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BIOL-2301 Final Exam > Chapter 6 and 7 > Flashcards

Chapter 6 and 7 Flashcards

1
Q

What is the unit of DNA replication

A

replicon

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2
Q

In prokaryotic and plasmid genomes, there is/are typically ____ origin(s) of replications

A

1

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3
Q

T/F DNA synthesis can be initiated without a template

A

false. DNA synthesis cannot be initiated, the nucleotides can only be added to an existing partially double stranded poly nucleotide sequence.

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4
Q

New nucleotides are added to the ____ end of the strand

A

3’ end

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5
Q

What kind of model did Meselson and Stahl propose for DNA replication? How did they achieve this?

A

They proposed the semi-conservative model, used 5-bromodeoxyuridine that replaced thiamine bases, and after two rounds of DNA replication, the sister chromatids had different chemical content, indicating that they were attached to an old strand.

They used equilibrium density gradient centrifugation that allowed the separation of molecules with only slightly different densities. This enabled parent and daughter strands to be separated and stained using different nitrogen isotopes.

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6
Q

What is theta replication? Which organisms use this sort of replication?

A

Theta replication is DNA replication in a circular formation used by organisms with circular DNA molecules, like bacteria.
Theta replication begins at a specific origin of replications, and terminates at the TERMINUS OF REPLICATION.

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7
Q

What is the terminus of replication?

A

the portion where circular dna replication ends.

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8
Q

In circular DNA molecules, replication is __directional from the replication forks

A

bidirection. it occurs both ways.

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9
Q

In eukaryotes, there are several replication ____ in every chromosome, and the bidirectional replication creates a _____ which fuse together

A

there are several replication origins in every chromosome, and the bidirectional replication creates a REPLICATION BUBBLE, which fuse together where the forks meet.

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10
Q

What’re the two main differences of replication between prokaryotic and eukaryotic DNA?

A

1) replication and synthesis rate- in eukaryotes, the synthesis is slower, but there are more origins located
2) number of DNA polymerases: Bacteria have 5 different polymerases numbered 1-5, and eukaryotes have at least 15 polymerases, the main ones being sigma, alpha and E

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11
Q

Which 3 polymerases are used for main chromosome replication in eukaryotic cells

A

sigma, alpha and E

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12
Q

What is the purpose of DnaA protein? is this used by prokaryotic or eukaryotic cells?

A

it recognizes the PROKARYOTIC origin and begins strand separation

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13
Q

What produces Helicase? What does it do and how does it power this process?

A

helicase is a protein produced by ecoli gene DNaB, and uses ATP to power the strand separation process once DNaA recognizes the origin.

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14
Q

T/F: Single stranded DNA is unstable and tends to reanneal after separation

A

true

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15
Q

What keeps the single stranded DNA from separating?

A

SSB- single stranded DNA binding protein coats the SS DNA to ensure availability of a template and to protect ssDNA from degradation.

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16
Q

T/F Unwinding the DNA causes tension

A

true.

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17
Q

What protein relieves the tension from DNA unwinding? How do they do this?

A

in prokaryotes, protein TOPOISOMERASE catalyzes teh cutting and rejoining of DNA molecules.

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18
Q

What does topoisomerase two do?

A

topoisomerase II cuts both strands of DNA

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19
Q

Where is gyrase found? what does it do?

A

gyrase topoisomerase cuts the DNA strands to release tension, swivels the broken strands, relieving the stress and reseal any nicks, allowing helix unwinding to continue.

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20
Q

What stage does origin recognition, unwinding, template stabilization and tension relief of prokaryotic DNA replication fall under?

A

Preinitiation stage.

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21
Q

What protein is needed for DNA Polymerase to initiate DNA synthesis? In prokaryotes, what is it made of? How about in Eukaryotes?

A

A primer is a short double stranded segment with a 3’ hydroxyl, which is needed for initiation. In prokaryotes, it is called a PRIMASE: an RNA primer. in eukaryotes, it is called a PRIMOSOME: a primer made of RNA and DNA.

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22
Q

What is pol III Holoenzyme?

A

a multiprotein complex used in chain elongation and proofreading in eukaryotes.

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23
Q

What is the beta clamp?

A

holds the pol III holoenzyme onto the template stand.

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24
Q

What is a replisome?

A

the entire molecular machine. multiprotein made of composed of a number of proteins including helicase, RFC, PCNA, gyrase/topoisomerase, SSB/RPA, primase, DNA polymerase III, RNAse H, and ligase. The replisome first unwinds double stranded DNA into two single strands. For each of the resulting single strands, a new complementary sequence of DNA is synthesized

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25
Q

What is a 3’-5’ exonuclease?

A

breaks the phosphodiester bond in the sugar-phosphate backbone of a nucleic acid chain and removes the terminal nucleotide FROM THE 3’ END if there is an error. aids in proofreading by correcting incorporation errors that occurred during polymerization

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26
Q

a template strand is read in a x’ to y’ manner, and DNA is synthesized in a y’ to x’ direction

A

a template strand is read in a 3’ to 5’ manner, and DNA is synthesized in a 5’ to 3’ direction.

27
Q

Which strand is the leading strand?

A

the leading strand is the strand that is running in a 3’ to 5’ manner and can thus be synthesized CONTINUOUSLY in a 5’ to 3’ manner.

28
Q

A lagging strand is synthesized in ____ fragments

A

okazaki fragments

29
Q

What is the job of Pol 1 Polymerase? What’re the three main enzymatic activities of poly 1 polymerase

A

it is in prokaryotic e.coli, and it removes the RNA primerase primer and inserts the appropriate deoxyribonucleotides.

1) pol 1 acts as a polymerase: inserts nucleotides in 5’-3’ direction
2) pol 1 acts as an exonuclease: proof reads in a 3’-5’ manner
3) pol 1 acts as an exonuclease in terms of removing RNA primerase (as mentioned above)

30
Q

T/F: each okazaki fragment needs a primer

A

true

31
Q

T/F: RNA removal and DNA addition is done base by base

A

true

32
Q

______ protein seals all the nicks once the entire RNA primer has been removed

A

DNA ligase.

33
Q

DNA polymerase III (pol III holoenzyme) is made of ____ dimers

A

2 pol III dimers, one for each strand

34
Q

Are helicase, SSB proteins and topoisomerases used in eukaryotic replication?

A

Yes they are, used for preinitiation and origin recognition

35
Q

In eukaryotes, what is polymerase alpha?

A

polymerase alpha is part of the primosome complex and produces the primer made of RNA and DNA

36
Q

Polymerase sigma is responsible for adding nucleotides to the ____ strand, and polymerase E is responsible for adding nucleotides to the _____ strand

A

Polymerase sigma is responsible for adding nucleotides to the LAGGING STRAND, and polymerase E is responsible for adding nucleotides to the LEADING STRAND

37
Q

Both polymerase sigma and polymerase E are part of the ______

A

DNA polymerase complex in eukaryotes

38
Q

Can polymerase sigma and polymerase E conduct proofreading?

A

yes

39
Q

What is the difference between primer removal in eukaryotic and prokaryotic DNA replication?

A

in eukaryotic replication, the primer segment is removed in one piece.

In prokaryotic replication, the primer segment is removed one base at a time and replaced with a deoxynucleotide

40
Q

How does primer removal on the lagging strand work?

A

polymerase sigma reaches the previous primer sequence (since it is working backwards and synthesizing in fragments) and replication protein A (RPA), a type of SSB, recuits an endonuclease to cleave the RNA. The polymerase sigma inserts the replacement complimentary nucleotides, and ligase selas the nicks together.

41
Q

What is the function of replication protein A

A

RPA is an SSB protein that stabilizes displaced RNA-DNA primer in eukaryotic cells and recruits an endonuclease to cleave the RNA so that the two lagging strand fragments can be sealed together.

42
Q

If the incoming nucleotide was to be missing a 3’ hydroxyl group, would replication keep going?

A

no, bases attach to the 3’ hydroxyl group. Recall, a 3’ hydroxyl on the deoxyribose sugar of the growing chain attaches to the 5’ phosphate of the incoming nucleotide.

43
Q

What is the ratio between DNA and histone in interphase/

A

50:50

44
Q

What makes up a histone octamer

A

2 of each of H2a H2b H3 and H4.

45
Q

What is a nucleosome

A

A bunch of histone octamers make up a nucleosome plus H1, which is a linking histone.

46
Q

What’re the two levels of DNA-histone organization?

A

1) DNA winds around a histone octamer

2) A bunch of octamers form a super coil, forming a nucleosome, which is stabilized by H1 linking protein

47
Q

What protein is responsible for DNA condensation?

A

condensins

48
Q

What happens to histones before DNA replication occurs?

A

they dissociate so that the DNA can get replicated, and then they immediately reform

49
Q

Are histones a part of the chromatin structure at every stage?

A

Yes. at every stage of replication besides the actual DNA replication in interphase, histones hold the DNA together in the sister chromatids.

50
Q

What’re the two factors that histones need to functioN?

A

CAF1- chromosome assembly factor carries the histones to the PCNA

PCNA; the eukayotic equivalent of the beta clamp and holds the histones and CAF to the DNA strands.

51
Q

What is the telomere?

A

the over hanging short tandem repeats at the end of the chromosomes. Shortens with every DNA cycle.

52
Q

What is telomerase?

A

protein responsible for maintaining the length of the telomere to prevent entire degradation. It contains RNA that is complementary to the telomere repeats and is used to extend the 3’ end of the telomere. (RIBONUCLEOPROTEIN)

53
Q

Besides telomerase, how else is the telomere protected against degradation

A
  • the telomere forms a loop by opening a double stranded section to bind its compliment.
  • proteins associate to protect the region from further degradation.
54
Q

What is the general process for rolling circle replication

A

begins with cleavage of sugar-phosphate backbone of one strand. DNA synthesis adds nucleotides to free 3’ydroxyl group. the Circle rolls and displaces SINGLE STRANDED DNA, creating a tail. Lagging strand DNA synthesis uses the tail as a template to create new double stranded DNA.

55
Q

How many DNA polymerase III’s are in the pol III holoenzyme?

A

2, each PolIII works on either the leading or the lagging strand.

56
Q

is the pol III holoenzyme the same as a replisome?

A

yes

57
Q

Is polymerase one found in prokaryotic or eukaryotic replication?

A

used for lagging strand replication in circular prophage replication. gets rid of fragment primer in prokaryotes (5’ to 3’ exonuclease of RNA) and adds nucleotides one by one from a 5’ to 3’, also a 3’ to 5’ exonuclease proofreader.`

58
Q

Compare and contrast prokaryotic and eukaryotic primers

A

Pro: made of RNA, formed by primase
Euk: made of RNA and DNA, formed by polymerase alpha of the primosome complex. Longer than a prokaryotic primer

59
Q

What protein has a 3’-5’ exonuclease capability?

A

polymerase 1 in prokaryotes. removes RNA primer on lagging strand one at a time and adds and proof reads nucelotides

60
Q

What protein is responsible for initiating the unwinding of double stranded DNA by separating the parental DNA strands?

A

DNA helicase

61
Q

What would happen if telomerase was defective?

A

telomerase is responsible for the maintenance of telomeres, therefore, the telomeres would get shorter every division.

62
Q

Is there a telomere in the ecoli DNA?

A

no, because the bacterial chromosome is circular and thus has no end.

63
Q

Are the 3’ overhang ends (telomeres) at both ends of the chromosomes compatible to form a duplex?

A

no. The telomeres at both ends would be the SAME, not the complement. you’d need complimentary pairs for them in order to join together.

BIOL-2301 Final Exam (6 decks)

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