genomics Flash Cards

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Title:	genomics
Description:	test 1
Number of Cards:	159
Save Count:	0
Author:	rajm8d10
Created:	2008-05-26
Tags:	genome
Private	No

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- Question
- Answer
- Side 3

- Define genome
- all the genetic material in an individual
- define genomics
- study of genomes
- What is the difference between genomics and molecular genetics
- genomics- study of entire genome
  molecular genetics- individual genes
- What kind of genomics do we study in vet med
- pathogen genes and domestic animal genomes
- What are some future applications of genomics
- gene and stem cell therapy
- what is pharmacogenetics
- optimizing drug therapy in light of individual patient makeup.
- What is pharmacogenetics used mainly for
- avoiding adverse drug reactions
- What is the difference between pharmacogenetics and genomics
- genetics-study of inherited differnces in drug metabolism/response. genomics-general study of many diff genes that determine drug behavior.
- What breed has ivermectin sensitivity
- collies
- When did human genome project begin
- 1986
- What was the goal of the human genome project
- form a complete sequence of euchromatic regions
- When was human genome sequence complete
- 2003
- what are the highly repetative parts of chrom. called
- heterochromatic regions
- the less repetative regions of a chrom are called
- euchromatic regions
- Before they sequence the human genome what else did they sequence
- smaller sequences(bacteria) to optimized methods
- Who designed the current DNA sequencing method
- Frederick Sanger
- what is function of ddNTP
- A chain terminator
- What is function of dNTP
- continues translation
- What length and cost of typical mammalian genome
- 3 million bp and $25 million
- What is the data obtained from a single Sanger reaction
- read
- How many base pairs does a single read contain
- 550bp
- Name 5 steps in completing genome projects
- 1.Accumulate reads
  2.Assemble reads in contigs
  3.Assemble contigs on scaffold
  4.Annotate genome sequences
  5.Indentify polymorphic sights
- What is a contig
- a contiguous sequence of DNA created by assembling overlapping sequenced fragments
- What does depth of coverage mean
- average # of lines a nucleotide appears
- What is the equation for depth of coverage
- total of of nt divided by the length of the genome
- What is a mobile element
- DNA sequence that has been inserted many times
- A series of sequence segments that are in the right order but not connect in contiunous stretch...is a
- scaffold
- What sequence did collins use
- hierachial sequence-11yr
- What sequence did Venter use
- Shotgun-1yr(company celera)
- What is the scaffold for tiling path of shotgun approach
- BAC clones
- What is a tiling path
- contiguous set of clones that completely spans a genomic region with minimum overlap
- What are tiling paths constructed from
- BAC-bacterial artificial chrom. (lengths 150,000)
- What is a draft sequence
- sequence produced by combining sequence info from individual reads
- Define finished sequence
- complete sequence with few gaps and 99.99% accuracy.
- What is sequence annotaion
- resulf of computer analysis of sequence to revel positions of genes/exons/mobile elements
- in the finished sequence the remaining 1% unsequenced part is distributed...
- in 308 gaps
- What is length of human euchromatic genome
- 2.88GB
- What is total length of human genome(with heterochromatic)
- 3.08 GB
- How many genes and pseudogenes in human genome
- 21,000
  20,000PG
- Define gene
- NT sequence that codes for RNA product
- Define pseudogene
- NT sequence that resembles gene but can't produce functional RNA product
- Name 2 NIH goals
- 2010 $100,000 sequence
  2015 $1,000 sequence
- what steps lead to annotation of genome
- cloninc, sequencing rxns, assembly sequence.
- What does a gene code for
- one protein or RNA(t or r)
- how long is one gene
- 1Kb
- What is the sequence for the start of a protein
- ATG
- The majority of bacterial genomes are
- circular(1)
- Vibrio is an example of
- 2 circular genomes
- Borrelia is an example of
- one linear genome
- Agrobacterium
- one circular and one linear genome
- what are ORF
- open reading frames(gene for a protein)
- Give examples of things that can be deduced from a genome sequence
- metabolic pathways, flagella, adhesion, toxins, surface proteins, antigenic variation
- What are slippery sequences mediate
- antigenic/phase variation
- Give examples of bacteria in which genomic approaches are good
- intracellular pathogens- chlamydia and rickettsia
- define comparitive genomics
- comparison of closely related species- for evolution/adaptation clues
- What do we find with the quantum leap in pathogen evolution
- pathogenicity islands
- What are hallmarks of lateral gene transfer
- different GC content, inserted into tRNA gene, presense of phage intergrase
- approximately how many genes are needed for PAI
- 35 to make strain virulent
- What is a microarray
- microscope slide with 20,000 genes
- What is a DNA chip
- hybridization fo mRNA/DNA to chip DNA. Then analyzed for gene profiles/transcriptome and genetic polymorphism
- Define proteome
- complete set of proteins encoded by a genome
- What are proteomes used for
- indentify which proteins are expressed under diff. conditions and growth in presense/absense of Antimicrobial
- What does a complete genome sequence reveal
- every candidate protein antigen- useful for detection and vax development
- What is function of reverse vaccinology
- shortens vaccine candidate search
- What are limitations of reverse vaccinology
- only protein components assessed and must avoid phase variable genes
- What are Metagenomics
- community sequence projects
- What has the smallest genome
- mycoplasms(1000Kb)
- Describe viral genomes
- compact, minimal untranslated regions, common overlapping frames
- are viral genomes composed of rna or dna
- either
- describe rna viruses
- small but lots of heterogeneity. Range from7-15 Kb
- describe dna viruses
- bigger than rna
- What is posive polarity the same as
- mRNA
- DS DNA, SS DNA, DS RNA, Positive and negative sense RNA, RNA and DNA reverse transcribing viruses are all
- 7 classifications of viral genomes
- What are quasispecies
- RNA virus populations are mixtures of many diff. genome sequences generated by random error
- Are viral genomes stable
- no