Molecular Biology II (PCB4524) Syllabus
Section 001: Spring 2023
3 credit hours
Lecture: TuTh 12:00-1:15pm
Nicholson School of Communication and Media
(NSC) room 101
As a graduate of this class and our BS in Biomedical Science’s program, students should be
able to differentiate the process of transcription and translation, as well as the steps and
proteins used by prokaryotes and eukaryotes.
Contact Information:
Camilla T. Ambivero, Ph.D.
Associate Professor
Burnett School of Biomedical Sciences, College of Medicine
Email: Camilla.Ambivero@ucf.edu
Office Hours: Posted during the first week of class
Prerequisites: Molecular Biology I (PCB 3522)
Course Text:
Molecular Biology: Principles and Practice; Michael M. Cox, Jennifer Doudna, Michael
O'Donnell; 2nd edition 2015, MacMillan Learning with Achieve (ISBN-13: 9781464182525)
Required Material that Supplements the Text:
The lectures closely follow the text, but some information found in the PowerPoints may come
from different textbooks and manuscripts as your instructor sees fit. Students are responsible for
all material covered in pre-recorded lecture as well as through any discussion.
Technical Requirements:
• Students need to have access to the internet.
• Students should check Canvas or their email daily to ensure they have the most up to
date information about the class. Failure to check Canvas or attend class can severely
impact your grade. Students are responsible for ensuring their e-mail address listed with
Conversations is accurate.
• The use of computers for activities other than note-taking during lecture is not permitted.
Cell phones should be silenced during class.
• Instructors will not discuss grades over email or Canvas messenger; please make an
appointment if you must discuss your class standing.
• You will be using Achieve from MacMillan for your homework grade, so please ensure
you have a compatible browser. Make sure to use your UCF Knights’ email address
when registering.
• We will be using UCF Here for attendance. Please download the app on your phone
before the end of the first week of class. It is available for both Android and Apple.
•
Students are responsible for technical related issues. Please contact the proper support
department (such as Canvas or MacMillan) for technical difficulties.
Class Attendance:
• Our discussions will be held in person and attendance taken via UCF Here.
• Please review the schedule posted on Canvas with the material you are responsible for
reviewing before lecture, as these correspond to the slide numbers in your pre-recorded
lectures.
• Attendance is not mandatory; however, we will have daily Canvas quizzes given during
lecture. These quizzes can be accessed via a computer or the Canvas app on your
phone and will be open for the first 15 minutes of lecture. These quizzes do not directly
impact your grade in a negative way. These quizzes are there to help identify
weaknesses and topics for further discussion.
Emails:
• We will not be using Canvas message to communicate with you, so please do not use
Canvas messages to communicate with us.
• When emailing the instructors include in the subject line of your email [PCB4524-001] so
I can best assist you with your question and concern.
• Emails should be written in a professional manner. Please avoid salutations using your
instructors’ first name, and make sure to always have your full name somewhere in the
email.
• If the answer to your email question can be found in this document, your email may not
be responded to.
• The professor will return all emails within 24 hours during business hours. During the
weekends you may receive replies within 72 hours.
• Emails at the end of the semester about grades will not be responded to.
• Please note that Florida has a very broad open records law (F.S. 119), which makes
emails subject to public disclosure.
Etiquette for emails:
The faculty and staff associated with Burnett School of Biomedical Sciences are your advocates
and want you to succeed in this course and program. You have every right to ask to review an
issue with the appropriate faculty or staff. It is NOT acceptable to write inflammatory emails or
use expletives in meetings. An individual who displays disruptive behavior will be asked to leave
the class and further departmental action may be taken.
Mandatory Quiz:
As of Fall 2014, all faculty members are required to document students' academic activity at the
beginning of each course. To document that you began this course and to remain enrolled,
please complete the following academic activity by the end of the first week of classes, or as
soon as possible after adding the course, but no later than January 13th. For those on financial
aid, failure to do so will result in a delay in the disbursement of your financial aid.
Important Dates:
Add/Drop
Withdrawal Deadline
January 13th by midnight
March 24th by midnight
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Grading:
Grades will be posted on Canvas. As this class is graded on total points and not percentage,
please keep that in consideration when calculating where you stand in the class. Students will
receive a rubric in regards how their weekly assignments will be graded with each assignment.
Course grades are assigned on an objective basis and without regard to the identity of the
student or other departmental, program or scholarship requirements. It is the student’s
responsibility to see that their course grades are above any minimum requirements mandated
by their department, program or scholarship provider. The class is based on overall points and
not percentage.
Evaluation Procedures:
Examinations
Points
First Exam
100
Second Exam
100
Third Exam
100
Fourth Exam
100
Cumulative Final
100
Achieve Assignments
100
TOTAL POINTS
Grading Scale:
• ≥ 89.50% A
• ≥ 79.50% B
•
•
≥ 69.50% C
≥ 59.50% D
600
•
≤ 59.49% F
Curving of Grades:
Overall class performance is taken into consideration. Do not count on a curve as we will have
extra questions built into the exams for extra credit.
Incomplete (I) & Withdrawal Grades:
The grade of “I” (incomplete) indicates that the student’s work is satisfactory (of passing quality)
as of the end of the semester but has not been completed. The grade of “I” will be given only if
the student meets all the following requirements and UCF policies:
1) The student must have completed a substantial part of the course work.
2) The completed work must be of passing quality. Incompletes are not given to students
who are failing the course.
3) The student must demonstrate the existence of hardship that renders it unjust to hold the
student to the time limits previously fixed for the completion of the work.
When a grade of “I” is given, the instructor’s record of the student’s class work remains until the
student completes the course work. Previously completed work (prior to receiving the “I”) is then
considered with the final work in assigning the course grade. The grade of “I” does not erase all
previous work in the course; rather, it allows the student to repeat the course without paying
additional credit-hour and laboratory fees. The grade of “I” simply extends the time allowed for
completion of the remaining work. Work must be completed within two weeks of the start of
the following semester.
All withdrawal options must be through the Registrar’s Office or Academic Services in Millican
Hall.
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A late withdrawal is a withdrawal from the course after the withdrawal deadline due to
exceptional circumstances. Students are given a Was Passing (WP) or Was Failing
(WF) grade. This is not available if the final exam is taken.
• A medical withdrawal is given only for urgent reasons related to extended illness or
distress that prevents a student from finishing the course. The student is then withdrawn
from all courses. Extended mid-semester absences would be more likely to fit under the
late withdrawal͟ or medical withdrawal͟ categories.
This class does not allow for “NC” (no credit) grades.
•
Homework Assignments:
• There are homework assignments through MacMillan’s Achieve which you should have
setup before the end of the first week.
• It is highly recommended that students do the assignments as we move through the
material and not the night before it is due. Assignments may take a few hours to
complete and failure to complete assignments by the deadline will severely impact your
grade. The homework assignment is graded on completion, even though that accuracy
will help you complete the assignments quicker.
• There will also be extra problems available for practice before the exam which will not
count towards your grade. These assignments are found in Achieve and are strictly
optional, even though they may help you better prepare for the exam.
• Students are expected to work alone on their homework assignments as well as their
chapter quizzes.
Exam Format and Grading:
• All exams count towards your final grade. No exam grade will be dropped.
• For the exception of the final, exams will most likely be 50 multiple choice questions.
Questions will come from all levels of Bloom’s Taxonomy. Students should be able to
recall information as well as apply the information they have learned to solve problems.
• Exam format may change as per the discretion of the professor; however, the number of
points will not change.
• Exams may include information from the PowerPoint slides, textbook material, lecture
notes and any other material covered in the classroom.
• It is the student’s responsibility to attend course lectures to obtain any information
regarding course announcements or other supplemental course information that is
provided during the lecture sessions.
• The exam must be completed within the allocated time. Any student who starts the exam
late will not be given extra time.
• Exams can be reviewed for one week during scheduled hours or with an appointment.
Students are not allowed to make notes or have their notes and/or electronics out.
• Once grades are posted, they are non-negotiable.
• Your final will be a 100 multiple-choice questions cumulative exam. Exam will be given
on Thursday, April 27th at 10:00am-12:50pm in accordance with UCF’s Final Exam
Schedule. Your instructor may not give you the full time to take the exam, but the
amount that seems to be the best fit.
• Cell phones, smart watches or any other technology cannot be used during any
examination. Anyone using one during an exam will be cheating. Cell phones are
expected to be on silent or turned off during an exam, not on vibrate.
• Exams are not to be removed from the classroom or the room where exam reviews are
being held. Anyone who is found to be in possession of an exam will be sent to Student
Conduct and UCFPD.
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Exam and Assignment Make-up:
• We will be using UCF’s pink/raspberry scantrons for your exams.
• These are not typically offered. Religious holidays and UCF approved team travel are
the two reasons an alternative test date would be approved without penalty as per UCF
policy. It is requested that students notify the instructor at the BEGINNING OF THE
SEMESTER for such accommodations. “Ask for permission, not forgiveness.”
• Military duty and jury duty will also be excused without penalty. Please contact your
professor as soon as you are made aware of any date conflicts.
• Alternative exams due to conflicts with other important, scheduled events related to
education, such as professional school interviews, will be considered. Please note that
work and work-related functions are not school sponsored events and therefore do not
fall under excused absences.
• Students with chronic medical conditions should contact Students Accessibility Services
(SAS) at the beginning of the semester in case something arises during the semester.
• If a student is under the care of a physician on the day of the exam, an alternative exam
date may be considered. Notes from an office visit are not considered “under a
physician’s care” and will not be accepted. Please note that this includes COVID-19.
• Due to an increase in falsified doctor’s notes, and to be fair to all students, the following
will be accepted forms of proof if a student is sick on exam or class day:
o Hospital discharge papers (please black out personal information, reason for
being seen, etc); must only include name of patient/student, DOB, date seen, and
doctor seen with contact information. Patient bracelet, which includes patient’s
name, DOB and date seen at the hospital.
o The instructor will contact the hospital and/or physician’s office to ensure the note
is authentic. The instructor will not ask why you were seen or any other personal
information, as to follow strict HIPAA (Health Insurance Portability and
Accountability Act) guidelines.
• The following will not be accepted as proof without further documentation:
o Any note that solely states “patient may return to work on” without discharge
papers or secondary proof.
o Any at-home COVID-19 test results.
• Any student who is found to have turned in a falsified document (doctor’s note, crash
report, interview invite, etc) will receive a zero for the assignment and submitted to
Student Conduct for further action.
• Instructor may not give you any extension if you fall ill before an exam, as students
should be studying as we go through the material and not cramming days prior. “A lack
of planning on your part does not constitute an emergency on my part.”
• Since homework assignments are due online, students on vacation or any other out-oftown trips will not be granted extensions.
• The professor holds the right to reject any request for an alternative test date that does
not include valid documentation. Professor also holds the right to withhold any curves
given to the class and/or change the exam format if the student takes the exam later.
Academic Honesty:
Many incidents of plagiarism result from students’ lack of understanding about what constitutes
plagiarism. You are expected to familiarize yourself with UCF’s policy on plagiarism. All work
you submit must be your own scholarly and creative efforts. UCF’s Golden Rule defines
plagiarism as follows: “whereby another’s work is used or appropriated without any indication of
the source, thereby attempting to convey the impression that such work is the student’s own.”
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Cheating will be subject to appropriate referral to the Office of Student Conduct for further
action. Penalties can include a failing grade in an assignment or in the course, suspension or
expulsion from the university, and/or a "Z Designation" on a student's official transcript indicating
academic dishonesty, where the final grade for this course will be preceded by the letter Z. For
more information about the Z Designation, see http://z.ucf.edu/.
Course Accessibility Statement:
The University of Central Florida is committed to providing access and inclusion for all persons
with disabilities. This syllabus is available in alternate formats upon request. Students with
disabilities who need specific access in this course, such as accommodations, should contact
the professor as soon as possible to discuss various access options. Students should also
connect with Student Accessibility Services (Ferrell Commons, 7F, Room 185, sas@ucf.edu,
phone (407) 823-2371). Through Student Accessibility Services, a Course Accessibility Letter
may be created and sent to professors, which informs faculty of potential access and
accommodations that might be reasonable.
FERPA and Privacy:
As a student, your educational records are considered confidential. Under FERPA (Family
Educational Rights and Privacy Act), your records are confidential and protected. Under most
circumstances your records will not be released without your written and signed consent.
However, some directory information may be released to third parties without your prior consent
unless a written request to restrict this is on file. You can learn more about student rights to
privacy at http://registrar.ucf.edu/ferpa.
Disruptive or Rude Behavior will NOT be Tolerated:
• Disruptive behavior will not be tolerated in this course.
o You may be asked to leave the class immediately.
o In cases of class dismissal, it will be necessary that you set an appointment time
with the instructor to discuss the disruptive/rude behavior prior to your being
allowed to return to class.
• Inappropriate use of Canvas links will result in the immediate and unannounced removal
of your access to the site.
o In cases of lost Canvas access, it will be necessary that you set an appointment
time with the instructor to discuss the inappropriate use of the Canvas site prior
to your access being restored.
Keys for Success:
Class attendance for the lecture sessions is highly recommended. Data support the idea that
class attendance improves learning. To do well in the course you must attend lecture and study
the lecture notes thoroughly between lectures. It is very important that you keep up with the
reading, studying and your assignments. If you are confused about your assignments or any
material, contact your professor as soon as possible to discuss how to improve. I am here to
help you learn. Most questions can be and are best addressed during lecture hours. Try to work
together! Come to class prepared to learn and seek the assistance of others. Keep in mind that
the two most important criteria for success, in either college or the workplace, are motivation
and hard work!
ASBMB Fundamental Concepts:
The American Society for Biochemistry and Molecular Biology (ASBMB) has set forth a list of
topics students who complete a class in molecular biology should be able to have an advanced
and/or basic understanding of the following:
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1. The genome: A genome is an organism’s complete set of DNA, including all of its genes.
Each genome contains all the information needed to build and maintain that organism.
Some noncoding sequences enable our cells to produce different amounts of proteins at
different times. For example, control sequences contain instructions to tell the cell how to
switch genes on and off. Other noncoding sequences are part of genes but do not directly
code for proteins. These are thought to help the cell generate a number of different proteins
from one gene. More than half of the DNA in our genome is made up of repeated
sequences, which appear to stabilize chromosomes; noncoding regions may have a role in
spacing out the coding sequences so that they can be activated independently.
a. Students should be able to define what a genome consists of and how the
information in the various genes and other sequence classes within each genome is
used to store and express genetic information.
b. Students should be able to discuss how the genome is organized and packaged in
prokaryotes and eukaryotes.
c. Students should be able to discuss tools used to study expression, conservation and
structure of an organism at the genome level.
d. Students should be able to explain the role of repetitive and non-repetitive DNA and
how its relative abundance varies from prokaryotes to eukaryotes.
2. Information in the gene: nucleotide sequence to biological function: The information
contained in the nucleotide sequence of a genome is organized into various elements,
including coding regions, which contain three base codons coding for amino acids, which
are transcribed to messenger RNA. The messenger RNA is translated to give the primary
sequence of a protein and regulatory elements. The transcribed coding region for a given
protein may contain introns and exons in eukaryotic cells. The amino acid sequence of a
protein gives rise to biological function through stably folded regions and/or intrinsically
disordered regions.
a. Students should be able to explain the central dogma of biology and relate the
commonality of the process to all of life.
b. Students should be able to explain the process of gene regulation connecting how
extracellular signals can result in a change of gene expression.
c. Students should be able to discuss how genes are organized and contrast the
different approaches used in prokaryotic and eukaryotic organisms.
d. Students should be able to explain how mRNA processing occurs and how splicing
affects the diversity of gene products in eukaryotic organisms.
3. Genome transmission from one generation to the next: The primary concern of cell
division is the maintenance of the original cell's genome. The genomic information that is
stored in chromosomes must be replicated, and the duplicated genome must be separated
cleanly between cells. Somatic cell lines are diploid (2n chromosome complement), and
mitotic division normally results in two daughter cells, each with chromosomes and genes
identical to those of the parent cell. Germline cells, called gametes, are haploid (having the
haploid or the n chromosomal complement) and reproduce by meiosis.
a. Students should be able to explain the differences of mitosis and meiosis and relate
them to the process of cellular division.
b. Students should be able to illustrate how DNA is replicated and genes are
transmitted from one generation to the next in multiple types of organisms including
bacteria, eukaryotes, viruses and retroviruses.
c. Students should be able to apply the concepts of segregation and independent
assortment to traits inherited from parent to offspring and discuss how they increase
genetic variation.
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4. Genome maintenance: Throughout its lifetime, the DNA in a cell is under constant
metabolic and environmental assault leading to damage. The ultraviolet (UV) component of
sunlight, ionizing radiation and numerous genotoxic chemicals, including the (by)products of
normal cellular metabolism (e.g. reactive oxygen species such as superoxide anions,
hydroxyl radicals and hydrogen peroxide), constitute a permanent enemy to DNA integrity.
Hydrolysis of nucleotide residues leaves non-instructive abasic sites. Spontaneous or
induced deamination of cytosine, adenine, guanine or 5-methylcytosine converts these
bases to the miscoding uracil, hypoxanthine, xanthine and thymine, respectively. Left
unchecked, the resulting genomic instability initiates cancer and other age-related disorders.
Inherited or acquired deficiencies in genome maintenance systems contribute significantly to
the onset of cancer. Over time, DNA accumulates changes that activate proto-oncogenes
and inactivate tumor-suppressor genes. Cells have evolved nucleotide- and base-excision
repair mechanisms, homologous recombination, end joining, mismatch repair and telomere
metabolism as mechanisms to maintain the integrity of the genome.
a. Students should be able to state how the cell ensures high fidelity DNA replication
and identify instances where the cell employs mechanism for damage repair.
b. Students should be able to explain what a mutation is at the molecular level, how it
arises and how it could potentially affect the organism from gene expression to
fitness.
c. Students should be able to construct relationships between chromosome and cellular
structures (e.g. telomere, centromeres and centrosomes) and explain how these
structures are responsible for and/or involved in genomic stability.
d. Students should be able to relate how the cell cycle and genome maintenance are
coordinated and how disruptions in this coordination could affect the organism.
e. Students should be able to list events that result in genomic instability and explain
how the cell responds to restore order and stability.
This syllabus is a tentative outline for the course.
Depending on conditions encountered during the semester,
Aspects of this syllabus may change accordingly.
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Tentative Schedule:
Week
Material(s) Being Covered
1
Syllabus, Introduction, Overview of
Molec I
2
Chapter 13: Recombinational DNA
Repair and Homologous
Recombination
3
Chapter 14: Site-Specific
Recombination and Transposition
4
EXAM 1
5
Chapter 15: Transcription: DNADependent Synthesis of RNA
6
Chapter 16: RNA Processing
7
EXAM 2
8
Chapter 17: The Genetic Code
9
Chapter 18: Protein Synthesis
10
Chapter 19: Regulating the Flow of
Information
11
EXAM 3
12
Chapter 20: The Regulation of
Gene Expression in Bacteria
13
Chapter 21: The Transcriptional
Regulation of Gene Expression in
Eukaryotes
Chapter 22: The Posttranscriptional
Regulation of Gene Expression in
Eukaryotes
14
EXAM 4
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CUMULATIVE FINAL
Dates Stop on Slide
Assignments
1/10
Complete Academic Activity by 1/13
at 11:59pm
1/12
Complete Molec I Review Quiz by
1/15 at 11:59pm
1/17
Chp 13, 28
1/19
Chp 13, 51
1/24
Chp 14, 24
1/26
Chp 14, 46
1/31
2/2
2/7
Chp 15, 25
Chp 15, 47
2/9
Chp 15, 74
2/14
Chp 15, 97
2/16
Chp 16, 21
2/21
Chp 16, 55
Complete Chapter 13 Achieve by
1/22 at 11:59pm
Complete Chapter 14 Achieve by
1/29 at 11:59pm
EXAM 1 (Chapters 13 & 14)
Complete Chapter 15 Achieve by
2/12 at 11:59pm
Complete Chapter 16 Achieve by
2/22 at 11:59pm
EXAM 2 (Chapters 15 & 16)
2/23
2/28
Chp 17, 22
3/2
Chp 17, 42
Complete Chapter 17 Achieve by 3/5
at 11:59pm
3/7
Chp 18, 33
3/9
Chp 18, 67
SPRING BREAK
3/21
Chp 18, 88
3/23
Chp 19, 21
3/28
Chp 19, 46
Complete Chapter 19 Achieve by
3/29 at 11:59pm
EXAM 3 (Chapters 17, 18 and 19)
3/30
4/4
Chp 20, 23
4/6
Chp 20, 41
4/11
Chp 21, 33
4/13
Chp 22, 34
Complete Chapter 20 Achieve by 4/9
at 11:59pm
Complete Chapter 21 Achieve by
4/12 at 11:59pm
Complete Chapter 22 Achieve by
4/17 at 11:59pm
EXAM 4 (Chapters 20, 21 and 22)
No class
UCF’s Study Day
4/18
4/20
4/25
5/27
Complete Chapter 18 Achieve by
3/22 at 11:59pm
10:00am
CUMULATIVE FINAL
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This schedule is subject to change at the instructor’s discretion.
Exam dates will not change unless there is a mandatory school closure.
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