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Flash Cards > molbio FINALLLL > Flashcards

molbio FINALLLL Flashcards

1
Q

Eukaryotic and bacterial genes are interrupted by non coding DNA (t/f)

A

false, only eukaryotic

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2
Q

RNA poly CANNOT distinguish between coding and non coding regions, it will transcribe everything (t/f)

A

true

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3
Q

Purpose of splicing

A

cell must remove non coding RNA from the primary transcript

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4
Q

Eukaryotes add ______ and ______ to the ends of a transcript

A

cap to 5’
poly A tail to 3’

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5
Q

splicing and capping occur in….

A

the nucleus, before mRNA moves to cystoplasm

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6
Q

post transcript process

A
  1. capping
  2. splicing
  3. poly adenylation
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7
Q

introns occur in…

A

mRNA, tRNA, rRNA

introns are surrounded by EXONs

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8
Q

how many introns do mRNA contain, vs tRNA

A

0-362
0-1

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9
Q

exons contain the sequence that will appear in a mature RNA product (t/f)

A

true

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10
Q

introns are present in ____ but not _____

A

genes, mature RNA

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11
Q

RNA splicing definition

A

cutting introns out of immature RNA, and stitching exons together
^^^simulstaneous

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12
Q

primary transcript has both ____ and ____

A

introns, exons

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13
Q

stages of mRNA synthesis/splicing

A

stage 1: synthesis of primary transcript
-an mRNA precursor, with introns copied from the gene
-the precursor is part of (hnRNAs)

stage 2: mRNA maturation
-splicing

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14
Q

splicing must be _____ , it cannot disrupt the _____

A

precise, codons

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15
Q

splicing signals in nuclear mRNA precursors are _____

A

uniform.

first 2 bases of introns will be GU
last 2 bases will be AG

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16
Q

5’ and 3’ splice sites have _________ , that extend beyond ______

A

consensus sequences
GU and AG motifs

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17
Q

whole ___________ - sequences are important to correct splicing

A

consensus

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18
Q

mutated consensus seq can lead to

A

abnormal splicing

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19
Q

splicing of nuclear mRNA precursors

A

the TWO STEP MODEL

  • 2’ OH’ group of adenosine nucleotide in the middle of the intron will attack the phosphodiester bond in between the 1st exon, and G beginning of intron.
    -forms loop lariat, and separates the first exon from intron.

-3’ OH group left at the end of the 1st exon will attack the phosphodiester bond linking the intron to the 2nd exon, forming the exon-exon phosphodiester bond, and releasing intron in lariat form at the same time

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20
Q

spliceosomes are created inside the

A

nucleus

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21
Q

splicing takes place on the

A

spliceosome

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22
Q

spliceosomes contain

A

pre mRNA
snRNPs
protein splicing factors

^^^these recognize key splicing signals and direct splicing.

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23
Q

snRNPs stands for ____ and contain ____

A

small nuclear ribonuclear proteins
rRNA+proteins

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24
Q

The five snRNAs

A

U1, 2, 4, 5, 6

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25
Q

All 5 snRNAs join the ______ to play crucial role in splicing

A

spliceosome

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26
Q

spliceosome components and cycle

A

-proteins and RNA
-assembly, splicing activity, disassembly

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27
Q

by controlling assembly of ____, a cell can regulate quality/quantity of splicing, to regulate ____

A

spliceosome
gene expression

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28
Q

spliceosome cycle: assembly

A

-starts by binding U1 to splicing substrate, forming commitment complex- used to splice out the intron

-U2 joins complex because of ATP, and is followed by the others

-U6 leaves U4, and dislocates U1 at the 5’, this step depends on ATP, and will activate the spliceosome, allowing U1 and U4 to be released.

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29
Q

alternative splicing

A
  • will have profound effects on genes protein products
  • can make a difference between secreted/membrane bound protein, and activity/inactivity
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30
Q

alternative splicing of ______ will mean many different products.

A

the same pre mRNA

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31
Q

many genes have ______ splicing patterns, some having thousands

A

more than 2

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32
Q

alternative splicing occurs in …

A

less than 50 % of human genes

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33
Q

self splicing RNAs occur ….

A

without a spliceosome- it splices naturally

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34
Q

example of self splicing RNA

A

tetrahymena 26s rRNA gene has an intron, and self splices

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35
Q

Group of self splicing RNAs

A

group 1 introns, some group 2 introns

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36
Q

group 1 inrons

A

self splicing:

reaction starts by attack by guanine nucleotide on 5’
-this will add G to the 5’ end of intron, and release first exon

now the first exon will attack the 3’
-this will ligate 2 exons together, and release the linear intron
-the intron will cycle twice, losing nucleotides each time, then linearize a last time.

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37
Q

group 2 introns

A

self splicing:

these self splice by using A-branched lariat intermediate, like a spliceosome lariat.
-this occurs w/ free guanosine attacking OH group

-secondary structures of the splicing complexes with sliceosome systems and group 2 introns are very similar

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38
Q

mRNAs will ____ at 5’ end and _______ at 3’ end

A

cap
polyadenylate

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39
Q

capping

A

a significant amount of methylation clustered at 5’ end of mRNA

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40
Q

cap studies used mRNA because

A

easier to purify

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41
Q

the B-phosphate of a nucleoside triphosphate….

A

remains only in the 1st nucleotide in an RNA
-linkage is a triphosphate

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42
Q

what is the 5’ cap made of

A

modified guanine: 7 methylguanosine

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43
Q

reovirus cap structure

A

the modified guanine (7methylguanosine) gives 1 positive charge

triphosphate link gives 3 negative charges

phosphodiester bond gives 1 negative charge

terminal phosphate gives 2 negative charges

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44
Q

reovirus cap is the…

A

base hydrolysis of viral mRNA followed by ion exchange chromatography

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45
Q

cap synthesis

A
  1. RNA triphosphate removes terminal phosphate from pre mRNA
  2. Guanylyltransferase adds capping GMP from GTP
  3. a methyltransferase will methylate N7 of capping guanosine
  4. methyltransferase catalyzes 2’ O methylation of penultimate nucleotide
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46
Q

cap synthesis occurs

A

early in transcription before chain gets to be 30 nt long.

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47
Q

guanylyl transferase function

A

–add

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48
Q

methyltransferase function

A

–add

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49
Q

What is the purpose of capping>

A
  1. protects mRNA from degradation
  2. enhance translation of mRNA
  3. transport mRNA out of nucleus
  4. helps splice mRNAs
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50
Q

polyadenylation is found…

A

in 3’ end of mature mRNA.
its not a part of DNA it is added.

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51
Q

polyadenylation

A

adding a poly A to RNA
-long chain of AMP residues is called poly A tail

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52
Q

heterogenous nuclear mRNA is…

A

a precursor to mRNA

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53
Q

the cut and falling of RNA poly is…

A

simultaneous.

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54
Q

eukaryotic mRNAs/their precursors have a chain of AMP residue about …

A

250nt long, at their 3’ ends

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55
Q

Poly A is added _______ by an enzyme called _____

A

post transcriptionally
poly A polymerase

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56
Q

poly A is not a product of transcription , it is not encoded in DNA (t/f)

A

true

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57
Q

functions of Poly A

A

-enhances lifetime and translation of mRNA
-required for transport of mRNAs from nucleus to cytoplasm

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58
Q

mechanism of poly A

A

-transcription of eukaryotic genes extends beyond polyadenylation site
-the transcript is cleaved, and polyadenylated at 3’ end

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59
Q

polyadenylation signals

A

-minimum polyad signal:

-AAUAA motif, about 20nt upstream of a polyad site in preMRNA
-followed 23 bp later by GU rich motif
-followed immediately by U rich motif

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60
Q

polyadenylation involves both:

A

-pre mRNA cleavage
-polyad at the cleavage site

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61
Q

cleavage in mammals requires these proteins:

A

CPSF, CstF, CF1, CF2, Poly A polym, RNA poly 2

^^^CF1 and CF2 are used to cut

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62
Q

Initiation of Polyad

A

-2 proteins participate in this initiation:
CPSF binds to the AAUAAA motif
Poly A polymerase

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63
Q

signal for initiation of Polyad

A

AAUAAA followed by 8nt
-when polyA reaches 10nt length, further polyad becomes independent of the AAUAAA signal, and will depend on the polyA itself.

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64
Q

elongation of PolyA

A

-requires a specificity factor: Poly A binding protein 2 (PAB2)
-PAB2 binds to a pre initiatied oligoA
-this will aid poly A polymerase in elongating the poly A to 250 nt or more.

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65
Q

PAB2

A

PAB2 acts independently of AAUAAA motif
PAB2 depends only on poly A
its activity is enhanced by CPSF

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66
Q

model for polyadenylation

A

-factors assemble on the pre mRNA, guided by motifs
-cleavage occurs
-polymerase initiates polyA synthesis
-PAB2 allows rapid extension of the oligo A to full length

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67
Q

RNA processing during transcription

A

all 3 RNA processes occur during transcription.

-splicing- occurs when transcript is still underway
-capping- occurs when nascent mRNA is 30nt long, and when the 5’ end of RNA emerges from polymerase
-polyadenylation occurs when mRNA is cut at the polyad site

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68
Q

binding CTD of RPB1 to mRNA process proteins

A

CTD of RPB1 of RNA poly 2 is involved in all 3 types of RNA processing,
capping, splicing, and polyad bind directly to the CTD which serves as a platform.

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69
Q

termination of transcription by RNA poly 2 occurs in 2 steps

A
  1. transcript will have a co -transcript cleavage (CoTC), within the termination region downstream of the polyad site
  2. cleavage and polyad occur at the polyA site, signals the polymerase to leave the template
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70
Q

translation is…

A

-ribosomes reading the genetic message in mRNA, and making the corresponding protein.

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71
Q

ribosomes are _______ factories

A

protein making

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72
Q

transfer RNAs (tRNAs) are ________ that bind an AA at one end, and _______ at the other end

A

adaptors
interact with mRNA

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73
Q

2 main components of translation

A

ribosome and tRNA

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74
Q

last three nucleotides of tRNA

A

CCA

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75
Q

what has to occur before initiating translation?

A

-make aminoacyl tRNAs: AAs must be covalently bound to tRNAs
-dissociation of ribosomes into their 2 subunits:
the cell will make the initiation complex on the small ribosomal subunit. the two subunits must separate.

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76
Q

translation initiation complex is assembled on …

A

small ribosomal subunits.

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77
Q

what is tRNA charging

A

the process of bonding tRNA to amino acids

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78
Q

all tRNAs have the same 3….

A

same 3 bases on the 3’ end (CCA)

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79
Q

terminal adenosine is the

A

target for charging with amino acid

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80
Q

during tRNA charging, an amino acid is attached by…

A

ester bonds between its carboxyl group and 2’ or 3’ hydroxyl group of terminal adenosine of tRNA

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81
Q

Two step charging

A

this is done for the aminoacyl tRNA synthetases to join amino acids to their tRNAs:

  1. activation of AA with AMP from ATP
  2. energy from aminoacyl-AMP is used to transfer the AA to the tRNA
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82
Q

E coli ribosomes dissociate into subunits at….

A

the end of each round of translation.

this is promoted by RRF and EF-G

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83
Q

RRF

A

ribosomal removal factor

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84
Q

IF3 binds to free 30S subunit to…

A

prevent reassociation with 50s subunit, to form a whole ribosome.

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85
Q

50s and 30s subunits combine to make…

A

70s subunit

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86
Q

IF3

A

binds by itself to the 30s subunit, stabilized by IF1 and IF2.

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87
Q

IF2

A

IF2 can bind alone, but it is stabilized with the help of IF1 and IF3.

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88
Q

IF1 cannot…

A

bind alone.

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89
Q

IF2 brings…

A

charged tRNA

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90
Q

Once the ribosomal subunits are dissociated, the cell builds a 30S initiation complex

A

includes:
-mRNA
-Aminoacyl tRNA (fMet-tRNA)
-Initiation factors (IFs)

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91
Q

when mRNA binds to 30s…

A

-16s rRNA can interact, and AUG will fit on top of the P site of 30s.
-tRNA will bind to the AUG, with an f-met unit.
-now, 50s subunit can bind, and it will bind with f-met unit.

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92
Q

Prokaryotic initiation codons:

A

AUG (most common)
GUG
UUG

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93
Q

the initiating aminoacyl tRNA

A

N-formyl-methionyl-tRNA

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94
Q

N formyl methione (fMet)

A

is the first amino acid incorporated to the polypeptide
-its usually removed from the mature protein

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95
Q

the 30s initiation complex is formed from…

A

a free 30s ribosomal subunit + mRNA + fMet-tRNA

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96
Q

the binding between the 30s prokaryotic ribosomal subunit and the initiation of mRNA depends on..

A

the base pairing with:
-Shine Dalgarno seq (upstream of the initiation)
-complementary seq of the 3’ end of 16s RNA

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97
Q

the Shine dalgarno seq is complementary to

A

the 3’ end of 16s e coli rRNA.

-mediated by IF3, all 3 IF factors will bind.
IF1 and 2 will assist.

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98
Q

ribosome binding occurs when theres…

A

3 or more base pairs

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99
Q

____ is the first tRNA and the major factor promoting the binding of fMet-tRNA to the _______

A

IF2.
-30s initiation complex.

** IF1 and IF3 are necessary for support.

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100
Q

______ is required for IF2 binding, but _____ is not hydrolyzed in the process.

A

GTP
GTP

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101
Q

the complete 30s initiation complex:

A

-30s ribosomal subunit
-mRNA
-fMET-tRNA
-GTP
-IF1, IF2, IF3

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102
Q

GTP is hydrolyzed after…

A

the 50s subunit joins the 30s complex to make the 70s initiation complex.

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103
Q

GTP hydrolysis is carried out by …

A

IF2 with the 50s ribosomal subunit.

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104
Q

Purpose of hydrolysis

A

-release IF2 and GTP from the complex so that the polypeptide elongation can start.

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105
Q

Bacterial translation initiation

A
  1. RRF + EF-G dissociate the 70s ribosome into 50s and 30s.
  2. IF3 binds to 30S, prevents subunit re associating
  3. IF1 and IF2/ GTP alongside IF3 binds.
  4. binding of mRNA and fMEt-tRNA to form the 30S initiation complex
  5. binding of 50s with loss of IF1 and IF3
  6. IF2 dissociation with simultaneous GTP hydrolysis.
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106
Q

binding of mRNA and fMEt-tRNA to form the 30S initiation complex

A

-can bind in any order
-IF2 sponsors fMET-tRNA
-IF3 sponsors mRNA

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107
Q

Eukaryotic initiation of translation

A

-starts with methionine
-initiating tRNA differs from interior tRNA
-no shine dalgarno
-mRNA have caps on 5’ end
-no ribosome binding site

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108
Q

bacterial initiation of translation

A

-n formyl methionine
-shine dalgarno sequence, shows ribosomes where to start

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109
Q

eukaryotic 40s ribosomal subunits locate the start codon by…

A

binding to 5’ cap first, then scanning downstream to find the 1st AUG that is favorable (Kozaks rules)
-5-10% of the time, the 1st AUG will be passed in search of a better one

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110
Q

Translation with a short ORF

A

-ribosomes will initiate at an upstream AUG
-translate short ORF
-continue scanning
-reinitiate at a downstream AUG

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111
Q

Secondary structure near the 5’ end of an mRNA can have pos or neg effects:

A

-a hairpin past an AUG can force a pause by ribosome subunit and stimulate translation

-stem loop between cap and initiation site can block scanning, and inhibit translation

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112
Q

bacterial and eukaryotic translation initiation both require IF’s (t/f)

A

true

113
Q

eukaryotic system is more complex than bacterial (t/f)

A

true.
-it has scanning process and factors to recognize the 5’ cap.

114
Q

the eIF4F

A

-cap binding protein
-composed of three parts: eIF4E, eIF4A, eIF4G
-the three parts together form eIF4F

115
Q

eIF4E

A

24kD, cap binding activity

116
Q

eIF4A

A

50kD

117
Q

eIF4G

A

220kD

118
Q

function of eIF4A

A

-RNA helicase:
-unwinds hairpins found in 5’ leaders of eukaryotic mRNA
-unwinding is ATP dependent
-eIF4A needs help from eIF4B (stims helicase and binding to mRNA)

119
Q

function of eIF4G

A

-scaffold protein, it will bind to other proteins:
eIF4E, eIF3, Pab1p
-interacting with these proteins lets eIF4G recruit 40s ribosomal subunits to mRNA, and stim translation

120
Q

eIF3

A

40s ribosomal subunit binding protein

121
Q

Pab1p

A

poly A binding protein

122
Q

polio virus shuts down host cell’s ability to…

A

translate any capped mRNA
-polio has RNA that serves as mRNA
-a viral protease cleaves off aminoterminal domain of eIF4G
-only viral RNA gets translated through IRES in viral mRNA

123
Q

during polio, the DNA is not capped/methylated, but ….

A

it is still translated in the cell

124
Q

IRES

A

internal ribosome entry site

125
Q

eIF4G as an Adaptor step 1

A
  1. cap recognition:
    eIF4G is an adapter between eIF4E (which is bound to the cap) and eIF3 (bound to 40s subunit) that helps recruit 40s subunit to a site near the cap
126
Q

eIF4G as an Adaptor step 2

A
  1. IRES recognition:
    IRES interacts with the remnant of eIF4G recruiting 40S subunit.
127
Q

eIF4G as an Adaptor step 3

A
  1. Cap and poly A recognition: synergism between cap and poly A.
    the eIF4E bound to the cap and Pab1p bound to poly A both bind to eIF4G
    -now the initiation process is done, and the ribosome will translate.
128
Q

The Shine-Dalgarno sequence is found in

A

mRNA

129
Q

This initiation factor is involved in binding tRNA to the ribosome.

A

eIF2

130
Q

This initiation factor is a Cap binding protein

A

eIF4F

131
Q

This initiation factor binds to the 40S subunit and inhibits reassociation of the 40S and 60S subunits

A

eIF3

132
Q

This initiation factor binds to the 60S subunit and inhibits reassociation of the 40S and 60S subunits

A

eIF6

133
Q

The first amino acid in all mature proteins in prokaryotes is an N-formyl-methionine (t/f)

A

false

134
Q

The 30S initiation complex does not include

A

5S rRNA

135
Q

this SnRNP base pairs with 5’ splice site of mRNA

A

U1

136
Q

this SnRNP base pairs with the conserved sequence at splicing branch point

A

U2

137
Q

this SnRNP associates with last nucleotide in one exon and the first nucleotide in the next exon

A

U5

138
Q

this SnRNP base pairs with 5’ end of the intron

A

U6

139
Q

The snRNPs are usually involved in which of the following?

A

splicing

140
Q

Splicing signal sequence has _________ bases at 5’ end, and _________ bases at the 3’ end of the introns.

A

GU, AG

141
Q

The process by which introns are removed from immature mRNA is called ______________.

A

RNA splicing

142
Q

The semidiscontinuous nature of DNA replication was proven by the discovery of _____________

A

Okazaki fragments.

143
Q

OriC is called an origin of DNA replication in ________.

A

E coli

144
Q

In _______________ replication of DNA the two parental strands stay together and the two new daughter strands are produced.

A

semiconservative

145
Q

_______________ introduces transient single stranded or double stranded breaks in DNA.

A

topoisomerase

146
Q

The correct order of the steps of 5’-Cap synthesis based on the following:

A

1 The terminal phosphate is removed from the pre-mRNA.
2 A capping GMP is added to the pre-mRNA.
3 N7 of the capping guanine is methylated.
4 The 2’-O-methyl group of the penultimate nucleotide is methylated

147
Q

Functions of the mRNA cap include all EXCEPT

A

helps regulate expression of the mRNA

148
Q

The poly(A) tail of eukaryotic mRNA is exactly 150 nucleotides in length. (t/f)

A

false. 250

149
Q

The polyadenylation of pre-mRNA does not require

A

RNA polymerase I

150
Q

The _______ has ribosome-dependent GTPase activity.

A

IF-2

151
Q

During protein translation, elongation takes place in this order:

A
  1. EF-Tu, with GTP, binds an aminoacyl-tRNA to the ribosomal A site.
  2. Peptidyl transferase forms a peptide bond between the peptide in the P site and the newly arrived aminoacyl-tRNA in the A site.
  3. EF-G, with GTP, translocates peptidyl-tRNA to the P site
152
Q

Ribosome recycling factor (RRF) resembles a tRNA molecule. (t/f)

A

true

153
Q

elongation is similar in bacteria and eukaryotes (t/f)

A

true

154
Q

mRNA read AND synthesized in the _ to _ direction

A

5’ to 3’

155
Q

proteins are made in the __ to ___ direction

A

amino to carboxyl

156
Q

the ______ terminal amino acid is added first

A

amino

157
Q

genetic code

A

set of 3 codons in mRNA that represent the 20 AA’s in proteins

158
Q

mutations show their effect….

A

down stream

159
Q

types of frameshift mutations

A

add a base
delete a base
cross _ and _
add 3 bases

160
Q

adding 3 bases to a sequence will change …. as opposed to adding 1 base

A

very little
1 base changes a lot

161
Q

in mRNA codons instruct the ribosome to…

A

incorporate specific AA’s into a polypeptide

162
Q

genetic code can overlap (t/f)

A

false. each base is apart of 1 codon only.

163
Q

the genetic code doesnt have gaps or commas (t/f)

A

true

164
Q

3 codon sequence for methionine

A

AUG

165
Q

the stop. codons

A

UAA
UAG
UGA

166
Q

Not all amino acids will make a tRNA…

A

this will conserve energy.

167
Q

types of degeneracy in genetic code:

A

-isoaccepting species of tRNA: bind to the same AA, but recognize different codons

-wobble

168
Q

wobble

A

the 3rd base of a codon is allowed to move slightly from its position to form a non-Watson Crick pair with the anticodon.

169
Q

wobble allows the same,,,

A

aminoacyl-tRNA to pair with more than one codon

170
Q

wobble pairs are….

A

GU
IA

171
Q

in wobble, _____ has to be W-C pairing,

A

2/3.
the third can wobble.

172
Q

genetic code is universal. (t/f)

A

false.

173
Q

eukaryotic nuclei and _____ along with at least one bacterium can have altered code

A

mitochondria

174
Q

mitochondrial genomes and nuclei of at least one….

A

yeast have sense of codon changed from one AA to another. theyll have their own cellular machinery.

175
Q

there can be ______ from the universal genetic code

A

deviations

176
Q

EF-T

A

T for transfer.
transfers aminoacyl tRNAs to the ribosome.
-involved in 1st step of elongation
-its made of 2 different proteins: Tu’s and T’s.

Ef-Tu: unstable
Ef-Ts: stable

177
Q

EF-G

A

-G for GTPase
-EF-G is in the 3rd step of elongation.

178
Q

GTP and _____are needed for translocation

A

EF-G

179
Q

a new round of elongation will occur if …

A

EF-G is released from the ribosome, which depends on GTP hydrolysis.

180
Q

as the elongation cycle repeats…

A

it will add AA’s one at a time
-it will grow the polypeptide, until ribosome reaches a stop codon-now time for termination.

181
Q

mutations can create termination codons in mRNA…

A

causing premature termination of translation.

182
Q

amber mutation

A

creates UAG

183
Q

ochre mutation

A

creates UAA

184
Q

opal mutation

A

creates UGA

185
Q

stop codon suppression

A

suppresses the stop codon, AUG to AUC

186
Q

release factors recognize…

A

stop codons

187
Q

prokaryotic tranlation termination is mediated by 3 factors:

A

-RF1 recognizes UAA and UAG
-RF2 recognizes UAA and UGA
-RF3 is GTP binding, helping bind RF1 and RF2 to ribosome.

188
Q

eukaryotes have 2 release factors:

A

eRF1 recognizes all 3 termination codons

eRF3 is ribosome dependent GTPase, helping eRF1 release the finished polypeptide

189
Q

eukaryotic ribosomes are released by

A

eIF3
-aided by eIF1, eIFA, and eIF3j

190
Q

prokaryotic ribosomes need help from ____ and ____

A

RRF
EF-G

-RRF resembles a tRNA, binding to ribosome A site, but using a position not normally taken by tRNA.
-collaborates w EF-G in releasing 50s subunit or the whole ribosome.

191
Q

double helix model states the two strands are

A

complementary

192
Q

DNA replication is….

A

bidirectional
semi conservative
requires primers
half discontinuous

193
Q

In DNAs semidiscontinuous replication …

A

template is read 3’ to 5’
synthesized 5’ to 3’

194
Q

The transcript bubbles limitation

A

it can only read 2kilo bp

195
Q

in semi discontinuous the _____ strand is replicated continuously, and the _______ strand is replicated discontinously in _______

A

leading
lagging
okazaki fragments

196
Q

okazaki fragments in e coli are initiated with rna primers ______ long

A

10-12 nt

197
Q

primers can be hard to detect in cells because of

A

enzymes that attack RNAs

198
Q

dna replication starts with bubble:

A

area where parental strands are seperated and new dna is synthesized

199
Q

bidirectional replication fork

A

two replicating forks moving oppositely away from the origin

200
Q

replicon

A

dna with one origin of replication

201
Q

there are _______ dna polymerases in E coli

A

pol 1
pol 2
pol 3

202
Q

dna pol 1

A

versatile enzyme with 3 activities:
-dna pol
- 3’ to 5’ exonuclease
-5’ to 3’ exonuclease

203
Q

proteolytic treatment of dna pol 1

A

creates 2 polypeptides:
klenow fragment
smaller fragment

204
Q

klenow fragment

A

has both polymerase, and the 3’ to 5’ exo nuclease activity, serving as proofreading.
if mistake, pol 1 pauses, exonuclease removes mistake.

205
Q

5’ to 3’ exonuclease

A

allows pol 1 to degrade the strand ahead of the polymerase
-in one pass it will remove and replace the strand.

206
Q

dna poly 2 and 3

A

pol 2 is NOT required for DNA replication
pol 3 is the only dna poly REQUIRED for dna replication, and is the enzyme to replicate bacterial DNA

207
Q

DNA pol 1 appears mostly active as….

A

DNA repair

208
Q

DNA pol 3 holoenzyme

A

-dna pol is in the alpha (aka synthesis)
-3’ to 5’ exonuclease is in the 3 subunit
-O subunit is unknown
-y is for atp-ase
-B subunit + the other 8 subunits make up the holoenzyme

209
Q

dna dependent ATPase is in the ….

A

y - complex , with 5 subunits .

210
Q

these subunits make up the core polymerase

A

alpha
3
O

211
Q

T subunit

A

helps in dimerization of core

212
Q

primers are made of ____ which helps mark them for degredation

A

RNA

213
Q

only a ________ can serve as a primer for pol 3 holoenzyme

A

base paired nucleotide

214
Q

strand unwinding

A

requires energy and enzymes
the helicase enzyme unwinds dsDNA, then its readu for SS DNA bind protein.

215
Q

prokaryotic single strand DNA binding proteins

A

bind ssDNA much more strongly than dsDNA
-help helicase
help it from re annealing
-protect from degradation
-ESSENTIAL for prokaryotes

216
Q

topoisomerases

A

helicase use ATP to unwind, causing supercoil.
topoisomerase will release stress and prevent supercoil

217
Q

two types of topoisomerase:

A

type 1: temporary nicks in the SS
type 2: (the GYRASE) introduce single or ds breaks in DNA and allow it to change form.

218
Q

topoisomerase process

A

binds with G-seg, uses T-seg, then repairs G-seg.
-holds onto one strand, allows T seg, repairs.

219
Q

mismatch repair recognizes parental strand by…

A

methylated A in GATC seq

220
Q

mismatch repair

A

-recognizes parental strand
-corrects mismatch in new strand
-eukaryotes use part of repair system
-distinguish strands at mismatch

221
Q

methylated =_____ DNA
unmethylated = _____ DNA

A

original
new

222
Q

the nick in a strand corresponds to a

A

methyl group

223
Q

exonuclease ___
DNA poly 3 holoenzyme ____
DNA ligase _____

A

cuts
extends
fills gap

224
Q

DNA ligase

A

makes phosphodiester bonds with opposing DNA ends

225
Q

DNA helicase will _____ DNA
primase will ensure the ____

A

open up
continuation of making protein

226
Q

initiation of DNA replication means….

A

primer synthesis

227
Q

DNA poly cant synthesize without ____ which is made by _____

A

primers
DNA primase (DNA G)

228
Q

primosome

A

collection of proteins needed to make primers

229
Q

in e coli the primosome contains

A

DNA helicase (DNA B)
DNA primase (DNA G)

230
Q

primosome is assembled at the….

A

oriC

231
Q

the e coli oriC is a ____ bp DNA with 2 regions:

A

245 bp
the DUE and the DOR (protein binding, and DNA unwinding)

232
Q

what does DOR stand for

A

DNA A oligomerization region

233
Q

DNA A, ATP, HU… will only bind at

A

oriC

234
Q

DNA A binds to oriC at the

A

DNA A boxes 9 mers
helps rna poly and HU protein melt DNA

235
Q

DNA B (helicase) binds to the

A

open complex and helps binding of primase to complete the primosome
-unwinds DNA as replisome progresses

236
Q

primosome will stay with the _____ and repeatedly prime the ______ synthesis on lagging strand

A

replisome
okazaki fragment

237
Q

pol 3 holoenzyme synthesizes DNA at a rate of

A

730nt/sec to 1000nt/sec

238
Q

pol 3 core alone

A

very poor polymerase
will fall off of template after 10 nt and take 1 min to reassociate

239
Q

the B subunit of holoenzyme

A

-keeps pol engaged with template
-called sliding clamp

240
Q

core poly + B subunit

A

replicates DNA processively at 1000nt/sec
-B subunit forms a ring shaped dimer to fit around DNA template, and interacts w alpha unit to tether the whole polymerase and template together

241
Q

in eukaryotes what is the processivity factor, similar to the B clamp

A

PCNA. PCNA will form trimer, which forms ring to encircle DNA and hold it to template

242
Q

the B clamp will be replaced with…

A

core subunit

243
Q

the B subunit needs help from…

A

y - complex to load onto DNA template, and y complex will not remain afterwards.

244
Q

clamp loading is _____ dependent

A

ATP

ATP changes shape of loader, so that the S subunit can bind to a B subunit, and allow for the encircling and opening of clamp

245
Q

the pol 3 holoenzyme is…..

A

double headed

246
Q

there are 2 core polymerases attached through two _ subunits to a ______

A

T
y complex.

one core ensures continuous synth of leading strand
one core performs discontinous synth of lagging strand

247
Q

the y comlpex serves as a …

A

clamp loader, to load the B clamp to a primed DNA template

248
Q

After the B clamp is loaded…

A

the B clamp loses affinity for y complex, and associates with core polymerase

249
Q

the y complex and B clamp help….

A

core poly with processive synthesis of Okazaki fragment

250
Q

when the okazaki fragment is complete, the B clamp…

A

loses affinity for the core poly, and associates again with y complex, clamp recycles.

251
Q

bacterial replication

A

2 replication forks approach each other at the terminus region

252
Q

termination of replication for phage

A

phage produces long/linear concatemers, that grow until the genome sized piece is cut off, and put onto the phage head.

253
Q

terminus region has ____ bp terminator sites, that bind to specific proteins: the ___

A

22
TUS

254
Q

TUS stands for

A

terminus utilization substance

255
Q

termination of DNA rep process

A

replicating forks enter terminus, pause, leave 2 daughter duplexes tangled, and must seperate.

256
Q

what enables decatenation

A

topoIV decatenates the daughter duplexes

257
Q

DNA _____ acts as a swivel during DNA replication

A

gyrase

258
Q

two stage model for decatenation

A

-denaturation of remaining parental double helix (it still remains tangled together)
-repair synthesis fills in the single stranded gaps
-decatenation (topoIV) seperates daughter duplexes

259
Q

where are telomeres located

A

the ends of eukaryotic chromosomes

260
Q

one strand of telemores contains:

A

-tandem repeats of short G rich regions

261
Q

Telomerase enzyme makes…

A

G rich telomere strand
Telomerase has a short RNA, that serves as a template for telomere synthesis.

262
Q

telomeres help …

A
  • prevent degradation
    -and extends chromosome ends by using their own template
    -then fold in on themselves to secure
263
Q

lagging strand is efficient because of

A

-differential affinity clamp B clamp
-looping
-Okazaki fragments

264
Q

the 5’ end can never be…

A

extended.

this means a gap is made, which can be aided by telomerase, which CAN extend the 3’ end.

265
Q

steps of telomere formation

A

-elongation
-translocation
-elongation
-primer synthesis
-DNA replication
-primer removal

266
Q

all eukaryotes protect their _______ from nucleases, and ds break repair enzymes

A

telomeres

267
Q

eukaryotes have telomere ________

A

binding proteins

268
Q

telomere binding proteins

A

protect from degradation
hide telomere ends from DNA repair factors

269
Q

telomeres are linear (t/f)

A

false.
they form a DNA t-loop.

270
Q

Why is t loop formed

A

single stranded 3’ end of telomere invading the ds telomere DNA upstream

271
Q

function of telomere

A

prevent chromosome degradation and prevent DNA repair from finding ends of chromosomes

272
Q

telomere binding proteins

A

called “shelterin”
theres 6:
TRF1
TRF2
TIN2
POT1
TPP1
RAP1

273
Q

TRF1 and TRF2…

A

homologous. they bind to the ds part of telomeres.

274
Q

telomere binding protein TRF1

A

-binds to ds part of telomeres, TTAGG repeat binding factor

275
Q

telomere binding protein TRF2

A

homologous to TRF1, binds to ds part of telomeres

276
Q

telomere binding protein POT1

A

protects telomeres, binds ss 3’ tail of telomeres

277
Q

telomere binding protein TPP1

A

POT1 binding protein

278
Q

telomere binding protein TIN2

A

TRF1 interacting factor, and organizes.

279
Q

telomere binding protein RAP1

A

repressor activator protein

Flash Cards (21 decks)

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