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

Chapter 12 Flashcards

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
Q

What are the four stages of Replication?

A
  1. initiation
  2. unwinding
  3. elongation
  4. termination
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26
Q

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:

A

Initiator Proteins

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27
Q

_______ 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

A

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
Q

In bacteria, helicase cannot ______ the unwinding of double-stranded DNA; the ____ _____ must first separate DNA strands at the origin

A

In bacteria, helicase cannot initiate the unwinding of double-stranded DNA; the initiator protein must first separate DNA strands at the origin

29
Q

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

A

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
Q

What are Single-strand-binding proteins (SSBs)?

A

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
Q

_______ control the supercoiling of DNA

A

Topoisomerases control the supercoiling of DNA

32
Q

_____ ______ (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

A

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
Q

How does DNA gyrase relieve the torsional strain?

Include:

  • effect on supercoiling
  • energy-dependent or independent
A

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
Q

What is the difference between the two major types of topoisomerase?

A
  1. Type I: alter supercoiling by making single-strand breaks in DNA
  2. Type II: create double-strand breaks
35
Q

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

A
  1. initiator protein
  2. helicase
  3. single-strand-binding protein
  4. DNA gyrase
36
Q

What do all DNA polymerases require in order to add new nucleotides?

A

A nucleotide with a 3’-OH group to which new nucleotides can be added

37
Q

What enzyme provides the 3’OH group that is required by DNA polymerases?

A

Primase

38
Q

What is Primase?

A

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
Q

All newly synthesised DNA molecules have short _______ embedded within them that are later removed and replaced with DNA nucleotides

A

All newly synthesised DNA molecules have short RNA Primers embedded within them that are later removed and replaced with DNA nucleotides

40
Q

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 _______

A

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
Q

Where are primers synthesized on the lagging strand?

A

At the beginning of every okazaki fragment

42
Q

After DNA has unwound and a primer has been added, DNA polymerases elongate the new polynucleotide strand by catalyzing ________ _______

A

After DNA has unwound and a primer has been added, DNA polymerases elongate the new polynucleotide strand by catalyzing DNA Polymerization

43
Q

All of E.coli’s DNA polymerases share 7 common features:

A
  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
Q

What is the function of an initiator protein (simplified)

A

Bind to origin and separate strands of DNA to initiate replication

45
Q

What is the function of DNA helicase (simplified)

A

Unwind DNA at the replication fork

46
Q

What is the function of Single-strand-binding proteins (simplified)

A

Attach to single-stranded DNA and prevent secondary structures from forming

47
Q

What is the function of DNA gyrase?

A

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
Q

What is the function of DNA primase?

A

Synthesize a short RNA primer to provide 3’OH group for the attachment of DNA nucleotides

49
Q

What is the function of DNA Polymerase III

A

Elongates new nucleotide strand from the 3’OH group provided by the primer

50
Q

What is the function of DNA polymerase I

A

Remove RNA primers and replaces them with DNA

51
Q

What is the function of DNA ligase?

A

Joins okazaki fragments by sealing breaks in the sugar-phosphate backbone of newly synthesized DNA

52
Q

Which bacterial enzyme removes the primers?

A

DNA polymerase I

53
Q

What are the 5 basic functions required by each active replication fork?

A
  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
Q

Most of the errors that do arise in nucleotide selection are corrected in a second process called ______

A

Proofreading

55
Q

Define proofreading

A

Process by which DNA polymerases remove and replace incorrectly paired nucleotides in the course of replication

56
Q

How does proofreading work?

A
  • 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
Q

In some DNA molecules, replication is terminated whenever _____ _____ _____ ____.

In others, specific _____ _____ called (____ sites) block further replication

A

In some DNA molecules, replication is terminated whenever two replication forks meet.

In others, specific termination sequences called (Ter sites) block further replication

58
Q

The process, _________ corrects errors after replication is complete

A

Mismatch pair

59
Q

What is Mismatch Repair?

A

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
Q

In E. coli, how does mismatch repair distinguish between the old and new strands of DNA?

A

Methyl groups are added to a particular nucleotide sequences after replication - thus, immediately after DNA synthesis, only the old DNA strand is methylated

61
Q

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 ______
A

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
Q

Eukaryotic chromosomes are _____ and thus have ends

A

Eukaryotic chromosomes are linear and thus have ends

63
Q

What is the “end-Replication problem”?

A

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
Q

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 ______

A

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
Q

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)

A

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
Q

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?

A

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
Q

There is strong evidence that telomere length is related to _____

A

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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