Genomes, Transcriptomes, and Proteomes

Flashcards for reviewing vocabulary related to genomes, transcriptomes, and proteomes.

Genome

The complete haploid genetic complement of a typical cell.

Genomics

The study of DNA on a cellular scale.

Contig

A contiguous stretch of chromosomal DNA assembled from overlapping clones.

Sequence Tagged Site (STS)

A unique and previously characterized sequence mapped to a particular region of a chromosome.

Expressed Sequence Tag (EST)

A gene whose expression can be monitored, used as a landmark in contigs.

Whole-Genome Shotgun Sequencing

A strategy that eliminates the step of assembling a physical map of the genome.

Genome Annotation

Yields a listing of information about the location and function of genes and other critical sequences.

Homologs

Any two genes with a demonstrable sequence similarity.

Orthologs

Genes in different species that possess a clear sequence and functional relationship to each other, derived from an ancestral gene.

Paralogs

Genes that are similarly related to each other but within a single species, arising from gene duplication.

Synteny

Conserved gene order on a chromosome.

Metagenomics

DNA is isolated not from a single bacterial species but from an entire community of microbial species.

Intervening Sequence (Intron)

Nontranslated DNA segments within a gene.

Exon

Coding segments of a gene.

Simple-Sequence Repeats (SSR)

Highly repetitive sequences, generally less than 10 bp long.

Single Nucleotide Polymorphisms (SNPs)

Single-base variations within the human population.

Haplotypes

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

Outgroup

A more distantly related organism used for comparison in genome sequencing.

Linkage Analysis

A method where the gene involved in a disease condition is mapped relative to genetic polymorphisms.

Systems Biology

The study of complex interconnected processes in biology.

Transcriptome

The genes expressed in a cell under a given set of conditions.

Transcriptomics

The subdiscipline focused on studying transcriptomes.

Proteome

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

Proteomics

The subdiscipline concerned with defining the proteome.

Last Universal Common Ancestor (LUCA)

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

Phylogeny

The evolutionary relationship among species, populations, or genes.

Phylogenetics

The study of evolutionary relationships.

Taxon

A grouping of organisms being studied in an evolutionary tree.

Horizontal gene transfer

The process where genes can be gained from other species, resulting in the sudden appearance of a gene in a particular evolutionary line.

Allopatric Speciation

Geographic isolation of a group of individuals followed by evolution to form a distinct species.

Genome Annotation

The area of genomics dedicated to identifying the functions of genes and other sequences.

Transcriptome

The sum of all RNA molecules in a cell.

Proteome

The full complement of proteins expressed in a cell.

Transcriptomics

The analysis of the genes that are expressed.

Proteomics

The global analysis of protein expression.

Comparative genomics

Comparing entire genomes of different species.

Phylogenetic profiling

Used for identifying specific genes, then determining which other genes are present in the same genomes.

Linkage analysis

Mapping one or more genetic factors responsible for a disorder.

Systems biology

Study of an organism as an integrated system.

Chromosome

The word genome was derived from combining gene and the final syllable of what?

Hans Winkler

Who coined the word genome?

Eukaryotic cells

What kind of organism does mitochondria occur in?

Photosynthetic organisms

What kind of organism does chloroplasts occur in?

Thomas H. Roderick

Who came up with the word Genomics as the name for a new journal?

Haemophilus influenzae

What bacterium was the first complete genome to be sequenced?

James Watson

Who led The Human Genome Project first?

Francis Collins

Who led The Human Genome Project after James Watson?

J. Craig Venter

Who led the Celera group that competed in sequencing the human genome?

To identify conserved genetic elements of functional significance

What is the purpose of most genome sequencing projects?

25,000

Approximately how many genes are in the human genome?

1.5%

Approximately what % of human DNA is coding(exon) DNA?

Barbara McClintock

Who first discovered transposable elements?

Single nucleotide polymorphisms

What does the term SNPs refer to?

Baylor University

Name 1 of the scientists/labs mentioned that independently analyzed the samples of HIV for the Lafayette case.

University of Michigan

Name 1 of the scientists/labs mentioned that independently analyzed the samples of HIV for the Lafayette case

Mitochondrial Eve

What is the name given to the female genetic ancestor of all living humans?

Y chromosome Adam

What is the name given to the male genetic ancestor of all living humans?

flagellar and basal body

If someone suffers from Bardet-Biedel syndrome, the BBS genes responsible are typically involved in the function of what human structure?

60%

At what percentage of completion was the draft equence released in 2009?

National Center for Biotechnology Information

What does NCBI stands for?

Thousands

Roughly how many complete bacterial genomes are there to date?

Hundreds

Roughly how many complete eukaryotic genomes are there to date?

13,601

How many protein-encoding genes does the fruit fly Genome have?

19,735

How many protein-encoding genes does the nematode worm genome have?

38,000

How many protein-encoding genes does the rice-plant genome have?

Proteomics

The study of the full set of proteins encoded by a genome is called what?

Isoelectric focusing

Method that separates proteins based on their isoelectric point (pI).

Whole-genome shotgun sequencing

Method involving sequencing DNA fragments from throughout the genome at random.

Gene expression levels

What does the method RNA-Seq provide about RNA?

Used tools, used small groups, buried their dead

What features were shared between Neanderthals and modern humans?

Particular protein

The loss or mutation of what may lead to slower growth, altered development, or even death?

Human Genome Project

Is performed by two competing teams that used different strategies of shotgun sequencing.

Phenotypic, cellular, molecular

What are the three levels protein and RNA function can be described on?

transcriptome

A listing of the genes that are expressed in a given cell under a defined set of conditions

proteome

A compilation of all the proteins present in a given cell under a defined set of conditions

Africa

Where do humans and chimpanzees share a common ancestor?

Splicing

The process of removing introns from a primary RNA transcript

D

The use of what sugar isomer found in cells?

L

The use of what amino-acid isomer found in protein synthesis?

smallest genome sequenced thus far for a defined organism

Why us the bacterium Mycoplasma genitalium useful?

taxon

An individual, species, population, or a genus

The common ancestor

An unrooted tree shows uncertainty about which relationship?

1.23%

What percentage of genomic distinctions are related to base pairs?

3%

What percentage of genomic distinctions are related to transposed insertions?

500,000 years ago

Homo sapiens evolved when?

Statistical methods of linkage analysis

What process can correlate the inheritance of additional, more closely spaced polymorphisms with the occurence of disease?

million

The number of genomic alteration that could lead to large brrain, language skill, tol-making ablility?

Proteins must be in native state

What is the potential issue in probing macromolecular interactions?

shotgun sequencing

The process of using computer analyses to indentify overlapping sequences to create longer contigs?

species evolution

What does this phylogenetic tree based on?: Bacteria->LUCA->Eukaryotes

closely

The comparison between two homologous chromosomes in two how related species reveals synteny?

genes arranged in the same order

In two related bacterial species, a cluster of 5 genes were found with?

doctor

Who is responsible for giving the vitamin shot, in the Lafayette, Lousiana case?

tumor cells

What kind of cells make up tumors that exhibit characteristic transcription patterns?

reconstructing genomes from metagenomics data

The process of creating one that uses computer programs to assemble overlapping genomic segments from individual genomes

effort to define minimum gene set

The minimum set of genes needed to support a living cell is studied with this research

Carl Woese

Who discovered a new domain of living creatures, the arcaebacteria?

two-dimensional gel electrophoresis

What technique has the most common approach to examining cellular proteome?

existing taxa

the ends of external branches of a phylogenetic tree represent?

Homo habilis

The name of the first species of our own genus