7/28/2019 04 Nucleic Acids and the RNA World
1/37
2011 Pearson Education, Inc.
Lectures by Stephanie Scher Pandolfi
BIOLOGICAL SCIENCE
FOURTH EDITION
SCOTT FREEMAN
4Nucleic Acids and the
RNA World
7/28/2019 04 Nucleic Acids and the RNA World
2/37
2011 Pearson Education, Inc.
Key Concepts
Nucleotides consist of a sugar, phosphate group, and nitrogen-
containing base. Ribonucleotides polymerize to form RNA.
Deoxyribonucleotides polymerize to form DNA.
DNAs primary structure consists of a sequence of nitrogen-
containing bases; its secondary structure consists of two DNA
strands running in opposite directions, held together by
complementary base pairing, and twisted into a double helix.
DNAs structure allows organisms to store and replicate the
information needed to grow and reproduce.
7/28/2019 04 Nucleic Acids and the RNA World
3/37
2011 Pearson Education, Inc.
Key Concepts
RNAs primary structure consists of a sequence of nitrogen-
containing bases. Its secondary structure includes short regions of
double helices and structures called hairpins.
RNA was likely the first self-replicating molecule and a
forerunner to the first life-form.
7/28/2019 04 Nucleic Acids and the RNA World
4/37
2011 Pearson Education, Inc.
What Is a Nucleic Acid?
A nucleic acid is a polymer ofnucleotide monomers.
Nucleotides are each composed of a phosphate group, a sugar, and
a nitrogenous base.
The sugar is ribosein ribonucleotides and deoxyribosein
deoxyribonucleotides.
There are two groups of nitrogenous bases:
purines (adenine, guanine)
pyrimidines (cytosine, uracil, and thymine)
Uracil (U) is found only in ribonucleotides, and thymine (T) is
found only in deoxyribonucleotides.
7/28/2019 04 Nucleic Acids and the RNA World
5/37
2011 Pearson Education, Inc.
7/28/2019 04 Nucleic Acids and the RNA World
6/37
2011 Pearson Education, Inc.
7/28/2019 04 Nucleic Acids and the RNA World
7/37 2011 Pearson Education, Inc.
7/28/2019 04 Nucleic Acids and the RNA World
8/37 2011 Pearson Education, Inc.
7/28/2019 04 Nucleic Acids and the RNA World
9/37 2011 Pearson Education, Inc.
Could Chemical Evolution Produce Nucleotides?
Simulations of chemical evolution have not yet produced
nucleotides.
Sugars and purines are easily made, but pyrimidines and ribose are
not easily synthesized.
Ribose problem: Ribose would have had to have been dominant on
ancient Earth for nucleic acids to form.
7/28/2019 04 Nucleic Acids and the RNA World
10/37 2011 Pearson Education, Inc.
Nucleotides Polymerize to Form Nucleic Acids
Nucleic acids form when nucleotides polymerize.
A condensation reaction forms a phosphodiester linkage
(phosphodiester bond)between the phosphate group on the 5
carbon of one nucleotide and theOH group on the 3 carbon of
another.
Types of nucleotides involved:
1. Ribonucleotides, which contain the sugar ribose and
form RNA2. Deoxyribonucleotides, whichcontain the sugar deoxyribose
andform DNA
7/28/2019 04 Nucleic Acids and the RNA World
11/37 2011 Pearson Education, Inc.
7/28/2019 04 Nucleic Acids and the RNA World
12/37
2011 Pearson Education, Inc.
The Sugar-Phosphate Backbone Is Directional
The sugar-phosphate backbone of a nucleic acid is directionalone
end has an unlinked 5 carbon, and the other end has an unlinked 3
carbon.
The nucleotide sequence is written in the 5 3 direction. This
reflects the sequence in which nucleotides are added to a growing
molecule.
This nucleotide sequence comprises the nucleic acids primary
structure.
7/28/2019 04 Nucleic Acids and the RNA World
13/37
2011 Pearson Education, Inc.
7/28/2019 04 Nucleic Acids and the RNA World
14/37
2011 Pearson Education, Inc.
The Polymerization of Nucleic Acids Is Endergonic
Polymerization of nucleic acids is an endergonic process catalyzed
by enzymes.
Energy for polymerization comes from the phosphorylation of the
nucleotides.
Phosphorylation is the transfer of one or more phosphate
groups to a substrate molecule. This raises the potential energy
of the substrate and enables endergonic reactions.
In nucleic acid polymerization, two phosphates are transferred,
creating a nucleoside triphosphate.
7/28/2019 04 Nucleic Acids and the RNA World
15/37
2011 Pearson Education, Inc.
7/28/2019 04 Nucleic Acids and the RNA World
16/37
2011 Pearson Education, Inc.
What Is the Nature of DNA's Secondary Structure?
Erwin Chargaff established two empirical rules for DNA:
1. The total number of purines and pyrimidines is the same.2. The numbers of As and Ts are equal and the numbers of Cs
and Gs are equal.
7/28/2019 04 Nucleic Acids and the RNA World
17/37
2011 Pearson Education, Inc.
Watson and Cricks Model of DNAs Secondary Structure
James Watson and Francis Crick determined:
1. DNA strands run in an antiparallelconfiguration.2. DNA strands form a double helix.
The hydrophilic sugar-phosphate backbone faces the
exterior.
Nitrogenous base pairs face the interior.3. Purines always pair with pyrimidines.
Specifically, strands form complementarybasepairs A-
T and G-C.
A-T have two hydrogen bonds. C-G have three hydrogen bonds.
4. DNA has two different sized grooves: the major groove and
the minor groove.
7/28/2019 04 Nucleic Acids and the RNA World
18/37
2011 Pearson Education, Inc.
7/28/2019 04 Nucleic Acids and the RNA World
19/37
2011 Pearson Education, Inc.
7/28/2019 04 Nucleic Acids and the RNA World
20/37
2011 Pearson Education, Inc.
7/28/2019 04 Nucleic Acids and the RNA World
21/37
2011 Pearson Education, Inc.
7/28/2019 04 Nucleic Acids and the RNA World
22/37
2011 Pearson Education, Inc.
The DNA Double Helix
BLAST Animation: DNA Double Helix
http://localhost/var/www/apps/conversion/tmp/scratch_11/DNA_double_helix.html7/28/2019 04 Nucleic Acids and the RNA World
23/37
2011 Pearson Education, Inc.
7/28/2019 04 Nucleic Acids and the RNA World
24/37
2011 Pearson Education, Inc.
Structure of RNA and DNA
Web Activity: Structure of RNA and DNA
http://localhost/var/www/apps/conversion/tmp/scratch_11/StructureOfRNAandDNA.html7/28/2019 04 Nucleic Acids and the RNA World
25/37
2011 Pearson Education, Inc.
Hydrogen Bonds in DNA
Web Activity: DNA Hydrogen Bonds
S f A S S
http://localhost/var/www/apps/conversion/tmp/scratch_11/Hydrogen_bonds_DNA.html7/28/2019 04 Nucleic Acids and the RNA World
26/37
2011 Pearson Education, Inc.
Summary of DNAs Secondary Structure
DNAs secondary structure consists of two antiparallel strands
twisted into a double helix. The molecule is stabilized by
hydrophobic interactions in its interior and by hydrogen bonding
between the complementary base pairs A-T and G-C.
DNA C i Bi l i l I f i
7/28/2019 04 Nucleic Acids and the RNA World
27/37
2011 Pearson Education, Inc.
DNA Contains Biological Information
DNA can store and transmit biological information.
The language of nucleic acids is contained in the sequence of the
bases.
DNA carries the information required for the growth andreproduction of all cells.
H D DNA R li ?
7/28/2019 04 Nucleic Acids and the RNA World
28/37
2011 Pearson Education, Inc.
How Does DNA Replicate?
Complementary base pairing provides a simple mechanism for
DNA replicationeach strand can serve as a template for the
formation of a new complementary strand.
DNA replication requires two steps:
1. Separation of the double helix
2. Hydrogen bonding of deoxyribonucleotides with
complementary bases on the original templatestrand,
followed by phosphodiester bond formation to form the
complementarystrand
7/28/2019 04 Nucleic Acids and the RNA World
29/37
2011 Pearson Education, Inc.
I DNA C t l ti M l l ?
7/28/2019 04 Nucleic Acids and the RNA World
30/37
2011 Pearson Education, Inc.
Is DNA a Catalytic Molecule?
DNAs stability makes it a reliable store for genetic information it
is less reactive than RNA but more resistant to chemical
degradation. Stable molecules such as DNA make poor catalysts.
Because DNA does not appear to be able to catalyze any chemical
reaction, biologists think that the first life-form was made of RNA,
not DNA.
RNA St t d F ti
7/28/2019 04 Nucleic Acids and the RNA World
31/37
2011 Pearson Education, Inc.
RNA Structure and Function
Like DNA, RNA has a primary structure consisting of a sugar-
phosphate backbone formed by phosphodiester linkages and,
extending from that backbone, a sequence of four types of
nitrogenous bases.
The primary structure of RNA differs from DNA in two ways:
1. RNA contains uracil instead of thymine.
2. RNA contains ribose instead of deoxyribose.
The presence of theOH group on ribose makes RNA much
more reactive and less stable than DNA.
RNA S d St t
7/28/2019 04 Nucleic Acids and the RNA World
32/37
2011 Pearson Education, Inc.
RNAs Secondary Structure
RNAs secondary structure results from complementary base
pairing.
The bases of RNA typically form hydrogen bonds with
complementary bases on thesame strand.
The RNA strand folds over, forming a hairpin structure: the
bases on one side of the fold align with an antiparallel RNA
segment on the other side of the fold.
RNA molecules can have tertiary and quaternary structures.
7/28/2019 04 Nucleic Acids and the RNA World
33/37
2011 Pearson Education, Inc.
7/28/2019 04 Nucleic Acids and the RNA World
34/37
2011 Pearson Education, Inc.
Differences Bet een DNA and RNA
7/28/2019 04 Nucleic Acids and the RNA World
35/37
2011 Pearson Education, Inc.
Differences Between DNA and RNA
BLAST Animation: DNA Versus RNA
RNAs Versatility
http://localhost/var/www/apps/conversion/tmp/scratch_11/DNA_versus_RNA.html7/28/2019 04 Nucleic Acids and the RNA World
36/37
2011 Pearson Education, Inc.
RNAs Versatility
RNA is structurally, chemically, and functionally intermediate
between DNA and proteins.
Like DNA, RNA can function as an information-containing
molecule, and is capable of self-replication.
RNA can function as a catalytic molecule.
Ribozymes are enzyme-like RNAs.
The First Life Form: RNA
7/28/2019 04 Nucleic Acids and the RNA World
37/37
The First Life-Form: RNA
RNA can both provide a template for copying itself and catalyze
the polymerization reactions that would link monomers into a
copy of that template. Thus, most origin-of-life researcherspropose that the first life-form was made of RNA.
RNA is not very stable, but might have survived long enough in
the prebiotic soup to replicate itself, becoming the first life-form.
Researchers found that a ribozyme called RNA replicase could be
isolated that could catalyze the addition of ribonucleotides to a
complementary RNA strand.