Genetics Lab Final Exam Study Guide
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Questions and Answers

What is the purpose of a negative control in an experiment?

  • To increase the effect of the treatment
  • To show what 'no treatment' looks like (correct)
  • To verify the accuracy of positive controls
  • To ensure that the experiment works

    • Which of the following best describes an exon?

  • An untranslated region of RNA
  • A non-coding segment of a gene
  • A coding segment of a gene (correct)
  • A type of paralog

    • What does BLAST stand for?

  • Biological Alignment Sequence Tester
  • Broad Local Alignment Sequence Test
  • Basic Linkage Alignment Software Tool
  • Basic Local Alignment Search Tool (correct)

    • When translating nucleotide sequences, what replaces thymine (T) in RNA?

    <p>Uracil (U) (A)</p> Signup and view all the answers

    What is the primary outcome of removing introns from pre-mRNA?

    <p>Production of mature mRNA (D)</p> Signup and view all the answers

    What is a key feature of paralogs?

    <p>They are created through gene duplication (C)</p> Signup and view all the answers

    Which of the following statements about column-based extraction techniques is accurate?

    <p>They purify DNA by lysing cellular membranes (D)</p> Signup and view all the answers

    What is the significance of understanding the relationship between micro- and milli- volumes in pipetting?

    <p>To ensure accurate volume measurements (C)</p> Signup and view all the answers

    What is homology in genetics primarily concerned with?

    <p>Similarity due to shared ancestry (B)</p> Signup and view all the answers

    Which organism was primarily used as a model organism in this course for studying hydrosensation?

    <p>Aedes aegypti (C)</p> Signup and view all the answers

    What is the role of sgRNAs in the CRISPR system?

    <p>To bind to target DNA sequences (C)</p> Signup and view all the answers

    Which of the following best describes reverse genetics?

    <p>Assessing the phenotype after creating a mutant genotype (A)</p> Signup and view all the answers

    In the context of experimental design, what does a 2 x 2 factorial design imply?

    <p>Two treatments and two genetic backgrounds (B)</p> Signup and view all the answers

    What are Ionotrophic Receptor 68a (IR68a) and Odorant Binding Protein 71 (OBP71) primarily involved in?

    <p>Sensing water in mosquitoes (C)</p> Signup and view all the answers

    What does one measure in a factorial design involving genetic backgrounds and treatments?

    <p>The interaction between genotype and environmental factors (A)</p> Signup and view all the answers

    Which of the following is a potential cause for the failure of an in-vitro CRISPR experiment?

    <p>Mismatch between sgRNA and target DNA (D)</p> Signup and view all the answers

    What is the primary purpose of the homogenization step in DNA extraction?

    <p>To break the specimen into smaller chunks. (C)</p> Signup and view all the answers

    Which reagent protects DNA from enzymatic degradation during the extraction process?

    <p>EDTA (B)</p> Signup and view all the answers

    In PCR, what happens during the denaturation step?

    <p>Heat breaks hydrogen bonds between DNA strands. (D)</p> Signup and view all the answers

    What is the main function of Taq polymerase in the PCR process?

    <p>To elongate the DNA strand. (D)</p> Signup and view all the answers

    How does gel electrophoresis separate DNA fragments?

    <p>By applying an electric current to move DNA through a matrix. (D)</p> Signup and view all the answers

    In gel electrophoresis, what does the distance a DNA fragment migrates indicate?

    <p>Its base pair length. (C)</p> Signup and view all the answers

    What role do primers play in the PCR process?

    <p>They bind to specific complementary sequences in the DNA. (D)</p> Signup and view all the answers

    What is a key advantage of Taq polymerase in PCR?

    <p>It remains stable at high temperatures during the denaturation step. (D)</p> Signup and view all the answers

    What is the alternative method used for detecting very small indels instead of gel electrophoresis?

    <p>Fragment analysis (D)</p> Signup and view all the answers

    What is the role of restriction enzymes in the context of CRISPR?

    <p>They cut DNA at specific sites to create mutations. (C)</p> Signup and view all the answers

    Which of the following is TRUE regarding ExoSAP?

    <p>It contains exonuclease I and shrimp alkaline phosphatase. (C)</p> Signup and view all the answers

    What distinguishes Sanger sequencing from standard PCR?

    <p>Incorporation of labeled ddNTPs in Sanger sequencing. (B)</p> Signup and view all the answers

    What is the function of a PAM in CRISPR-Cas9 genome editing?

    <p>It is a sequence where Cas9 can specifically cut DNA. (A)</p> Signup and view all the answers

    What is generated most commonly by CRISPR-Cas9 genome editing during repair?

    <p>A small insertion or deletion (indel). (C)</p> Signup and view all the answers

    How does genome editing differ from random mutagenesis?

    <p>Genome editing results in specific, targeted mutations. (A)</p> Signup and view all the answers

    What is the purpose of the process called NHEJ in CRISPR-Cas9?

    <p>To join DNA fragments after cutting. (B)</p> Signup and view all the answers

    Flashcards

    Homology in model organisms

    Similarity in genes or traits due to common ancestry, allowing inferences about one organism's function based on another's.

    Model organism

    An organism used to study a biological process or disease in another organism with similar traits (often due to homology).

    Reverse Genetics

    A methodology that starts with a modified gene and observes the resultant trait or phenotype.

    Forward Genetics

    A traditional method of identifying genes responsible for a particular phenotype (trait).

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    2x2 factorial design

    An experimental design using two independent variables (each with two levels) to observe their combined effects on a dependent variable.

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    Independent variable

    The factor manipulated by an experimenter to observe its effects on the dependent variable.

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    Dependent variable

    The factor measured or observed to determine the effect of the independent variable.

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    CRISPR sgRNA

    Guide RNA used to target specific DNA sequences(Cas9 enzyme) for modification in gene editing experiments, accompanied by an adjacent PAM sequence.

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    Positive Control

    A treatment group that is known to produce a positive result. It ensures the experiment is working correctly and protects against false negatives.

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    Negative Control

    A treatment group that should not produce a positive result. It shows what happens with 'no treatment' and helps identify false positives.

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    Paralog

    A gene that arises from duplication within the same genome. Paralogs within a species often have similar functions.

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    Ortholog

    A gene that arises from a speciation event and is found in related species. Orthologs often have similar functions.

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    BLAST

    Basic Local Alignment Search Tool. A program used to compare sequences and find regions of similarity.

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    E-value

    A measure of the likelihood that a BLAST alignment occurred by chance. Lower e-values indicate greater similarity.

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    Exon vs. Intron

    Exons are coding segments of a gene that are translated into protein. Introns are non-coding segments that are removed during mRNA processing.

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    UTR

    Untranslated region of a gene. These regions are transcribed but not translated into protein.

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    DNA Extraction - Step 1: Homogenization

    Breaking down a sample into smaller pieces to release DNA.

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    DNA Extraction - Step 2: Cell and Nuclear Lysis

    Breaking open cell and nuclear membranes to release DNA into solution.

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    DNA Extraction - Step 3: DNA Binding

    Attaching DNA to a filter or beads for separation.

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    DNA Extraction - Step 4: Washing

    Removing contaminants (proteins, etc.) from the DNA using ethanol.

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    DNA Extraction - Step 5: Elution

    Releasing DNA from the filter/beads into a solution.

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    PCR (Polymerase Chain Reaction) - Denaturation

    Heating DNA to separate the two strands and break hydrogen bonds.

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    PCR (Polymerase Chain Reaction) - Annealing

    Cooling DNA to allow primers to bind to their complementary sequences.

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    PCR (Polymerase Chain Reaction) - Elongation

    Taq polymerase extends the primers, creating a complete DNA copy.

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    Fragment analysis

    A technique similar to gel electrophoresis but using a capillary and producing a digital readout, making it ideal for detecting small indels (insertions & deletions).

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    Restriction digest

    A method utilizing enzymes that cut DNA at specific sequences, revealing mutations by the presence or absence of cutting at target sites.

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    ExoSAP

    A product containing exonuclease I (ExoI) and shrimp alkaline phosphatase (SAP). ExoI removes unconsumed primers, while SAP removes dNTPs, pre-sequencing sample cleanup.

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    Sanger sequencing

    A method for determining the sequence of DNA, using labelled ddNTPs (dideoxynucleotides) to terminate DNA synthesis, creating fragments of different length.

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    Polymorphism

    A variation in a DNA sequence that occurs in a significant proportion of the population. It can be a single base change (SNP) or more extensive variations.

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    CRISPR-Cas9

    A powerful genome editing tool that utilizes CRISPR associated protein 9 (Cas9) to cut DNA at specific sites guided by a small RNA sequence.

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    NHEJ

    Non-homologous end joining. A DNA repair mechanism that often introduces small insertions or deletions (indels) at the site of a CRISPR-Cas9 cut.

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    Study Notes

    Genetics Lab Final Exam Study Guide

    • The exam will be 30-35 questions, a mix of multiple choice, true/false, and written response.
    • It will cover both theoretical and practical applications of the course material.
    • Students should be able to explain homology and how it aids in developing model organisms.
    • Students must identify homologous genes from different organisms based on gene sequences.
    • Identifying sgRNAs with adjacent PAM domains is a required skill.
    • Understanding how to interpret CRISPR experiment results and identify potential errors is crucial.
    • Comprehending gel interpretation for experiments is essential.
    • Mastering micropipette techniques is necessary.

    Module 1

    • Mosquitoes, specifically Aedes aegypti, are used as a model organism to study water sensing.
    • This model is relevant due to Aedes aegypti's role as a vector for diseases like dengue and Zika.
    • Genes like Ionotrophic Receptor 68a (IR68a) and Odorant Binding Protein 71 (OBP71) are being studied, potentially involved in water sensing.
    • Homology (similarity due to shared ancestry) enables research in one organism to learn about others.

    Module 1, continued

    • Reverse genetics experiments involve creating a mutant genotype and assessing the resulting phenotype.
    • Forward genetics involves observing a mutant phenotype and identifying the responsible gene.
    • A 2x2 factorial design is used in reverse genetics; one variable is the genetic background (wild-type vs. mutant), the other is a treatment.
    • The dependent variable is the measurable factor across the treatments.
    • Positive control ensures the experiment works; negative control demonstrates the "no treatment" response.

    Module 2

    • Students will understand how to use pipettes and read volume dials.
    • Students will understand the relationship between different volume measurements.

    Module 3

    • Gene families arise from gene duplication events (paralogs), and speciation events (orthologs).
    • BLAST (Basic Local Alignment Search Tool) is a fundamental tool for sequence comparisons.
    • Various BLAST types exist, each with different output metrics (e-value, query cover, percent identity) used for similarity assessments.
    • Exons code for proteins; introns do not and are removed during mRNA processing.
    • Understanding the structure of genes (exons, introns, untranslated regions (UTRs)) is essential.
    • Students must be able to read a FASTA file.

    Module 4

    • Molecular biology extraction methods (column-based techniques) are crucial for DNA isolation.
    • Lysis of cell and nuclear membranes, protein removal, DNA binding, washing, and elution are critical steps in DNA purification.
    • Roles of detergents and EDTA in the process of DNA extraction.

    Module 5

    • PCR amplifies DNA regions including the CRISPR target site.
    • The polymerase chain reaction involves denaturation, annealing, and elongation cycles.
    • Purification of samples using ExoSAP (exonuclease and phosphatase) for downstream sequencing is crucial.
    • Sanger/Cycle sequencing is used to determine the sequences of amplified DNA fragments.
    • Understanding similarities and differences between PCR and Sanger sequencing is required.

    Module 8

    • Polymorphisms are differences in DNA sequences.
    • CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) technology is used for targeted genome editing.
    • CRISPR-Cas9 leads to small insertions or deletions in the genome.
    • A frameshift mutation is caused by insertions or deletions of base pairs that are not multiples of three.
    • Nonsense mutations lead to premature stop codons.
    • Missense mutations cause changes in amino acid sequences.

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    Genetics Lab Final Exam Study Guide Fall '24 PDF

    Description

    Prepare for your Genetics Lab final exam with this comprehensive study guide, covering crucial topics such as homologous genes, CRISPR techniques, and gel interpretation. This guide emphasizes practical applications and theoretical knowledge necessary for mastering the course material. Ensure you are well-versed in methodologies and model organisms relevant to genetic studies.

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