Section 2 - Module 7 Flashcards
1
Q
RNA molecules specific to Eukaryotes
A
MicroRNA (miRNA) and small interfering RNA (siRNA)
2
Q
RNAi in transcription
A
condenses chromatin to suppress transcription, mRNA is not made
3
Q
RNAi function
A
transcriptional gene silencing and post-transcriptional gene silencing
4
Q
RNAi with mRNA
A
The mRNA is destroyed before it is translated into protein
5
Q
RNAi in translation
A
Inhibit translation, protein is not made.
6
Q
what are miRNA precursors
A
primary miRNA (pri-miRNA)
7
Q
What encodes pri-miRNA
A
the genome. Relevant genomic regions are transcribed by RNA Pol II
8
Q
What cleaves nucleus, Pri-miRNA into pre-miRNA
A
Drosha (RNAase III enzyme)
9
Q
What structure is pre-miRNA
A
a stem-loop structure
10
Q
What in the cytosol cleaves the pre-miRNA into 19-25 nucleotide miRNA:miRNA duplex with no stem loop
A
Dicer
11
Q
Order or enzymes used in miRNA breakdown
A
Drosha, Exportin 5, Dicer
12
Q
RISC
A
RNA-induced silencing complex
13
Q
What type of protein dies RISC contain
A
Argonaute
14
Q
how long is siRNA nucleotide duplex
A
21-23
15
Q
how long is miRNA nucleotide duplex
A
19-25
16
Q
how many targets does siRNA have?
A
one
17
Q
how many targets does miRNA have?
A
multiple (could be over 100)
18
Q
How do siRNAs degrade mRNA
A
cleavage
19
Q
RITS (RNA-induced transcriptional silencing)
A
Effector complexes that are targeted to homologous sequences by base-pairing interactions involving the guide strand of the small RNA. Mediates gene silencing vis heterochromatin formation. RNAi mediated histone and DNA methylation.
20
Q
How many histone proteins in a nucleosome
A
eight
21
Q
What does a chromatosome consist of?
A
a nucleosome plus the H1 histone
22
Q
T/F changes in chromatin structure affect the expression of eukaryotic genes?
A
True
23
Q
Heterochromatin
A
Condensed inactive form of chromatin
24
Q
Euchromatin
A
open and active form of chromatin. Since open, transcription factors access the DNA and initiate transcription
25
How does histone modifications occur at multiple locations?
Acetylation, methylation, and phosphorylation
26
What percent of human genes are thought to tbe regualted by RNAi?
30%
27
When is gene regulation arguably most important?
Embryo development
28
What type of gene is RNAi an important research tool?
'knocking out' (silencing) particular genes
29
Colinearity
the concept that nucleotide sequences in genes dictate amino acid sequences in proteins.
30
How are nucleotides related to amino acids
continuous sequences of nucleotides encode a continuous sequence of amino acids. the number of nucleotides in a gene is proportional to the number of amino acids in the protein.
31
is the colinear model accurate for prokaryotes?
yes
32
is the colinear model accurate for eukaryotes?
no
33
what is included in a gene?
exons, introns, the sequences at the beginning and end of the RNA that are not translated into a protein
34
Shine-Dalgarno sequence
ONLY in prokaryotes. A ribosomal binding site located upstream of the AUG start codon
35
Do prokaryotes have pre-mRNA?
No
36
Splicing mechanism of nuclear pre-mRNA intron
spliceosomal
37
Location of the nuclear pre-mRNA intron
protein-encoding genes in the nucleus of eukaryotes.
38
Operon
operates as a unit utilizing a single transcription start site for multiple genes
39
Prokaryotic protein-coding genes
usually found in a contiguous array in the DNA called an operon
40
Eukaryotic protein-coding genes
each gene is transcribed from its own start site to yield a pre-mRNA that is processed into a functional mRNA encoding a single protein
41
Prokaryotes DNA genes and introns
Prokaryotic DNA genes contain little to no noncoding gaps (introns) and the DNA is transcribed directly into linear mRNA, which then is translated into protein while the mRNA is still being produced.
42
Addition of 5' cap post transcriptional modification in Eukaryotes
facilitates binding of ribosomes to 5' end of mRNA, increases mRNA stability, enhances RNA splicing
43
3' cleavage and addition of poly(A) tail in post transcriptional modification in Eukaryotes
increases stability of mRNA, aids in export of mRNA from the nucleus, and facilitates binding pf ribosome to mRNA
44
RNA splicing post transcriptional modification in Eukaryotes
Removes noncoding introns from pre-mRNA, facilitates export of mRNA to cytoplasm, allows for multiple proteins to be produced through alternative splicing
45
What are the modification for eukaryotic posttranslational modifications?
1) capping of the 5' end
2) polyadenylation of the 3' end
3) splicing (Removal) of introns
46
What type of nucleotide attached to the 5'-end of the pre-mRNA?
methylated (CH3) guanine (G)
47
How does the methylated guanine (G) join to the pre-mRNA?
5'-5' linkage involving 3 phosphate groups
48
What nucleotides are added to the 3'-end of the pre-mRNA?
50 to 250 adenine (A) nucleotides, known as polyadenylation to generate a poly(A) tail
49
How is the poly(A) tail added?
cleavage and polyadenylation
50
T/F. Modification is necessary for efficient initiation of translation, transport of mRNA from nucleus, protects mRNA from degradation, and enhances RNA splicing
True
51
What removes introns?
splicing
52
When does splicing occur?
between the pre-mRNA to mRNA
53
What are the three consensus sequences in the pre-mRNA?
5' splice site, 3' splice site, and branch point
54
What uses consensus sequences to recognize and remove introns?
spliceosome
55
In what forms are introns removed?
lariat
56
How are exons spliced together?
two successive reactions (then go to translation)
57
Where does splicing take place?
splicesome
58
snRNAs
small nuclear RNAs
59
What are the five snRNPs contained in the splicesome?
U1, U2, U4, U5, and U6
60
snRNP
snRNA + protein = snRNP. And are central to the activity of the spliceosome
61
T/F. The spliceosome assembles sequentially?
True
62
Where do snRNAs of U1 and U2 base pair with the consensus sequence?
5' splice site and the branch point site of the pre-mRNA
63
What mediates coupling of events?
The 'tail' or C-terminal repeat domain (CTD) of the largest subunit of Pol II.
64
Where are mRNA processing enzymes to during transcription?
CTD of Pol II
64
When is CAP added?
CAP is added as soon as the 5' end of the pre-mRNA emerges from the polymerase
64
When are capping enzymes recruited to the C-terminal domain (CTD) of RNA polymerase II?
early stages of transcription
65
How does the assembly of the spliceosome occur?
CO-transcriptionally while the RNA polymerase is still actively transcribing the template
65
During transcription termination what is recruited to the CTD of pol II
Polyadenylation factors
66
What end if RNA cleaved
Poly(a) 3' cleavage site
67
What does Rat1 degrading remaining RNA do?
terminates transcription
68
Proteome
protein complement of the cell
69
T/F. The proteome is more complex than the human genome?
True
70
Why is the proteome more complicated than the genome?
Because a single gene can give rise to a number of different proteins
71
What are the ways to process a single pre-mRNA to produce different mRNA molecules thereby translating to different proteins?
1) alternative splicing
2) alternative PolyA site
72
Alternative splicing
pre-mRNA can be spliced different ways. Since each mRNA produces a different combination of exons. When translated produce isoforms of protein
73
Alternative PolyA site
PolyA tail can be added at different 3' cleavage sites
74
Isoforms of proteins
different proteins
75
Patterns of alternative splicing
exon skipped, intron retention, alternative 5' or 3' splice site, mutually exclusive exons
76
What are 3' cleavage sites used for?
Used to determine the length of the mRNA transcript
77
Regulation of alterative processing
switch between the production of a functional or nonfunctional protein
78
What is transformer (Tra)
Protein in Drosophila sex determination
79
Male Tra protein phenotype
nonfunctional Tra protein
80
Female Tra protein phenotype
functional Tra protein
81
Male fly's splice site
upstream 3' slice site, results in premature stop codon of mRNA
82
Where is the female fly's slice site
downstream 3' splice site, and the termination codon is spliced out with the intron
83
T/F. Depending on RNA processing different forms of protein may be produced in different cell types
True
84
RNA processing in Thyroid is associated with
calcitonin
85
RNA processing in Brain cells is associated with
calcitonin-gene-regulated peptide (CGRP)
86
point mutation
single nucleotide mutation
87
Mutations can lead to exon_
skipping
88
Mutations can lead to intron __
retention
89
What results in gene loss of function?
Either nonfunctional proteins of altered stability of mRNA (mRNA is degraded and no protein is made)
90
Does exon skipping or intron retention occur more frequently?
Exon skipping
91
Cryptic splice site
a sequence not normally used for splicing
92
Beta-globin is a component of __
hemoglobin
93
What is beta thalassemia caused by?
mutations in the beta-globin which leads to incorrect splicing
94
What is beta thalassemia?
One of the most common human genetic diseases, it is a disorder resulting from excessive destruction of red blood cells, which leads to anemia.
95
What does RNA editing alter?
The coding information of the mRNA transcripts
96
Methods of RNA editing?
1) Substitution editing (base conversion)
2) insertion editing
97
Substitution editing
chemical alteration of individual nucleotide by specific enzymes.
98
Insertion editing
guide RNA (gRNA) adds nucleotides to be pre-mRNA that were not encoded by the DNA
99
What type of reactions splice together exons?
two transesterification reactions
100
What is the goal of alternative processing
increases protein diversity
