Chemistry 4140 (CRN 10526): General Biochemistry Lab Syllabus

Credit Hours: 1                           

Prerequisites: Credit or concurrent enrollment in CHEM 4340

Required Text: Fundamental Laboratory Approaches for Biochemistry & Biotechnology; Ninfa& Ballou (FLABB)

Course Structure: This course will introduce you to the fundamental biochemical principles, techniques and analytical methods that are integral to isolating and studying proteins, the biological molecules at the core of Biochemistry. These tools and techniques include: spectrophotometry, ion-exchange chromatography, gel electrophoresis, techniques for the analysis of enzyme kinetics and ultracentrifugation.

The topics and experiments covered in this course are not temporally correlated with CHEM 4340, so you will need to read the recommended text to acquire the appropriate background needed to understand and practice the techniques used in experiments for this course. Occasional homework problems will be assigned and consist of problems related to laboratory practice. Mastery of practice problems assigned by the instructor, assigned readings, calculations necessary to perform experiments, and understanding of experimental protocols will be critical for exam preparation. If you do not read the assigned chapters and do not work the assigned calculations you are likely to perform poorly on exams and laboratory reports. Blackboard Learn (BBL) will be used for discussion of experiments, dissemination of handouts, and submission of problem sets and lab reports.

Student Learning Outcomes

  1. Students will learn and demonstrate competence in using the basic tools and techniques used in the biochemistry laboratory. This will complement and integrate the nature of laboratory science with material learned from biochemistry lectures.
  2. Students will proficiently carry out biochemistry experiments and quantitatively analyze biochemical data. This will provide students with the experience necessary for competence in conducting and interpreting experiments in protein biochemistry in graduate school or the in their careers.
  3. Students will qualitatively assess biochemical data via the writing of professional-style laboratory reports similar to publications in the primary literature. This will provide students with the experience necessary to critically interpret biochemical data and the writing of publishable scientific reports.

Learning Outcomes Required for Writing Intensive Courses

  1. Identify and analyze a problem or issue pertinent to the field
  2. Craft and develop a theme, thesis statement, hypothesis, and/or research question, then organize and develop support for it
  3. Produce clear and correct writing that conforms to the standards and style of the discipline

Laboratory Safety: All students must comply with strict laboratory safety guidelines! Horseplay, practical jokes, experimental sabotage and/or threats in the laboratory will not be tolerated. Failure to comply with laboratory safety and rules will result in expulsion from the laboratory. Repeated offenses will result in permanent expulsion from the laboratory and failing of the course.

Minimum Safety Requirements for Lab Courses

Close toed shoes (no ballet flats, or high heels), lab coat and safety glasses.  Safety goggles are required if there is a liquid that would be dangerous if splashed in a student’s eye.  Students must purchase the glasses and have for labs where they are working with sharps, liquids, glassware. WHILE PERFORMING EXPERIMENTS, WEAR GLOVES AT ALL TIMES.

No food or drink allowed in lab at any time.  Students must put into backpack or throw away.   Failure to do so can result in a violation or fine for the university.

Laboratory Rules:

  1. Reagent Use
  2. Know the amount of reagent you wish to obtain. Avoid taking amounts greater than called for by your manual and/or instructor.
  3. Please be careful to avoid contaminating reagents for others and for your later use.
  4. To obtain a bulk (i.e., more than a few mL) liquid reagent, pour the reagent into a beaker from the bulk container. NEVER use micropipettors to obtain it from bulk container.
  5. Remove solids by shaking desired quantities from the bottle onto weighing paper. Use a clean spatula or spoon inside reagent bottles ONLY if solids will not shake freely from the bottle.
  6. NEVER return excess reagents to the containers. Check the needs of others before discarding excesses in the proper waste container.
  7. Do not use reagent containers without labels or with improper labels. Report these situations to your instructor.
  • Reagent Disposal
  • NEVER discard chemicals in sinks, or trash receptacles.
  • Place all organic wastes or other hazardous wastes in the properly designated containers (orange bags).
  • DO NOT MIX WASTES. Be sure to keep chlorinated and non-chlorinated liquid waste separate.
  • General
  • If you open it, close it.
  • If you turn it on, turn it off.
  • If you unlock it, lock it up.
  • If you break it, let your instructor know.
  • If you can’t fix it, leave it alone (report it to your instructor).
  • If you borrow it, return it.
  • If you make a mess, clean it up!!!
  • If you move it, put it back.
  • If it belongs to someone else, get permission to use it.
  • If you don’t know how to operate it, ask!
  • If you keep it, label it.
  • If you don’t need it anymore, dispose of it properly.

Homework: Instructor-designed problems relevant to laboratory experimentation will be assigned. It is critical that you read the assigned chapters relevant to the current experiment before coming to lab and have worked any relevant calculations. Not doing so will waste valuable laboratory time.

Attendance, Exams, Lab Reports, Peer Reviewed Summary: Your grade for this course will be assigned from a possible 600 total points earned throughout the semester. Attendance and participation in this laboratory is mandatory! Your active participation in this course is expected at all times.

Grading Rubric:

AssignmentsPercentage (%)Points
Lab Reports          (2 assignments, 100 points each)33%200 
Attendance/Participation4%25 
Peer Reviewed Summary12%75 
Quizzes     (4, 25 points each)17%100 
Final17%100 
Group Presentation17%100  
Total100%600 

Grading Scale and Policy: The following grade scale will be used:

90% – 100% = A.

80 % and 89% = B.

70% and 79% = C.

60% and 69% = D.

<  59% =  F.

  • Attendance: All absences will result in a 12.5 point deduction from your participation grade per absence. Missing more than two laboratories will result in failing the course. It is your responsibility to adjust your schedule to accommodate this laboratory.

Your failure to attend class or make contact with faculty to adequately explain your absence by the 10th class calendar day of the semester will result in you being administratively dropped from this course.  Being dropped from this course may affect your enrollment status and/or your financial aid eligibility.

  • Participation: The instructor will monitor student participation throughout the semester and deduct points for non-participation.
  • Quizzes: Four quizzes (25 points each) will be conducted to assess performance, theoretical and practical aspects of laboratory work (principles of protein isolation, micropipettor usage and calculations).
  • Final Exam: One 100-point exam will be administered covering experiments, calculations and principles/theory covered in the laboratory. The exam will consist of calculation problems, and applications and theory of experimental techniques.

Quizzes and the final exam are closed-book and closed-notes. Bonus point questions are likely on all quizzes/exam! There are no make-up tests given for a missed quiz/exam.

  • Peer Reviewed Report: (75 points) will be based on a peer reviewed article assigned to the student. This report will be evaluated for understanding of biochemistry concepts and methods on assigned peer reviewed paper. 1000 words.
  • Lab reports: Two lab reports will be turned in throughout the semester, each worth 100 points. Each report must be typed and strictly follow the guidelines given to you by the instructor. In addition, you must take each of your reports to the Writing Center (N 925) for proofreading. If you do not present proof of this by the due date of your report, you will be penalized five points on your report’s total grade. Lab reports are to be done individually! Late reports will not be accepted. All lab reports must be turned in for the course. More on this in relevant class meetings. 

If you do not turn in the lab reports, you will not pass this course.

  • Lab Report Structure: double space
    • Lab Report 1: (At least 2,000 words not including data and references)
      • Intro – 30 points
      • Methods – 10 points
      • Results – 30 points
      • Discussion – 30 points
  • Lab Report 2: (At least 3,000 words not including data and references)
    • Abstract – 5 points
      • Intro – 30 points
      • Methods – 5 points
      • Results – 30 points
      • Discussion – 30 points

Writing Guidelines for Lab Reports:

  1. Lab reports must be written professionally
    1. Avoid using active voice and the first person in writing (i.e. “I used …” or “we isolated..”).
    1. Must be written in 3rd person, use passive voice (i.e. “the solution was heated”).
    1. Avoid use of pronouns and weak words (got, be, it, they, that, etc).
    1. Edit your work for poor grammar, typos, spellings and imprecise terms.
  • Use precise terminology and appropriate vocabulary for discipline.
    • Every word and every sentence should be scrutinized as essential to the communication of the results and findings with an eye towards clarity, rigor, and precision.
    • Use biochemically precise and appropriate terminology.  For instance, do not call AP a molecule when it should be called a protein.
    • Use specific and precise language in describing what was done (avoid vague terminology and phrasing). For example, do not write “appropriate amount” – write “10 mls of….”; or do not write “closer results…”; instead, “our results may have given greater rates of catalysis if…..” Write biochemically specific sentences. For example do not write “certain parameters”. Instead please specify all the parameters. Do not write “negative results” unless you have defined what negative results are.
  • Clear and concise writing
    • No exposition, no flowery language in your scientific writing.
    • Please do not be wordy or repetitious!
    • Do not write that the experiments were a success without having comparing it to some quantifiable standard for success.
    • If a step requires particular diligence, do not just say that the diligence is required for the “experiment to work” – explain the biochemical reason with rigor and precision.
    • Figures and tables MUST have a detailed legend describing what is in the figure or table, without the need to dig through the text to figure it out.
    • Follow a logical flow in your scientific writing. For example in describing a biochemical experiment, start with the rationale of experiment followed by detailed experimental set up, results, conclusions and finally discussion.
  • Verb tense and prepositional phrases.
    • Use correct verb tense. Use past tense in explaining the experimental procedure and present tense in describing the theories and purpose of report.
    • Avoid the use of slang and the use of contractions. For instance do not include words like ‘wasn’t’ and didn’t. Instead write ‘was not’ and ‘did not’.
    • Do not use semicolons. Use two complete sentences instead.
    • Prepositional phrases at the beginning of the sentence tend to cause the main point to be lost. Avoid using prepositional phrases to be concise.
  • Use peer-reviewed sources for research.
    • NO QUOTES at all. This can be regarded as a sign of laziness or poor time management.
    • Unofficial websites that are not peer-reviewed and textbooks should be avoided.
    • Online scientific and medical journals are acceptable sources.
    • Cite your sources properly. Use parenthetical citations within your report (Author date). Format your references as:  Last name and initials, year, title, journal, volume, pages or retrieved from: (web page).

Tentative Course Schedule:

DateTopics Covered                         Reading AssignmentGroupNotes/Assignment Due  
Jan 19th    Discussion of Course policies and Structure Laboratory Safety and  Ethics Writing Lab Reports Calculations Test Lockdown BrowserChapter 2 Online      
Jan 26th    Measurements and Dilutions Making solutionsTheory of AP Isolation days 1-3Chapters 2, 5, 7, and 9 Quiz 1 – Calculations  
Feb 2nd  Training with micropipettes BCIP test Protein gel Electrophoresis of Alkaline PhosphataseChapters 2, 5 and 6  A, BQuiz 2- Take home; safety Due at 11:59 pm, Blackboard Turnitin)  
Feb 9th  Training with micropipettes BCIP test Protein gel Electrophoresis of Alkaline PhosphataseChapters 7 and 9C, DF2F    
Feb 16thQuantification of Alkaline PhosphataseChapters 3 and 7  A, BF2F
Feb 23rd   Quantification of Alkaline PhosphataseChapters 3 and 7  C, DF2F Peer Review Summary Due (at 11:59 pm, Blackboard Turnitin)  
Mar 2nd Intro to Enzyme Kinetics  Chapters 8 and 10 Online Quiz 3 – Isolation of AP (Days 1-3)    
Mar 9thReview for LR1 Data Analysis  Chapters 3 and 7 Online Peer Review Group Discussion        
Mar 16thSpring Break- No Classes    
Mar 23rdEnzyme Kinetics of Alkaline Phosphatase @ pH 7 and 8.0Chapters 8 and 10 A, BF2F Lab Report # 1 Due Date (at 11:59 pm, Blackboard Turnitin)
Mar 30th Enzyme Kinetics of Alkaline Phosphatase @ pH 7 and 8.0  Chapters 8 and 10C, DF2F  
Apr 6th Data Analysis Discussion of AP kinetics results Review for Final and LR2Chapters 8 and 10 Online Quiz 4 – Calculations, Theory of protein isolation, Micropipetting  
Apr 13thGroup Presentation     All GroupsOnline    
April 20thFinal Exam                Laboratory calculations                SDS-PAGE                Kinetics  Online      
Apr 27th   No Class  Lab Report # 2 Due Date (at 11:59 pm, Blackboard Turnitin)  

I RESERVE THE RIGHT TO CHANGE ANY PART OF THIS SYLLABUS OR COURSE POLICY TO MORE EFFECTIVELY MEET THE NEEDS OF THE STUDENTS.

Dropping or withdrawing from this course is as per University policy.  All students are subject to the UHD Academic Honesty policy, the course syllabus, and all University-wide policies set forth in the University Catalog and Student Handbook. Academic dishonesty, particularly with respect to exams and papers will result in automatic failure for the class (an immediate hold will be placed such that a W will be not be allowed).

Campus Carry:

As of August 1, 2016, the “Campus Carry Law” (SB 11) is in effect on the UHD campus.  Any individuals who hold a current and valid License to Carry may carry a concealed handgun on or about their person, where permitted on UHD property.  Certain areas of campus have been designated as gun-free areas, and there are notices or signs at those locations. 

Please refer to the UHD Campus Carry Policy (https://www.uhd.edu/administration/employment-services-operations/resources/Documents/PS01A16.pdf) for a list of the areas designated as gun-free and to understand your rights and responsibilities under the policy. 

NOTE THAT STB322/349 IS DESIGNATED AS A GUN-FREE AREA.

Disabled Students: The University of Houston-Downtown complies with Section 504 of the Rehabilitation Act of 1973 and the Americans with Disabilities Act of 1990, pertaining to the provision of reasonable academic adjustments/auxiliary aids for students with a disability.  In accordance with Section 504 and ADA guidelines, UHD strives to provide reasonable academic adjustments/auxiliary aids to students who request and require them.  If you believe that you have a documented disability requiring academic adjustments/auxiliary aids, please contact the Office of Disability Services, One Main St., Suite 409-South, Houston, TX 77002.  (Office) 713-226-5227 (Website) www.uhd.edu/disability/ (Email) disabilityservices@uhd.edu

Zoom Policies

This class will include required and optional virtual meetings. Whether meeting with classmates or the instructor, we will follow the guidelines below to maximize opportunities for all to engage and to provide a supportive environment:

  • While camera presence is not required for general class meetings, please consider using the camera whenever possible. You can use a virtual background following these instructions: virtual background for Zoom
  • Regardless of camera presence, everyone must include a photo and name visual when participating in live sessions. Look here for how to do this: customize Zoom
  • Full attention must be given during live sessions to the virtual meeting—be prepared to respond to chat, surveys, audio discussion, or other requested engagement during the entire session.
  • If we are using breakout rooms, be sure to accept the room assignment and participate actively in the task.
  • If you need to step away to handle a critical issue in your environment, send a private chat note to the instructor and indicate when you return. Do not disconnect from the session during this time unless you have indicated that you cannot return.
  • Respect the group by being on time and managing your volume, chat, and visual presence (use mute when not talking, do not use distracting or inappropriate background images, etc.)
  • If the instructor drops off or the virtual meeting ends unexpectedly, wait 5 minutes andtry to reenter the meeting. If that is not successful, check your Gatormail and class BB shell for information and instructions.
  • If your own connection drops during a class meeting or session, as soon as possible try to reengage and send a private chat note to your instructor. If you cannot reengage, email your instructor as soon as possible to explain what happened and ask what you missed. You may be required to carry out specific tasks to make up the absence.
  • Make a note of the meeting ID and passcode before you join via computer; if your connection fails, try to rejoin using a cell phone.
  • Specific course assignments and/or exams may require live video. I, as the instructor, will provide this information to you in advance of the assignment due date. If you have a concern regarding any requirement to participate in live video for specific course learning outcomes, please contact me as soon as possible to determine whether alternatives are available.

COVID-19 Policies

1. University Requirements: Disruptions, COVID Reporting, and Safety

To address issues related to disruption of university functions, COVID reporting, and safety protocols, as well as mandatory engagement with classes by the 10th class day, UHD has prepared a general set of requirements that can be found HERE.

These requirements are part of the expectations for this course. Any updates to the website will be communicated to students via their Gatormail accounts.

2. UHD Student Support Services

UHD has developed many resources to support your learning. We have developed a website that will offer a “one stop shop” for access to many of the resources you might need this semester to support your educational goals. Please access this website to get started: https://tinyurl.com/SSR2020. If you do not find the resource you need on this website, please contact your instructor, who will make every effort to connect you with the help you need.

3. Accessibility and Statement of Reasonable Accommodations

The University of Houston-Downtown (UHD), is committed to creating a learning environment that meets the needs of its diverse student population. Accordingly, UHD strives to provide reasonable academic accommodations to students who request and are eligible, as specified by Section 504 and ADA guidelines. Students with disabilities may work with the Office of Disability Services to discuss a range of options to removing barriers in this course, including official accommodations. If you have a disability, or think you may have a disability, please contact the Office of Disability Services, to begin this conversation or request an official accommodation. Office of Disability Services, One Main St., Suite GSB 314, Houston, TX 77002. (Office Phone) 713-221-5078 (Website) www.uhd.edu/disability/

(Email) disabilityservices@uhd.edu

4. Face Masks

Every individual must wear a face covering while in university buildings or facilities.

Please see the UHD FAQs on face masks for more information.

Plagiarism & Academic Honesty Policy

All students are subject to the UHD Academic Honesty Policy and all University-wide policies set forth in the University Catalog and Student Handbook. Specifically, the UHD Academic Honesty Policy (PS 03.A.19) states that “Students must be honest in all academic activities and must not tolerate dishonesty”. We highly encourage you to read PS 03.A.19 carefully; it is available online at www.uhd.edu.

The most common forms of academic dishonesty violations are cheating and plagiarism. Plagiarism is minimally defined as using the work or ideas of another in your own work without giving credit to the original source. It is also cheating if you and another student have the exact same sentences or answers or demonstrate any form of unacceptable collaboration. The UHD Academic Honesty Policy specifically states:

“Plagiarism includes, but is not limited to:

Directly quoting the words of others without using quotation marks or indented format to identify them.

Using sources of information (published or unpublished) without identifying them.

Paraphrasing materials or ideas of others without identifying the sources”

The UHD Academic Honesty Policy goes on to state that “Cheating includes, but is not limited to:

Submitting material that is not one’s own

Using information or devices that are not allowed by the faculty member

Obtaining and/or using unauthorized material”

Submitting substantially similar material in more than one course, even if it is one’s own work,    without the instructor’s permission.

The UHD Academic Honesty Policy also notes: “The penalty for academic honesty violation on a significant course requirement such as a term paper/project or final examination shall be an “F” for the course. The penalty for academic honesty violations in other coursework will be left to the discretion of the faculty member…”

Plagiarism is unacceptable in all forms as it (a) represents theft of the creative work of others and (b) an unwillingness by the student to fully engage in a fundamental goal of this course – the development of professional writing skills.

This document represents your one and only warning against plagiarism and cheating.

For all written assignments, the following general rules apply:

1) The only legitimate and credible sources and information that you may use are peer-reviewed publications listed on PubMed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed), and other websites run by NCBI, OMIM and ExPASY or similar websites explicitly approved by the instructor. Websites such as Ask.com, etc… are not credible scientific resources. Use of these sources in my course(s) will result in the loss of a full letter grade on the assignment for each infraction.  (Wikipedia may be used if the material can be verified by other sources.  If you are in doubt, ask the instructor.)

2) Information obtained from allowed sources must be cited within your writing, included in full bibliographic form in a bibliography/references section of your writing, and each source must be available to me electronically (e.g., through the UHD Library subscriptions or open access) or provided to me electronically or in hard copy upon submission of the assignment. 

3) Use of direct quotations is strictly forbidden. The use of direct quotes is reserved for unique passages of deep substance that linguistically has unique meaning – this happens in scientific writing only very rarely.  In student writing this action usually indicates an unwillingness of the student to work to develop her/his own voice or an unwillingness to think independently.  Ideas borrowed from credible and allowed resources should be paraphrased in your own words and cited appropriately.

4) All assignments must be turned in electronic format on Blackboard Learn via Mail.

5) Students must run all written assignments through the Plagiarism detection software, Turnitin, available in BbL, and the report generated by the software submitted with the assignment. This software is available to students through the University.  Any plagiarism detected by the software must be eliminated prior to turning in the assignment.  Work submitted without the Turnitin report will not be graded.

I have software designed to catch plagiarism. I will enter the electronic version of your assignments into this software to search for plagiarism.

If you violate any tenet of Academic Dishonesty, you will fail this course, not just the assignment.

UHD and other web resources have guidelines for identifying and avoiding plagiarism in your writing. I highly encourage you visit these sites. When in doubt, ask me directly, or simply do not use the source or take the chance of inadvertently plagiarizing.

You must acknowledge that you have read, understand, and accept the policies in this document by signing the statement below.  You first assignment will not be accepted without this completed form, and as such considered late until this is turned in.

Turn in:

Sign below and turn in this portion BEFORE the Second Class meeting. 

I, ____________________________________________ [print name, legibly], have read the attached document and understand the consequences for an academic honesty violation in this course. The first plagiarism or cheating violation will result in my failing of the course.

Signature: ____________________________________________________________________

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