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GAG WK3 Flashcards

1
Q

What are the 3 types of non-coding RNA

A
  • snRNA
  • snoRNA
  • piRNA
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2
Q

What is the function of snRNA

A
  • involved in splicing mRNA transcripts
  • removes introns and connects exons
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3
Q

Where are snRNA located

A

nucleus

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4
Q

What is another name for snRNA (and why)

A
  • U-RNA
  • they have a high content of uridine
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5
Q

Name all the short non coding RNA

A
  • miRNA
  • snRNA
  • siRNA
  • snoRNA
  • piRNA
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6
Q

Where are snoRNA found

A

nucleolus

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7
Q

What is the function of snoRNA

A

they are involved in modification of other RNA transcripts (rRNA, tRNA and snRNA)

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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
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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
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10
Q

Which of the 3 non-coding RNA is the largest class

A

piRNA

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11
Q

What are siRNAs

A

short double-stranded RNA that plays a role in gene silencing

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12
Q

How is siRNA formed

A
  • generated from any double-stranded RNA
  • double-stranded RNA is cleaved into small fragments by Dicer
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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
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14
Q

What are antisense oligonucleotides (ASOs)

A

short RNA sequences which bind to target mRNA

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15
Q

What is the effect of ASOs

A
  • binding of ASO to mRNA triggers degradation of mRNA
  • prevents translation
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16
Q

With which non-coding RNA do ASO degradation mechanisms with

A

siRNA

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17
Q

What does siRNA stand for

A

small interfering RNA

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18
Q

What does piRNA stand for

A

Piwi-interacting RNA

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19
Q

What does snoRNA stand for

A

small nucleolar RNA

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20
Q

What does snRNA stand for

A

small nuclear RNA

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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
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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

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23
Q

What is a motor neuron disease

A

a neurodegenerative disorder that cause the death of motor neurons resulting in paralysis and death

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24
Q

What does miRNA stand for

A

microRNA

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25
Q

What are miRNA

A

central regulators of gene expression

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26
Q

What is the difference between siRNA and miRNA (structure)

A
  • siRNA = double-stranded RNA
  • miRNA = single-stranded RNA
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27
Q

What is the difference between siRNA and miRNA (enzymes)

A
  • miRNA = processed by 2 enzymes (Drosha & Dicer)
  • siRNA = processed by 1 enzyme (Dicer)
28
Q

What is the difference between siRNA and miRNA (target genes)

A
  • miRNA = target 100s of genes
  • siRNA = target fewer genes
29
Q

What important cognitive process do miRNA influence

A

miRNA influences a network of genes involved in LTP

30
Q

How does miRNA regulate gene expression

A

based on complementarity to target mRNA

31
Q

What is the effect of miRNA on gene expression during complete complementarity

A
  • 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
Q

What is the effect of miRNA on gene expression during partial complementarity

A
  • 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
Q

Why is it important that microRNA can target multiple genes

A
  • can regulate many genes which allows rapid changes in pathway activation
34
Q

Why is it beneficial that many miRNAs can regulate a gene

A

provides stronger control over its expression

35
Q

Why does tRNA availability vary

A
  • not all codons are equally common
  • more anti-codons ensure smooth translation w/o delays
36
Q

What does it mean if mutation on rare codon happens

A

slows down translation and reduces gene expression

37
Q

How does tRNA availability affect translation speed

A
  • 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
Q

How does the tRNA pool change in different cell types

A
  • 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
Q

How does tRNA efficiency contribute to cancer

A
  • 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
Q

Name short non-coding RNA

A
  • miRNA
  • snoRNA
  • microRNA
  • piRNA
  • siRNA
41
Q

What are pseudogenes

A

they are copies of genes where the protein-coding sequence is removed & untranslated regions (UTRs) remain

42
Q

What is the purpose of these UTRs in pseudogenes

A
  • miRNA can bind to
  • it helps reduce miRNA interaction with the original gene and allows normal gene expression
43
Q

What happens if miRNA binds to these pseudogenes

A
  • less miRNA is available to block the real gene and block gene expression
  • this is bad if it affects important genes
44
Q

Outline an example of pseudogenes acting as decoys for miRNA

A
  • 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
Q

What does circRNA stand for

A

circular RNA

46
Q

What are circRNA

A
  • long non-coding RNA with joined ends forming a loop
  • they absorb excess miRNA and prevent over-regulation
47
Q

What is the effect of circRNA

A

it helps balance miRNA levels by providing multiple binding sites

48
Q

What are the 3 main functions of circRNA

A
  • 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
Q

How many circRNA are there approximately in human cells

A

over 15 000

50
Q

What is back-splicing error

A

where circRNA is made from a mistake during the RNA splicing process where parts of RNA are incorrectly joined

51
Q

How does back-splicing happen

A

donor and acceptor sites from different exons are incorrectly joined

52
Q

In which types of genes is back-splicing common

A

highly expressed gene where RNA splicing is frequent

53
Q

How can circRNA be promoted

A
  • Alu repeats can bind to each other and form a hairpin loop
  • splicing occurs after the introns are removed, leaving the circRNA intact
54
Q

What are long non-coding RNA

A

RNA molecules longer than 200 nucleotides with little or no coding potentials for proteins

55
Q

What is the function of lncRNA

A

they perform targeted specific regulatory functions unlike shorter non-coding RNA

56
Q

What are anti-sense stabilisation by lncRNA

A
  • 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
Q

What is an example of antisense stabilisation by lncRNA

A
  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
Q

What is meant by lncRNA act as sponges or decoys

A
  • lncRNA sock up RNA or proteins preventing them from working
  • they bind to important molecules and blocking their normal function
59
Q

What is an example of lncRNA acting as a sponge or decoy

A
  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
Q

How can lncRNA modulate epigenetic effects

A
  • 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
Q

How does X inactivation happen via lncRNA

A
  • XIST lncRNA controls X inactivation
  • XIST binds to DNA and attracts a protein complex that methylates histones and DNA –> inactivating X chromosome
62
Q

What are smORFs

A
  • lncRNA can produce proteins
63
Q

What are the features of smORFs

A
  • proteins are cell-specific
  • only made because lncRNA uses rare codons which slows translation
64
Q

Outline part 1 of how siRNAs silence genes

A
  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
Q

Outline part 2 of how siRNAs silence genes

A
  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
Q

What is the function of miRNA

A

they guide RISC complex to complementary target mRNA sequence and either degrade mRNA or prevent translation

Human Genomics & Genetics (7 decks)

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