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43 Cards in this Set

  • Front
  • Back

Study of content, organization, function, and evolution of entire genomes

Genomics

Genome sequencing: Type of sequencing involved in sequencing overlapping clones

Map-based sequencing

Genome sequencing that theres less sequencing and no need to assemble genome, but takes a lot of time to order the clones

Map-based sequencing

Type of genome sequencing where you sequence random fragments

Shotgun sequencing

Type of genome sequencing where you assemble the sequenced fragments into a complete chromosome by identifying sequence overlaps

Shotgun sequencing

Type of genome sequencing that requires more sequencing(10 genome equivalents) but no need to order clones

Shotgun sequencing

What type of sequencing can "complete" a human genome in two days? Ethical issues arise in individual genome sequences.

Next generation

Site in a genome where individual members of a species differ by a single base pair

Single-Nuceltodie Polymorphism (SNP)

What has a 1/1000 bp between individuals, with 3 million differences in entire genome?

SNP

What is linked to a disease-causing allele that tends to be inherited together(BRCA1 and BRCA2)?

SNP

What involves the use of numerous SNPs to identify genes that're associated with certain diseases?

Genomewide Association Studies (GWAS)

What involves the sequencing of non-cultured microbial communities to gain an understanding of types of bacteria living in a niche?

Metagenomics

What is used once a genome is completed and is required to derive meaning from the sequence?

Bioinformatics

In bioinformatics, what is identifying genes called? (ex: promoters, introns, exons, coding sequence, regulatory sites, etc)

Annotation of the genome

Bioinformatics: Homology search of the ______ _______ data base to identify gene function based on amino acid sequence similarity.

genomic sequence

What uses genomic approaches to study all of the gene products simultaneously?

Functional Genomics

What analyzes the expression patterns of all genes simultaneously under various growth conditions, times during development, when a regulatory protein is mutated, etc?

Transcriptome analysis

Microarray studies using ___ _____ measures RNA levels expressed from each gene

gene chips

Variation in gene expression can be used to predict the recurrence of breast cancer is detected by what?

Microarrays

Comparative Genomics


-What are closely related genes called?


Homologs

What has the same genetic locus inherited from a common ancestor(i.e. in different organisms)?

Orthologs

What are genes that are related via gene duplication events (i.e. in the same organism)?

Paralogs

Chimpanzee is the closest living relative to who?

Humans

Human and chimpanzees last common ancestor was how long ago? (1% DNA sequence divergence) (Additional insertions and deletions are evident)

6 million years

Humans and chimps have a total of how much sequence differences?

3%

30% of all what are identical in sequence?

Orthologous proteins

There are many prokaryotic _____ of unknown function.

Genes

25% of genes in a bacterial genome don't have a what in other sequenced genomes?

Homolog

What is the analysis of all proteins in a cell or organism?

Proteomics

What uses mass spectroscopy to identify changes in protein levels under various growth conditions, or times during development, when a regulatory protein is mutated, etc?

Proteome anlaysis

Proteome analysis is complementary to what but also identifies genes controlled at level of translation?

Transcriptome

What is involved in running 2-D gel, cutting out spots of interest, determining protein mass with mass spec, and identifying protein form sequenced genome?

Proteome analysis

What is repetitive DNA in genome? (45% of genome)

transposable elements

Introns are much bigger than what?

Exons

2% of genome codes for protein, because introns are much bigger than what?

exons

No introns in what genes?

Bacterial

What has 27,000 bp with 9 exons?

Average gene

24,000 human genes


About 3 alternative splicing pathways per gene on average, therefore the what is about 3x size of the genome?

proteome

There are more human what than human genes?

proteins

What characterizes the microbial communities found at several diff. sites on human body? (nasal passages, oral cavities, skin, etc)


-analyzes role of these microbes in human health and disease

human micro biome project

Most (90%) of cells in/on human body are what, not human?

Microbial

What is the identification of many phenotypes associated with the inactivation of each gene?




(Biolog; technology that scans biological proprieties of cells, tests 200 phenotypes, determines effect of genetic changes on cells, and determines effect of drug exposure on cells)

Phenome (phenotypic) analysis

Where you have fragment DNA and ligate adaptors on ends, capture single DNA molecules on beads, PCR to amplify DNA on beads, use one bead per well, and finally sequence individual DNAs in wells(by using different dNTP's to see if it will correspond with unknown sequence nucleotide)

(Next generation)


High-throughput sequencing