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49 Cards in this Set

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What are the three stages of genome sequencing?
Sequencing, Assembly, and Annotation
What was the intended goal of the human genome project?
The goal was to understand the networks of molecular interactions that bring each person to life in a unique way.
What was a secondary goal of the human genome project?
To provide an understanding of human genetic disease
What was the dispute between the two segments of scientists concerning the human genome project?
Discovery science versus hypothesis driven science
What was the primary argument against the human genome project?
2% of genes is coding, 98% junk, why bother. It will also inhibit hypothesis driven funding.
What was the logistical goal pertaining to actual mapping?
Physical, genetic and sequence maps of the human genome (map first, sequence later)
By measuring what during meiosis can a genetic map be constructed?
By measuring the reciprocal exchanges in meiosis a genetic map can be constructed.
What is genetic distance roughly correlated with?
It is roughly correlated with physical distance.
What do genetic and physical maps help identify?
They help identify genes responsible for specific processes.
What are the two strategies for sequencing of a genome?
Shotgun and Hierarchical
What happens in first step of the shotgun method of DNA sequencing?
The whole DNA is sheared and cloned into a vector (e.g., pUC, M13)
What is the second step in the shotgun method after the DNA has been cloned into a vector?
Sequence to 5-10 fold coverage.
After each of these individual parts are sequenced, what is the final step? of the shotgun method of DNA sequencing?
Assemble a complete, contiguous sequence in silico.
What does in silico mean?
It means: In or by means of a computer simulation.
What is the first step of the hierarchical (clone contig) method?
The first step is to construct a clone contig (mapped, ordered library of adjacent clones)
What is the second step of the hierarchical method?
After mapped, ordered library of adjacent clones has been created, the second step is to mimic the shotgun method by then sequencing the individual clones.
So to boil things down simply, what does one do for hierarchical sequencing?
First make a library and then order the clones.
What are three examples of large clones / vectors?
YACs, BACs and P1 clones
Imagine you have a clone. And a library. Using methods we have talked about, how would you find clones next to the one you have?
Sequence ends first and then design PCR primers or make probe
What are the two most common methods to build clone contigs?
Chromosome walking is the first and chromosome fingerprinting is the second method.
What is genome assembly?
It is when a computer is used to align overlaps
What else is used for genome assembly?
Celera's trick for repetitive DNA
What are the three ways to find genes in DNA?
Use open reading frames, use expressed sequence tags, or use BLAST.
What does BLAST stand for?
Basic Local Alignment Search Tool
What are some other less common ways of finding genes?
Use a genefinder
What does BLAST search for?
blastn-nucleotide-nucleotide, blastp-protein-protein, blastx-nucleotide-protein, tblastn-protein-translated nucleotide, tblastx-translated nucleotide-translated nucleotide
With a complete DNA sequence, what can be compared?
It becomes possible to compare sequences of DNA and proteins with all organisms whose sequences are in the database.
What is possible to learn by sequencing genomes?
We can learn what the basic genes for life are. What genes differentiate plants, animals, bacteria, and fungi. What genes change through evolution. We can identify candidate genes for diseases and oncogenes.
What are 3 classes of genes biochemically speaking?
Metabolism, DNA/RNA, Protein synthesis
Does the human genome have more or fewer gene families and larger or smaller gene families than the invertebrates?
The human genome has more and larger gene families than the invertebrates.
More than 50% of the human genome is composed of what?
Repeated sequences
What is one example of this and its percentage of the genome?
Retroviruses are contained in 8% of the genome.
After an RNA retrovirus has entered a cell and lost its envelope, what happens next?
The RNA leaves the unenveloped virus and uses the enzyme reverse transcriptase to produce a single strand of DNA.
What happens next?
The DNA strand is duplicated by the host cells machinery.
What are the two biggest concerning the human genome?
What are the specific roles of noncoding DNA. What are the functions of genes with no known domains or roles.
What is the primary purpose of model systems?
They are used to purify and express proteins to determine what their biochemical function is.
What can be determined by inactivating single / sets of genes?
It can be determined what the function of those genes are in the organisms.
What is this known as?
This is known as reverse genetics and defines genetic function.
What is the purpose of microarrays?
It becomes possible to test under what conditions genes are expressed.
What are expression microarrays also known as?
They are also known as global expression analysis.
What levels of RNA are analyzed in microarray analysis?
RNA levels of every gene in the genome are analyzed in paprallel.
How can microarrays be compared to northern blot?
Microarrays contain more information by many orders of magnitude.
How has microarray analysis of gene expression improved disease diagnostics from genomics?
Microarray analysis of gene expression allows multiple types of tumors to be analyzed at the same time.
What does this accomplish?
This allows grouping of gene expression patterns and shows very clear differences among the tumors.
How does this actually influence individual treatment of diseases?
It can be used to tailor therapy to individual needs.
Whatis pharmacogenomics?
It is when drug therapies are tailored to individuals.
How are these drug therapies designed?
They are designed based upon the individual's genome.
What do the subtle differences in genomes cause in drug therapy?
They cause differences in how one responds to drugs.
So ultimately, what does pharmacogenomics allow the determination of?
It enables the identification of those who will suffer harmful side effects from particular drugs.