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Losick Mango office hours
TODAY 3-5 PM
Kahne’s Office
October 21
Richard Losick
RNA and the Origin of Life
1. Ribozymes
2. Is the ribosome a molecular fossil
from an RNA world?
3. How did life evolve?
Goal: To understand how life might have
evolved from an RNA world.
Objectives:
1. Describe self-splicing.
2. Explain why RNase P is a true ribozyme.
3. Explain why the ribosome could be a
molecular fossil from an RNA world.
4. Describe how to select for ribozymes that
polymerize nucleotides.
5. Explain why evolution of self-replicating
ribozymes demands compartments.
With RNA we throw away many of the rules! If
DNA is straight-laced and uniform, RNA is freewheeling and audacious. RNA is the non-conformist.
It has ceded primacy as the repository of genetic
information to DNA but it has gained versatility. It is
a master architect, forming complex, threedimensional structures, and it can carry out
catalysis, a trick it learned long before proteins
knew how to be enzymes. In short, life probably
evolved from an ‘RNA world’.
- Y.
Truly
What is an enzyme?
•Enzymes are proteins that catalyze a chemical
reaction.
•Enzymes have an “active site” that binds
substrates through ionic, H-bonds, and/or van
der Waals interactions.
•Enzymes facilitate the formation of a transition
state, thereby lowering the activation energy.
•Enzymes have a turnover number greater than one.
James Sumner purified the first enzyme, urease,
in 1926 and showed it to be a protein.
+ H 2O
urease
CO2 + 2 NH3
Harvard class of 1910
For over half a century, it was believed that
only proteins are enzymes.
But RNA molecules can be enzymes too!
RNA enzymes are known as “ribozymes.”
We will consider ribozymes that:
• cleave phosphodiester bonds
• create phosphodiester bonds
• create peptide bonds
Recall mRNA splicing, which occurs in two transesterification reactions
Splicing is catalyzed by an enzyme complex
called the splicosome
Self-splicing requires no enzyme.
The intron mediates its own excision!
exon
intron
Self-splicing intron uses a free
guanine nucleotide as a
nucleophile.
Strictly speaking, is a self-splicing RNA a
ribozyme? Is it a catalyst?
Why or why not?
RNase P
•The first true RNA enzyme (ribozyme).
•It cleaves a precursor to tRNA molecules
(pre-tRNAs) at a specific site.
RNase P cleaves off a segment of RNA from the
transcription product of tRNA genes to generate the
mature tRNA
RNase P
RNA subunit
protein subunit
tRNA
substrate
Main points
1. Both RNA and protein can be
enzymes
2. Self-splicing introns and RNase P
act on phosphorous centers
2. Is the ribosome a molecular
fossil from an RNA world?
Self-splicing introns and RNase P act
on phosphorous centers.
One ribozyme is known that acts on a
carbon center.
It is the enzyme at the heart of the
ribosome that creates peptide bonds!
TheO phosphodiester
bond
OH
O
P O CH2
O
O
O
O
A
OH
P O CH2
O
OH
C
O
OH
3' end
The peptide bond
peptide bond formation is
catalyzed by “peptidyl
transferase”
The peptidyl transferase is a ribozyme!
• Peptidyl transferase is
composed of RNA.
• No proteins are close to
the catalytic site
• The ribozyme juxtaposes
the 3’ ends of the tRNAs
in the P and A sites.
Large subunit of the ribosome
Peptide bond formation is catalyzed by a
proton shuttle involving the 2’ OH
The 3’ oxygen captures a proton from the 2’ OH
The 2’ oxygen in turn captures a proton
from the nitrogen of the amino group.
Main points so far
1. The most fundamental reaction in the
“protein world” is catalyzed by a ribozyme.
2. The RNA component of the large subunit of
the ribosome is a ribozyme that catalyzes
peptide bond formation.
3. Both ribosomal RNA and tRNA participate
in catalysis.
4. Is the ribosome a fossil from an earlier,
“RNA world”?
3. How Did Life Evolve
The discovery of ribozymes simplified the
problem of the origin of life.
RNA could be the information carrier and
the replicase for its own duplication.
Eventually, a ribozyme evolved that could
synthesize proteins.
Did life evolve from an “RNA world”?
What is life?
Life is a system that is capable of selfreplication and that is subject to Darwinian
evolution.
Self-replication means the system relies only
on small molecules and energy.
Darwinian evolution implies variation (mutation)
and phenotypic expression.
Can we create an RNA molecule that is
capable of self-replication and variation?
Evolving an RNA replicase
1. Start with RNA molecules of random sequence.
2. Incubate RNAs with ribonucleoside triphosphates
and an RNA template.
3. Size select RNAs that are slightly larger (those with
polymerase activity!).
4. Mutagenize size-selected RNAs.
5. Repeat the cycle of size selection and mutagenesis.
Evolving RNA molecules that can
polymerize ribonucleoside triphosphates.
The best ribozyme with polymerizing activity to
date can generate 95-nucleotide long RNAs in a
template-directed manner.
Structure of an evolved ribozyme capable of
carrying out phosphodiester bond formation
How do we get from a ribozyme
replicaase to life?
Three conceptual problems:
1.The self-replication problem.
2.The Darwinian selection problem
3.The prebiotic chemistry problem.
The Self-replication Problem
One replicase would have to make a
complete copy of another.
The immediate product would be a
complement of the replicase.
The complement in turn would be a
template to make more replicases.
The Darwinian Selection Problem
How could this system evolve to select
for better and better replicases?
If a mutant ribozyme arose that worked
better, it would copy non-mutant
RNAs as well as mutant RNAs.
The solution to this dilemma is
compartmentalization.
Vesicles form spontaneously from lipids
Fatty acids and other lipids naturally form vesicles
Chronology of Life on Earth
1. Earth and its moon arose from a collison with a giant
projectile about 4.5 million years ago.
2. It took a few hundred years for Earth to cool off enough to
have oceans.
3. Layered structures called stromatolites in sedimentary
rocks indicate life as early as 3.6 million years ago.
4. So life likely arose between 4.2 and 3.6 million years ago.
life arises from an
RNA world?
The prebiotic chemistry problem
What was the nature of the prebiotic world that
spawned self-replicating RNA molecules?
In 1953, Stanley Miller and Harold Urey showed that
subjecting water, methane, ammonia, and hydrogen to
electrical discharges in sealed flasks generated amino
acids.
In 1969 the Murchison meteorite landed in
Australia, bringing amino acids and bases to
Earth from outer space!
Francis Crick and the Theory of Panspermia