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CONTACT INFORMATION
Dr. Jason C. Hurlbert
301B Sims Science Bldg
Rock Hill, SC 29733, USA
803/323-4928
803/323-2246 (fax)
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CHEM523: Biochemistry I (Fall 2018)

Course Specifics:

Instructor:       Dr. Jason C. Hurlbert
                          Office:  Sims 301B
                          Office hours:  M 10:30-11:30AM, W 2:00-3:00PM and by appointment
                          Phone:  323-4928
                          E-mail:  hurlbertj@winthrop.edu

Meeting Times: Wednesdays and Fridays: 12:30 - 1:45 PM
Location: Sims 113C

Virtual classroom at bluebutton.ddns01.com. This site will be used for inclement weather sessions (should they arise) and for evening office hours when scheduled.

Textbook: Fundamentals of Biochemistry: Life at the Molecular Level, 4th Edition, Voet, Voet and Pratt (required). The text may be rented, but if you are considering attending graduate or professional school after graduation, I would highly recommend purchasing and keeping the book.

Course Outline:       
Biochemistry is the branch of science focused on studying the structure, function and interactions of the molecules found in living systems. Its very name tells you that it is a hybrid discipline incorporating biology, organic chemistry, physcial chemistry and even physics into the study of the chemical reactions and interactions that allow life to exist. The goal of this course is to familiarize you with the vocabulary and concepts necessary to understand how living cells function at the molecular level. We will spend one third of the semester learning the basics of biological molecules: amino acids, proteins, sugars, polysaccharides and nucleic acids. In the second third of the semester, we will learn about the techniques necessary to study biological molecules and the rules governing enzymatic function. Finally, in the last part of the semester, we will look at the key reactions and processes that allow cells to convert the static information contained within the genome into functional proteins that allow the cell to adapt to its environment.

In order to accomplish these goals, we will rely upon various computational methods and current biochemical research papers in addition to the textbook and lecture notes. A large portion of your grade in the course will be based upon your implementation of these methods on your own as you describe and characterize proteins that have been assigned to you. Your efforts will culminate in a verbal presentation to the class and a 10 page review article discussing your proteins.

This is a 500 level course, which means that the concepts we will discuss are advanced and will require you to spend a lot of time and work outside of the classroom to fully understand and apply them. I have set up a virtual classroom at bluebutton.ddns01.com in order to be available and provide help to you after hours. This virtual classroom has full videoconferencing and whiteboard capabilities and, in the event of campus being closed due to inclement weather, will be used to hold class. Evening office hours in this virtual classroom will be determined and announced during the first week of class.

This class is meant to push you to your limits and will help you tie together concepts and information you have learned in general chemistry, organic chemistry and various biology courses you have taken during your college career. Every bit of effort you put into this class will be rewarded with a better understanding of the role of chemistry in biological systems and will be reflected in the grade you earn for the course. Go ahead and plan to work on the material for this class at least 10-15 hours a week.

Week Date Topic  
1

22 Aug

Course Introduction

Chapter 1: The Foundations of Biochemistry

1.1: Cellular Foundations

1.2: Chemical Foundations

1.3: Physical Foundations

1.4: Genetic Foundations

1.5: Evolutionary Foundations

24 Aug

Chapter 2: Water

2.1: Weak Interactions in Aqueous SYstems

2.2: Ionization of Water, Weak Acids and Weak Bases

2.3: Buffering against pH Changes in Biological Systems

2.4: Water as a Reactant

2.5: The Fitness of the Aqueous Environment for Living Organisms

2

29 Aug

Chapter 3: Amino Acids, Peptides and Proteins

3.1: Amino Acids

3.2: Peptides and Proteins

3.3: Working with Proteins

 

31 Aug

3.4: The Structure of Proteins: Primary Structure

Chapter 4: The 3D Structure of Proteins

4.1: Overview of Protein Structure

4.2: Protein Secondary Structure

3

5 Sept

Chapter 4: The 3D Structure of Proteins

4.3: Protein Tertiary and Quaternary Structures

4.4: Protein Denaturation and Folding

7 Sept

Computational Biology: Entrez, BLAST and Chimera

4

12 Sept

14 Sept

Test 1

5

19 Sept

Chapter 5: Protein Function

5.1: Reversible Binding of a Protein to a Ligand: Oxygen-binding Proteins

21 Sept

6

26 Sept

5.2: Complementary Interactions between Proteins and Ligands: The Immune System and Immunoglobulins

28 Sept

Chapter 6: Enzymes

6.1: An Introduction to Enzymes

6.2: How Enzymes Work

6.3: Enzyme Kinetics as an Approach to Understanding Mechanism

7

3 Oct

Chapter 6: Enzymes

6.4: Examples of Enzymatic Mechanisms

5 Oct

8

10 Oct

6.5: Regulation of Enzymatic Activty

12 Oct

FALL BREAK NO CLASS
9

17 Oct

Chapter 7: Carbohydrates and Glycobiology

7.1: Monosaccharides and Disaccharides

7.2: Polysaccharides

7.3: Glycoconjugates: Proteoglycans, Glycoproteins and Glycosphingolipids

7.4: Carbohydrates as Informational Molecules: The Sugar Code

 

19 Oct

Test 2

10

24 Oct

Chapter 10: Lipids

10.1: Storage Lipids

10.2: Structural Lipids in Membranes

10.3: Lipids as Signals, Cofactors and Pigments

Chapter 11: Biological Membranes

11.1: The Composition and Architecture of Membranes

11.2: Membrane Dynamics

11.3: Solute Transport Across Membranes

26 Oct

Chapter 12: Biosignaling

12.1: General Features of Signal Transduction

12.2: G-Protein Coupled Receptors and Second Messengers

11

31 Oct

Chapter 12: Biosignaling

12.3: Receptor Tyrosine Kinases

12.11: Regulation of Cell Cycle by Protein Kinases

2 Nov

12

7 Nov

Test 3

9 Nov

Chapter 8: Nucleotides and Nucleic Acids

8.1: Some Basics

8.2: Nucleic Acid Structure

8.3: Nucleic Acid Chemistry

8.4: Other Functions of Nucleotides

13

14 Nov

Chapter 25: DNA Metabolism

25.1: DNA Replication

16 Nov

Chapter 26: RNA Metabolism

26.1: DNA-dependent Synthesis of RNA

14 21 Nov

THANKSGIVING BREAK NO CLASS

23 Nov

THANKSGIVING BREAK NO CLASS

15

28 Nov

Chapter 27: Protein Metabolism

27.1: The Genetic Code

27.2: Protein Synthesis

30 Nov

Grading for the Course

Homework Problems
Because we cover so much material during the semester, you will have small homework assignments due EVERY time class meets.  These assignments are due at the start of each class session.  If you show up late to class, DO NOT COME TO THE FRONT OF THE ROOM AND TURN IN YOUR ASSIGNMENT!  Wait until class is over and turn it in.

Tests
Three tests will be administered during the semester. Understanding concepts from the beginning of the semester will be crucial to understanding concepts discussed at the end of the semester, so while the tests are not strictly cumulative, students are always responsible for material learned throughout the semester. Each exam will be worth 100 points. Exams will be taken during the class meeting time indicated on the Detailed Class Schedule webpage. 

Protein Project
During the semester, each student will be assigned two proteins. Students will be responsible for working with these proteins during the semester. As we learn different bioinformatic, computational and visualization techniques, students will apply them to their assigned proteins. Throughout the semester, these assignments will be collected and graded.
At the end of the semester, students will write a 10-14 page review article about their proteins. This article will be due on the last day of the semester. Grading rubrics for the paper will be available on the course website on the Student Protein Assignments Page.

Final Exam
A cumulative final exam will be given on the scheduled date at the end of the semester.

Extra Credit Opportunities
Throughout the semester you will be given several opportunities to earn extra credit points. These opportunities will be challenging and are meant to be difficult. Failure to complete the assignment exactly as instructed will result in no points being awarded. Extra credit assignments are always non-negotiable:  You do the assignment completely, you do the assignment well and you do the assignment in the manner it was intended to be done or you do not get any bonus points.

Final Grade

Homework Assignments: 13 x 10 points = 130 points
Bioinformatics Assignment: 25 points
Chimera Assignment: 25 points
Tests: 3 x 100 points = 300 points
Protein Assignment, Written: 50 points
Final Exam: 250 points
Total Number of Points for Course: 780 points

Grading Scale:

A: >93% of the total Points
A-: 90.0 - 92.9% of the total points
B+: 87 - 89.9% of the total Points
B: 83 - 86% of the total Points
B-: 80 - 82.9% of the total points
C+: 77 - 79.9% of the total Points
C: 70 - 76.9% of the total Points
D: 60 - 69.9% of the total Points
F: <60% of the total Points

Technology in the Classroom

No cellular phones may be used when class is meeting. Once class starts, all cellular telephones must be turned to silent mode for the duration of class. Should your cellular telephone ring while the class is meeting, you will be asked only once to silence it. A second violation of this policy will result in immediate removal from that class session. Anyone caught using these devices during class without prior permission will immediately be asked to leave the class. Anyone caught texting, using Facebook or other forms of social media during class will be immediately ejected from class. This policy is non-negotiable and will be enforced without exception. ANY and ALL violations of these rules will result in forfeiture of all earned bonus points and violators will also be ineligible for future extra credit opportunities.


Student Code of Conduct

As noted in the Student Conduct Code: “Responsibility for good conduct rests with students as adult individuals.” The policy on student academic misconduct is outlined in the “Student Conduct Code Academic Misconduct Policy” in the online Student Handbook.

Time Management and Your Role as a Student

As members of the Winthrop community of life-long learners, you are expected to treat your role as a student with the utmost respect and seriousness. Properly mangaging your time and effort is a big part of that and I urge you to begin working on assignments as early and often as possible. Not only will your life be a lot less stressful because you aren't trying to cram everything in at the last minute, but you can also identify things that you are having trouble understanding with enough time to ask me for help. If you know that you have a scheduling conflict with an assignment due in this course, please come talk to me about it as soon as possible. I will do everything I can to work with you, but I expect you to shoulder your responsibilities as part of the partnership.

Students with Disabilities/Need of Accommodations for Access:

Winthrop University is committed to providing access to education. If you have a condition which may adversely impact your ability to access academics and/or campus life, and you require specific accommodations to complete this course, contact the Office of Accessibility (OA) at 803-323-3290, or, accessibility@winthrop.edu. Please inform me as early as possible, once you have your official notice of accommodations from the Office of Accessibility.