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Questions and Answers
What is the first step in the DNA extraction process?
What is the first step in the DNA extraction process?
Which reagent is used to protect DNA from enzymatic degradation during extraction?
Which reagent is used to protect DNA from enzymatic degradation during extraction?
What is the main purpose of the elongation step in PCR?
What is the main purpose of the elongation step in PCR?
What principle allows DNA to be separated by size during gel electrophoresis?
What principle allows DNA to be separated by size during gel electrophoresis?
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Which of the following steps of PCR is directly affected by the temperature change?
Which of the following steps of PCR is directly affected by the temperature change?
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What does the term 'amplicon' refer to in the context of PCR?
What does the term 'amplicon' refer to in the context of PCR?
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How does the use of Taq polymerase enhance the PCR process?
How does the use of Taq polymerase enhance the PCR process?
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During washing in DNA extraction, what is primarily removed from the solution?
During washing in DNA extraction, what is primarily removed from the solution?
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What is the primary purpose of studying homologous genes in different organisms?
What is the primary purpose of studying homologous genes in different organisms?
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Which of the following genes is associated with water sensing in mosquitoes?
Which of the following genes is associated with water sensing in mosquitoes?
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What is the key difference between reverse genetics and forward genetics?
What is the key difference between reverse genetics and forward genetics?
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What is the expected format of the final exam based on the study guide?
What is the expected format of the final exam based on the study guide?
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What is the purpose of using a positive control in an experiment?
What is the purpose of using a positive control in an experiment?
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In a reverse genetics experiment, what is the dependent variable typically measured?
In a reverse genetics experiment, what is the dependent variable typically measured?
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What role does water play in the life cycle of mosquitoes, specifically Aedes aegypti?
What role does water play in the life cycle of mosquitoes, specifically Aedes aegypti?
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Which of the following represents the correct relationship between exons and introns?
Which of the following represents the correct relationship between exons and introns?
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Which factor is typically used as one of the independent variables in a 2 x 2 factorial design for reverse genetics experiments?
Which factor is typically used as one of the independent variables in a 2 x 2 factorial design for reverse genetics experiments?
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What does the e-value indicate in a BLAST search?
What does the e-value indicate in a BLAST search?
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What is the significance of the PAM domain in identifying sgRNAs?
What is the significance of the PAM domain in identifying sgRNAs?
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In DNA transcription, which base is replaced by Uracil in RNA?
In DNA transcription, which base is replaced by Uracil in RNA?
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What is a key step performed during the column-based extraction of DNA?
What is a key step performed during the column-based extraction of DNA?
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Which of the following statements about homologs is correct?
Which of the following statements about homologs is correct?
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What is the coding DNA sequence (CDS) formed from?
What is the coding DNA sequence (CDS) formed from?
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What is indicated by the term 'query cover' in a BLAST result?
What is indicated by the term 'query cover' in a BLAST result?
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Why is gel electrophoresis not efficient for detecting very small indels?
Why is gel electrophoresis not efficient for detecting very small indels?
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What is the function of ExoSAP in sample purification?
What is the function of ExoSAP in sample purification?
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How does Sanger sequencing differ from PCR?
How does Sanger sequencing differ from PCR?
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What are PAM sites important for in the CRISPR-Cas9 system?
What are PAM sites important for in the CRISPR-Cas9 system?
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What is a key difference between random mutagenesis and genome editing?
What is a key difference between random mutagenesis and genome editing?
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What does the term ‘indel’ refer to in the context of CRISPR-Cas9 genome editing?
What does the term ‘indel’ refer to in the context of CRISPR-Cas9 genome editing?
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Which enzyme class does Cas9 belong to?
Which enzyme class does Cas9 belong to?
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In Sanger sequencing, what is the role of ddNTPs?
In Sanger sequencing, what is the role of ddNTPs?
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Study Notes
Genetics Lab Final Exam Study Guide
- The exam will have 30-35 questions, a mix of multiple choice, true/false, and written response.
- It will cover both theoretical and practical applications.
- Students should be prepared to explain homology and its role in model organism development.
- Identifying homologous genes from different organisms given a gene sequence is important.
- Students need to identify sgRNAs with adjacent PAM domains.
- Understanding in-vitro CRISPR experiment results and identifying potential errors is crucial.
- Interpreting gel results from experiments is a key skill.
- Implementing correct micropipetting techniques is vital.
Module 1: Mosquitoes and Reverse Genetics
- Mosquitoes (order Diptera) have a strong water dependence.
- Aedes aegypti, a common vector for diseases, is a model organism studied in this course.
- The genes IR68a and OBP71 are potentially involved in mosquito water sensing.
- Homology in genes allows inferences about function across different organisms.
- Reverse genetics involves creating a mutant genotype and studying its phenotype.
- Forward genetics is the traditional approach of observing a mutant phenotype to find the causative gene.
- A 2x2 factorial design is used for reverse genetics experiments with a genetic background (e.g., wild-type or mutant) and a treatment variable.
- Positive controls ensure the experiment functions correctly, while negative controls show what "no treatment" looks like.
Module 2: Pipetting Techniques
- Students need to understand pipette usage, specifically the calibrated volumes and how to read the volume dial.
- Understanding volume relationships is crucial.
Module 3: Gene Families and BLAST
- Gene families are formed through gene duplication within a genome creating paralogs.
- Speciation creates orthologs.
- Homologous genes can be compared using BLAST tools.
- Students should be familiar with different BLAST types, how they function, and interpret outputs like e-value, query cover and percent identity.
Module 4: Gene Structure and DNA Extraction
- Exons code for proteins and introns do not.
- Exons, introns, and UTRs (untranslated regions) are transcribed into pre-mRNA.
- Pre-mRNA undergoes processing to produce mRNA with only exons.
- mRNA is translated into proteins.
- Gel electrophoresis is used to visualize DNA.
- Extraction techniques like homogenization, cell lysis, DNA binding, washing, and elution are used to purify DNA samples.
- Students should study the role of reagents in DNA extraction.
Module 5: Genotyping and PCR
- Genotyping typically starts by amplifying a region.
- PCR, or polymerase chain reaction, is used to amplify target sequences in repeated cycles.
- Each cycle doubles the target DNA amount.
- The PCR process includes denaturation, annealing, and elongation steps.
Module 6, 7: Gel Electrophoresis and Sequencing
- Gel electrophoresis separates DNA fragments by size.
- DNA is negatively charged and moves toward the positive electrode.
- Smaller fragments travel farther in the gel.
- Gel electrophoresis can be used to detect small indels (Insertions and/or Deletions).
- Techniques like fragment analysis give a digital output instead of a gel.
- Restriction digests can be used to identify mutations that disrupt restriction sites for identification.
- Cycle sequencing and Sanger sequencing are used to determine DNA sequences.
Module 8: CRISPR-Cas9
- CRISPR-Cas9 is a genome editing technology targeting DNA sequences using an RNA-guided nucleases.
- CRISPR-Cas9 creates small insertions or deletions (indels) in DNA.
- Methods used and their relationship to knock-out mutants and frameshift mutations.
- Frame-shift mutations disrupt the reading frame of codons.
- Understanding the use of PAM (protospacer adjacent motif) regions, and their relationship to the target sequence.
Review: Sanger Sequencing and Gel Electrophoresis
- Students should be able to interpret a Sanger sequencing gel electrophoresis.
- Understand the concept of polymorphism.
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Description
Prepare for your Genetics Lab final exam with this comprehensive study guide. It covers key concepts like gene homology, CRISPR applications, and practical skills such as micropipetting. Review theoretical knowledge and practical applications essential for the exam.
