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Questions and Answers
What does the term 'Omics' refer to in biological sciences?
What does the term 'Omics' refer to in biological sciences?
Which type of Omics specifically analyzes protein interactions?
Which type of Omics specifically analyzes protein interactions?
What reserve material do many bacteria accumulate when nutrients are unbalanced?
What reserve material do many bacteria accumulate when nutrients are unbalanced?
Which method was primarily used for the first complete genome sequencing of a cellular organism?
Which method was primarily used for the first complete genome sequencing of a cellular organism?
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Which organism's complete genome was sequenced using the random shotgun approach by Craig Venter?
Which organism's complete genome was sequenced using the random shotgun approach by Craig Venter?
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How does the size of the human genome compare with that of Haemophilus influenza?
How does the size of the human genome compare with that of Haemophilus influenza?
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What factor influences the type of reserve material bacteria accumulate?
What factor influences the type of reserve material bacteria accumulate?
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What analysis does epigenomics focus on?
What analysis does epigenomics focus on?
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Which organism has the smallest genome size among the listed prokaryotes?
Which organism has the smallest genome size among the listed prokaryotes?
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What is the significance of paralogous genes?
What is the significance of paralogous genes?
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What additional gene features are typically found in larger genomes?
What additional gene features are typically found in larger genomes?
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What mechanism contributes to the reduction of genome size in organisms with limited habitats?
What mechanism contributes to the reduction of genome size in organisms with limited habitats?
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Which organism contains a genomic island associated with N2-fixation?
Which organism contains a genomic island associated with N2-fixation?
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How many coding proteins does Mycoplasma genitalum encode?
How many coding proteins does Mycoplasma genitalum encode?
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Which of the following bacteria has the largest genome size?
Which of the following bacteria has the largest genome size?
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Why is Mycobacterium leprae's genome size considered unique?
Why is Mycobacterium leprae's genome size considered unique?
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Study Notes
Lecture 6: The World of Omics
- Omics is an umbrella term for large-scale biological studies
- These studies look at genomics, proteomics, transcriptomics, and other data sets
- The goal is to comprehensively understand structure, function, and dynamics of living systems
Types of Omics
- Genomics: Studies an organism's entire DNA sequence (genome)
- Transcriptomics: Focuses on RNA transcripts (gene expression patterns)
- Proteomics: Analyzes protein structure, function, and interactions
- Metabolomics: Studies small molecule metabolites (chemical fingerprints)
- Epigenomics: Examines epigenetic changes, such as DNA methylation
Polyesters
- Bacteria store reserve material. The type of reserve material depends on the organism's genotype and limiting nutrients
- If the carbon-to-nitrogen ratio is high or nitrogen, phosphorus, or oxygen are limiting, bacteria often store glycogen and/or aliphatic polyesters (PHAs) up to 80% of their cellular dry weight
Sequencing of Genomes
- Viral genome sequencing began in the late 1970s
- The Sanger dideoxy termination method was used for random fragment sequencing
- Phage and bacteriophage DNA sequencing, notably phage λ in 1980, was also achieved
- Initial efforts to sequence entire cellular genomes focused on Escherichia coli, but the "clone-by-clone shotgun" method was not suitable for large or complete genomes
Sequencing of Genomes (Continued)
- Craig Venter successfully sequenced the entire 1.8-megabase genome of Haemophilus influenzae using the completely random, shotgun sequencing approach
- Human genome sequencing, at 3 gigabases, is much larger and required massive data and processing
Prokaryotic Genomes
- Their genomes contain the minimal set of genes to allow cellular growth and replication
- Homologous genes and proteins are classified by homology using algorithms like BLAST
- Orthologs: Similar genes in two different species, arising from a common ancestral gene
- Paralogs: Similar genes within the same species, often arising from gene duplication
- Organisms like M. genitalum and H. influenzae have gene sets with about 300 and 1500 genes respectively for independent survival
Prokaryotic Genomes (Continued)
- Larger prokaryotic genomes (e.g., E.coli, P. aeruginosa, S. coelicolor) have more genes for different functional roles like environmental adaptation
- Genes involved in handling or adaptation to stress factors (e.g. nutritional limitations, toxins, antibiotics etc.)
- Some microorganisms have large genomic "islands" of genes obtained from horizontal transfer from other organisms (e.g., pathogenicity islands in Salmonella, and symbiosis islands in B. japonicum).
Genome Size
- Size of prokaryotic genomes can vary greatly
- H. influenzae: 1.8Mb
- Chlamydia trachomatis: 1.0 Mb
- Mycoplasma genitalum: 0.6 Mb
- E. coli: 4.6 Mb
- Pseudomonas aeruginosa: 6.3 Mb
- Streptomyces coelicolor: 8.7Mb
- Bradyrhizobium japonicum: 9.1 Mb
- Most archaeal genomes range from 1.5 to 3 Mb
Prokaryotic Genomes (Continued)
- In some cases, smaller genomes arise when genes are converted to pseudogenes (genes that no longer function). Example: Salmonella typhi genome, which has limited habitat adaptation, is smaller than other organisms
- Mycobacterium leprae only has 50% protein-coding genes.
Metagenomics
- Metagenomics is an approach to study microbial communities, many of which are currently uncultured
- Biotechnology allows expressing of foreign genes in microbial organisms like E. coli or yeast
- Direct cloning from soil samples can reveal widely diverse properties of proteins
- Metagenomic methods are now standard industrial techniques for gene cloning
Metagenomics (Continued)
- An example of metagenomic studies includes analyzing microbial communities from acid mine drainage, which provides insights into metabolic pathways of microorganisms
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Description
Explore the fascinating world of omics, which encompasses large-scale biological studies including genomics, proteomics, transcriptomics, and more. This quiz aims to deepen your understanding of the structure, function, and dynamics of living systems through various omics disciplines.
