Nucleic Acids and the RNA World

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Nucleic Acids and the RNA World

• Pages 74-89
• Chapter 4

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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

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RNA World Hypothesis

• This proposal is called the RNA World Hypothesis
• Again, this is still very HYPOTHetical
• THIS IS THE DELEMA OF

LIFE
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What is Life?????

• This is an age old question that scientists still
  debate!
• We dont 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

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Version 1 (The easy version)

• 1. All life is made of cells
• 2. Life reacts to its environment
• 3. Life reproduces
• 4. Life uses energy
• 5. Life grows at some point
• Sadly..it isnt so cut and dry!

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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!

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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

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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

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Nucleotide
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Components of a Nucleotide

• 3 components
• Phosphate group
• Sugar
• Nitrogenous (Contains a nitrogen) Base
• PAGE 75

Nitrogenous Base
Phosphate
Sugar
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Sugar

• Your sugar is an organic compound with a carbonyl
  group
• CO

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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

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DNAs Sugar-Phosphate Backbone
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RNAs Sugar Phosphate Backbone
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Count Your Primes
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Base Pairs
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Base Pairs
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Base Pairs
Adenine
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Base Pairs
Guanine
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Base Pairs
Thymine
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Base Pairs
Cytosine
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Chargaffs Theory

• Found that the of bases (Purines Pyrimidines)
  are the same
• The of As of Ts
• The of Cs of Gs
• Found that these bases must be relavent to its
  matching pair

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WATSON and CRICK

• Announced in 1953
• Used the results of other scientists to figure
  out the structure of DNA

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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 As
  and Ts were equal to the number of Cs and Gs
• This was called Chargaffs 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

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Scatter Pattern X-ray Diffraction
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Wilkins Franklin

• These measurements were from brilliant work done
  by Rosalind Franklin from Kings College
• Franklin, who was a leader in the field of X-ray
  crystallography, worked in Maurice Wilkins Lab
• Maurice Wilkins was the man charged with finding
  the structure of DNA in England
• Wilkins and Franklin were not friends But
  Wilkins, Watson, and Crick were friends
• Let the soap opera of science begin

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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)

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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

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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

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Major vs. Minor Grooves
Minor Groove
Major Groove
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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

A-T

C-G
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DNA Size

• Width of the helix 2.0nm
• Length of one full complete turn of helix 3.4nm
• Distance between bases .34nm

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DNA Size
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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 stable of a
  template act as a catalyst and fuel self
  replication
• In fact, never has it been observed to act as a
  catalyst in the laboratory
• Which means, without an external energy source,
  DNA is very unlikely to be able to sustainably
  self replicate
• And with the problem that DNA doesnt just
  replicate what could it be???

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RNA as a suspect for life

• .as a possible suspect for lifes roots
• Or maybe first we should ask

What about RNA???
What is RNA?
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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

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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

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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

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RNA Hairpin
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Hairpins

• These form WITHOUT energy input because they
  exergonic
• 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 because it can release bond energy
  required for replication

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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

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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

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DNA Replication

• DNA is not only an exceptional information
  carrying molecule it is also structurally made
  to replicate itself
• Through simple base pairing, DNA basically has
  two copies at all time
• All DNA polymerase (the protein that helps form
  the new DNA strand) has to do is unzip the
  molecule
• Once the molecule is unzipped, deoxyribose
  nucleotides will naturally make new base pairs

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DNA polymerase works in a 5-3 direction
5
3
Lagging Strand
Leading strand
3
5
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Leading Lagging

• Where the DNA strand is unzipped is known as the
  replication fork
• From this fork, each of the original strands acts
  as a template for replication
• The leading strand allows the new strand
  synthesized complementary to it, to be
  synthesized 5' to 3' in the same direction as the
  movement of the replication fork.
• The lagging strand starts away from the
  replication fork (moving towards it) and adds
  small fragments to template strand called Okazaki
  fragments
• DNA polymerase works in a 5-3 direction

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A lil bit of energy

• In order for the template strand to make a new
  complimentary strand an input of energy (a small
  amount) is required
• Compared to a protein, RNA is VERY STABLE and not
  (very) catalytically reactive
• However, in rare occurrences, RNA can form the
  necessary tertiary structures and transition
  forms for chemical catalysis to occur

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The unlikely catalyst

• If RNA can form the necessary tertiary structure
  to behave like a catalytic protein than it should
  be able to break bonds to release energy
• If the bonds break and the free energy is
  released, the energy could be absorbed by a
  templating molecule
• This molecule would then have the necessary
  energy to form the necessary bonds of a
  complimenting structure, and could affectively
  replicate itself

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Its alive. ITS ALIVE!!!

• This would adequately meet both of lifes
  (current) requirements
• Replication (Reproduction) would occur
• Energy would be used to effectively carry out the
  replication process
• Then, over a great deal of time, these
  replicating molecules would change (due to simple
  mutation) and likely increase in complexity
• Because RNA carries a code, complexity from
  mutation would seem very likely

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DNA in the LAB

• DNA has, for the last 50 years been considered to
  be the template of life
• Mostly because RNA is, for the most part, just a
  copy of DNA
• And because DNA contains the information that
  explains how to build proteins which are the
  functional units of life
• In the laboratory, two of the most important
  techniques for working with DNA is Gel
  Electrophoresis and DNA PCR

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Gel Electrophoresis

• Used daily by science laboratories and CSI units
• Requires DNA P.C.R (Copyng)
• Uses a ladder to compare the distance various
  DNA pieces move in a set amount of time.
• Generally, small pieces of DNA move more rapidly
  than large pieces
• Because the DNA is cut at similar base locations,
  each person has a unique gel electrograph
• This causes the individual DNA fingerprint!

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Gel Electro-graph
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Material
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Process
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PCR

• In nature, most organisms copy their DNA in the
  same way.
• The PCR mimics this process, only it does it in a
  test tube.
• When any cell divides, enzymes called polymerases
  make a copy of all the DNA in each chromosome.
• To copy DNA, polymerase requires two other
  components a supply of the four nucleotide bases
  and something called a primer.

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P.C.R.

• A PCR vial contains all the necessary components
  for DNA duplication
• a piece of DNA,
• large quantities of the four nucleotides,
• large quantities of the primer sequence,
• and DNA polymerase.

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DNA is Formed From Genes

• In biochemistry and genetics it has been genetic
  dogma that genes are parts of DNA
• However, recent research is showing that it may
  be more accurate to say that genes form your DNA
• To explain this story we have to think back a
  long long time ago Perhaps about 4.5 B.Y.A.

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The first Genes

• THE RNA WORLD HYPOTHESIS
• The prebiotic soup was composed of a multitude of
  compounds, most importantly
• Protein, Nucleic Acids, Lipids, Carbohydrates
• All of these molecules naturally form bonds in
  the presence of energy.
• The bond forming would last until the molecules
  were broken down by a different reaction (2nd law
  of thermodynamics)

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The RNA WORLD

• Through a generic form of natural selection, only
  macromolecules that resisted degradation from
  entropy would exist longer than any other
• Over time, the soup became dominated by
  macromolecules that were resistant to degradation
• This domination would be brief in the large
  scheme, because the molecule lacked the ability
  to template replication

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RNA Takes the Lead

• At some point, an RNA molecule (through random
  chance and bonding) Hairpin loops forming a
  ribozyme (RNA Catalyst)
• This molecule can split (through catalysis) and
  can form a template with free floating
  nucleotides (through base pairing)
• This allows it to rapidly replicate itself,
  giving it a chance to increase its numbers
  against the tide of entropy
• Over time, this replicating RNA becomes dominant
  in the prebiotic soup

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Now to Battle Entropy

• The RNA molecule, now commoner than any other
  molecule in the soup, over time will develop
  copying errors
• These errors, called mutations, cause some RNAs
  to differ from others
• Some strands get longer, some get shorter, and
  most importantly, some begin to interact with
  other macromolecules
• Some RNA molecules begin to interact with amino
  acids, forming bonds the eventually lead to the
  first tRNA (Transfer RNA)
• Some become intertwined with protiens, forming
  elaborate machines called ribosomes
• Some interact with free lipids forming fat
  bubbles that protect them from the degradation of
  entropy

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The Battle Continues

• Due to the RNA molecules success, the amount of
  free nucleotides in the prebiotic soup decreased
  dramatically
• As the RNA molecules became more and more
  different, (and free nucleotides became more rare
  in the soup)many of them began degrading other
  RNAs for free nucleotides
• Similar to a predator degrading its prey for
  nutrition
• Now it is a game of pure natural selection

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RNA to DNA

• The pressure was on RNA to become resistant to
  degradation (from entropy and predator RNAs)
• RNA was much safer from degradation in the
  hairpin loop form, but couldnt sustain this
  structure because of the nature of RNA (DICER
  naturally cuts it)
• One replicating RNA molecule had a writing error
  that allowed for a different Thymine nucleotide
  to replace the common Uracil (Only possible when
  the Sugar on the S-P backbone loses an oxygen)
• This one change allowed for the RNA to hairpin
  loop, and remain looped in the form of a double
  strand
• This new double stranded RNA with a thymine in
  the place of a uracil (called DNA) was extremely
  resistant to entropy (Stable) and made
  replication even easier

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And Then There Was DNA

• DNA was far more stable which allowed for a
  decrease in mutations
• Although this likely slowed down the rate at
  which differentiation occurred, it also
  dramatically decreased the chance that molecule
  would be degraded
• Over time, this molecule began to differentiate
  and compete much the same way the early RNA
  molecules did
• Some DNA molecules utilized the tRNA molecules to
  create strands of amino acids that it could use
  to become more specialized
• Others utilized lipids to form strong outer
  barriers that were only permeable to things the
  cell needed
• A new world, a world of cells, was beginning to
  emerge!

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Genes make DNA

• Each new useful (or negative) change that
  occurred within these first nucleic acids would
  today be called genes
• Selective pressure made it so only the most
  beneficial gene-containing organisms were
  able to make successful offspring
• But remember, the organism we are referring to
  is really just the same collection of genes that
  formed the RNA strand
• The genes that formed the more successful
  organism dominated the less successful and
  replaced them

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The Selfish Gene

• As natural selection pressures grew stronger, it
  became essential for the genes to cooperate and
  work together which allowed them to specialize
• This cooperation led to the formation of
  chromosomes (Groups of genes working together)
• Even internally genes fought to insure they would
  be successful in the next generation
• IE XY gene competition Formation of placenta
• Over time, this led to the formation of basic and
  eventually complex cellular organisms