ADVANCES IN MOLECULAR BIOLOGY
Bio 41001 & 41002
Syllabus - Laboratory and Lecture
LAB SECTION:
LECTURE:
Dr. James Bricker Office: BI 116 extension 2457
Dept. of Biology E-mail: bricker@tcnj.edu; Web Page: http://bricker.tcnj.edu
Office Hours: BI 116 or 112 (research lab)
Basic Information
Purpose statement: Advances in Molecular Biology is an upper level course, aimed at juniors and seniors. It is designed to give a good background in current Molecular Biology, which should allow for easy continuation to graduate or professional school courses. The major themes are Eukaryotic and Prokaryotic DNA replication, Chromosomal structure and function and Gene structure and function. Students will learn from current papers in the scientific literature, and will be expected to use concepts developed in the course in class, in the laboratory and in exams.
Molecular Biology is fundmental to the study of all living things. It describes, in its most basic form, the mechanisms of how organisms live, reproduce and evolve. It is basic to much of modern Biology, no matter what the field of study.
Course description: The purpose of this semester of Advances in Molecular Biology is to familiarize the student with those concepts that are basic to the functioning of prokaryotic and eukaryotic cells.
Lecture is the foundation of the course. Laboratories will not always coincide with the lecture topics. The student is responsible for assignments that add to the lecture and lab material. The student is encouraged to seek out related materials that are available, such as scientific journals (e.g. Cell, Nature, Scientific American), newspapers, magazines and television programs (e.g. channels 12 and 52) that relate to course topics. Lecture notes will be published on the internet at my home page before the given lecture.
There are three basic concepts in this course - the replication of DNA; the structure and function of chromosomes; and the structure and functioning of genes. They will be organized as indicated below.
Assignments: Selected articles; resource texts and reserve library materials as required. Watson et. al. Molecular Biology of the Gene ed. 5 (text) as assigned. Lectures cannot cover all that is in the text, and are designed to be complementary to, instead of a repetition of, the text. Exams will be on the lecture material and on those portions of the text and assigned papers relating to it. Assigned text readings are listed by chapter; a given lecture might not cover all the subjects in the chapter(s) listed. Recent papers will be assigned as needed, for each topic, and will be listed in the notes for that lecture. Most topics will be outlined in notes handed out prior to the lecture, if possible. These notes are study guides, not a description of what is required for exams.
Current materials and topics will be included when appropriate. Initiative on the part of each individual student in asking pertinent questions and inviting conversation on related outside topics will be noted in the final grade; the professor's evaluation of student participation in lecture and laboratory can be used to benefit hard working students and possibly enhance their grade if they are in a borderline position.
Prerequisites: Biology of the Eukaryotic Cell, Organic Chemistry.
Learning Goals
Content Goals: When they have finished the course, students will have been exposed to Molecular Biology laboratory techniques (DNA isolation and purification, recombinant DNA synthesis and cloning, gene detection,PCR and Southern and Western Blotting), which will be used to expand the student's appreciation and knowledge of the lecture material. The lectures cover Molecular Biology as a whole - the "central dogma" of Biology: DNA makes RNA which then makes protein. Out of this there arise three concepts - Eukaryotic and Prokaryotic DNA biosynthesis; Chromosomal structure and function (with associated proteins and functions); and Eukaryotic and Prokaryotic gene structure and function (mRNA, tRNA synthesis and function, including protein synthesis), and how they relate to basic biological and chemical concepts (such as the action of evolutionary processes on living things) learned in previous courses. In general, they should understand how our genomes function, including gene activation and deactivation, RNA synthesis and protein biosynthesis and be able to use this knowledge in their work and in the laboratory. Overall, emphasized and reemphasized in the course, and illustrated by specific examples and laboratory experiments, are the ways in which the above topics are interconnected, and factors used in one way are recycled to be used in another. This leads to interconnectiveness amongst the various cellular functions, and allows for signaling and controls between them. These principles should allow them to establish a firm connection between this course and other aspects of biology and give a foundation for future Molecular Biology courses and/or a good appreciation of concepts needed to make reasoned choices in their everyday lives.
Performance Goals: Students should acquire a good understanding of the concepts above. They should be able to show their mastery of them in oral and written form, in lecture, in the laboratory and in exams. They should be able to design experiments to isolate DNA, identify genes and gene products, interpret the data and communicate it.
Student Assessment
Advances in Molecular Biology is an upper level course, aimed at juniors and seniors that is designed for Biology majors who want to expand their knowledge of the biological world, in general, or for use in professional or graduate school. Students need to be able to understand both the concepts presented as well as have an understanding of the factual nature of the course, in order to go on to higher learning, or to better understand the world. To achieve that goal, feedback will be given on responses to questions asked in lecture and laboratory, questions asked by the student(s) in any setting, exams, and on the laboratory paper in as prompt fashion as possible so that the students will always understand how they stand.
GRADING:
| Exams - | 16.67% of final grade (x 3 exams): | 50%
|
| Final Exam - | 30% of final grade: | 30%
|
| Laboratory - | 20% of final grade* | 20%
|
| Totals | ... | 100%
|
*The laboratory grade is based mainly on the laboratory paper (normal scientific format, aprox. 8 pages, with a bibliography and internal referencing), as well as the instructor's assessment of the student's activity for the entire laboratory. Some laboratory based questions will appear on exams, especially including the final exam.
The professor's evaluation of student participation in lecture and laboratory can be used to benefit hard working students and possibly enhance their grade if they are in a borderline position.
Missed Exams: Call or contact Dr. Bricker before the exam if you must miss it. Leave messages with the Biology department office as soon as possible. All makeup exams will be given on the last Wednesday of classes (no exceptions).
Student Responsibilities: Attendance in laboratory and lecture is necessary and expected.
Student Input: Personal interests and ideas relating to the course are encouraged, and, where possible, incorporated into the course. If you have ideas or opinions, express them so that they can add to the appreciation of the course. The course is improved by responsible input from the student.
Learning Activities
These will consist of lectures, laboratory demonstrations, laboratory work, reading assigned scientific papers, writing a laboratory paper and answering those questions that are asked in lecture and laboratory. Outside the formal lecture / laboratory structure, the student is expected to read assignments in the text, as well as assigned papers from the scientific literature, and study the concepts presented in lecture, laboratory and in the text. Hopefully this mix of learning activities will create a deeper appreciation of Molecular Biology.
| | TOPIC | TEXT
|
|---|
| SECTION ONE: | DNA replication, repair and recombination |
|
|---|
| Introduction | Chapters 1 - 5
|
| Prokaryotic\Eukaryotic Cell Cycles | Chapters 6 & 7
|
| DNA Replication | Chapter 8
|
| DNA Replication | Ibid
|
| DNA Replication | Ibid
|
| DNA Repair | Chapter 9
|
| DNA Recombination | Chapter 10 & 11
|
| EXAM 1
|
| SECTION TWO: | Chromosome structure and function, chromatin, prokaryotic operon structure and function. |
|
|---|
| Chromosome Structure and Function | Chapter 7
|
| Chromatin | Ibid
|
| Chromatin | Ibid
|
|---|
| The Prokaryotic Operon: Promoters | Chapter 16
|
| The Prokaryotic Operon: Operators | Ibid
|
| The Prokaryotic Operon: Control | Ibid
|
| The Prokaryotic Operon: Control | Ibid
|
| EXAM 2
|
| SECTION THREE: | The eukaryotic operon structure and function, gene clusters, genes in organelles. |
|
|---|
| The Eukaryotic Operon: Organization | Chapter 2, 3, 17 & 18
|
| The Eukaryotic Operon: Implications | Ibid
|
| The Eukaryotic Operon: Transcription | Ibid
|
| The Eukaryotic Operon: Post-Transcriptional Processing | Ibid
|
| The Eukaryotic Operon: Gene Clusters |
|
| Genes in Organelles | Chapter 15 & 19
|
| EXAM 3
|
| SECTION FOUR: | Ribosomes, protein biosynthesis and transportation, eukaryotic and prokaryotic viruses, genetic engineering. |
|
|---|
| Ribosomes | Chapter 14 & 16
|
| Protein Translation | Ibid
|
| The Signal Hypothesis | Chapter 17
|
| Nuclear Transport | Chapter 13
|
| MAKEUP EXAMS | see above
|
| |
|
| Lab Report |
|
FINAL EXAM TBA All of the above
Laboratory Schedule - text: Human Molecular Biology - S. Surzycki
| week 1 | | Lab 7- 1 | | |
|
|---|
| week 2 |
| Lab 7 - 2 |
| week 3 | | Lab 7-3 & 4
|
| week 4 | | Lab 7-5
|
| week 5 | | Lab 7-6
|
| week 6 | | Lab 7-6
|
| week 7 | | Lab 7-7
|
| week 8 | | | Analysis
|
| week 9 | | | |
Lab 8-1
|
| week 10 | | | |
Lab 8-2
|
| week 11 | | | |
Lab 8-3
|
| week 12 | | | |
Lab "8-4"
|
| week 13 | | | |
| Analysis
|
The laboratory is designed to have students investigate advanced concepts in Molecular Biology, using the latest techniques.
| Human Telomere Length Experiment | | Laboratory Report due at End of Experiment
|
| Lab 7 Human Telomere Length Detection; 7-1 | | DNA Isolation
|
| Lab 7-2 | | DNA Purity and Concentration
|
| Lab 7-3 & 4 | | Restriction Digest & Agarose Gel Electrophoresis
|
| Lab 7-5 | | Southern Transfer
|
| Lab 7-6 | | DNA Hybridization
|
| Lab 7-7 | | TRF Length
|
| | |
|
| Human Gene Detection Experiment | | Question(s) asked on Final
|
| Lab 8 RT PCR; 8-1 | | RNA Purification
|
| Lab 8-2 | | RNA Agarose EP
|
| Lab 8-3 | | RT PCR Reaction
|
| "Lab 8-4" | | PCR Gel EP
|