2018 Fall Syllabus

Biochemistry I

Fall 2018, CHEM 4400

Dr. Koni Stone Phone: 667-3570 Email: ude.natsusc|enotsk#ude.natsusc|enotsk
Office: N 358 Office hours: M, W, F 1-2 and by appointment Text: Biochemistry by Roger Miesfeld and Megan McEvoy, ISBN: 9780393614022
Web page for the class: http://biochemistry-stanislaus.wikidot.com/biochemistry-i Smartwork: 61670

**Hard copies of this syllabus will not be available in class.*


Welcome to the first semester of a full year course in Biochemistry. You must have taken and passed (a C or better is highly recommended a C- is required), two semesters of Organic chemistry in order to register for this course. If you took the course at another institution, be prepared to show your transcripts to Dr. Stone. If you have not met this pre-requisite, you will be dropped from CHEM 4400.

The learning goals for this class are:

1. Learn biochemical facts, including the language used to describe biochemistry and the methods used to study it.

2. Gain understanding of some biochemical principles including
• Acid base chemistry and buffers
• Amino acids, peptides and proteins
• Protein structure and the relationship between structure and function
• Enzyme kinetics and mechanisms
• Regulation of biochemical reactions
• Biomolecules such lipids, carbohydrates and nucleic acids

3. Improve writing skills and learn how to find and use resources to answer questions.

4. Learn how to work with others as a member of a team.

The following devices will be used to assess your learning in this class.

Device Dates Points
Exams September 14, October 26, December 7. There are no make-up or early exams. 300
Class activities Random and announced activities, presentations, exercises and quizzes. November 21: Warrior Day Parade of Mechanisms, must be present to earn 20 points. (There may be more or less than 150 actual points, your percentage of the actual points x 150 will be entered.) No early or late or make-up work accepted 150
Smartworks, Class: 61670 Due at midnight on each due date (Your total percentage on all assignmentsx0.5 = your Smartworks points) 50
Comprehensive Final Exam Wednesday, December 12th 8:30-10:30 There are no make-up or early final exams. 200
Service Learning Tutoring in the CSU, Stanislaus Tutoring Center (5 hours a week), or coaching a Science Olympiad event or Helping at the Science Olympiad Saturday, submit your applications to Turnitin by Sept 22, then submit your reflections to Turnitin by Dec 13 50 points, Max
Literature paper selection: Selection of a primary literature paper from the Journal of Biological Chemistry or from Biochemistry Aug 31 10
Main purpose of selected paper October 5 10
Description of Results November 2 30
Description of Two Biochemical Experiments November 30 50

All papers are due at 11:59pm on the due date. Papers are submitted to Turnitin.com, class:18731900, stanislaus. Late submissions are penalized 10% per day or any fraction thereof.


Scores for the writing assignments and exams will be entered into the turnitin site. Other grades will be posted on blackboard.

This course is graded with letter grades using the following minimum scores:
A, 720; B, 640; C, 560; D, 480. There are no +/- grades for this course.
The last day to add this class is September 4th. The last day to withdraw from this course is September 19th.

Cheating (including plagiarism and other acts of academic dishonesty) will not be tolerated. Full reports will be submitted to the Dean of Students, an F on the assignment/test/quiz/paper will be entered in the grade book. A second offense will result in automatic failure of the class.

Use of electronic devices in class: if they become a distraction to Dr. Stone or other students, you will be asked to stop using them. No photography or recording is allowed in class. Take notes and then compare your notes with your classmates' notes. You will learn more and you will be successful in this class.

For the safety and comfort of all students and your instructor, please refrain from talking during lecture. Incessant chatter interferes with the navigational controls of your instructor. If you have a question or comment, please indicate so by raising your hand. When your instructor pauses to breath, you will have a chance to talk. Until you are recognized by your instructor, all verbal communication should be turned off.

Class activities and Smartworks

Presentations, exercises and quizzes will cover all information presented in class and all material in the required readings and end of chapter homework problems. End of chapter homework problems will not be collected or graded. These materials are designed to help you learn the material and help you determine your strengths and weaknesses.

Smartworks is an online system designed by the publisher to increase your comprehension. The Student Set ID is 61670. You should start by following this link: https://digital.wwnorton.com/biochem

Exam questions

Exam questions will be taken from the assigned problems, class activities, lectures and assigned readings. No make-up or early exams will be given. If you have extenuating circumstances that involve serious and compelling reasons for missing an exam, you are advised to schedule a consultation with Dr. Stone as soon as possible to develop an appropriate plan of action.

The final exam will be comprehensive and will be based on questions that were on the exams, worksheets and online homework. No Early or Late finals will be given.

Service based learning

Service based learning is a great way to learn while having fun. You can choose from several options:

1. 50 points: Work in the Stan State Tutoring Center: Go to the CSU, Tutoring Center get hired as a tutor for CHEM 2100 (Chemistry and Biochemistry for Nurses) or CHEM 1110 (General Chemistry II) or CHEM 3010 or CHEM 3020 (Organic I or II) for a minimum of 5 hours per week during the semester, 50 points. You must commit to five hours per week in the Stan State Tutoring center. You must apply for these tutoring positions and you must have earned a B or better in CHEM 1110 or CHEM 3010 or CHEM 3020. Deadline: Applications are due August 24. Apply at: How to Become a Tutor.

2. 50 points: Be an Science Olympiad Event Coach for the Turlock High School team. A list of events is on this web page: https://www.soinc.org/events/2018-division-c-events
Coaches will provide an organized set of content materials, meet with high school students on Wednesday afternoons (1:50-3:15) starting October 24th , and write a practice test. The rules for these events are quite complex, so your job will be to make sure the high school students understand the rules. Rules will be provided as hard copies. You will need to submit an application to be an Event Coach. Directions are on Turnitin.com, applications are due September 21.

3. 50 points: Design and lead a Science Olympiad event on Saturday December 1st, 10:00-2:00pm. There will be a set up meeting on November 30th (3:00) to train your team and get your materials organized. You will use the current rules to design a Science Olympiad practice event. You will then lead a team of students to deliver the event, score the event and then provide feedback to the high school participants. https://www.soinc.org/events/2019-division-c-events
You will need to submit an application to be an Event Coach. Directions are on Turnitin.com, applications are due September 21.

4. 20 points: Help with a Science Olympiad practice event on December 1st, 10-2. There will be a mandatory set-up/training meeting on November 30th (3:00). Go to the list of events is on this web page: https://www.soinc.org/events/2019-division-c-events.

For all Service Learning: In order to earn any service learning points, you must submit a written report to Turnitin. Please include the following:

1. What activity did you select and why did you select it?
2. Fully describe what you did.
3. How did this activity enhance your understanding of chemistry?
4. What advice do you have for future students that might select this activity?

Writing Assignment

Select a Primary Literature paper:

10 points, in class: August 27, please bring a hard copy of your literature paper, turnitin: August 31. Find a paper published in 2017-2018 in either: Biochemistry (an American Chemical Society publication, http://pubs.acs.org/journal/bichaw) or Journal of Biological Chemistry (jbc.org) If you select a JBC paper that is published in the last year, then you will need to do a DOI search on the CSU, Stanilaus web page: http://library.csustan.edu/doi-lookup.

Do not select a review article. Make sure it has experimental data that the authors collected (primary source).

Submit the complete bibliographic information for your paper, including title, authors, dates, journal, volume and pages.

No two students can have the same literature paper, so if your paper has been selected by another student, you will be asked to submit another paper. Submit your paper early!
All papers will be submitted via turnitin.com
http://turnitin.com course: 18731900 password: stanislaus

Main Idea,

20 points, Due: in class: October 1, Turnitin: October 5, 1-2 pages What is the main idea of the paper you selected? Summarize what this paper contributes to the knowledge of the topic. Where was this research done? Limit this summary to 2 typed, double spaced pages. Fully cite all of your references, including titles, authors, dates, journal, volume and pages. Do not use quotations. Describe the biochemical paper topic with your own words. All papers will be submitted via turnitin.com


30 points, Due: in class: October 29, Turnitin: November 2 Give a full description of the results presented in the paper you selected and how they contribute to the authors' conclusion(s). You will need to explain this at the molecular level. You will need to do research outside of our text and beyond google searches (although google scholar may work.) Describe the results using terminology that your science major classmates will understand. Do not cut and paste, do not paraphrase, do not use quotes. Use only your own words to explain your understanding of the results presented in your paper. Be sure to describe how the results support the authors' conclusions. Fully cite all of your references, including titles, authors, dates, journal, volume and pages.


50 points, Due: in class: November 26, Turnitin: November 30 Explain at least two experiments in the paper you selected. Carefully read the Experimental Methods section of the literature paper to determine how the experiments worked. You will need to consult other online sources (wikipedia and google work great) to understand what the researchers did. Describe how these experiments were done. Leave out the details related to temperature, volume and masses. Do explain any instruments (and the theory behind how the instruments work) that were used. Fully cite all of your references, including titles, authors, dates, journal, volume and pages. Use terminology that your science major classmates will understand. Do not cut and paste, do not paraphrase, do not use quotes. Use only your own words to explain these two experiments.

General Directions for the Writing Assignments:

All papers will be submitted via turnitin.com
See table at the top of the syllabus.
Every assignment has a grading rubric. Be sure to consult it.

These reports must be generated using a word processing computer program. No handwritten text, tables or graphics will be accepted. Please use double spacing and select a font that has 10-12 characters per inch. Both MacIntosh and IBM machines are available for your use in the computer labs in the Library building.

Fully cite all of your references, including titles, authors, dates, journal, volume and pages. Quotations are not allowed. Use your own words. The objectives of this assignment are to strengthen your literature research and writing skills. This will also give you the opportunity to learn about biochemical topics in more detail.

Papers will be used for a peer review writing exercise in class on Monday before it is due on Friday. Papers are due to turnitin by 11:59 on the above due dates. Late papers will be penalized 10% per 24 hour period or fraction thereof. Papers will be graded on content, thoroughness, validity, clarity, organization, punctuation and grammar. Every assignment has a grading rubric. Be sure to consult it.

Reading Schedule

Weeks Chapters Topics
1-3 1, 2 Intro,Cells, Genetic Information,Energy, IMF, Osmolarity, water,pH, buffers, cell membranes
4-8 3, 4 Nucleic acid structure and function, Protein structure
9-14 5,6,7 Techniques for studying proteins, Protein function,Enzymes

*Other supplemental reading material may be assigned
Note: This syllabus is intended to be used as a guide, it is not a legal contract. This syllabus may change, depending upon circumstances.

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