Biochemistry Syllabus Spring 2020 PDF

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Biochemistry Syllabus Spring 2020...

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Syllabus Biochemistry I 4190-001/5190-001 Spring 2020 Instructor: Dr. Michael Fannon Ball 210 Email: [email protected]

Required Text: Biochemistry, 9th edition, by Berg & Stryer, published by H. Freeman All students will need a calculator that is able to calculate logarithms to bring to exams. Biochemistry will be taught in a traditional format of lecture.

Daily quizzes – A quiz on the lecture from the previous class will be given in the following class, as indicated on the syllabus. The questions on these quizzes will be based on the book chapter, Power Points, and lecture. Students can use the slides in the Power Points labeled “practice” and “answers” as a guide to the quizzes. The quiz average will count as 16 % of the overall grade. The lowest quiz grade will be dropped when calculating this average. Class quizzes that are missed because of absence from class cannot be made up. If there is a justified excuse (including documentation) for missing the in-class quiz, you will be excused from that quiz. If there is no justified excuse, then a zero will be entered for that quiz grade.

Exams – Exams will be given on the days indicated in the syllabus during regular class time. Each of the four exams is worth 17% of the final grade and the final exam is worth 16%. If you are unable to take an exam due to extreme circumstances, and you notify the instructor ahead of time, you may be excused from that exam. NO MAKEUP EXAMS WILL BE GIVEN. If an excuse is granted, your grade will be determined using three exam scores instead of four. Excused absences will not be given for airline reservations, routine minor illness (colds, flu), or other common ailments. Excused absences will not be granted for misreading the syllabus, not finding a parking space, or sleeping through your alarm. Excused absences will generally not be given if no notice has been received prior to the exam except under unusual circumstances. Students with airline reservations are not automatically entitled to an excused absence. In those rare circumstances where a trip is sometimes necessary, please report it at the beginning of the semester and a decision will be made if the reason justifies other arrangements.

Practice Problems – Practice problems are also available for each chapter. These practice problems are for practice and are not graded! I recommend that you use these to assess your grasp of the material. These practice problems are designed to help you learn the material and prepare for the exams. While they are not required, it is strongly recommended that you complete them in a timely manner as a study tool. This will help you see what you don’t understand and get help before you are tested on the material.

Graduate students Students who are enrolled for graduate credit have additional requirements. Their exams will have an additional degree of difficulty and each will be required to make a presentation to the class. The presentation will be a component of the final exam grade. This will be discussed in greater detail during the first meeting.

Grades : Daily Quiz average Exam 1 – Exam 2 – Exam 3 – Exam 4 – Final Exam -

16% 17% 17% 17% 17% 16% 100%

Please note the date and time of the class exams and quizzes. You should read the appropriate chapter in the book prior to lecture. The lectures will serve to explain the material that is the most important to understand for the quizzes and exams and also gives you the opportunity to ask questions or have a concept clarified if it is unclear. As a courtesy to others in class, please TURN OFF all cell phones. It is very disruptive and is not fair to the students around you. LEARNING OBJECTIVES FOR BIOCHEMISTRY: 1. Demonstrate knowledge of pH, buffers, pKa and how they affect the chemistry, and the interactions between biological molecules and their cellular environment. 2. Explain what Gibbs free energy is, how it is affected by concentrations, temperatures, etc., and what the sign and magnitude of Gibbs free energy means. 3. Identify how the chemistry of amino acids determines the shape of a protein, including the secondary, tertiary, and quaternary structures. Be able to explain how a change in the amino acid sequence can change the shape and function of a protein. 4. Differentiate between different carbohydrates that are used for storage and how they are linked. Identify how carbohydrates are modified or are used to modify other molecules. 5. Explain the difference in structure between the different classes of lipids, and their functions. Explain how lipids are used to anchor proteins. 6. Demonstrate knowledge of the structure of membranes and explain how this structure functions to moderate the passage of molecules into and out of the cell. 7. Explain the structure of nucleotides, and how they combine to make the structure of DNA and RNA. 8. Explain how enzymes work to catalyze a reaction, and their kinetics. Differentiate between the ways that inhibitors can function to inhibit enzymes.

9. Demonstrate knowledge of how sugars are metabolized to provide energy for the cell. Differentiate between the key reactions used to break down sugars or synthesize them. Understand how those reactions are regulated. 10. Be able to explain the key reactions involved in the metabolism of fatty acids. Differentiate between the metabolism and synthesis of fatty acids. Predict what will cause these reactions to be induced or inhibited. 11. Identify the key reactions in the synthesis of nucleotides are synthesized. Differentiate between the ways that purines and pyrimidines are synthesized. Explain what the salvage pathways are and the consequences if they are defective. Explain the regulation of the key reactions in this synthesis. GENERAL UMass AND DEPARTMENTAL POLICIES Cheating, plagiarism or other acts of academic dishonesty by students is subject to the disciplinary process outlined under Academic Rules & Regulations in the Policies and Procedures section of the UMass Lowell Registrar’s Website. Academic work by students is expected to be undertaken with honesty and integrity Academic dishonesty includes but is not limited to: Cheating - use, or attempted use, of trickery, artifice, deception, breach of confidence, fraud, or misrepresentation of one's academic work. Submission of the same work in its entirety for credit in two courses without obtaining the permission of the instructors constitutes cheating. Collaborating with others when not explicitly allowed by the instructor constitutes cheating. For exams and quizzes - no books or notes are allowed to be used and NOTHING is allowed on your desk. For exams, phones, smartwatches, and backpacks must all be left in the front of the room. Leaving the room to use the bathroom is not allowed except in emergencies. Fabrication - falsification or invention of any information or citation in any academic exercise. Plagiarism - representing, whether intentionally or unintentionally, the words or ideas of another as one's own work in any academic exercise. Facilitating dishonesty - helping or attempting to help another commit an act of academic dishonesty, including substituting for another in an examination, misrepresenting oneself, or allowing others to represent as their own one's papers, reports, or academic works. Student Mental Health and Wellbeing We are a campus that cares about the mental health and well-being of all individuals in our campus community. Your personal health and well-being can impact your success in this course. Students sometimes experience mental health concerns or stressful experiences that interfere with academics and have a negative impact on everyday life. If you or someone you know are experiencing mental health challenges at UMass Lowell, please contact Counseling (information below). Their services are free and confidential, and same day appointments are available. I am available to talk with you about stresses related to your work in my class. Furthermore, I can assist you in reaching out to any one of a wide range of campus resources, including:

· Counseling Services provides crisis intervention, assessment, referrals, short-term individual counseling, group therapy, and on-call clinicians outside of business hours. They are located at University Crossing Suite 300 and their 24/7 phone number is 978-934-6800. UMatter2 is a university-wide initiative to support students and promote mental health. · The office may be reached at 978-934-6671. Consider also reaching out to a friend, faculty or family member you trust for help getting connected to the support that can help.

Day

Date

Chapter

Topic

Mon.

Jan 27

Chap. 1, 2

Water, pH, Acids, Bases, Buffers Protein Structure

Mon.

Feb 3

Chap. 4, 8

Quiz Ch. 1,2 DNA, RNA, Enzymes and Kinetics,

Mon.

Feb 10

Chap. 11

Quiz Ch. 4,8 Carbohydrates,

Mon.

Feb 17

Tue

Feb 18

Chap. 12

Monday class schedule Exam 1 Chap. 1, 2, 4, 8, 11 Lipids, Cell Membranes

Mon

Feb 24

Chap. 13

Quiz Ch. 12 Membrane Channels

Mon.

Mar 2

Chap. 16

Quiz Chap.13 Glycolysis, Gluconeogenesis

Mon.

Mar 9

Mon.

Mar 16

Chap. 17

Exam 2 Chap. 12, 13, 16 Citric Acid Cycle

Mon.

Mar 23

Chap. 18

Quiz Ch. 17 Oxidative Phosphorylation

Mon

Mar 30

Chap 21, 22A

Quiz Ch. 18

Holiday- no class

Spring recess

Glycogen Metabolism Fatty Acid Breakdown Mon.

Apr 6 Chap. 22B, 23

Exam 3 Chap. 17, 18, 21, 22A, Fatty Acid Synthesis,

Chap. 23

Amino Acid Breakdown

Mon.

Apr 13

Mon.

Apr 20

Fri.

Apr 24

Mon.

Apr 27

Exam 4 Chap. 22B, 23,24,25 Review, Graduate presentations

Mon.

May 4

Final Exam

Patriots Day No Class Chap. 24, 25

Grades 93 or above A 90 -92 A87-89 B+ 83 – 86 B 80 - 82 B77 - 79 C+ 73 - 76 C 70 - 72 C67 - 69 D+ 60 -67 D Below 60 F Graduate 93 90 -92 87-89 83 – 86 80 - 82 77 - 79 73 - 76 70 - 72 Below 70

A AB+ B BC+ C CF

Monday Schedule Quiz Ch. 22B. 23 Amino Acid Synthesis Nucleotides

TBA...