Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

AMB > AMB17 > Flashcards

AMB17 Flashcards

(51 cards)

Start Studying
1
Q

Describe nuclear splicing

A

2 transesterification reactions where an OH group
pre-mRNA - mRNA
attacks a phosphodiester bond.
Cuts at 5’ site and forms lariet by 5’ - 2’ bond connnecting from 5’G to 2’A branch site
Cut at 3’ site and join exons releasing the intron as a lariat.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

How is splicing initiated

A

SR proteins bind sequences within the exons and from there recurit U2AF and U1 snRNA to downstream 3’ and upstream 5’ intron splice sites respectively initiating assembly of machinery on correct sites

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

what are snRNPs

A

snRNPs (pronounced “snurps”), or small nuclear ribonucleic proteins, are RNA-protein complexes that combine with unmodified pre-mRNA and various other proteins to form a spliceosome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

how are introns marked

A 
introns are marked because of their consensus sequence, usually a a GU at 5' and a AG at 3' 
5' bound by U1 snRNPs 
branch site (AG) bound by U2 accessory faactor U2AF
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

how are exons marked

A

by interaction with proteins rich is serine and arginine SR proteins, which bidn to exon specific enhancers, stopping exons being spliced out.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

what is alternative splicing

A

when primary transcripts are spliced alternatively to produce different mRNA and thus different protein products (isoforms)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

how much of the human and drosophilia genome undego alternative splicing

A

40% of drosophila genes

up to 75% of human genes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Give an example of a human gene that is highly alternatively spliced

A

human slo gene
encodes pore forming alpha subunit of large conductance activated potatium channels in the NS
hundreds of isoforms can be formed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

give an example of a drosophilia gene that can be alternatiely spliced

A

Dscam gene
potentially encodes 38,000 proten isoforms, important in establishing neural networks in the brain, (synpatogenesis), also in the immune system, different isoforms recognise different antigens.
4 exons each with 12, 48, 33 and 2 alternative splicing respectively = 38000

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What happens in high iron concentration in the cell

A

iron is present and so binds with IRE binding proein (iron response element) making it no longer free to bind to transferrin mRNA, so transferrin is degraded and synthesis of the receptor inhibited
IRE can also not bind to ferritin mRNA so translation of ferritin proceeds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

what happens in low iron concentration

A

iron is absent so IRE binding protein binds to the 3; IRE of the transferrin receptor mRNA, protecting it from degradation by creating a loop in the position where ribonclease would begin degradation - allows it to be translated
IRE binding proteins binds to 5’ IRE of ferritin mRNA creating a looop before the start codon which prevents the ribosome binding stopping translation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

what does transferring mrna and ferritin mrna code for

A 
transferring = iron receptor to allow iron into cell
ferritin = iron binding protein to render toxic iron safe
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

what is the IRE binding protein?

A

aconitase - the TCA enzyme that requires iron as a cofactor for activity.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

gives examples of some non coding RNAs

A

tRNA
rRNA
snRNA (small nuclear)
snoRNA (small nucleolar)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

how large are micro RNAs

A

22pb ish

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

what is RNA interferance

A

process by which short 21-23nt antisense RNAs derived from longer dsRNAs can modulate expression of mRNA by translation inhibition or degradation.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

what is stRNA

A

(RNAi) short temporal RNA - miRNA that modulates mRNA expression during eukaryotic development

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

what is piRNA

A

(RNAi) regulates gene expression in germ line cells adn acts to silence transposable elements

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

what is si RNA

A

(RNAi) small interfering RNA complementary to viruses and transposable elements

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

how is RNAi generated

A

from longer precursors by Drosher and Dicer

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

what is Drosher

Study These Flashcards
A

nuclease endonuclease that processes ds prim-RNAs into short 70pb ish precursors for Dicer processing, exported to DIcer in the cytoplams

22
Q

what is Dicer

Study These Flashcards
A

endonuclease that processes ds precursor RNA to 21-23 nt RNAi molecules

23
Q

What are short RNA produced by Dicer recognised by

Study These Flashcards
A

RISC - RNA induced silencing complex - a ribonucleoprotein particle composed of a short ssRNA and a nuclease that cleaves mRNA complementary to siRNA, recieved from dicer and delivering it to mRNA

24
Q

desribe RISC

Study These Flashcards
A

The RNA-induced silencing complex, or RISC, is a multiprotein complex, specifically a ribonucleoprotein, which incorporates one strand of a double-stranded RNA (dsRNA) fragment, such as small interfering RNA (siRNA) or microRNA (miRNA).[1] The single strand acts as a template for RISC to recognize complementary messenger RNA (mRNA) transcript.

25
what kind of enzymes are Drosher and DIcer
RNAseIII
26
what determines whether the ssRNA bound to RISC is cleaved or translation repressed?
- degree of complementation between target mRNA and argonautes small associated RNA
27
what are loaded argonaute proteins guided to
complementary target mRNA to silence
28
what happens when RISC encounters a small RNA duplex and is not perfectly complementary - mismatches or bulges?
not substreas so become single stranded ina cleavage independent manner - by an unknown protein
29
how do micro RNAs regulate expression
by base pairing with complementary sequences in target mRNA
30
what does RNA interferance trigger?
degradation or translation inhibition of mRNAs complementary to miRNA or siRNA - or can also lead to mRNA activation
31
what are microRNAs
MicroRNAs (or miRNAs) comprise a novel class of small, non-coding endogenous RNAs that regulate gene expression by directing their target mRNAs for degradation or translational repression.
32
what is the difference between miRNA and siRNA
miRNAs derive from regions of RNA transcripts that fold back on themselves to form short hairpins, whereas siRNAs derive from longer regions of double-stranded RNA
33
what happens to primary miRNA in the nucleus
processed by Drosher and DGCR8 into precursor miRNA and then transported to cytoplasm by exportin 5/XPO5
34
what happens to precursor miRNA in the cytoplasm
bound by Dicer containg pre RISx and processed to make guide sequence loaded into holo RISC which contains all the components required for RNA silencing.
35
what is the catalytic core of risc
AGO2
36
what happens when RISC guide sequence meets to corresponding target seq
binds to 3' UTR of cellular mRNA if fully complemenatary to target site it triggers site specific cleavage and degradation of the mRNA through catalytic domain of AGO2
37
what happens if base pairing of RISC is incomplete but includes the seed region (nt 2-8) of the miRNA
translational inhibition occurs, which can be accompanied by non sequence specific degradation of the mRNA P bodies
38
What is shRNA
small hair pin RNA artificial RNA molecule with a tight hairpin turn that can be used to silence target gene expression via RNA interference (RNAi). Expression of shRNA in cells is typically accomplished by delivery of plasmids or through viral or bacterial vectors. shRNA is an advantageous mediator of RNAi in that it has a relatively low rate of degradation and turnover.
39
what happens to shRNA in cell
similar to miRNA they are transported to the cytoplasm by XPO5 dsRNA int he cytoplasm is recognised and processed by Dicer into 21-25nts siRNA fragments loaded into RISC can then target complementaty sewuences of cellular mRNA and trigger their degradation through AGO2 mediated cleavag
40
what happens when siRNAs are prsent in nucleus and complementary to the promoter region
can trigger chromatin remodelling and histone modification that result in transcriptional gene silencing. - details unknown, but include argonaute family proteins and accesory proteins TRBP and PACT
41
what happens after host cell is infected by a DNA virus
genome is transcribed in the nucleus to yeield both pri-mRNAs and mRNAs - pri mRNA is processed by host factors in the nucleaus to yeielf pre -miRNA intermediate which is exported to the cytoplasm where mature miRNA is generated and incorperated into RISC
42
What is gene knock down
cells transfected with siRNA made in vtro transgenic animals or trasnfected cells can be made to express dsRNA or shRNA from transgenes that will be processed by DIcer or Drosher from transcribed precursors siRNAs can be generated from long dsRNAs in vitro via recombinant dicer, transcribed in vitro from plasmids or chemically synthesised then RNAs trasnfected into cells to specifically target mRNAs and silence specific genes
43
What is the main problem with using the RNAi pathway to manippualte disease gene expression what are some solutions
- delivery. Viral delivery - using shRNA constructs chemical delivery - using reagent that will neutralise the -ve RNA and allow interaction and passage through the membrane
44
what is the potential of RNAi treatment
could turn off oncogene expression, anti sense RNA against oncogene and bring down expression of RNA correponding to oncogene
45
what are 6 in vitro delivery strategies for therapeutic siRNAs
1. cholesterol groups linked to modified siRNAs to enhance stability - eg. 2' Omethyluridine/ 2'fluorouridingec combined with phophorothioate linkages 2. polycation nanoparticles can direct delivery of siRNA to specific cells through use of surface ligands - such as trasnferrin,t hat bind to receptors on target cells 3. SNALPs encapsuakte modified siRNA in cationinc or neutral lipid bilayer coated with diffusable PEG lipid conjugates - allow siRNA to be taken up by cells and released by endosomes 4. masked endosomolytic agent - simialr to SNALPs but smaller and contain a ligand that allows targeted cell delivery 5. tagging seqeunce specific antibodies with proamine or pos charge to allow delivery to specific cell types via receptor mediated uptake 6. chemically linking or contranscribing siRNAs with RNA aptamers allows the targeted delivery of the siRNA to cells expressing appropriate receptors.
46
cholesterol based delivery strategy for therapeutic siRNAs
1. cholesterol groups linked to modified siRNAs to enhance stability - eg. 2' Omethyluridine/ 2'fluorouridingec combined with phophorothioate linkages
47
Polycation based delivery strategy for therapeutic siRNAs
polycation nanoparticles can direct delivery of siRNA to specific cells through use of surface ligands - such as trasnferrin,t hat bind to receptors on target cells
48
SNALPS based delivery strategy for therapeutic siRNAs
. SNALPs encapsuakte modified siRNA in cationinc or neutral lipid bilayer coated with diffusable PEG lipid conjugates - allow siRNA to be taken up by cells and released by endosomes
49
Masked endosomolytic agent based delivery strategy for therapeutic siRNAs
masked endosomolytic agent - simialr to SNALPs but smaller and contain a ligand that allows targeted cell delivery
50
antibody based delivery strategy for therapeutic siRNAs
tagging seqeunce specific antibodies with proamine or pos charge to allow delivery to specific cell types via receptor mediated uptake
51
chemically linked based delivery strategy for therapeutic siRNAs
chemically linking or contranscribing siRNAs with RNA aptamers allows the targeted delivery of the siRNA to cells expressing appropriate receptors.

AMB (21 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions