Txn, RNA and gene expression Flashcards
1
Q
Is RNA single-stranded or double-stranded?
A
single
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
3
Q
What does RNA Pol I produce?
A
rRNA (28S, 18S, 5.8S and 5S)
4
Q
What does RNA Pol III produce?
A
5S rRNA and tRNA
5
Q
What does RNA Pol II produce?
A
mRNA
6
Q
What is the function of the promoter?
A
to signal starting point of txn
7
Q
What are three common consensus sequences for txn?
A
TATA box, CAAT box and GC region
8
Q
Which consensus sequence is almost always found?
A
TATA box
9
Q
What is the TBP?
A
TATA-box binding protein
10
Q
Binding of TBP causes what other txn factors to associate?
A
TFIIE, TFIIF, TFIIH and Pol II
11
Q
Which txn factor has helicase activity?
A
TFIIH
12
Q
The basal txn complex can transcribe genes at what rate?
A
Low
13
Q
What does SP-1 bind?
A
GC-rich sequences
14
Q
NF-1 binds what DNA region?
A
CAAT box
15
Q
What do SP-1 and NF-1 do to rates of txn?
A
enhance them enormously
16
Q
alpha-amanitin is a potent inhibitor of what protein?
A
RNA Pol II
17
Q
What is the MOA of rifampicin?
A
inhibitor of prokaryotic RNA pol II
18
Q
What is rifampicin often used to treat?
A
TB
19
Q
What if the function of the mRNA cap?
A
allows the cell to distinguish mRNA from other types of RNA
20
Q
Does pre-mRNA contain introns, exons or both?
A
both
exons must be spliced out
21
Q
What is the spliceosome also referred to as?
A
snRNP
22
Q
What proteins recognize the intron and exon boundaries?
A
spliceosomes
23
Q
When making the lariat, what end is cut first?
A
5’ OH
24
Q
What nucleotide is involved in the lariat structure?
A
adenine
25
What is alternative splicing?
rearrangment of exon order in mRNA
26
What does alternative splicing help a cell do?
create tissue specific isoforms of proteins
27
What is the function of polyadenylation?
prevents premature mRNA degradation
28
What structures contain the poly A tail?
only mRNA
29
Degradation begins with what?
shortening of the polyA tail
30
What process begins by reduction of the polyA tail?
removing the 5' cap
31
What is the function of micro RNA's and miRNA?
contribute to mRNA stability
32
Reduced synthesis of what chain of hemoglobin results in beta-thalassemia?
beta-chain
33
Where does the error occur in beta-thalessemia synthesis?
nucleotide sequence between the first intron and exon boundary
34
Where is the mutation for PKU found?
single base change in 5' splice site
35
HATs acetylate what residue?
Lysine
36
What type of charge do HATs induce in histone?
reduces net positive charge
37
What residues in DNA can be methylated?
cytosine
38
Does methylation affect DNA base pairing?
no
39
Methylated DNA recruits what type of protein complex?
HDAC
40
Where do proteins generally bind DNA?
major groove
41
DNA binding proteins are active as what?
dimers
42
Homeobox proteins are what type of DNA binding motif?
helix-turn-helix
43
Zinc is usually coordinated to what residues in zinc fingers?
histidine and cysteine
44
What type of receptor is a common zinc-finger DNA binding protein?
glucocorticoid receptor
45
Do leucine zipper dimerize?
yes
46
leucine zipper proteins contain what amino acid at every 7th residue?
Leucine
47
What type of region of the protein interacts with DNA in a leucine zipper? Where does this region interact with the DNA?
positively charged
major groove
48
Fos and Jun are what type of DNA binding protein?
leucine zipper
49
DNA binding proteins often induce the binding of what other proteins?
HATs
50
The LDL receptor recognizes what two types of apoproteins?
ApoE and ApoB
51
Txn of the LDLR is increased in response to what?
low cellular cholesterol
52
SP-1 is what type of DNA binding protein?
zinc finger
53
Low cholesterol levels cause the entry of what into the nucleus?
SREBP-1a
54
What is SREBP-1a heterodimerized to?
SRE-1
55
When do SRE-1 and SREBP-1a heterodimerize?
upon their entry into the nucleus
56
What does this heterodimerization induce?
increased txn of the LDL-R
57
SREBP-1a is also involved in the metabolism of what two other energy sources?
cholesterol and fatty acids
58
How does cortisol activate txn?
inducing a conformational change in GR that allows it to function
59
What form form does the GR activate txn in?
homodimer
60
Where does the GR/hormone complex bind?
glucocorticoid responsive element (GRE)
61
What is the GRE classified as?
enhancer element
62
Where is the GRE often found?
in the promoter of GRE responsive genes
63
What two other genes can be regulated by GRE?
PEPCK and lipoprotein lipase
64
Where are thyroid receptor hormones found?
nucleus
65
What type of dimers do the thryoid hormone receptors bind DNA?
heterodimer
66
In the absence of liagand, what do thyroid hormone receptors function to do?
repress txn
67
What is the other partner in the thyroid hormone heterodimer?
retinoid X receptor
68
RxR/ThR recruit what to repress txn of target genes?
HDAC
69
Thyroid hormone binding results in what?
displacement of HDAC
70
What is the chain from glucagon to txn of PEPCK chain?
glucgon-->cAMP-->PKA-->CREB
| -->CRE's-->CBP-->EP300
71
What is the function of the EP300/CBP?
this complex acts as a HAT to increase txn of target genes
72
Rubenstein-Taybi syndrome is caused by mutations or deletions in what two proteins?
EP300 or CBP
73
rRNA is made by what RNA polymerase?
RNA polymerase I
74
tRNA is synthesized by what polymerase?
RNA polymerase III
75
What is the only rRNA not transcribed by pol I?
5S rRNA
76
What synthesizes 5S rRNA?
Pol III
77
What is the function of the promoter?
signals where txn of a gene is to start
78
What consensus sequence is almost invariably found in all sequences transcribed by Pol II?
TATA box
79
TATA box binding protein binds to what tx factor?
TFIID
80
What is the function of TBP?
"signpost"
81
DNA helicase activity is owned by what txn factor?
TFIIH
82
What is the mechanism of action for rifampicin?
inhibits bacterial polymerase
83
What is the function of the 5' cap?
to distinguish mRNA from other RNA's
84
What is the spliceosome referred to as?
small nuclear ribonucleoprotein
85
What type of RNA does the spliceosome contain?
snRNA
86
What base is featured during splicing of an intron?
adenine
87
Is this adenine on the 3' or the 5' end?
3'
88
What end of the mRNA is polyadenylated?
3'
89
What is the poly-A tail involved in?
mRNA stability
90
What triggers the removal of the 5' cap?
degradation of the 3' poly-A tail
91
Regarding mRNA, what do siRNA and miRNA influence?
mRNA stability
92
What two conditions can result from incorrect splicing of mRNA?
beta-thalassemia and phenylketonuria
93
Where does the mutation for beta-thalassemia occur?
junction of first intron and exon
94
Where is the DNA mutation regarding PKU?
5' site of an intron
95
Which DNA residues are methylated?
cytosine
96
The homeobox proteins are members of what protein family?
helix-turn-helix
97
What receptor is a member of the zinc finger protein family?
glucocorticoid receptor
98
Which two proteins are members of the leucine zipper family?
Fos and Jun
99
What region of the leucine zipper family interacts with DNA region of interest?
positively-charged region
100
What apolipoproteins does the LDL receptor recognize?
Apo B and Apo E
101
The promoter of the LDL receptor contains what sequence?
SRE-1
102
What protein binds SRE-1?
SREBP-1a
103
What causes SREBP-1a to translocate to the nucleus?
low level of intracellular cholesterol
104
Where does SREBP-1a bind to SRE-1?
in the nucleus
105
Where does SP-1 bind? What cofactor does SP-1 require?
GC box at promoter of LDLR
CRSP
106
What is the GRE? Where is the GRE found?
glucocorticoid responsive element
promoter of glucocorticoid gene
107
In the absence of hormone, what is the purpose of the THR is relation to gene txn?
repress txn
108
What is the thyroid receptor dimerized to? What protein can this complex recruit?
retinoid X receptor (RXR)
HDAC
109
How does PKA achieve transcriptional control?
via phosphorylation of CREB
110
How does CREB influence txn?
via binding to CREs (cyclic AMP responsive elements)
111
What protein does CREB recruit?
EP300
112
Rubinstein-Taybi patients feature mutations in what genes?
CBP or EP300
113
What RNA contains inosine?
tRNA
114
What txn factor contains the TATA box binding protein?
TFIID
115
What two additional txn factors are needed for a high txn rate?
SP1 and NF1
116
Where does SP-1 bind?
GC rich region
117
Where does NF1 bind?
CAAT box
118
What composes the 5' cap?
methylguanosine
119
What complex contains snRNA?
spliceosome
120
During splicing, where is the adenine found?
3' end
121
What signals the stop point for txn?
polyA signal
122
What can siRNAs do?
target specific mRNAs for degradation
123
The mutation for beta-thalassemia occurs where?
border of first exon and intron
124
On what base does methylation occur?
Cytosine
125
What two proteins are Leucine Zipper DNA binding proteins?
Fos and Jun
126
What two genes does the GR increase txn of?
PEPCK and lipoprotein lipase
127
What type of binding protein is SREBP-1a?
leucine zipper
