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Title: Nucleic Acids and the RNA World


1
Nucleic Acids and the RNA World
  • Pages 74-89
  • Chapter 4

2
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

3
RNA World Hypothesis
  • This proposal is called the RNA World Hypothesis
  • Again, this is still very HYPOTHetical
  • THIS IS THE DELEMA OF

LIFE
4
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

5
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!

6
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!

7
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

8
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

9
Nucleotide
10
Components of a Nucleotide
  • 3 components
  • Phosphate group
  • Sugar
  • Nitrogenous (Contains a nitrogen) Base
  • PAGE 75

Nitrogenous Base
Phosphate
Sugar
11
Sugar
  • Your sugar is an organic compound with a carbonyl
    group
  • CO

12
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

13
DNAs Sugar-Phosphate Backbone
14
RNAs Sugar Phosphate Backbone
15
Count Your Primes
16
Base Pairs
17
Base Pairs
18
Base Pairs
Adenine
19
Base Pairs
Guanine
20
Base Pairs
Thymine
21
Base Pairs
Cytosine
22
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

23
WATSON and CRICK
  • Announced in 1953
  • Used the results of other scientists to figure
    out the structure of DNA

24
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

25
Scatter Pattern X-ray Diffraction
26
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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28
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)

29
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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31
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

32
Major vs. Minor Grooves
Minor Groove
Major Groove
33
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
34
DNA Size
  • Width of the helix 2.0nm
  • Length of one full complete turn of helix 3.4nm
  • Distance between bases .34nm

35
DNA Size
36
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???

37
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?
38
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

39
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

40
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

41
RNA Hairpin
42
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

43
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

44
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

45
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46
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

47
DNA polymerase works in a 5-3 direction
5
3
Lagging Strand
Leading strand
3
5
48
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

49
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51
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

52
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

53
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54
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

55
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

56
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!

57
Gel Electro-graph
58
Material
59
Process
60
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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62
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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64
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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66
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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68
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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70
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

71
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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73
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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75
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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77
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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79
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

80
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
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