Lecture 8: Nucleic Acids and Chromosome Structure

Deoxyribonucleic Acid (DNA): Polymer made of nucleotides.
- Nucleotides consist of four bases: adenine (A), thymine (T), cytosine (C), guanine (G).
- Nucleotide base pairs:
- Adenine pairs with Thymine: A:T
- Cytosine pairs with Guanine: C:G
- Double Helix: DNA structure featuring two strands winding around each other.
- Different conformations: A-DNA, B-DNA, and Z-DNA.
Genetic Material: DNA is the primary genetic material of cells.
- Genes are encoded by long sequences of nucleotides, which subsequently transcribed into RNA.
- Cells contain extensive amounts of DNA, fundamentally essential for cellular functions.

Prokaryotic Bacteria:
- Contain a single, circular DNA molecule or chromosome ranging from 500,000 to 12 million base pairs.
- If stretched out, this DNA would be about 1,000 times longer than the cell.
Eukaryotic Cells:
- Made up of multiple, linear DNA molecules or chromosomes, with lengths varying from 10 million to over 100 billion base pairs in one cell.
- Human beings possess more than 6 billion base pairs across 23 pairs of chromosomes.
- When stretched out end-to-end, this DNA would exceed 6 feet in length.
DNA Packaging: Achieved by winding DNA around proteins to facilitate compaction.

Supercoiling: DNA can be altered by overwinding or underwinding.
- Causes strain in the molecule leading to folding in loops, enhancing compactness.
- Positive Supercoiling: Occurs with over-wound DNA.
- Negative Supercoiling: Occurs with underwound DNA.
- Topoisomerase Enzymes: Mediate the supercoiling processes within the cell.

Nucleoid Associated Proteins (NAPs): Assist in compacting and organizing bacterial chromosomes within the cytoplasm.
Plasmids: Small accessory DNA molecules within bacteria that replicate independently and can exist in multiple copies within a single cell.

Chromatin: Eukaryotic DNA complexed with proteins to maintain its structure and regulate gene expression.
- Euchromatin: Loosens during the cell cycle, making it available for transcription.
- Heterochromatin: Remains condensed throughout the cell cycle and is not involved in crossing over.
- Constitutive Heterochromatin: Permanently compacted regions (e.g., centromeres and telomeres).
- Facultative Heterochromatin: Developmentally regulated regions (e.g., Barr bodies).
Histones: Major proteins associated with eukaryotic chromatin (H1, H2A, H2B, H3, H4).
- Rich in arginine and lysine, giving them a net positive charge, which aids in DNA binding.

Nucleosome: Basic unit of chromatin consisting of DNA (~200 bp) wrapped around an octamer of histones.
Histone H1: Binds to nucleosomes, securing the DNA.
Nucleosome Function: Interact and pack tightly together, playing a role in DNA compaction and transcription regulation.
Histone Modifications:
- Histone Methylation: Condenses nucleosomes through reduced overall charge due to hydrophobic forces.
- Histone Acetylation: Loosens interaction with DNA by reducing the positive charge on histone tails, facilitating transcription.

Centromeres: Regions of heterochromatin with nucleosomes containing the variant histone CENP-A.
- Important for connecting sister chromatids after DNA replication.
- Various centromere positions:
- Telocentric: Joins chromatids at their tips.
- Acrocentric: Joins chromatids near their tips, resulting in short p arms and long q arms.
- Submetacentric: Joins chromatids closer to the center.
- Metacentric: Joins chromatids at the center, yielding symmetric arms.
- Acts as the site for kinetochore assembly and spindle microtubule attachment during cell division.

Telomeres: Repeated sequences at the ends of linear chromosomes.
- G-rich 3' Overhang: Binds to protective proteins, providing a buffer against chromosome shortening during replication.
- Lengthened in gametic cells by the enzyme telomerase.

Linked Genes: Genes that do not assort independently; exhibit lower recombination rates due to physical closeness on the same chromosome.
- A linkage group is composed of several genes (loci) that infrequently recombine.
Crossing-Over: Occurs during meiosis, leading to recombination of linked alleles.
- Recombination rate is proportional to the distance between genes on a chromosome.
- If genes are completely linked, a double heterozygote will produce only two gametes rather than four.
- Recombination frequency can be derived from the proportion of offspring displaying recombinant phenotypes.

Allele Configuration:
- Coupling: Alleles linked in cis configuration (e.g., A-B and a-b).
- Repulsion: Alleles linked in trans configuration (e.g., A-b and a-B).
Recombination frequencies lie on a continuum from complete linkage to near-independence.

Chi-squared Test: Utilized to assess deviations from independent assortment in genetic crosses.

Linkage Mapping: Involves measuring recombination rates to determine gene positions on chromosomes.
- Map Unit: One map unit equals a 1% recombination rate measured in centiMorgans (cM).
- Genetic distances are additive (e.g., distance from A to B plus B to C equals A to C).
- The order of genes is ascertainable using trihybrid crosses.
- Genes that are distanced apart on the same chromosome behave as though they are on separate chromosomes due to reaching a 50% recombination frequency.
- Double Crossovers: Between widely spaced genes can result in underestimating map distances.
Test Crosses:
- Two-point Test Cross: Involves mapping distances among multiple genes through a series of dihybrid test crosses.
- Three-point Test Cross: Employs three genes in one cross to determine their order.
- The two most common phenotypes will represent non-recombinant offspring resembling parents (e.g., A_B_C_ or aabbcc).
- The rarest phenotypes will be double crossover progeny resulting from two crossover events.

There exist three possible gene orders among the phenotypes, with the correct order corresponding to the observed phenotype.
Interference: Refers to one crossover event inhibiting additional crossovers in the same chromosomal region, resulting in fewer observed double crossovers than theoretically expected.
Coefficient of Coincidence: Ratio of observed to expected double crossovers.
- Interference Calculated: Given by the formula:
  ext{Interference} = 1 - ext{coefficient of coincidence}
- A higher interference value indicates a reduction in double crossover occurrences.
Multiple Crossovers: Can involve three or four chromatids resulting in an increased number of recombinant gametes due to participation of more than two recombinant chromatids.