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


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 selfassessed 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


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 grantedthis 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 doctors 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.


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
nights 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 dont 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


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 detailoriented; 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 2015Subject to Change
Date
Topic
Related Reading
Assignment
August 25
Course Overview
Syllabus
Introduction to Cell Physiology and Biochemistry
Chapters 1 and 2
*Review basic concepts in
acid/base chemistry on
your own
August 27
Class Policies Review
Syllabus
Importance of pH and Buffer Systems in Biochemistry
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
Chapter 4
Structural Proteins and the Cytoskeleton
September 8
Thermodynamics, Free Energy and Enzymes as
Assigned Reading (TBA)
Catalysts I
*Review Basic Concepts of
Thermodynamics on your
ownKeq and standard
free energy change
Chapter 6
September 10
Quiz 2 (Amino Acid and Peptide Charge)
Thermodynamics, Free Energy and Enzymes as
Review Basic Concepts in
Catalysts II
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
Chapter 7 pg. 108-112
Reticulum
Chapter 8 pg. 125-134


September 22

September 24
September 29
October 1
October 6

Quiz 3 (Thermodynamics and Enzyme Kinetics)

Protein Analysis
Allosteric Proteins
(End of Exam I materials)
Allosteric Proteins and Hemoglobin
Carbohydrates, Glycoproteins and Glycolipids
Cell Surface and the Extracellular Matrix I
Exam I
Carbohydrates, Glycoproteins and Glycolipids
Cell Surface and the Extracellular Matrix II

October 8
Quiz 4 (Hemoglobin and Carbohydrates)
Nucleic Acids and the Nucleus
Selected Topics DNA replication and mRNA
Transcription

October 13
October 15
October 20

October 22

October 27
October 29
November 3
November 5

November 10

November 12
November 17

Protein Synthesis and Localization: the Rough

Endoplasmic Reticulum
Ribosomes
Lipids
Cholesterol Synthesis and Endocytosis
Quiz 5 (Polysaccharides and Nucleic Acids)
Membrane Structure and Function
The Endomembrane System and Protein Trafficking
Cell Membrane Receptors and Signal Transduction
Western Blotting
Introduction to Digestion
(End of Exam II materials)
Cellular Energy Sources
Glycolysis
Fermentation
Exam II
Gluconeogenesis
Coordination of
Glycolysis and Gluconeogenesis
Quiz 6 (Glycolysis, Fermentation and
Gluconeogenesis)
Preparation for the Citric Acid Cycle
Citric Acid Cycle and Regulation
Quiz 7 (Regulation of Glycolysis and
Gluconeogenesis; Citric Acid Cycle)
Electron Transport Chain and the Mitochondria

Assigned Reading (TBA)

Chapter 5 pg. 67-78, 84-87
Chapter 7 pg. 112-118
Chapter 9
Chapter 10 pg. 157-166
Assigned Reading (TBA)
Chapter 10 pg. 167-175
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
Chapter 39 (pg. 680-685,
others as review)
Chapter 40 (pg. 689-702)
Chapter 11
Chapter 29 pg. 503-515
Assigned Reading (TBA)
Chapter 12
Chapter 13
Chapter 5 pg. 78-83
Chapter 14 (pg 237-242)
Chapter 15
Chapter 16

Chapter 17
Assigned Reading (TBA)
Chapter 18
Chapter 19
Chapter 20
Assigned Reading (TBA)

Oxidative Phosphorylation and Apoptosis

Quiz 8 (Electron Transport Chain and Oxidative
Phosphorylation)
Glycogen Degradation
6

Chapter 21
Chapter 24


November 19
November 24
December 1

(End Exam III materials)

Glycogen Synthesis
Exam III
Fatty Acid Degradation/Synthesis Overview

December 3

Metabolic Regulation, Diabetes and Obesity

December 15

Cumulative Final Examination

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

Chapter 25
Chapters 27 and 28
(selected topics)
Assigned Reading (TBA)
pp. 226-228, 243-244, 293294, 309, 443-445
4:30-6:30 PM in B110