Download BIMM 101 Recombinant DNA Techniques Credit by Exam Student

BIMM 101 Recombinant DNA Techniques
Credit by Exam Student Information Sheet
The equivalency exam for credit for BIMM 101 will consist of a written exam and a hands-on lab practical in which students must demonstrate
an understanding of the theoretical basis of, and proficiency with, various molecular biology techniques. Students must also demonstrate the
ability to interpret the results of experiments using these molecular biology techniques, as well as familiarity with commonly used bioinformatics
tools. The exam is based on the learning outcomes expected of students who take BIMM 101 and is therefore a comprehensive test of the
concepts and skills learned in BIMM 101. Before you decide whether or not to attempt credit by exam, it is highly recommended that you
carefully examine the course learning goals and expected outcomes included in these instructions. These outcomes are based on actual student
skill levels at the end of the course. It might also be useful to examine the lab manual to get an idea of the actual content.
This exam will be a combination of hands-on lab work and associated interpretation and analysis of results, bioinformatics problems, and a
written exam:
1. Wet-lab: approximately 2.5 hours consisting of bench work and written analysis of results
2. Bioinformatics and written exam: approximately 2.5 hours. The bioinformatics portion of the exam will be performed on a computer and will
require using various bioinformatics tools to analyze DNA sequences. The lab may provide a computer but it is advisable to confirm this
before the day of the exam. The written portion of the exam will consist of short answer, multiple choice, and essay questions.
Prior to the exam you will be required to complete the standard safety training administered to all students in the lab. This training should take
about 75 minutes and is mandatory regardless of whether you have had safety training elsewhere. Please let us know in advance if you have any
health conditions that would be impacted by working in a lab. These include but are not restricted to recent injury, allergies, pregnancy, and
health conditions that involve suppressed or reduced immune function. Your safety is our concern.
On the day of the lab, you should bring a lab coat, safety glasses or goggles, a scientific calculator, and pens/pencils. If you require a lab coat or
safety glasses, please inform the instructor well in advance. Gloves will be provided in the lab and are required for all bench work. These gloves
are the standard powdered gloves. You will need to provide your own gloves if you have any special glove requirements.
Grade distribution is based on the following scale:
Percentage
Grade range
100 - 90
89 - 80
79 – 70
69 – 60
< 60
A
B
C
D
F
Expected proficiencies upon entering BIMM101:
1. Knowledge of chemistry equivalent to successful completion of Chem 6A and Chem 6B
2. Knowledge of molecular and cell biology equivalent to the successful completion of BILD1
3. Competency in writing English
4. Basic math and calculator skills
5. Some knowledge of how to access and read scientific literature
Learning goals and outcomes for BIMM 101 students
Learning goals:
A. Related to general scientific skills and
competencies
1. Acquire strong quantitative skills
Specific outcomes – students will be able to:
a) Understand concept of concentration, how to work with
volume/mass units, and how to make up and dilute solutions
b) Know how to graph data
c) Do simple probability problems
2. Learn the importance of proper controls in
designing experiments and interpreting results
a) Define and identify negative and positive controls
3. Develop ability to record and interpret scientific
data
a) Interpret results and draw logical conclusions
4. Improve ability to find and interpret scientific
papers
a) Use search engines to find primary literature
5. Know lab safety essentials
a) Know and obey safety rules and regulations
b) Handle biological and chemical waste correctly
B. Related to specific concepts and methods
1. Understand basics tenets of molecular biology
2. Demonstrate mastery of basic molecular biology
techniques
b) Understand experimental design and the inclusion of proper controls
b) Present data in tables and graphs
b) Explain main purpose and conclusions of scientific papers
a) Identify the components of nucleic acids and describe the structure
of dsDNA
b) Explain how DNA is replicated in bacteria
c) Explain the function of a promoter and RNA polymerase
d) Understand how transcription and translation occur in bacteria
e) Explain how genes are organized into operons in bacteria
a) Demonstrate correct use of a pipetteman
b)
c)
d)
e)
f)
g)
Explain theory underlying agarose gels
Pour and run an agarose gel
Use an agarose gel to determine size and amount of DNA
Perform experiments using sterile techniques
Culture bacteria in liquid and solid media
Use a spectrophotometer to determine concentration and purity of
nucleic acids
3. Know how DNA is isolated from organisms
a) Outline the general strategy used to isolate DNA from organisms
b) Describe the characteristics of a gram negative bacteria
c) Explain how chromosomal DNA is isolated from bacteria using
phenol-chloroform method
d) Explain how plasmid DNA is isolated from bacteria using the alkaline
lysis method
4. Understand the importance of restriction
enzymes and ligases in gene cloning experiments
a) Describe the characteristics of Type ll restriction enzymes and the
factors which affect their activity
b) Determine the approximate sizes of DNA fragments generated by a
restriction digest of known DNA
c) Describe the characteristics of T4 ligase and the factors which affect
its activity
5. Know the structure and function of plasmids as
cloning vectors
a) Describe the different conformations of plasmids
6. Be able to utilize basic cloning techniques
a)
b)
c)
d)
e)
f)
7. Understand and be able to apply the polymerase
b) Describe how the different conformation of plasmids run on an
agarose gel
c) Explain the function of the ori
d) Explain the function of the Ampr gene and antibiotic resistance
e) Describe the structure and function of the polylinker region
f) Explain the theory underlying blue white screening (lacZalpha
complementation)
Outline the general strategy used to clone DNA
Set up and analyze the results of a restriction digest
Set up a ligation and analyze ligation results on a gel
Make competent cells and perform a transformation
Calculate transformation efficiency
Screen and expand colonies
a) Explain the theory underlying PCR and the factors which affect the
chain reaction method
b)
c)
d)
e)
PCR reaction
Describe the characteristics and enzyme activities of heat stable
polymerases
Design PCR primers and determine size of PCR products using Blast
Set up a PCR reaction and purify PCR products
Understand various strategies used to clone PCR products into
bacteria
8. Know the Sanger sequencing method
a) Explain the difference between a deoxy and dideoxynucleotide
b) Explain how DNA sequence is determined using the Sanger method
c) Interpret a sequencing chromatogram and assess the quality of a
sequencing run.
9. Be able to explain and apply RNA methods
a)
b)
c)
d)
10. Understand the basis of genetic diversity.
a) Give examples of polymorphisms that can occur in DNA sequences.
Describe different methods for measuring gene expression
Explain the theory underlying qRTPCR methodology
Outline the general strategy used to isolate RNA from an organism
Quantitate specific mRNAs using qRTPCR
b) Explain the difference between synonymous and non-synonymous
SNPs, and transitions and transversions.
c) Define a haplotype
d) Explain how to perform a CAPs assay
11. Demonstrate familiarity with bioinformatics
databases and applications.
a) Describe content of Genbank and how sequences are annotated
within Genbank
b) Perform a Blast on a DNA sequence and interpret the results
c) Use ORF finder to find open reading frames in DNA sequences
d) Do a ClustalW alignment and interpret the results