biol 3250 - chapter 11 and 12

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72 Terms

1
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dna replication occurs in a 5’ to ?

3’ direction with respect to dna structure and relies on the complementary of dna strands

  • AT/CG RULE

2
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the two complementary dna strands come apart at the ?

replication fork and each serves as the template strand for the synthesis of new complementary dna strands

3
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the two newly-made dna strands

daughter strands

4
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the two original strands

parental strands

5
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one replicated strand and the leading strand occur in what direction ?

towards the replication fork

6
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one replicated strand and the lagging strand occur in what direction ?

away from the replication fork

7
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DNAaA boxes

sites for the binding of DNaA protein

8
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at-rich regions

sites where the dna strands separate

9
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GATC methylation sites

sites that help to regulate dna replication

10
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initiation of replication only occurs when?

when dna is fully methylated

11
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dna synthesis requires a ?

rna or dna primer

12
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in the cell, both the lagging and leading replicated dna strands are synthesized by ?

DNA pol lll by using rna primers synthesized by the primase protein

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primosome

coordinates the actions of helicase and primase

14
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dna polymerase catalyzes ?

the formation of a covalent ester bond between the innermost phosphate group of the incoming deoxyribonucleoside triphosphate and 3’-OH of the sugar of the previous deoxynucleotide

15
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the last two phosphate of the incoming nucleotide are released how ?

in the form of pyrophosphate (PP)

16
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what polymerase is associated with the primase protein?

dna polymerase alpha

17
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polymerase switch

dna poly a is exchanged with dna polymerase epsilon to synthesize the leading strand and the dna polymerase delta to synthesize the lagging strand

18
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what features are dna polymerase defined by ?

  1. synthesize dna only in the 5’ to 3’ direction

  2. cannot start dna synthesis on an unprimed dna strand

19
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at the 3’ ends of linear chromosomes -

the end of the strand cannot be replicated !

20
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the telomerase protein binds to ?

telomeric repeat sequences in the telomeres at the ends of the chromosome using an rna primer

21
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what is the name of the rna primer used in telomerase protein ?

telomeric rna

  • replicated the ends of the chromosomes

22
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not all rna is ?

mrna

23
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what is mrna translated into ?

proteins

24
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the central dogma

dna - mrna - protein

25
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regulatory sequences

sites for the binding of regulatory proteins that influence the rate of transcription

26
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promoter

site for rna polymerase binding which signals the beginning of transcription

27
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terminator

signals the end of transcription

28
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ribosome-binding site

site for ribosome binding to mrna in bacteria which begins the translation of mrna into a protein

29
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codons

3 nucleotide sequences within the mrna that specify particular amino acids

  • the sequence of codons within mrna determines the sequence of amino acids within a polypeptide

30
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start codon

specifies the first amino acid in a polypeptide

sequence, usually a formylmethionine (bacteria)

and methionine (eukaryotes)

31
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stop codon

specifies the end of polypeptide synthesis

32
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the base sequence in the mrna is ?

identical to the coding or sense strand of dna

  • except for the sub of uracil in rna for thymine in dna

33
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the dna strand that is actually transcribed (template) is termed the ?

template strand and is complementary to the sense strand

34
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the mrna transcript is ?

complementary to the template strand

35
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what enzyme catalyzes the synthesis of rna ?

rna polymerase

36
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in e.coli, rna polymerase holoenzyme is composed of ?

rna polymerase core enzyme

  • five subunits, a2bb’w, sigma factor

37
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rna polymerase core enzyme

a2bb’w

38
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rna poly core enzyme + sigma factor =

rna polymerase holoenzyme

39
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rna polymerase core enzyme binds loosely to the dna -

then it scans along the dna , until it encounters a promoter

  • when it does, the sigma factor recognizes both the 35 and 10 sequences

  • a region within the sigma factor that contains a helix-turn-helix structure is involved in the binding to the dna

40
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rna polymerase does not need a ?

dna or rna primer to replicate dna to rna

41
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e. coli has two different mech. for termination

  1. rho-dependent termination

  2. rho-independent termination

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rho-dependent termination

requires a protein known as (rho)

43
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rho-independent termination

uses proteins other than rho

44
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rho-dependent termination uses the rho protein, which binds to a rho recognition site (rut), that is ?

transcribed in the rna and a stem-loop is formed by a stretch of GC nucleotide in the rna causes rna polymerase to stall and release from the dna

45
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rho independent termination use a GC rich stem loop structure at the end of the mrna that is followed by ?

a uracil-rich sequence, auxiliary proteins (nursa)

  • these bind to both the rna and rna polymerase causing it to pause at the stem-loop structure and release rna polymerase from the dna

46
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nuclear dna is transcribed by three different rna polymerases

rna pol 1

rna pol 2

rna pol 3

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rna pol1

transcribes all rrna genes (no 5s rrna)

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rna pol2

transcribes all mrnas

some snrnas genes needed for splicing

49
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rna pol3

transcribes all trna genes, 5s rrna gene, microrna genes

50
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regulatory elements are short dna sequences that affect the binding of rna polymerase to the core promoter. transcription factors (proteins) bind to these elements and influence ?

the rate of transcription

51
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enhancers

stimulate transcription

52
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silencers

inhibit transcription

53
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enhancers and silencers locations

-50 to -100 region upstream of the promoter

54
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regulatory elements are ?

cis with respect to the gene they regulate

55
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transcription factors are ?

trans with respect to the gene that they regulate

56
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cis acting elements

dna sequences that exert their effect only over a particular gene, like TATA box, enhancers and silencers

  • found near the gene that they regulate and are on the same chromosome the has the regulated gene

57
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trans acting factors

regulatory proteins that bind to the promoter region of genes

  • control many genes and the genes that encode them are not located near the gene that they regulate

58
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rna polymerase ll

five different proteins called general transcription factors

  • protein complex called mediator

59
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mrnas are modified by cleavage near their 3’ end with subsequent attachment of a string of adenines to form a ?

polyadenylated (polyA) tail

-can happen in bacteria

60
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termination according to the allosteric model is ?

aided by termination factors

61
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termination according to the torpedo model is ?

aided by exonucleases

62
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most eukaryotic mrnas have introns that are removed from the ?

mrna before its translated into a protein

63
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ribosomal rna is also ?

processed from a larger precursor in bacteria

64
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eukaryotic trna is also processed from a ?

large precursor

65
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intron rna is spacer rna that is ?

removed from the final rna

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exon rna is the rna that is ?

contained in the final rna

67
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rna splicing occurs in ?

both bacteria and eukaryotes

  • but splicing using a spliceosome only happens in eukaryotes

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are there spliceosomes in bacteria ?

no

69
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does alternative splicing of mrna happen in bacteria ?

alternative splicing of mrna does not happen in bacteria

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bacterial mrna does not have a ?

7-methyl-guanosine cap at their 5’ end

71
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some bacterial mrna have a ?

polyA tail

72
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does rna editing occur in bacteria ?

yes