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Biochem > 6: The Nucleus > Flashcards

6: The Nucleus Flashcards

1
Q

what’s included inside nucleus

A

histone = protein that binds to DNA from eukaryotic chromosomes
nucleosome = protein-DNA complex containing 8 histone proteins
chromatin = repeating nucleosome structure
chromosome = defined region of chromatin that carries information specific to genes
sister chromatids = identical copes of the same chromosome

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2
Q

how does DNA become protein

A
  1. transcription in nucleus - requires specific enzymes called RNA polymerases that read DNA and turn it into mRNA
  2. translation on ribosomes in cytosol - specific amino acids are matched to mRNA sequences to form a polypeptide
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3
Q

what is the nucleus

A

biggest single organelle within eukaryotic cells
contains genetic material called DNA
DNA is packaged as chromatin
site of RNA synthesis - known as transcription
contains nucleolus

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4
Q

nucleus features

A

nuclear envelope = inner and outer membrane separated by perinuclear space
nucleolus = dark stained region
nuclear pore complex = connects nucleoplasm to cytosol
nuclear lamina = part of cytoskeleton to maintain structure
ribosomes = site of protein synthesis (on outside of nucleus membrane)

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5
Q

nuclear pore complex (NPC)

A

channel connecting nucleoplasm to cytoplasm, allowing water soluble molecules to diffuse passively
made of protein called nucleoporins (30 different types)
anything less than 5 KDa can diffuse through freely
proteins up to 60 KDa can diffuse through - takes longer
proteins over 60 KDa cannot diffuse through, requires specialised mechanism and energy

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6
Q

signal sequences

A

nuclear localisation signals (NLSs) tell a protein to go into the nucleus
proteins are synthesised on a cytosolic ribosome
NLSs recognised by specific nuclear import receptors NIR, called importins
NIR bind to FG repeats on nucleoporins in NPC
proteins move through NPC binding sequentially to FG repeats

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7
Q

nuclear import

A
  1. protein synthesised on ribosome with an NLS in its primary sequence
  2. NLS recognised by NIR and the import receptor binds to the signal sequence and the proteins itself
  3. protein complex binds to cytosolic fibrils of the NPC
  4. protein complex moves through NPC by binding, dissociated and rebind with special nucleoporins containing FG-repeats
  5. the protein complex arrives in the nucleoplasm
  6. ran-GTP binds to NIR
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8
Q

nuclear import (part 2)

A
  1. NIR releases protein cargo into nucleoplasm
  2. empty NIR bound to ran-GTP moves back through NPC to cytoplasm
  3. ran-GTP binds to ran binding protein to release NIR
  4. ran-GAP hydrolyses ran-GTP to leave ran-GDP + Pi
  5. ran-GDP transported back to nucleus through NPC
  6. ran-GEF converts ran-GDP to ran-GDP
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9
Q

nuclear export

A
  1. ran-GTP binds to nuclear export receptor (NER)
  2. a protein to be exported from nucleus binds to NER
  3. NER binds to nucleoporins on nuclear basket
  4. sequentially binds to FG-repeats
  5. protein arrives at cytoplasm
  6. ran-GTP bound by a ran binding protein and ran-GAP to hydrolyse GTP to GDP
  7. NER releases its cargo and ran-GDP
  8. ran-GDP moves back to nucleoplasm through NPC
  9. ran-GEF converts ran-GDP to ran-GTP
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10
Q

mRNA processing

A

modified after transcription by splicing and addition of 5’ cap and poly-A tail
happens while still in nucleus in order to become a mature mRNA

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11
Q

mRNA export out nucleus

A

mature mRNA is complexed with proteins - now called messenger ribonucleoprotein (mRNP)
mRNP exports using NER that bind to adapter proteins
adapter proteins bind to the 5’ end of the mRNA interacting with the cap binding complex (CBC)
adapter proteins can only bind if mRNA has been correctly processed

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12
Q

the nucleolus

A

chromatin exists in 2 forms - heterochromatin and euchromatin
heterochromatin is transcriptionally inactive and densely packed making the dark regions
euchromatin is transcriptionally inactive and loosely packed (light regions)
nucleolus packed full of RNA’s and proteins
region where ribosomes are synthesised - ribosomal biogenesis

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13
Q

structure of ribosomes

A

made of 2/3 rRNA and 1/3 protein
large subunit = 60S = made of 5S, 5.8S and 28S rRNA complexed to 49 proteins
small subunit = 40S = made of 18S rRNA and 33 proteins
comes together together as 80S

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14
Q

rRNA genes

A

rRNA genes are clustered together on a DNA sequence called tandem repeats - have spacer regions and coding DNA sequences repeated through a chain
18S, 5.8S and 28S rRNA transcribed in nucleolus by RNA polymerase I
5S rRNA transcribed in nucleoplasm by RNA polymerase III and transported to nucleolus
single strand of 18S, 5.8S and 28S rRNA genes transcribed into 45S pre-rRNA

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15
Q

additional of ribosomal proteins

A

addition of ribosomal proteins (the 1/3 protein) enter via NPC
forms huge structure called 90S pre-ribosome (45S pre-rRNA and proteins bound)
90S pre-ribosome is then modified to to form the three rRNA’s needed

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16
Q

snoRNP’s

A

small nucleolar ribonucleoproteins (snoRNPs) are small nucleolar RNAs (snoRNAs) complexed with proteins
snoRNAs recognise specific areas of rRNA that require modification

17
Q

3 modifications of RNA

A
  1. methylation of hydroxyl groups = OH is changed to OCH3, stabilises and tags RNA so snoRNA can chop it out
  2. conversion of uridine to pseudo uridine = isomerisation catalysed by enzyme psi synthase, improves affinity of RNA to tRNA during protein synthesis
  3. cleavage of the 45S pre-rRNA
18
Q

cleavage of ETS (externally transcribed spaces) and ITS (internally)

A

spacers still in the way of 90S so need to be chopped out
snoRNPs that have just bound to RNA contain enzymes called exoribonucleases that remove ETS
enzymes called endoribonucleases remove ITS
now left with 3 discrete sequences (18s, 28S and 5.8S)

19
Q

export

A

5S rRNA from nucleoplasm combines with 5.8S and 28S rRNA to form the 60S subunit
40S and 60S subunits are transported to the cytoplasm separately and re-combine
export through NPC

Biochem (10 decks)

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