exam 3

Question 1

four main parts of mass spec

Answer 1

separation source front end
ionization like MALDI
mass separater
detector

Question 2

dideoxy sequencing

Answer 2

3' Oh group is gone
stop short
modern diff color per end
or run each column differently
modern is color capillary

Question 3

Pacbio

Answer 3

single long strand
stuck in well with poly adding one at at time
suuuuper long DNA

Question 4

ilumina

Answer 4

blob with primers

added one at a time to get colors

Question 5

RNAseq

Answer 5

make cDNA with reverse transcriptase
use something like illumina
know what relative levels are active
super expensive though

Question 6

microarray

Answer 6

littlespots
use cDNA again
has oligonucleotides single stranded
bind complimentary
to probe for a bunch of genes and concentrations 
intercalated dies

Question 7

HPLC

Answer 7

high pressure liquid chromatography
samples are run ofer a column w/ high pressure columns containg resins like (affinity, pH, size exclusiong) to attract specific samples samples bound to resin can be taken in a specific order by washing organic solven in increaseing concentrations over the column

Question 8

PCR

Answer 8

polymerase chain reaction
melt - 94
anneal primers - 50-65
elongate/amplify -70s is when taq polymerase is most active

Question 9

Tm

Answer 9

50% of primer is bound

hotter than that less primer is bound

Question 10

where when pluripotent mouse ESC

Answer 10

inner cell mass of a 3.5 day old mouse blastocyte

Question 11

yeast 2 hybrid model

Answer 11

for proteins
half of an enhancer on each of 2 proteins
if they interact they activate enhancer to turn on promoter on a reporter gene

Question 12

Northern Blots

Answer 12

RNA
run through a gel
hybridize to probe
peel and loook

Question 13

Southern Blots

Answer 13

DNA

same steps

Question 14

Western Blots

Answer 14

Protein
denature first
antibodies to do bait and hook

Question 15

CRISPR-Cas

Answer 15

target specific gene with CAS9 and guide protein in 0.5 fertilized egg (pronucleus) then transfered to pseudopregnant female mouse

Question 16

RNA absourbance

Answer 16

260/280

about 2

Question 17

RNA absorbance

Answer 17

260/280

about 2

Question 18

DNA absirbance

Answer 18

260/280

about 1.8

Question 19

ligase independent

Answer 19

how do they associate

Question 20

ligase independent

Answer 20

use false sticky ends instead

Question 21

genome library

Answer 21

restriction enzyme to randomly cut
cut vector the same
transform bacteria 
grow
harvest
see if hybridize with probe

Question 22

cDNA library

Answer 22

put it in plasmid
up-regulate
find exons and introns
cut and see if DNA binds to it

Question 23

CRISPR

Answer 23

delete need two
add need two and donor plasmid
insertion need one and donor 
in the one cell stage 
into zygote 
gRNA can be bought if we know sequence 
makes humans homo

Question 24

ZFN and TALENS

Answer 24

same as crisper but find it with their modules

Question 25

RNA interference

Answer 25

in something feed words putting in si and miRNA because double stranded RNA is unnatural can be incorporated

Question 26

Cre-lox

Answer 26

intersect of reporters for cre and the gene tissue specific can be in adults not just embryos can knock out things later that would be fatal to embryos

Question 27

2d electrophoresis

Answer 27

for proteins step one by PI second By SDS to do by size mass ratio s stain after blue

Question 28

stain first

Answer 28

DNA gels ethidium bromide

Question 29

pull down

Answer 29

tag with antibodies size similar to affinity chromatography

Question 30

sucrose gradient centrifugation

Answer 30

dense on bottome settle in and then collect bottom layer first S units

Question 31

FPLC

Answer 31

doesnt denature | size exclusion

Question 32

reverse phase HPLC

Answer 32

hydrophilicity phobic column polar solvent normally phases are opposite

Question 33

MALDI

Answer 33

laser bounces off dish

Question 34

DESI

Answer 34

spray evaporate hit

Question 35

Quadripole

Answer 35

narrow hole

Question 36

tof

Answer 36

mirrors | longer bigger

Question 37

orbitrap

Answer 37

round a magnet | longer bigger

Question 38

SRM MRM

Answer 38

single and multiple reaction monitoring | single vs multiple proteins during like MS

Question 39

MudPIT

Answer 39

multiple dimensional Protein ID Tech proteins to poly peptides compare to known bottom up

Question 40

iTraq vs silac

Answer 40

isobaric attatch known size to protein | silac is heavy light from tagging with 15N

Question 41

imaging MS

Answer 41

MS with pic instead of electron multiplier tells you location slice not cell sized kinda like a heat map

Question 42

gene targeting in embryonic stem cells

Answer 42

long arms in yeast | cut elsehwer