FULL CH 8 and 7

What is a genome?

What is a genome?

The entire hereditary information of an organism encoded by DNA or RNA, including all genes and regulatory sequences. In humans, this spans over 3 billion base pairs.

What is genomics?

The study of the entire genome, focusing on mapping, sequencing, and understanding gene functions and interactions.

What are the three subfields of genomics?

Structural genomics (mapping and sequencing), functional genomics (studying gene functions), and comparative genomics (comparing genomes across species).

What is the Human Genome Project (HGP)?

An international effort begun in 1990 to sequence the entire human genome, which contains approximately 3.3 billion base pairs.

What is the C-value paradox?

An observation that genome size does not correlate with organism complexity (e.g., some plants and amoebas have larger genomes than humans).

What is a Cot curve?

A plot used to measure genome complexity, based on the reassociation rate of single-stranded DNA. More complex genomes reassociate more slowly.

What is genetic mapping?

A process to locate genes on chromosomes by examining recombination frequencies, often used in large-scale genome projects like the HGP.

What is physical mapping?

Creating a map of genetic markers by directly analyzing genomic DNA, rather than through recombination, to determine the physical locations of genes.

What is the mapping-based approach to sequencing?

Sequencing method that first maps the genome using markers, then sequences fragments systematically (used by the HGP).

What is whole-genome shotgun sequencing?

A sequencing approach that randomly breaks DNA into small fragments, sequences each fragment, and then assembles the genome (used by Celera Genomics).

What are molecular markers?

Markers like microsatellites or STRs (short tandem repeats) used to identify specific DNA sequences for mapping and genetic analysis.

What is a clone contig map?

A set of ordered, partially overlapping DNA clones covering a chromosome or genome segment, forming a basis for sequencing.

What are ESTs (Expressed Sequence Tags)?

Markers derived from cDNA sequences that identify gene-expressed regions in the genome, useful in locating genes.

What are YACs and BACs?

Yeast Artificial Chromosomes (YACs) and Bacterial Artificial Chromosomes (BACs) are vectors used to clone large DNA fragments for sequencing.

What is spectral karyotyping (SKY)?

A technique using fluorescent dyes to visualize chromosomes in different colors, helpful in identifying chromosomal abnormalities.

What is a restriction map?

A map showing the locations of restriction enzyme sites on DNA, used to analyze the physical structure of genomes.

What are sequence-tagged sites (STS)?

Unique DNA sequences that serve as markers in genetic mapping, enabling researchers to locate specific genome regions.

What is a genetic linkage map?

A map showing the positions of genes or markers based on recombination frequencies, used in studying inheritance and traits.

What is a transposable element?

A "jumping gene" that can move within the genome, potentially causing mutations or altering gene function.

What are LINEs and SINEs?

Long Interspersed Nuclear Elements (LINEs) and Short Interspersed Nuclear Elements (SINEs) are repetitive DNA sequences with roles in genome structure and regulation.

What are forward and reverse mutations?

Forward mutations change a gene from wild type to mutant, while reverse mutations restore a gene from mutant back to wild type.

What is base excision repair?

A DNA repair mechanism that removes and replaces damaged bases to maintain genome integrity.

Who discovered transposable elements?

Barbara McClintock discovered transposable elements in the 1950s while studying genetics in corn.

What is the Ac/Ds system?

A transposon system in plants where Ac (Activator) helps Ds (Dissociation) elements move, impacting gene function.

What is DNA ligase's role in repair?

DNA ligase seals breaks in the DNA backbone, completing the repair of single-strand damage.

What is a polyribosome?

A complex of multiple ribosomes translating the same mRNA, allowing simultaneous protein synthesis.

What is the C0t curve used for?

Analyzing genome size and complexity by measuring the reassociation rates of DNA sequences in a given genome.

What is the role of G-banding?

A chromosomal staining technique that divides chromosomes into bands, aiding in identifying structural changes.

What are functional genomics studies?

Studies that focus on understanding the functions of genes, regulatory elements, and noncoding sequences in the genome.

What is comparative genomics?

The study of comparing genomes across species to learn about evolutionary relationships and gene functions. Here are 40 flashcards combining concepts from the genomics information in all three documents provided:

---

What is whole-genome shotgun sequencing?

What are paired-end reads, and why are they essential?

Paired-end reads sequence from both ends of long inserts. This approach improves assembly efficiency as pairs have known spacing and orientation, which helps in reconstructing sequences containing repetitive elements.

What was significant about the sequencing infrastructure used by Celera?

Celera used powerful computing infrastructure with 4-processor SMPs and 16-processor NUMA machines, totaling around 20,000 CPU hours, to run its genome assembly operations.

What was the controversy between Celera and the public genome project?

Celera was criticized for not achieving a true "whole-genome shotgun assembly" as it relied on publicly available data from the Human Genome Project, which sparked a dispute over the extent of their independent contributions.

What distinguishes the human genome's composition?

Only 1.1% of the human genome comprises exons, 24% are introns, and 75% is intergenic DNA. The genome also includes diverse regions with gene clusters, gene deserts, and high proportions of transposable elements (around 45%).

What is the Sanger sequencing method?

It involves using dideoxynucleotide triphosphates (ddNTPs) to terminate DNA elongation at specific bases, allowing for DNA sequencing by generating fragments ending at each nucleotide.

What is "next-generation sequencing"?

It refers to advanced, high-throughput sequencing technologies that succeeded Sanger sequencing, enabling massive parallel sequencing by methods developed by companies like Roche, Illumina, and Life Technologies.

How do comparative genomics studies benefit from species like the pufferfish?

Pufferfish have smaller genomes with fewer introns and repetitive DNA, making it easier to study genes homologous to humans, especially in identifying functional counterparts.

Why is sequence coverage important in genome sequencing?

Higher coverage increases accuracy in sequencing by providing more data points per region, which is essential to accurately assemble complex genomes and account for errors.

What are SNPs, and why are they significant in human genomics?

SNPs (Single Nucleotide Polymorphisms) are variations at a single nucleotide position in the genome. They play a key role in genetic diversity and can influence traits and susceptibility to diseases.

What are transposable elements, and how prevalent are they in the human genome?

Transposable elements are DNA sequences that can move to different positions within the genome. They make up about 45% of the human genome, although many are inactive.

How does recombination vary across the human genome?

Recombination rates are higher in distal (end) regions of chromosomes and on shorter chromosome arms, which promotes crossovers during meiosis and increases genetic diversity.

What role does alternative splicing play in gene complexity?

Alternative splicing allows a single gene to produce multiple protein products, increasing protein diversity and functional complexity beyond the number of genes in the genome.

Describe the relationship between GC content and genomic regions.

Regions with high GC content are often gene-dense and play a role in regulating gene expression, while lower GC regions may have fewer genes and different functional elements.

What distinguishes vertebrate genomes from invertebrates at the protein level?

Vertebrates have unique protein domains and motifs, contributing to increased complexity in their proteomes, especially in neuronal, immune, and tissue-specific developmental functions.

What are CpG islands, and where are they commonly found?

CpG islands are regions with a high frequency of CG dinucleotides, often found near gene promoters. They are involved in gene regulation and are typically methylated to control gene expression.

What is the significance of horizontal gene transfer in human evolution?

Some human genes may have originated from bacteria through horizontal gene transfer, suggesting a complex evolutionary history involving genetic material from other species.

What are segmental duplications, and why are they important?

Segmental duplications are large DNA sequences duplicated in multiple locations in the genome, which contribute to genomic variation and can lead to evolutionary innovations or disease susceptibility.

Explain the difference between dNTPs and ddNTPs in Sanger sequencing.

dNTPs are standard nucleotides that allow DNA chain elongation, while ddNTPs lack a 3'-hydroxyl group, causing chain termination when incorporated into a DNA strand, which enables sequence determination.

What was the impact of automated sample preparation in sequencing?

Automation increased sequencing efficiency and reduced errors, enabling large-scale genomic projects like the Human Genome Project by streamlining sample handling and preparation.

How does the mutation rate differ between male and female meiosis?

Mutation rates are approximately twice as high in male meiosis compared to female meiosis, suggesting that most mutations in the human genome arise from paternal contributions.

Describe the structure of DNA in relation to Sanger sequencing.

DNA is composed of nucleotides connected by phosphodiester bonds. Sanger sequencing uses ddNTPs to randomly terminate synthesis, allowing the sequence to be inferred from fragment lengths.

What is a reference genome, and why is it used?

A reference genome is a previously sequenced genome used as a template for comparing new genomes, which accelerates the assembly and analysis of newly sequenced genomes.

How do gene deserts contribute to genome organization?

Gene deserts are large regions with few or no genes, thought to play roles in chromosomal organization and may contain regulatory elements affecting distant genes.

What is the proteome, and how does it relate to genomics?

The proteome is the full set of proteins expressed by a genome. It’s more complex in vertebrates due to alternative splicing and specific protein motifs, influencing organismal complexity.

Why is the pufferfish genome significant in human genomics?

The pufferfish genome is compact with fewer introns and repetitive sequences, making it easier to study homologous genes and gain insights into human gene function.

What was a major advancement in next-generation sequencing?

The development of massively parallel sequencing technologies allowed for rapid sequencing of large amounts of DNA, transforming genomic research and clinical applications.

What is primer walking in sequencing?

Primer walking is a method where new primers are designed from each successive DNA sequence read, allowing systematic sequencing of long DNA fragments.

What role do tandem repeats play in the genome?

Tandem repeats are sequences repeated consecutively and can affect genome stability, gene regulation, and are often used as markers in genetic studies.

Why is sequencing difficult for genomes with high repeat content?

High repeat content complicates assembly because identical or similar sequences can align incorrectly, making it challenging to accurately reconstruct the original sequence.

What are the two subunits of a ribosome?

The ribosome has a small and a large subunit. In humans, the small subunit has one large RNA molecule and ~32 proteins, while the large subunit has three RNA molecules and ~46 proteins.

What is the purpose of a polyribosome?

A polyribosome is a complex of several ribosomes translating the same mRNA, allowing for simultaneous synthesis of multiple copies of a polypeptide.

What is a forward mutation?

It is a mutation that changes the genotype from the wild type to a mutant.

What is a reverse mutation?

It is a mutation that changes the genotype from a mutant back to the wild type.

What are transposable elements?

Also known as transposons or "jumping genes," transposable elements are DNA sequences that can move to different positions within the genome, sometimes causing mutations.

What is the function of DNA glycosylase in base excision repair?

DNA glycosylase recognizes and removes damaged bases, initiating the repair of DNA through base excision repair.

What are LINEs in human DNA?

Long interspersed nuclear elements (LINEs) are long repeated sequences, over 5,000 bp, comprising about 20% of the human genome and encoding enzymes for retrotransposition.

What are SINEs in human DNA?

Short interspersed nuclear elements (SINEs) are shorter repetitive DNA sequences, like Alu elements, that do not encode transposition enzymes and depend on other elements for movement.

Who discovered transposable elements?

Barbara McClintock discovered transposable elements, or "jumping genes," in the 1950s while studying corn genetics.

What is the Ac/Ds system in plants?

Ac/Ds is a two-element transposable system in plants, where Ac (Activator) is necessary for movement, while Ds (Dissociation) elements require Ac to transpose.

What are the two types of DNA mutations?

Small-scale mutations (e.g., point mutations) involve changes at the base level, while large-scale mutations (e.g., chromosomal rearrangements) involve insertions, deletions, and other structural changes.

What is a mutagen?

A mutagen is an agent, physical or chemical, that induces mutations in the DNA of an organism, either through direct interaction or causing damage that leads to errors in replication