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74 Cards in this Set
- Front
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high throughput sequencing |
rapid DNA sequencing on micro scale in which many DNA fragments sequenced simultaneously |
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functional genomics |
use sequencing information to identify functions of various parts of genomes |
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open reading frames |
DNA sequence with no stop codon, encodes part of protein |
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intron consensus sequence |
boundary btw intron and exon |
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regulatory sequence |
promoters and terminators for tanscription |
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comparative genomics |
use sequencing info to compare newly seq genome with sequences from other organisms |
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genetic determinism |
FALSE notion that phenotype only determined by genotype |
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proteomics |
to identify and characterize all proteins |
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proteome |
sum total of all proteins produced by organism |
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metabolomics |
to desxribe metabolic profile of tissue/organism under particular environmental conditions |
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metabolome |
complete set of small molecules in cell/tissue/organism |
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primary metabolites |
involved in normal processes, such as intermediates in glycolysis, hormones, signaling molecules |
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secondary metabolites |
unique to particular organisms/groups involved in special responses to environment ex. defense chemicals in plants |
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plasmid |
circular DNA molecules that can be transferred btw prokaryotic cells |
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metagenomics |
practice of analyzing DNA from environmental samples without isolating intact organisms |
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example of metagenomics |
sequencing sea water to see viruses and bacteria |
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transposons |
segments of DNA that can move from place to place in genome can cause mutations |
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gene families |
set of similar genes derived from single parent gene |
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pseudogenes |
nonfunctional genes in gene families that result from mutations that cause LOSS of funciotn |
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highly repetitive sequences |
short sequences repeated 1000s of times NOT transcribed associated with heterochromatin (inactive) |
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short tandem repeats |
2-5 bp repeated up to 100xm |
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moderately repetitive seuqnce |
repeated 10-1000x in euks include genes YES TRANSCRIBED to produces tRNA and rRNA |
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transposons make up _______ of human genome |
40% |
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most _______ sequences are transposons |
moderately repetitive |
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retrotransposons |
make RNA copies of themselves, copied back into DNA before translocation insertion |
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DNA transposons |
do not use RNA intermediates excised from origin, inserted elsewhere WITHOUT being replicated |
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DNA fingerprinting |
short tandem repeats analyzed, one's unique pattern becomes apparent |
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pharmacogenomics |
study of how one's genome affects drug response to personalize drug treatment |
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2 approaches to DNA cloning |
standard cloning and PCR |
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cloning vector |
DNA molecule that can self-reproduce |
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how to do standard DNA cloning? |
restriction enzymes "cut" DNA strands, sticky ends, attach gene of interest with ligase, recombinant DNA formed then recomb DNA replicates and produces many copies of gene of interest |
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restriction enzymes |
cut DNA strands at restriction sites (staggered not clean cut) |
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palindrome |
symmetrical sequence of 4-8 nucleotides running in opposite directions on two strands complementary and template strands identical, can flip flop |
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transformation |
bacteria take up genetic info from environment insert recombinant DNA into host cell |
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how do bacteria protect their own DNA from being chopped up by restriction enzymes? |
methylation |
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PCR |
isolate and amplify DNA quickly |
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steps of PCR |
heated to denature and separate strands cooled to let primers attach, DNA pol does its job heated again, repeat 35-40x |
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gene therapy |
replace defective copy of gene with normal copy within patient's own DNA and cells |
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Ashanti deSilva |
low WBC count, defective gene for ADA (breaks down toxic intermediates) |
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no ADA = |
toxins in WBC, killing them |
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what fixed Ashanti |
retrovirus with functional ADA gene infected WBC, allowed WBC with ADA to divide
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goals of human genome project |
1. determine entire DNA sequence of human genes 2. identify, map, determine function of genes |
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when was human genome project finished |
2003 |
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how many genes in human genome? |
21,000 protein-coding genes |
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how much of human genome DIRECTLY codes for protein? |
less than 1%
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how much of human genome is junk DNA? |
10% repetitive ancient retroviruses that entered and never left! |
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transposable elements |
useless pieces of DNA that copy themselves and shift around chromosome = junk DNA |
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which is bigger: genome or proteome |
MORE PROTEOME (more proteins than total DNA) |
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how does proteome have over 200,000 proteins? |
alternative splicing- some exons removed, one gene, many mRNAs, many proteins |
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gel electrophoresis |
separates DNA fragments DNA negatively charged, move to positive end smaller fragments move faster |
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vector |
plasmid or virus that carries inserted piece of DNA into bacterium for cloning purposes |
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examples of vectors |
plasmids as vectors plasmic vectors for plants viruses as vectors |
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cDNA |
complementary DNA formed by reverse transcriptase acting with RNA template no introns |
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RT-PCR |
RNA isolated from cell, reverse transcriptase used to make cDNA then PCR amplifies sequence from cDNA |
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homologous recombination |
exchange of segments btw 2 DNA molecules based on sequence similarity btw molecules, they cross over |
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what is homologous recombination used for? |
to knockout (inactivate) mutants in mice and other organisms |
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stem cell |
unspecialized cell that divides and differentiates into specialized cells |
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RNA interference (RNAi) |
mechanism for preventing mRNA translation double-stranded RNA processed into small, single-stranded RNA whose binding to a target mRNA results in breakdown of mRNA |
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antisense RNA |
complementary to, thus targeted against, mRNA of interest to block transcription |
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difference between microRNA and siRNA sequencing |
siRNAs target specific mRNA molecules because their sequences exactly match mRNA sequence microRNAs do NOT match targets |
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DNA microarray can be used to examine patterns of __________ in different tissues and under different conditions ALSO to identify organisms with _______ |
examine patterns of gene expression, identify organisms with mutations |
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expression vector |
have all characteristics of typical vector PLUS extra sequence needed for foreign gene to be expressed in host cell (transcription and translation) |
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expression vector can include _____ promoter, which responds to specific signal |
inducible
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expression vector can include _____ promoter, which is expressed only in certain tissue at certain time |
tissue-specific |
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human insulin was originally made in ______, now made in ____ |
E.coli, now yeast |
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pharming |
production of pharmaceuticals from farm animals (milk) or plants |
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explain process of pharming |
expression vector carrying desired gene put into animal egg, implanted into surrogate mom transgenic offspring produces new protein in their milk milk harvested and protein isolated for patients |
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advantages of recombinant DNA technology over traditional breeding |
ability to identify specific genes ability to introduce any gene from any organism into plant or animal ability to generate new organisms quickly |
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example of plant making its own insecticide |
bacteria bacillus thirungoifoiefoifoi produces protein (Bt) that kills insects B toxin gene isolated, cloned, modified to be produced by crop plants |
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instead of manipulating environment to suit plant, biotechnology allows us to adapt __________ |
adapt plant to environment |
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haplotype |
piece of chromosome with set of linked SNPs this is sentence, SNPs are words |
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DNA microarray |
grid of microscopic spots, pattern of spots reveal haplotype |
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reporter gene |
genetic marker in recombinant DNA to indicate presence of recombinant DNA |
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selectable marker |
gene that can be used to identify cells with recombinant DNA among large population of untransformed cells |
