DNA Structure and Repair Quiz

Study Notes

DNA comprises two deoxynucleotide chains connected by phosphodiester bonds, forming a right-handed double helix, running anti-parallel.
In coding regions, the 5' to 3' strand is the coding strand; the 3' to 5' strand serves as the template strand for daughter strand assembly.
Sequences are typically written in the 5' to 3' direction.
DNA's negative charge stems from exposed phosphate groups; hydrophobic bases stack internally, forming G–C and A–T base pairs.
G–C pairs, connected by three hydrogen bonds, are more stable compared to A–T pairs, which have two hydrogen bonds.
DNA is chemically and physically stable but denatures into single strands at a temperature dependent on length and G–C content, showing a hyperchromic shift during denaturation.
DNA hybridization enables technologies like "genes on a chip," used to identify mutations and expression patterns in cancers.

A chromosome consists of a single DNA molecule, compacted about 10,000 times into chromatin.
Chromatin exists as heterochromatin (highly condensed) and euchromatin (loosely condensed, active in transcription).
Composed of nucleosomes (histones and DNA), chromatin is organized into solenoid fibers and loops.
Histones carry a positive charge, which helps them bind to DNA; their dissociation during replication and transcription is facilitated by acetylation.

During cell division, chromosomes duplicate, forming dyads (two chromatids) bound by a centromere.
Telomeres protect chromosome ends, distinguishing them from DNA breaks.
Genomic DNA types include unique sequences (single or mid-range copy genes), moderately repetitive DNA (transcription regulatory regions, LINES, SINES), and highly repetitive DNA (tandem repeats).

LINES (Long Interspersed Nuclear Elements) contain genes for reverse transcriptase, enabling retrotransposition with SINES (Short Interspersed Nuclear Elements) like Alu.
Transposons utilize cut-and-paste mechanisms for mobility; many retrotransposons are remnants of ancient retroviruses.
Histone acetyltransferases (HATs) and histone deacetylases (HDACs) regulate DNA accessibility; HDAC inhibitors are in development as anticancer therapies.
Germline and cancer cells express telomerase, essential for maintaining telomeric length.

Short tandem repeat sequences vary among individuals, making them valuable for forensic analysis.
Repeat sequences can increase susceptibility to replication errors through mechanisms like mismatch, slippage, or unequal crossover.
Alu repeats may link to genetic conditions such as hemophilia and hypercholesterolemia due to their insertional dependencies.
HIV integrates its proviral DNA into gene-rich chromosome regions to enhance transcription levels.

Understanding the organization of genomic DNA helps in appreciating its various sequence types.
Telomeres and telomerase present promising targets for anticancer therapy development.