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Biochemistry > Chapter 25: DNA Metabolism > Flashcards

Chapter 25: DNA Metabolism Flashcards

1
Q

TRUE/FALSE:

DNA is stable and not static

A

True

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2
Q

DNA metabolism includes the

processes of ____, _____, and ____

A

replication, repair, and recombination.

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3
Q

Proteins (sometimes Eukaryotic proteins) are usually written in Roman type and the first letter is capitalized. Example?

A

IspA, IspB, IspC, IspD, etc. (isoprene biosynthesis)

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4
Q

Bacterial genes (sometimes Eukaryotic genes) are written in lowercase italics, generally using three letters.

A

isp (isoprene biosynthesis)

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5
Q

If several bacterial genes are important for the same process, a fourth letter is added and it is capitalized.
Example?

A

ispA, ispB, ispC, ispD

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6
Q

DNA replication is_______ since each strand can act as a template for the synthesis of a perfect copy of the other strand.

A

semiconservative

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7
Q

What are the enzymes responsible for DNA replication?

A

DNA Polymerase

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8
Q

DNA Polymerase utilizes single stranded DNA

templates and adds nucleotides in what direction?

A

5’ to 3’

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9
Q

DNA molecule consists of one _____ and

one ____ .

A

old strand, new strand

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10
Q

replication “bubbles”

A

separation of two strands of DNA accompanied by synthesis of their complementary strands.

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11
Q

Origin of replication (oriC), a unique point, is where?

A

Replication always begins

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12
Q

Branch point in a replication bubble

A

Replication Fork

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13
Q

Most replication forks appear to be in what direction?

A

Bidirectional

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14
Q

New DNA base added to the ____ of the previously

added base

A

3’ OH

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15
Q

Semidiscontinuous Replication Model:

A
  • Leading strand, is continuously
    synthesized in the 5’ to 3’ direction.
  • Lagging strand, is synthesized in
    the 5’ to 3’ direction in a discontinuous manner.
  • DNA ligase is required to join the discontinuous Okazaki fragments together into a continuous piece of DNA.
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16
Q

Because both strands are REPLICATED

simultaneously _____

A

both strands cannot be SYNTHESIZED continuously

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17
Q

What 8 proteins are required in replication?

A
  1. Nucleases
  2. DNA topoisomerases
  3. Helicases to separate DNA at the replication fork.
  4. Proteins to prevent reannealing
  5. Primases to synthesize RNA primers
  6. DNA polymerase
  7. An enzyme to remove the RNA primers
  8. Ligase to link together Okazaki fragments
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18
Q

What nucleases remove DNA only from the

ENDS of DNA strands?

A

Exonucleases

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19
Q

Most exonucleases operate in WHAT direction(s) ?

A

5’→3’ or the 3’→5’
(Most polymerases have a 3’→5’ exonuclease
activity)

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20
Q

What nucleases degrade DNA from the interior of a DNA strand (hydrolyze the phosphodiester bond)?

A

Endonucleases

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21
Q

Most endonucleases cut DNA internally with what enzymes?

A

restriction enzymes

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22
Q

DNA Polymerase:
Synthesize _____
Adds the incoming ____ to the 3’ OH of the growing
chain, releasing ___ in the process.
• This is a favorable reaction due to the subsequent hydrolysis of PPi and the additional base stacking and base pairing interactions that
occur.
• DNA polymerase requires a template that it can copy; it cannot
synthesize random sequences of DNA on its own.
• It also requires a primer with a free 3’-hydroxyl to which it can add
additional nucleotide bases. This primer generates a short
sequence of double stranded nucleotide. Most primers are actually
short stretches of RNA.
• After adding a nucleotide, the DNA polymerase can either move
along the strand and add the next base, or it can dissociate from the
strand.

A

DNA.

deoxyribonucleotide, PPi

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23
Q

What’s the name for dNTP?

A

Deoxynucleoside Triphosphate

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24
Q

DNA polymerase error rate is every

A

10^4 or 10^5

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25
E. coli error rate is every
10^9 or 10^10
26
Proofreading and increases accuracy by 102- to
remove incorrect bases
27
principle replication enzyme
DNA Polymerase III
28
responsible for a variety of clean up functions | during replication, recombination, and repair
DNA Polymerase II
29
DNA polymerase II, IV, and V
involved in DNA repair
30
DNA Polymerase I contains ___ exonuclease activity
5’→3’
31
Which DNA Polymerase removes a short stretch of RNA or DNA and replaces it with a new sequence of DNA (nick translation)?
DNA Polymerase I
32
What enzyme creates RNA primers on the Okazaki fragments in E. coli?
Primase
33
DNA polymerase III requires a _____ for | addition of the next nucleotide,
free 3’ hydroxyl
34
Okazaki fragments' 5’ ends consist of what?
RNA segments
35
In Prokaryotes, what DNA gyrase introduces negative supercoils (unwinding) into DNA replication, allowing the process to proceed
topoisomerase
36
What accessory proteins are needed to help DNA Pol III unwind?
DnaB helicase | Single-strand binding protein (SSB)
37
Can DNA Pol III unwind DNA?
No.
38
A hexameric ring is found in?
DNA Helicases
39
DnaB cycles between what three conformations?
NTP bound, hydrolysis, and release of products.
40
Single-Strand Binding Protein
Single stranded DNA (ssDNA) likes to anneal to form | dsDNA
41
DNA ligase is responsible for
ligating two pieces of DNA together to form a contiguous strand.
42
Energy for a DNA Ligase reaction is supplied by
either ATP hydrolysis to AMP + PPi or NAD+ hydrolysis to NMN+ + AMP
43
What are E. Coli replication steps?
initiation, elongation, and termination
44
Initiation takes place where?
Origin of replication (oriC)
45
Origin of replication (oriC) region denatures what and where?
which is an easily denatured 245 bp AT rich region
46
10 proteins involved in initiation?
1. DnaA 2. DnaB (Helicase) 3. DnaC protein 4. DnaG protein (Primase) 5. HU 6. FIS 7. IHF 8. Single-Strand DNA binding protein 9. DNA gyrase (topoisomerase II) 10. DAM methylase
47
Binding of an ATP-bound DnaA to the five 9 bp repeats in the origin. ....complex denatures DNA in the three 13 bp DUE sequences also located in the oriC. The DnaC protein then loads DnaB onto the unwound segment of DNA. The DnaB hexamers act as helicases and begin to unwind the DNA in both directions, creating the replication fork.
E. Coli Replication
48
The oriC DNA is methylated on N6 of adenine residues in the GATC sequences by Dam methylase. 11 of these sequences occur at the origin.
E. Coli Regulation
49
E. Coli Elongation requires synthesis of what?
synthesis of the leading strand and | the lagging strand
50
DNA helicases (DnaB) are required to unwind the DNA, with the resulting stress relieved by topoisomerases. SSB binds to the single strands. Primase (DnaG) then lays down short (10-60 nucleotide) RNA primers at the origin. DNA Pol III begins adding deoxyribonucleotides in a continuous fashion to create the leading strand. ... interacts with DnaB and travels along the replication fork
E. Coli Elongation
51
Synthesis of the next Okazaki fragment:
Okazaki fragment reaches the previous fragment, a | new  clamp loads onto the next primer and associates with the lagging strand polymerase.
52
Replisome
the complex of proteins located at the replication fork
53
When an Okazaki fragment | is completed, what occurs?
1) . DNA Pol I removes the RNA primer and replaces it with DNA. 2) . DNA ligase then seals the "nick" to make a contiguous piece of DNA.
54
The two replication forks make their way around the E. coli circular genome, eventually meeting on the other side. Multiple copies of a 20 bp termination sequence (Ter) are found at the opposite end; they trap the first replication fork to arrive. The other replication fork stops when it meets the first one and the few hundred bases between the forks are replicated by an unknown mechanism. Two circular chromosomes are interlinked (catenated). Topoisomerase IV separates the two chromosomes and they are segregated into daughter cells.
E. Coli Termination
55
TRUE/FALSE: Eukaryotic Replication is more complex than E. Coli and involves linear chromosomes.
True
56
TRUE/FALSE: Eukaryotic AND Prokaryotic replication have the same basic mechanism
True
57
Mutations
are permanent changes in the genomic nucleotide sequence
58
What can cause Mutations?
Base changes or the Addition/Deletion of base pairs
59
Silent mutations
Have no effect on gene function
60
Most mutations are what type of mutation?
Silent Mutations
61
Though essential, repair systems are _____ and use ____ __ ____.
inefficient, lots of energy
62
Why is DNA repair possible?
Opposite strand will (hopefully) encode the | correct sequence.
63
TRUE/FALSE: Mismatch Repair is a expensive process since 1000 bp or more may be hydrolyzed to repair a single mismatch.
True
64
When is the Mut Repair System required?
In prokaryotes, repair at sites distant from replication
65
MutL and MutS proteins form a complex and bind to the mismatch site (except C-C mismatches). MutH then binds to MutL and the three proteins thread the DNA through the complex. Once a hemimethylated GATC sequence is encountered, the unmethylated strand is cut by MutH, marking it as the strand for repair. DNA is unwound to the site of mismatch and the new strand is degraded. DNA is re-synthesized to generate a proper DNA copy.
Mismatch Repair
66
Mismatch Repair corrects DNA using the | sequence of the ___ ___.
template strand
67
In Mismatch Repair, we monitor methylation of what residues?
Adenine
68
Homologs of MutS
bind to DNA as dimers
69
Homologs of MutS
MSH2, MSH3, and MSH6
70
Homologs of MutL
stabilize MSH complexes
71
Homologs of MutL
MLH1 and PMS1
72
TRUE/FALSE: Defects in DNA repair proteins lead to increased susceptibility to cancer and other diseases.
True
73
TRUE/FALSE: Methylation of GATC residues is not used to identify newly synthesized DNA strands.
True
74
Which homologs have been identified in humans and not well known?
MutH
75
``` DNA lesions (modifications of a base) are fixed by ```
base-excision repair
76
DNA glycosylase removes damaged base by cleaving Nglycosyl bond. The deoxyribose 5’-phosphate left behind (apurine or apyrimidine site) is removed by an AP endonuclease. Removal often takes out a segment of DNA. DNA polymerase I replaces the removed DNA before DNA ligase seals the remaining "nick".
Base-Excision Repair
77
When is Nucleotide Excision Repair used?
repair large distortions in the helical structure of DNA
78
In Nucleotide Excision Repair, multisubunit enzyme ___ ____ (includes the Uvr proteins A, B, C, and D) hydrolyzes two phosphodiester bonds, one on either side of the distortion.
ABC excinuclease
79
What type of repair occurs when damage is repaired without having to remove the damaged base?
Direct Repair
80
When excessive DNA damage occurs, what type of repair in bacteria?
SOS Repair System
81
Which DNA Polymerase is activated in SOS Repair System?
DNA polymerase (pol V)
82
Though essential to the survival of the bacterial population, the SOS response leads to ___ __ ___
high error rates
83
What disease is associated with nucleotide excision repair?
Xeroderma pigmentosum (XP) :extremely light sensitive because they are unable to repair pyrimidine dimers formed by UV light absorption.
84
What mismatch repair genes are associated with Hereditary nonpolyposis colon cancer?
MLH1 and MSH2
85
What mutations account for 10% of known breast cancer cases?
BRCA1 and BRCA2 (involved in DNA maintenance and | repair)

Biochemistry (5 decks)

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