GAG WK3 Flashcards
1
Q
What are the 3 types of non-coding RNA
A
- snRNA
- snoRNA
- piRNA
2
Q
What is the function of snRNA
A
- involved in splicing mRNA transcripts
- removes introns and connects exons
3
Q
Where are snRNA located
A
nucleus
4
Q
What is another name for snRNA (and why)
A
- U-RNA
- they have a high content of uridine
5
Q
Name all the short non coding RNA
A
- miRNA
- snRNA
- siRNA
- snoRNA
- piRNA
6
Q
Where are snoRNA found
A
nucleolus
7
Q
What is the function of snoRNA
A
they are involved in modification of other RNA transcripts (rRNA, tRNA and snRNA)
8
Q
What are the 2 main types of snoRNA & functions
A
- C/D box snoRNA = involved w/ methylation
- H/ACA box snoRNA = involved w/ pseudouridylation
- affect RNA translation and stability
9
Q
What is the function of piRNA
A
- guide Piwi proteins guide piRNA to target sequences
- silence transposablele elements
- prevents harmful transposable elements from causing mutations
10
Q
Which of the 3 non-coding RNA is the largest class
A
piRNA
11
Q
What are siRNAs
A
short double-stranded RNA that plays a role in gene silencing
12
Q
How is siRNA formed
A
- generated from any double-stranded RNA
- double-stranded RNA is cleaved into small fragments by Dicer
13
Q
What are the 3 functions of siRNA
A
- gene silencing (causes degradation of target RNA)
- involved in immune response against viral infections by degrading viral RNA
- target specific disease-related genes for gene therapy
14
Q
What are antisense oligonucleotides (ASOs)
A
short RNA sequences which bind to target mRNA
15
Q
What is the effect of ASOs
A
- binding of ASO to mRNA triggers degradation of mRNA
- prevents translation
16
Q
With which non-coding RNA do ASO degradation mechanisms with
A
siRNA
17
Q
What does siRNA stand for
A
small interfering RNA
18
Q
What does piRNA stand for
A
Piwi-interacting RNA
19
Q
What does snoRNA stand for
A
small nucleolar RNA
20
Q
What does snRNA stand for
A
small nuclear RNA
21
Q
What is the effect of ASO therapy on motor neuron disease
A
- Adding ASO knocks down the expression of mutant SOD1
- slows down disease and reduces SOD1 protein levels
22
Q
What is the cause of motor neuron disease
A
a mutation in the gene SOD1 which causes abnormal function and altered protein/gene expression
23
Q
What is a motor neuron disease
A
a neurodegenerative disorder that cause the death of motor neurons resulting in paralysis and death
24
Q
What does miRNA stand for
A
microRNA
25
What are miRNA
central regulators of gene expression
26
What is the difference between siRNA and miRNA (structure)
- siRNA = double-stranded RNA
- miRNA = single-stranded RNA
27
What is the difference between siRNA and miRNA (enzymes)
- miRNA = processed by 2 enzymes (Drosha & Dicer)
- siRNA = processed by 1 enzyme (Dicer)
28
What is the difference between siRNA and miRNA (target genes)
- miRNA = target 100s of genes
- siRNA = target fewer genes
29
What important cognitive process do miRNA influence
miRNA influences a network of genes involved in LTP
30
How does miRNA regulate gene expression
based on complementarity to target mRNA
31
What is the effect of miRNA on gene expression during complete complementarity
- mRNA poly-A tail is cleaved (degradation of mRNA)
- base pairs between miRNA and mRNA match perfectly
- this allows miRNA bind tightly to mRNA
32
What is the effect of miRNA on gene expression during partial complementarity
- translation is inhibited because RISC blocks ribosome movement
- the base pairs between mRNA and miRNA don't match perfectly
- miRNA blocks translation w/o degrading mRNA
33
Why is it important that microRNA can target multiple genes
- can regulate many genes which allows rapid changes in pathway activation
34
Why is it beneficial that many miRNAs can regulate a gene
provides stronger control over its expression
35
Why does tRNA availability vary
- not all codons are equally common
- more anti-codons ensure smooth translation w/o delays
36
What does it mean if mutation on rare codon happens
slows down translation and reduces gene expression
37
How does tRNA availability affect translation speed
- optimal codon-anticodon match = enables fast translation
- non-optimal codon = ribosome stalls & slow translation
- wobble-base pairing = mismatch at 3rd base is less efficient tRNA binding slower than optimal codon-anticodon match
38
How does the tRNA pool change in different cell types
- proliferating cells = tRNA pool supports genes in cell division and DNA replication
- terminally differentiated cells = tRNA pool supports genes in cell adhesion and multicellular functions
39
How does tRNA efficiency contribute to cancer
- mutations to rare codons slow down translation
- reduces cell's ability to respond to stress or damage
- increased tRNA for rare codons in oncogenes
- increases production of oncogenic proteins leads to cancer
40
Name short non-coding RNA
- miRNA
- snoRNA
- microRNA
- piRNA
- siRNA
41
What are pseudogenes
they are copies of genes where the protein-coding sequence is removed & untranslated regions (UTRs) remain
42
What is the purpose of these UTRs in pseudogenes
- miRNA can bind to
- it helps reduce miRNA interaction with the original gene and allows normal gene expression
43
What happens if miRNA binds to these pseudogenes
- less miRNA is available to block the real gene and block gene expression
- this is bad if it affects important genes
44
Outline an example of pseudogenes acting as decoys for miRNA
- PTEN gene produces protein critical for cell division
- if blocked by miRNA too much (downregulated) it can lead to cancer
- PTENP1 (pseudogene) protects PTEn from being downregulated and helps maintain proper PTEn levels
- miRNA binds to PTENP1
45
What does circRNA stand for
circular RNA
46
What are circRNA
- long non-coding RNA with joined ends forming a loop
- they absorb excess miRNA and prevent over-regulation
47
What is the effect of circRNA
it helps balance miRNA levels by providing multiple binding sites
48
What are the 3 main functions of circRNA
- regulation of miRNA = absorb excess miRNA
- promote transcription by binding to DNA
- more stable than linear RNA because they lack free ends = resistant to degradation by exonucleases
49
How many circRNA are there approximately in human cells
over 15 000
50
What is back-splicing error
where circRNA is made from a mistake during the RNA splicing process where parts of RNA are incorrectly joined
51
How does back-splicing happen
donor and acceptor sites from different exons are incorrectly joined
52
In which types of genes is back-splicing common
highly expressed gene where RNA splicing is frequent
53
How can circRNA be promoted
- Alu repeats can bind to each other and form a hairpin loop
- splicing occurs after the introns are removed, leaving the circRNA intact
54
What are long non-coding RNA
RNA molecules longer than 200 nucleotides with little or no coding potentials for proteins
55
What is the function of lncRNA
they perform targeted specific regulatory functions unlike shorter non-coding RNA
56
What are anti-sense stabilisation by lncRNA
- some lncRNA are made from anti-sense DNA strand = making them complementary to gene transcript
- complementary lncRNA binds to mRNA to stabilise it
- this prevents original gene from being destroyed by microRNA
57
What is an example of antisense stabilisation by lncRNA
1. BACE1 gene (involved in Alzheimer) has an antisense lncRNA
2. antisense lncRNA binds to BACE1 transcript
3. It increases stability leading to more amyloid-B plaque production
4. too much stabilisation can be harmful
58
What is meant by lncRNA act as sponges or decoys
- lncRNA sock up RNA or proteins preventing them from working
- they bind to important molecules and blocking their normal function
59
What is an example of lncRNA acting as a sponge or decoy
1. PANDA is an lncRNA that binds to a transcription factor NF-YA
2. When NF_YA binds to PANDA it can't trigger gene related to cell death
3. lncRNA prevents apoptosis
60
How can lncRNA modulate epigenetic effects
- lncRNA can block proteins that modify DNA preventing them from acting
- lncRNA can add methyl groups to DNA or histones = silencing genes
- lncRNA can bring epigenetic proteins to correct DNA site as some proteins cannot bind to DNA directly
61
How does X inactivation happen via lncRNA
- XIST lncRNA controls X inactivation
- XIST binds to DNA and attracts a protein complex that methylates histones and DNA --> inactivating X chromosome
62
What are smORFs
- lncRNA can produce proteins
63
What are the features of smORFs
- proteins are cell-specific
- only made because lncRNA uses rare codons which slows translation
64
Outline part 1 of how siRNAs silence genes
1. Dicer (enzyme) cleaves double-stranded RNA into small fragments called siRNA
2. siRNAs have 2 strands: guide strand & passenger strand
3. The guide strand is complementary to the target mRNA so arg binds to guide strand
65
Outline part 2 of how siRNAs silence genes
1. Arg and guide strand bind they form the RISC complex which is responsible for silencing genes
2. The guide strand (inside RISC) recognises target mRNA
3. Arg cleaves the target mRNA and the cleaved mRNA is degraded
4. preventing it from being silenced
66
What is the function of miRNA
they guide RISC complex to complementary target mRNA sequence and either degrade mRNA or prevent translation
