EM

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.