Study Notes on Virology and Genomics

Overview of Coronaviruses

  • Coronaviruses are classified as single-stranded RNA viruses.

    • Other notable examples of single-stranded RNA viruses include:

    • Ebola virus

    • HIV (Human Immunodeficiency Virus)

Viral Life Cycle

Phases

  • Lytic Phase

    • This is the phase of active viral replication.

    • The virus makes multiple copies of itself, leading to the death of the host cell as it releases new viral particles.

  • Lysogenic Phase

    • In this phase, viral DNA integrates into the host cell's genome without immediately destroying it.

Prokaryotic Viruses

  • Prokaryotic viruses include bacteriophages such as:

    • Bacteriophage T4

    • Bacteriophage T7

Genomics

Introduction to Genomics

  • Genomics is the study of whole genomes.

  • The concept of genomics led to the emergence of various fields of "omics" in biology.

    • Proteomics focuses on the study of all expressed proteins in a cell.

The Human Genome

  • The approximate number of nucleotide bases in the diploid human genome is around:

    • 7,000,000,000 (some estimates range between 7,000,000,000 and 8,000,000,000 bases).

    • For context, the entire genome of HIV consists of approximately 10,000 bases.

Sequencing Methods

Typical DNA Sequencing

  • Traditional sequencing methods require careful and systematic approaches, often done in separate laboratories.

Shotgun Sequencing

  • Description: In shotgun sequencing, the genome is fragmented into small pieces (e.g., 100-500 bases), sequenced, and then computer algorithms are employed to align and reconstruct the original DNA sequence.

  • This method replaced more deliberate approaches to sequencing due to its efficiency.

Human Genome Project (HGP)

  • Craig Venter introduced shotgun sequencing, claiming it could expedite the sequencing process and successfully led a press conference proclaiming accomplishments in sequencing the human genome.

  • A joint announcement was made with the Human Genome Project, indicating both parties had sequenced about 99% of the human genome.

  • Venter emphasized the collaborative nature of this scientific endeavor and clarified that both approaches were required to achieve the 1% they were missing.

Sequencing Statistics

  • Several hundred large animal genomes have been sequenced; the total for bacteria and other organisms exceeds 10,000 to 20,000 genomes.

  • Efforts such as the $100 genome project aim to make personal genome sequencing economically accessible.

Gene Density and Complexity

Human Gene Count

  • Humans possess approximately 20,000 to 30,000 genes within their genome of 7,000,000,000 bases.

  • The low gene percentage has intrigued researchers, leading to discussions around the complexity of genetic design compared to other entities (e.g., machines).

  • Early interpretations suggested that less than 2% of the genome is utilized for coding expressible genes.

Junk DNA vs. Functional DNA

  • Historically termed "junk DNA", it is now understood that this portion serves significant regulatory functions within the genome.

    • Approximately 1.5% of human DNA is considered actual coding genes.

    • Regulatory Sequences: About 20% of the genome is implicated in regulation of gene expression and is crucial for orchestrating complex traits.

Transposons

  • Discovered by Barbara McClintock, transposable elements (or transposons), allow portions of DNA to move around within the genome without necessarily being linked to specific gene functions.

  • Transposable elements have significant implications on genetic variation and stability across generations.

Formation of New Genes

Mechanisms

  • Processes that can contribute to the evolution of new genes include:

    • Transposition: Movement of genes or segments within the genome.

    • Exon Shuffling: Combination of exons from different genes to craft new functional units.

    • Exon Duplication: Copying of exons leading to gene families that can diverge functionally.

    • Point Mutations: These may yield advantageous changes in gene function, albeit rarely.

Implications of Gene Evolution

  • The slow evolution of genes is underscored by the fact that significant evolutionary change does not typically happen within a short time frame.

  • Homologous recombination during meiosis is a critical mechanism that supports genetic diversity, which may not be viable if it occurs between non-homologous chromosomes.

Summary of Key Concepts

Gene Expression

  • The gene expression is tightly regulated, and patterns of expression exhibit variations across different tissues and developmental stages.

  • Repetitive sequences in the genome are often used in forensic genetics to identify individuals based on DNA profiling.

Gene Functionality

  • There remains vast unexplored realms concerning the functionality of much of the non-coding DNA, which is not classified as junk due to its influencing roles in genetic expression and genomic stability.