Unit 2 - DNA Replication

Question 1

recognize origin sequences (A-T rich region) and separate the DNA strands locally, forming a replication bubble.

Answer 1

origin binding proteins

Question 2

A-T rich region,

Answer 2

origins of replication

Question 3

Required to extend the movement of the fork. Catalyzes separation of dsDNA, moving from 5’ to 3’ direction. Requires ATP.

Answer 3

DNA helicase

Question 4

Stabilizes the single-stranded molecules, preventing re-association of the two strands to protect the DNA from degradation. They bind cooperatively and are NOT enzymes.

Answer 4

SSB Proteins (SSBP)

Question 5

dNTPs (deoxynucleotide triphosphates), Single-stranded template, a free 3’-OH group, RNA primer.

Answer 5

Key components for replication

Question 6

Helicases, ssBP, primase, DNA polymerasea, Rnase H, DNA ligase, topoisomerases.

Answer 6

Major proteins involved in Replication

Question 7

energy of the triphosphate. (NOT ATP hydrolysis)

Answer 7

Energy for incorporation of nucleotide

Question 8

Covalently attach nucleotides to the 3’-OH end of the growing daughter strand one at a time. add bases ONLY to existing chains, and can ONLY extend from 5’ to 3’ direction.

Answer 8

DNA polymerase (DNA pol)

Question 9

Synthesizes short stretches of RNA that are complementary to the DNA template, called RNA primer.

Answer 9

Primase

Question 10

Provides a short, double stranded region consisting of RNA base-paired to the DNA template with a free 3’-OH group,the starting point for DNA polymerase.

Answer 10

RNA primer

Question 11

Blocks viral DNA replication because it does not have a hydroxyl group on the 3’-carbon so when incorporated into viral DNA, no additional nucleotides can be added. Blocks HIV reverse transcriptase, an HIV enzyme, preventing HIV from replicating and lowers the amount of HIV in the blood.

Answer 11

nucleoside reverse transcriptase inhibitor (NRTI)

Question 12

nucleoside reverse transcriptase inhibitor (NRTI) examples.

Answer 12

didanosine(ddI) and zidovudine (ZDV)

Question 13

Strand that is being synthesized continuously in the 5’à 3’ direction towards the replication fork.

Answer 13

Leading strand

Question 14

Strand synthesized in the direction away from the replication fork as short pieces (“Okazaki fragments”) of DNA in the 5’ to 3’ direction. These discontinuous pieces are eventually joined together to form a continuous DNA strand.

Answer 14

Lagging strand

Question 15

the major replicative enzyme

Answer 15

Polymerase delta

Question 16

Recognizes RNA-DNA duplexes and removes the primer, leaving DNA portion intact. a target for drug development to block HIV genome replication.

Answer 16

RNase H

Question 17

joins Okazaki fragments together by forming a phosphordiester bond.

Answer 17

DNA ligase

Question 18

Create nicks or cuts in DNA to relieve the torsional tension caused by twisting, then sealing the nicks. This allows the normal unwinding of DNA to occur during replication.

Answer 18

Topoisomerases

Question 19

transiently cuts one strand of DNA.

Answer 19

Topoisomerase I

Question 20

Transiently cuts both strands of the DNA

Answer 20

Topoisomerase II

Question 21

Topoisomerase I inhibitor, DNA supercoild won’t replicate quickly. Anti-Cancer.

Answer 21

camptothecin

Question 22

Topoisomerase II inhibitor

Answer 22

doxorubicin

Question 23

1) stably bind to DNA thus not generating a single strand DNA as a template for DNA replication. 2) prevent topoisomerases from re-sealing the DNA. Both will stop DNA replication.

Answer 23

Topoimerase inhibitor mechanism of action

Question 24

Ends of the linear chromosome composed of thousands of repetitive sequences of non-coding DNA that protect chromosome from damage. Single and double stranded.

Answer 24

Telomeres

Question 25

If the newly-made DNA strands are not sufficiently replicated, successive rounds of DNA replication will produce daughter strands that are progressively shorter because there is no room to synthesize a new RNA primer at the extreme 3' end.

Answer 25

“end-replication problem"

Question 26

RNA-dependent DNA polymerase (ribonucleoprotein), uses its own RNA template to synthesize DNA, not the primer (see the next slide). Contains an RNA component (RNA template), and it uses the telomeric DNA sequences to extend the parental DNA.

Answer 26

telomerase

Question 27

i. Semi-conservative ii. Starts at the ‘origin’ iii. Bidirectional iv. Semi-discontinuous v. Synthesis always in the 5’to 3’ direction vi. RNA primers required

Answer 27

Basic Rules of DNA replication

Question 28

consists of 8 proteins: 2 molecules each of histones H2A, H2B, H3, and H4.

Answer 28

histone core

Question 29

nucleosome

Answer 29

nucleosome

Question 30

DNA, the core histones, and histone H1.

Answer 30

chromatosome

Question 31

is involved in stabilizing higher order chromatin structures. It is not part of the nucleosome core.

Answer 31

Histone H1

Question 32

condensed 10-nm fiber structure stabilized by: Histone H1 (linker histone), Histone N-terminal tails, Linker DNA. Foundin interface euchromatin.

Answer 32

30-nm fiber

Question 33

transcriptionally active decondensed 10-nm and 30-nm fibers organized as loop domains

Answer 33

euchromatin

Question 34

DNA sequences that are generally not transcribed (such as centromeres or telomeres).

Answer 34

Constitutive heterochromatin

Question 35

genes that are not transcribed in that particular cell, but may be transcribed in other cell types.

Answer 35

Facultative heterochromatin

Question 36

The processes by which the lysine residues within the N-terminal tail protruding from the histone core of the nucleosome are acetylated and deacetylated as part of gene regulation.

Answer 36

Histone acetylation and deacetylation

Question 37

cause DNA to loosen by adding an acetyl group to histone tails, resulting in increased transciption.

Answer 37

Histone acetyltransferases (HATs)

Question 38

removes acetyl groups from histone tails, restoring the DNA/histone interaction and tightening the DNA resulting in transcription supression.

Answer 38

Histone deacetylases (HDACs)