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BCH311 L1-5
RNA Structure
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Amit Zaidman
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Cards (25)
What is the secondary structure of tRNAs?
Cloverleaf
shape,
“CAA”
acceptor stem,
4
distinct loops
What is the “CAA” acceptor stem?
Amino acid attachment point
; added
post-synthesis
What are the 4 loops in the secondary structure of tRNAs?
D loop
,
Anticodon loop
,
Variable loop
,
TΨC loop
What does the D loop contain?
Abundant
dihydrouridine
What does the anticodon loop contain?
Specific
trinucleotide
sequence (corresponding to an
amino acid
)
What does the TΨC loop contain?
T
,
Ψ
,
C
nucleotides (
invariant
)
What is the tertiary structure of a tRNA?
L-shape
What are the base-pairing interaction that form the tertiary structure of a tRNA?
D loop
with
variable
and
TΨC
loops
What interactions occur within a tRNA molecule?
Watson-Crick
base pairs,
Non-Watson-Crick
base pairs,
triple
base pairs,
Metal ion
/
polyamine
binding
What is the purpose of metal ions/polyamines in RNA structure?
Shield
negatively
charged
phosphate groups
, stabilize
tertiary
structure
What are some examples of divalent metal ions/polyamines?
Mg2+
and
Spermine
(contains amine, NH2 groups)
What is the purpose of rRNAs?
Provide
structural
foundation for
ribosomal
proteins
What modified nucleotides are found in rRNAs?
Ribothymidine
(T) and
Pseudouridine
(Ψ)
How are different rRNA species classified?
Via
sedimentation coefficients
(prokaryotic ribosome → 70S; consists of 50S and 30S rRNA strands)
What is the structure of rRNAs?
Complex
secondary
and
tertiary
structures, extremely
varied
sequences, structures nearly
homologous
How can RNA molecules play a role in catalysis?
Via
hydrolytic
or
transesterification
reactions
What processes the 5’-ends of a tRNA molecule?
RNAse P
(type of ribonuclease)
What is a ribozyme?
A piece of RNA that is
catalytic
and uses either
itself
or another piece of
RNA
to
cleave
something
What is the spliceosome and what does it do?
Multiple
ribozymes; carries out
splicing
of
introns
from pre-mRNA
What are riboswitches?
Regulatory segments
found in
ssRNA
What do riboswitches do?
Turn RNAs
on
or
off
through
small molecule binding
What do ligands bind to in riboswitches and what does that cause?
Ligands bind to an
aptamer domain
leading to
RNA structural changes
What are the two forms of regulation that riboswitches are involved in?
Regulation of
transcription
and
translation
What are aptamers?
Sequences that form
3D structures
that can be used to
identify
specific types of
biomarkers
on certain cells
What can ribozymes cleave?
Self
(phosphate backbone) or
other
pieces of RNA