BIOL 308 2.1- mid 2.5 readings

Chargaff's Rules

The molar concentrations where [A] = [T] and [G] = [C].

Species-Specific G+C Content

The percentage of G+C content in DNA, which ranges widely from 22% to 73% depending on the organism.

Ribose vs. Deoxyribose

Deoxyribose has an H on the 2' carbon, whereas ribose has an OH group.

Purines vs. Pyrimidines

Purines (A, G) have a double ring; pyrimidines (T, C, U) have a single ring.

Nucleoside Definition

A 5-carbon sugar covalently linked to a nitrogenous base at the 1'-carbon.

Nucleotide Definition

A nucleoside with a phosphate group attached to its 5'-carbon.

Phosphodiester Linkage

A bond linking the 3'-carbon of one sugar to the 5'-phosphate of another.

DNA Strand Polarity

Directionality defined by the 5'-phosphate end and the 3'-hydroxyl end.

Watson-Crick Base Pairing

Adenine pairs with Thymine via 2 H-bonds; Guanine pairs with Cytosine via 3 H-bonds.

Antiparallel Strands

The two DNA strands run in opposite directions (5' to 3' and 3' to 5').

Base Stacking

Hydrophobic interactions and van der Waals forces between stacked bases that stabilize the double helix.

Major Groove Function

A wide gap where sequence-specific proteins read base-pair donor/acceptor hydrogen bonding patterns.

Minor Groove Exception

TATA-binding protein (TBP) binds to the minor groove at the TATA box.

B-DNA Characteristics

The predominant physiological right-handed helix with 10.5 base pairs per turn.

A-DNA Characteristics

A right-handed helix with 11 base pairs per turn, common in RNA and lower-water conditions.

Z-DNA Characteristics

A left-handed helix with 12 base pairs per turn, associated with GC repeats and gene regulation.

Hyperchromicity

The increase in UV absorption at 260 nm when DNA strands separate during denaturation.

Melting Temperature (Tm)

The temperature at which half of the base pairs in double-stranded DNA have denatured.

G+C Content Effect on Tm

Higher G+C content raises the melting temperature due to extra hydrogen bonds and stronger base stacking.

Cot Graph Axes

X-axis is log(C0t); Y-axis is the fraction of single-stranded DNA remaining (C/C0).

Slipped Structure

Single-stranded loops formed at tandem repeats due to strand misalignment.

Cruciform Structure

Stem-loop structures formed by inverted repeats (palindromes) when AT-rich regions unwind.

Triple Helix DNA Binding

A third strand joins the double helix via Hoogsteen base pairing in purine-pyrimidine stretches.

G-Quadruplex

Four-stranded structures formed by guanine tandem repeats (G-tetrads), often found at telomeres.

Supercoiling Equation

Linking number equals twist plus supercoiling (L = T + supercoiling).