Course Description (from the University Catalog)

Laboratory course in protein biochemistry and enzymology. Topics covered include spectrophotometry, enzyme kinetics, electrophoresis and chromatography. In addition to one 4-hour laboratory sessions and one lecture per week, the course requires substantial out-of-class work involving computer-based data analysis and molecular modeling. Students need to take CHEM/BIOL 3510 prior to taking, or simultaneously with, this course.

Course Mechanics for Spring 2021

Because of the COVID-19 pandemic, BIOL 3515/CHEM 3515 is being taught online this semester, as an Instructional Video Conferencing (IVC) class. Both lecture and lab sessions will be held at the scheduled times via Zoom. Quizzes and exams will also be administered online. Participation in the course will depend on having access to a computer and broadband internet connection, as well as being able to use Canvas, Zoom and other online resources effectively. Please contact the instructor as soon as possible if you have concerns about these requirements. Further details are provided in the sections below.

Instructor and Teaching Assistants

Instructor:

David P. Goldenberg
Office: 306 Aline Skaggs Biology Building
Telephone: (801) 581-3885
E-mail:
Office hours (via Zoom):
  • Tuesdays: 11:00 AM - noon
  • Wednesdays: 2:00 PM - 3:00 PM (starting Tuesday, 22 Jan.)
Occasionally, conflicts may arise, and I will have to cancel office hours for a day. I will announce any changes on Canvas.
I am also happy to meet with students at other times. The best way to contact me to set up an appointment is by e-mail, using the address above.

Teaching Assistants:

Tuesday:
Wednesday:
Thursday:
At large:

Laboratory Sessions

The class will be divided into three laboratory sections, each meeting once a week on Tues., Wed. or Thurs. All sections will meet from 1:00 to 5:00 PM, via Zoom. The laboratory sessions will be designed to emulate as closely as possible the normal lab experience, with video demonstrations, virtual experiments and data analysis.
There will be no lab sessions during the first week of classes, the week of 6 January, or during the week of 8 March (in honor of the spring break that was canceled).

Laboratory Manual

A special manual, entitled "Laboratory Experiments in Biochemistry" has been prepared and will be provided electronically on Canvas.

Electronic Laboratory Notebooks

You will be keeping notes, storing data and preparing the lab reports using an online electronic notebook system called LabArchives. Shortly before classes start, you should receive an e-mail message containing a web link for setting up a LabArchives account. These links will also be available on the Canvas page for this course.
When setting up your account it is very important to use your University of Utah UMail e-mail address, of the form uNID@utah.edu. Do no not use an alias to your UMail account (such as my.name@utah.edu) or another account, such as a gmail account. Sorting things out once an account has been created using the wrong e-mail address is painful for everyone involved. But, once the account is set up with a proper UMail address, it is easy to change the address associated with the account.
After logging on to LabArchives, you should find an online notebook set up for this class, containing a page named "Getting Started". On this page you will find links to some tutorial material, and you should start getting to know the system before your first lab session.

Laboratory Reports

For each of the six experiments, a summary report will be due approximately two weeks after the completion of the experiment. The due dates for the individual lab reports are indicated on the Laboratory Schedule. This report will include:
  • All of the data collected in the lab, including computer files.
  • Data analysis, as specified in the lab manual
  • For experiments 3, 4 and 5, molecular modeling files.
The reports are to be created within LabArchives and will be submitted electronically as a pdf file.
A common question is whether or not the lab reports should include sections such as an introduction, methods, results or discussion. The answer is NO! Only the elements listed above are required.
Reports will be accepted up to 7 days late, but a 10-penalty for each day late will be imposed. Reports will not be accepted after 7 days beyond the due date.
Although you will be working in groups of three in the laboratory, and you should share responsibility for recording data in the lab, each of you is responsible for preparing your own reports. You may certainly consult the instructor, the TAs or other students as you work. But, the actual work handed in (other than the primary lab data) must be your own. Any, data analysis files, molecular modeling files and text must be clearly distinguishable from that of other students. Other sources must be properly cited. Text from other sources must be clearly identified by quotation marks. Furthermore, extensive quotations, even with proper citation, will not be considered satisfactory answers to questions. Copying and pasting does not demonstrate mastery of the material!
If two or more students turn in work that that is identical, their action will be considered academic misconduct and appropriate sanctions will be imposed. At a minimum, the sanction will include the loss of credit for the copied work, and more severe sanctions may be imposed for more extensive infractions. (See additional information below regarding Academic Conduct.)
Additional instructions for the laboratory reports are provided in the laboratory manual.

Lecture Sessions

Two lecture sessions per week will be held, on Tuesday and Thursday mornings from 9:40 - 10:30 AM. All class sessions will be held via video conferencing, using Zoom, and regular attendance is expected. The class sessions will have a mixed lecture-discussion format, and engaged participation is essential for learning. The Zoom sessions will be recorded and made available online to accomodate unavoidable absences, and slides from the lectures will be posted on Canvas (after the class session). But, these resources should not be viewed as a general substitute for attending class. During the period between 1 March through 12 March, all University of Utah classes will be online. For this class, there will be no change in format during these periods.

Clickers

The iClicker audience response system will be used to facilitate interactive learning during the IVC lecture sessions. The responses will be graded and will count for 5% of the course grade. For some questions, credit will be given for any answer, but for others points will only be given for correct answers.

Before the first class you should create an iClicker Reef account and set it up for this course, as follows:
  1. If you do not already have an iClicker Reef account, you will need to create one before classes begin, following the instructions at:
    How to Create an iClicker Reef Student Account
  2. Then, add this course to your account, as described here:
    Add Your Instructor's Course in Reef
    The course should be listed with the title, "Physical Principles in Biology"", and the course ID, "Biol 3550/3551.
  3. When you create a new iClicker Reef account, you will receive a free two-week trial license. At the end of this period, however, you will need to purchase a license. A license for six months costs $15.99, and other pricing options are listed here:
    https://www.iclicker.com/pricing
  4. As a final step, you must synchronize your iClicker account with Canvas. To do this, click on the iClicker Sync in the second-to-left column of the course Canvas page and follow the instructions there.
  5. To submit your responses during class, you can either install the iClicker Reef app on a mobile device or use the web interface. Links to the app for iOS and Android devices are found here:
    https://www.iclicker.com/students/apps-and-remotes/apps
    To use the web interface, login to your Reef account at:
    https://app.reef-education.com/#/login
Bonus clicker points can be earned by finding errors in the lab manual or lecture slides. To earn points, though, you must be the first to let the instructor know about the error!

Text book

There is no required text book for this course. There is, however, a recommended text entitled "Fundamental Laboratory Approaches for Biochemistry and Biotechnology" (2nd ed.), by A.J. Ninfa, D.P. Ballou and M. Benore. Copies of this text are available at the bookstore, and copies will be placed on reserve at Marriott Library. In addition, it may be helpful to review material from a standard biochemistry text, such as those by Berg, Tymoczko and Stryer or by Voet and Voet.

Quizzes and Final Exam

There will be two quizzes during the lecture sessions on the following dates:
  • Thursday, 18 February
  • Thursday, 18 March
Each of the first two quizzes will be about 25 minutes long and will cover material from the lectures and laboratory sessions since the previous quiz.
A cumulative, 1-hour final exam will be held during the scheduled exam period for this class:
  • Thursday, 29 April. 10:30--11:30 A.M.
The quizzes and and final exam will be administered via Canvas, and will be subject to an honor code. For each quiz or exam, students will be required to sign an honor-code statement, stating that they have not communicated with anyone during the exam period or used any online or other resources. Violations of this honor code will be considered academic misconduct and appropriate sanctions will be imposed. At a minimum, a grade of zero will be recorded for the quiz or exam. If the grade is for a quiz, it will be dropped from the course average. Repeated offence will be subject to additional sanctions.

Grades

The course grade will be based on the laboratory reports, quizzes and responses to in class questions (via clickers), weighted as follows:
  • Laboratory reports: 65%
  • Quizzes: 15%
  • Final exam: 15%
  • In class clicker responses: 5%
The following represent maximum cutoffs for determining class letter grades:
  • A: 92-100% (including A-)
  • B: 82-91% (including B- and B+)
  • C: 70-81% (including C- and C+)
  • D: 60-69%
  • E: < 60%
Depending on how things go, the grade cutoffs may be revised downwards, i.e. to make the grading more generous. The cutoffs will not be moved upwards to make the grading less generous.

Important Dates

  • Last day to add classes: Friday, 29 January.
  • Last day to drop (delete) classes: Friday, 29 January (No tuition penalty; class does not appear on record.)
  • Last day to withdraw from classes: Friday, 12 March (No tuition refund, ``W'' appears on transcript.)
  • Last day to elect CR/NC option: Friday, 9 April.
  • Last day to reverse CR/NC option: Friday, 23 April.
  • Last day of classes: Tuesday, 27 April.

Excused Absences

If you must miss a lab session because of illness, family emergency or an official University of Utah activity, please let the instructor and your TA know as soon as possible. If it can be arranged, you may be able to do the lab work by joining another lab group on a different day of the week. If this cannot be arranged, you can obtain the lab data from the other members of your group and complete the lab report using that data.
If you miss a lecture because of illness, family emergency or an official University of Utah activity, please notify the instructor. Any clicker points missed because of an authorized absence will not be included in calculating the average for your clicker responses.

Unexcused Absences

Attendance will be taken in each lab session. If you miss a lab session without an accepted excuse, you may complete your lab report using the data recorded by your lab partners. However, there will be a 20-point penalty applied to your lab report grade for each missed session.
If you miss a lecture without an accepted excuse, there will be no make up for any missed clicker questions.

University Policies

Faculty and Student Responsibilities

All students are expected to maintain professional behavior in the classroom setting, according to the Student Code. Students have specific rights in the classroom as detailed in Section II of the Code. The Code also specifies expectations of student behavior (Section III). Students should read the Code carefully and know they are responsible for the content. According to Faculty Rules and Regulations, it is the faculty responsibility to enforce responsible classroom behaviors, beginning with verbal warnings and progressing to dismissal from class and a failing grade. Students have the right to appeal such action to the Student Behavior Committee.

Special Accommodations

The University of Utah seeks to provide equal access to its programs, services and activities for people with disabilities. If you will need accommodations in the class, reasonable prior notice needs to be given to the Center for Disability and Access. CDA will work with you and the instructor to make arrangements for accommodations.

Academic Conduct

In order to ensure that the highest standards of academic conduct are promoted and supported at the University, students must adhere to generally accepted standards of academic honesty. Acts of academic misconduct include cheating, plagiarizing, research misconduct, misrepresenting one's work, and inappropriately collaborating. Suspected cases of academic misconduct will be dealt with according to the rules found in the Student Code, University Policy 6-400(V) . Instances of academic misconduct will be recorded in a database that may be made available to other University of Utah Departments and Colleges.

Title IX: Addressing Sexual Misconduct

Title IX makes it clear that violence and harassment based on sex and gender (which Includes sexual orientation and gender identity/expression) is a civil rights offense subject to the same kinds of accountability and the same kinds of support applied to offenses against other protected categories such as race, national origin, color, religion, age, status as a person with a disability, veteran's status or genetic information. If you or someone you know has been harassed or assaulted, you are encouraged to report it to the Title IX Coordinator in the Office of Equal Opportunity and Affirmative Action, 135 Park Building, 801-581-8365, or the Office of the Dean of Students, 270 Union Building, 801-581-7066. For support and confidential consultation, contact the Center for Student Wellness, 426 SSB, 801-581-7776. To report to the police, contact the Department of Public Safety, 801-585-2677(COPS).

University Safety Statement

The University of Utah values the safety of all campus community members. To report suspicious activity or to request a courtesy escort, call campus police at 801-585-COPS (801-585-2677). You will receive important emergency alerts and safety messages regarding campus safety via text message. For more information regarding safety and to view available training resources, including helpful videos, visit safeu.utah.edu.

Disclaimer

The information provided here and in the syllabus does not represent a binding legal contract. It may be modified by the instructor when students are given reasonable notice of the change.