Introduction to Biological Databases
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Questions and Answers

What is the product of the catalytic activity described in the content?

  • Hydrogen
  • L-Cysteine (correct)
  • L-Cystathionine
  • Oxobutanoate

    • What is the substrate used in the described enzymatic reaction?

  • Oxaloacetate
  • O-Butyric acid
  • L-Cystathionine (correct)
  • L-Cysteine

    • Which cofactor is mentioned as necessary for the associated enzymatic activity?

  • Pyridoxal phosphate (correct)
  • Coenzyme A
  • Flavin adenine dinucleotide
  • NADH

    • Which enzyme category is suggested by the gene product associated with CY S3?

    <p>Cystathionine synthase</p> Signup and view all the answers

    From which organism is the strain mentioned in the content derived?

    <p>Saccharomyces cerevisiae</p> Signup and view all the answers

    What is the main advantage of using a relational database over a flat file?

    <p>Relational databases allow for easier data management and output choices.</p> Signup and view all the answers

    What is a key characteristic of a biological database?

    <p>Data is organized for easy access, management, and updating.</p> Signup and view all the answers

    Which term is used when information is retrieved from a database?

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

    In the context of databases, what does unnecessary redundancy refer to?

    <p>Duplicating data within the database.</p> Signup and view all the answers

    Which statement best describes a database system?

    <p>It is an integrated collection of related files with data management capabilities.</p> Signup and view all the answers

    What does the term 'multi-user system' imply in the context of databases?

    <p>The database is accessible to multiple users simultaneously.</p> Signup and view all the answers

    What is one of the first steps in preparing a database?

    <p>Collecting data in an accessible form.</p> Signup and view all the answers

    Which of the following statements about databases is false?

    <p>A database must always have a physical backup.</p> Signup and view all the answers

    Which program was used for refinement according to the data?

    <p>X-PLOR</p> Signup and view all the answers

    What is the R value reported in the refinement results?

    <p>0.216</p> Signup and view all the answers

    How many reflections were included in the refinement?

    <p>3296</p> Signup and view all the answers

    What is the percentage completion of the data collected?

    <p>98.2</p> Signup and view all the answers

    What is the RMSD bond distances reported?

    <p>0.020 Angstroms</p> Signup and view all the answers

    What range of resolution is indicated in the data?

    <p>10.0 - 3.0 Angstroms</p> Signup and view all the answers

    How many protein atoms are included in this refinement?

    <p>456</p> Signup and view all the answers

    What is the expected result for the Y coordinate using its transformation?

    <p>Y SYMM + 117.32</p> Signup and view all the answers

    What transformation matrix is used on the coordinates X, Y, Z?

    <p>0 -1 0</p> Signup and view all the answers

    What does the remark about amino acids numbering indicate?

    <p>It corresponds to 281 amino acids.</p> Signup and view all the answers

    Which amino acids are present in the first sequence of SEQRES?

    <p>ILE, VAL, PRO, GLU</p> Signup and view all the answers

    What do the coordinates (35.313, 108.011, 15.140) represent in the ATOM records?

    <p>Position of the atom CA</p> Signup and view all the answers

    How many residues are listed in the first SEQRES entry for chain A?

    <p>62</p> Signup and view all the answers

    What is represented by the 'HELIX' record in the provided data?

    <p>The specific sequence of amino acids forming a helical region</p> Signup and view all the answers

    What does the term 'CRYST1' indicate in the content?

    <p>The crystallographic parameters</p> Signup and view all the answers

    How many total atoms are noted in the MASTER record?

    <p>844</p> Signup and view all the answers

    What does the 'TER' record signify in the molecular data?

    <p>The end of a chain of residues</p> Signup and view all the answers

    What is the source organism listed in the data for GCN4?

    <p>Saccharomyces cerevisiae</p> Signup and view all the answers

    What is the primary purpose of the SCOP database?

    <p>To provide a manual classification of protein structural domains</p> Signup and view all the answers

    Which of the following is NOT a principal level of classification within SCOP?

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

    What distinguishes a superfamily from a family in the SCOP hierarchy?

    <p>A superfamily includes domains with a distant common ancestor.</p> Signup and view all the answers

    Which statement correctly describes how proteins are organized in SCOP?

    <p>Proteins can be organized by individual domains or by whole multi-domain proteins.</p> Signup and view all the answers

    Which level of SCOP classification describes the types of folds, such as beta sheets?

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

    What challenge does the SCOP database face in classifying proteins?

    <p>The entities being organized are not homogeneous in nature.</p> Signup and view all the answers

    Which tool or external resource does SCOP provide access to for further information?

    <p>Protein Data Bank (PDB)</p> Signup and view all the answers

    What is the primary role of manual inspection in the SCOP classification process?

    <p>To provide accurate classification through visual comparison of structures.</p> Signup and view all the answers

    Study Notes

    Database Introduction

    • Biological database is a collection of biological data that is easily accessible, managed and updated
    • Preparing the database involves data collection and making it available to the user.
    • Databases are collections of related data that are stored in a computerized archives so that information can be retrieved easily.
    • Databases are used to store and organize data without unnecessary redundancies (duplicate data)
    • a database system is used to define, interpret, manipulate and maintain data.
    • A query is used to retrieve specific information from a database.

    SCOP Database

    • SCOP - Structural Classification of Proteins database
    • The SCOP database is a classification of protein structural domains based on similarities of their structures and amino acid sequences.
    • The SCOP database is maintained by the labs of molecular biology, and the center for protein engineering at MRC.
    • The SCOP database aims to provide a detailed description of the structural and evolutionary relationships between all proteins.
    • The SCOP database includes all entries in the Protein Data Bank (PDB).
    • The SCOP database provides links to PDB entries, sequences, references, images, and interactive display systems.
    • Automatic sequence and structure comparison tools are not sufficient for identifying all relationships between proteins.
    • The SCOP classification of proteins has been constructed manually through visual inspection and comparison of structures.
    • SCOP classification is challenging because of the variety of proteins.
    • SCOP classification is done at different levels - family, super family and fold.
    • The SCOP database is hierarchical and organized into Class, Fold, Superfamily, Family, Protein Domain, Species and Domain.
    • A protein domain is often only a portion of a larger protein.

    CATH Database

    • CATH database is a hierarchical classification of protein domain structures.
    • CATH database is also used to classify protein structural domains.
    • CATH database classifies protein structures based on Class, Architecture, Topology, Homology.

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    Molecular Biology Database Resources PDF

    Description

    Explore the fundamentals of biological databases, focusing on their structure, management, and utility in storing biological data. Learn about specific examples such as the SCOP database, which classifies protein structural domains based on their features. This quiz will deepen your understanding of how databases facilitate data retrieval and organization.

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