Lecture Notes on Genomics and Genetics

Understanding Genome Terminology

Common Terms in Cell and Genomics Study

• Similar to studying cells and cell organelles, certain common terminologies are used in genomics.
• Importance of understanding concepts clearly to avoid confusion when studying molecular genetics.
• Definition and variation of genomes across different organisms.

Defining Genome

• Narrow Definition: Often defined as the sum total of all DNA, genes, or chromosomes present in an organism.
• Broad Definition: Best defined as the sum total of all genetic material (DNA or RNA) present in an organism (cellular or non-cellular).
• Genomic material includes nuclear DNA, extra-nuclear DNA (like mitochondrial or plastid DNA).

Notes on Genetic Material

• Genetic material is not always DNA; RNA can also be genetic material (e.g., in some viruses).
• Genomic DNA can include chromosomal DNA and plasmid DNA (e.g., in bacteria).
• Chromosomal DNA is always present in bacteria, whereas plasmid DNA might or might not be present.

Supercoiling in DNA

Types of Supercoiling

• Plectonemic Supercoiling: Seen in chromosomal DNA, mainly negative supercoiling.
• Solenoidal Supercoiling: Involves histone protein complexes (seen in eukaryotic chromosomal DNA).

Genome Nature in Organisms

Prokaryotic Genome

• Components: Chromosomal DNA (essential), Plasmid DNA (non-essential, can be absent).
• Properties: Generally circular and negatively supercoiled.
• Variations: Some bacteria have linear DNA and more than one chromosome.

Eukaryotic Genome

• Nuclear DNA: More than one chromosome, linear in shape, solenoidal supercoiling.
• Extra-nuclear DNA: Found in mitochondria and plastids, can be circular or linear.

RNA-based Genomes

RNA Genomes

• Found in some viruses, can be single-stranded (common) or double-stranded (rare).
• Sense Types: Positive (acts as mRNA) or Negative (serves as a template for mRNA).
• Classification: Monopartite, Multipartite, or Segmented.

Genome Size and Complexity

Range and Trends

• Genome size ranges from less than 10^6 base pairs to more than 10^11 base pairs.
• Trend: Prokaryotic genomes are smaller; lower eukaryotic genomes are bigger; higher eukaryotic genomes are the biggest.
• Smallest Genome: Mycoplasma genitalium.

Factors Influencing Genome Size

• Increase in number of different genes (mainly protein-coding genes).
• Size of genes and presence of non-coding sequences (e.g., introns).
• Multiple copies of genes (gene duplication).

C-value Paradox

• No direct correlation between genome size and organism complexity. Example: larger genomes can be found in less complex organisms and vice versa.
• This lack of correlation is termed C-value Paradox.

Gene Definition and Classification

Evolution of Gene Definition

• Historical: One gene-one enzyme hypothesis evolved to one gene-one protein and then one gene-one polypeptide.
• Current: Genes are defined as functional segments of genetic material, which can be DNA or RNA.

Gene Types

• Interrupted Genes (Split Genes): Containing introns, common in higher eukaryotes.
• Uninterrupted Genes (Non-split Genes): Lacking introns, common in prokaryotes.
• Gene Duplication Fates: No divergence, related function, or become pseudogenes.

Gene Homology

Homologous Genes

• Orthologs: Homologous genes separated by speciation (different species).
• Paralogs: Homologous genes within the same genome (result of gene duplication).
• Homology vs. Similarity: Critical difference; homology means shared ancestry, not just similarity.

Concluding Notes and Recommendations

• Read the provided books to complement the notes for a better understanding of the subject.
• Pay attention to terminology differences across different sources.