M116 Midterm Questions With Complete Solutions
are lncRNAs critical for the survival of the organism Correct
Answers Yes ..
A series of lncRNA gene knockouts in mice have led to severe,
often lethal defects in development. Defects included
bottom-up approach Correct Answers Digest proteins to
peptides
Fractionate peptides (if LC-MS)
Isolate/fragment individual peptides inside the mass
spectrometer
Infer protein identities Identify peptide sequences
Can we predict RNA secondary structures, specifically helices ?
Correct Answers Yes, we can predict helical regions by, e.g.
'Free energy minimization'
Computer algorithm searches
However, the above algorithms are not very reliable: There may
be many alternate (equally stable) base-pairing arrangements
coaxially- stacked helices Correct Answers Two covalently
discontinuous helices, on the axis of the green line
Compartmentalized bead tagging aim Correct Answers evolve
a polymerase that can act free in solution
Compartmentalized bead tagging result Correct Answers An
RNA polymerase ribozyme that could
extend template by up to 95 nt with 99% fidelity! It was also
able to successfully replicate a hammerhead ribozyme.
, Core of Hammerhead ribozyme Correct Answers small, self-
cleaving ribozyme from a viroid (a viroid is an infectious RNA
molecule),
Data-dependent aquisition Correct Answers Tandem MS The
choice of ion to fragment is dependent upon on characteristics of
the initial mass spectrum
from high to low intensity
Electrospray Ionization (ESI) Correct Answers In mass
spectrometry, an ionization technique in which the compound is
first dissolved in a solvent and then sprayed via a high-voltage
needle into a vacuum chamber. The tiny droplets of solution
become charged by the needle, and subsequent evaporation
forms gas-phase molecular ions that typically carry one or more
charges.
first catalysts Correct Answers clay minerals such as greigite
(Fe5NiS8) or montmorillonite
HOTAIR ("HOX transcript antisense intergenic RNA" Correct
Answers Regulator of epidermal tissue development.
Particularly abundant in peripheral tissues of the human body
How can you determine RNA secondary structure
experimentally Correct Answers co-variation analysis', and by
physical probing
are lncRNAs critical for the survival of the organism Correct
Answers Yes ..
A series of lncRNA gene knockouts in mice have led to severe,
often lethal defects in development. Defects included
bottom-up approach Correct Answers Digest proteins to
peptides
Fractionate peptides (if LC-MS)
Isolate/fragment individual peptides inside the mass
spectrometer
Infer protein identities Identify peptide sequences
Can we predict RNA secondary structures, specifically helices ?
Correct Answers Yes, we can predict helical regions by, e.g.
'Free energy minimization'
Computer algorithm searches
However, the above algorithms are not very reliable: There may
be many alternate (equally stable) base-pairing arrangements
coaxially- stacked helices Correct Answers Two covalently
discontinuous helices, on the axis of the green line
Compartmentalized bead tagging aim Correct Answers evolve
a polymerase that can act free in solution
Compartmentalized bead tagging result Correct Answers An
RNA polymerase ribozyme that could
extend template by up to 95 nt with 99% fidelity! It was also
able to successfully replicate a hammerhead ribozyme.
, Core of Hammerhead ribozyme Correct Answers small, self-
cleaving ribozyme from a viroid (a viroid is an infectious RNA
molecule),
Data-dependent aquisition Correct Answers Tandem MS The
choice of ion to fragment is dependent upon on characteristics of
the initial mass spectrum
from high to low intensity
Electrospray Ionization (ESI) Correct Answers In mass
spectrometry, an ionization technique in which the compound is
first dissolved in a solvent and then sprayed via a high-voltage
needle into a vacuum chamber. The tiny droplets of solution
become charged by the needle, and subsequent evaporation
forms gas-phase molecular ions that typically carry one or more
charges.
first catalysts Correct Answers clay minerals such as greigite
(Fe5NiS8) or montmorillonite
HOTAIR ("HOX transcript antisense intergenic RNA" Correct
Answers Regulator of epidermal tissue development.
Particularly abundant in peripheral tissues of the human body
How can you determine RNA secondary structure
experimentally Correct Answers co-variation analysis', and by
physical probing
