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nucleic acids > Quiz 2 > Flashcards

Quiz 2 Flashcards

1
Q

leading strand vs. Lagging strand

A

leading strand is continuous and DNA Polymerase chases the replication fork in 5->3’ direction from an exposed 3’ hydroxyl (-OH). The first RNA primer is synthesized by (DnaG) primase
Lagging strand has discontinuous synthesis and needs to wait for upstream DNA 3’-OH to be exposed. needs many primers

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2
Q

what are Okazaki fragments and how do they compare in prokaryotes and eukaryotes

A

=newly synthesized stretches of DNA on the lagging strand

  • in prokaryotes, usually 1000-2000 nucleotides
  • in eukaryotes, usually 100-400 nucleotides
  • Length due to processivity
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3
Q

what does RNA Polymerase usually need to bind to the DNA so it can provide a short primer in which DNA can expand upon

A

Short DNA sequence trimer motif (GTA in E. coli.)

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4
Q

what enzymes remove RNA primers?

A

RNase H and 5’ exonuclease

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5
Q

describe the removal of the RNA template/primer to copied DNA strand

A

RNase H only bind to RNA bound to DNA and removes almost all the primer except for one which is removed by 5’exonuclease. DNA Pol then fills in the gap and DNA ligase seals the nick

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6
Q

compare the type of ligase used for E coli DNA vs T4 virus and eukaryote DNA ligase

A

E. coli ligase uses NAD+ as a cofactor

Eukaryotes use Mg+ATP

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7
Q

describe the structure/role of DNA helicase

A

unwinds DNA at the replication fork

  • they are hexameric proteins that encircle one of the DNA strands
  • highly processive: unwind multiple bases, don’t fall off.
  • needs ATP to break the H-bonds between bases and to move along the DNA
  • they are loaded onto DNA
  • they activate primases/primers
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8
Q

how is unwound DNA stabilized ?

A

by single stranded DNA binding proteins (SSB)

  • the first one that binds facilitates others to bind and protect DNA, getting it ready for replication
  • SSBs bind to the phosphodiester backbone and stack with nucleotide bases
  • SSBs dont form Hydrogen bonds with the ssDNA like other DNA binding proteins do
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9
Q

what is the role of topoisomerase in DNA replication

A

DNA topoisomerase 11 relieves positive supercoiling caused by replication by cutting both DNA strands and holding onto them both.
-acts on unreplicated DNA ahead of the replication fork to reduce linking number (cut about every 10 base pairs)

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10
Q

list the steps in how DNA replisome proteins function at the replication fork to duplicate DNA

A
  1. Helicase unzips DNA with ATP
  2. DNA topoisomerase II unwinds
  3. SSBs bind & protect DNA for replication
  4. Primase adds in temporary template
  5. DNA polymerase (III) extends DNA
  6. DNA polymerase I replaces gaps
    where RNase H removed RNA primer
    and seals nicks in DNA (nick ligation with ligase)
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11
Q

How are DNA polymerase isoforms distinguished ?

A

by enzyme kinetics (how fast they work), subunit composition, specific function and abundance

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12
Q

compare DNA Pol 1 and DNA Pol III isoforms (Prokaryotes)

A

DNA Pol III: highly processive since it replicates
4.6 Mb E. coli genome from only 2 replication forks

DNA Pol I: not processive (20-100nt/binding), removes upstream RNA from Okazaki fragment, fills in gap left by RNase H, has own built in 5′ exonuclease activity

  • Both these have proof-reading ability, other 3 isoforms do not (repair only)
  • Prokaryotes have 5 DNA Pol isoforms, 2 “hi-fi” for replication, 3 for repair only
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13
Q

Compare the three replication DNA Polymerase isoforms in eukaryotes

READING p269-278

A

3 genome replicating polymerases: DNA Pol α, ε and δ
- DNA Pol α/primase H starts off
with primase activity then DNA pol
activity (but has low processivity)
* DNA Pol α does both primer and DNA lay down but its slow so it switches)
-Replication shifts into ‘top gear’ with
highly processive DNA pol ε and δ
(this is called “polymerase switching”)

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14
Q

what is the function of the sliding clamp for DNA replication?

A

the sliding clamp encircles DNA, binds to DNA Pol and keeps it from diffusing away and on track

  • DNA Pol dissociates from 3′-OH every 20-100 bases but sliding clamp prevents loss
  • vastly improves processivity of DNA Pol
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15
Q

how/when does the sliding clamp-DNA Pol complex separate?

A

=dissociates when it hits double-stranded DNA
-DNA Pol recognizes dsDNA, active site has low affinity for dsDNA (as opposed to high affinity for RNA primer:DNA template junction)
-DNA Pol undergoes conformation change,
sliding clamp has low affinity for this DNA Pol’
-DNA Pol′ diffuses away but sliding clamp (PCNA)
remains for nucleosome assembly role

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16
Q

how does the sliding clamp get put on/taken off the DNA strand

A
  • Sliding clamp loaders bind and use ATP to crack open sliding clamp ring
  • The ‘open’ hexamer can then encircle a DNA strand, recruit, bind DNA Pol
  • When DNA Pol , nucleosome packing done, sliding clamp loaders also remove sliding clamps from the DNA strand (so DNA bases can pair)
  • Presence of primer:template junction serves as recruitment signal for sliding clamp (during replication, also during DNA repair)
  • DNA Pol and sliding clamp loaders compete for same binding domain on the sliding clamp itself -> so loader can’t interfere with active DNA Pol
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17
Q

describe the steps (a-e) of how the slide clamp is loaded onto the DNA strand

A

(a) Slide clamp loader protein (‘З-like’ protein) senses
primer:template junction
(b) binding of ATP, conformational change
(c) binds to protein:protein interaction domain of
sliding clamp protein, breaks hexameric ring
(d) recognizes p:t junction, slips ring onto DNA strand
(e) DNA binding causes ATP hydrolysis by altering
conformational shape, causing dissociation,
DNA is left encircled by clamp protein

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18
Q

what is the name of the Slide clamp loader protein in pro and eukaryotes

A

Slide clamp loader protein is γ-complex in E. coli,

Replication Factor C (RF-C) in eukaryotes

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19
Q

describe the makeup of the DNA Pol III holoenzyme

A

a complex of DNA Pol, clamp loader, & sliding clamp

  • E. coli DNA replication can be coordinated by physically linking enzymes (DNA Pol III holoenzyme)
  • Tau (τ)-protein links clamp loader with two DNA Pol III subunits (1 for leading + 2 for lagging strand synthesis)
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20
Q

what is faster, DNA Pol III or primase?

https://www.youtube.com/watch?v=I9ArIJWYZHI

A

DNA Pol III is faster than primase, so DNA Pol III is always
waiting for primase to dissociate (get out of the way)

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21
Q

DNA Pol III replicates as fast as helicase unwinds it, but only when….?

A

only when helicase interacts with τ -protein
(When helicase is not binding the τ –protein, activity falls 10-fold, allowing DNA Pol to catch up and preventing “helicase runaway”)
*Interactions of helicase and τ –protein help coordinate DNA Pol and helicase speed

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22
Q

how do Interactions of helicase and primase regulate Okazaki fragment length ?

A
  • Helicase also has protein-protein interaction with DNA primase, Interaction stimulates primase activity 1000 X’s
  • Stronger association gives more primers, shorter Okazaki fragments
  • Weaker gives less primers, longer Okazaki fragments
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23
Q

replicon = ?

A

all DNA replicated from 1 origin of replication (circular chromosome=1 replicon)

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24
Q

how does replication start? Origins of replication …

A

=Initiator protein binds replicator DNA motif at origin of replication to start DNA replication

-Need replicator (DNA sequence motif sufficient to
direct initiation of DNA replication), part of origin of
replication but not always be the entire origin in
eukaryotes (may need other DNA sequences)
-Need initiator (protein) to recognize DNA motif in replicator to activate replication
(uses ATP, recruits other proteins in to bind it or other DNA
structures, e.g., primer:template junction)

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25
Q

Known replicator sites share 2 common features

READING= p278-292

A
  1. Binding site for initiator
  2. AT-rich DNA motif that unwinds fairly easily….
    * Replicator DNA sequences have binding & unwinding, initial DNA synthesis sites
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26
Q

what are the two main jobs of Initiator proteins?

A
  1. Bind to replicator regions’ DNA sequence

2. Recruit proteins/replisome units for DNA replication

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27
Q

what is the additional role of initiator proteins in prokaryote DNA? (E. coli)

A

Facilitate unwinding of DNA

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28
Q

compare initiator proteins in E coli and eukaryotes

A
  • E. coli DnaA protein binds 9 & 13 mer regions, helps unwind DNA, recruits proteins
  • origin replication protein complex (ORC) is eukaryotic equivalent to DnaA, binds to origin element, helps recruit helicase (+ATP…) & all other proteins, BUT does not unwind DNA
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29
Q

explain how the DnaA initiator protein binds and starts the rep. process

A

DnaA bind oriC area and DnaA complex ‘melts’ the DNA repeats to form an “open complex“ (ATP also needed)
-Helicase + loading protein binds to melted area to form a “prepriming complex“, loading protein drops off and activates helicase
-In the presence of SSB plus DNA gyrase, helicase
unwinds the DNA further.
-Helicase recruits DnaG primase which makes a primer
-Helicase action displaces the DnaA initiator protein as oriC is fully unwound

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30
Q

To avoid catastrophic gene changes, only replicate chromosomes once during S phase
Rereplication of any DNA is difficult to fix, what may happen when attempting to fix this

A

Attempts to fix this often leads to gene duplication, increased expression that causes unwanted biological response
-Incomplete duplication followed by
premature segregation (pulling apart
of chromosomes) breaks DNA

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31
Q

how many replication origins are there on our chromosomes and how spaced out are they? when does it get inactivated?

A
  • one replication origin every ~30kb
  • 1500-8200 replication origins on our chromosomes
  • the origin gets inactivated once it starts replicating, or is (passively) replicated from another origin so **No origin can initiate replication once it has been replicated itself

(Ensures requirement of replicating chromosome once per cycle! )

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32
Q

what is the first step in the

initiation of replication in eukaryotes

A

helicase loading

33
Q

Two phases during replication?

A
  1. Identification, selection, ORC initiator binding to
    replicator during G1 phase (before S phase)
  2. Origin activation during S phase to trigger helicase (McM2-7) activity , DNA Pol recruitment
34
Q

ORC has 2 helicase loaders which are?

A

Cdc6 and Cdt1

*Cdc6/ORC/Cdt1 (Prereplicative complex) assembles in G1 phase and waits for S phase signal before actoin

35
Q

S phase signal is ??

A

S phase signal is phosphorylation activation of helicase binding cascade

36
Q

Two protein kinases activated in S phase?

A

CDK =(Cyclin Dependent Kinase)

DDK= (Dbf4-Dependent kinase)

37
Q

CDK and DDK phosphorylate what? what is the result?

A

DDK phosphorylates helicase, CDK phosphorylates CMG helicase complex(Sld2/3, Dpb11 -> facilitating GINS, Cdc45 binding to helicase)

  • Cdc6, Cdt1 helicase loader is even proteolyzed due to phosphorylation
  • DNA Pol α/primase, then other DNA Pol are also recruited, preceding 1st RNA primer
38
Q

CDKs have 2 key functions;

A

1) activate helicases to start DNA replication

2) also inhibit new helicases formation

39
Q

how is CDK activity regulated to allow only a single round of replication during each cell cycle?

A

CDK activity is regulated – low during G1 phase
(allows helicase loading, but not activation)

CDK activity high during S phase (G2 &M also)
(causes helicase activation, stops helicase loading)
*ensures only 1 chance for helicase loading in G1 phase with only 1 chance to activate helicase in S phase

40
Q

what allows the proper segregation of daughter

chromosomes after replication?

A
  • Both circular and large linear chromosomes need to be decatenated or untangled/unknotted, respectively
  • Type II topoisomerases finish circular DNA replication by decatenation
41
Q

large linear chromosomes have another problem after replication, what is it?

A

Lagging-strand synthesis is unable to copy the extreme
ends of linear chromosomes because there is a requirement for RNA primer
-therefore because primase runs out of space to bind last part of DNA, 1 chromosome is incompletely replicated

42
Q

how does telomerase fix the problem of the lagging strand being unable to copy the ends of the linear chromosome?

A

because it is a novel DNA polymerase that
does not require an exogenous template and uses its ribonucleoprotein component to extend the 3′ end with reverse transcriptase activity
-Telomerase uses its own RNA to bind to DNA, then use 3′OH of ssDNA to extend DNA with a telomerase subunit that is a reverse transcriptase (uses RNA as template for making DNA)
-Newly added 3′ end DNA gives primase room to add RNA template, allow DNA Pol III to extend the DNA fragment again
-Still leaves extra 3′ end overhang but this can extend telomeres

43
Q

Unregulated telomere extension is unwanted so how is it regulated? describe the proteins in yeast and humans

A

=Telomere-binding proteins regulate telomerase activity and tail
-Telomeres bound by ‘shelterins’ which regulate length
by governing telomerase-extension activity
-In yeast, Cdc13 binds ssDNA, recruits telomerase. it also has Rap1 (dsDNA-binder), recruits Rif1, Rif2
-Humans also have specialized Telomere Repeat binding Factors (TRFs) like yeast but unlike yeast, ssDNA binder POT1 inhibits activity of telomerase (more shelterin protein/POT1 = less telomere extension)

44
Q

how do Telomere-binding proteins protect chromosome tails?

READING: pg 293-310

A

Human telomeres apparently form T-loops with
help of TRF2 (this works in vitro)
-3′ ssDNA folds back on itself, invades dsDNA
region of telomere, binds DNA and then is
not recognized as dsDNA break (is protected as it is hidden)

45
Q

Mutations in DNA are almost always negative and need to be reversed so cells must do what two things?

A

Cells must 1) detect damaged DNA 2) repair and restore DNA code

46
Q

Mutations can arise due to DNA replication inaccuracy or chemical damage and can either ?

A
  1. change DNA code forever-> Allow use of DNA… but changes genetic code (cytosine deamination to uracil ->C:G to T:A…)
  2. make DNA unusable-> Block use of DNA in transcription, replication (DNA break, thymine dimer)

-Needs to be fixed before 2nd round of DNA replication or it is permanent

47
Q

why is there no cure for cancer?

A

because they are so many types of cancer and it changes from person to person and even within the same person

  • cancer is not a single mutation but a whole bunch of possible mutations
  • instead you need to find a million cures for a million different kinds of cancer
  • cancer has found ways to cheat death in all its forms
48
Q

Simplest mutations are changes to single bases: two types of substitutions?

A

Transitions (pyrimidine-pyrimidine, purine-purine)

Transversions (purine to pyrimidine & vice versa)

49
Q

Insertions & deletions are more complex mutations that are caused by?

A

Insertions caused by Transposons (‘jumping genes’)
Deletions caused by recombination reactions
-These can cause frameshift mutations, ± 1 or 2 bp
(can be due to DNA intercalating mutagens, cause ‘slippage’ during DNA replication)

50
Q

describe how the “mismatch repair system” is the last line of defence for DNA replication (in E coli)

A

-Improves fidelity 2-3 orders of magnitude
MutS (=MutationScanner) in E. coli repairs mismatched DNA bases and has two functions:

1) Rapidly scan genome for mismatches
(backbone distortion induced by mispairing)

2) Correct repair of mismatch on daughter,
not parental template strand

51
Q

how does MutS act to recruit proteins that clip,

degrade, refill & seal mismatched area?

A

-first, MutS binds to mismatch distortion and undergoes conformational change (MutS′)
-then, it recruits MutL(oader), MutH(ealer)
-MutL activates MutH, an endonuclease that nicks DNA, UrvD helicase (UV response D) unwinds DNA
-An exonuclease removes DNA to clear area
-DNA Pol III fills in new gap, nick sealed by
a DNA ligase to finish repair

52
Q

how does MutS′ know which strand is the parent and daughter? (in bacteria)

A

Transient methylation of Adenine in parental DNA by DexoyAdenosine Methylase (DAM) which acts on GATC about every 256bp
-Daughter DNA duplex only methylated solely on
parental strand for short time after replication so MutS′ must act before DAM methylase catches up and methylates new daughter DNA…
-MutH recognizes hemimethylated DNA so MutL & MutS can activate the endonuclease activity
(MutH binds nonmethylated DNA strand)
( our DNA is not methylated like bacteria’s)

53
Q

what are the different exonucleases recruited depending on what side of MutS makes nick

A

If nick is on 5′ side of mismatch: Exonuclease VII (5′-> 3′) removes DNA between the nick caused by MutH and the site of the mismatch

If nick is on 3′ side of mismatch: Exonuclease I (3′-> 5′) removes DNA between the nick caused by MutH and the site of the mismatch

54
Q

DNA is Damaged Spontaneously by ? and ?

A

Hydrolysis & Deamination

55
Q

how is DNA damaged by water?

A

->DNA is damaged by the action of water that causes deamination
- C->U transversion happens in mammalian cells
at rate of 100 events/day (most common)
-Adenine, Guanine susceptible too
-Uracil is unnatural in DNA, makes bond with
adenine (instead of proper C-G!)
-DNA is also depurinated by water: Guanine depurinated
to nothing (abasic site causes loss of a base in the DNA helix)

56
Q

why isnt uracil used in DNA?

A

because there is no way to know if it is there due to deliberate inclusion or because a cytosine was deaminated!

57
Q

Deamination of DNA bases can be chemical too (nitrosamine ->forms N oxides)
Nitrosamine comes from ??

A

comes from nitrates and nitrites that
are common food preservatives (also in beer,
tobacco, fried bacon, cured meats, nonfat dry milk)

58
Q

deamination of what gives normal base (T) ?

A

-5-methylcytosine (epigenetics) deamination gives normal base (T) so these are mutation “hotspots”

59
Q

how is DNA Damaged by alkylation

A

Alkylation transfers methyl/ethyl groups
to bases, phosphates in backbone

O6-methylguanosine leads to a G:CA:T
mutation

60
Q

how is the very mutagenic oxoG (7,8-dihydro-8-oxoguanine) made?

A

made by reactive oxygen species (oxidation) and can pair with both adenine and cytosine

61
Q

what is the most common mutation in cancer

A

oxoG (7,8-dihydro-8-oxoguanine)

62
Q

how is DNA damaged by radiation?

A

UV radiation causes thymine dimer formation,
stops replication of DNA

Radiation causes dsDNA strand breaks, stops replication

63
Q

what are Base analogs and how can they cause DNA mutation

A

Base analogs chemically resemble the proper DNA bases, but can be improperly incorporated, leading to improper base pairing -> mutation

64
Q

what are Intercalating agents and how can they cause DNA mutation

READING: pg 313-324

A

Intercalating agents are flat, can slip between bases of DNA

-Can cause deletion/insertion of a base or few bases (frameshift)

65
Q

what are the 4 categories of DNA repair systems

A
  1. reversal of damage by enzyme (most simple repair)
  2. Excision repair = damage removed, not reversed (more complex)
    - >Undamaged DNA becomes template for DNA polymerase (Either a single, or a stretch of nucleotides is replaced)
  3. Recombinational =double-strand break: repair uses info from 2nd copy of chromosome *most cytotoxic DNA damage
  4. If replication blocked by damaged base, translesion DNA polymerase copies across it without proper base-pairing (last-chance system, mutagenic)
66
Q

describe photoreactivation

A

=Best example of simple repair by reversal

  • Thymine bases damaged by UV radiation -> cyclobutane ring formed
  • DNA photolyase can use light energy to break ring’s covalent bonds
67
Q

role of methyltransferase in simple DNA repair by reversal? where is the enzyme expressed?

A

methyltransferase removes the methyl group from O6-methylguanine (from alkylation reaction)->but it destroys the methyltransferase!
-Enzyme is expressed mainly in liver ->where metabolism of toxic nitrosamines happens (beer, bacon, smokes)

68
Q

how can Alkylation of adenine and cytosine be reversed

A

by AlkB in newly discovered pathway

  • AlkB carries out oxidative demethylation reaction and will attack methyladenine and methylcytosine
  • Oxidized methyl groups are released as formaldehyde (toxic by itself…)
69
Q

how do Base excision repair enzymes remove damaged bases?

A

remove damaged bases by a base-flipping mechanism:
-DNA glycosylases scan along minor groove until damaged base encountered (base flipped out), then glycosylase active site binds base (has two chances to act)

70
Q

describe how DNA glycosylase has one more chance if it fails to remove damaged base before replication

A
  • oxoG can mispair with A, but “fail-safe” repair removes A and replaces with proper base (C)
  • OR, 5-methylcytosine is deaminated to thymine (natural base), gives T:G pairing instead but repair system replaces the T with a C (assumes it is an error)
71
Q

nucleotide excision repair enzymes differ from DNA gycosylase in that they do ? rather than recognizing damaged bases

A

recognize distorted DNA (thymine dimer, bulky adduct)

72
Q

describe the steps in how Nucleotide excision repair enzymes (Uvr_) remove and replace a stretch of bad DNA (5 steps)

A
  • UvrA2B complex scans DNA
  • UvrA(ssessor) dissociates from UvrB when distortion found
  • UvrB(inder) opens DNA, recruits UvrC
  • UvrC(hopper) cuts on either side of UvrB
  • helicase (UvrD) unwinds DNA, allows DNA polymerase, ligase to replace it
73
Q

what is xeroderma pigmentosum (XP)

A

mutations in XP protein leading to extreme UV sensitivity

*2000-4000x’s normal rate of skin, eye cancer in X.P.

74
Q

“transcription-coupled repair”

A

Targets repair enzymes to genes in use
->Critical nucleotide excision repair enzymes prioritize actively transcribed genes (help rescue stalled RNA
polymerase)
(Transcription-coupled repair systems also exist in prokaryotes)

75
Q

how does DNA recombination help to repair DNA lesions that block replication fork

A

Undamaged template of the other daughter strand can be used for template
-and then damage to parent strand can be fixed like other type 2 excision repairs

76
Q

when/how is ‘Non-Homologous End Joining” (NHEJ) used to repair Double-stranded breaks (DSB) in DNA

A

when there is only 1 chromosome (early cell cycle) to get info from
-(Ku70/80) proteins bind to ends of DNA
-DNA protein kinase (DNA-PKcs) recruited,
recruit Artemis endo/exonuclease
and phosphorylate it (activates)
-Artemis-processed ends then joined by ligase
-While mutagenic, still the lesser of 2 evils…

77
Q

how does Translesion DNA synthesis enable

replication to go across DNA damage

A

bypass damage sites, replication continues:
-special template-independent DNA
Pol IV, V replicate across lesion,
then DNA Pol III resumes
-Highly error-prone but cell has little choice (replicate or die)
-DNA Pol IV, V only expressed when DNA damage is sensed (SOS response – DNA damage destroys LexA repressor protein ->allows expression of these
DNA Pol IV, V isoforms and causes activation of Pol V)

78
Q

Eukaryotes bypass and fix lesions by ubiquitinating regular DNA polymerases. what two ways can this happen?

READING: p325-338

A

a) May happen by polymerase switching (a) where stalled replicative polymerase gets ‘Ub tagged’ on its sliding clamp then and swapped out for translesion polymerase
b) May happen by “gap filling” (b) where replicative DNA Pol allowed to skip lesion, translesion polymerase fixes it later

nucleic acids (5 decks)

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