DNA replication and recombination (exam 2 - 1)

The amount of DNA that is replicated from a single origin of replication is referred to as a(n) ________.

replicon

DNA replication occurs by adding ________.

dNTPs to the 3' end of the daughter strand

Which terms accurately reflect the nature of replication of the chromosome in E. coli?

bidirectional and fixed point of initiation

DNA Pol III is believed to be responsible for removing the primer. T/F

false - DNA Pol I removes the primer

DNA Pol I, II, and III all possess 3' to 5' exonuclease activity. T/F

True

DNA Pol I, II, and III all possess 5' to 3' exonuclease activity. T/F

False - Only DNA Pol I

DNA synthesis in bacteria involves five DNA polymerases (DNA Pol). T/F

True

DNA polymerases can all perform 5' to 3' polymerization. T/F

True

DNA polymerases are important in various aspects of DNA repair. T/F

True - Especially DNA Pol I, II, IV, and V (1, 2, 4, 5)

DNA polymerases can all initiate DNA synthesis on a template on their own.T/F

False

Which activity of E. coli DNA polymerase I is responsible for proofreading the newly synthesized DNA?

3' to 5'; exonuclease

The protein responsible for the initial step in unwinding the DNA helix during replication of the bacterial chromosome is coded for by the ________ gene.

dnaA

During DNA replication, ________ are 1000-2000 nucleotide long strands synthesized on the ________ strand to maintain the ________ of replication.

Okazaki fragments; lagging; bidirectionality

Which enzyme is responsible for relieving the tension ahead of the fork that results when the DNA unwinds to form the replication "bubble" or "eye"?

DNA gyrase

Which of the following statements about DNA replication is true?

DNA synthesis is continuous on the leading strand and discontinuous on the lagging strand.

As unwinding of the helix occurs during DNA replication, tension referred to as ________ is created ahead of the replication fork. This tension is relieved by the action of ________.

supercoiling; DNA gyrase

Explain the need for, and action of, DNA gyrase in bacterial DNA replication.

_________ enzyme: ________ supercoiling (tension) in the parental DNA as it processes.

_________ enzyme: _________ this tension so that replication fork progression can continue without grinding to a halt.

DNA helicase; induces

DNA gyrase; relieves

The new DNA strand that grows continuously in the 5' to 3' direction is called the __________ .

leading strand

During DNA replication, an open section of DNA, in which a DNA polymerase can replicate DNA, is called a __________.

replication fork

The enzyme that can replicate DNA is called __________ .

DNA polymerase

After replication is complete, the strand of new DNA, called __________ , is complementary to the parental strand.

daughter DNA

__________ are the short sections of DNA that are synthesized on the lagging strand of the replicating DNA.

Okazaki fragments

When cells divide or multiply, the DNA must be copied, or replicated. All known organisms replicate their DNA by a method known as __________ , in which each of the two strands of the parent DNA becomes part of the daughter DNA.

semi-conservative replication

DNA replication in eukaryotes ________.

initiates at multiple origins

Chromatin is defined as ________.

DNA complexed with protein

Compare and contrast DNA replication in prokaryotes and eukaryotes.

Continuous on one strand and discontinuous on the other strand.

Prokaryotic and eukaryotic replication

Compare and contrast DNA replication in prokaryotes and eukaryotes.

The only replication origin in a chromosome

prokaryotic replication

Compare and contrast DNA replication in prokaryotes and eukaryotes.

Euchromatin and heterochromatin replicate at different times

eukaryotic replication

Compare and contrast DNA replication in prokaryotes and eukaryotes.

Long Okazaki fragments (about 1000 nucleotides)

eukaryotic replication

Compare and contrast DNA replication in prokaryotes and eukaryotes.

Multiple replication origins

eukaryotic replication

Compare and contrast DNA replication in prokaryotes and eukaryotes.

Bidirectional

prokaryotic replication

Compare and contrast DNA replication in prokaryotes and eukaryotes.

Short Okazaki fragments (about 100 nucleotides)

prokaryotic replication

The process of making DNA from an RNA template is referred to as ________.

reverse transcription

Which term describes a genetic exchange between two DNA molecules with substantial DNA sequence homology?

homologous recombination

The new DNA in the daughter strand is interspersed among the old pieces

dispersive

The old DNA is completely conserved

Conservative

Each daughter strand is composed of one old DNA strand and one new DNA strand

Semiconservative

Separation of the individual covalent, phosphodiester bonds is required for this mode of replication

Dispersive

The original DNA strand is broken into pieces

Dispersive

The original double helix remains as a complete unit

Conservative

The new DNA double helix is produced as a single unit

Conservative

Kornberg showed that nucleotides are added to the 3'-end of each growing DNA strand.

In what way does an exposed 3'-OH group participate in strand elongation?

It directly participates in the formation of a covalent bond with the nucleotide being added

Can you distinguish between (a) unidirectional and bidirectional synthesis, and (b) continuous and discontinuous synthesis of DNA?

This diagram depicts an origin of replication, with the direction of the movement of the replication fork indicated.

What type of DNA synthesis is shown?

unidirectional

Given the direction of replication and the orientation of the two DNA strands, which of the following is true?

Select the two true statements.

The bottom strand (blue) is the lagging strand; it is being synthesized discontinuously

 

The top strand (pink) is the leading strand; it is being synthesized continuously

Identify the function of the proteins that unwind DNA during in vivo DNA synthesis.

Primase

Not involved in the unwinding of DNA for replication

DNA gyrase (topoisomerase)

Releases supercoiling by nicking DNA

DNA polymerase

Not involved in the unwinding of DNA for replication

Helicase

Opens DNA double helix

DnaA replication initiation factor protein

Not involved in the unwinding of DNA for replication

Single-stranded binding protein

Stabilizes the open conformation

DNA ligase

Not involved in the unwinding of DNA for replication

Can you define and identify the significance of Okazaki fragments, DNA ligase, and primer RNA during DNA replication?

Okazaki fragments are short DNA fragments synthesized in a __________ manner.

Okazaki fragments appear on the _________ strand during DNA replication.

DNA ligase forms _______ bonds in gaps between DNA Okazaki fragments.

These gaps are generated when _________ removes the RNA primers.

RNA primers are formed by _________ and serve as an initiation point for DNA synthesis on the template.

discontinuous ; lagging ; phosphodiester ; DNA polymerase I ; RNA primase (RNA polymerase)

Consider the drawing of a dinucleotide below.

Is it DNA or RNA ?

DNA

Consider the drawing of a dinucleotide below.

Is the arrow closest to the 5' or the 3' end?

3’

DNA strands have an arrangement, its nature of nitrogenous bases allow it to _____ __ _____

serve as a templates

what are the three modes of DNA Replication?

Semiconservative

Conservative

Dispersive

Semiconservative

each replicated DNA molecule consists of one “old” and one “new” strand ; prokaryotes and eukaryotes have this mode!

Conservative

two newly synthesized strands come together - original helix is conserved

Dispersive

parental strands are dispersed into new double helix - more complex

DNA replication begins at the _____ (Origin of _____)

at the site of replication, helix is unwound, creating a ________ ____ - this appears at the ____ __ _____ and moves along the DNA replication

replication is ______; therefore, there are _____ replication forks; this happens in _______ and _______

________: unit of length of DNA replicated

ORI ; Replication

replication fork ; point of origin

bidirectional ; two ; prokaryotes ; eukaryotes

replicon

bacteria on have ____ ORI

DNA synthesis originates at _____

_____ replicon consists of entire genome

one ; OriC ; E.coli

In order for DNA polymerase to work there are several requirements what are they?

DNA template

Primer

All four deoxyribonucleoside triphosphates (dNTP’s)

what are the four deoxyribonucleoside triphosphates?

dATP, dTTP, dCTP, dGTP

Chain elongation by DNA polymerase I occurs in ____’ to ____’ direction adding one ____ at a time to the 3’ end

nucleotide added will have ____ terminal phosphates cleaved off providing a newly exposed ___’ - OH

___’ - OH will be exposed to add another ____ as DNA ______ Proceeds

5’ to 3’ ; nucleotide

two ; 3

3 ; nucleotide ; synthesis

DNA polymerase I, II, III

can elongate existing DNA strand (Primer)

______ initiate DNA Synthesis

all three possess 3’ to 5’ exonuclease activity: ______ newly synthesized DNA, Remove/replace incorrect ______

5’ to 3’ ______

Cannot

proofread ; nucleotides

polymerization

DNA polymerase I

exonuclease activity ____’ to ____’ : excises ____ - fills gaps left behind

5’ to 3’ ; primers

DNA polymerase I, II, IV, V

allow for _______

Exposure of ____ light can cause damage to DNA repair

DNA repair

UV

DNA polymerase III

also known as _______: contains core enzyme complexes made up of ______

Subunits each have seperate functions

• α (alpha) 5’ to 3’ __________

• ε (epsilon) _’ to _’ exonuclease

• θ (theta) ____ ___

Holoenzyme ; subunits

polymerization

3’ to 5’

core assembly

seven key issues must be resolved during DNA replication

• _______ of helix

• Reduce increased _____ generated due to ______

• Synthesis of ____ tell enzymes where to initiate

• Discontinuous synthesis of _____ strand - will have 2 strands, ______ one will be discontinued

• removal of the _____ _____

• joining of _____-____ DNA to adjacent strand

• _______

unwinding

coiling ; unwinding

primers

second ; lagging

RNA primers

gap-filling

proofreading

dnaA

_____ protein is encoded by this gene → binds to ____ causing conformation change → this causes helix to _____ and open up → it then exposes ____ (single strand DNA)

initiator ; ORI ; destabilize ; ssDNA

DNA helicase

made of Dna__ _____

Recruits holoenzyme to bind _____ ___ and initiate _____

helicases require energy supplied by hydrolysis of ____ - _____ hydrogen bonds and stabilizes double helix

B polypeptides

replication fork ; replication

ATP ; denatures

SSBP’s

____ -____ _____ ____

bind specifically to single strands of ____

______ the open conformation of helix

single-stranded binding proteins

DNA

stabilize

DNA gyrase

prevents _____, enzyme relieves coiled tension from unwinding of ____

member of larger enzyme group: ____ ______

makes single- or double-stranded cuts

driven by energy released during ____ ____

supercoiling ; helix

DNA topoisomerases

ATP Hydrolysis

Primase formed by ____ ______

• recruited to replication form by ____

• primase _____ RNA primer

• provides ___ 3’ - OH required by DNA polymerase III for ____

RNA Polymerase

helicase

synthesizes

free ; elongation

DNA polymerase I

• ______ primer and ______ it with _____

RNA ___

• happens in bacteria, _____ and several ______ organisms

removes ; replaces ; DNA

priming

viruses ; eukaryotic

Two strand of double helix are antiparallel: ___’ to ___ ’ and ___’ to ___’

• DNA pol III ONLY synthesizes __’ to _’

Continuous DNA synthesis = _____

Discountinuous DNA synthesis = ______

• replicates away from the _____ _____, creating _______ fragments

5’ to 3’ and 3’ to 5’

5’ to 3’

leading strand

lagging strand

replication fork ; Okazaki