Molecular Biology Techniques

Molecular Biology Techniques


Spring 2011
01/18/2011 - 05/15/2011

Course Information

Section 001
MW 18:05 - 19:30
EVC9 9101
Jack O'Grady

Section 001
MW 19:40 - 21:25
EVC9 9101
Jack O'Grady

Office Hours

No office hours have been entered for this term


The infromation posted on this site addresses the syllabus information required by Texas House BIll 2504. The syllabus handed out in class will contain complete class information in more detail. The complete syllabus will also be posted on my ACC website ( as well as on Blackboard. The schedule posted here is subject to change. Any changes will be announced in class and posted to Blackboard.

Complete Syllabi can be found on my website:

Course Requirements

1.      Lecture Exams.   (350 points)  Two exams will be given in class on the days listed in the course schedule.  The midterm exam is worth 150 points, and the final comprehensive exam is worth 200 points. Both will cover topics and concepts covered by lecture, lab and assigned reading materials.  The format of these exams will be diverse, and may include short answer, definitions, problems, discussions, and analysis, graphing and multiple choice questions. Questions on these exams will emphasize higher-level critical thinking skills as mandated by the ACC Biotechnology Department and will challenge students to be able to use their factual knowledge in order to answer the questions.

2.      Homework.(100 points). There will be 4 homework assignments given throughout the semester. Each homework assignment is 25 points. Homework due dates are posted on the schedule. Students will be given homework assignments outside of the classroom that correspond to the topics being covered in the course.  These may include outside readings from the scientific literature in addition to readings from the textbook.  The homework will reflect the expectations in the course examinations in both content material and format:  they may include short answers, thought problems, discussions, and multiple choice questions.  Student collaborations in homework assignments are encouraged, but each student must produce their own work written by themselves

3.      Class Participation. (50 points). For every Biotechnology class with lab, the student will receive a “Work Performance & Technical Abilities Evaluation” from the instructor. The instructor will meet with the student individually to review the evaluation, give the student a copy and the department will retain a copy.  Attendance is taken every class. You will be graded on preparing for class, participation in class, team work and safe behavior in the lab. Part of being a good technician is being able to work effectively in a team and this evaluation is designed to help the student achieve that goal. This evaluation will cover areas such as technical skills, initiation and follow through, independence and dependability, prioritization and organization, problem solving, quality of work and leadership.

4.      Lab Notebook. (50 points) Students will maintain a laboratory notebook as instructed in the lab manual. This notebook will be submitted for grading close to the end of the semester. Turn-in date posted on the schedule.

5.      Lab Reports.(350 points)  Students will turn in written lab reports as assigned. Lab exercises are due one week after all the data has been collected for that exercise. Students may collaborate with their team on the writing of lab reports, but each student must produce their own tables and graphs, and write their own lab report in their own words.  Photocopies or computer generated copies of others’ works will NOT be accepted and will be considered plagiarism.

6.      Lab Practical.(100 points). There will be one lab practical given during the semester. Date is posted on the schedule. This lab practical will be independent work only and will cover material in the laboratory. The format of the lab practical will be both a laboratory hands-on exercise and written portion. The written portion format may include multiple choice and short answer questions, as well as problem solving calculations and graphing.


Grades will be assigned according to the following scale (there will be no “curving” of grades)    


2 Exams                                                            350

4 homework assignments                            100

Attendance and In-class participation           50

Lab Reports                                                     350

Lab Notebook                                                    50

Lab Practical                                                    100                            

Total Lecture Points                                     1000    (Divide total points by 10 = Grade %)


Grading Scale:            90‑100% = A; 80‑89% = B; 70‑79% = C; 60‑69% = D; < 60% = F                                                            Percentage scores will be rounded to the nearest whole number


Textbooks:     1. Molecular Diagnostics:  Fundamentals, Methods, & Clinical Applicationsby Lela Buckingham & Maribeth L. Flaws, F.A.Davis Co (2007)

2. Seidman & Moore, Basic Laboratory Methods for Biotechnology:  Textbook & Laboratory Reference, 2nd edition. 2009. Prentice Hall. ISBN: 0321570146

Lab Manual:  “Molecular Biology Techniques” L. Fletcher et al 2011. ISBN: BITC2441S2011.One copy of the lab manual will be supplied.


Week of

Lecture Schedule

Reading Assignment (Buckingham&Flaws)

Laboratory Schedule


Jan 17


(No Classes Monday Jan 17th)

Syllabus Review

Unit 1: Introduction & Lab Safety

Unit 1: Competency Refresher


Jan 24

CH 16 QA/QC in the Molecular Biology Lab

Homework 1 due

Unit2: Quality Systems in the Molecular Biology Lab



Jan 31

CH 1: DNA, CH 2: RNA, CH 3: Proteins

*note: these chapters should be a review of your prerequisite classes.

CH 29 (Seidman)

Unit 3: Nucleic Acid Isolations


Feb 7

CH: 13 (Campbell): Nucleic Acid Biotechnology Techniques Review

CH 25 (Seidman): Spectrophotometry

Unit 4: Nucleic Acid Quantity & Quality



Feb 14

CH4: Nucleic Acid Extraction Methods

Homework 2 due

Unit 5: Cloning GAPDH from Plants

             Part 1: Genomic DNA Extraction


Feb 21

CH 7: Nucleic Acid Amplification

CH 24/Pt VI (Seidman): PCR Assays

Unit 5: Cloning GAPDH from Plants

             Part 2: Long PCR



Feb 28

CH 5: Resolution & Detection of Nucleic Acids


Unit 5: Cloning GAPDH from Plants

             Part 3: Nested PCR

             Part 4: PCR Analysis & Ligation



CH 6: Analysis & Characterization of Nucleic Acids & Proteins (pp94-112)

Homework 3 due

Unit 5: Cloning GAPDH from Plants

             Part 5: Transformation

Lab Practical

Mar 14

No classes March Break:  March 14-20th




Mar 21

Midterm Exam

(CH 1-7, 16, & Seidman, Campbell chapters)

Unit 5: Cloning GAPDH from Plants

             Part 6:Mini-prep Plasmid isolation

             Part 7: Restriction Digest


Mar 28

CH 10: Sequencing

Unit 5: Cloning GAPDH from Plants

             Part 8: DNA Sequencing


Apr 4

CH 8: Chromosomal Structure & Chromosomal Mutations

CH 9: Gene Mutations

Unit 6: Gene Expression Analysis

             Part 1: Design of Universal Primers


Apr 11

CH 11: DNA Polymorphisms & Human Identification

Unit 6: Gene Expression Analysis

             Part 1: Design of Universal Primers

             Part 2:Real Time PCR


Apr 18

Ch 6: Array based Hybridizations: Microarrays (pp112-118)

Additional Readings from the literature

Unit 6: Gene Expression Analysis

             Part 2:Real Time PCR

Unit 5: Cloning GAPDH from Plants

             Part 9: Analysis of Sequencing Data



CH 13:Molecular Detection of Inherited Diseases

Unit 5: Cloning GAPDH from Plants

             Part 9: Analysis of Sequencing Data


May 2

Class Review

Homework 4 due

Unit 6: Gene Expression Analysis

             Part 3: Southern or Western Blot


May 9

Comprehensive Final Exam


Notebooks due

Workplace Evaluations

Course Subjects

See Detailed Reading Assignment above.

Course Description: An introduction to the theory and laboratory techniques in molecular biology with an emphasis on DNA replication, transcription, gene expression and regulation, recombinant DNA and RNA techniques such as transformation, RT-PCR, Northern Blots, microarray analysis and DNA bioinformatic tools. Skills: O

Student Learning Outcomes/Learning Objectives

Course Objectives/Outcomes:   The competency outcomes for this course reflect skills necessary in the biotechnology workforce which emphasize communication skills, punctuality, and teamwork in addition to molecular biology skills. The TSSB recognized Skill Standards for this course can be found here: ACAP competencies are available on Blackboard.


A1 Maintain laboratory and equipment

A3 Operate equipment

A5 Clean and prepare items for lab

A6 Prepare biological and/or chemical materials

B1 Assist in designing experiments

B2 Perform assays and experiments

B3 Troubleshoot experiments and equipment

B4 Perform data analysis

B5 Communicate results

B6 Investigate new technologies and methodologies

C1 Participate in employer-sponsored safety training

C2 Participate in emergency drills and emergency response teams

C3 Identify unsafe conditions and take corrective action

C4 Suggest continuous improvements

C5 Coordinate with work team

C7 Handle and dispose of hazardous materials

C8 Maintain security

D1 Maintain lab notebook

D2 Create documents

D3 Enter and manage laboratory information electronically