Biology 4307

Biochemistry and Physiology of the Cell Fall 2015

Section 01 Tuesdays and Thursdays 3:30-4:45 PM BSB B110

Instructor: Dr. Erika Abel Office Location: BSB A126 Office Hours: by appointment only – use Canvas to schedule Email: Erika_Abel@baylor.edu Supplemental Instructor: Ms. Brittany Schall Supplemental Instructor Email: Brittany_Schall@baylor.edu Supplemental Instruction Meeting Times: TBA I. Course Description

1. This course explores the roles of biologically important molecules in cellular structure and function, emphasizing an integrated understanding of the characteristics of the four major classes of biological molecules and the chemical interactions that support living systems

2. Undergraduates who successfully complete this course will be awarded 3 hours of advanced credit toward their degree. Undergraduate biology majors who take this class to fulfill the requirements of their degree plan must earn a grade of C- or better, and those majors who choose this course to fulfill the physiology requirement of their degree plan (i.e. BS/BA BIO general plan) must take both BIO 4307 and BIO 4107. (BS/BA BIO PHC prehealthcare students are NOT required to enroll in BIO 4107).

3. Graduate students taking BIO 4307 for graduate credit are required to complete an additional 50 point project. Please schedule an appointment via Canvas to discuss.

4. The intended audience for this course is junior or senior biology majors interested in careers in research or healthcare. Students from other disciplines may also find the course helpful in preparing for similar careers.

5. The prerequisites for BIO 4307 are successful completion of either BIO 1105, 1305 or BIO 1405; AND either BIO 1106, 1306 or BIO 1406; AND CHE 3331. CHE 4341 is NOT a prerequisite for BIO 4307. As would be expected, those who have already been exposed to biochemistry often find the material less challenging upon second exposure; however, each semester, students without prior exposure to the subject matter are among the highest scoring quartile of the class. Conversely, those students who have already earned credit for CHE 4341 are encouraged to be vigilant in their study of the material. The material is presented from the perspective of a biologist for biologists. You will be asked to apply and extend knowledge of biochemistry to cellular and organismal function; similar grades in CHE 4341 and BIO 4307 are not guaranteed.

II. Goals and Learning Outcomes

1. Goals: The chief goal of this course is for you to gain a deeper understanding of cellular and organismal function by studying the structure, interactions, and metabolism of the component molecules.

2. Learning Outcomes: By the end of the semester, if all goes well, you will: i. have learned, or reviewed, the characteristics of the major cellular macromolecules

ii. have learned, or reviewed, the principles that guide macromolecular and/or cellular function iii. be able to relate the chemical and physical characteristics of cellular macromolecules to

cellular structure and function and, by extension, to organismal physiology iv. be able to articulate the major metabolic pathways and mechanisms whereby cells extract

energy from fuel sources v. be able to interpret scientific data related to the role of biochemistry in normal cellular and

organismal function or pathology

 

  2  

III. Textbooks, Readings, and Other Materials 1. Textbooks

i. Reading the textbook PRIOR to attending class and working the suggested end-of-chapter problems after class are necessary for adequate performance in this course. The required textbook for BIO 4307 is:

1. Biochemistry: A Short Course" by Tymoczko, Berg and Stryer, 2011, W.H. Freeman and Company. Second edition.

Note: The international version of this textbook is not a suitable substitute for the required text.

ii. For further, optional reading you may wish to consult: 1. Becker's World of the Cell 8th Edition, ISBN 9780321716026 2. Lehninger Principles of Biochemistry, ISBN 9780716771081

2. Journal Articles: Throughout the semester, you will be instructed to read current and/or seminal research journal articles either as preparation for an upcoming lecture or as an extension of themes presented in class.

3. Turning Technologies “Clicker”: Ability to utilize this student response system during class is mandatory (see below for further information).

4. You will need a non-programmable calculator that is Log and Ln capable for select exams and quizzes. If the calculator is equipped with a cover, you will be asked to leave it in your backpack during exams and quizzes.

5. Study Guides: I provide study guides on Blackboard to help you prioritize, order and place in context the information presented during lecture. Material not included or referenced on the study guide will not be on exams. Questions included on the study guide are particularly important. Referenced end-of-chapter problems from the textbook are highly important (especially when mathematical equations or relationships are addressed). *****I cannot emphasize enough how important it is to use the study guide as you prepare for class and for the examinations******

IV. Overall Structure of the Course

BIO 4307 is largely lecture-based; however, my goal is to rely upon scientifically validated teaching methods during lecture. In particular, I will introduce active learning modules and discussion of primary literature sources to reinforce concepts presented in your text. Out of class homework problems may also be assigned. While these problems are CRITICAL for your intellectual development, they are self-assessed using the answers provided. I also intend to employ frequent formative assessment during class using the Turning Technologies Student Response System (Clickers). Each of these teaching methods has been repeatedly shown to produce greater and longer-lasting learning gains. In order for you to be successful in an active learning environment, you must be prepared (read before class), present (and awake), and intellectually engaged (not on social media!). Your participation will account for approximately 10% of your grade. Quizzes account for 10% of your grade, and each summative exam (3 regular exams and 1 cumulative final exam) will account for 20% of your grade.

V. Course Policies

1. As a faculty member, it is my duty to encourage standards of professionalism in my students. Further, it is my duty to insure that your learning environment is free of distractions. For these reasons, I will correct rude, dishonest, or unethical behavior. Rude behaviors include internet surfing, studying other topics, entering/exiting the room in a distracting manner during lecture, or talking while another person is talking. Computers are NOT permitted due to the distraction they cause to neighboring students when misused in class. Be assured that I will do my best to eliminate disruptive behaviors, which impede your ability to focus during lecture. I will not hesitate to ask your classmates to leave if their behavior is disruptive. I ask you to join me in maintaining classroom decorum by correcting your peers in a discreet manner.

2. Office Hours: My office hours are by appointment only. Please utilize the Canvas appointment

scheduling tool to reserve a time to speak with me. I will not accept ‘drop in’ meeting requests and

 

  3  

you must schedule the appointment at least 3 hours in advance. You are welcome and encouraged to make a group appointment to speak with me.

3. Email: I encourage the use of email for simple notifications and requests. My goal is to answer

every email within 24 hours, and I am generally quite available via email. However, using email to request accommodations on quizzes/exams/attendance requirements during the evening hours before the event is unacceptable. It is often the case that responding to your request with essentially no notice is impossible. Bottom Line: If you email me with accommodation requests in the evening prior to an exam/etc, do not expect to have your request granted—this is inadequate notice for requests pertaining to events of the next day. I am in the business of preparing you for a professional future, and this behavior is not to be tolerated.

4. Examination Policies: In-class examinations and the final exam will consist of multiple-choice

questions only. The final exam will be entirely comprehensive in nature. With regard to the three in-class exams, there will be 1-2 early morning or weeknight meeting times during which we will review the content of the exam at a specified time. Please come during those times, as exams will not be made available at alternative times. Offering exam content review times is a courtesy I extend, not a requirement. Only re-grade requests that address a blatant error in calculating your grade will be addressed.

5. Required Use of “Clickers”: The Turning Technologies Student Response system will be used to

assess your attendance, participation and/or quiz performance during most lectures. Ability to utilize this system during lecture is a requirement. You are NOT permitted to use the cellphone/computer app; therefore, the Response Card RF-LCD by Turning Technologies is required. You can purchase it (or rent it) at the bookstore. You can use this “Clicker” for any of your classes that require this type of clicker.

6. Cell Phones and Other Electronic Devices: The use of cell phones, tablets or computers during

class is prohibited. I am committed to insuring that you are able to concentrate in my class, and I will not hesitate to ask your classmates to leave the classroom if this rule is not respected. I will rely on you, as peers, to correct behavior in a more discreet manner as well.

7. Policies on Missed Quizzes and Lectures: Make-up quizzes or ‘participation points’ will not be

granted and no ‘early’ quizzes will be granted. (Bear in mind that there will be a total of at least 8 quizzes, and only the top 5 grades will count.) The one exception to the ‘no make-up’ rule is multiple absences due to graduate/professional school interviews and/or MCAT/DAT/LSAT exams. If you can provide documentation of your missing two prior quizzes for these reasons, I will allow you to make up a quiz should you have a third interview, etc. that conflicts with the class schedule. Do not expect a response to requests for other exceptions.

8. Policies on Missed Examinations: No ‘early’ examinations will be granted under any circumstances.

If an exam is missed for a legitimate reason, contact me by email within 24 hours. You must provide me with a) a doctor’s note stating that you were too ill to take the exam on the exam date or b) adequate proof of missing the exam due to a graduate/professional school interview in order to take a make-up exam. You will be docked 5% of your points for each day that you are late in taking the exam. The make-up exam must be taken within 2 days of the missed exam. ***Important**** Exercise restraint in requesting a make-up exam, as a make-up exam may be granted ONCE and once only during the semester. Two exceptions to this rule exist: proof of your hospitalization or multiple missed exams due to multiple graduate/professional school interviews. You may not ‘combine’ one missed exam due to illness with one missed exam due to interviews. Do not ask for further exceptions to these rules.

9. Drop Policy: Refer to University regulations regarding the drop policy.

 

  4  

10. Academic Honesty: Cheating will not be tolerated. Dishonest behavior will be punished to the full extent allowed by the University, including an automatic zero on your exam/quiz as well as, potentially, the exam/assignment from which you cheated. The seats in this room are crowded. It is your job to insure that you leave NO DOUBT in my mind as to your integrity. If I have to ask you to keep your eyes on your own paper, I will record your name. Should I have to prompt you a second time, you WILL BE REPORTED to the honor council.

11. Exam Day: A calculator will be necessary during most examinations and several of the quizzes.

Only simple Ln/Log capable calculators (without a cover) will be allowed; no cell phones or other devices wherein ‘cheat sheets’ may be stored will be allowed. You may not borrow from a friend or from me during the quizzes or examinations. No caps during exams, and backpacks will be placed along the walls of the classroom. For all quizzes and exams, be seated in every other seat to the extent possible, in straight columns. If you are forced to sit in a seat adjacent to your classmate, move to the front of the room to do so.

VI. Assessment and Grading

1. Student Performance Evaluation: i. Quizzes: On 8 designated days, a short “Cell Fizz Quiz” will be administered during class

(see dates below). Quizzes will cover new material presented since the last quiz or exam as indicated. Each quiz will be worth 10 points, and the 3 lowest quiz scores will be dropped. Therefore, quizzes will cumulatively account for 50 points. Please note that quizzes are intended simply to keep you on track with memory work and use of mathematical equations. Quizzes are not reflective of the rigor of the examinations. Studying only well enough to perform well on quizzes will not result in a top grade in BIO 4307. You should be studying all of the indicated information in depth each week to earn an A or B grade.

ii. Participation in class will be assessed using “Clickers” as well occasional out of class

assignments or the products of in-class activities. Your ability to participate will often rely on your having read assigned articles and the textbook. Periodically, questions over the prior night’s assigned reading will be asked and will ‘count’ toward your participation grade.

A total of 50 participation points may be earned. To receive the full 50 participation points, you must earn at least 80% of the credit available via Clicker entries or other assignments. You must earn at least 70% of the available credit to earn 40 participation points. If you earn 50% of the available credit you will be awarded 30 participation points, while earning 30% of the available credit will result in 20 points being awarded. Students earning fewer than 30% of the available credit will not be awarded participation points. The relatively ‘low bar’ set for earning full participation acknowledges that many of you are in the process of interviewing for professional or graduate school and that, on occasion, clickers fail. Therefore, I have already accounted for these issues and I may also account for these issues prior to assigning final grades for the class as a whole. I WILL NOT adjust your individual clicker score on a given day for any reason. Please don’t ask.

iii. Exams: Three in-class exams and one final exam will also be administered. The final exam will be comprehensive of all material presented during the course. Each exam will be worth 100 possible points.

50 Cell Fizz Quiz points (5 highest scores of 8 total count toward grade; 10 pts per quiz) 50 Participation points 100 Exam I Points 100 Exam II Points 100 Exam III Points 100 Final Exam Points

 

  5  

Total Possible Points: 500

Those individuals who earn 450-500 points are guaranteed an “A”. To guarantee a “B+” one must earn 435-449 points. To guarantee a “B”, one must earn 400-434 points. To guarantee a “C+”, one must earn 385-399 points. To guarantee at least a “C”, one must earn 350-384 points. A “D” will be assigned to those earning, 300-349 points. A failing grade will be assigned to those who earn fewer than 300 points.

2. Statement on Final Grade Assignment and Suggestions for Student Success: Your

performance in this course is your responsibility. Seniors expecting to graduate at the end of the semester are strongly encouraged to avoid falling behind. Biochemistry is complex and detail-oriented; “cramming” is not advisable. Use your study guide after each lecture. If you are experiencing difficulties, visit my office or SI sessions before the situation is irreversible. No special assignments, ‘re-takes’ or extra points will be granted to individuals for grade improvement. All end of semester grades are FINAL.

3. Graduate Students: Graduate students taking BIO 4307 for graduate credit are required to

complete an additional 50 point project (total 550 course points for graduate students). The project due date is December 1. Please make an appointment during office hours to discuss.

VII. Course Outline/Course Schedule

BIO 4307 Course Schedule APPROXIMATION Spring 2015—Subject to Change Date Topic Related Reading

Assignment August 25 Course Overview

Introduction to Cell Physiology and Biochemistry Syllabus

Chapters 1 and 2 *Review basic concepts in

acid/base chemistry on your own

August 27 Class Policies Review Importance of pH and Buffer Systems in Biochemistry

Syllabus Chapter 2

September 1 Introduction to Amino Acids and Protein Assigned Reading (TBA) Chapters 3 and 4

September 3 Quiz 1 (pH and buffer systems; Amino Acid Structures and Characteristics)

Protein Charge and Structural Elements Structural Proteins and the Cytoskeleton

Chapter 4

September 8 Thermodynamics, Free Energy and Enzymes as Catalysts I

Assigned Reading (TBA) *Review Basic Concepts of Thermodynamics on your own—Keq and standard

free energy change Chapter 6

September 10 Quiz 2 (Amino Acid and Peptide Charge) Thermodynamics, Free Energy and Enzymes as

Catalysts II

Review Basic Concepts in

catalysis on your own Chapter 6

Chapter 8 pg. 134-138 September 15 Enzyme Kinetics I Chapter 7 pg. 105-108 September 17 Enzyme Kinetics II and the Smooth Endoplasmic

Reticulum Chapter 7 pg. 108-112 Chapter 8 pg. 125-134

 

  6  

September 22 Quiz 3 (Thermodynamics and Enzyme Kinetics) Protein Analysis

Allosteric Proteins (End of Exam I materials)

Assigned Reading (TBA) Chapter 5 pg. 67-78, 84-87

Chapter 7 pg. 112-118

September 24 Allosteric Proteins and Hemoglobin Chapter 9 September 29 Carbohydrates, Glycoproteins and Glycolipids

Cell Surface and the Extracellular Matrix I

Chapter 10 pg. 157-166 October 1 Exam I October 6 Carbohydrates, Glycoproteins and Glycolipids

Cell Surface and the Extracellular Matrix II Assigned Reading (TBA) Chapter 10 pg. 167-175

October 8 Quiz 4 (Hemoglobin and Carbohydrates)

Nucleic Acids and the Nucleus Selected Topics DNA replication and mRNA

Transcription

Chapter 33 Chapters 32 pg. 555-563

Review the Central Dogma

of Biology Selected Topics--Chapters 34 (pg 597-601), 36 (pg. 629-633), 37 and 39 (pg.

675-679) or BIO 2306 notes

October 13 Protein Synthesis and Localization: the Rough Endoplasmic Reticulum

Ribosomes

Chapter 39 (pg. 680-685, others as review)

Chapter 40 (pg. 689-702) October 15 Lipids

Cholesterol Synthesis and Endocytosis Chapter 11

Chapter 29 pg. 503-515 October 20 Quiz 5 (Polysaccharides and Nucleic Acids)

Membrane Structure and Function The Endomembrane System and Protein Trafficking

Assigned Reading (TBA)

Chapter 12

October 22 Cell Membrane Receptors and Signal Transduction Western Blotting

Introduction to Digestion (End of Exam II materials)

Chapter 13 Chapter 5 pg. 78-83

Chapter 14 (pg 237-242)

October 27 Cellular Energy Sources Glycolysis

Fermentation

Chapter 15 Chapter 16

October 29 Exam II November 3 Gluconeogenesis

Coordination of Glycolysis and Gluconeogenesis

Chapter 17 Assigned Reading (TBA)

November 5 Quiz 6 (Glycolysis, Fermentation and Gluconeogenesis)

Preparation for the Citric Acid Cycle Citric Acid Cycle and Regulation

Chapter 18 Chapter 19

November 10 Quiz 7 (Regulation of Glycolysis and Gluconeogenesis; Citric Acid Cycle)

Electron Transport Chain and the Mitochondria

Chapter 20 Assigned Reading (TBA)

November 12 Oxidative Phosphorylation and Apoptosis Chapter 21

November 17 Quiz 8 (Electron Transport Chain and Oxidative Phosphorylation)

Glycogen Degradation

Chapter 24

 

  7  

*For review, consult your introductory chemistry or biology course text

(End Exam III materials) November 19 Glycogen Synthesis Chapter 25 November 24 Exam III December 1 Fatty Acid Degradation/Synthesis Overview Chapters 27 and 28

(selected topics) December 3 Metabolic Regulation, Diabetes and Obesity Assigned Reading (TBA)

pp. 226-228, 243-244, 293-294, 309, 443-445

December 15 Cumulative Final Examination 4:30-6:30 PM in B110