J. A. CAPPUCCIO, CHEM 434 FALL 2021 1

SYLLABUS: CHEM 434, BIOCHEMISTRY I

Course Information • CHEM 434. Biochemistry I (3 units) • Fall 2021 • 434, 41256: Mo We Fr 10:00 – 10:50 • Hyflex, synchronous • Zoom link: https://humboldtstate.zoom.us/j/87568669344 • Meeting ID: 875 6866 9344 • Passcode: chem434

Instructor Information Instructor name: Dr. Jenny A. Cappuccio Email: jc3534@humboldt.edu Phone: 826-3109, preferred contact is email Zoom Office Hours: Office Hours are by appointment email jc3534@humboldt.edu Or at the following zoom link Monday 11:30-1:00, Wed 11-12:30 https://humboldtstate.zoom.us/j/87293882611 Meeting ID: 872 9388 2611 Passcode: JennyOH

How and when to contact instructor: office hours and email are the best options. Link to Instructor bio: http://www2.humboldt.edu/chemistry/faculty/cappuccio.html

Course Description: CHEM 434. Biochemistry I (3). First semester lecture of a one-year sequence. Biochemical energetics, introductory metabolism, nature and mechanism of action of enzymes. [Prereq: CHEM110; any calculus course; CHEM 228 or (CHEM 325 and CHEM 325L) all with a C- or higher.] Instruction Modes and Dates: The first two weeks of class are fully virtual and synchronous. Just log on through zoom at the scheduled class time. After these two week there will be hyflex instruction. Hyflex in CHEM 434 means that you can either attend in-person (FGYM 148, next to science A) or you may attend synchronously through zoom. All students are required to be fully masked and vaccinated due to the contagiousness of the new SARS-CoV-2 variants. This may make group work challenging on activity days. If this proves to be so we will move activity days to a virtual format with breakout rooms. Either way attendance at the scheduled class time is expected. It is highly encouraged for your engagement and mental health that you keep your camera on during virtual attendance. Online instruction Hyflex - FGYM 148

08/23/2021 - 09/03/2021 09/07/2021 - 12/10/2021

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Required Textbook/Course Materials Please read the Technical Skills and Requirements to understand the Minimum Hardware and Software needed for this course. Required Textbooks:

• Lehninger Principles of Biochemistry, 8th edition By Nelson and Cox (lecture text) and Achieve Homework package. I recommend either the electronic version (2 term access – don’t pay twice!) Course Id: fwa3ey ISBN:9781319322298 $114

• Or if you still prefer paper as I do, the loose leaf version with the Achieve 2-term ISBN:9781319408930 $154.99 (2 term access)

Other Required Materials:

• Non-programmable scientific calculator with logarithmic and exponential function capabilities that you know how to use. WiFi, Bluetooth and IR calculators are not allowed for quizzes or examinations.

Recommended Materials (optional): • The Absolute Ultimate Guide to Lehninger Principles of Biochemistry, Osgood and Ocorr

Student Learning Outcomes Institutional Learning Outcomes • Information Literacy – HSU graduates will be able to locate, evaluate, and employ

information effectively and ethically for a wide range of purposes. • Critical Thinking – HSU graduates will be able to critically evaluate issues, ideas, artifacts,

and evidence to guide their thinking. • Written Communication – HSU graduates will be able to develop and express ideas

effectively in writing. • Oral Communication – HSU graduates will be able to effectively communicate orally for

informational, persuasive, and expressive purposes. • Quantitative Reasoning – HSU graduates will be able to apply math concepts and skills to

the interpretation and analysis of quantitative information in context. Course Learning Outcomes Upon completion of this course series, you will be able to:

• SLO 1: Students will complete the American Chemical Society standardized exams to demonstrate knowledge in the sub-discipline of biochemistry (end of second semester).

• SLO 2: Students will use three-dimensional models to aid in the understanding of biochemical structures and properties and to proficiently translate those models into two-dimensional representations to interpret chemical processes, and will also use modern computational methods to develop an in-depth understanding of chemical reactivity and chemical structure.

• SLO 4: Students will utilize library resources in biochemistry to proficiently locate, evaluate cite and interpret biochemistry literature for a variety of purposes.

• SLO 5: Students will prepare and orally communicate a chemical topic in biochemistry, demonstrating their breadth of knowledge of biochemical topics to a diverse audience.

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Table 1. CHEM 434 Lecture, Course on a Pages Schedule, Fall 2021 Week Date Lecture Topic Quizzes Reading Homework

1 8/23 Intro &Syllabus, activity Intro 1 Quiz 1. Intro 2.1-2.3 Pre-activity1. syllabus 8/25 Chapt. 2: Water 2.4-2.5 8/27 Pre-activity2

2 8/30 Activity 2 3.1-3.3 9/1 Ch3: Amino Acid Peptide & Protein Quiz 2, Chapt 2 9/3 3.4 HW ch2 due 9/4

3 9/6 Labor Day Holiday Drop date Pre-miniactivity 3 9/8 HW ch3 due 9/14

9/10 4 9/13 Ch 4: 3-D structure of Proteins Quiz 3 Chapt. 3 4.1-4.2 Pre-activity 3

9/15 Activity 3 4.3-4.4 9/17 Pre-activity 4

5 9/20 Ch5: Protein Function, Activity4 ch 5 Quiz 4, Chapt 4 5.1-5.2 HW ch4 due 9/19 9/22 5.3 HW ch5 9/24 Pre-activity 5-PDB

6 9/27 Protein Data Bank Activity 5 9/29 Ch 6: Enzymes Quiz 5 Chapter 5 6.1-6.3 10/1 6.4-6.5 Pre-activity 6

7 10/4 Activity 6 10/6 10/8 PDB Paper 10/10 Group1. Pres upload

8 10/11 PDB In Class Presentation Group 1. Group2. Pres upload 10/13 PDB In Class Presentation Group2. 10/15 Quiz 6 Chapt 6 HW ch6

9 10/18 Ch 7: Carbohydrates 7.1-7.2 Pre-activity 7 10/20 Activity7 7.3-7.5 10/22

10 10/25 Ch 8: Nucleotides & Nucleic Acids Quiz 7 Chapt 7 8.1-8.2 HW ch7 10/27 Activity8 8.1-8.2 Pre-Activity 8 11/29 8.3-8.4 HW ch8

11 11/1 Ch 9: DNA-Technology. Quiz 8. Chapt 8 9.1-9.3 Pre-Activity 9 11/3 Activity9 Activity 7 HW ch9 11/5 Pre-Activity 10

12 11/8 Ch 10: Lipids Quiz 9 Chapter 9 10.1-10.4 HW ch10 11/10 Activity 10 11/12

13 11/15 Chapter 11: Membranes Quiz 10. Chapt 10 11.1-3 Pre-activity 11 11/17 Activity 11 HW ch11 11/19 Virtual material

x 11/22-26 Holiday - Fall Break 14 11/29 Quiz 11. Chapt 11

12/1 Chapter 12: Biosignaling 12.1-11 Pre-activity 12 12/3 Activity 12

15 12/6 Quiz 12. Chapt.12 Upload Presentation 12/8 Lipid / Carb. Pres. - Paper Due Group 1 Paper Due Upload Paper

12/10 Lipid / Carbohydrate Pres Group 2 HW CH12 16 12/14-17 Final Examination: 12/17/2021, Friday 10:20AM - 12:10PM

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Course Schedule Check the Course Schedule for more detail on the topics for this semester. (Course schedule as listed and in Canvas) Messages from your instructor will be sent to you at the email address used in your Humboldt State profile. Lesson/Instructional Materials Pre-Activities and Assignments will be listed on canvas and the Online homework Platform Sapling. Course Overview CHEM 434 This lecture class is being synchronously online with additional online content. As a professional senior level course preparing you for your future careers it is expected that student will come prepared and ready to learn, and ready to contribute to group work. This is not a self-paced class. You will need to use Canvas and the online Homework system to find materials, take quizzes, and submit completed works electronically. You should do your work in this course with a high priority and complete reading assignments and pre-activities. This will also ensure you are ready for any quizzes or discussions. Course requirements

• Class participation in activities and discussions. Collegial attitudes with peers and the instructor.

• Chapter quizzes, homework in Macmillian Sapling, readings in the text book and other sources.

• Two presentations with two 3-4 page papers with cited primary scientific literature. • A cumulative final.

Quizzes Quizzes will be given for each chapter covered, on canvas or in Achieve from the canvas link. They will relate to either the lecture material or readings. There will be 12 quizzes worth 20 points each (lowest 2 dropped) for 200 points. These quizzes will be timed. They will prepare you for the final examination. Pre-Activity and Activity These active learning assignments will have two components. 1. The Pre-Activity where the individual students do pre-reading on new material and answer some questions or complete a task. This will be turned in on canvas, where they will be checked for completion. 2. The Activity where students will assemble into groups of 4 using the POGIL (Process Oriented Guided Inquiry Learning) method. Here you will complete a worksheet and develop key insights from your discovery. This is a proven higher order learning strategy, and contributes both to the

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individual learning and the soft skills that the Biotech and Medical industries list as their number one attribute in candidates. These work sheets should be saved and used as study guides for the exams and final. Each of 12 pre-activity and participation in the activity are worth 10 points total for 100 points. (Lowest two dropped)

Homework You will be using the online homework platform Achieve from the book publisher Macmillian, which will be assigned for both practice and reading (ungraded) and homework (graded). Each chapter will have 10 points of homework with the lowest two scores dropped for 100 pts. We will also use the case studies which will be 5 points each and in-class participation for 50 points. Total of 150 points. I will select some of the questions for the quizzes and final from the homework graded and ungraded assignments. Below are the instructions for Launching Achieve in Canvas. It is fully integrated STUDENT INSTRUCTIONS I have enabled single-sign-on with Canvas, use these instructions to access Achieve.

1. Follow the Achieve assignment link from the course page (Canvas). 2. For initial registration, Achieve must be accessed through that link. After logging in once

using this link, you can log in to subsequent sessions from your instructor's course page or from the Achieve home page.

3. If you already have an Achieve account, enter your username and password in the login box. If the login box is disabled, click the Create Account link to create an account. Once your account is created, you will be returned to the login page where you can enter your new username and password and click Log In.

4. If the course requires payment and is past the grace period, you will be required to pay before you can access the assignments.

5. Need Help? Answers to many common questions are found in our Student Support Community. If you need direct assistance you can also contact technical support: https://macmillan.force.com/macmillanlearning/s/.

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In Class Presentation and Papers Each student prepare two short presentations for the class accompanied with two 3-4 page papers that cite primary scientific literature. The first assignment is the PDB presentation and paper, where each student will choose a protein data bank http://www.rcsb.org/ protein entry and discuss the biochemistry, biological function and structural information about their protein of choice with the class. The presentation style will be the “quad chart” format which is a single slide used for pitching ideas in the biotech industry and governmental agencies. https://en.wikipedia.org/wiki/Quad_chart This talk and brief paper will reference the primary scientific literature and also incorporate images you will generate using protein molecular modeling software. Such as UCSF ChimeraX. (https://www.rbvi.ucsf.edu/chimerax/) a free program. The second assignment will be a student choice of a lipid and/or carbohydrate related topic in biochemistry. Again the primary scientific literature will be cited in a brief 3-4 page paper and presentation. The format of this presentation is to be determined. Combined the Papers and presentations are worth 100 points.

Final and Testing Statement The final exam will be timed and online on canvas. Accommodations are welcome, but must be made in advance with documentation.

Methods of Evaluation/Grading Policy The above grading information is summarized in the table below.

Table 2. Grading information for CHEM 434L

Grade Items Points % Quizzes 200 26.7 Activities 100 13.3 Homework (100) and case studies & participation (50) 150 20 PDB Paper and Presentation 50 6.7 Lipid/Carbohydrate Paper and Presentation 50 6.7 Comprehensive Final Exam 200 26.7 Total Points 750 100

Your performance will be evaluated based on your scores on assignments compared to that of your peers. I reserve the right to adjust the grades downward (e.g. 92-100% = A) but will never adjust grades upward from the following base grading scale:

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Table 4. CHEM 434L Grading scale BASE GRADING SCALE A 94 -100% A- 90 – 93% B+ 87 - 89% B 83 – 86% B- 80 – 82% C+ 77 -79% C 71 – 76% C- 65 – 70% D+ 61 - 64% D 55 – 60% F Under 55%

Attendance Policy Lecture attendance is mandatory and will be recorded. Students are responsible for knowing policy regarding attendance and disruptive behavior: Class Attendance and Disruptive Behavior. I would prefer that you have your camera on for zoom meeting as it helps with the course dynamics, however I am flexible due to limited wifi access.

Supplemental Help Please attend faculty zoom office hours. Students who attend office hours perform better in this course. Biochemistry students often find it helpful to study in groups. Create a study group early and create a schedule so that you can work together to master content.

Academic Honesty Students are responsible for knowing policy regarding academic honesty. For more information, visit: Academic Honesty Policy or HSU Catalog Academic dishonesty is the intentional act of fraud, in which an individual seeks to claim credit for the work and efforts of another or uses unauthorized material or fabricated information in any academic exercise. Academic dishonesty also includes, but is not limited to: (1) Forgery/fabrication/falsification/plagiarism of academic documents; (2) Intentionally impeding or damaging the academic work of others; (3) Assisting others in acts of academic dishonesty; (4) Cheating in the online classroom; (5) Unauthorized attendance; (6) Multiple submissions; and (7) Unauthorized collaboration or use of online platforms. Netiquette “Netiquette” refers to the etiquette by which you should abide when using online services for your classes and campus communications. This includes email, social media, online chat, blogs, online discussions or message boards, instant messages,

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etc. Although you are participating in course activities and using course materials online, the HSU code of conduct still applies.

https://studentrights.humboldt.edu/ Online participants are expected to behave in a respectful manner that is supportive to other learners, participants, and faculty.

General Student Services Students with Disabilities Persons who wish to request disability-related accommodations should contact me immediately so I can assist you in a timely manner. If you have not yet done so, please request services with the Student Disability Resource Center, temporarily located in the Campus Events Field, #6, 826-4678 (voice) or 826-5392 (TDD). Some accommodations may take up to several weeks to arrange. Student Disability Resource Center. HSU Policy and Procedures for Accommodating Individuals with Disabilities Statement Executive Memorandum EM P02-01 states: It is the policy of Humboldt State University to provide equal access and reasonable accommodation for individuals with disabilities to participate in any program, service, or opportunity by the campus, including access to the content and services of the World Wide Web pages authored by the University. Request for accommodation in pursuit of student's academic programs should be made to the Student Disability Resource Center. Our campus learning management system is Canvas. Here is a link to the Accessibility within Canvas statement. This course was built with accessibility in mind. However, if you discover something in the course that is not as accessible as it could be, please alert your instructor as soon as possible. Technical Assistance It is crucial to seek help when you can’t access Canvas or you have difficulty with your computer settings or browser: For technical assistance contact HSU’s Help Desk at 707.826.HELP (4357) or send an email to help@humboldt.edu For Canvas support, please use the Help button located on the bottom left of your course. Please see the Canvas Student Guides to learn more about specific Canvas functions. https://community.canvaslms.com/docs/DOC-4121

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Mental Health Support Counseling and Psychological Services (CAPS) provides short-term individual, couples, and group psychotherapy and counseling, crisis services, and assessment/referral services for enrolled HSU students. More information may be found at the CAPS website: http://www2.humboldt.edu/counseling/index.html About Counseling Services

• If you are feeling overwhelmed, counselors are ready to listen. • If you are feeling stuck and can't decide how to proceed, counselors can help

you gain a new perspective. • If you are ready for a change, counselors can help you make it happen. • When you see a counselor... • They will be non-judgmental. • You will get professional feedback. • Your conversations will be private and confidential. • You will be safe to discuss whatever is on your mind. • Counseling will not be a part of your HSU records.

Inclusivity Students in this class are encouraged and required to speak up and participate in-class and online. Each of us must show respect for each other because our class represents a diversity of beliefs, backgrounds, and experiences. I believe that this is what will enrich all of our experiences together. I recognize that our individual differences can deepen our understanding of one another and the world around us, rather than divide us. In this class, people of all ethnicities, genders and gender identities, religions, ages, sexual orientations, disabilities, socioeconomic backgrounds, regions, and nationalities are strongly encouraged to share their rich array of perspectives and experiences. If you feel your differences may in some way isolate you from our classroom community or if you have a specific need, please speak with me early in the semester so that we can work together to help you become an active and engaged member of our class and community. Emergency Procedures

• During an emergency, information can be found on campus conditions at 707-826-INFO or the HSU Emergency website.

Email Policy All HSU students are responsible for checking their HSU email account for official communications. While students may elect to redirect messages sent to their official HSU email address to another address, those who redirect their email to another address do so at their own risk. HSU Email Policy.

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Student Support Services

Resources and Options for the HSU Student Community Find a full list of services for HSU students here: http://www2.humboldt.edu/studentaffairs/student-resources

Learning Center The HSU Learning Center has a wide range of academic support services. HSU Learning Center

Writing Studio The Writing Center offers free peer assistance with writing assignments and standardized writing examination preparation. The Writing Studio's web site can be accessed at HSU Writing Studio

Improving Study Skills Find a variety of resources to improve your study skills. HSU RAMP Academic Resources

Tutoring Services The Learning Center provides tutorial assistance to students having difficulties in specific Courses. The Tutoring Services web site can be accessed at HSU Tutorial Services

Advising The Academic and Career Advising Center supports students' pursuit of educational goals. HSU Academic & Career Advising Center

Mentoring Peer academic support through Retention Through Academic Mentoring Program (RAMP) HSU RAMP Program

Registration The Office of the Registrar can guide you through all your registration information. HSU Office of the Registrar

Counseling The Counseling & Psychological Services Center supports the wellbeing of HSU students. HSU Counseling & Psychological Services