Genes and Chromosomes

• DNA molecules in bacteriophages are dramatically longer than the viral particles that contain them
• The T2 bacteriophage DNA is approximately 290 times longer than the viral particle itself
• This creates a fundamental packaging challenge: fitting an extremely long molecule (60,800 nm for T2) into a confined space (210 nm)
• This remarkable compaction requires specialized molecular mechanisms for:
  • DNA condensation without tangling
  • Ordered packing that allows for subsequent release
  • Maintaining DNA integrity despite extreme bending and twisting

Example: T2 bacteriophage contains a 168,889 bp linear DNA molecule that must be precisely packed into its head structure through a combination of DNA condensation proteins and a specialized motor that drives DNA into the capsid.

DNA uses a template strand for transcription because:

• RNA polymerase synthesizes RNA in the 5'→3' direction complementary to the template • The template strand (3'→5') ensures the mRNA will have the correct sequence for translation • The coding strand has the same sequence as the mRNA (except U replaces T)

If the wrong strand were transcribed: • The resulting mRNA would be complementary to the coding strand • This would create a completely different codon sequence • Translation would yield an entirely different amino acid sequence • The protein would have no structural or functional similarity to the intended protein • This incorrect protein would likely be non-functional or potentially harmful

Example: If the coding sequence in DNA is 5'-ATG-3' (coding for Met), transcribing the wrong strand would produce 5'-CAU-3' in mRNA (coding for His) instead of 5'-AUG-3'.

Note: Cells prevent this by having specific promoter sequences that orient RNA polymerase correctly and create strand specificity.

• Mitochondrial division employs dynamin-related proteins (DRPs) that constrict the organelle at the division site, while bacteria use FtsZ proteins to form a Z-ring
• Mitochondrial fission requires coordination with the host cell through ER-mitochondria contact sites, unlike autonomous bacterial division
• Both processes maintain circular DNA integrity during division, supporting the endosymbiotic theory
• Mitochondrial division retains some bacterial-like features but has evolved specialized mechanisms integrated with eukaryotic cellular systems
• Unlike bacteria, mitochondria cannot form de novo and must arise from pre-existing mitochondria

Example: When cells need more ATP during exercise, mitochondrial fission increases, but uses eukaryotic-specific mechanisms while still preserving the bacterial-like circular DNA segregation patterns.

• Impaired mitochondrial fission leads to elongated, interconnected mitochondrial networks that cannot distribute properly during cell division
• Excessive fission produces fragmented mitochondria with disrupted energy production and increased reactive oxygen species
• Mutations in division machinery (e.g., DRP1) cause neurodegenerative diseases by disrupting energy supply in neurons
• Dysregulated division can lead to heteroplasmy (uneven distribution of wild-type and mutant mtDNA)
• Mitochondrial dynamics are essential for mitophagy (removal of damaged mitochondria), and disruption leads to accumulation of dysfunctional organelles

Example: In Charcot-Marie-Tooth disease type 2A, mutations in mitofusin 2 disrupt the balance between mitochondrial fusion and fission, leading to peripheral nerve degeneration due to energy deficits in long axons that require precisely positioned mitochondria.

Chromosome condensation:

• Progressively compacts DNA during prophase of mitosis
• Transforms diffuse chromatin into distinct, visible chromosomes
• Reaches maximum compaction during metaphase
• Serves multiple critical functions:
  1. Enables proper chromosome segregation by preventing tangling
  2. Facilitates attachment of spindle fibers to kinetochores
  3. Allows organized movement of large DNA molecules during anaphase
  4. Prevents DNA damage during physical separation

After cell division, chromosomes decondense during telophase, allowing transcription and replication to resume in the new G1 phase. Condensation represents a remarkable packaging solution - human chromosomes become approximately 10,000× more compact compared to their interphase state.

Underwound circular DNA accommodates structural strain through three main mechanisms:

1. Supercoiling (writhe):

   • DNA axis coils upon itself in space
   • Forms plectonemic (extended) or solenoidal (wrapped) structures
   • Preserves most base pairing
   • Dominant mechanism in most cellular conditions

2. Changes in twist:

   • Increases bp/turn from canonical 10.5 to higher values
   • Distorts ideal B-DNA geometry
   • Maintains linear DNA axis

3. Local strand separation:

   • Breaks hydrogen bonds between complementary bases
   • Creates single-stranded regions
   • Important for initiating replication/transcription

Energetic considerations:

• Base pairing (hydrogen bonds): ~2-3 kcal/mol per bp
• Base stacking: ~4-10 kcal/mol per bp
• Bending/writhing: ~2 kcal/mol per 10 bp of supercoiling

Strain relief dominance is determined by:

• Temperature (higher temperatures favor strand separation)
• Ionic conditions (low salt favors strand separation)
• DNA sequence (AT-rich regions separate more easily)
• Protein binding (can stabilize any of the three forms)
• Degree of underwinding (extreme underwinding forces strand separation)

Normally, supercoiling dominates because it preserves the energetically favorable base pairing and stacking interactions while alleviating the torsional strain.

This process is called DNA supercoiling, which:

• Forms a new helix (superhelix) when the axis of the DNA double helix coils on itself
• Creates a higher-order DNA structure beyond the primary double helix
• Results in a more compact DNA arrangement
• Is an intrinsic property of DNA tertiary structure in all cells
• Serves crucial biological functions including DNA packaging and regulation of gene expression

In biological terms, supercoiling represents a form of stored energy that can facilitate processes requiring DNA strand separation.

• DNA supercoiling represents stored energy that cells can harness for DNA metabolism
• Cells actively maintain negative supercoiling (underwound DNA) to:
  • Facilitate DNA compaction through solenoidal coiling
  • Make strand separation energetically more favorable
  • Aid processes requiring strand separation (replication, transcription)
  • Promote formation of alternative DNA structures at specific sequences
  • Regulate gene expression through structural transitions
• The degree of supercoiling is precisely regulated through topoisomerase enzymes
• In prokaryotes: Gyrase introduces negative supercoils; topoisomerase I relaxes them
• In eukaryotes: Chromatin proteins help maintain and regulate DNA topology

Example: When RNA polymerase moves along DNA during transcription, positive supercoils accumulate ahead of the enzyme while negative supercoils form behind it. Topoisomerases must continually resolve these topological challenges for transcription to proceed efficiently.

1. Relaxed circular DNA starts with no supercoiling
2. Condensin binds to DNA, creating:
   • Positive supercoils (+) at binding sites
   • Compensatory negative supercoils (−) elsewhere in the DNA
3. Topoisomerase I specifically relaxes the negative supercoils
4. This results in net positive supercoiling being retained
5. The remaining positive supercoils contribute to DNA condensation
6. Condensin is eventually released, but the changed topology remains
7. This process is essential for chromosome condensation during mitosis

DNA can adopt several distinct structural states in response to underwinding (negative supercoiling):

1. Relaxed DNA (baseline state):

   • Standard B-form with ~10.5 base pairs per helical turn
   • No torsional strain present
   • Linear helical axis

2. Strained/Underwound DNA:

   • Contains fewer helical turns than expected for its length
   • Base pairs must accommodate different helical pitch (e.g., 12.0 bp/turn)
   • Thermodynamically unstable due to suboptimal base stacking
   • Common in circular DNA where free rotation is constrained

3. Supercoiled DNA:

   • Primary cellular solution to underwinding strain
   • DNA axis coils upon itself, forming superhelical turns
   • Preserves base pairing while accommodating reduced twist
   • Most efficient way to manage topological stress in circular DNA

4. Strand-separated DNA:

   • Partial melting of the double helix
   • Underwinding facilitates separation by reducing energy needed to break base pairs
   • Critical for initiating replication and transcription
   • Often occurs at AT-rich regions (weaker base pairing)

5. Cruciform DNA:

   • Forms at palindromic sequences under negative supercoiling
   • Features two hairpin-like structures projecting from main helix
   • Base pairing switches from interstrand to intrastrand
   • More extreme structural adaptation than simple underwinding

Note: When one helical turn is removed, DNA initially experiences strain that is typically resolved through a combination of these states, with supercoiling being energetically favored over maintaining the strained conformation.