Course Mechanics for Spring 2022

Both the lecture and laboratory sessions for this course are currently scheduled to meet in person. The lectures will be recorded (with only the audio and slides) and these recordings, along with the slides, will be posted on Canvas. But the sessions will not be live-streamed. Accommodations will be made for those unable to attend lecture or lab sessions because of COVID-19 or other unavoidable absences.

COVID-19 Precautions and Information

Given the current rates of COVID-19 infections in Utah, wearing a face mask in class is strongly encouraged. According to the CDC, wearing a mask remains an effective means of preventing infection for both unvaccinated and vaccinated people. Regardless of what someone chooses (mask or no mask), the university seeks to foster a sense of community and asks everyone on campus to be respectful of individual decisions on mask wearing.
Current university COVID information can be found at these sites: For absences related to COVID, please request an accommodations by filling out the online form at:
https://www.biology.utah.edu/secure/covid-accommodations
For absences due to other illnesses, family emergency or an official University of Utah activity, please contact the instructor by e-mail at.

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.

Instructor and Teaching Assistants

Instructor:

David P. Goldenberg
Office: 306 Aline Skaggs Biology Building
Telephone: (801) 581-3885
E-mail:
Office hours (via Zoom, starting Tuesday, 18 Jan.):
  • Tuesdays: 11:00 AM - noon
  • Wednesdays: 2:00 PM - 3:00 PM
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:

Monday:
Tuesday:
Wednesday:
Thursday:

Laboratory Sessions

The class will be divided into four laboratory sections, each meeting once a week on Mon., Tues., Wed. or Thurs. Except for the computer sessions during the weeks of 31 January and 7 February, the laboratory sessions will be held in Room 143 in the Crocker Science Center (CSC).
During the first week of classes, the week of 6 January, only the Monday lab section will meet.

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. Instructions and links for setting up your LabArchives account wil be provided 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 Safety

  • No food or drink are allowed in the lab.
  • Safety glasses are required for all laboratory sessions.
  • Shoes must fully cover your feet for protection from broken glassware and other hazards.
  • Full-length trousers or equivalent are required.
  • Lab coats will be provided at no cost, and must be worn in the lab.
  • Gloves must be worn when handling reagents.
  • Personal electronic devices, including phones, tablet computers and laptop computers, will not be allowed in the laboratory. This is to avoid both distractions and possible chemical contamination that could be spread outside the lab. There is a classroom immediately adjacent to the lab, and reserved for the course, where you are free to use your laptop for working on lab reports.
  • Information about the reagents that we will be using can be found on the Chemical Safety page.

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, in Room 208 of the Crocker Science Center (CSC). Regular class attendance is expected of all students. Although slides from many of the lectures will be posted on the class web site, these should not be viewed as a substitute for attending class.

Electronic Device Policy

In order to encourage student engagement and create a more effective learning environment for everyone, the use of cell phones, tablet computers or laptop computers will not be allowed during class. Cell phones may be accessed during class only in cases of emergencies. Exceptions to this policy will be made for students who need to use an electronic device as part of an approved accommodation. See the section below on Special Accommodations for information about applying for an accommodation through the Center for Disability Services.

Clickers

The iClicker audience response system will be used to facilitate interactive learning during the class 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.
Although there is an iClicker app for mobile devices, it will not be supported in this class. (See the electronic device policy above.) You will thus need to purchase or rent one of the following two remote devices, if you don't already have one: The Campus Store will have the less-expensive iClicker+ available for sale for $44.99 and will buy back the device at the end of the term, though the amount to paid has not yet been determined. . Alternatively, the links above provide information for purchasing or renting the devices directly.
To use the device with this class, the following steps are required:
  1. If you do not already have an iClicker account, you will need to create one before classes begin, following the instructions at:
    How-to-Create-an-iClicker-Student-Account
  2. Register your iClicker remote device so that it is linked to your account:
    How-to-Register-an-iClicker-Remote
    Follow the instructions under the heading "My instructor is using iClicker Cloud"
  3. Add Biol 3515/Chem 3515 to your account, as described here:
    Add-Your-Instructor-s-Course-in-the-iClicker-Student-App
    The course should be listed with the title, ``Biological Chemistry Laboratory'', and the course ID, ``Biol 3515/Chem 3515''.
  4. Use of the iClicker system requires a license. If your clicker was purchased new, it will come with a five-year license, and there will be no additional charges. If, however, you buy a second-hand clicker that was previously registered to another account, you will need to purchase a license. Similarly, rented clickers do not include a license.
    When you create a new iClicker account, you will receive a free two-week trial license. At the end of this period, however, you will need to purchase a license (if you don't already have one). A license for six months costs $15.99, and other pricing options are listed here:
    https://www.iclicker.com/pricing
For each class session where the clickers are used, there will be a total possible score of 5~points, divided evenly among the number of questions asked. There will also be 1 possible participation point per lecture, which is earned by answering at least 75% of the questions (correctly or otherwise),
To allow for unavoidable absences, the lowest four clicker point scores will be dropped when calculating the course grade.
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 have been 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, 10 February
  • Thursday, 24 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:
  • Friday, 29 April. 10:30--11:30 A.M.

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: 70%
  • Quizzes: 12.5%
  • Final exam: 12.5%
  • 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, 21 January.
  • Last day to elect CR/NC option: Friday, 21 January.
  • Last day to drop (delete) classes: Friday, 21 January (No tuition penalty; class does not appear on record.)
  • Last day to withdraw from classes: Friday, 4 March (No tuition refund, ``W'' appears on transcript.)
  • Last day to reverse CR/NC option: Friday, 22 April.
  • Last day of classes: Tuesday, 26 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.