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YEAR 2 S1 MOLECULAR > Gerber L3 Cytoplasm > Flashcards

Gerber L3 Cytoplasm Flashcards

1
Q

is there correlation between mRNA levels and protein levels

A 
limited correlation (0.2-0.6)
- proteins are on avg ~2,800x more abundant than mRNAs
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2
Q

what are the reasons for RNA localisation

A
  • Target protein to appropriate Region in the cell
  • Prevents expression elsewhere
  • Response to local requirement (e.g. neurotransmitter production in neurons)
  • Independent control in different cellular regions (local control apart from central control)
  • Localized synthesis necessary for assembly of protein complexes. If a big complex has to be set up, its logical to produce the parts in the same localization.
  • More efficient transport (one mRNA molecule vs. many proteins)
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3
Q

what are the adv of RNA localisation

A

Is better to locally produce the product instead to waste energy in transport. The energy used for protein production is high.
- The protein effect can be very local and maybe the presence of the protein in some cell parts could have a detrimental effect

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4
Q

what are the 3 main fates of mRNA in cytoplasm

A

translation
localisation/storage
decay

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5
Q

give an example of mRNA localisation in neurons

A
  • allows for local synthesis
  • mRNA is localised to the SYNAPSES for protein production
  • more efficient to transport mRNA
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6
Q

give examples of RNA localisation during developmental processes

A
  • gradients of morphogens
    (Nanos mRNA at the posterior pole of Drosphila embryos)
  • cell lineage specification
    (Vg1 mRNA localisation to VEGETAL pole of Xenopus stage III-IV oocyte)
  • achieve high protein concentrations
    (Beta-actin mRNA localised to the leading process in chicken fibroblasts and in dendrites of neurons)
  • establishment of assymentry for the development of new cells
    (ASH1 mRNA localisation to the bud tip of dividing yeast cells)
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7
Q

molecular mechanisms to localise mRNAs NO1

A
  • neuronal RNPs along microtubules, ASH1 mRNA along ACTIN to bud-tip in yeast
  • mRNA brought to a region where protein needs to be synth
  • microtubules
  • eg yeast
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8
Q

molecular mechanisms to localise mRNAs NO2

A
  • Drosophila mRNAs enriched in pole plasa in post pole of embryo
  • RNA floating in cytoplasm is CAUGHT by receptor in prot.synth regions
  • extended by degradation of mRNAs in OTHER AREAS where it is unwanted
  • eg where a protein is harmful
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9
Q

give an example of a ‘ZIP’ code used for mRNA localisation

A
  • Localization signals most often reside in 3’UTR -but not exclusively (eg ASH1 in yeast)
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10
Q

give the example of ASH1 in yeast

A
  • daughter cells remain same as mother (alpha) O no HO expression. Ash1 protein is a TRANSCRIPTIONAL REPRESSOR of HO. It is transported to the D cell only
  • change mating type in MOTHER from alpha to A, this is done by transcription factor HO (req for mating type switching)
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11
Q

how can we visualise localised mRNAs in vivo

A

use U1A-GFP fusion protein

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12
Q

how can we visualise localised mRNAs in vivo

A

use U1A-GFP fusion protein

  • U1A is part of a splicing factor and MS2 is a bacteria protein
  • U1A-GFP fusion protein is tethered to mRNA via U1A binding sites, this enables visualization of mRNA viaGFP
  • they make an interaction with a HAIR PIN (an artificial RNA that cont ASH1)
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13
Q

what are the 2 major modes of translational regulation

A

1) Global regulation: modification of translation-inhibition factors or their regulators
2) mRNA specific regulation:
- RNA structure
- specific RNA binding proteins
- microRNAs

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14
Q

where are CIS- acting regulatory elements usually found

POSITIVE elements

A

in UTRs

  • 5’ cap
  • internal ribosome entry sites (IRES) (can directly recruit ribosomes to initiate translation) common in viruses, oncogenic genes
  • poly A tail
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15
Q

where are CIS- acting regulatory elements usually found

NEGATIVE elements

A
  • RPB binding site
  • UTRs
  • micro RNA binding sites
  • secondary structures like HAIRPINS can block translation initiation
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16
Q

give an example of how regulatory proteins prevent recruitment of small ribosome subunit

A

IRON REGULATORY PROTEINS

  • binds to IRON RESPONSE ELEMENT (IRE) prventing recruitment of small ribsome subunit to the mRNA-bound eukaryotic initiation factors (eIF4F) complex by steric hindrance
  • At the 5´end of the mRNA there is a 4E Cap initiation complex. Proteins interact with the cap. These are required to initiate translation, to prepare the mRNA. The IRP binds to the hair pin very close to the start (cap initiation). By doing this prevents the assembly of the complex by ribosome factors like the ribosomal units. It blocks the assembly for the factors. Steric blockage. This is important because many proteins bind and block in other stages.
17
Q

how does iron starvation affect post trans modif

A
  • ferretin is req for Fe storage
  • if low Fe, CYTOSOLIC ACONITASE binds to an element in the 5’ UTR of ferretin mRNA and blocks translation O no Fe storage
  • IRON RESPONSE PROTEIN binds to 3’ UTR of TRANSFERRIN receptor mRNA (for Fe import into cell)
  • inc Fe transport into cell
18
Q

how does excess iron affect

A
  • iron binds to ACONITASE, changing its conformation, O it binds IRON instead of RNA
  • ferritin is made because of the RELEASE of the ACONITASE from the 3’ UTR
  • O hairpin= exposed
  • ENDONUCLEASE has access to RNA, it is degraded O no more transferrin receptor
19
Q

how can RNA binding proteins affect translation at different steps

A
  • binding to 3’ UTR can affect stability
  • assembly of translation initiation complexes interfere in the binding of CAP protein
  • repress joining of ribosomalsubunits
  • control length of poly A tail, poly A tail controls translation
20
Q

what is the life expectancy of mRNAs and proteins in humans

A

mRNA: 9 hours
proteins: 36 hours: they are 5x more stable than mRNA

no correlation between their half lives

21
Q

how are euk mRNAs degraded

A

1) poly A tail is SHORTENED to 10-20 adenosines by deadenylation complex called PARN
the 2 possibilities:
1) 5’ cap removed by DCP1 and 2
- XRN1 decays the rest from 5’ to 3’
2) EXOSOME degrades it from 3’ to 5’, then the leftover cap is further degraded

22
Q

where is the exosome found, what does it do

A

found in nucleus (degrades introns)

cytoplasm too: degrades

23
Q

what is the structure of the core human exosome

A
  • 9 DIFFERENT protein subunits
  • make a ring structure
  • RNA passes through the central pore and is degraded by RNAses at the other end
  • have additional associated proteins Rrp6 and Rrp7 that specify activity on distinct RNA classes
24
Q

where is mRNA degraded

A

Decappingand degradation of mRNAs takes place in so-called Processing bodies (P-bodies)
P-bodies are condense aggregates of mRNAs and proteins/ncRNAs in the cytoplasm
P-bodies are especially visible in stressed cells (leading to rapid shut-down of translation

YEAR 2 S1 MOLECULAR (7 decks)

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