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Flashcards in Final Exam Recap Deck (108):
1

DNA protein complex that makes up eukaryotic chromasomes is called ______

chromatin

2

What do histones bind to and what do they do

Positively charged histones bind to chromatin and counteract the negative charge on DNA backbone

3

How does Eukaryotic DNA packaging work

Two H3-H4 dimers associate with DNA, Two H2A- H2B dimers associate to form octamer, in left handed direction, negatively supercoiled

4

Acetylation promotes _______

euchromatin

5

Deacetylation promotes _______

heterochromatin

6

How may ori per chromosome for prokaryotes

one

7

how many ori per chromosome in eukaryotes

many

8

what specifies replication termination in prokaryotes

ter

9

What directs chromosme segregation in eukaryotes

centromeres

10

what stabilizes the end of chromosomes in eukaryotes

telomeres

11

where does replication start

ori

12

DNA synthesis is _' --> _'

5 -> 3'

13

DNA synthesis needs a ____

primer

14

Initiator proteins bind to ____

origins

15

What is the initiator in E.coli

DnaA

16

What is the initiator in eukaryotes

ORC

17

ATP binding by ____ required for ORC to bind to DNA

Orc1

18

What two helicase proteins does ORC recruit

Cdc6 and Cdt1

19

how is initiation regulated in e.coli

DnaA binds and multimerizes at oriC when bound to ATP, after initiation, sliding calmp and Hda stimulate hydrolysis of DnaA-ATP

20

What is the major regulatory step preventing initiation

RIDA

21

In eukaroytes origins are selected in __ phase and activated in __ phase

G1 phase, S phase

22

what is the helicase used in replication initiation for eukaryotes called

MCM

23

what is the helicase used in replication initiation for prokaryotes called

DnaB

24

what two proteins assist DNA polymerase during replication elongaion

clamp loader and sliding clamp

25

when does termination occur in eukaryotes

when two different forks meet, when fork reaches end of chromosome or when polymerase meets previously replicated strand

26

What connects adjacent strands in eukaryotes

DNA ligase

27

where does termination occur in prokaryotes

at ter site, on opposite side of the chromosome from ori

28

ter is bound by ___

Tus

29

entangled daughter chromosomes are resolved by _____

topoisomerases

30

when errors are found by DNA polymerase ____ remove the incorrect nucleotide

exonucleases

31

what do the two magnesium ions at the active site do

one activates the 3' OH, the other interacts with the incoming dNTP and stabilizes the negative leaving oxygen

32

what are the three steps in PCR

Denaturation, Annealing, Extension

33

What is chain-determination dideoxynucleotide sequence

a single primer is annealed and the primer is extended with the DNA polymerase, contains deoxy bases and some dideoxy bases

34

What is illumina sequencing

Requires more upfront preparation, fragment capture, amplification and sequencing

35

in tRNA, ____ of the double helices are formed by ____

three, hairpins

36

what is a riboswitch

bind a small molecule that control the RNA secondary structure

37

what are the two regions in riboswitches

aptamer that binds to the metabolite, and the expression platform

38

effects of different riboswitches vary to ____ or ____ transcription or translation

promote or prevent

39

T or F: splicing occurs in all acracea, bacteria and eukaryotes

True

40

T or F: 5' capping occurs in all archaea, bacteria and eukaryotes

F, only in eukaryotes

41

T or F: polyadenylation occurs in only eukaryotes

True

42

What does splicing do

joins two exons from either side of an intron

43

T or F: 5' cap is needed for efficient transcription elongation and termination

T

44

polyadenylation occurs at the __' end after a __

3', CA

45

T or F: a larger protein complex is required for polyadenylation than for 5' capping

T

46

what is the C-terminal domain responsible for

mediating mRNA processing

47

C-terminal domain is part of a RNA polymerase subunit called ___

Rpb1

48

What happens when CTD is phosphorylated

when transcription has not yet begun; 'ready to go' RNA polymerase

49

What happens when CTD is party phosphorylated

during transcription initation, recruits the capping enzyme

50

Wht happens when CTD is fully phosphorylated

during transcription elongation, recruits splicing machinery

51

RNA stability is affected by what factors

-structures at 5' and 3' ends
-5' cap in eukaryotic mRNAs protects against exonuclease
-3' end stem loops in bacteria
-3' poly(A) tail increases stability in eukaryotic mRNA

52

what is the first base to be transcribed in transcription

TSS

53

RNA is transcribed _' -> _'

5' -> 3'

54

___ repairs behind the enzyme, maintaining the transcription bubble

DNA

55

What are the three additional types of enzymes required in eukaryotic transcription

Nucleosome remodeling enzymes, histone chaperones, and enzymes that reevrisbly modify histones

56

What are nucleosome remodeling enzymes

reposition histones away from the DNA

57

What are histone chaperones

dissasemble and assemble the histone octamer

58

Which polymerase is ATP required to open the transcription bubble

Polymerase II

59

what is protein is involved in abortive initiation in bacteria

sigma factor

60

what protein is involved in abortive initiation in eukaryotes

TFIIB

61

what do sigma factor and TFIIB have in common

both have a loop that extends to the RNA polymerase active site, loop can block the elongating transcript

62

what happens during promoter clearance

RNA polymerase undergoaes conformational change that associates it stably with DNA and loosens its grip on initiation factors

63

how is transcription initiation regulated in bacteria

Trp repressor protein

64

all eukaryotic polymerases need the ____ to initiate transcription

TTA binding protein (TBP)

65

T or F: elongation can backtrack when there is a pause in RNA synthesis

T

66

how does transcription enhance endonuclease activity

transcription cleavage factors chop 3' protruding RNA

67

when RNA polymerase makes mRNA its not usually in final active form, so called _____

pre-mRNA

68

what are the two terminator sequences in bacteria

intrinsic and Rho-dependant

69

what is intrinsic termination

inverted repeat sequences that when transcribed form a stem-loop in RNA, weak base pairing in transcription bubble thought to arrest transcription

70

what is rho-dependant termination

dont have a hairpin or poly(A) structures, Rho is a hexameric ATPase that binds to C-rich areas of RNA, and once bound, closes the ring, ATP hydrolysis drives pulling of RNA

71

What is antitermination

some phage lambda genes are transcribed only when transcription termination is actively prevented, N binds to nut sites in a stem loop form

72

What are the two main models in eukaryotic transcirption termination

allosteric and torpedo

73

what happens in allosteric termination

RNA polymerase II transcribes thorugh poly(A) and 3' processing signals, cleavage or recognition causes conformtional changes that leads to dissociation of Polymerase II from DNA

74

what happens in torpedo termination

RNA downtream of poly(A) tail digested by 5-3' exonuclease (Rat1)

75

What happens in eukaryotic transcirption regulation antitermination

tar site forms a stem loop called TAR element, Tat binds to tar along with cellular kinase that phosphorylates RNA Poly II

76

what does RNA-seq determine

determines which genes are on or offf

77

what are the three steps in RNA-seq

Purify DNA, Reverse- transcribe RNA to cDNA, equence dna fragments

78

what does CRISPR/Cas9 complex do

Cas9 targets a specific DNA site

79

What are the four stages of translation

Initiation, Elongation, Termination, and ribosome recycling

80

What are the initiation factors needed in bacteria

IFI, IF2, IF3

81

IFI binds to _ site of SSU

A

82

IF3 binds to _ site of SSU

E

83

IF2 provides _____ to join ____ + _____

energy, LSU and SSU

84

what is invlolved in eukaryotic translation initiation

mRNA 5' cap and 3' poly(A) tail, cap bound by E1F4E and tail by PABP, forms a closed loop complex

85

What are the three steps in Translation elongation

decoding, peptide bond formation, and translocation

86

what happens in decoding

aminoacyl-tRNA with anticoding that is complementary to mRNA

87

what happens in peptide bond formation

invovles the transfer of polypeptide chain to the aminoacyl tRNA in the A site, binding allows peptidyl tRNA to be positioned in active site

88

what happens in translocation

mRNA bound to tRA in A+P site, EF-G can bind in the A site

89

What recognizes stop codons in translation termination

Class I release factors (tRNAs)

90

What is needed for bacterial termination

Class II Rfs and GTPases, RF3 promote dissociation of RF1/2 after peptide release

91

What is needed for eukaryotic termination tranlsation

eukaryotic class II eRF3 interacting with eRFI before association with ribosome, couples GTP hydrolysis to peptide release

92

What happens during ribosome recycling in bacteria

ribosome recycling factor (RRF) acts with eFG and promotes dissasembly, tRNA and mRNA fall off small subuinit and is stabilized by iF3

93

What happens during eukaryotic ribosome recycling

eRF1 remains bound after ppetide is released, helps dissociation with ATPase ABCEI.

94

what initiation factors in eukaryoes bind to help stabilize the dissociated ribosomal subuits

eFI,eIFIa, and eIF3

95

Bacterial mRNAs are ___cistronic, meaning ______

polycistronic, meaning they have more than one open reading frame

96

T or F: Eukaryotic mRNAs are monocistronic

T

97

uncarged tRNAs are a sign of low _____ abundance

amino acid

98

what is the strignent response

uncharged tRNAs compete with charged tRNAs for binding at ribosomal A site, translation cannot proceed with an uncharged tRNA in A site

99

in eukaryotic translation regulation, uncharged tRNA binds to what

Gcn2

100

phosphorylated eIF2 binds strongly to _____

eIF23

101

What happens to Shine-Delgarno sequence when temperatures are low

base pariing render S-D inacessible

102

What happne sto Shine-Delgarno sequene when temperatures are high

sequence becomes acessible and translation can occur

103

What does affinity purification do

separates mixtures based on anitgen and antibody and antigen enzyme and substrate.

104

what are the three steps in affinity purification

bind, wash, elute

105

what does SDS_PAGE separate based off of

sexe

106

what are the three steps in SDS-PAGE

prepare samples, denature and add charge

107

what does the western blot do

Antibody recognition gives evidence of protein identity and sensitivity

108

what are the two things you can use western blot to target

antibody or His-tag