Stuff i need to memorise

Question 1

miRNAs and siRNAs

Answer 1

exert their function by associating with argonaute (AGO) proteins to form ribonucleoprotein silencing complexes that can either decrease mRNA translation or induce mRNA degradation

Question 2

miRNA biogenesis and function

Answer 2

he human genome encodes > 2000 miRNA genes.
* miRNAs are transcribed by RNAPII as a much longer transcript called Pri-miRNA.
* The Pri-miRNA folds back on itself to form at least one distinctive hairpin structure.
* The hairpin structure within Pri-miRNA is cleaved by the microprocessor complex to release Pre-miRNA.
* After export to the cytoplasm, the Pre-miRNA is cleaved by the endoribonuclease Dicer to produce a
~ 20 nt miRNA duplex with a 5’ phosphate and a 2 nt 3’ overhang at each end.
* One strand of the miRNA duplex - the mature miRNA - is loaded into the guide-strand channel of an AGO protein to form a silencing complex, the other strand is degraded.
* The silencing complex targets mRNA complementary to the guide miRNA. mRNAs with perfect complementarity are degraded and translation of mRNAs with incomplete complementarity is decreased

Question 3

Summary of selected posttranscriptional
gene regulatory mechanisms

Answer 3

• Decapping and/or deadenylation triggers degradation of mRNA.
• Alternative splicing results in different mRNAs from a single pre-mRNA and thus allows to express several proteins with distinct primary structure from a single gene.
• RNA editing introduces changes to mRNA sequences post transcription, and can therefore also result in expression of distinct protein variants from a single gene.
• Short non-coding RNAs (miRNAs and siRNAs) regulate mRNA stability and mRNA translation through complementary base pairing in the context of ribonucleoprotein silencing complexes

Question 4

RNA editing

Answer 4

Posttranscriptional processes that lead to nucleotide changes at specific positions in RNA molecules, including
* nucleobase modifications, such as adenine-to-inosine and cytosine-to-uracil deamination.
* non-template nucleotide additions or deletions.

Question 5

5

Answer 5

5’- capping occurs co-transcriptionally shortly after transcription initiation, when the nascent RNA reaches a length of 25 - 30 nt.

Question 6

3

Answer 6

polyadenylation occurs during transcription termination; the length of poly A tails varies
in different organisms (~ 200 nt in mammals, ~ 70 nt in yeast

Question 7

The helix-turn-helix (HTH) DNA-binding motif

Answer 7

• Two α-helices joined by a short turn
• A recognition helix is locked in place by
  an adjacent α-helix
• A recognition helix is locked in place by
  an adjacent α-helix.

Question 8

The basic leucine zipper (bZip) DNA-binding motif

Answer 8

Coiled-coil dimerization of monomers is
stabilised by hydrophobic interactions.

Basic regions in the extended α-helical
Region of monomers interact with DNA
through adjacent major groove

Question 9

Sequence-specific DNA-binding proteins

Answer 9

• Base pairs in DNA display a characteristic set of functional groups in the major
  and minor grooves of DNA.
• DNA binding proteins recognize specific sequences predominantly based on
  their specific chemical signatures in the DNA major groove.
• A common architectural principle of DNA-binding motifs is a recognition helix,
  placed into the major groove of the DNA, and positioned by another secondary
  structure.
• DNA-binding proteins containing leucine zipper and helix-loop-helix motifs must
  form dimers in order to bind DNA in a sequence-specific manner.
• Dimeric DNA-binding proteins recognize bipartite DNA sequences, consisting
  of pairs of conserved half-site sequences separated by non-conserved nucleotide sequences of varying lengths.
• Heterodimerisation of sequence-specific DNA-binding transcription factors
  allows for combinatorial regulation of gene transcription