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Biochem 451 Exam 2 > DNA Replication > Flashcards

DNA Replication Flashcards

1
Q

Each strand of the DNA helix is a polymer of nucleotides joined together in ___ ___ that have alternating sugar-phosphate-sugar-phosphate links. On the inside of the double helix are the complementary ___ ___ held together by ___ ___.

A
  • phosphodiester linkages
  • base pairs
  • hydrogen bonds
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2
Q

The arrangement of the double helix is in an ___-___ fashion, meaning that one strand oriented in the 5’ to 3’ direction is directly paired to a ___ strand oriented in the 3’ to 5’ direction.

A
  • anti-parallel

- complementary

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3
Q

Phosphodiester bonds involve linkage between the __ ___ ___ of the incoming nucleotide and the __ ____ of the previous nucleotide in the chain.

A
  • 5’ phosphate group

- 3’ hydroxyl

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4
Q

DNA contains four bases - A,T,C, and G arranged with A paired with __ and G paired with __ on the internal portion of the double helix.

A
  • T

- C

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5
Q

Hydrogen bonds stabilize these base pairs: __ for the A-T pair and ___ for the G-C pair. Thus, ___ pairs are harder to break than ___ pairs.

A
  • two
  • three
  • G-C
  • A-T
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6
Q

DNA has a ___ and a ___ groove arising from ___ ___ linkages between the deoxyribose ___ and each ___ in the double helix.

A
  • major and a minor
  • asymmetric glycosidic
  • sugar
  • base
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7
Q

DNA has three major forms -

A

A, B , and Z

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8
Q

The A and B forms are ___-__ ____, whereas the Z form is a ___-___ ____.

A
  • right-handed helices

- left-handed helix

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9
Q

The B form of DNA is the ___ ___ one and contains about ___ bases per turn of the helix.

A
  • most prevalent

- 10.5

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10
Q

Z-DNA may have roles in:

A

marking the location of genes in eukaryotic chromosomes

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11
Q

The A form (actually discovered by Rosalind Franklin) is more _____ and is also a right handed helix. The A form is the form assumed by ___ ___ ___ or ___-__ ____ as well.

A
  • compressed
  • double strand RNA
  • RNA-DNA duplexes
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12
Q

____ _____ ___ is an enzyme that has three enzymatic activities.

A

-DNA polymerase I

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13
Q

What are the 3 activities of DNA Polymerase I?

A
  1. a 5’ to 3’ DNA polymerase activity to make DNA
  2. a 3’ to 5’ exonuclease activity (also called proofreading)
  3. a 5’ to 3’ exonuclease activity.
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14
Q

All DNA polymerases require a ____ to start ___ ____. This requirement is formed inside of cells by a special RNA polymerase known as ____. (RNA polymerase does not require a primer)

A
  • primer
  • DNA synthesis
  • primase
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15
Q

DNA replication proceeds by ___ distinct mechanisms (both ____)- ___ on each strand.

A
  • two
  • 5’ to 3’
  • one
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16
Q

Leading strand and lagging strand synthesis occur by different mechanisms, but both are catalyzed by the same ___ ____ ____ (___ __, in the case of E. coli).

A
  • DNA replication complex

- Pol III

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17
Q

Leading strand synthesis is ____ in the __ to __ direction.

A
  • continuous

- 5’ to 3’

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18
Q

Lagging strand synthesis can only occur when the leading strand synthesis ___ __ a new single stranded region for replication. The __ to __ syntheses of the lagging strand are ______.

A
  • opens up
  • 5’ to 3’
  • discontinuous
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19
Q

The many pieces of lagging strand synthesis are called:

A

Okazaki fragments

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20
Q

To combine the okazaki fragments, the ___ _____ must be removed from each one. The 5’ to 3’ _____ ____ of DNA Polymerase I is needed to remove the initial ___ ____ of leading strand synthesis, but is needed frequently to remove the ____ of lagging strand synthesis.

A
  • RNA primer
  • exonuclease activity
  • RNA primer
  • primers
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21
Q

___ ____ is an enzyme that creates ______ bonds between adjacent nucleotides between _____ ____.

A
  • DNA ligase
  • phosphodiester
  • Okazaki fragments
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22
Q

Biotechnologists use DNA ligase to join DNA fragments together to create:

A

-recombinant molecules

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23
Q

E. coli DNA replication occurs at ____ base pairs per second. At __ base pairs per turn, this represents a machine turning at ___ to ___ rpm.

A
  • 1000
  • 10
  • 5000 to 6000
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24
Q

E. coli’s helicase protein (___-__: part of the __ ____) unwinds DNA at a rate of at least ____ rpm. The protein separates strands ahead of the ___ ___ __ so as to make single strands ____ for replication.

A
  • DNA B
  • BC complex
  • 5000
  • DNA Pol III
  • accessible
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25
Q

Unwinding of strands causes ____ ____ to increase ____ of the helicase.

A
  • superhelical tension

- ahead

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26
Q

The enzyme _____ __ (____) relieves the tension created by the helicase and is essential for ____ to proceed efficiently.

A
  • Topoisomerase II (gyrase)

- replication

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27
Q

DNA Polymerase III is very ____ in its action, meaning that once it gets onto a DNA molecule, it stays on it for a ____ ____, _____ it. DNA Polymerase I is NOT very _____.

A
  • processive
  • long time
  • replicating
  • processive
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28
Q

In E. coli DNA replication, a ___ of ___ _____ __ is at the replication fork and performs most of the DNA replication in the cell. One portion of it replicates the ____ ___ and the other replicates the ____ ____.

A
  • dimer
  • DNA Polymerase III
  • leading strand
  • lagging strand
29
Q

Leading strand synthesis is ___, so the lagging strand template sometimes ____ ____ in a ____-like fashion when the lagging strand replication ____ ____.

A
  • faster
  • loops out
  • trombone
  • falls behind
30
Q

Proteins near replication fork include:

A

primase, SSB, DNA gyrase, , Pol I, DNA ligase, and helicase

31
Q

Primase:

A

makes RNA primers necessary for the DNA polymerase to act on

32
Q

SSB:

A

single stranded binding protein - protects single-stranded DNA and interacts with the replication proteins

33
Q

DNA gyrase

A

topoisomerase II - relieves the superhelical tension created by helicase

34
Q

Pol I

A

removes RNA primers

35
Q

DNA ligase

A

joins DNA fragments together by catalyzing synthesis of phosphodiester bonds at nick sites

36
Q

helicase

A

unwinds double helix

37
Q

As DNA polymerase I’s exonuclease removes RNA primers at the front end of the enzyme, what does DNA polymerase do?

A

It fills in the space behind it and moves along.

38
Q

____ will cause double strands to ___ ___ each other and thus allow the DNA helix to go back to approximately ___ base pairs per turn.

A
  • Supercoiling
  • twist over
  • 10.5
39
Q

Topoisomerases come in two types:

A

Type I and Type II

40
Q

Topoisomerase Type I enzymes act by ___ ___ strand, ____ the number of twists, and then ____ the _____ bond.

A
  • cutting one
  • altering
  • remaking
  • phosphodiester
41
Q

Type II topoisomerases (DNA gyrase is an example) act by ___ ___ strands, ____ the number of twists, and then ______ ____ phosphodiester bonds.

A
  • cutting both
  • altering
  • re-sealing both
42
Q

Drugs that ____ topoisomerases can be effective antibiotics. Examples include ____ ___ and _____.

A
  • inhibit
  • naladixic acid
  • ciprofloxacin
43
Q

The linking number (L) of a DNA is the sum of:

Thus the equation is:

A

the number of twists (T) of a DNA plus the number of writhes (W).
-L= T+W

44
Q

The twists are the number of:

The writhe is the number of:

A
  • times two the two helices cross each other.

- superhelical turns found in a DNA.

45
Q

Writhes can be ____ or ____ and in either case, when the W is a non-zero value, the molecule is said to be ____ = to have _____.

A
  • positive
  • negative
  • superhelical
  • superhelicity
46
Q

Writhing of DNA occurs in an attempt by a DNA molecule to:

A

-relax

47
Q

A DNA molecule is relaxed when its number of base pairs (bp) per twist (T) is that of __-___ (___-___ bp per turn).

A
  • B-DNA

- 10.4-10.5

48
Q

If one takes a circular DNA, opens it and removes two twists from it and then closes it, the number of twists will ____, but the number of base pairs ___ __ ___.

A
  • decrease

- remains the same

49
Q

If the number of twists decrease but the number of base pairs stay the same, the number of base pairs per twist will:

A

Increase

50
Q

Increase in number of base pairs per twist causes a ____ that is relieved by the DNA ___ ___ ___. This will cause the ____ to compensate by forming two negative superhelical turns, giving W a value of negative two. Note that the ____ number remains the same.

A
  • tension
  • twisting two turns
  • writhe
  • negative
  • negative two
  • linking
51
Q

On the other hand if one takes a circular DNA, opens it and adds twists to it and then closes it, the number of twists will ____, but the number of base pairs ___ ___ ___. In this case, the numbers of bp per twist will _____.

A
  • increase
  • remains the same
  • decrease
52
Q

If base pairs per twists decrease, DNA will relax by _____ ___ ____, which will cause the ___ increase to a value of ____ ___.

A
  • untwisting two turns
  • writhe
  • positive two
53
Q

Initiation of replication in E. coli occurs at a specific site on the E. coli genomic DNA, known as:

A

OriC, in the cell’s circular chromosome.

54
Q

The OriC site contains three repeats of what? near what?

A

AT rich sequence near some sequences bound by the DNA A protein.

55
Q

Replication initiation begins with:

A

binding of the several copies of the dnaA protein to the OriC site.

56
Q

Bending and wrapping of the DNA around dnaA proteins causes the AT-rich sequences noted above to become:

A

single-stranded.

57
Q

Once sequences become single stranded, the ____ ____ binds the ____ ____ (____) to each of the single strands in ____ orientations. The ___ protein is released in the process.

A
  • dnaBC complex
  • dnaB protein (helicase)
  • opposite
  • dnaC
58
Q

After dnaC protein is released, ___ and ____ bind the exposed single-stranded regions and cause ___ ____ to be released.

A
  • SSB
  • primase
  • DNA-A protein
59
Q

After DNA-a protein is released, the ____ begin synthesizing RNA primers (remember - 5’ to 3’ RNA synthesis only also) in _____ directions on each strand.

A
  • primases

- opposite

60
Q

The primases __ __ require a _____ ____ to function.

A
  • do not

- pre-existing primer

61
Q

Eukaryotic chromosomes differ from prokaryotic DNAs in being ____. The linear ends of the chromosomes are called _____.

A
  • linear

- telomeres

62
Q

Telomeric sequences have:

A

thousands of copies of repeats of short sequences.

63
Q

The enzyme that builds telomeres is called? and is found?

A

telomerase and is found predominantly in fetal and cancer cells, as well as fertilized eggs.

64
Q

Differentiated cells for the most part do not appear to have an:

A

active telomerase.

65
Q

With each round of DNA replication, linear chromosomes in eukaryotes ____. Thus, the more telomeric sequences a chromosome has, the ____ divisions it can undergo before the telomeres are “eaten up”.

A
  • shorten

- more

66
Q

Telomerase is a:

A

reverse transcriptase

67
Q

What is a reverse transcriptase?

A

an enzyme that uses an RNA template (a circular RNA that it carries) to synthesize DNA.

68
Q

Other reverse transcriptases are found:

A

in retroviruses, such as HIV.

Biochem 451 Exam 2 (6 decks)

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