Week 2

Question 1

dynamic points where parent DNA is being unwound and the separated strands are replicated

Answer 1

replication forks

Question 2

Cairins found that radioactive DNA isolated from ____ cells during replication showed and extra ____ of DNA. He concluded that the extra lop resulted from the formation of two radioactive ____ strands. He also showed that both DNA strands are replicated ____. Variations on his experiment showed that replication of bacterial chromosomes is ____.

Answer 2

e. coli, loops, daughter, simultaneously, bidirectional

Question 3

Using ___ ___ Inman showed that DNA could be selectively denatured at sequences unusually rich in ___ base pairs, generating a reproducible pattern of _____ ____. Using these points as reference, they found that replication loops always initiated at a unique point called a ____. For circular DNA the two replication forks meet at a point on the side of the circle ___ to the origin

Answer 3

denaturation mapping, A-T, single-strand bubbles, origin, opposite

Question 4

A new strand of DNA is always synthesized in the ___ direction, with the free ____ as the point at which DNA is elongated. The template is read from _____.

Answer 4

5’–>3’ , 3’OH, 3’->5’

Question 5

One DNA strand is synthesized ____ and is called the ____ strand while the other is synthesized discontinuously in ___ ____ and is called the ___ strand.

Answer 5

continuously, leading, okazaki fragments, lagging

Question 6

nucleases that degrade nucleic acids from one end of the molecule

Answer 6

exonucleases

Question 7

nucleases that begin to degrade at specific internal sites in a nucleic acid strand, reducing it to smaller and smaller fragments

Answer 7

endonucleases

Question 8

The reaction for DNA synthesis seems to proceed with only a ___ change in free energy, given that one ____ bond is formed at the expensive of a somewhat less stable ___ ___. However ____ ___ and ____ interactions provide additional stabilization to the lengthened DNA product relative to the free nucleotide.

Answer 8

minimal, phosphodiester, phosphate anhydride, noncovalent base-stacking base-pairing

Question 9

The formation of the products of DNA synthesis is facilitated in the cell by the _____ kj/mol generated in the subsequent ___ of the ___ product by the enzyme ____

Answer 9

19, hydrolysis, pyrophosphate, pyrophosphatase

Question 10

DNA polymerases require a DNA ____ and an ____ ____ with a free ____ group to which a nucleotide can be added,

Answer 10

template, RNA primer, 3’OH

Question 11

The incoming nucleotide is initially positioned in the ______ ____ of the DNA pol. Once the ____ bond is formed, the polymerase slides forward on the DNA and the new base pair is positioned in the ___ ____. After adding a nucleotide to a growing DNA strand, a DNA pol either ___ or moves along the template to add another nucleotide.

Answer 11

insertion site, phosphodiester, postinsertion site, dissociates

Question 12

the average number of nucleotides added before a polymerase dissociates

Answer 12

processivity

Question 13

The active site of DNA pol ___ accomodates only base pairs with the geometry of standard ____ and ___ base pairs. Incorrect bases can be ____ before the phosphodiester bond is formed

Answer 13

I, C-G, A-T, rejected

Question 14

DNA polymerases insert one incorrect nucleotide for every ____ to ___ correct ones. These mistakes sometimes occur because a base is briefly in an unusual ____ form, allowing it to ____ with an incorrect partner. In vivo, the error rate is reduced by additional ___ mechanisms

Answer 14

10E4, 10E5, tautomeric, hydrogen-bond, enzymatic

Question 15

Many DNA pols have a separate ____ ____ activity that double checks each nucleotide after it is added If the polymerase has added the wrong nucleotide, ___ of the enzyme to the position where the next nucleotide is to be added is _____. This proofreading activity requires _____ ____ bonds. In DNA pol I, the polymerizing and proofreading activities have separate ___ ___ within the same polypeptide

Answer 15

3’–>5’, translocation, inhibited, 3 high-energy, active sites

Question 16

DNA pol’s rate at which it adds nucleotides is too ______, it has a relatively low _____, and it does not act ____. Cairns also found a bacterial strain that produced ____ pol I that still had ___ DNA

Answer 16

slow, processivity, alone, inactive, viable

Question 17

DNA pol II has ____ exonuclease activity and an ____ polymerization rate and _____.

Answer 17

3’->5’, intermediate, processivity

Question 18

DNA pol III has ____ exonuclease activity as well has the highest ____ rate and ___

Answer 18

3’->5’, polymerization, processivity

Question 19

DNA pol I has _____ and ____ exonuclease activity, as well the lowest rate of polymerization and ____

Answer 19

3’->5’, 5’->3’, processivity

Question 20

The 5’->3’ proofreading activity if DNA pol is located in a ___ ___ that can be separated from the rest of the enzyme by mild ____ treatment. When it is removed the remaining fragment, the ___ / ____ fragment, retains the ___ and ___ activities

Answer 20

structural domain, protease, large, klenow, polymerization, proofreading

Question 21

DNA pol III is much more complex than DNA pol I with ___ subunits. The polymerization activity resides in its ____ subunit and its proofreading activity residues in its ___ subunit. The ___ associates with both subunits. The ___ subunits increase processivity

Answer 21

9, alpha, eta, theta, beta

Question 22

enzymes that move along DNA and separate the strands using chemical energy from ATP

Answer 22

helicases

Question 23

enzymes that relieve topological stress in the helical DNA structure

Answer 23

topoisomerases

Question 24

Proteins that stabilize separated DNA strands

Answer 24

DNA-binding proteins

Question 25

enzymes that synthesizes short segments of RNA primers

Answer 25

primases

Question 26

DNA pol I and ______ ____ removes the RNA primers after DNA synthesis and the remaining gap is filled in with ____. The nick is sealed with ___ ___

Answer 26

RNase H1, DNA, DNA ligase

Question 27

In the kornberg experiment, the isolated e. coli fraction was radiolabeled with _____. ____ was added to the reaction after some time, and ____ separated the mixture into two fractions. The acid soluble mixture contains the _____ and ____. The acid insoluble mixture contains the ____, indicating polymerase is in the mixture. To verify this, ____ was added to the insoluble pellet, and the radioactivity ended up in the ____ layer as the soluble fraction. This experiment was also repeated using radioactive ____

Answer 27

dT, acid, centrifugation, nucleotides, nucleosides, polynucleotides, DNase, supernatent, dTTP

Question 28

Messelson and Stahl grew e. coli in the presence of ____ nitrogen to label the bacteria’s DNA. Then they moved the bacteria to a normal ____ containing medium and allowed the cells to divide ___. The resulting DNA were separated by ____. After 2 generations, the DNA is either all ____ or a mixture of heavy and light, supporting the ____ model

Answer 28

N15, N14, once, density, light, semiconservative

Question 29

On a ___ ___ density gradient, the heavier DNA runs ____ down the gradient

Answer 29

cesium chloride, further

Question 30

The DNA pol III clamp loading complex is an ____ + _____. This complex binds to __ and to the new ___ sliding clamp. The binding imparts ___ on the dimeric clamp, opening up the ring at one subunit ____. The newly primed lagging strand is slipped into the ring through the resulting ___. The clamp loader then _____ ATP, releasing the ___ ___ and allowing it to close around the ___.

Answer 30

AAA, ATP, ATP, beta, strain, interface, hydrolyzes, sliding clamp, DNA

Question 31

Spontaneous deamination of cytosine converts this base to ___. Uracil is chemically very similar to ____ and can base pair with ___. This uracil is recognized as foreign in __ and removed via __ ___ ___

Answer 31

uracil, thymine, adenine, DNA , base exicision repair

Question 32

hydrolysis of the N-beta-glycosyl bond between the base and the pentose; more common with purines

Answer 32

depurination

Question 33

reactive oxygen species such as hydrogen ____, ____ ____, and ___ radicals damage DNA. ___ ___ are responsible for most oxidative DNA damage. A common form of this damage is the formation of _____ which due to the extra carbonyl group will now favor a ___ conformation around the glycosyl bond and then base pairs with __ instead of C.

Answer 33

peroxide, hydroxyl radicals, superoxide, hydroxyl radicals, 8-oxo-guanine syn, A

Question 34

UV light causes ___ _____ dimers and 6-4 ______.

Answer 34

cyclobutane pyrimidine, photoproduct

Question 35

ionizing radiation such as x rays and ___ rays cause ___ opening, base ____, and breaks in the ___ backbone of nucleic acids.

Answer 35

gamma, ring, fragmentation, covalent

Question 36

____ is a modified nucleotide that forms in the presence of alkylating agents. This is a __ and highly ____ lesion, and results in a pair with ___ rather than cytosine

Answer 36

O6-methylguanine, common, mutagenic, thymine

Question 37

enzymes that recognize common DNA lesions and remove the affected base by cleaving the N-glycosyl bond in the process of BEA

Answer 37

DNA glycosylases

Question 38

_____ specifically removes from DNA the uracil that results from spontaneous deamination of cytosine. It does not remove uracil residues from ___ or thymine residues from ___. The deamination is ___ fold faster in ______

Answer 38

uracil DNA glycosylases, RNA, DNA, 100, ssDNA

Question 39

Programmed double strand breaks are due to ____ and ___ recombination

Answer 39

meiosis, V(D)J

Question 40

Damage that leads to double strand breaks are _____ NER or BER repair pathways and subsequent DNA ____, _____ ____ or ___ damage, and replication ____.

Answer 40

incomplete, replication, UV, IR, stalling

Question 41

NHEJ will join two broken strands using very small _______. This can result in small ___ or ____.

Answer 41

microhomology, deletions, insertions

Question 42

homologous recombination is _____ repair of break. ___ ____ are used to repair breaks

Answer 42

template-driven, sister chromosomes

Question 43

In TALENs, the __ nuclease can be engineered to be targeted to specific regions of the genome by attaching it to ____ ___ ___ that will recognize a specific and unique sequence of DNA. This is ____ as each newly engineered DNA-binding motif needs to be validated for ___ and potential ___ effects

Answer 43

FokI, engineered DNA-binding motifs, labor-intensive, specificity, off-target

Question 44

For HIV to enter a ____ it must be able to bind to the ____ ___ and the _____ _____. A naturally occurring variant in the human population is immune to HIV, and they have a variant of the _____ that is missing ___ base pairs in an ___ loop, and HIV cannot enter these cells

Answer 44

t-cell, CD4 receptor, CCR5 co-receptor, CCR5, 32, exofacial

Question 45

CRISPR evolved in bacteria as a mechanism to protect themselves from ___ attacks. The bacteria integrate a small piece of the DNA from the ____ ___ into a specific region of their genome and transcribe it to a _____ The RNA molecules guide the ____ to cleave the viral DNA

Answer 45

viral, invading virus, TracrRNA, CRISPR-cas9

Question 46

Cas9 has a disordered ___ recognition domain. Binding of the TracrRNA and _____, together the ____, induce folding of the PAM recognition domain. Then the PAM recognition region can recognize the ___ in the target sequence

Answer 46

PAM, crRNA, sgRNA, PAM

Question 47

After PAM is recognized, the Crispr-Cas9 complex ___ the target DNA at the PAM. If the sgRNA is ___ to the target DNA, it will continue to unwind and expand the ____. If fully complementary, the ____ domain moves over the cut site on the ____ strand and the ___ domain over the ___ strand and hydrolyze the backbone

Answer 47

melts, complementary, R-loop, HNH, 3’, RuvC, 5’

Question 48

There is large scale ___ of the ___ domain during binding of the ___ and target. Cleavage is only possible with these changes.

Answer 48

reorganization, HNH, sgRNA

Question 49

NHEJ repair which is favored in humans, will often result in a small ___ and ___, leading to a gene disruption. HR repair will repair the break with high ___ in S or ___ phase.

Answer 49

insertions, deletions, fidelity, G2

Question 50

if you provide the cell with a repair ____, one that is identical to the sequences on either side of the ___ ___, you can add genetic material. During HR repair, ___ ___ will amplify these regionsq

Answer 50

template, CRISPR DSB, DNA pol