BIO380: Biochemistry.Fall 2024

FALL 2024
UNION COLLEGE, SCHENECTADY, NY

Location and Meeting Time: WOLD 225 MWF 10:30AM-11:35AM
Laboratory: WOLD 201,  WEDNESDAY 1:50-4:40 PM or THURSDAY  1:55-4:50 PM

SYLLABUS OF STUDY (DRAFT 2024/08/13)

COURSE OBJECTIVES

The main objective of this course are to understand the structure-function relationships of non-protein molecules including nucleic acids, carbohydrates, and lipids. The challenge will be to move away from traditional aspects of these molecules. For example:

• Non-genomic functions of nucleic acids- instead of thinking about DNA and RNA in their traditional role in the flow of genetic information, we will focus on concepts like the use of RNA in the formation of aptamers and aptamer based drugs
• Non-metabolic functions of carbohydrates and lipids- the role of glycosylation in protein function and the role of lipids in cell membranes

1. 1. TEXTBOOK (required)
      • Lehninger Principles of Biochemistry, Eighth Edition by David Nelson and Michael Cox (2021), published by WH Freeman
        • This textbook is required, as there will be assigned readings (please see lecture schedule) that will either complement or expand upon the material presented during lectures.  However, the lecture period remains the most important and efficient way of learning the material in the course.
   2. LECTURE PRESENTATIONS
      Presentations will make use of traditional teaching tools as well as assorted electronic resources.
      • This course contains a lot of material and the pace may seem quite intense especially in a ten week format.  It is important to pay close attention to lectures.  ASK QUESTIONS if you don’t understand or if something requires clarification.  If a certain concept eludes you, please don’t delay in coming to see me.  As we proceed in the course, you’ll find that much of the material requires an understanding of the processes discussed during the first few weeks.
      • Reviewing your lecture notes every day after class will help you to identify confusion points and get answers quickly
      • Course Materials on Nexus
        • I am using Nexus as the online repository of information related to this course. The site can be found at: http://nexus.union.edu/
      • The three-plus hours of class time per week are designed to be interactive.  Lectures still take up the bulk of the time; however, discussion will be encouraged.
      • Presentations will primarily make use of assorted electronic resources (Power Point, videos, and animations). Almost all of the lecture material will be available as powerpoint documents on Nexus.
        • Many students find it helpful to make hard copies of the lecture figures and bring them to class.
        • You may also use laptops or tablets to take notes directly onto the individual slides.
      • You will be responsible for all material covered during lectures, as well as any textbook readings, handouts or assignments (whether provided in this syllabus or at a later time).  Moreover, the lectures will contain new information not covered in the textbook.  Therefore, you should make every effort to attend lecture and take complete and accurate notes.
      • Want more information on how to do well in class? Follow this link: How to do well in a Cohen class
   3. LABORATORY
      Students enrolled in the course will be required to attend lab as scheduled each week.  Labs will be held in the Wold Center Room 201 WEDNESDAY AND THURSDAY.  If you cannot make your scheduled lab period a particular week, you must coordinate with me to make it up at another time.  Failure to do so will result in a failing grade for the lab section of the course.
   4. OTHER INFORMATION
      • Attendance
        • Attendance in lecture is expected, but not mandatory
          • You will not be able to get classroom participation points if you are not in the classroom
          • Exam questions will come from lecture material (hand-outs, discussions, etc.).  Topics discussed during class may also prove to be useful when writing your lab reports.
        • Laboratory attendance is mandatory; missing lab may result in failure in the course. You must watch the laboratory safety video and take the quiz before you can take the lab.  You can gain access to the video and quiz on Nexus.
        • If you read this please email me and you can come to get a prize from my prize bag (don’t get too excited- we’re talking pens, stickers, a few stress balls, etc)
      • Students Requiring Academic Accommodations
        • Union College facilitates the implementation of reasonable accommodations, including resources and services, for students with disabilities, chronic medical conditions and temporary disabilities resulting in difficulties accessing learning opportunities. All students needing services must first register with Accommodative Services located in Reamer 303. It is strongly recommended that accommodations be requested within first two weeks of the term. Last minute requests can be denied.
        • At the beginning of the term, please discuss with me the accommodations needed to facilitate your learning and test taking. Discussions will remain confidential. Appropriate documentation from the Accommodative Services Office is required.
      • Academic Honesty
        • Union College recognizes the need to create an environment of mutual trust as part of its educational mission. Responsible participation in an academic community requires respect for and acknowledgement of the thoughts and work of others, whether expressed in the present or in some distant time and place.
        • Matriculation at the College is taken to signify implicit agreement with the Academic Honor Code, available at honorcode.union.edu. It is each student’s responsibility to ensure that submitted work is his or her own and does not involve any form of academic misconduct. Students are expected to ask their course instructors for clarification regarding, but not limited to, collaboration, citations, and plagiarism. Ignorance is not an excuse for breaching academic integrity.
          • Because of the implicit agreement I do not require you to affix an Honor Code Affirmation on each item of coursework submitted for grading but I expect that you will abide by this code
        • Suspected breaches of the Honor Code (plagiarism, use of notes during exams, solicitation of help from other students during exams, providing assistance to other students during exams, theft or destruction of laboratory materials or other offenses not listed) will result in a minimum penalty of “0” for the assignment, and will automatically be reported to the Student Chair of the Honor Council and/ or the Dean of Studies.
      • Instructor/Course Policy on Quizzes, Tests (Exams) & Final Exam
        • Anyone who misses an exam can take a make-up (provided you have a Dean’s or medical excuse).  If you anticipate an absence on one of the exam days, see me immediately.  Unexcused absence (absence without documentation or preapproval) from a test will result in a grade of ZERO.
        • All grading mistakes on tests must be discussed within a week of getting the test returned.
        • It is Biology Department policy that all students will take the final exam at the time scheduled by the Registrar except if missing class for an official Union College activity.  Please do not make travel plans that conflict with the date of the final.
      • AI Generated Content
        • Understanding how to live and work with digital tools and platforms – from statistical software to data visualization tools to artificial intelligence tools – is an essential skill for all students in this day in age.
        • However, as with any other resource you use to aid your work in this course, you must acknowledge any and all AI tools that you use in the development of your work. You must also substantially revise any writing or work produced by an AI tool before submitting it for credit in this course.
          • If you use an AI tool at any point in the development and/or creation of your work for this course – including discussion board posts, exams, and projects – you must include appropriate citations and the acknowledgment below in your Reference list:
            • Name of publisher/tool producer. (year). Name of AI tool (version date) [Large language model].
            • You must also include a full transcript of the writing or work produced by the AI tool in an appendix to your work.
            • For more details on how to cite ChatGPT and other generative AI tools see this resource from the American Psychological Association (apastyle.apa.org/blog/how-to-cite-chatgpt).
      • Inclusion
        • It is my goal that all students in this course feel they are working in an environment in which they can comfortably and productively learn. To that end, I want to be explicit that diversity of background (including, but not limited to: race, gender, ethnicity, sexual orientation, age, socioeconomic status, religion, ability) is an asset to all of us. Diversity of voices, of minds, makes our ability to do science and answer questions about the world we all inhabit stronger. In fact, research has shown that papers authored by more diverse teams of scientists generate papers that are more highly cited than work from more homogenous groups (see this example).
        • Accordingly, I will seek to provide primary literature from diverse voices of scientists presently working in our field, but I also acknowledge that many of the foundational articles we will read have been authored by a small subset of privileged voices (James Watson will be one of our prime examples of this).
        • In addition, as part of this class, we all agree to refer to others by the names and pronouns they use. If your name or pronouns change over the course of the term, feel free to reach out to me at any point so that I can ensure that we all refer to each other properly. Finally, you should all feel comfortable to let me know (in person, over email, or anonymously) if you feel that your learning is being adversely affected by experiences in or outside of class.
        • For more information about Union College’s commitment to diversity, equity, inclusion, and belonging, please visit: union.edu/campus-diversity-inclusion/dei-statement
      • Mental Wellbeing
        • As a college student, there may be times when personal stressors interfere with your academic performance and/or negatively impact your daily life. If you or someone you know is experiencing mental health challenges at Union College, please contact the Counseling Center located in the Wicker Wellness Center or call 518-388-6161 between the hours of 8:30 A.M. to 5:00 P.M.  Counseling services are free and confidential. In a crisis situation, or after hours, contact Campus Safety at 518-388-6911.  The National Suicide Prevention hotline also offers a 24-hour hotline at 800-273-825.
      • Office of Title IX & Equal Opportunity
        • Union College faculty are committed to helping create a safe and open learning environment for all students. If you (or someone you know) have experienced any form of gender-based misconduct, including sexual assault, intimate partner violence, stalking, or sexual harassment know that help and support are available. The College strongly encourages all members of the community to take action, seek support and report incidents of gender-based misconduct.
        • Please be aware that under Title IX of the Education Amendments of 1972, I am designated as a “responsible employee” and am required to disclose information about gender-based misconduct to the Office of TitleIX & Equal Opportunity. The purpose of responsible employees is to ensure that all students are aware of their rights and resources. Please know that while I am required to disclose incidents of gender-based misconduct, students can never be required to participate in an adjudicative process and all communications relative to reports remain private.
        • If you wish to speak to a confidential employee who does not have this reporting responsibility, you can contact Eppler-Wolff Counseling Center at (518) 388-6161, which has daily walk-in hours available. For more information about reporting options, support services, and resources at Union College and within the local community the community, please visit: union.edu/titleix.
   5. GRADES
      1. Lecture-based term-tests/final exam, a final paper and in-class participation will account for 66% of your final grade as follows:
         

         Item		Percentage of final grade
         Exam 1- 9/20		12%
         Exam 2- 10/11		12%
         Exam 3- 10/28		12%
         Exam 4 (during final period)		12%
         BiochemTract (what’s that?)		18%
         Breakdown of BiochemTract assignment
         Purpose Statement	1.5%
         Background draft	15%
         Peer review: Background	4.5%
         Approach & Accomplishments draft	15%
         Peer review: Approach & Accomplishments	4.5%
         Commentary draft	15%
         Peer review: commentary	4.5%
         Final paper	40%

      2. Lab-based grades will account for 28% of your final grade as follows:
         

         Restriction digest lab		5%
         Breakdown of Restriction digest lab assignments
         Figure and legend	50%
         Virtual lab	50%
         PCR lab results and discussion		8%
         Glycoprotein lab introduction		5%
         Final lab report		10%

      3. Other grades will account for 6% of your grade
         

         Other assignments	3%
         Instructor evaluation/class participation	3%

      4. Sample Grade Scale: The following scale will be used to convert numerical grades on individual assignments into equivalent letter grades for the course. You are not competing against your classmates.
         

         Score	≥93	90-92	87-89	83-86	80-82	77-79	73-76	70-72	60-69	<60
         Letter	A	A-	B+	B	B-	C+	C	C-	D	F