BIOCHEMISTRY I Fall 2019 - University of Toledo · • Study Guide and Solutions Manual: The Absolute, Ultimate Guide to Lehninger Principles of Biochemistry 7th Edition. ISBN-13:

BIOCHEMISTRY I Fall 2019

CHEM 3510-001 Department of Chemistry and Biochemistry

College of Natural Sciences and Mathematics The University of Toledo

Instructor: Dr. John Bellizzi Class Location: Memorial Field House 2100 E-mail: [email protected] Class Day/Time: Mon/Wed/Fri 10:20-11:15 am Office: Wolfe Hall 4203A Credit Hours: 3 Office Hours: Mon 2:00-3:50 pm, Wed 5:00-5:50 pm, Thu 2:00-3:50 pm and by appointment Office Phone: 419-530-5926

CATALOG DESCRIPTION: Chemical structure and molecular transformation in biological systems. COURSE OVERVIEW: As the first semester in the two-semester biochemistry sequence, CHEM 3510 applies the fundamental concepts about structure and mechanism you learned in organic chemistry to the structures, properties and functions of the major classes of biomolecules – proteins, carbohydrates, nucleic acids, and lipids. This gives us a framework for describing and understanding molecular and cellular phenomena (such as catalysis by enzymes, transport of oxygen, and action potential generation by neurons) in terms of physical interactions and chemical reactions of specific biomolecules. STUDENT LEARNING OUTCOMES: Upon successful completion of this course, students will be able to: 1. Identify, name, and draw chemical structures of amino acids, nucleotides, monosaccharides, disaccharides,

polysaccharides, and common storage and membrane lipids. 2. Understand how intermolecular forces and the hydrophobic effect lead to the formation of three-dimensional

structures of biomolecules and intermolecular complexes. 3. Describe how the biological functions of proteins, nucleic acids, polysaccharides, and lipid assemblies are dependent

on their covalent structures, stereochemistry, conformations, and the properties and reactivities of their component functional groups.

4. Use the Henderson-Hasselbalch equation to relate pH, pKa and concentrations of weak acids and conjugate bases. 5. Calculate isoelectric points and net charges for amino acids, peptides and other molecular ions. 6. Interpret protein and nucleic acid sequencing data. 7. Classify enzymes on the basis of the type of reaction they catalyze. 8. Mathematically and graphically describe protein-ligand equilibria and the kinetics of enzyme-catalyzed reactions. 9. Draw the chemical mechanisms of enzyme-catalyzed reactions using curved arrow notation, and extrapolate from

specific reactions studied in class to propose mechanisms for other enzymes that carry out similar reactions. 10. Recognize, classify, and explain important cellular functions carried out by proteins, including transport of solutes

across membranes and intracellular signal transduction, and describe general principles and specific examples of these pathways.

11. Integrate knowledge from other courses and fields (e.g. organic chemistry, biology) with biochemistry.

2

PREREQUISITE: The prerequisite for this course is a C- or better in CHEM 2420 Organic Chemistry II (D- or better for students with a catalog year prior to Fall 2017). Students not satisfying the prerequisite will be dropped from the course. There many important concepts critical to mastering biochemistry that you are expected to already know from General and Organic Chemistry. If you do not feel proficient in the areas below you are advised to go back and review them. • Lewis structures, formal charges, and resonance • Covalent bonding, hybridization, and molecular geometry (VSEPR) • Conformational analysis of open chains (staggered/eclipsed/gauche/anti) and rings (puckered/boat/chair) • Stereochemistry – cis/trans and chiral centers (enantiomers, diastereomers) • Intermolecular forces (electrostatic, dipole-dipole, dispersion forces, hydrogen bonds) • Thermodynamics (ΔG, ΔH, ΔS), equilibrium (Keq), kinetics (first order and second order rate equations) • Ionization of weak acids; acid/base strength (pKa, pH) • Structures, properties and names of organic functional groups • Reactions and mechanisms

• Acid-base reactions • Carbonyl reactions (additions, eliminations, acyl substitutions) • Nucleophilic substitution and β-elimination

• How to use curved arrows to trace the flow of electron pairs in reaction mechanisms

REQUIRED INSTRUCTIONAL MATERIALS: • Required Homework Access: SaplingPlus Access Code (includes Lehninger 7th edition e-book), This will be used

for both CHEM 3510 and CHEM 3520 (if you will be taking CHEM 3520 in the Spring, you will save money if you buy the two-semester access code). http://www.saplinglearning.com

• Required Textbook: Nelson, D.L. and Cox, M.M. Lehninger Principles of Biochemistry (7th Edition, 2017). W.H. Freeman and Co. (New York, NY). This text will be used for both CHEM 3510 and CHEM 3520. The e-book comes bundled with SaplingPlus, so you do not have to purchase it separately unless you want a physical copy.

• Required Clicker: Turning Technologies clicker license (UT students should already have this from general and organic chemistry). http://account.turningtechnologies.com Please read the following information carefully! When you purchase the required Sapling Plus Access Code it is integrated with the e-book version of the Lehninger textbook so unless you want a physical book you can just purchase the access code. • The least expensive option for CHEM 3510 is to purchase a one-semester SaplingPlus access + Lehninger E-

book for $72.99 directly at http://www.saplinglearning.com. • If you will be taking CHEM 3520 in Spring 2020, you can buy a two-semester access code at

http://www.saplinglearning.com for $103.99, which will cover homework and text for both CHEM 3510 and 3520. • You can also purchase the one-semester and two-semester Sapling Plus access codes (+ Lehninger e-book) at

the bookstore; however, the price will be higher ($83.25 for one semester and $118.90 for two semesters). For those of you who want a physical copy of the textbook in addition to the e-book, the information is below. • Hardcover textbook + SaplingPlus/E-book. ISBN-13: 9781319125875. Bookstore Price $326.50 New. • Loose-leaf textbook + SaplingPlus/E-book ISBN-13: 9781319125745. Bookstore Price $213.30 New. • If you buy either of these books at the bookstore, they are bundled with the two-semester SaplingPlus access

code and E-book, so you don’t have to buy anything else. If you buy the books elsewhere, they may or may not come bundled with SaplingPlus, so you may have to purchase it separately. Make sure you know what you are buying before purchasing.

OPTIONAL MATERIALS: • Study Guide and Solutions Manual: The Absolute, Ultimate Guide to Lehninger Principles of Biochemistry 7th

Edition. ISBN-13: 9781464187971. Bookstore Price $98.75. • Molecular Model Kit. Many students benefit from having a model kit. If you don’t already have one from organic

chemistry, a good inexpensive one is the Molecular Student Set from Duluth Labs: MM-005 for about $18 or MM-006 for about $28 at Amazon.com.

3

TECHNOLOGY REQUIREMENTS: • Students will need an active Turning Technologies license code and either a clicker or a compatible device running

the TurningPoint app. • Students will need to have access to a computer and a reliable Internet connection to complete weekly homework

assignments on SaplingPlus and use the course Blackboard site. Students should check Blackboard regularly for announcements, handouts, lecture outlines and practice exams. A discussion board will be available for posting questions to the instructor and the rest of the class.

• Students will need to use their UT Rockets e-mail account regularly. Messages sent to the instructor from other e-mail accounts may be caught by spam filters and not received. In addition, official class announcements will be send out via Blackboard, which delivers messages to the UT Rockets e-mail accounts.

COURSE EXPECTATIONS: • Students are responsible for all material covered in the assigned chapters (even material that is not explicitly

discussed in lecture), as well as material covered in lecture that is not in the textbook. Reading assignments relevant to each week’s lecture and homework topics are on the schedule on the last page of the syllabus, and it is highly recommended that you complete the reading before lecture.

• Students with challenges that require special assistance should contact the Student Disability Services Office and follow up with me by e-mail to arrange the accommodations specified by the electronic memo.

• I am available outside of class to answer questions during posted office hours, at other times by appointment (please contact me via e-mail to arrange a meeting). The discussion board on Blackboard is also a good way to have questions answered (and see what your fellow students are asking about). When e-mailing, use your UT Rockets e-mail account and include CHEM 3510 in the subject of your e-mail.

• Please be considerate of me and of your fellow students by silencing your electronic devices and keeping conversation and other disruptions to a minimum. I know that a number of students have class on the opposite side of campus immediately before or after lecture; if late arrival or departure from class is unavoidable, use the rear doors of the lecture hall and do not disturb your neighbors.

ASSESSMENT AND GRADING: Final Grading: Final grades will be calculated based on a total of 500 points.

Three mid-term exams 60% 300 points Cumulative final exam 20% 100 points Homework (Sapling Plus) 12% 60 points Lecture quizzes 4% 20 points Clickers (attendance/participation) 4% 20 points

Exam grades and course grades will not be curved. Final course grades will be assigned based on the following cutoffs for percentage of total possible points. Depending on exam averages and final grade distributions, these cutoffs may be lowered slightly but will not be raised.

A ≥90% 90%> A- ≥88% 88%> B+ ≥86% 86%> B ≥80% 80%> B- ≥78% 78%> C+ ≥76% 76%> C ≥70% 70%> C- ≥68% 68%> D+ ≥66% 66%> D ≥60% 60%> D- ≥58% 58% > F

Midterm Grading: Midterm grades (for advisory purposes and to officially track course participation) will be assigned in Late October (after Exam II) and will be based on your percentage of total possible points earned on Exams I and II, quizzes 1 and 2 and SaplingPlus assignments 1-7 converted to letter grades using the above scale. The U.S. Department of Education requires the University to document both active participation and satisfactory academic progress as part of the compliance with federal financial aid regulations. Students receiving Title IV Federal Aid funds are required to have regular attendance and satisfactory academic progress in their courses to receive federal aid. Students may also use the midterm grade to help make a decision in regards to withdrawing from the course.

4

Assignment/Assessment Descriptions • Examinations (Mid-Term Exams and Final): There will be three mid-term exams given in class on the dates listed on

the last page of the syllabus. Each exam will be worth 100 points. The lowest of your three mid-term exam scores will be dropped and replaced with the average of your other two exam scores. You should have a calculator for the exams.

• Lecture Quizzes: There will be three 5-minute quizzes given in class on the dates listed on the last page of the syllabus. Each quiz will be worth 10 points and the lowest of the three quiz scores will be dropped. You will need to have a blank sheet of paper in class to turn in for each quiz.

• Homework (SaplingPlus): There will be a graded homework assignment of variable length due on SaplingPlus each week (Wednesday at 11:55 pm). Each assignment is worth 5 points, and there are 13 assignments (worth a total of 5 x 13 = 65 points). SaplingPlus is worth 60 points, so you can still get full credit even if you don’t get perfect scores on each assignment) or get up to 5 points extra credit. You may attempt each question unlimited times, but you will lose 5% of the points for the question for each incorrect attempt. Late problem sets will lose 20% of the possible credit per day until they are completed. You will also have access to ungraded review material, reading quizzes, and exercises in addition to the graded problem sets, along with links to the e-book and other resources.

• Clickers: Clicker questions will be asked in class beginning on Wednesday September 5. Clicker questions will be asked periodically in lecture. You will receive a clicker attendance/participation grade of up to 20 points based on the percentage of lectures in which you respond to at least one clicker question.

§ Attendance/participation below 50%: 0 points § Attendance/participation 90% or higher: 20 points § Attendance/participation <90% and >50%: Points = (% attendance – 50%) x 0.5

Note that you can fail to respond in up to 10% of lectures and still get the maximum 20 points. As a result, there will be no makeups for missed classes or forgotten clickers. Clickers will also be used to track attendance for financial aid reporting.

ACADEMIC POLICIES: Course Academic Honesty Policies • Academic Honesty: The University of Toledo policy on academic honesty will be strictly enforced.

https://www.utoledo.edu/policies/academic/undergraduate/pdfs/3364-71-04 Academic dishonesty.pdf • Students are permitted to collaborate on homework assignments but each student must submit their own answers

while logged into their own SaplingPlus account. • Any student caught cheating in any way on an exam or quiz or facilitating the cheating of others will receive a 0 for

that exam/quiz and will be required to take any remaining exams in the Field House Testing Center. A second violation will result in an F in the course and referral to the Dean’s Office. This includes but is not limited to talking during an exam/quiz, looking at notes or other unauthorized material, looking at another student’s paper, or allowing other students to copy your answers. If you want two extra credit points, e-mail your instructor a picture of a dog with the word “dog” in the subject line of your message.

• Students are prohibited from using the clickers/devices of other students or allowing other students to use their clickers/devices to answer clicker questions.

Examination Policies • Three mid-term exams will be given in class on the dates listed on p. 4 of this syllabus. Exams will begin promptly at

10:20 and papers will be collected at 11:15. If you arrive late for an exam you will NOT be given extra time to finish. • I will drop the lowest of the three mid-term exam scores and replace it with the average of the other two exam scores. • There will be no make-up exams given after the scheduled exam date/time.

o An excused absence from an exam will be granted only for documented circumstances meeting the criteria of the UT Missed Class Policy (personal emergencies, including, but not limited to, illness of the student or of a dependent of the student or death in the family; religious observances that prevent the student from attending class; participation in University-sponsored activities, approved by the appropriate University authority, such as intercollegiate athletic competitions, activities approved by academic units, including artistic performances, R.O.T.C. functions, academic field trips, and special events connected with coursework; government-required activities, such as military assignments, jury duty, or court appearances). Appropriate documentation must be provided before an excused absence will be considered. For more details, consult: https://www.utoledo.edu/policies/academic/undergraduate/pdfs/3364-71-14 Missed class policy.pdf

5

o If you have a conflict for an approved student activity or other obligation satisfying the criteria of the missed class policy, provide me with documentation and I will arrange for you to take the exam early. It is your responsibility to contact me to make these arrangements as soon as you are aware of the conflict.

o For legal absences with no prior notice (such as medical emergencies), acceptable written documentation justifying the absence is required before an excused absence will be considered. If you are granted an excused absence from a mid-term exam, your final grade will be calculated out of 400 rather than 500 points.

o Missing an exam for any reason other than a qualified legal absence according to the UT Missed Class policy (including but not limited to lack of preparation, travel, transportation difficulties, oversleeping, job conflicts, etc.) will result in a grade of 0 for the missed exam with no opportunity to make it up. Plan accordingly.

• A comprehensive final exam will be held during final exam week on Mon, December 9 from 10:15 am to 12:15 pm. Missing the final for a legal absence will result in a grade of incomplete for the course; missing the final exam for any reason other than a legal absence will result in a grade of 0 for the final. The final exam can only be taken at the date and time specified by the exam schedule. Be sure your travel plans at the end of the semester take this into account.

• Exam Re-grading Policy: Graded mid-term exams may be picked up in office hours after the grades are posted. If you believe that there was an error in grading your exam or calculating your exam score, you may make a single request for re-evaluation of your exam within 2 weeks (14 days) of the date the exam grades are posted to Blackboard. If you want your exam reevaluated, return it to me with an attached note describing specifically why you think your grade is incorrect. Your entire exam will then be re-graded.

University Policies and Regulations • Your safely and well-being as a University of Toledo student is important to the faculty, staff, and administration; as

such please take a minute to review the following university policies that apply to you as a student of the University. Students can find these policy along with other university policies listed by audience on the University Policy webpage

The University of Toledo's Title IX (Sexual Misconduct) Policy - 3364-50-01 Nondiscrimination 3364-50-02 Nondiscrimination on the basis of disability - Americans with Disability Act compliance 3354-50-03 Consensual romantic and/or sexual relationships - Policy 3364-25-65 Student Code of Conduct 3364-30-04

• Academic Accommodations: The University of Toledo embraces the inclusion of students with disabilities. We are committed to ensuring equal opportunity and seamless access for full participation in all courses. For students who have an accommodations memo from Student Disability Services, I invite you to correspond with me as soon as possible so that we can communicate confidentially about implementing accommodations in this course. For students who have not established affiliation with Student Disability Services and are experiencing disability access barriers or are interested in a referral to healthcare resources for a potential disability or would like information regarding eligibility for academic accommodations, please contact the Student Disability Services Office by calling 419.530.4981 or sending an email to [email protected]

• Drop/Withdraw: The course may be dropped on the web no later than Monday September 9, and you may withdraw from the course (with a grade of W) no later than Friday November 1.

• Academic and Support Services: Please follow this link to view a comprehensive list of Student Academic and Support Services.

• Safety and Health Services for UT Students. Please use this link to view a comprehensive list of Campus Health and Safety Services available to you as a student.

6

SCHEDULE

Schedule Lecture Topics In-Class Assessment Student Learning Outcomes

Week 1 8/26-8/30

Biochemistry – the big picture

1, 2, 4, 11

Homework for Week 1: Read Ch. 1-2, set up SaplingPlus account, complete SaplingPlus review exercises (ungraded) make sure your Turning technologies response device is licensed and registered Week 2 9/2-9/6

No Lecture Mon 9/2 (Labor Day) Carbohydrates

Clickers begin Wed 9/4 1, 2, 3

Homework for Week 2: Read Chapter 7, Complete SaplingPlus Assignment 1 by Wed 9/4 at 11:55 pm Week 3 9/9-9/13

Carbohydrates Lipids

Lecture Quiz 1 Mon 9/9 Mon 9/9 last day to drop

1, 2, 3


Lipids

Mid-term Exam I Fri 9/20 (Covers Week 1 and carbohydrates, lipids)

1, 2, 3

Homework for Week 4: Review Ch 1, 2, 7, 10 for Exam I. Complete SaplingPlus Assignment 3 by Wed 9/18 at 11:55 pm Week 5 9/23-9/27

Nucleotides and nucleic acids 1, 2, 3

Homework for Week 5: Read Chapter 8 and 9, Complete SaplingPlus Assignment 4 by Wed 9/25 at 11:55 pm Week 6 9/30-10/4

Nucleotides and nucleic acids Amino acids, peptides and proteins

1, 2, 3, 5, 6


Protein three-dimensional structure No Lecture Fri 10/11 (Fall Break)

Lecture Quiz 2 Mon 10/7 1, 2, 3, 5, 6


Proteins Mid-term Exam II Fri 10/18 (covers Exam I material plus nucleotides, nucleic acids, amino acids, proteins)

1, 2, 3, 5, 6

Homework for Week 8: Review Ch 3, 4, 8, 9 for Exam II. Complete SaplingPlus Assignment 7 by Wed 10/16 at 11:55 pm Week 9 10/21-10/25

Protein-ligand interactions 8, 10, 11


Enzymes – principles of catalysis, kinetics

Fri 11/1 last day to withdraw 8, 9, 10, 11


Enzyme Mechanisms Lecture Quiz 3 Mon 11/4 8, 9, 10, 11


No Lecture Mon 11/11 (Veterans Day) Membranes and membrane transport

8, 9, 10, 11


Membrane transport

Mid-Term Exam III Fri 11/22 (covers Exam I and II material plus protein-ligand interactions and enzymes)

Homework for Week 13: Review Ch 5 and 6 for Mid-Term Exam III, Complete SaplingPlus Assignment 12 by Wed 11/20 at 11:55 pm Week 14 11/25-11/29

Signal transduction No Lecture Wed 11/27 and Fri 11/29 (Thanksgiving Break)

10, 11

Homework for Week 14: Read Chapter 12 Week 15 12/2-12/6

Signal transduction 10, 11

Homework for Week 15: Read Chapter 12, Complete SaplingPlus Assignment 13 by Fri 12/6 at 11:55 pm Final Exam Monday December 9 10:15-12:15

Documents

BIOCHEMISTRY I Fall 2019 - University of Toledo · • Study Guide and Solutions Manual: The Absolute, Ultimate Guide to Lehninger Principles of Biochemistry 7th Edition. ISBN-13: