Genomes, Transcriptomes, and Proteomes

Flashcards covering key concepts from lecture notes on genomes, transcriptomes, and proteomes.

What is a genome?

The complete haploid genetic complement of a typical cell.

What is the modern science of genomics dedicated to?

The study of DNA on a cellular scale.

What was the first complete genome to be sequenced?

Haemophilus influenzae (bacterium) in 1995.

When was the draft sequence of the human genome published?

February 2001.

What are contigs?

Long contiguous stretches of chromosomal DNA, identified by hybridization and other methods, organized from overlapping clones from digested genomes.

What is a sequence tagged site (STS)?

A unique and previously characterized sequence.

What is an expressed sequence tag (EST)?

A gene whose expression can be monitored.

Who led the Celera Corporation in 1997 in a commercial effort to sequence the human genome?

J. Craig Venter.

What is whole-genome shotgun sequencing?

A strategy that eliminates the step of assembling a physical map of the genome by sequencing DNA segments from throughout the genome at random.

What is genome annotation?

The critical process that yields a listing of information about the location and function of genes and other critical sequences.

What is phenotypic function?

Describes the effects of a gene product on the entire organism.

What is cellular function?

A description of the metabolic processes in which a gene product participates and of the interactions of that gene product with other proteins or RNAs in the cell.

What is molecular function?

Refers to the precise biochemical activity of a protein or an RNA, such as the reactions an enzyme catalyzes, the ligands a receptor binds, or the complex formed between a specific RNA and a protein.

What is BLAST?

Basic Local Alignment Search Tool, used to search genome databases for related sequences.

What is comparative genomics?

Assigning gene functions by genome comparisons.

What are homologs?

Any two genes with a demonstrable sequence similarity, whether or not they are closely related by function.

What are orthologs?

Genes derived from an ancestral gene in the last common ancestor of two species.

What are paralogs?

Genes that are similarly related to each other but within a single species.

What is conserved gene order, or synteny?

Provides additional evidence for an orthologous relationship between genes at identical locations in related segments.

What is a gene knockout collection?

Each strain in an organism’s collection has a different inactivated gene, and every genomic gene is represented.

What class of viruses contains the most abundant viral genome type?

Single-stranded, positive-sense RNA.

What is metagenomics?

A subdiscipline of genomics where DNA is isolated not from a single bacterial species, but from an entire community of microbial species.

What are archaea?

Single-celled organisms that share some properties with both bacteria and eukaryotes and have evolved as an independent line.

What are introns?

Nontranslated inserts that interrupt the otherwise colinear relationship between a gene’s nucleotide sequence and the amino acid sequence of the encoded polypeptide.

What are exons?

Coding segments of DNA.

What are single nucleotide polymorphisms, or SNPs?

Single-base variations within the human population.

What are haplotypes?

Groups of SNPs and other genetic differences that are close together on a chromosome are rarely affected by recombination and are usually inherited together.

What is the primary purpose of sequencing the human genome?

To find differences between our genome and those of other organisms in order to reveal the molecular basis of human genetic diseases and identify genes that contribute to human characteristics.

What are some human lineage genomic alterations?

Segmental duplication, transposition, and recombination which can lead to inversions.

What is linkage analysis?

A method where a gene involved in a disease condition is mapped relative to well-characterized genetic polymorphisms that occur throughout the human genome.

In the context of transcriptomics, what are transcriptional profiles?

Characteristic patterns of gene expression exhibited by tumor cells that can provide a tumor fingerprint, used to predict a patient’s prognosis and/or select the most beneficial therapies.

In the context of transcriptomics, what is the RNA-Seq method?

A method using high-throughput DNA sequencing technologies to map gene expression levels across genes, chromosomes, and entire genomes.

What constitutes a cell's proteome?

The complement of proteins present in that cell under a given set of conditions.

What does the subdiscipline of proteomics include?

Efforts to define the proteome.

What is two-dimensional gel electrophoresis?

A technique used to separate proteins on the basis of different properties by carrying out two electrophoretic steps in succession.

What is isoelectric focusing?

A method that separates proteins on the basis of their isoelectric point (pI) during the first step (or dimension) of two-dimensional gel electrophoresis.

What is the role of mass spectrometry in proteomics?

Used to partially sequence individual peptides derived from spots on electrophoresis gels and to assign each to a protein.

In the context of genome sequencing, what is phylogenetic profiling?

Searching the genome databases for specific genes, then determining which other genes are present in the same genomes to hint at protein function.

What is a protein chip?

Proteins, like nucleic acids, can be immobilized on a solid surface to detect the presence or absence of other proteins in a sample.

In what ways do proteins function?

By interacting with other molecules; from small metabolites to nucleic acids, and other proteins.

What is systems biology?

The study of complex interconnected processes in biology.

How does comparative genomics relate to assigning gene functions?

The avaliability of many genome sequences in online databases enables researchers to assign gene functions by genome comparisons.

What is the signifance of phylogenetic profiling?

The consistent appearance of two genes together in a genome suggests that the proteins they encode may be functionally related.

How can comparative genomics be used?

Comaprisons of genome composition, although not evidence of direct association, can hint at protein function.

What types of molecules do proteins interact with?

Other proteins, small metabolites, and nucleic acids.

What are key attributes of orthologs and paralogs?

Two genes in different species that possess a clear and functional relationship to each other, related to each other within a single specices and arise most often from gene duplication.

How does phylogenetic profiling help?

Can search the databases for specific genes, then determine which other genes are present in the same genome.

What does genome sequencing allow modern biology to do?

Reconstruct the complete tree of life.

What is a phylogeny?

The evolutionary relationship among species, populations or genes.

What is phylogenetics?

The study of evolution and genetic relationships.

What is a taxon?

A species, genus, class, or a population of a species.

What is the last universal common ancestor (LUCA)?

The successful living entity that gave rise to all non-viral life on Earth.

What is horizontal gene transfer?

Species that transfer their genes to other species non-linearly.

What is allopatric speciation?

Geographic isolation of a group of individuals followed by evolution to form a distinct species that no longer can interbreed with the original one.

What is genetic drift?

The frequency of particular mutations in a population changes more or less randomly over time.

What does phylogenetics help biologists do?

Classify organisms, reveal evolution information, and helps criminal invesitgations.

In the context of a phylogenetic tree, what does a node represent?

An extinct ancestral species common to the two connected branches.

What do numbers next to tree branches indicate?

The level of confidence the investigator has in the information contained in the branch.

What does it mean for a tree to be unrooted?

The positioning of the common ancestors is uncertain.

What does genome research study?

When groups of organisms colonize new regions and environemnts, their migrations may subject them to new and different selective pressures.

When did Homo sapiens evolve?

500,000 years ago.

When did genomic diversity split into populations?

During evolutional bottlenecks.

When did life diversity in humans first colonize Asia?

Arose roughly 50,000 years ago.

What are some factors that affects human evolution?

Mutation, natural selection, genetics and migrations.

When did Human journey start

Seven million years ago with evolution of of african ancestor evolving into chimpanzees and bonobos plus current men.

When did HAemophilus influenzae first sequence

1995.

What is minimal sequence

Directed efforts to disrupt individual genes has revealed that the bacterium can dispense with only 97 of them and still retain viability in the laboratory, giving a minimal complement of

What does DNA testing find

Genetic markers and that enables species in modern science.

WHat came first during HAemophilus Influenzae

Mechanical breaking of the DNA in fragments and selection by size

What does an outgroup comparison determine?

Comparing two species to a third to see the differences.

Who is mitochondrial eve

African woman who lived ago 150 years with DNA that led to now.

Who came after homo Habilis

H Erectus who used tools.

What is a bottleneck

When an evolutionary event significantly reduces the size of a population.

What is different in Proteome's testing

It test for isoelectric points or pi to find data regarding protein's net charge.

What is the goal of expression testing

Discover every possible protein that will contribute to cellular metabolism.

What is looked for in cellular testing.

Broad array tech to updated testing to understand the cellular level.

What are the primary targets of scientific investigation by genome annotation?

Genes encoding RNA and protein.

What process occurs more frequently in humans than worms allowing for greater complexity?

Alternative modes of gene expression and RNA splicing.

Why are bacterial genomes the starting point for searching for the minimal genome?

These cells can grow in stress-free laboratory environments with constant temperature and abundant resources.

What human genetic disease aided in elucidating linkage analysis?

Alzheimer's disease.

Which scientists pioneered the study in HIV-1 with phylogenetic analysis in a trial for court?

Metzker, M.L. et al (2002).

RNA transcripts have sequence changes not present in the DNA genes, these changes are known as?

RNA editing.

The International HapMap project lead in what significant finding?

Mitochondrial Eve and the Y chromosome Adam finding.

What does mass spectrometry measure and how is it beneficial?

It detects bound cofactors, metal ions, covalent modifications to help reveal protein functions to assist in gene function.

What factors are critical to keep in mind of an evolutionary tree?

The overall number of species in the test and constant mutation rates.

The search for the genetic underpinnings of special human characteristics depend on what complementary search?

Where extreme changes have occurred or that are involved in relevant human diseases.

What are the steps to establish disease or origin with linkage analysis?

1.) collect DNA smaples from affected members 2.) localize to a chromosome 3.) co-inheritance of markers.

What are common problems on the road to establishing gene linkage?

Co-inheritance which can imply there could be an underlying problem.

What are the classes of protein genes that are accelerated to the human?

Genes in Chemosensory perception, immune function, and reproduction.

What happens in Phylogenetic analyses of species evolution for genetics?

Rely on gene mutations or genetic differences to evolve and establish.

What technique can elucidate and determine location on a protein by protein location?

Two way elecrophorisis.

What method is best for measuring genetic data on marine organisms?

Metagenomic.

What do scientists take into account when constructing models based on RNA

Estimated mutation rates, selection, genetic drift, and other factors.

What is a potential drawback of only using transcriptional profiles for analysis of tumors?

Tumors are complex and heterogeneous, leading transcriptional profiles to vary greatly from one tumor to the next in a non-trivial way.

How do researchers select the markers for establishing the location for

Researchers first localize the regions is associated with specific chromosomes or where it is commonly observed.

What kind of diseases benefit the most from the studies of genomics?

Study of mitochondrial DNA,Y , and genetics

In relation to diseases, what does the study of metagenomics look at?

The evolution of viral diseases on an molecular and individual level to predict possible mutations.

In relation to plants, what can analysis of genomics find?

Analysis of genomic history can revel lost genetic diversity in plant or crop strains that might prove useful to to farmers or agriculture

What can we know about a trait's origin if a large diversity of its possible haplotypes are carried in African DNA

This tells us the trait evolved early in the human timeline. Any DNA in the rest of the world, has some but with lower diversity.

In relation to genomics what is a gene knockout collection?

When every strain in an organisms genomic profile collection has a different expression pattern.