Nucleic Acids and the RNA World

BIOLOGICAL SCIENCE
FOURTH EDITION

SCOTT FREEMAN
Lectures by Stephanie Scher Pandolfi
2011 Pearson Education, Inc.

Key Concepts
Nucleotides consist of a sugar, phosphate group, and nitrogencontaining base. Ribonucleotides polymerize to form RNA. Deoxyribonucleotides polymerize to form DNA. DNAs primary structure consists of a sequence of nitrogencontaining 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.

2011 Pearson Education, Inc.

Key Concepts
RNAs primary structure consists of a sequence of nitrogencontaining 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.

2011 Pearson Education, Inc.

What Is a Nucleic Acid?

A nucleic acid is a polymer of nucleotide monomers. Nucleotides are each composed of a phosphate group, a sugar, and a nitrogenous base. The sugar is ribose in ribonucleotides and deoxyribose in 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.
2011 Pearson Education, Inc.

 2011 Pearson Education, Inc.

 2011 Pearson Education, Inc.

 2011 Pearson Education, Inc.

 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.

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 the OH group on the 3 carbon of another.

Types of nucleotides involved: 1. Ribonucleotides, which contain the sugar ribose and form RNA 2. Deoxyribonucleotides, which contain the sugar deoxyribose and form DNA

2011 Pearson Education, Inc.

 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.

2011 Pearson Education, Inc.

 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.

2011 Pearson Education, Inc.

 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.

2011 Pearson Education, Inc.

Watson and Cricks Model of DNAs Secondary Structure

James Watson and Francis Crick determined: 1. DNA strands run in an antiparallel configuration. 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 complementary base pairs AT 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.
2011 Pearson Education, Inc.

 2011 Pearson Education, Inc.

 2011 Pearson Education, Inc.

 2011 Pearson Education, Inc.

 2011 Pearson Education, Inc.

The DNA Double Helix

BLAST Animation: DNA Double Helix

2011 Pearson Education, Inc.

 2011 Pearson Education, Inc.

Structure of RNA and DNA

Web Activity: Structure of RNA and DNA

2011 Pearson Education, Inc.

Hydrogen Bonds in DNA

Web Activity: DNA Hydrogen Bonds

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.

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 and reproduction of all cells.

2011 Pearson Education, Inc.

How Does DNA Replicate?

Complementary base pairing provides a simple mechanism for DNA replication each 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 template strand, followed by phosphodiester bond formation to form the complementary strand

2011 Pearson Education, Inc.

 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.

2011 Pearson Education, Inc.

RNA Structure and Function

Like DNA, RNA has a primary structure consisting of a sugarphosphate 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 the OH group on ribose makes RNA much more reactive and less stable than DNA.

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 the same 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.

2011 Pearson Education, Inc.

 2011 Pearson Education, Inc.

 2011 Pearson Education, Inc.

Differences Between DNA and RNA

BLAST Animation: DNA Versus RNA

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.

2011 Pearson Education, Inc.

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 researchers propose 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.

2011 Pearson Education, Inc.