Introduction to Molecular Biology and Biochemistry Research (01:694:315)
This course is open first to declared Molecular Biology and Biochemistry (694) majors.This course is also intended for second year students who plan to become Molecular Biology and Biochemistry majors and have completed the prerequisites courses. The course is also open to non-MBB majors.
Offered: For the Spring 2021 semester, this course will be taught in a synchronous remote manner:
On line Lecture/Discussion sessions will be held T3 (Tues 12:00-1:20 PM) and H3* (Thurs. 12:15-1:10 PM)
Lab Sessions will be used to answer questions and go over problems.
Lab Section 01 T45 (Tues 1:40-4:40 PM)
Lab Section 02 W45 (Wed 1:40-4:40 PM)
Credits: 3 (Credit not given for both this course and 01:447:315, 694:215 or 694:214.)
Prerequisites: General Biology 01:119:116, 117 and General Chemistry 01:160:162 or 01:160:164.
Learning Goals: The purpose of this course is to train students in many of the techniques used in modern molecular biology and biochemistry by giving them as much "hands on" experience as possible. In designing this course, we wanted to avoid the problems of lab courses in which the experimental outcome is already known and the aim of the laboratory exercises is to simply reproduce the expected results as closely as possible. We have therefore developed a course in which students will carry out a research project for which the results are unknown.
The project: After some initial training in techniques commonly used in molecular biology, students will start to work on their main research project. The project involves sequencing random clones from a cDNA library. The sequences derived from these experiments will be used to query a database for sequence similarity using the appropriate computer software. When matches are found, students will then search the scientific literature for information on the genes that they have identified. Students have the potential of identifying novel genes.
Tentative Lecture and Lab Schedule
|Week||Topic (Download lecture and lab notes and figures from the Canvas site)|
|1||Lecture: Introduction, Project, Ch. 1-The Central Dogma|
|Lab: Lab Introduction and Rules|
|2||Lecture: Ch. 2 - Cloning Vectors, DNA libraries|
|3||Lecture: Ch. 3- Analyzing DNA - Restriction enzymes & PCR,|
|Lab: Basic Techniques: Dilutions, DNA concentration by comparison, Plating Library|
|4||Lecture: Ch. 4 & 5 -Sequencing DNA, Crop and edit DNA sequences|
|Lab: DNA concentration by OD, Colony streakouts|
|5||Lecture: Ch. 6- Bioinformatics Analysis Part I: BLASTN,|
|Lab: Set up bacterial cultures|
|6||Lecture: Ch. 7 - Bioinformatics Analysis Part II: BLASTX|
|Lab: Plasmid DNA Minipreps|
|7||Lecture: In Class Exam (Lectures & Labs for weeks 1-6)|
|Lab: Restriction Digests & PCR, DNA sequence analysis|
|8||Lecture: Ch. 7- Bioinformatics Analysis Part III: ORF, BLASTP|
|Lab: Gel Electrophoresis, Choose clones to sequence, DNA Sequence Analysis of Practice Clones,|
|9||No Class or labs - Spring Break|
|10||Lecture: Ch. 8- Bioinformatics Analysis Part IV: Determining the function of the protein-Literature and database searches|
|Lab: Set up cultures II, DNA Sequence Analysis of PCs|
|11||Lecture: Ch. 9 - Clustal, Protein structure and modeling|
|Lab: Plasmid DNA Minipreps II, PCR II, Restriction Digests II, DNA Sequence Analysis Due: Analysis of Practice Clones 1-3 completed|
|12||Lecture: Ch. 10 - Tools of Molecular Biology|
|Lab: Gel Electrophoresis II, Choose clones to sequence, Sequence Analysis of Unknown Clones|
|13||Lecture: Ch. 11 - Tools of Molecular Biology (cont)|
|Lab: Sequence Analysis of Unknown Clones|
|14||Lecture: Ch. 12 - RNAi and CRIPR,|
|Lab: Sequence analysis|
|15||Lecture: Careers in Biomedical Sciences, Choice of Majors Help Sessions.|
|Lab: Sequence analysis, Analysis of ALL clones must be completed|
Course satisfies the following MBB Dept. Learning Goals:
1. Students should demonstrate an understanding of the knowledge that is needed to begin biomedical research and that is required for post-graduate exams and studies.
2. Students should demonstrate the ability to find and evaluate information about specific biological systems or problems.
3. Students should demonstrate the ability to design experiments and critically analyze data.
4. Students should demonstrate the ability to communicate their research and findings orally through seminar and poster presentations and through written research papers.
Core Curriculum Learning Goals met by this course:
NS e. Understand and apply basic principles and concepts in the physical or biological sciences.
NS f. Explain and be able to assess the relationship among assumptions, method, evidence, arguments, and theory in scientific analysis.
IRT y. Employ current technologies to access information, to conduct research, and to communicate findings.
IRT z. Analyze and critically assess information from traditional and emergent technologies.
1. Exams (40%): The mid-term and the final exam will focus on the material covered in the lectures, labs, and assigned reading.
2. Quizzes (30%): There will be two forms of quizzes.
A) Chapter Review Quizzes: After watching the video or reading the lecture notes on a chapter students will take quizzes posted on Canvas on the material. These will be used for the students to gauge their basic understanding of the material. These will be self-paced, but must be completed before the topics are discussed in the on-line meetings. These will represent 10% of the grade.
B) Analysis Quizzes: These quizzes will be given over a 4 hr period or in class to gauge the understanding of the material that was presented in the lecture notes and videos and then covered in the online discussion sections in the previous week. These quizzes will account for 20% of your grade.
3. Lab Reports (20%): During the semester, students will be expected to turn a series of Lab Reports in which they will report about the data they collected. Students will be expected to mock up their data and answer questions about their conclusions from the analysis of their data. These reports will be submitted through the Assignments page on the course’s Sakai site.
To simplify and better organize the analysis of your DNA sequences we have developed an online tool, the DNA Sequence Analysis Program (DSAP), to help guide students in the analysis of their DNA sequences and record their data. During the course, each student will analyze a series of practice DNA sequences, called PCs for practice clones, as well as their own unknown clones. At various points during the semester, students will need to submit this analysis for review by the staff. If the analysis is not correct, the students will be notified what needs to be changed to correctly complete the analysis. Although students will not be penalized if the answers are incorrect, the submission and completion of the analysis on time will be graded.
4. Assignments (10%) Workshops in the course will be used to review material that was covered in the lectures and labs, as well as discuss specific aspects of the material more in depth. Attendance at the workshops is mandatory and there may be quizzes and clicker questions administered during these periods. To help instructors to know what material to review for the worshops, each student must submit a question on the material that was covered in the lecture or lab that week. Submission of a question each week will be calculated into the grade. Although the questions themselves are not graded, it is hoped that the students put thought into these and ask things that are unclear or confusing. However, questions that are clear examples of no thought process (i.e. What is DNA?) will not get full credit. Other homework, problem sets and work sheets may also be assigned and graded.
Course Materials: A laboratory and lecture manual is posted on the course Canvas site.
Dr. Bryce Nickels
Waksman Institute, Room 335
Dr. Andrew Vershon
Waksman Institute, Rm 233
Phone: 445-2905 (note this now infrequently checked)
Office Hours: 7:00 -10:00 AM Tuesdays
Dr. Janet Mead
Waksman Institute, Rm 231
Office Hours: This course is designed to provide students with a unique, specialized laboratory experience. Thus, course participants are likely to require individualized attention at irregular and unpredictable intervals. In order to accommodate this unusual situation, the instructors have arranged to be as accessible as possible. Faculty are present during the entire laboratory period to answer questions.