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CSF final > Final Review Block 2 > Flashcards

Final Review Block 2 Flashcards

1
Q

6 ways that prokaryotic transcription differs from eukaryotic transcription

A
  • in the cytoplasm (not nucleus)
  • no histones
  • transcription and translation at the same time
  • operons
  • polycistronic
  • attenuation
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2
Q

what is the role of sigma factor?

A

present in prokaryotes, unites RNA polymerase and DNA promoter sequences, responsible for unwinding DNA strands, released after 10 nt added

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3
Q

rho independent termination

A

GC rich hairpin followed by series of Us, the series of Us weakness the assoc between RNA pol and DNA and RNA pol falls off

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4
Q

rho-dependent termination

A

weak hairpin that is NOT followed by Us is present, this slows the RNA pol down, the rho protein associates and removes RNA pol from DNA

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5
Q

what is encoded for by the trp operon?

A

5 structural enzymes that form tryptophan synthetase

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6
Q

what occurs when trp is high?

A

trp binds to the repressor protein, repressor protein is activated and binds promoter/shielding in from RNA pol

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7
Q

describe attenuation

A

premature stop mechanism using “leader sequence”, with hairpins 1-2, 3-4

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8
Q

describe attenuation when trp is high

A

when trp is high, ribosome can add 2 trp without delay, 3-4 hairpin forms, rho independent termination occurs and ribosome falls off – premature termination

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9
Q

describe attenuation when trp is low

A

when trp is low, ribosome stalls waiting for 2 trp to add, it stalls over region 1 and 1-2 cannot form, but 2-3 forms instead, thus 3-4 cannot form and ribosome continues

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10
Q

what is controlled by the lac operon?

A

expression of LacZ protein- codes for enzymes that are used to digest lactose

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11
Q

describe (+) glucose, no lactose

A

operon is repressed, no LacZ

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12
Q

describe (+) glucose, (+) lactose

A

presence of lactose inhibits repressor, polymerase is able to bind, yields low expression of LacZ

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13
Q

describe no glucose, (+) lactose

A

catabolic activating protein present, no repressor, high LacZ expression

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14
Q

what is synthesized by the different RNA polymerases?

A

RNA pol I- 5.8s, 18s, 28s rRNA
RNA pol II- mRNA, sno/sn/miRNA
RNA pol III- tRNA, 5s rRNA

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15
Q

what is significant about the -35 and -25 sites in eukaryotic transcription?

A
  • 35- GC rich recognition site

- 25- TATA box

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16
Q

what are the steps in formation of the pre-recognition complex?

A

DBFEH

dogs bark and bite people frequently every halloween

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17
Q

action of TFIID

A

bind TBP and together they bind TATA box

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18
Q

action of TFIIH

A

acts as helices, phosphorylates 5th serine on CTD on RNA pol II leading to release of transcription factors

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19
Q

describe RNA pol I initiation and termination

A

initiation- upstream binding factor, SL1 (TBP+TFs)

termination- rho dependent-like

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20
Q

describe RNA pol III initiation and termination

A

initiaiton- ses internal control regions (except U6 snRNA)

termination- rho independent-like

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21
Q

where is mRNA processed?

A

in the nucleus

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22
Q

describe addition of 5’cap

A

occurs when mRNA about 25 nt long (during transcription), 5’triphosphate is removed by phosphohydrolase, GTP is added in unique 5’-5’ fashion by guanylyl transferase, methyl groups are added

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23
Q

3 functions of 5’cap

A

prevent exonuclease activity
for positioning on ribosome
to delineate 5’ end for splicing

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24
Q

describe addition of poly-A tail

A

cleavage proteins and PAP detect and bind to AAUAAA and GU motif at 3’ end, complex cleaves 10-35 nt, PAP adds 12 A slow, PABPII adds 200-250 As fast

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25
Q

2 functions of poly-A tail

A

prevent exonuclease activity at 3’end, recognition signal for mRNA transport into cytoplasm

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26
Q

what composes the sliceosome?

A

snRNA (U1,U2,U4, U5,U6) + splicing factor proteins

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27
Q

what are the conserved sequences for splicing

A

5’ GU
branch point- A
3’ AG

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28
Q

3 steps of splicing

A

1-adenine residue 2’OH attacks phosphodiester bond at 5’splice site
2-3’OH on exon is exposed, attack 3’ splice spot
3- intronis removed in “lariat” shape and exons are fused together

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29
Q

what is eukaryotic splicing similar to?

A

group 2 self splicing- mito of fungi, chloroplasts and cyanobacteria, also have lariat byproduct

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30
Q

clinical correlation to splicing

A

b-thalassemia- mutation oin b-globulin gene leads to alteration in splice sits and abnormal product (longer exon 3)

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31
Q

A-I editing

A

Adenosine changed to Inosine (like guanine)

enzyme is ADAR

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32
Q

C-U editing

A

cytosine to uracil

enzyme is cytidine deaminase

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33
Q

clinical example of C-U editing

A

in gut, C-U editing yeilds shorter ApoB product (changes from glutamine to stop codon)

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34
Q

editing in pathogenic trypanosomes

A

extensive editing

uracil edits by uridylyl transferase and guide RNAs

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35
Q

what is responsible for rRNA edition?

A

snoRNA

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36
Q

what is the action of snoRNA?

A

will cleave 45s into 5.8s, 18s, 28s units, can also directly methylate and pseudouridylate

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37
Q

what are the 4 ways in which tRNAs are edited?

A

cleavage- 3’ end by RNase D, 5’ end by RNase P
splicing- facilitated by proteins
RNA editing- uracil at 3’end changed to CAA
chemical modifications by snoRNA

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38
Q

what is the significant of 3’CAA in tRNA?

A

responsible for charging tRNA with aa

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39
Q

what is meant by the genetic code is “degenerate”?

A

61 codons for only 20 aa (repeats)

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40
Q

what are the start and stop codons?

A

start- AUG

stop- UGA, UAG, UAA

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41
Q

what aa only have 1 codon?

A

Met and Trp

42
Q

what enzyme will “charge” tRNAs? how many are there?

A

aminoacyl tRNA synthetase, 20- one for each aa

43
Q

what is the wobble position?

A

3rd nt on mRNA, 1st nt on tRNA, allows for non-standaed base pairing

44
Q

describe prokaryotic ribosome

A 
large= 50s (23s + 5s + 31 proteins)
small = 30s (16s + 21 proteins)
overall = 70s
45
Q

describe eukaryotic ribosome

A

large=60s (28s+5.8s+50 proteins)
small= 40s (18s+33 proteins)
overall=80s

46
Q

what are the 3 sites on a ribosome?

A

A site- aminoacyl
P site- peptidyl
E site- exit

47
Q

differentiate between the 2 tRNAs for Met

A

one can only initiate protein synthesis, the other is for incorporation of Met into a growing chain; both have same aminoacyl synthetase

48
Q

where does tRNAi-Met bind?

A

binds to the P site, all other tRNAs bind the A site

49
Q

describe DNA methylation

A

methyl groups added to cytosines in CpG islands located within the gene promoter region by DNA methyltransferase

50
Q

what is the effect of hyper vs. hypo methylation?

A

hyper- silencing

hypo-activating

51
Q

how does methylation silence gene expression?

A

1-makes it harder for transcription factors to bind
2- recruits methyl binding proteins that recruit enzymes that modify chromatin and make it hard for transcription factors to bind

52
Q

rett syndrome

A

caused by dysfunction of MECP2- methyl binding protein

53
Q

what is the overall effect of histone acetylation? why?

A

activation, acetylation of histones will shield DNA from (+) lysine and will decrease the attraction between DNA and histone, decreased interaction = looser DNA = increase access

54
Q

what enzyme is responsible for histone acetylation?

A

histone acetyltransferases

55
Q

describe bromodomains

A

found on transcription factor proteins, able to bind acetylated lysine’s

56
Q

what is the effect of histone methylation?

A

activating or silencing

57
Q

H3K9

A

when methylated- decreased gene expression, will recruit HP1, leads to more methylation
when acetylated- will increase gene expression

58
Q

H3K4

A

when methylated, will increase gene expression

59
Q

describe the actions of nucleosome remodeling engines?

A

use ATP to shift the position of nucleosomes that will result in varied access to gene promoters

60
Q

where are repressors and activators working?

A

at the promoter proximal region (-200 to -100), both can directly bind DNA

61
Q

what is the action of corepressors/coactivators?

A

bind to transcription factors, NOT directly to DNA

62
Q

what works at a distance to influence expression?

A

enhancers- can be 200 bp to 5kbp up or down stream. allow for synergistic binding of transcription factors

63
Q

example of coactivators

A

scaffold proteins

64
Q

example of corepressors

A

histone deacetylase - removes acetyl groups and can also recruit methyltransferases to methylate

65
Q

describe translational control in times of low iron

A

increase receptor: IRE-BP binds to AU rich hairpin in 3’UTR to protect from endonucleases
decrease ferritin: IRE-BP stablizes 5’ hairpin and ribosome cannot start translation

66
Q

describe translational control in times of high iron

A

increase ferritin: no IRE-BP, ribosome translates ferritin

decrease receptor: no IRE-BP, mRNA is degraded by endonucleases

67
Q

describe siRNA in the 3’UTR

A

exogenous
perfect mRNA binding
results in mRNA cleavage

68
Q

describe micorRNA in the 3’UTR

A

endogenous (from RNA pol II)
imperfect mRNA binding
results in translational repression or mRNA degradation

69
Q

describe the nuclear localization signal

A

basic aa sequence

70
Q

describe the 5 steps in nuclear import

A
  • NLS assoc with import in
  • (p+importin) travel through NPC via hydrophobic interactions with FC nucleoporins
  • (P+importin) bind GTP and protein is released
  • (GTP+importin) exit through NPC
  • in cytoplasm, GTP interacts with GAP, and is converted to GDP, releasing importin
71
Q

what is GAP?

A

GTP –> GDP in cytoplasm

72
Q

what is GEF?

A

exchanges GTP for GDP in nucleus

73
Q

describe the nuclear export signal

A

hydrophobic with leucine residues

74
Q

describe the 3 steps in nuclear export

A

1-(p+exportin+GTP)pass through NPC
2- GTP interacts with GAP in cytoplasm and is changed to GDP, thereby releasing protein and exportin
3- exportin assoc with GDP and travels back into nucleus

75
Q

describe the mitochondrial targeting sequence

A

amipathic a-helix with hydrophobic residues on one side and basic residues on the other side

76
Q

what is unique about mito import?

A

proteins must be unfolded to enter mito, thus they are accompanied by chaperones

77
Q

describe contact site on mito membrane

A

contact sites exist between inner and outer membranes so that proteins are transported directly into mito matrix

78
Q

what sequence targets for ER?

A

signal sequence at N-terminus- (+) charge followed by hydrophobic residues

79
Q

where do proteins end up if they are inside of ER lumen?

A

outside of the cell

80
Q

what allows entry into ER lumen?

A

translocons

81
Q

describe type I integral membrane proteins

A

have COO- in cytoplasm

82
Q

where is the signal sequence in type I integral membrane proteins?

A

at N-terminus

83
Q

what is the significance of STA sequence?

A

Stop-Transfer-Anchor sequence will span the membrane, closes the translocon so that the remaining portion of the protein (COO- end) will be in cytoplasm

84
Q

describe type II integral membrane proteins

A

have NH3+ in cytoplasm

85
Q

what types of sequences are found in type II integral membrane proteins?

A

Signal sequence- bind and opens translocon
anchor sequence- spans membrane
*No stop sequences- translation continues into ER lumen

86
Q

what targets to COPI vesicles?

A

KDEL

87
Q

what targets to lysosome vis clathrin?

A

mannose-6-phosphate

88
Q

what targets to COPII?

A

diacidic motif

89
Q

what is the activity of COPI vesicles?

A

retrograde transport from golgi to ER

90
Q

what is the activity of clarthin vesicles?

A

incoming from cell surface or to lysosomes, dynamic help with “pinching”

91
Q

southern blot, probe?

A

used to assess DNA with nucleic acid probe

92
Q

PCR

A

for DNA quantification, specificity convey via primers

93
Q

sequencing

A

melt DNA, add primer and modified bases

actual DNA is complimentary to what is found experimentally

94
Q

northern blot, probe?

A

RNA with nucleic acid probe

must denature to ensure linearity, use formaldehyde probe

95
Q

RT-PCR

A

for mRNA, use RT to make cDNA

96
Q

western blot

A

use to assess protein levels with antibody probe

97
Q

mutation that causes CF

A

mutation in CFTR leading to faulty Cl channel

98
Q

what can be used to treat class I CF?

A

gentamycin by suppressing recognition of premature stop codon

99
Q

what class is the mc/ cause of CF?

A

class II- DF508, within NBD1 domain, leads to increased levels of misfolded proteins, increased ubiquitination and increased turnover at cell surface

100
Q

describe folding of wild type CFTR

A

up to 50% wild type CFTR is misfolded, chaperones in ER will help. if incorrectly folded, will lack diacidic motif and will not be incorporated into COPII vesicles

101
Q

2 classes of DF508 treatment

A

correctors- enhance folding/trafficking to membrane

potentiatiors- decrease turnover and increase activity of channel

102
Q

testing for CF

A

prenatal- multiplex PCR assay or NextGen sequencing

post-natal- sweat test

CSF final (3 decks)

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