Chem 221 Biochemistry Information and Syllabus, Spring 2017

  • Kim-Lien Thi Dinh, Assistant Professor of Chemistry, Los Angeles City College
  • Email: dinhkt@lacitycollege.edu, phone: 323.953.4000 x 1602 (please leave a message)
  • Spring 2017 Office Hours in SCI 324H: MW 12:30 pm – 1:35 pm, TTh 3:00 pm – 5:00 pm or by appt.

Section 0265

  • Lecture & Conference:  MW 1:45 pm – 3:10 pm, 3:20 pm – 4:20 pm (SCI 314)                 
  • Lab:  MW 4:30 pm – 6:35 pm (SCI 304) 

Prerequisites

  • Chem 211 with a minimum grade of “C” or equivalent.

Required Materials

  • Text: Biochemistry: Concepts and Connections by Appling (Pearson 2016)
  • Safety goggles, even if you wear glasses! Like these or theselab coat, closed-toe shoes, protective gloves, hot mitt or dishtowel.
  • Scientific calculator, need logarithm functions and scientific notation keys. No graphing calculator, no sharing.  Something like this or similar will work.
  • Laboratory Experiments
  • Lab notebook, the kind with carbonless duplicate pages, 50 or 100 pages.
  • Scantrons, form 882-E
  • Safety quiz, completed and turned in to lab instructor by the second class meeting.
  • 221 Lab Check-in Sheet, printed and filled out on the day of lab check-in.

Optional

  • Write Like a Chemist by M. Robinson
  • ChemDraw structure drawing software by CambridgeSoft (request student pricing) or other chemical structure drawing software. 

Grading

A total of 1000 points are possible as indicated below:

  • Final (comprehensive), 250 points
  • Exams (2, 150 points each), 300 points
  • Quizzes (4, 25 points each), 100 points
  • Presentations (2, 50 points each), 100 points
  • Laboratory Work (normalized total), 250 points

Course grades* will be assigned according to the following breakdown:

A 85.0-100%        B 75.0-84.9%       C 60.0-74.9%       D 50.0-59.9%       F less than 50%

*LACC does not have a +/– grading system.  Only A, B, C, D, F, I**, W, P/NP will be used.

**Incomplete academic work for unforeseeable emergency and justifiable reasons at the end of the term may result in an “I” symbol being entered in a student’s record.  The “I” must be made up no later than one year following the end of the term in which it was assigned.  The policies can be found here.  Further more, the following will be applied.  You must currently be passing the course for an incomplete.  You must satisfactorily complete 7 out of the 7 laboratory assignments.  A score of “0” will be recorded for any unfinished assignments and can not be made up.  You must have completed all exams and 3 out of 4 quizzes. A score of “0” will be recorded for the 4th quiz and can not be made up. The final must be taken within a year and a letter grade will be recorded after its completion. Do not assume you will be granted an incomplete without consulting with me first. 

Course Description: Chemistry 221 is a short course in biochemistry for science majors but not usually for those pursuing a B.S. degree in Chemistry or Biochemistry.  The course is accepted by pharmacy and health professional programs unless the specific requirement is an upper division biochemistry class.  The course covers the chemical structure and function of the major classes of biomolecules: proteins, carbohydrates, lipids and nucleic acids.  It also reviews bioenergetics and the main metabolic pathways, both catabolic and anabolic.  Laboratory work includes isolation and characterization of biomolecules by qualitative and quantitative methods, assays of enzyme kinetics, graphical analysis of data, individual report writing, and oral presentation of work on current topics of interest in biochemistry.

Student Learning Outcomes:  On completing this course, students will:

  • Understand the chemical nature of the building blocks of the 4 major classes of biomolecules (protein, polysaccharide, lipid and nucleic acid) and be able to construct a segment of the polymer for any of these.
  • Understand the main metabolic pathways that maintain living organisms.

Financial Aid:  If you need help paying for books and other college expenses, call the Financial Aid Office at (323) 953-4000 ext.2010.

Academic Integrity: All students at LACC are expected to follow the rules of ethical conduct stated in the Student Policies section of the Schedule of Classes.  The complete schedule of classes in PDF format is found here.

Information for Students with Disabilities: Students with a verified disability who may need authorized accommodation(s) for this class are encouraged to notify the instructor and the Office of Special Services (SSV 100, 323-953-4000, ext. 2270) as soon as possible.  All information will remain confidential.

Audio/video recording is not permitted unless accommodation letter states otherwise.

Cheating will not be tolerated!  Violations of academic integrity include, but are not limited to, the following actions: cheating on an exam, plagiarism (the act of copying another’s written work and submitting it as your own), faking or falsifying experimental data, copying another’s lab report, data, and published work, working together on an assignment, paper or project when the instructor has specifically stated students should not do so, submitting the same term paper to more than one instructor, or allowing another individual to assume one’s identity for the purpose of enhancing one’s grade (see LACCD Board Rule 9803.28). Such actions (which are often illegal in the “real world”) may result in a grade of zero on an exam or paper, and suspension or dismissal from the course and the college. These consequences will also apply to those that help others cheat.  

Drop Date Information!  For classes from 2/6/17 to 6/5/17, the deadline to drop without a “W” on your transcript is Monday, February 20, 2017. Effective July 1, 2012 students are allowed three (3) attempts to pass a single class within the Los Angeles Community College District. If a student gets a “W” or grade of “D”, “F”, or “NP” in a class, that counts as an attempt. If you think you will not be able to complete this course with a C or better, drop by Sunday, May 7, 2017. If the class begins or ends on a different date, please refer to Admissions Important Dates page.  If you have any questions, please don’t hesitate to talk to me.  You may also see a counselor in the Counseling Center in AD 108. 

You will be excluded (dropped) from the course for any one of the following:  If you missed the first meeting of class, if you are absent more hours than the number of hours the class meets per week, or if you do not enroll in Canvas. However, you should not assume that the instructor will drop you. It is your responsibility to formally withdraw from the class through Admissions and Records should you decide you no longer wish to be enrolled, otherwise you will receive an “F” in the course. I do not exclude students once they have attended class and have turned in assignments. If you are absent, it is your responsibility to make sure work is handed in on time and to find out what you missed in class.

Computer Resources: The Chemistry and Earth Sciences Department has a computer classroom located in SCI 316.  The classroom is normally open 8:00 AM – 10:00 PM Monday-Thursday.  If the room is locked, you can ask one of the faculty or lab technicians to open it for you.  This classroom can be reserved for class meetings by department faculty.  If the classroom is unavailable, the all-campus computer lab for student use is located on the second floor of the Martin Luther King Library and is available during the library’s normal business hours.  Please contact ext. 2396 for more information about the all-campus lab.  For information about computer access, including information regarding computer login, email accounts and wireless access, please go to the following site.

Policy on Cell Phones and other Electronic Devices:  The use of cell phones or any other electronic devices for any purpose, including smart phone calculator apps, on exams/quizzes is prohibited.  All phones are to be turned off during exams and stored.  Students caught using phones during exam may be subject to receiving a score of “0” on the exam/quiz and referral for further disciplinary action.

Description of Coursework

Final: Everyone, regardless of grade at the time, is required to take the final examination. The date is listed in the schedule below. Failure to take the final will result in an automatic fail for this course, regardless of your grade prior to the final. The final will not be returned to you. Your score will be posted in Canvas.

Exams: Two exams will be given and no scores will be dropped. The dates are listed in the schedule below. The exam starts at the beginning of lecture and if you are late to an exam, you will have the remainder of that time to complete your exam. If you need to make-up an exam or both exams, a penalty of 20%, per day-weekend counts, will be assessed for the first exam take late, and a larger penalty, 40%, per day, for any additional exam that needs to be made up. Once an exam has been returned and reviewed (2-7 days), there will be no more make-up. It is your responsibility to re-schedule your exam, not your instructor’s. Send an email and I will confirm the date, time, and location of your make-up exam. If you do not show up, a score of “0” will be recorded and no further make-up will be allowed.

Quizzes: Four quizzes will be given and no scores will be dropped.  The dates are listed in the schedule below. There are no make up.  Each quiz starts at the beginning of class and if you are late, you will have the remainder of that time to complete your quiz.

Presentations:  Each student will have two oral presentations, a presentation of the structure and function of a polypeptide (10 minutes), and a presentation on the molecular basis of a genetic or metabolic disease (15 minutes).  The presentation date, time, and topic are listed the schedule below.  You have been pre-assigned to the presentations but you may trade with a willing classmate if it conflicts with your schedule, but no more than two students may present in any given day or have the same presentation topic. Only if time permits, a make up is allowed and a 40% penalty will be applied. An iPad and a laser pointer are available. You will need to save your presentation as a pdf in Dropbox before your presentation starts.  If you want to use your own computer, you will need a VGA adaptor for the projector.

Laboratory work:  The laboratory component is designed to give you hands-on experience with some of the concepts learned in lecture. All laboratory experiments and reports are done independently by each individual. There will be no makeup labs. You must satisfactorily complete all laboratory assignments in order to achieve a grade of “C” or higher, regardless of total score.  Completing lab consists of performing the experiment and handing in the lab report.  Typed lab reports are due one week from the date the experiment is completed.  There is a 20% penalty for each day that your report is late (weekend counts).  After a report has been graded and returned, you will only receive one point for that assignment, but it counts as being completed.  All chemical structures in lab reports and presentations must be electronically drawn, no hand-written insertions.  ChemDraw is installed on the department’s computers.  Please schedule time to learn the software and to use it at LACC if necessary. No points will be credited to one student for lab work completed by another student; that is cheating. 

Safety goggles are to be worn by all students in the laboratory at all times.  Students who repeatedly are found not wearing goggles (to protect their eyes) will be subject to removal from the laboratory for that entire period.  

You are responsible for all of the equipment in your locker. You will lose two points for each equipment you break or lose. It is best not to share equipment, and if you absolutely must share, be sure to return any shared equipment to your locker before you leave for the day.  Make sure you have put away all equipment and locked your drawer before leaving. 

All students are required to keep a lab notebook. The notebook must have carbonless duplicates. You are required to prepare your notebook for data collection prior to coming to class. You will record all data directly in your notebook and you will turn in the carbon copies of your data sheets. Notebook policies are described in more detail here

You are responsible for printing out your experiments prior to coming to lab.  I will not print them for you.

For each minute you stay after lab is over (at 6:35 pm), you will lose two points. Please set a timer so that you have enough time to clean up. Everyone is responsible for cleaning up the lab, 10 points will be deducted if you don’t.

Enrollment in Canvas is mandatory!  I do not use eTudes, Blackboard, or Moodle.  This program serves as my course management system.  You will not have any recorded scores until you enroll.  Graded and returned work are your responsibility. 

Study Guides for Exams and Extra Credit:  There are none, please don’t ask.  

Chemistry 221 Tentative Lecture, Conference, and Lab Schedule

Your instructor reserves the right to alter this schedule, including exam and quiz dates. 

Wk Date Lecture Topics Conference

Student Pres: Polypeptide (10 min) Grading Rubric and Peer Review

Student Pres: Molec Basis of Disease (15 min) Grading Rubric and Peer Review

Laboratory
1 M 2/6 Ch 1 Intro to Biochemistry none none Safety Video, Safety Quiz, Writing 101
W 2/8 Ch 2 – Weak Interactions in Aqueous Environment none none Exp 01-pH and Buffers – pH measurement, buffer preparation
2 M 2/13 Ch 3 – Energetics of Life none none Check-In

pH and Buffers – pH measurement, buffer preparation

W 2/15 Ch 5 – Amino Acids P1-chymotrypsin D20-Cystic fibrosis pH and Buffers – buffer properties and titration
3 M 2/20 Holiday
W 2/22 Ch 6 – 3D Structure of Proteins P2-catalase D19-Hemophilia A pH and Buffers – titration
4 M 2/27 Quiz 1:   Ch 1, 2, 3

Ch 7 – Protein Function

P3-hemoglobin D18-Achondroplascia Exp 02-Amino Acid Titration – determination of the pK’s of an amino acid
W 3/1 Ch 8 – Enzymes P4-hexokinase D17-sickle cell anemia Amino Acid Titration – complete titration; graphical analysis
5 M 3/6 Ch 9 – Carbohydrates: Sugars, Saccharides, Glycan P5-carbonic anhydrase D16-galactosemia Amino Acid Titration – graphical analysis
W 3/8 Ch 10 – Lipids, Membranes & Cellular Transport P6-myoglobin D15-lactose intolerance Exp 03-Protein Purification – Virtual Lab (in Canvas)

Note: You can use this day to work on Exp 2.

6 M 3/13 Quiz 2:   Ch 5, 6, 7, 8

Ch 11 – Metabolism

P7-beta galactosidase D14-Tay-Sachs disease Exp 04-Enzyme Behavior – purification
W 3/15 Ch 12 – Carbohydrates Metabolism: Glycolysis, Gluconeogenesis none none Enzyme Behavior – purification and kinetic characteristics
7 M 3/20 Exam 1 Ch 1-9 none none Enzyme Behavior – complete purification; initial activity determination
W 3/22 Ch 12 – Carbohydrates Metabolism: Glycogen Metabolism & Pentose Phosphate Pathway P8-alcohol dehydrogenase D13-Gaucher’s disease Enzyme Behavior – assay and effect on an inhibitor
8 M 3/27 Ch 13 – Citric Acid Cycle P9-pyruvate carboxylase D11-Fragile X syndrome Enzyme Behavior – assay and effect on an inhibitor
W 3/29 Ch 14 – Electron Transport, Oxidative Phosphorylation, and Oxygen Metabolism P10-cytochrome c D12-trimethylaminuria Enzyme Behavior – assay and effect on an inhibitor
Spring Break Sat 4/1- Fri 4/7
9 M 4/10 Ch 15 – Photosynthesis P11-insulin D10-neurofibromatosis (NF-2) Enzyme Behavior – assay and effect on an inhibitor
W 4/12 Quiz 3:   Ch 10, 11, 12, 13

Ch 16 – Lipid Metabolism

P12-RuBisCO D9-Wilson’s Disease     Exp 05-Isolation of Nutmeg Lipid – isolation and purification of triglyceride
10 M 4/17 Ch 17 – Interorgan & Intracellular Coordination of Energy Metabolism in Vertebrates P13-myosin D8- Porphyria Isolation of Nutmeg Lipid – isolation and purification of triglyceride
W 4/19 Ch 18 – Amino Acid & Nitrogen Metabolism P14-tyrosine aminotransferase D7-Maple syrup urine disease Isolation of Nutmeg Lipid – saponification, characterization
11 M 4/24 Ch 4 – Nucleic Acids P15-actin D6-Lesch-Nyhan syndrome Isolation of Nutmeg Lipid – melting point determination
W 4/26 Ch 19 – Nucleotide Metabolism P16 aminoacyl-tRNA synthase D5- Retinoblastoma Exp 06-β-Carotene – isolation & extraction
12 M 5/1 Quiz 4:   Ch 14, 15, 16, 17

Ch 20 – Mechanisms of Signal Transduction

P17-glutamine synthetase D4- Osteogenesis imperfecta β-Carotene – UV/VIS scan
W 5/3 Ch 21 – Genes, Genomes, and Chromosomes none none β-Carotene – UV/VIS scan
13 M 5/8 Exam 2 Ch 10-18 none none β-Carotene – spectrophotometric determination
W 5/10 Ch 22 – DNA Replication P18-RNA polymerase D3- VLCAD β-Carotene – spectrophotometric determination
14 M 5/15 Ch 23 – DNA Repair, Recombination and Rearrangement P19-EcoRV restriction endonuclease D2- Crigler-Najjar syndrome Exp 07-Carbohydrates – qualitative characteristics
W 5/17 Ch 24 – Transcription & Post-Transcriptional Processing P20-acetylcholinesterase, AChE D1- Ellis-van Crevald syndrome               Carbohydrates – hydrolysis and analysis
15 M 5/22 Ch 25 – Translation & Post-Translational Protein Processing none none Carbohydrates –analysis
W 5/24 Ch 26 – Regulation of Gene Expression none none Carbohydrates –analysis

Check Out

16 M 6/5 Cumulative Final Monday June 5 2:30 – 4:30 pm, SCI 314