Genomics II: Functional Genomics, Proteomics, and Bioinformatics Quiz
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What is the primary function of DNA microarrays?

  • To amplify gene fragments
  • To identify genes that are not transcribed
  • To monitor thousands of genes simultaneously (correct)
  • To synthesize genes

    • What is the advantage of using DNA microarrays over traditional methods?

  • They can monitor only a few genes at a time
  • They can analyze thousands of genes simultaneously (correct)
  • They are more expensive
  • They can identify genes that are not transcribed

    • What is the purpose of the DNA sequences on a microarray?

  • To amplify gene fragments
  • To identify genes that are not transcribed
  • To act as probes to identify genes that are transcribed (correct)
  • To synthesize genes

    • How are the DNA fragments on a microarray typically prepared?

    <p>They are amplified by PCR and then spotted onto the microarray</p> Signup and view all the answers

    What is the purpose of a single slide on a DNA microarray?

    <p>To analyze thousands of genes simultaneously</p> Signup and view all the answers

    What is the technology used to make DNA microarrays similar to?

    <p>An inkjet printer</p> Signup and view all the answers

    What is an application of DNA microarrays?

    <p>To compare microarray data using cDNAs derived from RNA of different cell types</p> Signup and view all the answers

    What is the result of using a DNA microarray as a hybridization tool?

    <p>The identification of genes that are transcribed</p> Signup and view all the answers

    What is the primary goal of functional genomics in a given species?

    <p>To elucidate the roles of genetic sequences</p> Signup and view all the answers

    What is the term used to describe the entire collection of proteins that an organism can make?

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

    What is the primary focus of epigenomics?

    <p>To study the chemicals that can tell the genome what to do</p> Signup and view all the answers

    What is the term used to describe the large-scale study of small molecules within cells, biofluids, tissues or organisms?

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

    What is the primary focus of bioinformatics?

    <p>To extract information from genetic data using a mathematical approach</p> Signup and view all the answers

    What is the term used to describe the analysis of the complete set of gene expression?

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

    What is the term used to describe the sum of constituents within a cell at all levels?

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

    What is the primary goal of proteomics?

    <p>To understand the interplay among many different proteins</p> Signup and view all the answers

    What is the primary purpose of functional microarrays?

    <p>To probe the function of proteins</p> Signup and view all the answers

    What is the term for the marriage between genetics and biocomputing?

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

    What are the three basic components of computer analysis of genetic sequences?

    <p>Computer, data, and program</p> Signup and view all the answers

    What is the primary function of a computer program in bioinformatics?

    <p>To analyze data in a desired way</p> Signup and view all the answers

    What is the purpose of generating a computer data file?

    <p>To collect genetic data in a form suitable for storage and manipulation by a computer</p> Signup and view all the answers

    How are genetic sequences typically entered into a computer file?

    <p>Manually and by instruments</p> Signup and view all the answers

    What is one of the ways genetic sequences can be analyzed?

    <p>To identify functional sequences</p> Signup and view all the answers

    What is the term for the study of the evolutionary relationship between genetic sequences?

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

    What is the primary goal of gene prediction?

    <p>To identify regions of genomic DNA that encode genes</p> Signup and view all the answers

    What strategy do computer programs use to locate genes by searching for specific signals?

    <p>Searching for an organization of known sequence elements</p> Signup and view all the answers

    What is the primary difference between search by signal and search by content strategies?

    <p>Search by signal searches for known sequence elements, while search by content searches for sequences that differ significantly from a random distribution</p> Signup and view all the answers

    What is an open reading frame (ORF)?

    <p>A nucleotide sequence that does not contain any stop codons</p> Signup and view all the answers

    Why are there six possible reading frames in a newly discovered sequence?

    <p>Because there are three reading frames in each direction (5' to 3' and 3' to 5')</p> Signup and view all the answers

    What is the significance of homologous genes?

    <p>They are derived from the same ancestral gene</p> Signup and view all the answers

    What is the purpose of translating a genomic DNA sequence in all three reading frames?

    <p>To locate coding regions within a DNA sequence</p> Signup and view all the answers

    Why are long ORFs contained within chromosomal gene sequences in prokaryotes?

    <p>Because introns are not present in prokaryotes</p> Signup and view all the answers

    What is the primary goal of using a tool like BLAST?

    <p>To identify the function of genetic sequences</p> Signup and view all the answers

    What does a small E-value in BLAST indicate?

    <p>That the similarity is unlikely to be due to random events</p> Signup and view all the answers

    Why is homology among protein sequences easier to identify than is DNA sequence homology?

    <p>Because the genetic code is degenerate</p> Signup and view all the answers

    What is the purpose of the E-value in BLAST?

    <p>To represent the number of times a match would be expected to occur by random chance</p> Signup and view all the answers

    What is the result of using a query sequence in BLAST?

    <p>A list of homologous sequences with corresponding E-values</p> Signup and view all the answers

    Why are the results of a BLAST search typically sorted by E-value?

    <p>Because the E-value determines the significance of the match</p> Signup and view all the answers

    What is the advantage of using BLAST over other sequence comparison methods?

    <p>BLAST can search large databases quickly</p> Signup and view all the answers

    What is the primary input for a BLAST search?

    <p>A query sequence</p> Signup and view all the answers

    What is the purpose of multiple sequence alignment?

    <p>To identify conserved sites among homologs</p> Signup and view all the answers

    What is the characteristic of conserved sites in homologs?

    <p>They are identical or similar across multiple homologs</p> Signup and view all the answers

    How many paralogs of the globin gene family are functionally expressed in humans?

    <p>9</p> Signup and view all the answers

    What is the composition of hemoglobin protein?

    <p>Two α-chains and two β-chains</p> Signup and view all the answers

    During what stage of development are the ζ and ε genes expressed?

    <p>Early embryonic development</p> Signup and view all the answers

    What can be inferred from the high degree of sequence similarity between species?

    <p>The function of the sequence is similar</p> Signup and view all the answers

    Who originally proposed the multiple sequence alignment approach?

    <p>Saul Needleman and Christian Wunsch</p> Signup and view all the answers

    What is the result of comparing the sequences of the hemoglobin chains?

    <p>Insight into their structure and function</p> Signup and view all the answers

    What is the category of the β gene in the globin gene family?

    <p>β-chains</p> Signup and view all the answers

    What is the purpose of multiple sequence alignment in the globin gene family?

    <p>To compare the sequences of the hemoglobin chains</p> Signup and view all the answers

    Study Notes

    Omics

    • In biology, the word "omics" refers to the sum of constituents within a cell at all levels.
    • There are several types of omics, including:
      • Epigenomics: deals with chemicals that can tell the genome what to do
      • Proteomics: studies the entire collection of proteins that an organism can make
      • Bioinformatics: analyzes biological information using a mathematical/computational approach
      • Transcriptomics: analyzes the complete set of gene expression
      • Metabolomics: is the large-scale study of small molecules, commonly known as metabolites, within cells, biofluids, tissues, or organisms

    Functional Genomics

    • The goal of functional genomics is to elucidate the roles of genetic sequences in a given species.
    • It aims to understand gene function and the interplay among many different genes.
    • Recent genome-sequencing projects have enabled the study of gene function at a more complex level.
    • We can now examine groups of many genes simultaneously.

    DNA Microarrays

    • DNA microarrays (also called gene chips) are a technology that makes it possible to monitor thousands of genes simultaneously.
    • A DNA microarray is a small silica, glass, or plastic slide that is dotted with many sequences of DNA.
    • Each of these sequences corresponds to a known gene.
    • The DNA fragments on a microarray can be either amplified by PCR and then spotted onto the microarray or synthesized directly on the microarray itself.
    • A single slide contains tens of thousands of different spots in an area the size of a postage stamp.
    • The technology for making DNA microarrays is quite amazing, involving spotting technologies that are quite similar to the way that an inkjet printer works.

    Applications of DNA Microarrays

    • DNA microarrays can be used to:
      • Compare microarray data using cDNAs derived from RNA of different cell types to identify genes that are expressed in a cell-specific manner.
      • Identify genes that are expressed in a cell-specific manner.
      • Probe the function of proteins.

    Bioinformatics

    • The computer has become an important tool in genetic studies.
    • The marriage between genetics and biocomputing has yielded an important branch of science: bioinformatics.
    • Computer analysis of genetic sequences usually relies on three basic components: a computer, a computer program, and some type of data.
    • A computer program is a defined series of operations that can analyze data in a desired way.
    • A first step in the computer analysis of genetic data is the generation of a computer data file.
    • The genetic sequence can be analyzed in many ways, including:
      • Does a sequence contain a gene?
      • Where are functional sequences, such as promoters and splice sites?
      • Does a sequence encode a polypeptide?
      • Is a sequence homologous to other sequences?
      • What is the evolutionary relationship between two or more genetic sequences?

    Approaches to Identify Genes

    • Gene prediction refers to the process of identifying regions of genomic DNA that encode genes.
    • Computer programs can employ different strategies to locate genes, including:
      • Search by signal: looking for an organization of known sequence elements that are normally found within a gene.
      • Search by content: looking for sequences that differ significantly from a random distribution due to codon bias within protein-encoding genes.

    Open Reading Frames

    • Another way to locate coding regions within a DNA sequence is to examine reading frames.
    • In a DNA sequence, the reading of codons could begin with the first, second, or third nucleotide.
    • These are called reading frame 1, 2, and 3, respectively.
    • An open reading frame (ORF) is a nucleotide sequence that does not contain any stop codons.
    • In prokaryotes, long ORFs are contained within the chromosomal gene sequences.
    • In eukaryotes, however, the chromosomal coding sequences may be interrupted by introns.

    Homologous Genes

    • When comparing genetic sequences, researchers sometimes find two or more similar sequences.
    • Homology between genetic sequences can be identified by computer programs and databases.
    • A strong correlation is typically found between homology and function.
    • Homologous genes are derived from the same ancestral gene.

    BLAST

    • BLAST (Basic Local Alignment Search Tool) is a program that starts with a genetic sequence and then locates homologous sequences in a large database.
    • Homology among protein sequences is easier to identify than is DNA sequence homology.
    • The relationship between the query sequence and each matching sequence is given an E-value (Expect value).
    • The E-value represents the number of times that the match or a better one would be expected to occur purely by random chance in the entire database.

    Proteomics

    • Proteomics is the study of the functional roles of proteins in a species.
    • The entire collection of proteins in a species is known as the proteome.
    • Genomic data can provide insights into the proteome, but may not accurately measure protein abundance.

    The Proteome is Larger than the Genome

    • The proteome is larger than the genome due to cellular processes such as:
      • Alternative splicing
      • RNA editing
      • Post-translational covalent modification

    Alterations that Affect the Proteome

    • Alternative splicing:
      • Occurs in eukaryotes
      • A single pre-mRNA is spliced into multiple versions
      • Splicing is often cell-specific or related to environmental conditions
    • RNA editing:
      • Less common than alternative splicing
      • Leads to changes in the coding sequence of mRNA after it is made

    DNA Microarrays

    • A DNA microarray is a technology that allows for the simultaneous monitoring of thousands of genes.
    • It consists of a small silica, glass, or plastic slide dotted with many DNA sequences, each corresponding to a known gene.
    • The DNA fragments on the microarray can be:
      • Amplified by PCR and then spotted onto the microarray
      • Synthesized directly on the microarray
    • A single slide can contain tens of thousands of different spots, with the relative location of each spot known.

    Applications of DNA Microarrays

    • Cell-specific gene expression: Comparing microarray data using cDNAs derived from RNA of different cell types can identify genes that are expressed in a cell-specific manner.
    • Functional microarrays: Consist of many different cellular proteins, used to probe the function of proteins.

    Bioinformatics

    • The computer has become an important tool in genetic studies, combining genetics and biocomputing to form the field of bioinformatics.
    • Computer analysis of genetic sequences relies on three basic components:
      • A computer
      • A computer program
      • Some type of data

    Sequence Files and Computer Programs

    • A computer program is a defined series of operations that can analyze data in a desired way.
    • A computer data file is a collection of information in a form suitable for storage and manipulation by a computer.
    • Entering data into a computer file can be done manually or by instruments that read data directly from a sequencing ladder.

    Analyzing Genetic Sequences

    • Computer analysis of genetic sequences can answer questions such as:
      • Does a sequence contain a gene?
      • Where are functional sequences, such as promoters and splice sites?
      • Does a sequence encode a polypeptide?
      • Is a sequence homologous to other sequences?
      • What is the evolutionary relationship between two or more genetic sequences?

    Homologous Genes

    • Homologous genes are genes that have evolved from a common ancestral gene.
    • Orthologs: Homologous genes found in different species.
    • Paralogs: Homologous genes found in a single organism.
    • A gene family consists of two or more copies of homologous genes within the genome of a single organism.

    Computer Databases

    • Computer databases store large amounts of genetic information generated by researchers.
    • Databases contain annotations, including the genetic sequence and a concise description of it, as well as other features of significance.
    • Examples of major computer databases include GenBank, EMBL, and DDBJ.

    Multiple Sequence Alignment

    • This approach compares homologous genes to identify conserved sites and understand their structure and function.
    • It was originally proposed by Saul Needleman and Christian Wunsch in 1970.
    • The globin gene family in humans is an example of multiple sequence alignment.

    Globin Gene Family

    • The globin gene family consists of 9 paralogs that are functionally expressed in humans.
    • The 9 paralogs fall into two categories: α-chains and β-chains.
    • The composition of hemoglobin changes during development, with different genes expressed during early embryonic development and in the adult.
    • Comparing the sequences of the hemoglobin chains can give insight into their structure and function.

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    Description

    Test your understanding of functional genomics, proteomics, and bioinformatics with this quiz. Covers key concepts from Chapter 23 of Genetics: Analysis & Principles by Robert J. Brooker.

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