DNA Polymerase in Lab vs. Cells

Question 1

DNA Polymerase in the cell has ________ timed replication of long chromosomes, ______ per cycle, and are done at _______ temperature.

Answer 1

precisely, once, same

Question 2

Because synthesis is 5’ to 3’, replication of complementary DNA strands in the cell is ________ and is ______________.

Answer 2

asymmetric, semi-discontinuous

Question 3

Many ____________ enzymes are required for fast high ________ replication of genomes such as helicase, DNA primase, and DNA ligase.

Answer 3

accessory, fidelity

Question 4

In the lab, _______ _______ reaction amplifies short sequences of interest with steps controlled by ______

Answer 4

polymerase chain, temperature

Question 5

DNA Polymerase active site has _______ , 3’ OH of ______ strand, nucleoside 5’triphosphate, 2Mg+.

Answer 5

template, growing

Question 6

DNA ________ is the stepwise, directional addition of ______ to a growing DNA chain.

Answer 6

synthesis, dNTPs

Question 7

DNA synthesis by polymerases require a _______ strand and a _______.

Answer 7

template, primer

Question 8

DNA strands must be ________ prior to DNA synthesis.

Answer 8

separated

Question 9

DNA polymerization always occurs in the ___ to ___ direction.

Answer 9

5’ , 3’

Question 10

DNA double helix must be denatured for _________. In cells, denaturation is localized and starts at an ______ of replication.

Answer 10

replication, origin

Question 11

A __________ _______ is where DNA replication in cells require many more components than the polymerase.

Answer 11

replication fork

Question 12

The _________ of DNA strands is an ________-_________ process carried out by special enzymes.

Answer 12

separation, energy dependent

Question 13

DNA helicases hydrolyze ____ to induce cyclic conformational changes and mechanical forces which are moving wedges that _____ the helix _____.

Answer 13

ATP, pry, apart

Question 14

_____ _____ ______ proteins bind to the unwound strands of DNA to keep them separate and stop them from forming a helix again.

Answer 14

single strand binding

Question 15

Because the DNA Double Helix is antiparallel, the synthesis of one DNA strand is __________ whereas it’s complementary strand is synthesized in ________.

Answer 15

continuous, fragments

Question 16

DNA polymerases need an ____ primer. DNA primase is an ____ polymerase.

Answer 16

RNA, RNA

Question 17

synthesis of the _______ strand leaves gaps that must be _______ by DNA _______.

Answer 17

lagging, sealed, ligase

Question 18

DNA _______ seals gaps by charging the 5’ phosphate with ____ in the nick, which is subsequently attacked by 3’OH, sealing the DNA with phosphate.

Answer 18

ligase, AMP

Question 19

_______ unwind DNA double helix ______ of the replication fork.

Answer 19

helicases, infront

Question 20

IN PCR, the template is provided by ______ and can vary widely in ______.

Answer 20

you, quality

Question 21

In PCR, DNA primers are provided by _______ and direct where synthesis ________.

Answer 21

you, starts

Question 22

In PCR, the DNA strand is separated by ________ but a DNA polymerase that can _________ heat is required.

Answer 22

heating, withstand

Question 23

PCR amplifies DNA through successive rounds of _________, _________, and __________ all regulated by temperature.

Answer 23

denaturation, annealing, extension

Question 24

PCR results in the ___________ amplification of DNA molecules.

Answer 24

exponential

Question 25

primer design requires finding the right _______ temperatures to balance specificity and structure.

Answer 25

melting

Question 26

the melting temp (____) of a primer is the temp at which ___ of the DNA Duplex is denatured into single strand DNA. this reflects the _______ of the DNA sequence.

Answer 26

Tm, 1/2, stability

Question 27

the Tm of primers depend on its ___________. It’s best predicted by _____ _________ calculations which account for basepair h bonds and base stacking stabilization.

Answer 27

sequence, nearest neighbor

Question 28

_______ gel electrophoresis separates nucleic acids based on _____.

Answer 28

agarose, size

Question 29

________ transcriptase allows for detection of RNA in addition to DNA

Answer 29

reverse

Question 30

PCR can be used to amplify _________ DNA sequences from complex DNA mixtures.

Answer 30

specific

Question 31

the power of PCR to single out specific DNA molecules can be exploited in the ______

Answer 31

clinic

Question 32

Ex of Clinical use of PCR.
1. take blood sample from infected person
2. remove cells by _________
3. extract _____
4. _______ transcription and _____ amplification of particle
5. run sample through _____ _________ with column of uninfected person

Answer 32

centrifugation, RNA, reverse, PCR, gel electrophoresis

Question 33

DNA tells what a cell ____ do, RNA tells what a cell ____ do.

Answer 33

can, does

Question 34

reverse transcriptase is an RNA dependent DNA polymerase; it ______ RNA and ______ DNA

Answer 34

reads, writes

Question 35

reverse transcriptase can be used to make ______ libraries. which are libraries of ________ after post transcriptional processing.

Answer 35

cDNA, mRNA’s

Question 36

agarose gel electrophoresis doesnt require ______ as linear DNA molecules naturally have similar _____ and _____ proportional to their size.

Answer 36

SDS, shape, size

Question 37

________ PCR directly detects the exponential growth of PCR products during the PCR in order to _____ specific DNA molecules. an example is the use of fluorophore to know when the strand has ______

Answer 37

quantitative, quantify, binded

Question 38

in quantitative PCR a ________ ______ of known DNA quantities allows you to calculate the original concentration of DNA of known sequence from the ____.

Answer 38

standard curve, Ct

Question 39

amount of DNA is _______ proportional to the cycle number.

Answer 39

inversely

Question 40

________ sequencing is sequencing DNA using dideoxynucleotides (ddNTP) as chain __________. These have a 3’ H instead of OH.

Answer 40

sanger, terminators

Question 41

____________ of nucleic acids facilitates easy detection of labeled probe sequences (florescent)

Answer 41

hybridization

Question 42

microarray is an array of synthesized single stranded _____ corresponding to regions of a genome of interest

Answer 42

DNA

Question 43

ChIP + detection
- cut DNA into _______
- immunoprecipitate ___ on a DNA binding protein
- detect bound ______
-detects where proteins bind

Answer 43

fragments
pull
DNA