Syllabus

Bio444/Chem444 – Biochemistry – Spring 2010

Instructor: Jeffrey D. Newman

Room: Heim 107

Phone: 570-321-4386

email: newman@lycoming.edu

office hours: Mon. 3:30-4:30 PM

Tues. 3:30-4:30 PM

Instructor: Chriss McDonald

Room: Heim 233

Phone: 570-321-4186

email: mcdonald@lycoming.edu

office hours: I'm almost always around
from 8:15 – 5:00

Lecture meets MF 2:00 –3:15 PM in Heim G-40

Lab meets W 2:00 – 4:50 PM in Heim 106

Course Web Site: http://moodle.lycoming.edu/moodle/login/index.php

Text: Berg, Timoczko & Stryer, Biochemistry, 6^th ed, 2007, WH Freeman Publishers.

Catalog Description of Course: Emphasis is given to the metabolism of carbohydrates, lipids, amino acids, proteins, and nucleic acids; integration of metabolism; and biochemical control mechanisms, including allosteric control, induction, repression, signal transduction as well as the various types of inhibitive control mechanisms.

Grades will be determined based on the following assessments:

Exams 3 x 100 pts = 300 pts

Final Exam 150 pts

Prep Papers 22 x 3 pts = 66 pts

Phosphatase Lab Report 50 pts

Lipid Analysis Lab Report 50 pts

Metabolic Reconstruction 50 pts

Homework up to 74 pts

Quizzes 3 x 20 pts = 60 pts

Total possible 800 pts

Attending Chemistry colloquium will earn 3 bonus points, with a maximum of 15 bonus points permitted

	B+ = 86.7 - 89.9%	C+ = 76.7 – 79.9%	D+ = 66.7 - 69.9%
A = 93.3 – 100%	B = 83.3 – 86.6%	C = 73.3 – 76.6%	D = 63.3 – 66.6%	F= below 60%
A- = 90.0 – 93.2%	B- = 80.0 – 83.2%	C- = 70.0 – 73.2%	D- = 60.0 – 63.2%

Attendance Policy: Attendance of all lectures and laboratories is expected. Absences will be noted by the instructor, and if excessive (more than 1 lab or 4 lectures), may result in a reduction of the course grade. Absences and participation will be used to determine borderline (within 0.5%) grades. Documentation (note from school nurse, physician, documentation of job interview, etc.) for excused absences must be provided to the instructor as soon as possible.

Daily “Prep Papers” are due at the beginning of each class to encourage the use of writing to organize your thoughts about the course material.

Guidelines:

Name and date should be indicated on top of page
0.5 page summarizing key points from previous class and asking questions in bold.
0.5 page summarizing key points from reading assignment and asking questions in bold.
Each paper that meets guidelines earns 3 points
66 points are built into the grading scale

If you do 22 prep papers, you score 100% on 66 point part of your grade
If you do 26 prep papers, you score 100% on 66 point part of your grade and get 12 bonus points
If you do 18 prep papers, you score 85% on 66 point part of your grade

If prep papers are not done, a sign-in sheet will be available to confirm attendance
Prep papers may be submitted for missed classes only when accompanied by a documented excuse (Note from Health Care Provider or coach).
If a class is missed, the prep paper that is submitted upon return to class should summarize the last class attended and the reading assignment given on that day.

Guidelines for Attending Chemistry Colloquium:

i. Be on time.

ii. The speaker has expended a lot of effort to prepare for the talk. Be attentive and polite.

iii. If you can’t stay for 45 minutes for an internal speaker or 60 minutes for an external speaker, don’t come (please do not ask the speaker how long the talk will last).

iv. Realize that questions for the speaker at the end is part of the talk and you will be expected to stay for that as well.

A few words about learning biochemistry. Studying biochemistry is hard work for most people (this is certainly true for us). We would recommend that you work on the lecture material outside of class for at least one hour per day, 7 days/week. Once you see how things are going this amount can be adjusted as needed (We suggest a significant increase in study time prior to an exam). If you are having trouble, make sure and come and talk to us. You will be responsible for all of the material listed on the following schedule for the indicated exams and quizzes. It is not sufficient to learn the material from the lecture alone. You are expected to read and think about the material prior to the lecture. We must necessarily cover a large amount of material so our pace must be geared towards those who are ready to learn. The exams will be somewhat cumulative in the sense that we need to know the earlier material to comprehend the latter.

We will spend a great deal of effort studying biochemical pathways in this course. Your understanding of these pathways will be substantially enhanced by becoming familiar with the structures of important biomolecules. Throughout the course of the semester you should strive to learn the following structures.

General structures: amino acids, monosaccharides, fatty acids, sphingomyelin, phosphatidylcholine, polypeptide structure (1^o, 2^o, 3^o)

Specific structures: the 20 most important amino acids, glucose (acyclic, cyclic), amylose, amylopectin, glycogen, starting compounds, intermediates, and products of the following pathways – glycolysis, gluconeogenesis, b oxidation, and fatty acid synthesis

Tentative Schedule-2010

Lecture Topics

Lab Activities (Wed.)

Week 1
1/11 – 1/15

ch. 1,2

M – Introduction, Concept reviews
(JN & CM)

F – Amino Acids, Peptide Bonds (CM)

Biochemical Composition of Foods, Nutrition Facts Tables

Week 2

1/18 – 1/22

ch. 2, 6

M - Protein Structure (JN)

F – Protein Sequences & Evolution (JN)

Protein structure and sequence analysis with Chime/Protein Explorer.

(computer lab) (text ch 3.6)

Week 3

1/25 – 1/29

ch. 7, 8

M - Quiz 1 (1/25)
M – Hemoglobin (JN)

F – Enzyme Kinetics (JN)

Measurement of phosphatase activity: Effect of enzyme concentration and pH.

Week 4

2/1 – 2/5

ch. 9,10

M – Enzyme Catalysis (CM)

F – Enzyme Regulation (JN)

Phosphatase kinetic analysis: Effect of substrate concentration and inhibitors.

Week 5

2/8 – 2/12

ch. 12

M – Catch-up, review for exam

F - Lipids (CM)

Exam 1 (2/10)

Week 6

2/15 – 2/19

ch.12,13

M – Membranes (JN)

F – Membrane Transport (JN)

SDS-PAGE, Phosphatase Data Analysis

Week 7

2/22 – 2/26

ch 14

M - Signal Transduction (JN)
F – Signal Transduction (JN)

Membrane Permeability, Quiz 2 (2/24)

Enzyme lab report due 2/26

Week 8

3/8 – 3/12

ch 11, 15

M - Carbohydrates (CM)

F – Metabolic concepts (CM)

Exam 2 (3/10)

Week 9

3/15 – 3/19

ch 16

M – Glycolysis (CM)

F – Gluconeogenesis (CM)

GC/HNMR analysis of membrane lipids: Extract, transesterify to form methyl esters.

Week 10

3/22 – 3/26

ch 21, 20

Quiz 3 (3/22)

M - Glycogen Metabolism (JN)

F - Calvin Cycle & Pentose Phosphate pathway (JN)

GC/HNMR analysis of membrane lipids. Load samples, analyze data.

Week 11

3/29 – 4/2

ch 17

M – Catch-up, review for exam

F – Good Friday

Exam 3 (3/31)

Week 12

4/5 – 4/9

ch. 18,22

M – Citric Acid Cycle (JN)

F – Electron Transport (JN)

Lipid Analysis Lab report due 4/7 Metabolic Reconstruction from Genome Sequences

Week 13

4/12 – 4/16

ch. 22, 23

M - Lipid Catabolism (CM)

F - Lipid Synthesis (CM)

Metabolic Reconstruction from Genome Sequences

Week 14

4/19 – 4/23

ch 24, 27

M - Amino Acid Metabolism (JN)

F - Integration of Metabolism (JN)

Journal Club: Diabetes, Obesity, Metabolic Syndrome papers