UTD Instrumental Analysis: Academic Fall 2021 Syllabus PDF

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This document will show the academic syllabus for CHEM 3472 (Instrumental Analysis). This contents in this document contain the standards that are expected to be held being within the class, the dates and assignments of when they are due, and the grading system for the class....

Description

Course Syllabus – Fall 2021 ________________________________________________________________ Course Information BIOL/CHEM 3361 section 001 Biochemistry 1

Fall 2021 MWF, 3.00-3.50pm, SCI 1.220 ________________________________________________________________ Professor Contact Information Dr. Lin Jia, BSB 12.510, [email protected] Dr. Stephen Spiro, RL 2.708, [email protected] Office Hours Dr. Jia: Tuesday and Thursday, 11am - noon Dr. Spiro: Tuesday and Thursday, 11am - noon ________________________________________________________________ Course Pre-requisites, Co-requisites, and/or Other Restrictions CHEM 2323 (or equivalent); CHEM 2325 (or equivalent). Concurrent registration in Biochemistry Workshop I (BIOL 3161, Sections 001 – 014) is required for both BIOL and CHEM 3361 students. ________________________________________________________________ Course Description Structures and chemical properties of amino acids; protein purification and characterization; protein structure and thermodynamics of polypeptide chain folding; catalytic mechanisms, kinetics and regulation of enzymes; energetics of biochemical reactions; metabolism; roles of coenzymes and prosthetic groups in redox reactions; pathways for carbohydrate oxidation; glycogen metabolism; glucose synthesis; electron transport and oxidative phosphorylation. ______________________________________________________ Student Learning Objectives/Outcomes This undergraduate core course is the first of a two-course sequence that provides students with a working knowledge of the macromolecules and fundamental metabolic pathways of prokaryotes and eukaryotes, with emphasis on human systems. Biochemistry I is devoted to mastering: 1) the structure and function of amino acids and proteins, and 2) central metabolism and energy conservation, as a means of understanding biological processes in general and developing problem-solving skills in biochemistry. Fundamental thermodynamic principles that drive life processes and the regulatory mechanisms that fine-tune them are stressed to provide the rationale and framework for students to master the necessary molecular structure and pathways. Relevance to human physiology, medicine, and genetics is used to stimulate students to begin the integration of biochemistry with other disciplines.

Course Syllabus

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At the end of the course, students will be able to: 1. Explain the basic thermodynamics governing biochemical reactions and use this information to solve problems involving biochemical thermodynamics. 2. Recognize the molecular structures and describe the chemical properties of proteins, their amino acid residues, and carbohydrates; and solve related pH problems. 3. Explain enzyme catalysis and regulation and apply enzyme kinetics in problem solving. 4. Describe the central pathways for the catabolism of glucose and complex carbohydrates, and gluconeogenesis, and apply them in problem solving. 5. Understand the organization of electron transport chains and the different mechanisms for ATP synthesis, and apply them in problem solving. ________________________________________________________________ Required Textbooks and Materials R.H. Garrett and C.M. Grisham: Biochemistry, 6h edition, from Cengage Learning. eBook Purchasing Options: 1. Direct purchase through Blackboard Click on the “eBook” link on the left navigation of your course homepage on eLearning/BbCollaborate. When you purchase the Cengage eBook directly through Blackboard, you will not need an ISBN. OR 2. Purchase through Bookstore When you purchase through the bookstore, you will purchase Cengage Unlimited eTextbooks ISBN 9780357693933 The text is available either alone or bundled with OWLv2. OWLv2 is an online set of study materials for each of the 15 chapters covered in the course, which you may wish to use. To register and log in go to login.cengagebrain.com. If you need an ID, use your UTD net ID. The OWLv2 questions will NOT be graded by UTD staff, and OWLv2 is NOT required for the course. But, it may be cheaper to buy the text with OWLv2, rather than the text alone. Textbooks and some other bookstore materials can be ordered online or purchased at the UT Dallas Bookstore. ___________________________________________________________

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Classroom Safety and COVID-19To help preserve the University’s in-person learning environment, UT Dallas recommends the following: Adhere to the University’s CDC Updated Guidelines (https://evites.utdallas.edu/coronavirus/43.html) issued on July 30, 2021. All Comets are strongly encouraged to wear face coverings indoors regardless of vaccination status. Please note this represents a change in the campus guidance (https://evites.utdallas.edu/coronavirus/39.html) issued on May 20, 2021. See the end of the syllabus foradditional Covid information and resources. Arrangements for the first three weeks of the semester. As you know, we are required to occupy the lecture room at a reduced density for at least the first three weeks of the semester. Please attend class in-person as follows: Last name A through Ji Jo through Pas Pat through Z

In person attendance Monday Wednesday Friday

So, if your last name is Jimmy you should attend class in-person on Monday, if your last name is Joanne, you should attend class in person on Wednesday, and so on. It is essential that you comply with this pattern so that we can maintain the appropriate density in the classroom, and in case there needs to be any contact tracing done. On days when you do not attend in-person, class will be live streamed vis MS Teams. The link for the live stream (also posted on eLearning) is: https://teams.microsoft.com/l/meetupjoin/19%3ameeting_YjliY2YxM2EtN2RlNi00ZWU3LTg1MjYtOWM4ZDIyNDdhNT Ji%40thread.v2/0?context=%7b%22Tid%22%3a%228d281d1d-9c4d-4bf7-b16e032d15de9f6c%22%2c%22Oid%22%3a%22899907ba-b9c7-470d-b8a9e0adf6f782c7%22%7d

Course Syllabus

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Assignments & Academic Calendar DATE Mon Aug 23 Wed Aug 25 Fri Aug 27 Mon Aug 30

TOPIC(S) Lecture 1: Introduction Lecture 2: Weak interactions / Water Lecture 3: Acid/Base Properties Lecture 4: Thermodynamics of Biological Systems I

Wed Sep 1

Lecture 5: Thermodynamics of Biological Systems II

Fri Sep 3

Lecture 6: Thermodynamics of Biological Systems III / Hydrophobic interactions

Mon Sep 6 Wed Sep 8 Fri Sep 10

LABOR DAY Lecture 7: Amino Acids I Lecture 8: Amino Acids II

Mon Sep 13

Lecture 9: Protein Purification and Characterization I Lecture 10: Protein Purification and Characterization II PS1 due Exam 1 Lecture 11: Proteins: Primary structure, Sequencing and Mass spectrometry I Lecture 12: Proteins: Mass spectrometry II, Sequence Alignments and Structures Lecture 13: Protein Structure and Protein Folding

Wed Sep 15 Fri Sep 17 Mon Sep 20 Wed Sep 22 Fri Sep 24 Mon Sep 27

Wed Sep 29 Fri Oct 1 Mon Oct 4 Wed Oct 6 Fri Oct 8 Mon Oct 11 Tue Oct 12

Lecture 14: Enzyme kinetics I Lecture 15: Enzyme kinetics II and Inhibition kinetics I Lecture 16: Inhibition kinetics II Lecture 17: Bisubstrate Reactions Lecture 18: Enzyme mechanisms I Lecture 19: Enzyme mechanisms II PS2 due

Course Syllabus

Book Chapter Chap 1 Chap 1 & Chap 2 Chap 2 Handout on eLearning as substitute for Chap 3 Handout on eLearning as substitute for Chap 3 Handout on eLearning as substitute for Chap 3

Instructor Jia Jia Jia Jia

Chap 4 Chap 4

Jia Jia

Chap 4.7 & 5.1-5.2, 5.7-5.8 Chap 4.7 & 5.1-5.2, 5.7-5.8

Jia

Jia

Jia

Jia

Chap 4.7 & 5.3-5.6; Chap 6 Chap 4.7 & 5.3-5.6 Chap 6 Chap 6 and Chap 31.1 on pp 1132-1140 Chap 13 Chap 13

Jia

Jia Jia

Chap 13 Chap 14 Chap 14 Chap 14

Jia Jia Jia Jia

Jia Jia

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Wed Oct 13 Fri Oct 15 Mon Oct 18 Wed Oct 20 Fri Oct 22 Mon Oct 25 Wed Oct 27 Fri Oct 29 Mon Nov 1 Wed Nov 3 Fri Nov 5 Fri Nov 5 Mon Nov 8 Wed Nov 10 Fri Nov 12 Mon Nov 15 Wed Nov 17 Fri Nov 19 Nov 22-24 Fri Nov 26 Mon Nov 29 Wed Dec 1 Fri Dec 3 Mon Dec 6 Mon Dec 6 Mon Dec 13

Exam 2 Lecture 20: Enzyme regulation Lecture 21: Enzyme regulation II Lecture 22: Allostery in hemoglobin Lecture 23: Introduction to metabolism Lecture 24: Carbohydrates Lecture 25: Glycolysis I Lecture 26: Glycolysis II Lecture 27: Glycolysis III Lecture 28: Gluconeogenesis Lecture 29: Glycogen metabolism PS3 due Exam 3 Lecture 30: Pentose phosphate pathway Lecture 31: TCA cycle I Lecture 32: TCA cycle II Lecture 33: TCA cycle III Lecture 34: Electron transport I FALL BREAK, NO LECTURES THANKSGIVING Lecture 35: Electron transport II Lecture 36: Electron transport III Lecture 37: ATP synthesis I Lecture 38: ATP synthesis II PS4 due Exam 4 (date subject to confirmation)

Chap 15 Chap 15 Chap 15 Chap 17

Spiro Spiro Spiro Spiro

Chap 7 Chap 18 Chap 18 Chap 18 Chap 22 (part 1)

Spiro Spiro Spiro Spiro Spiro

Chap 22 (part 2) Chap 22 (part 2) Chap 19 Chap 19 Chap 19

Spiro Spiro Spiro Spiro Spiro

Chap 20 Chap 20 Chap 20 Chap 20

Spiro Spiro Spiro Spiro

Undergraduate Teaching Assistants Hamza Dahshi [email protected] Rohan Jupelly [email protected] Elodie Tan [email protected] Rabia Ahmed [email protected] Eashana Arora [email protected] Caiden Golder [email protected] Radhika Vaishnav [email protected] Sara Taleb [email protected] Prabhleen Kaur [email protected] Prashanth Gowda [email protected] Ramtin Kohandel [email protected] James Widner [email protected] Pouya Modareszadeh [email protected] Parsa Modareszadeh [email protected]

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Graduate Teaching Assistants Rafah Falah Ibrahim Salaudeen Zakia Akter Nicholas Mercado Muneer Oladipupo Yaqub Dannie Zhabilov Shelby Phelps

[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected]

Workshop Sections BIOCHEMISTRY WORKSHOP I* Section Day Time Room 001 Tu Noon SCI 2.210 002 Tu 3.00pm CR 1.202 003 Tu 8.30am SLC 1.202 004 Tu 3.00pm SCI 2.230 005 Tu 4.00pm SCI 2.230 006 Wed 9.00am JSOM 11.202 007 Wed 3.00pm HH 2.502 008 Wed 4.00pm SLC 2.303 009 Th 8.00am SCI 2.210 010 Th Noon ECSS 2.201 011 Th 8.30am SLC 1.202 012 Fri Noon FO 3.616 013 Th 3.00pm CR 1.202 014 Th 4.00pm CR 1.202

TA Hamza Dashi Rohan Jupelly Elodie Tan Rabia Ahmed Eashana Arora Caiden Golder Radhika Vaishnav Sara Taleb Prabhleen Kaur Prashanth Gowda Ramtin Kohandel James Widner Pouya Modareszadeh Parsa Modareszadeh

Intern will organize a workshop section and needs to post materials and send email Workshop Schedule Week 1 Week 2 Week 3 Week 4 Week 5 Week 6 Week 7 Week 8 Week 9 Week 10 Week 11 Week 12

Course Syllabus

8/24 – 8/27 8/31 – 9/3 9/7 – 9/10 9/14 – 9/17 9/21 – 9/24 9/28 – 10/1 10/5 – 10/8 10/12 – 10/15 10/19 – 10/22 10/26 – 10/29 11/2 – 11/5 11/9 – 11/12

pH calculations, HH equation pH calculations, Thermodynamics Thermodynamics ; Protein purification Exam prep – No workshops Enzyme kinetics Enzyme kinetics; Enzyme mechanisms Protein structure Exam week – No workshops Enzyme regulation Metabolism; Carbohydrates Glycolysis and Gluconeogenesis Glycogen metabolism and TCA cycle

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Week 13 Week 14 Week 15

11/16 – 11/19 11/23 – 11/26 11/30 – 12/3

TCA cycle and electron transport Thanksgiving – No workshops ATP synthesis

________________________________________________________________ Grading Policy

Four (4) exams (20% each, 80% total) + adjusted workshop problem set score (20%, see below). Workshop Problem Sets: There will be four assigned problem sets, which will be posted successively online at eLearning, starting at the beginning of the semester and immediately after each examination. Completed problems must be turned in by the following dates and times: Set 1 Friday September 17th by 5:00 PM Set 2 Tuesday October 12th by 5:00 PM Set 3 Friday November 5th by 5:00 PM Set 4 Monday December 6th by 5:00 PM These due dates were set to allow all students to meet the same number of workshop sessions before each turn-in date. On these dates the problems sets will be due by 5:00 PM and submitted via eLearning. You may also turn in your problems sets before the due date. For full credit, all steps to the solution of problems must be shown. Complete answers to problems will be posted on eLearning following the due date. If you have a question regarding the grading of your problem sets, first contact the Head TA, who oversees the grading. Adjusted workshop problem score: Your workshop problem-set average will be calculated after dropping the lowest of the four scores. *Grades- At the end of the semester an average of your four exam scores plus your adjusted problem-set score will be computed and scaled between 0 and 100 points. Your final letter grade will be no worse than that based on the following scale:

Letter Grade

Course Syllabus

Score Range

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A- to A+

85-100

B- to B+

75-84

C- to C+

65-74

D- to D+

55-64

F

< 55

If your final mean numerical score is fractional it will be rounded off to the nearest integer value: i.e., 0.5 - 0.9 will be rounded up to the next highest whole number. In other words, 84.5 would be rounded to 85 and the student would receive an Agrade, but 84.4 would be rounded to 84 and the student would receive a B+ grade. You will receive the same letter grade in both BIOL/CHEM 3361 and BIOL 3161 ________________________________________________________________ Course & Instructor Policies Make-up exams There will be no make-up exams except for the most extreme of documented circumstances or for religious holidays as described under University Policy below. If you do miss an exam, the score will be recorded as 0. Late Work Problem sets will not be accepted after the due dates. If you do miss a due date, the score will be recorded as 0. Class Participation Notes and slides used in lecture, problem sets, class announcements, scores, and practice exams will be posted on eLearning, which is accessible through Orion on the UT Dallas Homepage. Classroom Citizenship Please avoid using cellphones and other behaviors that distract students around you. ________________________________________________________________

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Class Materials The instructor may provide class materials that will be made available to all students registered for this class as they are intended to supplement the classroom experience. These materials may be downloaded during the course, however, these materials are for registered students' use only. Classroom materials may not be reproduced or shared with those not in class, or uploaded to other online environments except to implement an approved Office of Student AccessAbility accommodation. Failure to comply with these University requirements is a violation of the Student Code of Conduct. ________________________________________________________________ Classroom Conduct Requirements Related to Public Health Measures UT Dallas will follow the public health and safety guidelines put forth by the Centers for Disease Control and Prevention (CDC), the Texas Department of State Health Services (DSHS), and local public health agencies that are in effect at that time during the Fall 2021 semester. ________________________________________________________________ Class Attendance The University’s attendance policy requirement is that individual faculty set their course attendance requirements. Regular and punctual class attendance is expected. Students who fail to attend class regularly are inviting scholastic difficulty. In some courses, instructors may have special attendance requirements; these should be made known to students during the first week of classes. ________________________________________________________________ Class Recordings Students are expected to follow appropriate University policies and maintain the security of passwords used to access recorded lectures. Unless the Office of Student AccessAbility has approved the student to record the instruction, students are expressly prohibited from recording any part of this course. Recordings may not be published, reproduced, or shared with those not in the class, or uploaded to other online environments except to implement an approved Office of Student AccessAbility accommodation. Failure to comply with these University requirements is a violation of the Student Code of Conduct. ________________________________________________________________ Comet Creed This creed was voted on by the UT Dallas student body in 2014. It is a standard that Comets choose to live by and encourage others to do the same: “As a Comet, I pledge honesty, integrity, and service in all that I do.”

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________________________________________________________________ Academic Support Resources The information contained in the following link lists the University’s academic support resources for all students. Please see http://go.utdallas.edu/academic-support-resources. ________________________________________________________________ UT Dallas Syllabus Policies and Procedures The information contained in the following link constitutes the University’s policies and procedures segment of the course syllabus. Please review the catalog sections regarding the credit/no credit or pass/fail grading option and withdrawal from class. Please go to http://go.utdallas.edu/syllabus-policies for these policies.

COVID-19 Guidelines and Resources Masks and Vaccinations

Classroom Safety and COVID-19

Please remember that Texas Governor Greg Abbott’s Executive Order GA-38 prohibits us from mandating vaccines and face coverings for UT Dallas employees, students and members of the public on our campus. However, we strongly encourage all Comets to get vaccinated and wear face coverings as recommended by the CDC. The University of Texas at Dallas (UT Dallas) will continue to share more information and guidance as we get closer to the fall semester. To help preserve the University’s in-person learning environment, UT Dallas recommends the following: Adhere to the University’s CDC Updated Guidelines issued on July 30, 2021. All Comets are strongly encouraged to wear face coverings indoors regardless of vaccination status. Please note this represents a change in the campus guidance issued on May 20, 2021.

Accommodations Students Who Miss Class for Reasons Unrelated to COVID-19: Please contact the instructor and TA as soon as possible. Students Who Must Isolate or Quarantine Due to COVID-19: To keep the UT Dallas community as safe as possible, the University requires students who test positive for COVID-19 or who are close contacts as determined by the campus contact tracing program to isolate or quarantine as applicable. Faculty will be notified by the Dean of Students' Office if a student in their class has been required to isolate (positive case) or quarantine Course Syllabus

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(exposed). We will make lectures and course materials available for those students during the period the students must isolate or quarantine. Absences due to COVID-19 will not be counted against an isolated or quarantined student. Verifying COVID19 Isolation or Quarantine

Student Safety

Student Resources including COVID-19 Resources

Students need to self-report COVID-19 positive results or exposures via an online form so that university campus trac...