BIOL 302: Molecular and General Genetics

Fall 2013

Module 5: Recombinant DNA and Biotechnology

Reading Guide and Goals: Chapters 7, 10, 16, 17, 18, and 21 (dont panicjust
sections of these chapters)
Learning Goals for the Unit:
Students will be able to compare and contrast Southern, Northern, Western, RT PCR, and
RT qPCR methodshow they are performed, and what they are used for

Students will be able to explain how basic genetics is used in biotechnology to improve human
quality of life

Students will be able to explain how Next Generation Sequencing (NGS) is being applied to
medical diagnostics and basic research

Students will be able to explain how biotechnology can help to clarify basic genetics.

Reading Requirements for the Module 5 iRAT and tRAT, Oct. 28

Chapter 7: Review Chapter 7.5.
Chapter 10: Read Chapter 10.2.
Scitable Article: Genetically Modified Organisms (GMOs): Transgenic Crops and Recombinant DNA
Technology
http://www.nature.com/scitable/topicpage/genetically-modified-organisms-gmos-transgenic-cropsnbsp-732
Scitable Article: Recombinant DNA Technology and Transgenic Animals
http://www.nature.com/scitable/topicpage/recombinant-dna-technology-and-transgenic-animals-34513
Scitable Article: The Biotechnology Revolution: PCR and the Use of Reverse Transcriptase to Clone
Expressed Genes
http://www.nature.com/scitable/topicpage/the-biotechnology-revolution-pcr-and-the-use-553
Scitable Article: Paternity Testing: Blood Types and DNA
http://www.nature.com/scitable/topicpage/paternity-testing-blood-types-and-dna-374
Online animation on RFLP analysis:
http://bcs.whfreeman.com/thelifewire/content/chp17/1702001.html)
Watch video on Illumina sequencing:
http://gep.wustl.edu/curriculum/course_materials_WU/introduction_to_genomics/nextgen_tour/2.mov
Scitable Article on GWAS and human disease: http://www.nature.com/scitable/topicpage/geneticvariation-and-disease-gwas-682

BIOL 302: Molecular and General Genetics

Fall 2013

Suggested MG Web Activity on RFLP analysis (not required for iRAT):

http://media.pearsoncmg.com/bc/bc_0media_gen/animations/ch22/22_1/22_1.html
Reading/Video Requirements for Module 5, Oct. 30
Chapter 16: Read Chapter 16.2 and 16.4.
Chapter 17: Read Chapter 17.1.
View MG Web activity (chapter 16) on DNA Cloning:
http://wps.aw.com/bc_sanders_genetics_1_msa/150/38504/9857072.cw/index.html
View MG Web activity (chapter 16) on Cloning Libraries:
http://media.pearsoncmg.com/bc/bc_0media_gen/animations/ch19/19_4/19_4.html
View MG Web activity (chapter 16) on restriction mapping:
http://media.pearsoncmg.com/bc/bc_0media_gen/animations/ch19/19_5/19_5.html
Reading/Video Requirements for Module 5, Nov. 4
Chapter 21: Read Chapter 21.4.
View animation on paternity testing:
http://www.sumanasinc.com/webcontent/animations/content/paternitytesting.html)
View YouTube video on how DNA microarrays can be used to detect SNPs:
http://www.youtube.com/watch?v=AhnTT6-Jgcg
Reading/Video Requirements for Module 5, Nov. 6
Chapter 16: Read Chapter 16.3
Chapter 18: Read Chapter 18.3 (up to Other -Omes and -Omics
Watch YouTube video on Illumina sequencing: http://www.youtube.com/watch?v=HMyCqWhwB8E
Read case study on use of NGS to quickly diagnose a pathogen: A Diagnosis Just in Time:
http://www.ucsf.edu/news/2014/06/115116/teen%E2%80%99s-recovery-shows-value%E2%80%9Cnext-generation%E2%80%9D-dna-sequencing
View video on real-time PCR (through SYBR green detection; can ignore Taq-Man detection):
https://www3.appliedbiosystems.com/cms/groups/portal/documents/web_content/cms_055079.swf
View MG Web Activity (chapter 18) on Analysis of Gene Expression Using Microarrays:
http://wps.aw.com/bc_sanders_genetics_1_msa/150/38504/9857072.cw/index.html
Optional YouTube tutorial on microarrays to analyze gene expression:
http://www.youtube.com/watch?v=_6ZMEZK-alM
Reading/Video Requirements for Module 5, Nov. 11

NoneTeam contest/review

BIOL 302: Molecular and General Genetics

Fall 2013

Learning Objectives
October 28:

Compare and contrast the Southern, Northern, and western blotting techniques and the kinds of
information that can be obtained from each

Explain how reverse transcriptase (RT) PCR works and what it can be used for

October 30:

Explain what a transgenic organism is

Explain what recombinant DNA technology is and enumerate steps and sub-steps to create a
transgenic organism using recombinant DNA (rDNA) technology

Describe what a DNA library is and how to build one

Enumerate the three general steps of molecular cloning

Design a protocol to produce a protein such as recombinant human growth hormone (HGH) in
Escherichia coli

October 28-31 (Discussion 8)

Choose the right cloning vector based on insert size and application
Construct a restriction map

November 4:

Explain how human genotyping is done and used

Explain how SNPs are identified using PCR and restriction enzyme digestion or by microarray

Describe what quantitative trait loci (QTLs) are and explain how QTLs are used in GenomeWide Association Studies (GWAS)

Explain what GWAS are used for and Design a GWAS

November 6:

Schematize how Illumina next-generation sequencing (NGS) works compared to traditional

Sanger sequencing

Explain how NGS can be used to diagnose infectious disease

Explain how RT qPCR is used to analyze expression of individual genes

Explain how microarrays and NGS are used to analyze global gene expression

BIOL 302: Molecular and General Genetics

Fall 2013

November 4-7 (Discussion 9)

Design a complete PCR reaction, writing out all the steps, and including primer location
depending on the product to amplify
Identify a SNP, using PCR and restriction enzyme digestion
Determine relative likelihood of different kinds of mutations to affect phenotype

November 11:

Review

Key wordsterms the student should be able to define:

Chapter 10: Agarose, blunt end, electrophoretic mobility, ethidium bromide, gel electrophoresis,
hybridization, molecular probe, northern blotting, polyacrylamide gel, restriction enzyme, restriction
fragment length polymorphism (RFLP), single nucleotide polymorphism (SNP), Southern blotting,
sticky end, western blotting
Chapter 16:Bacterial artificial chromosome (BAC), cohesive ends, cohesive end sequence (cos) sites,
complementary DNA (cDNA) library, cosmid vector, directional cloning, DNA library, genomic
library, multiple cloning site (MCS), recombinant DNA, restriction enzyme, restriction map, reverse
transcriptase, sticky ends, vector, yeast artificial chromosome (YAC)
Chapter 17: Eukaryotic expression vector, expression vector, fusion gene, fusion protein, gene
knockout, genetic chimera, homologous recombination, illegitimate recombination, site-directed
mutagenesis, site-specific recombination, transgene, transgenic, transgenic organism
Chapter 18: DNA microarray, expression array, transcriptomics
Chapter 21: Genome-Wide Association Studies (GWAS)*, quantitative trait locus (QTL), QTL
mapping.
Assignment due dates at a glance
Tuesday 10/28 (8:30 am/10 am) in class i/tRAT #4
Wednesday 10/29 (11:59 pm) Bb pre-class reading quiz #11
Sunday 11/02 (11:59 pm) MG homework set #7
Monday 11/3 (11:59 pm) Bb pre-class reading quiz #11
Wednesday 11/5 (11:59 pm) Bb pre-class reading quiz #12
Sunday 11/9 (11:59 pm) MG homework set #8
Monday 11/10 (11:59) Bb pre-class reading quiz #13
Sunday 11/16 (11:59) MG homework set #9

BIOL 302: Molecular and General Genetics

Fall 2013

Chapter Problems to Practice (not graded)

Chapter 10: 4, 5, 6, 7, 8, 10, 11, 12, 13, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31.
Chapter 16: 2, 3, 4, 6, 9, 15, 16, 17, 18, 19, 20, 26.
Chapter 17: 2, 5, e2 13, 15, 20, 24, 25.
Chapter 18: 1, 2, 12, 14, 15, 24, 25.
Chapter 21: 1