Class 15 transcript DS

Nucleotide Building Blocks

The three components that make up DNA and RNA: 1) A five-carbon sugar (ribose or deoxyribose), 2) One or more phosphate groups, and 3) A nitrogenous base (A, T, G, C, or U). The sugar and phosphate form the backbone, while the bases allow for base pairing.

DNA Function: Information Storage

DNA's primary role is to safely store genetic information within the cell, even when genes are not being actively expressed.

DNA Function: Template

DNA acts as a template for two key processes: for RNA polymerase during transcription, and for DNA polymerase during DNA replication.

DNA Function: Protein Binding

Proteins can bind to DNA in a sequence-specific manner (e.g., transcription factors binding to enhancers) or in a non-sequence-specific manner (e.g., histones binding via electrostatic attraction to the negatively charged backbone).

Nucleic Acid Synthesis Direction

The synthesis of new nucleic acid strands always proceeds in the 5' to 3' direction. The 5' end retains the triphosphate group, while the new nucleotides are added to the 3' hydroxyl (OH) group.

Nucleotide Addition Mechanism

The chemical reaction for adding a nucleotide involves a nucleophilic attack. The 3' OH group of the last nucleotide in the chain attacks the alpha phosphate of the incoming nucleotide, forming a new bond and releasing pyrophosphate (beta and gamma phosphates).

DNA vs. RNA Sugar Backbone

The key chemical difference is at the 2' carbon of the sugar: DNA has a Hydrogen (H) atom (deoxyribose), making it stable. RNA has a Hydroxyl group (OH) (ribose), making it more reactive and less stable.

RNA Reactivity & Splicing

The 2' OH group in RNA is crucial for its function in processes like splicing, where it initiates a nucleophilic attack on the 5' splice site to form the lariat structure. This same reactivity also makes RNA prone to spontaneous breakdown.

DNA Stability

DNA is an extremely stable molecule due to the lack of a 2' OH group, which prevents self-cleavage. This stability allows DNA to be preserved for long periods, as evidenced by the sequencing of 45,000-year-old DNA from Siberian remains.

Forces Stabilizing Double Helix

Three main non-covalent forces: 1) Hydrogen bonding (between complementary bases), 2) Van der Waals forces (from base stacking), and 3) The Hydrophobic Effect (burying the non-polar bases in the core, away from water).

Hydrophobic Effect (in DNA)

The strongest force stabilizing the double helix. It drives the non-polar, hydrophobic nitrogenous bases to stack in the core of the helix, while the polar, hydrophilic sugar-phosphate backbone faces the external, aqueous environment.

Intermolecular vs. Intramolecular Duplex

An intermolecular duplex is formed between two separate strands (e.g., DNA double helix). An intramolecular duplex is formed when a single strand base-pairs with itself (e.g., RNA hairpins or stem-loop structures).

B Form DNA

The most common and biologically relevant form of DNA inside cells. It is a right-handed helix with 10 base pairs per turn and a constant diameter, maintained by the purine-pyrimidine base pairing rule.

Constant Helix Diameter

The diameter of the DNA double helix remains constant because a purine (two-ringed base) always pairs with a pyrimidine (one-ringed base). This ensures a uniform width, preventing bulges or constrictions.

A Form DNA

An alternative helical structure that forms under dehydrated conditions or in DNA-RNA hybrids. It is more compact and has a larger diameter than B form DNA.

Z Form DNA

A left-handed helical form of DNA observed in vitro, characterized by a zig-zag backbone. It is uncommon in cells, but its existence is supported by the presence of specific proteins (like ADAR1) that bind to it.

Major Groove

The wider groove in the B form DNA double helix. It exposes more variation in hydrogen bond donors and acceptors, allowing proteins to recognize and bind to specific DNA sequences.

Minor Groove

The narrower groove in the B form DNA double helix. It exposes less distinct information about the base pair identity and is less commonly used for specific protein recognition.

Origin of Major & Minor Groove

The grooves are formed because the glycosidic bonds of the two base-paired nucleotides are not directly opposite each other. The "longer path" around the helix between the glycosidic bonds creates the major groove, while the "shorter path" creates the minor groove.

Historical DNA Structure Hypotheses

Linus Pauling proposed an incorrect triple helix model with the sugar-phosphate backbone on the inside and bases pointing outwards. The correct double helix structure was determined by Watson and Crick using data from Rosalind Franklin without her permission.

Purine-Pyrimidine Base Pairing Rule

In double-stranded DNA, adenine (A, purine) always pairs with thymine (T, pyrimidine), and guanine (G, purine) always pairs with cytosine (C, pyrimidine). This rule is fundamental for maintaining a constant helix diameter and for accurate replication.

5' Carbon Identification

The 5' carbon in the ribose sugar is the carbon atom attached to the phosphate group(s). It is the starting point of the nucleic acid strand's directionality.

3' Carbon Identification

The 3' carbon in the ribose sugar has a hydroxyl (OH) group and is the site where new nucleotides are added during strand synthesis. It defines the growing end of the nucleic acid chain.

DNA Identification Feature

A molecule can be identified as DNA (and not RNA) by the presence of a single Hydrogen (H) atom on the 2' carbon of the sugar, instead of a Hydroxyl (OH) group.

Major Groove Location (Per Base Pair)

Every base pair in a double helix has both a major groove side and a minor groove side. As the helix twists, each base pair is accessible from both grooves, but the major groove side contains more sequence-specific information