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biochem lec > Replication of DNA > Flashcards

Replication of DNA Flashcards

1
Q

The DNA in the chromosomes carries out two functions:

A
  • It reproduces itself. This process is called
    replication.
  • It supplies the information necessary to make all
    the RNA and proteins in the body, including enzymes.
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2
Q

The sequence of bases in DNA encodes _________

A

genetic information

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3
Q

The duplication of DNA, giving rise to a new DNA molecule with the same base sequence as the original, is necessary whenever a cell divides to produce daughter cells. This duplication process is called __________

A

replication

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4
Q

The actual formation of gene
products requires RNA; the production of RNA on a DNA template is called _______________

A

transcription

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5
Q

The process by
which the base sequence directs the amino acid sequence is called ____________

A

translation

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6
Q

In some viruses, RNA can direct its own synthesis as well as that of DNA. What enzyme____________ catalyzes this process.

A

reverse transcriptase

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7
Q

Virus which RNA, rather than DNA, is the genetic
material.

A

retroviruses

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8
Q

the cell also must protect the unwound portions of DNA from the action of __________ that preferentially attack single-stranded
DNA.

A

nucleases

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9
Q

the mode in which DNA reproduces itself, such that
one strand comes from parent DNA and the other strand is newly formed

A

semiconservative replication

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10
Q

the point at which the
DNA double helix begins to unwind at the start of replication

A

origin of replication

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11
Q

in DNA replication, the
points at which new DNA strands are formed

A

replication forks

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12
Q

A ___________ of newly synthesized DNA between regions of the original
DNA is a manifestation of the advance of the two replication forks in opposite directions.

A

“bubble”

also called an “eye”

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13
Q

synthesis can take place in both directions from the origin of replication

A

bidirectional

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14
Q

All synthesis of nucleotide chains occurs in the ________ from the perspective of the chain being synthesized.

A

5’ to 3’ direction

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15
Q

Each gene is a section of a DNA molecule that contains a specific sequence typically comprising about

A

1000 to 2000 nucleotides.

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16
Q

One of the syntheses is continuous along the 3’-to-5’ strand

A

leading strand

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17
Q

Along the other strand that runs in the 5’¡3’ direction, the synthesis is discontinuous.

A

lagging strand

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18
Q

carries the information necessary to produce one protein
or RNA molecule

A

base sequence of a gene

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19
Q

The actual reaction occurring is a nucleophilic attack by the ________ of the deoxyribose of one nucleotide against the _________ on the 5’ carbon of the incoming nucleoside triphosphate

A
  • 3’-hydroxyl
  • first phosphate
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20
Q

DNA Replication steps

During replication, the very condensed superstructure of chromosomes must be opened so that it becomes accessible to enzymes and other proteins. What mechanism accomplishes this feat?

Opening Up the Superstructure

A

signal transduction mechanism

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21
Q

DNA Replication steps

One notable step of the
signal transduction is the ________ and ________ of key lysine residues of histones.

Opening Up the Superstructure

A

acetylation and deacetylation

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22
Q

DNA Replication steps

an enzyme, puts acetyl
groups on key lysine residues, some positive charges are eliminated and the strength of the DNA–histone interaction is weakened

. Opening Up the Superstructure

A

histone acetylase

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23
Q

DNA Replication steps

removes these acetyl groups, the positive charges are reestablished. That, in turn, facilitates regaining the highly condensed structure of chromatin.

. Opening Up the Superstructure

A

histone deacetylase

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24
Q

DNA Replication steps

are enzymes that facilitate the relaxation of supercoiling in DNA.

Relaxation of Higher-Order Structures of DNA

A

Topoisomerases
(also called gyrases)

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25
Q

DNA Replication steps

The transient break forms a phosphodiester bond between a __________ of the enzyme and either the _____________ on the DNA.

Relaxation of Higher-Order Structures of DNA

A
  • tyrosyl residue
  • 5’ or 3’ end of a phosphate
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26
Q

DNA Replication steps

are also involved in the untangling of the replicated chromosomes, before cell division can occur.

Relaxation of Higher-Order Structures of DNA

A

Topoisomerases

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27
Q

DNA Replication steps

Special unwinding protein molecules, called ______ attach themselves to one DNA strand and cause the separation of the double helix.

Unwinding the DNA Double Helix

A

helicases

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28
Q

DNA Replication steps

Helicases of eukaryotes are made of how many protein subunits?

Unwinding the DNA Double Helix

A

six

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29
Q

DNA Replication steps

How long are primers

Primers/Primases

A

4 to 15 nucleotides long

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30
Q

DNA Replication steps

RNA
oligonucleotides synthesized from ribonucleoside triphosphates

Primers/Primases

A

Primers

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31
Q

DNA Replication steps

form complexes with DNA polymerase in eukaryotes.

Primers/Primases

A

Primases

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32
Q

DNA Replication steps

The enzyme catalyzing this synthesis of both daughter strands

Primers/Primases

A

Primases

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33
Q

DNA Replication steps

Primers are placed about
every _______ in the lagging-strand synthesis.

Primers/Primases

A

50 nucleotides

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34
Q

DNA Replication steps

DNA Polymerase surrounds the end of the ___________, creating a specifically shaped pocket for the incoming nucleotide.

DNA Polymerase

A

DNA template– primer complex

35
Q

DNA Replication steps

While the bases of the newly arrived nucleotides are being hydrogen-bonded to their partners, polymerases join the ____________

DNA Polymerase

A

nucleotide backbones.

36
Q

DNA Replication steps

Short DNA segments made of about 20 nucleotides in higher organisms eukaryotes) and of 2000 nucleotides
in prokaryotes

DNA Polymerase

A

Okazaki fragments

37
Q

DNA Replication steps

The Okazaki fragments and any nicks remaining are eventually joined together by another enzyme,

Ligation

A

DNA ligase

38
Q

Components of Replisomes and Their Functions

Unwinds the DNA double helix

A

Helicase

39
Q

Components of Replisomes and Their Functions

Synthesizes short oligonucleotides (primers)

A

Primase

40
Q

Components of Replisomes and Their Functions

Allows the leading strand to be threaded through

A

Clamp protein

41
Q

Components of Replisomes and Their Functions

Joins the assembled nucleotides

A

DNA polymerase

42
Q

Components of Replisomes and Their Functions

Joins Okazaki fragments in the lagging strand

A

Ligase

43
Q

Components of Replisomes and Their Functions

Protects the single-stranded regions from degradation
during replication

A

Single-stranded binding
protein (SSB)

44
Q

the protein whose binding
prepares for the start of DNA
replication in eukaryotes

A

Replication activator proteins (RAP)

45
Q

When a cell divides into two each of the two cells has one or has retained one of the original (template strands) and one of
the new strands (daughter strands) that will partner with the leading strands through the complementary base pairing and now there will be 2 daughter DNAs

A

semi conservative replication

46
Q

all synthesis of nucleotide chains occurs in the 5’ to 3’ direction from the perspective of the chain being synthesized.

A

semi discontinuous DNA replication

47
Q

The 5 DNA Polymerases in Prokayotes

involved in
proofreading and repair processes

A

DNA Polymerase 1 & 2

48
Q

The 5 DNA Polymerases in Prokayotes

replaces the primer with
deoxynucleotide (deoxy as it is in DNA and the sugar present is deoxyribose)

A

Polymerase 1

49
Q

The 5 DNA Polymerases in Prokayotes

principal enzyme responsible for the synthesis of new DNA or
new daughter strands of DNA and it is a multi-subunit enzyme

A

DNA Polymerase 3

50
Q

The 5 DNA Polymerases in Prokayotes

Not studied extensively

A

DNA Polymerase 4 & 5

51
Q

The primer and the protein at the replication fork as a whole are called

A

primosome

52
Q

The entire complex including the DNA polymerase (important roles of DNA polymerase 1&3) is what you call the

A

replisome

53
Q

In what phase of the Eukaryotic cell cycle does DNA Replication occur?

A

S phase

54
Q

5 DNA polymerases

5 DNA polymerases in eukaryotes

A
  • Alpha
  • Beta
  • Gamma
  • Theta
  • Epsilon
55
Q

5 DNA polymerases

Principal synthesizer of DNA and is equivalent to Polymerase III in
prokaryotes.

A

Gamma

56
Q

. ERRORS IN DNA REPLICATION

There is a fidelity in the binding of the base pairs. But there are occasions, due to tear and wear, where some _______ could happen during base-pairing, as well as in transcription and translation.

A

mutations

57
Q

. ERRORS IN DNA REPLICATION

The viability of cells depends on ________ that can detect, recognize, and remove mutations from DNA

A

DNA repair enzymes

58
Q

. ERRORS IN DNA REPLICATION

Externally, ________ or ________, may damage a base.

A
  • UV radiation
  • highly reactive oxidizing agents (superoxide)
59
Q

. ERRORS IN DNA REPLICATION

Errors in copying or internal chemical reactions, such as _________ can create damage internally

A

deamination of a base

60
Q

. ERRORS IN DNA REPLICATION

Deamination of cytosine turns it into ______, which creates a mismatch.

A

uracil

61
Q

. ERRORS IN DNA REPLICATION

One of the most common base repairs prepare means is called

A

BER (Base Excision Repair)

62
Q

. ERRORS IN DNA REPLICATION

It is the job of Polymerase I and III, but sometimes during the proofreading by codons (by 3s), these commit mistakes

Kinds of Mutation

A

spontaneous mutation.

63
Q

. ERRORS IN DNA REPLICATION

The result of error in natural biological
processes.

Kinds of Mutation

A

SPONTANEOUS MUTATION

64
Q

. ERRORS IN DNA REPLICATION

This mutation is due to chemical agents and could be physical agents in the environment that can cause change in the DNA structure

Kinds of Mutation

A

INDUCED MUTATION

65
Q

. ERRORS IN DNA REPLICATION

Physical agents such as heat and UV
radiation can cause this mutation

Kinds of Mutation

A

INDUCED MUTATION

66
Q

. ERRORS IN DNA REPLICATION

UV is known to give ____________, so instead of the regular binding (A-T), it now becomes T-T, causing now an intercalation leading to the cancer of the skin.

Kinds of Mutation

A

thymine-thymine dimer

67
Q

. ERRORS IN DNA REPLICATION

Chemical agents such as benzo-(a)-pyrene which you can get from the charred portion of broiled meat and fish can cause this mutation

Kinds of Mutation

A

INDUCED MUTATION

68
Q

. ERRORS IN DNA REPLICATION

It is a good intercalating agent as it inserts into the DNA base-pairing.

Kinds of Mutation

A

benzo-(a)-pyrene

69
Q

. ERRORS IN DNA REPLICATION

If it happens during S phase of the replication, then now you can perpetuate the mutations and can come up with different products.

Kinds of Mutation

A

benzo-(a)-pyrene

70
Q

. ERRORS IN DNA REPLICATION

Due to oxidizing agents one of the commonest types of mutation would be _______ and _______

Kinds of Mutation

A

depurination and deamination

71
Q

. ERRORS IN DNA REPLICATION

(removal of the amino groups from the bases) of the pyrimidine and purine bases.

Kinds of Mutation

A

deamination

72
Q

. ERRORS IN DNA REPLICATION

can be caused by
depurination and deamination reaction.

Kinds of Mutation

A

Spontaneous mutation

73
Q

. ERRORS IN DNA REPLICATION

is the kind of intervention of the
glycosidic bond linkage due to chemical instability of the purine and pyrimidine bases.

Kinds of Mutation

A

Depurination

74
Q

BASE EXCISION REPAIR (BER)

Important enzymes in part 1

A
  1. DNA glycolase
  2. Endonuclease
  3. Exonuclease
75
Q

BASE EXCISION REPAIR (BER)

Important enzymes in part 2

A
  1. DNA polymerase
  2. DNA ligase
76
Q

BASE EXCISION REPAIR (BER)

Recognizes the damaged base and catalyzes hydrolysis of B-glycosidic bond between the base and deoxyribose.

A

DNA glycolase

77
Q

BASE EXCISION REPAIR (BER)

The sugar-phosphate backbone here is
still intact.

A

DNA glycolase

77
Q

BASE EXCISION REPAIR (BER)

releases the damaged base completing the excision (like scissors)

A

DNA glycolase

78
Q

BASE EXCISION REPAIR (BER)

cleaves the backbone at the AP (apurinic or apyrimidinic site)

A

Endonuclease

79
Q

BASE EXCISION REPAIR (BER)

Helps in the excision repair of the sugarphosphate backbone to separate the apurinic and apyrimidinic site

A

Endonuclease

80
Q

BASE EXCISION REPAIR (BER)

Liberates the sugar-phosphate unit of the
damaged size.

A

Exonuclease

81
Q

BASE EXCISION REPAIR (BER)

inserts the correct nucleotide,
becoming an automatic repair system that detects the occurrence of a mutation and it
instantaneously repair through the insertion of the correct nucleotide (such as cytidine for
example)

A

DNA
polymerase

82
Q

BASE EXCISION REPAIR (BER)

seals the backbone to complete the repair

A

DNA ligase

biochem lec (10 decks)

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