Genomic Analysis - Lecture Notes

Flashcards created from lecture notes on genomic analysis covering topics like sequencing, gene functions, bioinformatics, and more.

What is genomics?

The study of genomes.

What does Whole-Genome Sequencing allow for?

Sequencing and assembling entire genomes.

What does DNA sequence analysis rely on?

Bioinformatics applications and genomic databases.

What is functional genomics?

The study that establishes gene functions and identifies regulatory elements in a genome.

What was the aim of the Human Genome Project?

To sequence and identify all genes of the human genome.

What is comparative genomics?

Analyzes and compares genomes from different organisms.

What is metagenomics?

Applies genomics techniques to environmental samples.

What does transcriptome analysis reveal?

Profiles of expressed genes in cells and tissues.

What is proteomics?

Identification and analysis of the protein composition of cells.

What are contigs?

Continuous fragments formed by overlapping DNA fragments that create one continuous DNA molecule.

What is the shotgun cloning method?

A strategy for whole-genome sequencing where genomic DNA is cut into fragments and assembled by computer programs.

What are algorithm-based software programs used for?

Creating DNA-sequence alignment for genomic purposes.

What is the significance of high-throughput sequencing?

It enabled rapid sequencing of large amounts of DNA, essential for projects like the Human Genome Project.

What is clone-by-clone mapping?

A map-based cloning approach where DNA fragments are aligned to create a restriction map.

What are SNPs?

Single-nucleotide polymorphisms, variations in a single nucleotide in the genome.

What is annotation in genomics?

The process of identifying genes, their regulatory sequences, and their functions.

What does BLAST stand for?

Basic Local Alignment Search Tool.

What is the role of bioinformatics in genomics?

To organize, share, and analyze genetic data.

What does the term 'sequence alignment' refer to?

Aligning similar sequences for comparison to identify overlaps.

What is structural genomics?

Analyzing nucleotide sequences to identify gene sequences and regulatory elements.

What characterizes protein-coding regions?

Identifiable features like promoter sequences, initiation sequences, and exons.

What is an open reading frame (ORF)?

A sequence of triplet nucleotides that can be translated into a protein.

What do alternative splicing patterns accomplish?

They generate multiple mRNA molecules, leading to diverse protein production from a single gene.

What does functional categories assignment involve?

Categorizing genes based on their functions and similarities to known genes.

What are homologous genes?

Genes that are evolutionarily related.

What is the purpose of chromatin immunoprecipitation (ChIP)?

To map protein–DNA interactions.

What significant aspect of the human genome was revealed by the HGP?

Humans share a common set of essential genes with other species.

What is the average size of a human gene?

About 25 kilobytes.

What percentage of the human genome is made up of protein-coding sequences?

Approximately 2 percent.

What is the function of microarrays in transcriptome analysis?

To study global gene expression levels and compare them.

How do scientists use DNA microarrays?

By hybridizing cDNA to DNA spots to indicate gene expression levels.

What are the main outcomes of transcriptome analysis in sea urchins?

Revealed that 52% of genes are active during early development.

What is Two-dimensional gel electrophoresis (2DGE) used for?

Separating proteins with high resolution based on charge and molecular mass.

What is the principle behind SDS-PAGE?

Separates proteins by molecular mass after isoelectric focusing.

What is mass spectrometry (MS) used for in proteomics?

For protein identification and analyzing ionized samples.

What are the major sequencing techniques?

Automated Sanger sequencing, 454 pyrosequencing, sequencing by synthesis, sequencing by ligation, third-generation sequencing.

What are the challenges in the analysis of the human genome?

Identifying functions for many genes with no known molecular function.

What is the significance of gene-rich clusters in the human genome?

They are separated by gene-poor deserts, influencing gene distribution on chromosomes.

What is gene mapping?

Creating a restriction map to visualize gene locations on chromosomes.

What do evolutionary biologists analyze in comparative genomics?

Similarities and differences in genomes across species.

What is the primary goal of DNA sequence analysis?

To determine the order of nucleotides in a DNA fragment.

What is the ratio of DNA sequences shared among individuals?

99.9 percent similar.

What is alternative splicing?

A process that allows genes to code for multiple proteins.

What does proteomics compare?

Proteins in normal vs. diseased tissues.

How do humans utilize the information from the Human Genome Project?

To identify disease genes and develop treatment strategies.

What encompasses the ‘Omics’ revolution?

Diverse biological research areas including proteomics and metabolomics.

What do most genes in the human genome exhibit?

High degrees of similarity to genes in other organisms.

What percentage of human genes have no known function?

More than 40 percent.

What is the largest known human gene?

The dystrophin gene.

What do transposable elements contribute to the genome?

They make up at least 50 percent of the human genome.

What is the role of RNA in functional genomics?

Based on resulting RNAs to determine gene function.

What are the next-generation sequencing methods?

Advanced techniques for rapid sequencing of genomes using automated equipment.

What is the molecular weight separation achieved by in 2DGE?

Proteins migrate based on charge and mass in the gel.

What feature of genes contributes to their variability?

Single-nucleotide polymorphisms (SNPs) and copy number variations (CNVs).

What is the main focus of gene annotation?

Identifying gene functions and regulatory sequences.

What does the ‘E Value’ in BLAST indicate?

The expected value based on matches in the database by chance.

What is the importance of having diverse protein domains?

It allows proteins to perform various functional roles in the organism.

What fields of biology are supported by genomics?

Medicine, environmental science, agriculture, and others.

How does transcriptome analysis differ from DNA sequencing?

It focuses on measuring gene expression rather than sequence determination.

What is the primary method for protein identification in proteomics?

Mass spectrometry.

What can functional categories of genes indicate?

They can suggest the roles that genes play in biological processes.

How do researchers predict the function of unknown genes?

By searching for similarities to known genes in databases.

What is the significance of gene deserts in the human genome?

They are regions between gene-rich areas that influence gene distribution.

What is the fundamental goal of functional genomics?

To determine the roles of genes and their interactions.

What approach do scientists use in metagenomics?

Analyzing genetic material from environmental samples.

What technologies facilitate genomic research?

High-throughput sequencing, computational analysis, and various data-sharing platforms.

How does alternative splicing benefit a single gene?

It enables the production of multiple protein isoforms from one gene.

Why is bioinformatics crucial in genomics?

It helps manage and analyze large genetic datasets effectively.

What does the term 'genomic database' refer to?

A repository for storing and retrieving genomic sequences.

What role do regulatory elements play in a genome?

They control the expression of genes.

What does the percentage of GPCRs in trained tissue indicate?

It reflects the abundance of specific signaling pathways active in that tissue.

What tools are commonly used in transcriptome analysis?

Microarrays, RNA-seq, and quantitative PCR.

What do functional assays in genomics analyze?

The impact of genetic variations on protein functions.

What is the impact of technologies like ChIP on genomics?

They allow for investigating how proteins interact with DNA.