Module Five Flashcards
How do genome size, gene number, and gene density differ between prokaryotes and eukaryotes?
Prokaryotes:
Smaller genome size (usually less than 10 Mb).
Fewer genes (typically 1,000–5,000).
Higher gene density (genes are tightly packed with fewer noncoding regions).
Eukaryotes:
Larger genome size (ranging from 10 Mb to hundreds of Gb).
More genes (5,000–40,000+).
Lower gene density (due to introns, regulatory sequences, and repetitive DNA).
What is the history of genome sequencing and what are the methods for whole genome sequencing?
History:
1977: First genome sequenced (bacteriophage ΦX174) using Sanger sequencing.
1990–2003: Human Genome Project sequenced the first human genome.
Advances in sequencing technologies reduced costs and time required for sequencing.
Methods:
Sanger Sequencing: Uses chain-terminating nucleotides for sequence determination.
Next-Generation Sequencing (NGS):
Parallel processing of millions of DNA fragments.
Produces massive amounts of data quickly and cost-effectively.
Third-Generation Sequencing:
Real-time sequencing of single DNA molecules (e.g., nanopore sequencing).
What are the principles of bioinformatics and systems biology, and what questions do they address?
Bioinformatics:
Combines biology, computer science, and mathematics.
Principles:
Analyzes and compares DNA, RNA, and protein sequences.
Identifies genes, regulatory elements, and evolutionary relationships.
Questions Addressed:
What are the functions of genes and proteins?
How are genes regulated and expressed?
Systems Biology:
Focuses on the interactions within biological systems.
Principles:
Integrates data from genomics, proteomics, and metabolomics.
Models and predicts system behaviors.
Questions Addressed:
How do networks of genes and proteins coordinate cellular functions?
How do perturbations affect the system (e.g., in diseases)?
What are transposable elements, and how do they impact genomes?
Transposable Elements (TEs):
DNA sequences that can move within the genome.
Types:
Retrotransposons: Move via RNA intermediate (copy-paste mechanism).
DNA Transposons: Move directly as DNA (cut-paste mechanism).
Impacts on Genomes:
Increase genome size.
Create mutations by inserting into functional genes.
Promote recombination, leading to genome rearrangements.
Provide raw material for evolutionary innovation.
What are the types of repetitive DNA?
Tandem Repeats: Short sequences repeated one after another. Examples: microsatellites and minisatellites.
Interspersed Repeats: Repeated sequences scattered throughout the genome, often derived from transposable elements.
Satellite DNA: Found in centromeric and telomeric regions; aids in chromosome stability and segregation.
What are the mechanisms by which genome structure can change?
Gene Duplication: Creates additional copies of genes, leading to new functions.
Chromosomal
Rearrangements:
Deletions, duplications, inversions, and translocations alter chromosome structure.
Horizontal Gene Transfer: Acquisition of genes from other species (common in prokaryotes).
Polyploidy: Duplication of the entire genome (common in plants).
Transposable Element Activity: Rearranges genes and regulatory sequences.
How do multigene families and new protein functions evolve?
Multigene Families:
Arise through gene duplication.
Subsequent mutations allow specialized or novel functions (e.g., hemoglobin and myoglobin).
New Protein Functions:
Exon Shuffling: Recombination events combine exons from different genes.
Gene Fusion: Two genes merge, creating a hybrid protein.
Adaptive Evolution: Positive selection for mutations that enhance protein functionality.
