Chapter 4- Nucleic Acids and an RNA World

4.1 What Is a Nucleic Acid?

Nucleic acids are polymers, just as proteins are polymers.
Nucleic acids are made up of monomers called nucleotides.
There are three components of a nucleotide:
- A phosphate group
- A five-carbon sugar
- A nitrogenous base
The monomers of ribonucleic acid (RNA) are referred to as ribonucleotides.
The monomers of deoxyribonucleic acid (DNA) are called deoxyribonucleotides.
The purines are adenine (A) and guanine (G).
The pyrimidines are cytosine (C), uracil (U), and thymine (T).
Ribonucleotides use uracil (U), while deoxyribonucleotides use thymine (T).
The bridge formed by the phosphate group is called a phosphodiester linkage-also frequently referred to as a phosphodiester bond.

4.2 DNA Structure and Function

The primary structure of DNA is somewhat similar to the primary structure of proteins.
By bombarding DNA with X-rays and analyzing how it scattered the radiation, Rosalind Franklin and Maurice Wilkins had calculated the distances between groups of atoms in the molecule. The technique they used is called X-ray crystallography.
Watson and Crick had discovered complementary base pairing between the A-T and G-C bases.
In fact, the term Watson-Crick pairing is now used interchangeably with the phrase “complementary base pairing.”
The two strands are further stabilized by base stacking, which results from van der Waals interactions between the tightly packed adjacent bases.
DNA’s secondary structure consists of two anti parallel strands twisted into a double helix.
The double helix is shaped and stabilized by hydrogen bonding between the complementary base pairs, hydrophobic interactions, and van der Waals interactions.

The difference between RNA and DNA is that:
- The sugar in the sugar-phosphate backbone of RNA is ribose, not deoxyribose as in DNA.
- The pyrimidine base thymine does not exist in RNA. Instead, RNA contains the closely related pyrimidine base uracil.
These RNAs are called ribozymes, or RNA enzymes, because they catalyze reactions similar to protein enzymes.
The three-dimensional nature of ribozymes is vital to their catalytic activity. To catalyze a chemical reaction, substrates must be brought together in an environment that will promote the reaction

To make a copy of itself, that first living molecule had to
- provide a template that could be copied
- catalyze polymerization reactions that would link monomers into a copy of that template.
After this milestone, three of the five fundamental characteristics of life would have been solidly in place:
- Information: Proteins and ribozymes would be processing information stored in nucleic acids for the synthesis of more proteins.
- Replication: Proteins and ribozymes would be processing information stored in nucleic acids for the synthesis of more proteins.
- Evolution: Random changes in the nucleic acids would lead to the synthesis of different proteins and ribozymes. Selective advantages resulting from some of these changes would allow for the evolution of new functions.

Nucleic acids are polymers, just as proteins are polymers.
Nucleic acids are made up of monomers called nucleotides.
There are three components of a nucleotide:
- A phosphate group
- A five-carbon sugar
- A nitrogenous base
The monomers of ribonucleic acid (RNA) are referred to as ribonucleotides.
The monomers of deoxyribonucleic acid (DNA) are called deoxyribonucleotides.
The purines are adenine (A) and guanine (G).
The pyrimidines are cytosine (C), uracil (U), and thymine (T).
Ribonucleotides use uracil (U), while deoxyribonucleotides use thymine (T).
The bridge formed by the phosphate group is called a phosphodiester linkage-also frequently referred to as a phosphodiester bond.

The primary structure of DNA is somewhat similar to the primary structure of proteins.
By bombarding DNA with X-rays and analyzing how it scattered the radiation, Rosalind Franklin and Maurice Wilkins had calculated the distances between groups of atoms in the molecule. The technique they used is called X-ray crystallography.
Watson and Crick had discovered complementary base pairing between the A-T and G-C bases.
In fact, the term Watson-Crick pairing is now used interchangeably with the phrase “complementary base pairing.”
The two strands are further stabilized by base stacking, which results from van der Waals interactions between the tightly packed adjacent bases.
DNA’s secondary structure consists of two anti parallel strands twisted into a double helix.
The double helix is shaped and stabilized by hydrogen bonding between the complementary base pairs, hydrophobic interactions, and van der Waals interactions.

The difference between RNA and DNA is that:
- The sugar in the sugar-phosphate backbone of RNA is ribose, not deoxyribose as in DNA.
- The pyrimidine base thymine does not exist in RNA. Instead, RNA contains the closely related pyrimidine base uracil.
These RNAs are called ribozymes, or RNA enzymes, because they catalyze reactions similar to protein enzymes.
The three-dimensional nature of ribozymes is vital to their catalytic activity. To catalyze a chemical reaction, substrates must be brought together in an environment that will promote the reaction

To make a copy of itself, that first living molecule had to
- provide a template that could be copied
- catalyze polymerization reactions that would link monomers into a copy of that template.
After this milestone, three of the five fundamental characteristics of life would have been solidly in place:
- Information: Proteins and ribozymes would be processing information stored in nucleic acids for the synthesis of more proteins.
- Replication: Proteins and ribozymes would be processing information stored in nucleic acids for the synthesis of more proteins.
- Evolution: Random changes in the nucleic acids would lead to the synthesis of different proteins and ribozymes. Selective advantages resulting from some of these changes would allow for the evolution of new functions.