HUBI 2004 (MUN) - Chapter 15 Questions and Definitions

Shotgun Sequencing

A laboratory method involving randomly fragmenting and sequencing DNA, followed by a computational re-assembly and re-constitution of the genome.

What is a challenge of repetitive DNA sequences?

Since repeat DNA sequences are identical, they cannot be assigned to a unique genomic location. So, the relative locations and orientations of other DNA sequences cannot be determined.

What is the function of third-generation sequencing?

It can detect unmethylated and methylated DNA.

Which type of sequencing technology is used for pair-end sequencing?

Next generation/Illumina sequencing

Genomics

A field of molecular biology that studies the entire genome of organisms, including genome structure, function, evolution, mapping, and editing.

What are the different subcategories of genomics?

- Structural Genomics

- Functional Genomics

- Comparative Genomics

- Pharmaco-Genomics

- Metagenomics

- Epigenomics

Structural Genomics

The study of the structural organization of the genome and its encoded proteins in an organism.

What are the three sequencing techniques involved with structural genomics?

- DNA sequencing

- Gene mapping

- 3D protein structure

What is the role of DNA sequencing in structural genomics?

It determines the exact sequence of nucleotides (bases).

What is the role of gene mapping in structural genomics?

It locates the gene within a chromosome or genome.

What is the role of the 3D protein structure in structural genomics?

It determines the tertiary structure of the polypeptide chain.

Metagenomics

The study of the structure and function of nucleotide sequences isolated and analyzed from the microbial populations that live in/on humans and in the environment.

What is the purpose of metagenomics?

- It develops species diversity and relative population levels in a given environment

- It identifies gene sequences of organisms living in a particular environment

Genome Annotation

The process of describing the genes' structure and attaching a biochemical and biological function to the products encoded by these genes.

What are the two types of genome annotation?

- Structural Annotation

- Functional Annotation

Functional Annotation

A type of genome annotation that aims to describe biochemical and biological functions of gene sequences.

Biological Functions

The role or purpose of a molecule within a cell in a living organism.

Biochemical Functions

The specific chemical reactions and mechanisms at the molecular level that a molecule performs.

Structural Annotations

A type of genomic annotation that aims to identify genes and map their structural components, including transcribing, coding, and regulatory sequences.

What are some examples of experimental approaches in structural annotation?

- Complexity of genome organization

- Variability

- Repetitive DNA

- Technology-related limitations

- Epigenetic modifications

What are some examples of computational approaches in structural annotation?

- Prediction of gene structures

- Helping address the deficit in knowledge

- Improving algorithms

- Guidance of experimental designs

Functional Genomics

The study of the function, expression, and interaction of gene products.

Comparative Genomics

The study of comparing similarities and differences in gene content, function, and organization among genomes of different organisms.

What are the roles of interspecific comparisons of genes in comparative genomics?

- It identifies conserved gene sequences over evolutionary time

- It provides insights into the evolution of genes and the diversity of species

- It facilitates genome annotation

What are the roles of intraspecific comparisons of genes in comparative genomics?

- It identifies sequence variations that are responsible for genetic differences

- It provides insights into evolutionary selective pressure and adaptations

- It identifies polymorphic markers and the structure of populations

What are some examples of different gene derivation methods throughout evolution?

- Exon shuffling

- Reverse Transcription

- Lateral Transfer

- De novo Derivation

- Fusion-Fission

- Duplication

- Unequal Crossover

Lateral Gene Transfer

The movement of genes from one species into the genome of another species.

Pseudogenes

Genes that lose their function over evolutionary time.

Ortholog Genes

Genes that have evolved from an ancestral gene through speciation.

Transcriptomics

The study of the structure, function, and evolution of the transcriptome of a given cell, tissue or organism, under a variety of conditions.

What are some examples of sequencing-based techniques in transcriptomics?

- Bulk RNAseq

- scRNAseq

- snRNAseq

- Spatial Transcriptomics

Expression Maps

Identify patterns of gene expression that can be correlated with a specific disease type or subtype, treatment response, etc.

What is the function of expression maps?

They compare gene expression levels between different samples, like healthy tissues vs. diseased tissues.