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BIOL 207 Lecture (Genetics: A conceptual Approach 6th/7th Ed) > Chapter 12 > Flashcards

Chapter 12 Flashcards

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1
Q

How many bands of DNA would be expected in Meselson and Stahls experiment after two rounds of conservative replication?

A

2 bands

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2
Q

the segment of DNA that undergoes replication is called the:

A

Replicon

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3
Q

Each replicon contains and origin of replication, what is that?

A

Site where DNA replication is initiated

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4
Q

How do bacterial chromosomes and eukaryotic chromosomes differ in origin of replication?

A

bacterial chromosomes have one while eukaryotic chromosomes have many

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5
Q

what is theta replication?

A

Replication of circular DNA that is initiated by the unwinding of the two nucleotide strands, producing a replication bubble. Unwinding continues at one or both ends of the bubble, making it progressively larger. DNA replication on both of the template strands is simultaneous with unwinding until the two replication forks meet.

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6
Q

Theta replication is the replication of DNA that is initiated by , producing a . Unwinding continues at one or both ends of the bubble, making it progressively larger. DNA replication on both of the template strands is with unwinding until the two replication forks meet.

A

Theta replication is the replication of circular DNA that is initiated by the unwinding of the two nucleotide strands, producing a replication bubble. Unwinding continues at one or both ends of the bubble, making it progressively larger. DNA replication on both of the template strands is simultaneous with unwinding until the two replication forks meet.

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7
Q

what is bidirectional replication?

A

replication at both ends of the replication bubble

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8
Q

What is rolling circle replication?

A

Replication of circular DNA that is initiated by a break in one of the nucleotide strands, producing a double-stranded circular DNA molecule and a single-stranded linear DNA molecule, the latter of which may circularize and serve as a template for the synthesis of a complementary strand.

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9
Q

What initiates rolling circle replication?

A

a break in one of the nucleotide strands which exposes a 3’OH group and a 5’phosphate group

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10
Q

After the 3’OH is exposed in rolling circle replication, what happens?

A

New nucleotides are added to the 3’ end of the broken strand using the inner (unbroken) strand as a template

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11
Q

In rolling circle replication, as new nucleotides are being added to the 3’ end of the broken strand, what happens to the 5’ end?

A

the 5’ end is displaced from the template “rolling out like thread being pulled from a spool”

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12
Q

What are the enzymes that synthesise DNA called?

A

DNA polymerases

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13
Q

What three groups of components are required for the process of replication?

A
  1. A template consisting of single-stranded DNA
  2. Raw materials (substrates) to be assembled into a new nucleotide strand
  3. Enzymes and other proteins that “read” the template and assemble the substrates into a DNA molecule
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14
Q

Because of the semiconservative nature of DNA replication, a double-stranded DNA molecule must ______ to expose the bases that act as a template for assembly of new polynucleotide strands, which will be ______ and _____ to the template strands

A

Because of the semiconservative nature of DNA replication, a double-stranded DNA molecule must unwind to expose the bases that act as a template for assembly of new polynucleotide strands, which will be complementary and antiparallel to the template strands

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15
Q

The raw materials from which new DNA molecules are synthesized are called ________

A

The raw materials from which new DNA molecules are synthesized are called deoxyribonucleoside triphosphates (dNTPs)

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16
Q

What do deoxyribonucleoside triphosphates (dNTPs) consist of?

A

a nucleoside (deoxyribose sugar and a base) attached to 3 phosphate groups

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17
Q

In DNA synthesis, nucleotides are added to the _________ of the growing nucleotide strand (Figure 12.7b). The 3′-OH group of the last nucleotide on the strand attacks the ________ of the incoming dNTP.

Two phosphate groups are cleaved from the incoming _____, and a ______ bond is created between the two nucleotides.

A

In DNA synthesis, nucleotides are added to the 3′-OH group of the growing nucleotide strand (Figure 12.7b). The 3′-OH group of the last nucleotide on the strand attacks the 5′-phosphate group of the incoming dNTP.

Two phosphate groups are cleaved from the incoming dNTP, and a phosphodiester bond is created between the two nucleotides.

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18
Q

Concept check:

DNA synthesis requires a ____ _____ DNA template, ______ _______, a growing _______ strand, and a group of ______ and ______

A

DNA synthesis requires a single-stranded DNA template, deoxyribonucleoside triphosphates (dNTPs), a growing nucleotide strand, and a group of enzymes and proteins

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19
Q

Because two template strands of DNA are antiparallel, and DNA synthesis is always 5’ to 3’:

DNA synthesis takes place from _____ to _____ on one strand

and

_____ to _____ on the other strand.

A

Because two template strands of DNA are antiparallel, and DNA synthesis is always 5’ to 3’:

DNA synthesis takes place from left to right on one strand

and

right to left on the other strand.

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20
Q

The DNA template strand that is exposed in the 3’ to 5’ direction allows the new strand to be synthesized continuously (in the 5’ to 3’ direction) and is called the:

A

Leading strand

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21
Q

What is continuous replication?

A

Replication of the leading strand (exposed 3’ to 5’) in the same direction as that of unwinding, allowing new nucleotides to be added continuously to the 3’ end of the new strand as the template is exposed

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22
Q

What is the lagging strand of DNA?

A

DNA strand that is replicated discontinuously:

  • strand exposed 5’ to 3’, short length of DNA is unwound - synthesis proceeds 5’ to 3’ (opposite unwinding)
  • replication machinery runs out of template
  • more DNA is unwound = new template at the 5’ end
  • short discontinuous bursts of synthesis
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23
Q

The short lengths of DNA produced by discontinuous replication of the lagging strand are called:

A

Okazaki fragments

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24
Q

Concept Check:

Discontinuous replication is the result of which property of DNA?

a) complementary bases
b) charged phosphate group
c) Antiparallel nucleotide strands
d) Five-carbon sugar

A

Concept Check:

Discontinuous replication is the result of which property of DNA?

a) complementary bases
b) charged phosphate group

c) Antiparallel nucleotide strands

d) Five-carbon sugar

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25
What are the four stages of Replication?
1. initiation 2. unwinding 3. elongation 4. termination
26
Proteins that bind to the origin of replication and cause a short section of DNA to unwind (allowing helicase and other proteins to attach) are called:
Initiator Proteins
27
\_\_\_\_\_\_\_ is an enzyme that breaks the hydrogen bonds that exist between the bases of the two nucleotide strands in a DNA molecule, thus serving to **unwind** the double-stranded DNA
_DNA Helicase_ is an enzyme that breaks the hydrogen bonds that exist between the bases of the two nucleotide strands in a DNA molecule, thus serving to **unwind** the double-stranded DNA
28
In bacteria, helicase cannot ______ the unwinding of double-stranded DNA; the ____ \_\_\_\_\_ must first separate DNA strands at the origin
In bacteria, helicase cannot _initiate_ the unwinding of double-stranded DNA; the _initiator protein_ must first separate DNA strands at the origin
29
After DNA has been unwound by helicase, ___________ attach tightly to the exposed single-stranded DNA to protect the single-stranded nucleotide chains and prevent the formation of secondary structures (eg hairpins) that would interfere with replication
After DNA has been unwound by helicase, _single-strand-binding proteins (SSBs)_ attach tightly to the exposed single-stranded DNA to protect the single-stranded nucleotide chains and prevent the formation of secondary structures (eg hairpins) that would interfere with replication
30
What are Single-strand-binding proteins (SSBs)?
Proteins that attach tightly to the exposed single-stranded DNA during replication and prevent the formation of secondary structures that would interfere with replication
31
\_\_\_\_\_\_\_ control the supercoiling of DNA
_Topoisomerases_ control the supercoiling of DNA
32
\_\_\_\_\_ ______ (a topoisomerase in E.coli) relieves the torsional strain that builds up ahead of the replication fork ie. reduces the torque that builds up as a result of unwinding
_DNA Gyrase_ (a topoisomerase in E.coli) relieves the torsional strain that builds up ahead of the replication fork ie. reduces the torque that builds up as a result of unwinding
33
How does DNA gyrase relieve the torsional strain? Include: * effect on supercoiling * energy-dependent or independent
DNA gyrase reduces the torque by making a double-strand break in one segment of the DNA helix, passing another segment of the helix through the break, and then resealing the broken ends of the DNA. This action, which **requires ATP**, removes a twist in the DNA and **reduces the supercoiling**
34
What is the difference between the two major types of topoisomerase?
1. Type I: alter supercoiling by making single-strand breaks in DNA 2. Type II: create double-strand breaks
35
Place the following components in the order in which they are first used in the course of replication: helicase; single-strand-binding proteins; DNA gyrase; initiator protein
1. initiator protein 2. helicase 3. single-strand-binding protein 4. DNA gyrase
36
What do all DNA polymerases require in order to add new nucleotides?
A nucleotide with a 3'-OH group to which new nucleotides can be added
37
What enzyme provides the 3'OH group that is required by DNA polymerases?
Primase
38
What is Primase?
An enzyme that synthesizes a short stretch of RNA on a DNA template - called **primers** Provides a 3'-OH group for the attachment of a DNA nucleotide
39
All newly synthesised DNA molecules have short _______ embedded within them that are later removed and replaced with DNA nucleotides
All newly synthesised DNA molecules have short _RNA Primers_ embedded within them that are later removed and replaced with DNA nucleotides
40
On the leading strand at a replication fork (where DNA synthesis is \_\_\_\_\_\_), a primer is required only at the _____ end. On the lagging strand (where DNA synthesis is \_\_\_\_\_\_) a new primer must be generated at the beginning of each \_\_\_\_\_\_\_
On the leading strand at a replication fork (where DNA synthesis is _continuous_), a primer is required only at the _5'_ end. On the lagging strand (where DNA synthesis is _discontinuous_) a new primer must be generated at the beginning of each _Okazaki fragment_
41
Where are primers synthesized on the **lagging** strand?
At the beginning of every okazaki fragment
42
After DNA has unwound and a primer has been added, DNA polymerases elongate the new polynucleotide strand by catalyzing ________ \_\_\_\_\_\_\_
After DNA has unwound and a primer has been added, DNA polymerases elongate the new polynucleotide strand by catalyzing _DNA Polymerization_
43
All of E.coli's DNA polymerases share 7 common features:
1. synthesize any sequence specified by the template strand 2. synthesize in the 5' to 3' direction by adding nucleotides to a 3'-OH group 3. use dNTPs to synthesize new DNA 4. Require a 3'OH group to initiate synthesis 5. catalyze the formation of a phosphodiester bond by joining the 5'phosphate group of the incoming nucleotide to the 3' OH group of the preceding nucleotide (cleaving off 2 phosphates in the process) 6. produce newly synthesized strands that are complementary and antiparallel to the template strands 7. are associated with a number of other proteins
44
What is the function of an initiator protein (simplified)
Bind to origin and separate strands of DNA to initiate replication
45
What is the function of DNA helicase (simplified)
Unwind DNA at the replication fork
46
What is the function of Single-strand-binding proteins (simplified)
Attach to single-stranded DNA and prevent secondary structures from forming
47
What is the function of DNA gyrase?
Moves ahead of the replication fork, making and resealing breaks in the double-helical DNA to release the torque that builds up as a result of unwinding at the fork
48
What is the function of DNA primase?
Synthesize a short RNA primer to provide 3'OH group for the attachment of DNA nucleotides
49
What is the function of DNA Polymerase III
Elongates new nucleotide strand from the 3'OH group provided by the primer
50
What is the function of DNA polymerase I
Remove RNA primers and replaces them with DNA
51
What is the function of DNA ligase?
Joins okazaki fragments by sealing breaks in the sugar-phosphate backbone of newly synthesized DNA
52
Which bacterial enzyme removes the primers?
DNA polymerase I
53
What are the 5 basic functions required by each active replication fork?
1. Helicase to unwind the DNA 2. Single-strand-binding proteins to protect the single nucleotide strands 3. DNA gyrase to remove strain ahead of the replication fork 4. Primase to synthesize primers with a 3'OH group at the beginning of each DNA fragment 5. DNA polymerase to synthesize the leading and lagging nucleotide strands
54
Most of the errors that do arise in nucleotide selection are corrected in a second process called \_\_\_\_\_\_
Proofreading
55
Define proofreading
Process by which DNA polymerases remove and replace incorrectly paired nucleotides in the course of replication
56
How does proofreading work?
* DNA polymerase inserts wrong nucleotide * the 3'OH group of mispaired nucleotide is incorrectly positioned in active site of DNA polymerase = can't accept next nucleotide * stalls polymerization * the 3' → 5' exonuclease activity of DNA polymerase removes the incorrectly paired nucleotide * inserts correct nucleotide
57
In some DNA molecules, replication is terminated whenever _____ \_\_\_\_\_ _____ \_\_\_\_. In others, specific _____ \_\_\_\_\_ called (\_\_\_\_ sites) block further replication
In some DNA molecules, replication is terminated whenever _two replication forks meet_. In others, specific _termination sequences_ called (*_Ter_* sites) block further replication
58
The process, _________ corrects errors after replication is complete
Mismatch pair
59
What is Mismatch Repair?
Process that corrects mismatched nucleotides in DNA after replication has been completed Enzymes excise incorrectly paired nucleotides from the newly synthesized strand and use the original nucleotide strand as a template for replacing them
60
In E. coli, how does mismatch repair distinguish between the old and new strands of DNA?
Methyl groups are added to a particular nucleotide sequences *after* replication - thus, immediately after DNA synthesis, only the old DNA strand is methylated
61
There are 8 basic rules of Replication: 1. Replication is always \_\_\_\_\_\_\_ 2. Replication begins at sequences called ____ \_ \_\_\_\_\_ 3. DNA synthesis begins with the synthesis of short RNA sequences called \_\_\_\_\_\_ 4. Elongation of DNA always occurs in the _____ direction 5. New DNA is synthesized from \_\_\_\_\_; in the polymerization of DNA, two ______ groups are cleaved from _____ and the resulting nucleotide is added to the _____ group of the growing nucleotide strand 6. Replication is ______ on the leading strand and ______ on the lagging strand 7. New nucleotide strands are ______ and ______ to their template strands 8. Replication takes place at very high rates and is astonishingly accurate thanks to precise \_\_\_\_\_\_, ______ and \_\_\_\_\_\_
There are 8 basic rules of Replication: 1. Replication is always _semiconservative_ 2. Replication begins at sequences called _origins of replication_ 3. DNA synthesis begins with the synthesis of short RNA sequences called _primers_ 4. Elongation of DNA always occurs in the _5' to 3'_ direction 5. New DNA is synthesized from _dNTPs (deoxyribonucleotide triphosphate)_; in the polymerization of DNA, two _phosphate_ groups are cleaved from _dNTP_ and the resulting nucleotide is added to the _3'-OH_ group of the growing nucleotide strand 6. Replication is _continuous_ on the leading strand and _discontinuous_ on the lagging strand 7. New nucleotide strands are _antiparallel_ and _complementary_ to their template strands 8. Replication takes place at very high rates and is astonishingly accurate thanks to precise _nucleotide selection_, _proofreading_ and _mismatch repair_
62
Eukaryotic chromosomes are _____ and thus have ends
Eukaryotic chromosomes are _linear_ and thus have ends
63
What is the "end-Replication problem"?
In eukaryotic DNA replication, there are multiple origins of replication - the elongation of DNA in adjacent replicons provides a 3'OH group preceding each primer. At the very end of a linear chromosome, there isn't an adjacent stretch to provide the 3'Oh Therefore, when the terminal primer is removed from the end, it leaves a gap on the end of the chromosome -suggests that chromosomes would get shorter with each round of replication
64
The ends of eukaryotic chromosomes - called ______ - possess several unique features, one of which is the presence of many copies of a ____ \_\_\_\_ ____ in humans this is \_\_\_\_\_\_
The ends of eukaryotic chromosomes - called _telomeres_ - possess several unique features, one of which is the presence of many copies of a _short-repeated sequence;_ in humans this is _TTAGGG_
65
The single-stranded protruding end of the telomere, known as the \_\_\_\_\_\_\_\_, can be extended by ______ an enzyme that has both protein and RNA component (ribonucleoprotein)
The single-stranded protruding end of the telomere, known as the _G-rich 3' overhang_, can be extended by _telomerase_ an enzyme that has both protein and RNA component (ribonucleoprotein)
66
What would be the result if an organisms telomerase were mutated and nonfunctional? a) no DNA replication would occur b) the DNA polymerase enzyme would stall at the telomere c) chromosomes would shorten with each new generation d) RNA primers could not be removed?
What would be the result if an organisms telomerase were mutated and nonfunctional? a) no DNA replication would occur b) the DNA polymerase enzyme would stall at the telomere **c) chromosomes would shorten with each new generation** d) RNA primers could not be removed?
67
There is strong evidence that telomere length is related to \_\_\_\_\_
There is strong evidence that telomere length is related to _aging_

BIOL 207 Lecture (Genetics: A conceptual Approach 6th/7th Ed) (9 decks)

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