2022 Fall Syllabus

Biochemistry I

Fall 2022, CHEM 4400

Dr. Koni Stone Phone: (209) 667-3570 Email: please come to class to get my email address
Office: N358 office hours: MWF 11:30-12:30 Text: Biochemistry by Roger Miesfeld and Megan McEvoy, 2nd edition ISBN: 9780393690453
Web page for the class: http://biochemistry-stanislaus.wikidot.com/biochemistry-i


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 Sept 19, Oct 17, Dec 5 100 points each = 300
Group Enzyme mechanism presentation Dec 7 and 9 80
Comprehensive Final Exam Friday December 16, 8:30-10:30 200
Literature paper selection: Selection of a primary literature paper from the Journal of Biological Chemistry or from The American Chemical Society Journal, Biochemistry Sept 2 20
Main purpose of selected paper September 30 40
Description of Results November 4 60
Description of Two Biochemical Experiments December 2 100

All papers are due at 11:59pm on the due date. Papers are submitted to Turnitin.com, **this is outside of Canvas, the Class ID and password will be given in class.


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

This course is graded with letter grades using the following minimum scores:
A, 90%; B, 80%; C, 70%; D, 60%. There are no +/- grades for this course.
The last day to add this class is September 19th. 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. If you copy materials from the internet, that is plagiarism. Be sure to write everything in your own words. It is important for you to demonstrate your understanding of the material.

Class activities

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.

Exam questions

Exam questions will be taken from the assigned problems, class activities, lectures and assigned readings. 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 class activities.

Group enzyme mechanism presentation: groups will organize and present an enzyme mechanism by acting it out.

Writing Assignments

Select a Primary Literature paper:

20 points, turnitin. Find a paper published in 2019-2021 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. ONLY these journals are acceptable. Only primary research papers are acceptable. Primary research papers have original data and experimental details for how the experiments were done. No review articles are allowed.

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, see Canvas for the class ID and password

Main Idea,

40 points, Turnitin 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


60 points, Turnitin 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.


100 points, Due: Turnitin 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.

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 are due to turnitin by 11:59pm on the above due dates. 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.

Unless otherwise stated, the content of this page is licensed under Creative Commons Attribution-NonCommercial-ShareAlike 3.0 License