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BIO 3060 > TEST 5 > Flashcards

TEST 5 Flashcards

(69 cards)

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1
Q

Forward genetic screens

A

discovers gene due to known phenotype

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2
Q

Reverse genetics screens

A

alteration of genotype to find phenotype
discovers phenotype due to known genotype

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3
Q

amplifying

A

PCR

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4
Q

large scale analysis

A

GWAS

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5
Q

Restriction enzyme

A

molecular scissors

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6
Q

sticky end cut

A

leaves an over hang for future possible complementary paring

ex. AAGCTT
TTCGAACGTACGTA

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7
Q

blunt end cut

A

cut at same spot on both strands of DNA, harder to add on to

ex. AAGCTT
TTCGAA

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8
Q

programmable nuclease examples

A

Meganucleases
ZFN (zinc finger nucleases)
TALEN
Cas9- only one that has a guide RNA

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9
Q

function of programmable nucleases

A

restriction enzymes that have a programmed sequence to cut out of a genome

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10
Q

longer recognition sequences in restriction enzymes leads to what

A

leads to less cuts in the genome as longer sequences are more specific, meaning less parts in the DNA will bond to it

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11
Q

3 parts to a cloning vector

A

Cloning site
origin of replication
selectable marker

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12
Q

cloning site

A

sequences that are easily recognized by restriction enzymes

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13
Q

selectable marker

A

gene that is easily identifiable allowing you to see which genes got sucessfully into the new DNA
ex kanamycin resistance

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14
Q

cloning vector

A

DNA molecule where one inserts genes for amplification etc.

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15
Q

transformation

A

uptake of foreign DNA in environment into genome

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16
Q

ligation

A

ligation of foreign DNA into cloning vector may not be sucessful.
Plasmid can close on itself, or not close at all.
To sort between the cells that sucessfully ligated and those that didn’t additional tests are needed

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17
Q

Clone vector examples

A

Smallest to largest- insertion sequences
plasmids
phages
cosmids (plasmid w/phage gene, can be in a phage)
BAC- bacterial artificial chromosome
YAC- yeast artificial chromosome

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18
Q

Blue white screening

A

cloning vector contains bacterial resistance gene that also codes for blue coloring when no new gene has been transformed into the plasmid

recombinant colonies will inhibit blue gene, will be white
nonrecombinant colonies will not inhibit the blue gene, will be blue

can be doubly selective, agar plates can be covered with bacterial resistance that cloning vector must code for to survive

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19
Q

cDNA library

A

only have DNA sequences that transcribe genes into mRNA
this is done through the harvesting of all mRNA, conversion of mRNA into DNA

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20
Q

Genomic Fragments

A

genome treated with restriction enzyme all genome is broken into fragments

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21
Q

Sanger/Dideoxy sequencing

A

dNTP-normal nucleotide
ddNTP-dideoxy- has H instead of OH in 3’ position
this forces a stop to DNA synthesis in the chain as no new nucleotides are able to join after a ddNTP

take DNA, copy it many times, each time DNA is copied add ddNTPs.
over many generations whole sequence will be found through the analysis of the ddNTP ends

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22
Q

Cycle sequencing

A

automated computer version of sanger sequencing

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23
Q

Next generation sequencing

A

1) break DNA into fragments
2) add primer sequences to each fragment DNA is single stranded
3) each DNA fragment is added to a bead and surrounded by reagents for assisting PCR
4) amplified using pcr
5) each bead is forced into a well
6) DNA synthesis occurs
7) solution w/dATP is added
8) when nucleotide is added two phosphate groups leaving producing light
9) instrament records light
10)light is proportrional to # of nucleotides added
11) repeats steps 7-10 with dCTP, dGTP, dTTP.

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24
Q

PCR steps

A

Template DNA placed into solution with primers, nucleotides, all DNA pol, and PCR buffer

1) template strand is denatured with heat
2) single stranded DNA is cooled to allow for primers to bond
3) raise temp to allow DNA pol to work
4) repeat as many times as needed

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25
STR/ microsatellites
short tandem repeats variable number of copies of repeat sequences
26
hybridization
hybridization of nucleic acids, for example single stranded nucleic acid bonds with another creating a complex
27
genetic maps/linkage maps
low resolution recombination % is higher when genes are further apart
28
markers
unique sequences that provide orientation points in the genome landscape
29
physical maps
directly determines the order and spacing of genes bp by bp
30
physical map methods
DNA sequencing and restriction mapping
31
structural genomics
organization and sequence of genetic info in a genome
32
proteomics
study of all proteins in genome
33
metabolomics
technique for measuring large numbers of metabolites present in biological samples finds metabolic products
34
transcriptomics
study of all RNA molecules transcribed from a genome
35
functional genomics
develop compuational methods to bypass process of isolating and characterizing individual proteins
36
human genome project methods
map based sequencing whole genome shotgun sequencing
37
whole genome shotgun sequencing
1) fragment DNA 2) clone fragments through bacterial plasmid means 3) sequence through computer, computer matches similar ends
38
map based sequencing
1) partially digest DNA into large fragments 2) markers are used to build a continuous piece of DNA from the fragments 3) subset of fragments that cover the entire genome are selected and clone and sequenced
39
GWAS
use numerous SNPs scattered across genome to find genes of interest
40
SNPs
single nucleotide polymorphisms
41
Haplotype
set of SNPs and other genetic variants observed on a chromosome SNPs within a haplotype are physically linked and are inherited together
42
Bioinformatics
field combining computer science and biological data
43
Metagenomics
field where genome sequences of entire group of organisms that inhabit a common environment are sampled
44
synthetic biology
creation of novel organisms
45
microarrays
rely on known DNA fragment used as a probe to find complementary sequences numerous known DNA fragments are fixed to solid support in an array the probes correspond to known genes from a particular organism then mRNA/DNA/cDNA from experimental cells is labeled with flourescent nucleotides and applied to the array if hybridization occurs flourescence will be emitted
46
prokaryotic genomes
mostly singular circular chromosome small genome 1-3million bp # genes is around 1-2k only 50% of genes have known function gene density is constant
47
eukaryotic genomes
no relation between genome size and # of genes more euk genes than prok many euk genes have introns
48
human genome
27000bp each gene has around 2/3 different mRNAs
49
human genome
27000bp each gene has around 2/3 different mRNAs 3,2 billion bps
50
protein microarray chips
immobilization of purified proteins on glass slides
51
analytical protein microarray
antibody array, proteins are detected after antibody capture using direct protein labeling
52
functional protein microarray
constructed using individually purified proteins enable study of biochemical properties of proteins ex. protein-protein, protein-DNA, protein-drug
53
protooncogene to oncogene
gain of function dominant
54
tumor suppressor gene mutation
loss of ability to trigger apoptosis due to mutation recessive
55
benign
localized and self contained
56
malignant
not self contained spreads
57
2 characteristics of cancer
1)proliferate in defiance of normal constrants 2)invade and colonize territories for other tissues
58
how cancer develops
through clonal evolution
59
cyclins
oscillate in concentration during cell cycle
60
retinoblastoma protein function
regulates progression of G1 to s phase -when not phosphorylated it inhibits transcription factor that replicates DNA -when phosphorylated it releases the transcription factor which replicates DNA
61
northern blotting technique
detects RNA
62
southern blotting technique
detects DNA sequences
63
western blotting technique
detects proteins
64
eastern blotting technique
detects carbs
65
what is the chromosomal abnormalities is associated with chronic myelogenous leukemia
reciprocal translocation
66
function of RB protein
regulates progression of G1 to S phase
67
reporter sequence
an easily observed product used to track the expression of a gene of interest
68
nucleic acid hybridization
using a known DNA fragment as a probe to find a complementary sequence
69
2D PAGE technique
run an electrophoresis for the proteins based on pH, low pH will travel the furthest place 1st electrophoresis horizontally to a second electrophoresis when electrified the proteins will now separate based on size with the largest traveling the least

BIO 3060 (6 decks)

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