Gene Expression Analysis Techniques
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Questions and Answers

What is the primary function of transposons?

  • To terminate DNA replication
  • To synthesize proteins
  • To amplify DNA fragments
  • To move within the genome (correct)

    • Polyploidy can result in the gain of new genetic functions.

    True

    What is the definition of a genotype?

  • The sum of all DNA in a cell
  • Observable characteristics of an individual
  • The set of alleles possessed by an individual (correct)
  • The chromosomal location of a gene

    • Transposable elements can be categorized into two types: ___________ and ___________.

    <p>Cut and Paste, Copy and Paste</p> Signup and view all the answers

    Define functional genomics.

    <p>Functional genomics is the study of the relationship between genotype and phenotype.</p> Signup and view all the answers

    Homozygous means having two different alleles for a gene.

    <p>False</p> Signup and view all the answers

    What is the Law of Segregation?

    <p>The two alleles for a trait segregate into haploid gametes.</p> Signup and view all the answers

    Match the genomic variations with their definitions:

    <p>SNPs = Variations in DNA where at least 1% of individuals show differences CNVs = Regions in the genome where some individuals have multiple copies of a gene Transposons = Mobile genetic elements that can relocate within the genome Multigene Families = Clusters of similar genes usually arising from gene duplication</p> Signup and view all the answers

    Which of the following best defines the transcriptome?

    <p>The sum of all mRNA expressed by a cell or organism</p> Signup and view all the answers

    A phenotype is the __________ characteristic(s) resulting from a genotype.

    <p>observable</p> Signup and view all the answers

    Copy Number Variants (CNVs) are typically associated with pseudogenes.

    <p>False</p> Signup and view all the answers

    Match the following terms with their definitions:

    <p>Allele = One variant of a gene Homologous Chromosomes = Chromosomes coding for the same set of genes Heterozygous = Having two different alleles for a gene True Breeding = Homozygous for a trait</p> Signup and view all the answers

    What do we call the sum of all proteins expressed by a cell or organism?

    <p>Proteome</p> Signup and view all the answers

    Which of the following describes codominance?

    <p>Both alleles are completely expressed</p> Signup and view all the answers

    The process by which stem cells become more specialized is called __________.

    <p>cell differentiation</p> Signup and view all the answers

    The dihybrid cross follows two variations of a single trait.

    <p>False</p> Signup and view all the answers

    What type of cross is a test cross?

    <p>A cross between an organism with the dominant phenotype and a homozygous recessive organism for the same trait.</p> Signup and view all the answers

    What are retrotransposons primarily known for?

    <p>Duplicating and inserting cDNA</p> Signup and view all the answers

    What technique allows for the detection and quantification of all RNA expressed in a sample?

    <p>RNA-seq</p> Signup and view all the answers

    Genome mapping includes the absolute positions of genetic markers in nucleotides.

    <p>True</p> Signup and view all the answers

    What is Genomics?

    <p>The study of all the DNA in an organism.</p> Signup and view all the answers

    The sum of all DNA in a cell or organism is called the ______.

    <p>genome</p> Signup and view all the answers

    Match the following terminology with their definitions:

    <p>Bioinformatics = Application of computational analysis to biological data Metagenomics = Study of genetic material from environmental samples Expressed Sequence Tag (EST) = Small sequence of cDNA mapped onto the genome Shotgun Sequencing = Fragmented DNA sequenced in overlapping segments</p> Signup and view all the answers

    Which sequencing method uses fluorescently labeled dideoxy nucleotides?

    <p>Sanger Sequencing</p> Signup and view all the answers

    Gene annotation refers to the process of sequencing DNA.

    <p>False</p> Signup and view all the answers

    What is the purpose of the Enzyme-Linked Immunosorbent Assay (ELISA)?

    <p>To detect a specific antigen in a sample.</p> Signup and view all the answers

    What is the role of repressor proteins in prokaryotic gene expression?

    <p>They bind to operators, decreasing transcription initiation.</p> Signup and view all the answers

    The trp operon is induced when tryptophan is present.

    <p>False</p> Signup and view all the answers

    What molecule acts as a corepressor in the trp operon mechanism?

    <p>Tryptophan</p> Signup and view all the answers

    The lac operon is normally _____ but can be induced by the presence of lactose.

    <p>off</p> Signup and view all the answers

    What must be present for the lac operon to be induced?

    <p>Lactose and absence of glucose</p> Signup and view all the answers

    Match the following operons with their control mechanism:

    <p>Trp Operon = Negative Control Lac Operon = Inducible Operon Repressible Operon = Normally On Inducible Operon = Normally Off</p> Signup and view all the answers

    CAMP levels are high when glucose is abundant, promoting the induction of the lac operon.

    <p>False</p> Signup and view all the answers

    What protein binds to the operator of the lac operon to prevent transcription?

    <p>Lac Repressor</p> Signup and view all the answers

    What is the basic functional unit of chromatin?

    <p>Nucleosome</p> Signup and view all the answers

    Histone acetylation typically leads to more condensed chromatin structure.

    <p>False</p> Signup and view all the answers

    What is the term for changes that do not involve a change in the DNA sequence but can be passed to subsequent generations?

    <p>epigenetic changes</p> Signup and view all the answers

    DNA methylation typically occurs on ________ residues.

    <p>cytosine</p> Signup and view all the answers

    Match the following types of chromatin modifications with their effects:

    <p>Histone Acetylation = Promotes transcription Histone Methylation = Reduces transcription DNA Methylation = Associated with inactive genes Non-coding RNAs = Involved in chromatin remodeling</p> Signup and view all the answers

    Which of the following is a factor that can influence epigenetics?

    <p>Environmental changes</p> Signup and view all the answers

    Changes in epigenetics are often permanent and cannot be reversed.

    <p>False</p> Signup and view all the answers

    What type of chromatin is typically found in regions of low gene expression?

    <p>heterochromatin</p> Signup and view all the answers

    The Barr body is an example of an ________ X-chromosome.

    <p>inactive</p> Signup and view all the answers

    Which of the following conditions has been linked to changes in epigenetics?

    <p>Heart disease</p> Signup and view all the answers

    What is the primary advantage of RNA-seq compared to DNA microarrays?

    <p>It can detect and quantify all RNAs expressed in a sample.</p> Signup and view all the answers

    The genome includes all RNA in a cell or organism.

    <p>False</p> Signup and view all the answers

    What does the term 'metagenomics' refer to?

    <p>The study of all genetic material from an environmental sample.</p> Signup and view all the answers

    The process of creating a __________ involves sequencing fragmented DNA and identifying overlapping regions.

    <p>shotgun sequencing</p> Signup and view all the answers

    Match the following terms with their descriptions:

    <p>Genome = The sum of all DNA in a cell/organism Bioinformatics = The application of computational analysis to interpret biological data Gene Annotation = Identification of protein-encoding genes in a genome DNA Sequencing = Determining the sequence of a DNA molecule</p> Signup and view all the answers

    What is the role of general transcription factors in eukaryotes?

    <p>To enhance the binding of RNA polymerase to the promoter</p> Signup and view all the answers

    Enhancers can only be located upstream of the gene they regulate.

    <p>False</p> Signup and view all the answers

    What is the effect of steroid hormones on gene expression?

    <p>They bind to inducible activators that influence specific enhancers.</p> Signup and view all the answers

    The process by which regulatory proteins control which exons are used during alternative splicing is called __________.

    <p>regulation</p> Signup and view all the answers

    Match the following components of gene regulation with their functions:

    <p>Activators = Bind to enhancers to upregulate transcription Repressors = Bind to enhancers or activators to downregulate transcription General transcription factors = Facilitate RNA polymerase binding to the promoter Silencers = Regions that inhibit transcription when bound by repressors</p> Signup and view all the answers

    What determines the stability of an mRNA transcript?

    <p>Both B and C</p> Signup and view all the answers

    Repressors can only inhibit transcription at the promoter region.

    <p>False</p> Signup and view all the answers

    Why do non-steroid hormones bind receptors at the cell surface?

    <p>Because they cannot diffuse across the cell membrane.</p> Signup and view all the answers

    Greater than 90% of protein-coding genes undergo __________ splicing.

    <p>alternative</p> Signup and view all the answers

    How do enhancers and promoters interact in DNA?

    <p>They can be brought together through DNA looping.</p> Signup and view all the answers

    What is the primary function of recombinant DNA?

    <p>To combine DNA from multiple sources.</p> Signup and view all the answers

    Ubiquitin tagging is a method used to increase protein stability in cells.

    <p>False</p> Signup and view all the answers

    What is the process of RNA interference (RNAi) associated with?

    <p>Silencing genes by degrading mRNA or blocking translation.</p> Signup and view all the answers

    The process of amplifying specific DNA using primers and DNA replication is known as __________.

    <p>Polymerase Chain Reaction (PCR)</p> Signup and view all the answers

    Match the following techniques with their descriptions:

    <p>Restriction Endonucleases = Cut DNA at specific sequences Gel Electrophoresis = Separation of DNA fragments by size Reverse Transcription PCR = Amplification of RNA into DNA Ubiquitin tagging = Marking proteins for degradation</p> Signup and view all the answers

    What role do microRNA (miRNA) and small interfering RNA (siRNA) play in gene expression?

    <p>They lead to degradation of mRNA</p> Signup and view all the answers

    Gel electrophoresis separates DNA fragments based on their charge rather than their size.

    <p>False</p> Signup and view all the answers

    What is the effect of a shorter half-life of mRNA on gene expression?

    <p>Decreases overall gene expression</p> Signup and view all the answers

    The primary purpose of a plasmid in gene cloning is to facilitate the identification of transformed cells.

    <p>True</p> Signup and view all the answers

    MRNA is translated into proteins during the stage known as __________.

    <p>translation</p> Signup and view all the answers

    Study Notes

    Gene Expression Analysis

    • DNA probes are used in measuring differential gene expression, with RNAs converted to cDNA via reverse transcriptase and tagged with fluorescent markers.
    • Fluorescence intensity indicates the level of gene expression.
    • RNA-seq detects and quantifies all RNAs in a sample, more comprehensive than DNA microarrays but also more costly.
    • RNA-seq involves converting RNAs to cDNA, followed by sequencing using Next-Generation Sequencing (NGS).

    Genomics Overview

    • Genomics studies the total DNA, including genes, within an organism.
    • The genome encompasses all DNA in a cell or organism.
    • Bioinformatics applies computational methods to analyze and interpret biological data.
    • Metagenomics examines all genetic material from environmental samples.

    Genome Mapping

    • Gene Mapping identifies the relative positions of genetic markers within a genome.
    • Genetic Maps show positions based on recombination frequencies, measured in centimorgans (cM).
    • Physical Maps provide exact positions of markers in base pairs.
    • Expressed Sequence Tags (ESTs) are short cDNA sequences mapped to a genome.

    DNA Sequencing Techniques

    • Shotgun Sequencing fragments DNA for sequencing, utilizing overlaps to reconstruct full sequences.
    • Sanger Sequencing uses labeled dideoxy nucleotides to terminate DNA strands for sequencing analysis.
    • Next-Generation Sequencing amplifies and sequences DNA fragments massively and concurrently.

    Human Genome Characteristics

    • Prokaryotic genomes range from 0 to 6 million base pairs (bp); eukaryotic genomes range from 12 to 149 billion bp; the human genome is approximately 3 billion bp.
    • Humans have about 20,000 genes, with the genome comprising 1.5% protein-coding genes, 24% introns, and 45% transposable elements.

    Transposable Elements

    • Transposons are mobile genetic elements that can relocate within the genome by "cut and paste" or "copy and paste" mechanisms.
    • Retrotransposons move by converting RNA to cDNA and inserting at new locations.

    Genetic Variations

    • Single Nucleotide Polymorphisms (SNPs) are genomic loci with variations present in at least 1% of a population.
    • Copy Number Variants (CNVs) involve variations in gene copy number among individuals.

    Comparative and Functional Genomics

    • Comparative Genomics allows the comparison of different genomes for function and relatedness analysis.
    • Functional Genomics explores the relationship between genotype and phenotype, covering expressed RNA (transcriptome) and proteins (proteome).

    Fundamentals of Genetics

    • Genes are DNA sequences for producing specific products, such as proteins or RNA.
    • Genotypes represent an individual's allele composition; phenotypes reflect observable traits.
    • Complete Dominance occurs when one allele masks another, while Incomplete Dominance results in blended traits.
    • Codominance sees both alleles expressed distinctly, as demonstrated in blood types.
    • Key genetic laws include Segregation and Independent Assortment, guiding allele distribution in gametes.

    Breeding Crosses

    • Monohybrid Crosses study two variations of a single trait; Dihybrid Crosses consider two traits.
    • Test Crosses determine an organism's genotype by crossing with homozygous recessive individuals.

    Prokaryotic Regulation of Gene Expression

    • Regulatory proteins interact with DNA affecting RNA polymerase binding to promoters.
    • Control of gene expression allows prokaryotic cells to adapt to environmental changes.

    Negative Control

    • Repressor proteins bind to operators, decreasing transcription initiation.
    • Effectors can either increase or decrease repressor binding to DNA.

    Positive Control

    • Activator proteins bind DNA to enhance transcription initiation.
    • Effectors can influence activator binding similarly.

    Trp Operon (Negative Control)

    • Repressible Operon: normally active but can be repressed by effectors.
    • Involves synthesis of tryptophan; induced in absence of tryptophan.
    • Trp repressor binds operator when tryptophan is present, blocking transcription.

    Lac Operon

    • Inducible Operon: usually inactive but can be activated by effectors.
    • Allows lactose catabolism; induced when lactose is present and glucose is absent.
    • Lac repressor binds operator, preventing transcription when lactose is absent.
    • Allolactose, the isomer of lactose, acts as an inducer, enabling transcription.

    Glucose Repression (Positive Control)

    • Presence of glucose prevents lac operon induction.
    • Requires binding of catabolite activator protein (CAP) with cAMP when glucose levels are low.

    Eukaryotic Regulation of Gene Expression

    • More complex than prokaryotic regulation with several pathways.

    Regulation of Chromatin Structure

    • DNA packaged as chromatin; nucleosome structure affects gene accessibility.
    • Histone acetylation promotes transcription by loosening chromatin, while methylation typically represses it.
    • DNA methylation is often associated with inactive genes (e.g., Barr body).
    • Non-coding RNAs (ncRNAs) play significant roles in chromatin remodeling.
    • Epigenetic changes influence differential gene expression and are heritable.

    Transcriptional Regulation via Transcription Factors

    • RNA polymerase interacts with general transcription factors that bind DNA (TATA box) facilitating transcription.
    • Specific transcription factors (activators) bind to enhancers to increase transcription rates.
    • Enhancers can be distant from the gene; DNA loops bring them in proximity to the promoter.
    • Repressors can block activators or bind silencers to reduce transcription.

    Post-transcriptional Regulation

    • Alternative splicing allows varied protein products from single pre-mRNA.
    • mRNA stability is enhanced by the 5’ CAP and poly-A tail; sequences in the 3’ UTR affect degradation.
    • Translation initiation is regulated by proteins binding to untranslated regions.
    • Protein degradation involves ubiquitin tagging for proteolytic degradation.
    • miRNA and siRNA can bind mRNA, leading to silencing through degradation or translation blocking (RNA interference).

    Biotechnology

    • Recombinant DNA involves DNA from multiple sources.
    • Restriction endonucleases cut DNA at specific sequences, creating 'sticky ends.'
    • DNA/gene cloning incorporates specific genes into plasmids for expression in bacteria.
    • Gel electrophoresis separates DNA fragments by size using an electric current.

    Polymerase Chain Reaction (PCR)

    • PCR amplifies specific DNA sequences through cycles of denaturation, annealing, and elongation.

    cDNA and RNA Amplification Techniques

    • cDNA produced from mRNA using reverse transcriptase.
    • RT-PCR amplifies RNA into DNA for gene expression measurement using fluorescent markers.
    • RNA-seq detects all expressed RNAs using Next-Generation Sequencing (NGS).

    Enzyme-Linked Immunosorbent Assay (ELISA)

    • Quickly detects specific antigens using antibodies linked with enzymes for diagnostic purposes.

    Genomics

    • The study of the complete DNA content, encompassing all genes within a cell.
    • Bioinformatics applies computational methods for biological data analysis.

    Genome Mapping

    • Gene mapping identifies relative gene positions, using genetic maps (centimorgans) and physical maps (base pairs).

    DNA Sequencing Techniques

    • Shotgun sequencing fragments DNA for overlapping sequence reconstruction.
    • Sanger sequencing uses dideoxy nucleotides for chain termination in DNA sequencing.

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    Description

    This quiz covers techniques for measuring gene expression, particularly focusing on the use of DNA probes on a chip and RNA sequencing (RNA-seq). It explains the processes involved in converting RNA to cDNA and the significance of fluorescence in gene expression analysis. Test your understanding of these molecular biology methods.

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