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Questions and Answers
What is the name of the process that refers to programmed cell death?
What is the name of the process that refers to programmed cell death?
Apoptosis
What is the challenge faced in identifying homologous sequences outside of a limited taxonomic range?
What is the challenge faced in identifying homologous sequences outside of a limited taxonomic range?
The challenge is that homologous sequences can become undetectable by sequence search methods due to sequence divergence.
What does the term "open reading frame" refer to?
What does the term "open reading frame" refer to?
The open reading frame refers to a stretch of DNA that can be translated into a protein and does not contain any stop codons.
A protein molecule is constructed from a series of domains, each having a different structure and function.
A protein molecule is constructed from a series of domains, each having a different structure and function.
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What is the function of the 'death domain' in a protein?
What is the function of the 'death domain' in a protein?
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What is the fundamental unit of tertiary structure?
What is the fundamental unit of tertiary structure?
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How are domains built?
How are domains built?
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Identify three main classes of protein structures.
Identify three main classes of protein structures.
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What are the practical steps to classify a gene into a specific gene family? (Select all that apply)
What are the practical steps to classify a gene into a specific gene family? (Select all that apply)
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How is the sequence of a gene of interest obtained?
How is the sequence of a gene of interest obtained?
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What is the purpose of aligning the gene sequence with known sequences of genes in the gene family of interest?
What is the purpose of aligning the gene sequence with known sequences of genes in the gene family of interest?
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What type of analysis can be performed to further characterize the gene within the gene family?
What type of analysis can be performed to further characterize the gene within the gene family?
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What is the name of the circular structure that represents the complete gene map of the E. coli K12 genome?
What is the name of the circular structure that represents the complete gene map of the E. coli K12 genome?
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The complete circular gene map of the E. coli K12 genome shows that non-coding DNA accounts for only 11% of the total DNA.
The complete circular gene map of the E. coli K12 genome shows that non-coding DNA accounts for only 11% of the total DNA.
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Prokaryotic genomes have a significant amount of wasted space due to large stretches of non-coding DNA between genes.
Prokaryotic genomes have a significant amount of wasted space due to large stretches of non-coding DNA between genes.
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What is the suggested benefit of the compact organization of prokaryotic genomes?
What is the suggested benefit of the compact organization of prokaryotic genomes?
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What is a stop codon?
What is a stop codon?
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An open reading frame is a sequence of DNA that includes a stop codon.
An open reading frame is a sequence of DNA that includes a stop codon.
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An operon is a group of genes that are located adjacent to each other and expressed as a single unit.
An operon is a group of genes that are located adjacent to each other and expressed as a single unit.
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What is the name of the first operon discovered by Jacob and Monod?
What is the name of the first operon discovered by Jacob and Monod?
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What are the three genes found in the lactose operon?
What are the three genes found in the lactose operon?
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What is the function of the LacY gene?
What is the function of the LacY gene?
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What is the function of the LacZ and LacA genes?
What is the function of the LacZ and LacA genes?
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An operon is a group of genes whose functions are typically not related.
An operon is a group of genes whose functions are typically not related.
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The E. coli K12 genome contains almost 600 operons.
The E. coli K12 genome contains almost 600 operons.
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Bacillus subtilis contains a similar number of operons as E. coli K12.
Bacillus subtilis contains a similar number of operons as E. coli K12.
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What tool can be used to find an ORF?
What tool can be used to find an ORF?
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Study Notes
Gene Families
- Gene classification can be based on the purpose of study, e.g., cancer biology uses oncogenes, while evolutionary biology and bioinformatics use orthologues and paralogues.
- One method for classifying genes is by function, as shown in Figure 40. This approach has the benefit of broad functional categories that can be further broken down.
- However, assigning functions to many genes is not yet complete, limiting the scope of this categorization approach.
- Another challenge in classification is lineage-specific genes, also called "orphan" genes. Homologous sequences may not be found outside a certain taxonomic range. Sequence divergence may make these genes undetectable.
- A more powerful method uses protein structures instead of function. Proteins are made of domains with specific biochemical functions. Examples include zinc fingers for DNA binding and death domains in apoptosis.
- Protein domain sequences, determined by the nucleotide sequence of their gene, can aid classification.
- This structural approach is beneficial for genes lacking known functions, as this broader technique better identifies more genes.
Practical Steps to Classify a Gene
- Gene classification involves several steps—methods may vary depending on the gene family and organisms studied.
- Sequence Retrieval: Obtain the target gene sequence from databases like GenBank, Ensembl, or UniProt.
- Sequence Alignment: Match the target gene with known sequences of genes within its family using tools such as BLAST, Clustal Omega, or MAFFT.
- Phylogenetic Analysis: Create a phylogenetic tree to analyze the evolutionary relationships between the target gene and other genes in its family using aligned sequences.
- Conserved Domain Analysis: Use tools such as InterProScan or Pfam to find conserved domains or motifs within the target gene sequence, useful in classification.
- Functional Annotation: Investigate the functions of genes (from the gene family) to gain insights into the target gene's role.
- Gene Family Database Search: Consult databases (e.g., Pfam, PROSITE, or Gene Ontology) to ascertain if the target gene matches any known gene families.
- Literature Review: Study the scientific literature to understand the family's characteristics and classification criteria.
- Validation: Compare the characteristics/properties of the target gene to those of other members in the same family and consult subject-matter experts for validation.
- Document the process: Clearly record and include all methods, data sources, rationale and conclusions for your classification.
- Further analysis: Conduct additional analyses to improve characterization. This could include protein structure prediction, expression patterns, and functional studies.
The Genetic Map
- Bacterial genomes are tightly organized with minimal space between genes.
- The E. coli K12 genome map (Figure 36) demonstrates the compact structure.
- Non-coding DNA in bacterial genomes is relatively less than 11%, dispersed throughout the genome.
- Prokaryotic genomes are compact to support fast replication. However, there's no strong experimental evidence confirming this theoretical benefit.
Open Reading Frames
- An open reading frame (ORF) is a portion of a DNA sequence from a start to a stop codon.
- These codons are important for signaling the continuation or termination of protein synthesis.
- The majority of genes contain one or more ORFs, where each ORF codes for one protein.
- The process of "reading" is to produce a sequence of amino acids, which forms the protein.
Operons
- Operons are characteristic of prokaryotic genomes (e.g., E. coli).
- Operons are groupings of genes adjacent within the genome.
- The arrangement facilitates the coordinated expression of a group of genes. (A single regulatory system controls the function of all genes in the operon simultaneously).
- A key example is the lactose operon (Jacob and Monod, 1961), which controls lactose metabolism in E. coli, allowing a coordinated function for lactose utilization.
- Generally, the operon will not be expressed outside of E. coli's natural habitat. When lactose is available, the operon becomes active with protein production.
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Description
This quiz explores the classification of gene families based on various biological studies such as cancer biology and evolutionary biology. It covers methods for classifying genes by function and structure, along with challenges such as orphan genes and lineage-specific sequences. Test your knowledge on how protein domains contribute to gene classification.
