DNA Structure, Function, and Replication

Maurice Wilkins and Ray Gosling (1950): Produced the first clear crystalline X-ray diffraction patterns from DNA fibres.
Alec Stokes: Suggested that the diffraction patterns indicated a helical structure for DNA.
Rosalind Franklin (1952): An expert X-ray crystallographer who obtained pivotal images of DNA; her work was essential for the structure hypothesis.
James Watson and Francis Crick (1953): Proposed the double helix ladder model consisting of two twisted chains of nucleotides.
Nobel Prize (1962): Awarded to Wilkins, Watson, and Crick; Rosalind Franklin was not awarded posthumously following her death in 1958.

Nucleotide Construction: Composed of a $5$ -carbon deoxyribose sugar, a negatively charged phosphate group, and a nitrogenous base.
Nitrogenous Bases: DNA contains Adenine ( $A$ ), Thymine ( $T$ ), Guanine ( $G$ ), and Cytosine ( $C$ ). RNA uses Uracil ( $U$ ) instead of Thymine.
Complementary Base Pairing: $A$ always pairs with $T$ ( $2$ hydrogen bonds) and $G$ pairs with $C$ ( $3$ hydrogen bonds).
Directionality: DNA strands are anti-parallel, running in opposite directions, referred to as the $5'$ end and the $3'$ end.
DNA vs. RNA: RNA is single-stranded, contains ribose sugar, and facilitates protein synthesis through ribosomes.

Chromatin and Histones: DNA winds around histone proteins to form chromatin.
Euchromatin and Heterochromatin: Euchromatin is loosely wound and active for transcription; heterochromatin is tightly condensed and carries few active genes.
Chromosomes: Massive structures of condensed chromatin containing linear gene arrays. Duplicated chromosomes form an $X$ shape with two identical sister chromatids joined at a centromere.
Genes and Loci: Genes are hereditary units located at specific positions called gene loci (e.g., the $PRSS53$ gene on chromosome $16$ ).
Alleles: Different molecular forms of a gene at the same locus on homologous chromosomes.
Telomeres: Repetitive non-coding DNA at the ends of chromosomes that protect genes from damage and shorten with aging.
Gene Structure: Includes promoter regions (expression control), introns (non-coding regions spliced out), and exons (coding regions).

Prokaryotic DNA: Generally a single circular chromosome located in a cytoplasm space called the nucleoid; lacks a membrane-bound nucleus.
Plasmids: Small, independent rings of DNA that replicate separately and often carry antibiotic resistance genes.
Endosymbiotic Theory: Mitochondria and chloroplasts contain circular DNA similar to prokaryotes, supporting the theory they originated as independent organisms.
Maternal Inheritance: Mitochondrial and chloroplast DNA is inherited from the female parent via the egg.

Semiconservative Replication: Results in two identical DNA molecules, each containing one original parental strand and one new daughter strand.
DNA Helicase: Unzips the double helix by breaking weak hydrogen bonds between base pairs to create a replication fork.
DNA Polymerase: Adds free nucleotides to the template strand in the $5'$ to $3'$ direction.
Leading Strand: Synthesized continuously toward the replication fork.
Lagging Strand: Synthesized discontinuously away from the fork in short segments called Okazaki fragments.
DNA Ligase: Stitches together Okazaki fragments to form a continuous strand.
Proofreading: DNA polymerase reduces mistakes from $1$ in $100,000$ nucleotides ( $120,000$ per cycle) down to approximately $1,200$ per cycle.

Point Mutations: Caused by permanent base substitutions; typically have limited cellular effects if they occur in non-coding regions or produce the same amino acid.
Frameshift Mutations: Caused by permanent insertions or deletions; they alter the entire reading frame for protein synthesis, usually resulting in major negative effects.
Mutagens: Physical factors such as UV radiation (breaks nucleotide bonds/causes deletions) and chemical factors like nitrosamines in tobacco damage DNA sequences.

In what way is the DNA of prokaryotes and eukaryotes similar and different? Both use the same chemical code, but prokaryotes have circular DNA in the nucleoid while eukaryotes have linear DNA in a nucleus.
What structural features of DNA make it suitable to carry information from one generation to the next? Its helical structure and specific complementary base pairing enable stable storage and accurate copying.
How is DNA copied to enable transmission to the next generation? Through a multi-enzyme replication process specifically resulting in two identical double helix molecules.
Describe how chromosomes are ordered in a karyotype. They are matched in homologous pairs and ordered by length from longest to shortest, with sex chromosomes ( $X$ and $Y$ ) placed last.
Distinguish between euchromatin and heterochromatin. Euchromatin is densely populated with active genes and is loosely wound; heterochromatin is tightly condensed and carries few active genes.
Explain why chromosomes are generally depicted as an $X$ shape even though they are usually linear. They only appear as an $X$ after DNA replication when two identical sister chromatids are joined at the centromere prior to cell division.