Nucleic Acid Notes

1. Structure of Nucleic Acids

Nucleic acids are biopolymers made of nucleotides linked by phosphodiester linkages. They are the chemical carriers of genetic information and exist in two forms: DNA (2-deoxyribonucleic acid) and RNA (ribonucleic acid). 

What Are Nucleic Acids?

• Biopolymers made up of nucleotides linked by phosphodiester linkages

• Chemical carriers of genetic information

• Two main forms: DNA and RNA

The Three Components of a Nucleotide:

• Aldopentose sugar:

• Ribose in RNA (contains OH at the 2' carbon). 

• 2-deoxyribose in DNA (lacks oxygen at the 2' carbon). 

• Phosphate group: Joins the 3' carbon of one sugar to the 5' carbon of the next. 

• Heterocyclic base (amine): Categorized into two groups: 

• Purines (2-ring 6&5 sides): Adenine (A) and Guanine (G).  (nitrogenous bases attached at N-9)

• Pyrimidines:(1-ring 6 sides) Cytosine (C), Thymine (T) - found in DNA, and Uracil (U) - found in RNA.  (nitrogenous bases attached at N-1)

Components

• An aldopentose sugar (5-carbon sugar)

• A phosphate group

• A heterocyclic base (nitrogenous base)

Two Forms of Nucleic Acids

Important Terminology:

• Nucleoside: Sugar + Base. 

• Nucleotide: Sugar + Base + Phosphate. 

• Primary Structure: The sequence of nucleotides. By convention, sequences are written from the 5' end to the 3' end. 

Nucleoside vs. Nucleotide

• Nucleoside: Sugar + Base (NO phosphate)

• Nucleotide: Sugar + Base + Phosphate group

The Sugar Component

Two aldopentose sugars are found in nucleic acids:

Nitrogenous Bases

Bases are classified into two types:

Purines (Double-ring) → 6 sides and 5 sides

• Adenine (A) - Found in both DNA and RNA

• Guanine (G) - Found in both DNA and RNA

Pyrimidines (Single-ring) → 6 sides

• Cytosine (C) - Found in both DNA and RNA

• Thymine (T) - Found ONLY in DNA

• Uracil (U) - Found ONLY in RNA

Characteristics of Nitrogenous Bases

• Flat structures

• Basic in nature

• Contain aromatic rings

• Have conjugated double bonds

• Capable of hydrogen bonding

Chapter 3: Nucleosides and Nucleotides in DNA and RNA

DNA Nucleosides

RNA Nucleosides

2. DNA Secondary Structure: The Double Helix

DNA consists of two strands held together by hydrogen bonding between complementary bases. 

• Antiparallel Strands: One strand runs in the 5' to 3' direction, while the other runs 3' to 5'. 

• Complementary Base Pairing:

• A pairs with T (2 hydrogen bonds). 

• G pairs with C (3 hydrogen bonds). 

• Chargaff's Rule: In a double-stranded DNA molecule, the amount of purines equals the amount of pyrimidines (A+G=T+C). 

• Helical Stability: The interior consists of stacked N-bases, which maximizes hydrophobic interactions to stabilize the molecule. 

3. DNA Tertiary Structure & Packaging

To fit approximately 6 feet of human DNA into a microscopic nucleus, it must be highly condensed. 

• Chromatin: A complex of DNA and histone proteins in roughly equal proportions. 

• Nucleosomes: The basic unit of DNA packaging, where DNA is wrapped around histones. 

• Euchromatin: "Open" or loosely packed chromatin where transcription can occur. 

• Heterochromatin: "Closed" or densely packed chromatin where transcription cannot occur. 

4. DNA Replication

Replication is the process of making identical copies of DNA before cell division. 

Key Characteristics:

• Semiconservative: Each new daughter duplex contains one original parent strand and one newly synthesized strand. 

• Bidirectional: Replication occurs in two opposite directions from the origin of replication. 

• Semidiscontinuous: Synthesis always occurs in the 5' to 3' direction. 

Key Enzymes and Proteins:

5. Other Functions of Nucleotides

Beyond being precursors for DNA/RNA, nucleotides serve several other vital roles: 

• Energy Metabolism: ATP and GTP are used as energy currency. 

• Coenzymes: Components of carriers like NAD+ and FAD. 

• Regulatory Molecules: Cyclic AMP (cAMP) and cyclic GMP (cGMP) act as chemical signals. 

• Carriers of Activated Molecules: For example, UDP-glucose used in carbohydrate synthesis. 

Supplemental Lecture Notes: Advanced Nucleic Acid Specifics

The following notes provide more granular details from the lecture material to supplement your exam preparation.

I. Chemical Properties and Characteristics

• Nitrogenous Base Characteristics: These heterocyclic amines are structurally flat, aromatic rings with conjugated double bonds, making them basic and capable of hydrogen bonding.

• Phosphoester vs. Glycosidic Bonds: * The β-N-glycosidic bond connects the 1′ carbon of the sugar to the nitrogenous base.

• The phosphoester linkage connects the phosphate group to the 5′ carbon of the sugar.

  • Ribonucleotide vs. Deoxyribonucleotide: The structural difference is located at the 2′ carbon of the pentose sugar; ribose has an -OH group, while deoxyribose has a hydrogen ("no O").

Extended Functions of Nucleotides

• Regulatory Signaling: Cyclic nucleotides like cAMP and cGMP serve as regulatory molecules.

• Molecular Carriers: Nucleotides act as carriers for activated molecules, such as UDP-glucose, which is a "sugar nucleotide" used in metabolism.

• Acyl Group Transfer: Coenzyme A (CoA) utilizes an adenosine moiety to function in acyl group transfer reactions via a thioester linkage.

• Electron and Hydride Transfer: NAD+ functions specifically in hydride transfers, while FAD (derived from riboflavin) functions in electron transfers.

IV. Genomic and Chromosomal Structure

• Gene Definition: A segment of a DNA molecule containing the specific information required to synthesize a functional biological product (protein or RNA).

• The Genome: Refers to the totality of DNA within an organism's cell.

Chromosome Organization:

• Autosomes: Chromosomes 1 through 22 in somatic cells.

• Sex Chromosomes: X and Y for males; X and X for females.

• Sister Chromatids: Two thin, rod-like structures of DNA that make up a duplicated chromosome.

• Centromere: The constricted region where intertwined DNA and proteins join two sister chromatids.

V. Details of DNA Replication Requirements

For replication to occur, four specific requirements must be met:

1. Template: Provides the essential sequence information.

2. Primer: Provides the necessary free 3'-OH group to which new nucleotides are added.

3. Precursors: Deoxynucleoside triphosphates (dNTPs).

4. Proteins/Enzymes: Specifically, DNA Polymerase III is the enzyme responsible for the actual catalytic chain elongation.

Table 1: RNA Nomenclature (Ribose Sugar)

Table 2: DNA Nomenclature (Deoxyribose Sugar)

Key Structural Distinctions

• The Sugar Difference: RNA uses ribose , which has an -OH group at the 2′ carbon. DNA uses deoxyribose , which lacks the oxygen at the 2′ carbon ("no O").

• Naming Convention: For DNA, the prefix "deoxy-" is added to both the nucleoside and nucleotide names to indicate the absence of oxygen on the sugar.

• The Thymine/Uracil Rule: Thymine is unique to DNA nucleosides and nucleotides , whereas Uracil is unique to RNA.

 Functions of Nucleic Acids

1. As Repeating Units / Precursors of Genetic Material

A segment of DNA containing information for synthesis of a functional biological product is called a gene.

2. In Energy Metabolism

• ATP (Adenosine triphosphate)

• GTP (Guanosine triphosphate)

3. As Components of Coenzymes and Reductants

• NAD+ (Nicotinamide adenine dinucleotide)

• FAD (Flavin adenine dinucleotide)

4. As Regulatory Molecules

• cAMP (cyclic AMP)

• cGMP (cyclic GMP)

5. As Carriers of Activated Molecules

• UDP-glucose

Chapter 5: DNA Structure

What is DNA?

• Genetic material that stores biological information

• Governs cellular activities

• Polymer of four nucleotides (A, T, G, C)

Primary Structure

Main Features:

• Alternating sugar-phosphate groups form the backbone

• Bases attached to sugars

• Phosphodiester bonds connect 3' carbon to 5' carbon (covalent bond)

• Order of bases encodes genetic information

• Binded by hydrogen bonding

• Written 5' to 3' direction (Example: 5'-ATTTCAGACC-3')

Secondary Structure: The Double Helix

Key Characteristics:

• DNA consists of TWO strands

• Strands are antiparallel

• Strands are held by hydrogen bonds between bases

• Bases are complementary

Complementary Base Pairing

• Adenine (A) pairs with Thymine (T) - 2 hydrogen bonds

• Guanine (G) pairs with Cytosine (C) - 3 hydrogen bonds

Key Definitions

Essential Terms

Adenine: Purine base found in DNA and RNA

Cytosine: Pyrimidine base found in DNA and RNA

Deoxyribose: 5-carbon sugar in DNA

DNA: Deoxyribonucleic acid; stores genetic information

Gene: DNA segment coding for a protein or RNA

Guanine: Purine base found in DNA and RNA

Nucleoside: Sugar + Base (no phosphate)

Nucleotide: Sugar + Base + Phosphate

Phosphodiester Bond: Covalent bond in sugar-phosphate backbone

Purine: Two-ring base (A, G)

Pyrimidine: Single-ring base (C, T, U)

Ribose: 5-carbon sugar in RNA

RNA: Ribonucleic acid; used in protein synthesis

Thymine: Pyrimidine base in DNA only

Uracil: Pyrimidine base in RNA only

Review Questions

1. What are the three components of a nucleotide?

2. What is the difference between a nucleoside and a nucleotide?

3. Name the two pentose sugars and identify where each is found.

4. What is the key structural difference between DNA and RNA?

5. Classify the nitrogenous bases into purines and pyrimidines.

6. Which bases are found in DNA only, RNA only, and both?

7. Describe the primary structure of DNA.

8. What is a phosphodiester bond?

9. Explain complementary base pairing.

10. How many hydrogen bonds form between A-T and G-C?

11. What does antiparallel mean?

12. List five functions of nucleic acids.

Quick Reference

DNA vs RNA

Base Pairing Rules

In DNA:

• A pairs with T (2 hydrogen bonds)

• G pairs with C (3 hydrogen bonds)

In RNA:

• A pairs with U (2 hydrogen bonds)

• G pairs with C (3 hydrogen bonds)

Purines vs Pyrimidines