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Biochem IV > Txn, RNA and gene expression > Flashcards

Txn, RNA and gene expression Flashcards

1
Q

Is RNA single-stranded or double-stranded?

A

single

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2
Q

What are two major differences between RNA and DNA polymerases?

A

RNA pol. does not need a primer

RNA pol. is much more error prone

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3
Q

What does RNA Pol I produce?

A

rRNA (28S, 18S, 5.8S and 5S)

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4
Q

What does RNA Pol III produce?

A

5S rRNA and tRNA

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5
Q

What does RNA Pol II produce?

A

mRNA

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6
Q

What is the function of the promoter?

A

to signal starting point of txn

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7
Q

What are three common consensus sequences for txn?

A

TATA box, CAAT box and GC region

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8
Q

Which consensus sequence is almost always found?

A

TATA box

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9
Q

What is the TBP?

A

TATA-box binding protein

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10
Q

Binding of TBP causes what other txn factors to associate?

A

TFIIE, TFIIF, TFIIH and Pol II

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11
Q

Which txn factor has helicase activity?

A

TFIIH

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12
Q

The basal txn complex can transcribe genes at what rate?

A

Low

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13
Q

What does SP-1 bind?

A

GC-rich sequences

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14
Q

NF-1 binds what DNA region?

A

CAAT box

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15
Q

What do SP-1 and NF-1 do to rates of txn?

A

enhance them enormously

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16
Q

alpha-amanitin is a potent inhibitor of what protein?

A

RNA Pol II

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17
Q

What is the MOA of rifampicin?

A

inhibitor of prokaryotic RNA pol II

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18
Q

What is rifampicin often used to treat?

A

TB

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19
Q

What if the function of the mRNA cap?

A

allows the cell to distinguish mRNA from other types of RNA

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20
Q

Does pre-mRNA contain introns, exons or both?

A

both

exons must be spliced out

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21
Q

What is the spliceosome also referred to as?

A

snRNP

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22
Q

What proteins recognize the intron and exon boundaries?

A

spliceosomes

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23
Q

When making the lariat, what end is cut first?

A

5’ OH

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24
Q

What nucleotide is involved in the lariat structure?

A

adenine

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25
Q

What is alternative splicing?

A

rearrangment of exon order in mRNA

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26
Q

What does alternative splicing help a cell do?

A

create tissue specific isoforms of proteins

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27
Q

What is the function of polyadenylation?

A

prevents premature mRNA degradation

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28
Q

What structures contain the poly A tail?

A

only mRNA

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29
Q

Degradation begins with what?

A

shortening of the polyA tail

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30
Q

What process begins by reduction of the polyA tail?

A

removing the 5’ cap

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31
Q

What is the function of micro RNA’s and miRNA?

A

contribute to mRNA stability

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32
Q

Reduced synthesis of what chain of hemoglobin results in beta-thalassemia?

A

beta-chain

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33
Q

Where does the error occur in beta-thalessemia synthesis?

A

nucleotide sequence between the first intron and exon boundary

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34
Q

Where is the mutation for PKU found?

A

single base change in 5’ splice site

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35
Q

HATs acetylate what residue?

A

Lysine

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36
Q

What type of charge do HATs induce in histone?

A

reduces net positive charge

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37
Q

What residues in DNA can be methylated?

A

cytosine

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38
Q

Does methylation affect DNA base pairing?

A

no

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39
Q

Methylated DNA recruits what type of protein complex?

A

HDAC

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40
Q

Where do proteins generally bind DNA?

A

major groove

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41
Q

DNA binding proteins are active as what?

A

dimers

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42
Q

Homeobox proteins are what type of DNA binding motif?

A

helix-turn-helix

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43
Q

Zinc is usually coordinated to what residues in zinc fingers?

A

histidine and cysteine

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44
Q

What type of receptor is a common zinc-finger DNA binding protein?

A

glucocorticoid receptor

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45
Q

Do leucine zipper dimerize?

A

yes

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46
Q

leucine zipper proteins contain what amino acid at every 7th residue?

A

Leucine

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47
Q

What type of region of the protein interacts with DNA in a leucine zipper? Where does this region interact with the DNA?

A

positively charged

major groove

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48
Q

Fos and Jun are what type of DNA binding protein?

A

leucine zipper

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49
Q

DNA binding proteins often induce the binding of what other proteins?

A

HATs

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50
Q

The LDL receptor recognizes what two types of apoproteins?

A

ApoE and ApoB

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51
Q

Txn of the LDLR is increased in response to what?

A

low cellular cholesterol

52
Q

SP-1 is what type of DNA binding protein?

A

zinc finger

53
Q

Low cholesterol levels cause the entry of what into the nucleus?

A

SREBP-1a

54
Q

What is SREBP-1a heterodimerized to?

A

SRE-1

55
Q

When do SRE-1 and SREBP-1a heterodimerize?

A

upon their entry into the nucleus

56
Q

What does this heterodimerization induce?

A

increased txn of the LDL-R

57
Q

SREBP-1a is also involved in the metabolism of what two other energy sources?

A

cholesterol and fatty acids

58
Q

How does cortisol activate txn?

A

inducing a conformational change in GR that allows it to function

59
Q

What form form does the GR activate txn in?

A

homodimer

60
Q

Where does the GR/hormone complex bind?

A

glucocorticoid responsive element (GRE)

61
Q

What is the GRE classified as?

A

enhancer element

62
Q

Where is the GRE often found?

A

in the promoter of GRE responsive genes

63
Q

What two other genes can be regulated by GRE?

A

PEPCK and lipoprotein lipase

64
Q

Where are thyroid receptor hormones found?

A

nucleus

65
Q

What type of dimers do the thryoid hormone receptors bind DNA?

A

heterodimer

66
Q

In the absence of liagand, what do thyroid hormone receptors function to do?

A

repress txn

67
Q

What is the other partner in the thyroid hormone heterodimer?

A

retinoid X receptor

68
Q

RxR/ThR recruit what to repress txn of target genes?

A

HDAC

69
Q

Thyroid hormone binding results in what?

A

displacement of HDAC

70
Q

What is the chain from glucagon to txn of PEPCK chain?

A

glucgon–>cAMP–>PKA–>CREB

–>CRE’s–>CBP–>EP300

71
Q

What is the function of the EP300/CBP?

A

this complex acts as a HAT to increase txn of target genes

72
Q

Rubenstein-Taybi syndrome is caused by mutations or deletions in what two proteins?

A

EP300 or CBP

73
Q

rRNA is made by what RNA polymerase?

A

RNA polymerase I

74
Q

tRNA is synthesized by what polymerase?

A

RNA polymerase III

75
Q

What is the only rRNA not transcribed by pol I?

A

5S rRNA

76
Q

What synthesizes 5S rRNA?

A

Pol III

77
Q

What is the function of the promoter?

A

signals where txn of a gene is to start

78
Q

What consensus sequence is almost invariably found in all sequences transcribed by Pol II?

A

TATA box

79
Q

TATA box binding protein binds to what tx factor?

A

TFIID

80
Q

What is the function of TBP?

A

“signpost”

81
Q

DNA helicase activity is owned by what txn factor?

A

TFIIH

82
Q

What is the mechanism of action for rifampicin?

A

inhibits bacterial polymerase

83
Q

What is the function of the 5’ cap?

A

to distinguish mRNA from other RNA’s

84
Q

What is the spliceosome referred to as?

A

small nuclear ribonucleoprotein

85
Q

What type of RNA does the spliceosome contain?

A

snRNA

86
Q

What base is featured during splicing of an intron?

A

adenine

87
Q

Is this adenine on the 3’ or the 5’ end?

A

3’

88
Q

What end of the mRNA is polyadenylated?

A

3’

89
Q

What is the poly-A tail involved in?

A

mRNA stability

90
Q

What triggers the removal of the 5’ cap?

A

degradation of the 3’ poly-A tail

91
Q

Regarding mRNA, what do siRNA and miRNA influence?

A

mRNA stability

92
Q

What two conditions can result from incorrect splicing of mRNA?

A

beta-thalassemia and phenylketonuria

93
Q

Where does the mutation for beta-thalassemia occur?

A

junction of first intron and exon

94
Q

Where is the DNA mutation regarding PKU?

A

5’ site of an intron

95
Q

Which DNA residues are methylated?

A

cytosine

96
Q

The homeobox proteins are members of what protein family?

A

helix-turn-helix

97
Q

What receptor is a member of the zinc finger protein family?

A

glucocorticoid receptor

98
Q

Which two proteins are members of the leucine zipper family?

A

Fos and Jun

99
Q

What region of the leucine zipper family interacts with DNA region of interest?

A

positively-charged region

100
Q

What apolipoproteins does the LDL receptor recognize?

A

Apo B and Apo E

101
Q

The promoter of the LDL receptor contains what sequence?

A

SRE-1

102
Q

What protein binds SRE-1?

A

SREBP-1a

103
Q

What causes SREBP-1a to translocate to the nucleus?

A

low level of intracellular cholesterol

104
Q

Where does SREBP-1a bind to SRE-1?

A

in the nucleus

105
Q

Where does SP-1 bind? What cofactor does SP-1 require?

A

GC box at promoter of LDLR

CRSP

106
Q

What is the GRE? Where is the GRE found?

A

glucocorticoid responsive element

promoter of glucocorticoid gene

107
Q

In the absence of hormone, what is the purpose of the THR is relation to gene txn?

A

repress txn

108
Q

What is the thyroid receptor dimerized to? What protein can this complex recruit?

A

retinoid X receptor (RXR)

HDAC

109
Q

How does PKA achieve transcriptional control?

A

via phosphorylation of CREB

110
Q

How does CREB influence txn?

A

via binding to CREs (cyclic AMP responsive elements)

111
Q

What protein does CREB recruit?

A

EP300

112
Q

Rubinstein-Taybi patients feature mutations in what genes?

A

CBP or EP300

113
Q

What RNA contains inosine?

A

tRNA

114
Q

What txn factor contains the TATA box binding protein?

A

TFIID

115
Q

What two additional txn factors are needed for a high txn rate?

A

SP1 and NF1

116
Q

Where does SP-1 bind?

A

GC rich region

117
Q

Where does NF1 bind?

A

CAAT box

118
Q

What composes the 5’ cap?

A

methylguanosine

119
Q

What complex contains snRNA?

A

spliceosome

120
Q

During splicing, where is the adenine found?

A

3’ end

121
Q

What signals the stop point for txn?

A

polyA signal

122
Q

What can siRNAs do?

A

target specific mRNAs for degradation

123
Q

The mutation for beta-thalassemia occurs where?

A

border of first exon and intron

124
Q

On what base does methylation occur?

A

Cytosine

125
Q

What two proteins are Leucine Zipper DNA binding proteins?

A

Fos and Jun

126
Q

What two genes does the GR increase txn of?

A

PEPCK and lipoprotein lipase

127
Q

What type of binding protein is SREBP-1a?

A

leucine zipper

Biochem IV (6 decks)

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