BIO306 Exam 3 Review - Vocabulary

Wrapping DNA Into a Package

Bacteria

• Circular genome located in the nucleoid region.
• Genome is mostly coding region with a single origin of replication and some repetitive DNAs.
• Genome compaction achieved through loop domains and DNA supercoiling.

Eukaryotes

• Chromosomes consist of millions of nucleotides of double-stranded DNA (dsDNA).

• Contain centromeres, origins of replication every 100 kb, telomeres, and genes with introns (1-2% coding).

• Repetitive DNA includes rRNA repeat regions, telomeres, transposable elements, and other repetitive DNA sequences.

• Transposable Elements (TEs):

  • Small DNAs that can move from one location to another within the genome.
  • Two main mechanisms of movement: simple transposition and retrotransposition.
  • TEs can act as mutagens.

• Packaging Details:

  • Nucleosomes: DNA wrapped around an octamer of histone proteins (two each of histones H2A, H2B, H3, and H4), with histone H1 acting as a stabilizer.
  • Supercoiling of nucleosomes into a shorter, thicker 30nm fiber.
  • DNA matrix attachment regions (MARs) form radial loops attached to a protein scaffold made of nonhistone proteins.
  • Further condensation occurs during prophase in mitosis and meiosis.

• Heterochromatin: Typically contains no required genes.

• Euchromatin: Contains genes.

Chromosome Rearrangements and Changes in Number

Rearrangements

• Types: Deletions, Duplications, Inversions, Translocations.
• Understanding:
  • How each type of rearrangement occurs.
  • The effects of each on the cell or organism, considering whether there is a loss or gain of DNA material or if there are breakpoint effects.
  • Under what circumstances these rearrangements might reduce fertility.

Changes in Chromosome Number

• Aneuploidy:
  • Includes monosomies and trisomies.
  • Results from meiotic nondisjunction (NDJ) or mitotic NDJ/chromosome loss.
• Euploidy:
  • Includes monoploid, diploid, triploid, and other polyploid states.
• Polyploids:
  • Consequences for meiosis depend on whether there is an odd or even number of each chromosome.

Mutations

• Forward or reverse mutations.
• Germline or somatic mutations.
• Types:
  • Base substitutions, additions, and deletions.
• Effects:
  • Silent, conservative or non-conservative missense, nonsense, frameshift.
• Mutations Outside Coding Regions:
  • Mutations outside of the coding regions of genes can still cause mutant phenotypes.
• Suppressors:
  • Intragenic vs. intergenic suppressors.
• Position Effect Mutations
• Null vs. hypomorphic vs. haploinsufficiency vs. hypermorphic vs. dominant negative vs. neomorphic.
  • Understanding which are recessive and dominant, and which represent a loss of function or gain of function.
• Spontaneous Mutation Rate:
  • Low, approximately 1 in 100,000 to 1 in 1 billion.
• Spontaneous Mutations:
  • Are random (as demonstrated by the replica plating test).
• Process:
  • Lesions (damage) occur first, followed by either repair or no repair.
  • If there is no repair, permanent mutations can be introduced during DNA replication.
  • Once a legitimate base pair is established, the change can no longer be recognized as a mistake to be repaired.
• Causes of Spontaneous Mutation:
  • Depurination, deamination, tautomeric shifts, reactive oxygen species (ROS) damage.
  • Chromosome rearrangements, TEs, changes in chromosome number, and mistakes by DNA polymerase during replication.
• Causes of Induced Mutations:
  • Chemical: deamination, alkylating agents, intercalating agents, and base analogs.
  • Physical: X-rays/gamma rays, UV light.
• Mutagen-base change relationship:
  • If given that a mutagen alters a base (e.g., A) so it pairs like another base (e.g., G), explain why/how this lesion leads to a mutation after replication.
  • Recognize the change as a transition or transversion.
• Ames Test:
  • Understand how it works and how to interpret the data.

DNA Repair

• Focus on the types of lesions each repair system addresses.
  • Direct Repair: corrects specific types of damage; two examples and the respective lesions fixed.
  • Base Excision Repair (BER): replaces oxidized, damaged, or inappropriate bases.
  • Nucleotide Excision Repair (NER): removes thymine dimers.
  • Mismatch Repair (MMR): corrects mistakes made by DNA polymerase that were not caught by proofreading.
  • Homologous Recombination Repair (HRR): fixes double-strand breaks (DSBs) using a sister chromatid as a template.
  • Non-Homologous End-Joining (NHEJ): fixes DSBs but is not perfect and can introduce errors.

Gene Regulation in Prokaryotes

• Review of transcription (txn) and translation in prokaryotes.

Control Mechanisms

• Negative vs. Positive Control:
  • Repressors, activators, inducers, co-repressors, inhibitors.
  • Inducible genes vs. repressible genes.

lac Operon

• Inducible catabolic system.
• Negative control by a repressor.
• Positive control by CAP-cAMP.
• Key components: operator, repressor, promoter, inducer.
• Interpret the phenotype of merozygotes (bacteria with two copies of the lac operon) containing various mutations.

trp Operon

• Repressible anabolic system.
• Negative control by a repressor.
• Attenuation (neither positive nor negative control).
• Key components: operator, repressor, promoter, co-repressor.

Gene Regulation in Eukaryotes

Transcriptional Control

• Promoters, enhancers, and silencers (DNA sequences) vs. transcription factors (TFs, activators/repressors).
• TFs:
  • DNA binding domains (helix-turn-helix or zinc finger).
  • Protein binding domains (leucine zippers) to form homodimers or heterodimers.

Chromatin Remodeling

• Closed or open conformations by changing positions of nucleosomes, removing histones, or replacing histones with variants.
• Covalent modification of histone N-terminal tails leads to remodeling (histone code).
• ChIP assays determined that active genes are nucleosome-free at their beginnings and ends.
• Model for transcription of genes.

Post-Transcriptional Control

• RNA splicing.
• RNA stability.
• RNA interference:
  • miRNAs/siRNAs cause degradation or translation block.
• Protein stability.
• Protein modification.

Sex determination in fruit flies Example

• Ratio of number of X chromosomes (produce numerator elements) to number of sets of autosomes (produce denominator elements).
• NEs can homodimerize to activate txn of Sxl which activates other gene txn that ultimately activates female-specific genes.
• NEs can also heterodimerize with DEs and NOT activate txn of Sxl so if ratio of NEs:DEs is low, then default pathway of male-specific gene activation occurs.
• Alternative splicing is also involved in producing male- or female-specific spliced mRNAs.