Download Nucleic Acids and the RNA World

Nucleic Acids and the RNA
World
Pages 74-89
Chapter 4
RNA vs. Protein
• Chemical Evolution stated that life evolved
from a polymer called a protein.
• HOWEVER, now many scientists question
this.
• There is currently a large scientific motion
towards a polymer called a Nucleic Acid.
– Specifically, a RiboNucleic Acid
• RNA
RNA World Hypothesis
• This proposal is called the RNA World
Hypothesis
• Again, this is still very HYPOTHetical
• THIS IS THE DELEMA OF
What is Life?????
• This is an age old question that scientists
still debate!
• We don’t have a simple explanation, and
therefore discussing the origin of life is
nearly impossible
• There are 2 versions of the story…
– We will need to use the 2nd version
Version 1 (The easy version)
•
•
•
•
•
1.
2.
3.
4.
5.
All life is made of cells
Life reacts to its environment
Life reproduces
Life uses energy
Life grows at some point
– Sadly…..it isn’t so cut and dry!
Version 2 (Our version)
• Because scientists constantly debate this
issue, we only use two of these rules to
discuss LIFE in high end Biology
• 1. The ability to reproduce!
• 2. The ability to acquire particular
molecules and use them in
CONTROLLED CHEMICAL REACTIONS
that maintain conditions suitable for life
& contribute to growth!
What About the Other 3
Requirements
• They are there…. They are just used as
subcategories at this level of Biology.
– IE: Chemical reactions (Rule 2) are precisely
controlled because chemicals and reactants
are bound by a Plasma Membrane.
– Therefore, it is required for life… it is just no
longer the rule!
– The problem is that if it is debated, it becomes
an uncertain theory
– Remember, even the “rules” are JUST
theories
All Polymers are Proteins?
• Thus far, every polymer we have learned
about IS a protein.
• HOWEVER, we now are learning of a new
polymer.
• Proteins are the result of polymerization of
monomers called Amino Acids
• Nucleic Acids are the result of
polymerization of monomers called
Nucleotides
Amino Acid
Nucleotide
Components of a Nucleotide
• 3 components
– Phosphate group
– Sugar
– Nitrogenous (Contains a nitrogen) Base
• PAGE 75
Sugar
• Your sugar is an organic compound with a
carbonyl group
– C=O
How do Nucleotides Polymerize
• Figure 4.2 on page 76
• It starts with a phosphodiester linkage
– This condensation reaction is the formation of the
bond between the phosphate group of one nucleotide
and the hydroxyl group of the sugar component.
• If the nucleotides involved contain the sugar
RIBOSE, the polymer is called RNA
• If the nucleotides involved contain the sugar
DEOXYRIBOSE, the polymer is called DNA
DNA’s Sugar-Phosphate Backbone
RNA’s Sugar Phosphate Backbone
Count Your Primes
Base Pairs
Base Pairs
Base Pairs
Base Pairs
Base Pairs
Base Pairs
Chargaff’s Theory
• Found that the #of bases (Purines &
Pyrimidines) are the same
– The # of A’s = # of T’s
– The # of C’s = # of G’s
• Found that these bases must be relavent
to its matching pair
WATSON and CRICK
• Announced in 1953
• Used the results of other scientists to
figure out the structure of DNA
Watson & Crick Model
• Chemists found that DNA polymerized through
the formation of phosphodiester linkages
– This concluded a sugar-phosphate backbone
• By analyzing the total number of purines and
pyrimidines it was found that the number of A’s
and T’s were equal to the number of C’s and G’s
– This was called Chargaff’s rule after Erwin Chargaff
• X-ray diffraction showed a repeating scatter
pattern (.34 nm, 2.0nm, 3.4nm)
– This repeating pattern only makes sense if the
molecule is shaped as a double helix
• Pages 79-82
Scatter Pattern X-ray Diffraction
Scatter Pattern X-ray Diffraction
• Watson & Crick began to analyze the size and
geometry of deoxyribose, phosphate groups,
and nitrogenous bases.
• Using things like bond angles, and
measurements, they were able to devise 2.0nm
probably represented the width of the helix, and
.34 was likely the distance between bases
stacked in the spiral
• They arranged two strands of DNA running in
opposite directions (5`-3` and 3`-5`)
Base Pairing
• Using the x-ray diffraction patterns and
measurements, it was found only to work
if:
• Adenine always bonded with Thymine
• Guanine always bonded with Cytosine
• This phenomena is called Complimentary
Base Pairing
Polarity of DNA
• DNA is put together like a ladder with the
sugar-phosphate bonds form the supports
and the base pais form the rungs of the
ladder
• The tight packing of the nitrogenous bases
are the hydrophobic interior that is hard to
break apart
• The exterior, sugar-phosphate backbone
IS, however, hydrophilic, causing the
molecule to be water soluble
Major vs. Minor Grooves
Letters of a Book
• Watson & Cricks Model of DNA was
revolutionary because it explained how
DNA worked
• In the structure of DNA alone we can see
how the different sequences of bases in
DNA act like the letters in a book
=
DNA Size
• Width of the helix = 2.0nm
• Length of one full complete turn of helix =
3.4nm
• Distance between bases = .34nm
DNA Size
PROBLEM with DNA
• As we have mentioned, DNA seems like a great
suspect for the first polymer to reproduce itself
• ONE PROBLEM
• DNA is WAYYYYYyyyyy to simple and staple of
a template act as a catalyst and fuel self
replication
• In fact, never has it been observed to act as a
good enough catalyst to convince scientists that
it alone could do this
• And with the problem that “DNA doesn’t just
replicate” what could it be???
RNA as a suspect for life
• RNA now surfaces as a possible suspect
for life’s “roots”
• So what is RNA??
DNA vs. RNA
• Both have a sugar phosphate backbone
formed by phosphodiester linkages
• However there are 2 main differences:
– The pyrimidine base THYMINE does not exist
in RNA. Instead, RNA contains the the
closely related pyrimidine base URACIL
– The sugar in the sugar-phosphate backbone
of RNA is RIBOSE, not deoxyribose as in
DNA
RNA
• The second point is CRITICAL when
comparing the two (and understanding
RNA)
• The hydroxyl group on the 2`-carbon of
RIBOSE is MUCH more reactive
• This is the main difference that makes
DNA stable and RNA reactive
• The absence of Thymine and presence of
Uracil makes them easy to distinguish
RNA Hairpin
• Another difference between RNA and DNA
is in their secondary structures
• Very often, RNA is denoted as a single
strand (where DNA is a double strand)
• However, RNA can appear to be a double
stranded helix during what is called a
Hairpin
• This is when the secondary structure of
RNA loops and forms a double stranded
“stem”
RNA Hairpin
Hairpins
• These form WITHOUT energy input
because they energetically
– Hydrogen bond formation is exothermic and
exergonic
• Though they do release the entropy of the
strand, this is a “flag” for being the first
reproducing molecule
RNA Contains Information
• RNA contains a sequence of bases that is
analogous to the letters in a word
• This allows it to carry information
• Because hydrogen bonding occurs
specifically between A-U and G-C in RNA,
it is THEORETICALLY possible that it can
make a copy of itself
• Figure 4.14
Template & Complimentary
• When considering the replication process,
it is important to know the terminology for
each strand
– Template Strand: Original strand
– Complimentary Strand: New strand being
created
• It is called this because it needs to match the
template as a perfect compliment
The Ribozyme
• So as long as RNA is catalytic, then it does
make sense that it is possible to replicate itself if
the perfect situation arises
• RNA is catalytic through RNA enzymes called
RIBOZYMES.
• It has been observed in an experiment that the
ribozymes that were isolated had the ability to
catalyze BOTH the hydrolysis and condensation
reaction of phosphodiester linkages
• This is why the majority of scientific evolutionists
believe in RNA as the first LIFE
– This is called the RNA WORLD HYPOTHESIS
– This has still never been successfully shown in a
laboratory