Genomics Quiz: Components and Mapping

Major Components of Genomics

• Genomics is the study of entire genomes, focusing on structure, function, and evolution.
• Key components include sequencing, mapping, annotation, and analysis.

Genetic Map vs. Physical Map

• Genetic map shows the relative locations of genes based on recombination frequencies.
• Genetic map units are expressed as map units or centiMorgans (cM).
• Example: A genetic map showing the relative positions of genes on a chromosome involved in eye color or wing shape in fruit flies.
• Physical map depicts the exact locations of DNA segments on a chromosome based on physical distances (base pairs).
• Example: A physical map showing the precise location of a gene on a chromosome responsible for a genetic disorder or a specific gene related to cancer.
• Units: base pairs.

DNA Sequencing Methods

• DNA sequencing is the process of determining the order of nucleotides in a DNA molecule.
• Automated sequencing: uses fluorescently labeled chain-terminating nucleotides and an automated DNA sequencer.
• Next-generation sequencing (NGS): high-throughput methods that sequence millions or billions of DNA fragments simultaneously, enabling rapid genome sequencing.

Clone-Contig vs. Shotgun Sequencing

• Clone-contig method: involves creating overlapping DNA fragments (clones), assembling them, and then sequencing the entire genome.
• Shotgun method: uses random DNA fragmentation, sequencing of the fragments, and then assembling the fragments to reconstruct the complete genome.

Genome Annotation

• Genome annotation is the process of identifying genes, regulatory sequences, and other functional elements within a genome sequence.
• Importance lies in understanding the functions of genes and genome-wide processes.

Non-Coding DNA

• Non-coding DNA is DNA that does not code for proteins.
• Potential roles include regulatory sequences, structural elements, and transposable elements.

Comparative Genomics, Functional Genomics, and Proteomics

• Comparative genomics: compares genomes of different species to understand evolutionary relationships and identify conserved genes.
• Functional genomics: investigates the functions of all genes in an organism or the gene products (proteins).
• Proteomics: the study of the entire set of proteins in an organism (the proteome).

Applications of Genomics

• Automated sequencing: enabling highly efficient genome sequencing.
• Bioinformatics: the application of computational tools and techniques to analyze genomic data and gene functions.
• Base-pairs: units used to measure DNA, RNA, and gene lengths.
• BLAST: Basic Local Alignment Search Tool, used to identify regions of similarity between sequences.
• Chain-terminating nucleotides: used in DNA sequencing to stop the synthesis of DNA at specific points.
• Clone-contig method: used for constructing physical maps of a genome.
• Coding DNA: regions of DNA that encode proteins.
• Comparative genomics: compares genomes among different organisms.
• Dideoxynucleotides: used in sequencing reactions to terminate DNA synthesis.
• DNA microarray: used to analyze gene expression levels.
• Encyclopedia of DNA Elements (ENCODE): a project that maps regions of the human genome with functional significance.
• Chromosome maps: representations showing gene locations on chromosomes.
• Functional genomics: studies the role and functions of all the genes in an organism.
• GenBank: a database of DNA sequences.
• Genetic map: maps based on recombination frequencies.
• Genomics: the study of entire genome sequences.
• Human Genome Project: a project aimed at determining the complete sequence of the human genome.
• Kilobase-pairs: units used to measure long DNA sequences.
• Mass spectrophotometry (mass spec): used for protein identification and analysis.
• Next-generation sequencing (NGS): high-throughput DNA sequencing technologies.
• Noncoding DNA: DNA sequences that do not code for proteins.
• Open reading frame (ORF): sequence of DNA or RNA that potentially encodes a protein.
• Physical map: maps based on physical distances between DNA segments.
• Protein microarrays: used to analyze protein interactions or functions.
• Proteome: the complete set of proteins encoded by a genome.
• Proteomics: the study of the entire set of proteins in a cell.
• Pseudogenes: non-functional copies of genes.
• Restriction maps: maps showing the locations of restriction enzyme recognition sites.
• Segmental duplications: duplicated segments of DNA within a genome.
• Sequence-tagged site (STS): sequence markers used to position genes on chromosomes.
• Shotgun method: used to sequence entire genomes.
• Simple sequence repeats: short repeated DNA sequences.
• Structural DNA: DNA that plays a structural role in the chromosome.
• Synteny: conserved arrangement of genes between two or more species.
• Synthetic biology: the design and construction of new biological parts, devices, and systems.
• Transcriptome: the complete set of RNA transcripts in a cell.
• Transposable elements: DNA sequences that can move around the genome.