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Questions and Answers
What is the product of the catalytic activity described in the content?
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?
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?
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?
Which enzyme category is suggested by the gene product associated with CY S3?
From which organism is the strain mentioned in the content derived?
From which organism is the strain mentioned in the content derived?
What is the main advantage of using a relational database over a flat file?
What is the main advantage of using a relational database over a flat file?
What is a key characteristic of a biological database?
What is a key characteristic of a biological database?
Which term is used when information is retrieved from a database?
Which term is used when information is retrieved from a database?
In the context of databases, what does unnecessary redundancy refer to?
In the context of databases, what does unnecessary redundancy refer to?
Which statement best describes a database system?
Which statement best describes a database system?
What does the term 'multi-user system' imply in the context of databases?
What does the term 'multi-user system' imply in the context of databases?
What is one of the first steps in preparing a database?
What is one of the first steps in preparing a database?
Which of the following statements about databases is false?
Which of the following statements about databases is false?
Which program was used for refinement according to the data?
Which program was used for refinement according to the data?
What is the R value reported in the refinement results?
What is the R value reported in the refinement results?
How many reflections were included in the refinement?
How many reflections were included in the refinement?
What is the percentage completion of the data collected?
What is the percentage completion of the data collected?
What is the RMSD bond distances reported?
What is the RMSD bond distances reported?
What range of resolution is indicated in the data?
What range of resolution is indicated in the data?
How many protein atoms are included in this refinement?
How many protein atoms are included in this refinement?
What is the expected result for the Y coordinate using its transformation?
What is the expected result for the Y coordinate using its transformation?
What transformation matrix is used on the coordinates X, Y, Z?
What transformation matrix is used on the coordinates X, Y, Z?
What does the remark about amino acids numbering indicate?
What does the remark about amino acids numbering indicate?
Which amino acids are present in the first sequence of SEQRES?
Which amino acids are present in the first sequence of SEQRES?
What do the coordinates (35.313, 108.011, 15.140) represent in the ATOM records?
What do the coordinates (35.313, 108.011, 15.140) represent in the ATOM records?
How many residues are listed in the first SEQRES entry for chain A?
How many residues are listed in the first SEQRES entry for chain A?
What is represented by the 'HELIX' record in the provided data?
What is represented by the 'HELIX' record in the provided data?
What does the term 'CRYST1' indicate in the content?
What does the term 'CRYST1' indicate in the content?
How many total atoms are noted in the MASTER record?
How many total atoms are noted in the MASTER record?
What does the 'TER' record signify in the molecular data?
What does the 'TER' record signify in the molecular data?
What is the source organism listed in the data for GCN4?
What is the source organism listed in the data for GCN4?
What is the primary purpose of the SCOP database?
What is the primary purpose of the SCOP database?
Which of the following is NOT a principal level of classification within SCOP?
Which of the following is NOT a principal level of classification within SCOP?
What distinguishes a superfamily from a family in the SCOP hierarchy?
What distinguishes a superfamily from a family in the SCOP hierarchy?
Which statement correctly describes how proteins are organized in SCOP?
Which statement correctly describes how proteins are organized in SCOP?
Which level of SCOP classification describes the types of folds, such as beta sheets?
Which level of SCOP classification describes the types of folds, such as beta sheets?
What challenge does the SCOP database face in classifying proteins?
What challenge does the SCOP database face in classifying proteins?
Which tool or external resource does SCOP provide access to for further information?
Which tool or external resource does SCOP provide access to for further information?
What is the primary role of manual inspection in the SCOP classification process?
What is the primary role of manual inspection in the SCOP classification process?
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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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.
