information about this assignment will
be posted on Blackboard under Course Documents.
Lab Exam: The exam will test your understanding of the topics and
exercises covered in the laboratory sessions. Exam will consist of short
answers, fill-in-the blanks, and calculations.
Missed Lab Exam: It is your responsibility to make it to exam. If you
miss the exam due to a serious illness (e.g., admission to the hospital) or
a true emergency (e.g., traffic accident, fire, flood) that you could not
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attend school, you must present a valid excuse to the no later than 48
hours of the missed exam. A valid excuse must include names and
phone numbers for verification purposes. If you have a valid excuse,
you can either take the exam in another lab section or take a make-up
exam in the following week. If you do not have a valid excuse (or fail to
provide it within the allotted time), you will receive zero points for the
exam.
Posting Grades: All grades, lecture and lab assignments, are posted in
the LAB SECTION gradebook. It is the student’s responsibility to notify
your TA or the Lab Director as soon as possible if errors are found.
Laboratory score normalization: If necessary, the laboratory scores
will be normalized at the end of the semester by the Laboratory Director
to correct for differences in grading between TA’s.
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