GER lecture 1

• Prokaryotic cell


  • No nucleus with non-membrane nucleoid
  • Linked transcription & translation
  • Genes expressed in operons
  • Have a common promoter
• Eukaryotic cell


  • Nucleus with compartments
  • Unlinked transcription and translation
  • Transcription in nucleus
  • Translation in cytoplasm
  • Multiple levels of gene regulation (e.g. enhancers, splicing, imprinting)
• Operons


  Functional units of prokaryotic DNA, consisting of genes with related functions and regulatory elements that regulate their expression
• Imprinting

  Gender-specific gene regulation
• Important for understanding diseases, such as cancer, diabetes, Parkinson's
• Chromatin


  • DNA is packaged into chromatin that assembles into higher order structures
  • Main protector of DNA
  • Compacts DNA into the nucleus (DNA → nucleosome → beads → fiber → higher order chromatin)
  • Regulates gene expression
• Epigenetics


  The study of heritable changes in gene function that do not involve changes to the underlying DNA sequence
• Nucleosome


  • The basic unit of chromatin
  • One nucleosome is made up of DNA wrapped around 8 histone proteins – i.e. octamer histone core
  • DNA wraps 1.75 turns around histone core
  • 1 nucleosome always has 146 DNA bps because they are always the same size
  • Nucleosome is where transcription factors bind DNA
  • Each histone protein has a tail (disordered protein) that can be epigenetically modified
  • Instructs how DNA-binding proteins (e.g. transcription factors) should interact with it
• Linker DNA


  • Binds to a H1 histone protein (linker histone)
  • Less tightly packaged – where some transcription factors bind
• If a transcription factor is bound to a linker DNA, it protects it from digestion and allows us to find out where the TF binds
• Chromatin remodelling


  • Regulates gene expression
  • Acetylation stretches linker DNA, which separates the nucleosomes (relaxed chromatin = open chromatin = euchromatin)
  • Removing the acetylation allows nucleosomes to be closer together (condensed chromatin = closed chromatin = heterochromatin)
  • Heterochromatin is usually found near the nuclear membrane, whereas transcriptionally active chromatin (euchromatin) is found towards the middle of the nucleus
  • ATP-independent remodelers change chromatin dynamics
• Histone modifications


  • Can be either permissive or repressive depending on which specific histone residue/tail is modified and the degree of modification
  • Histone tail modifications spread out the nucleosomes, leading to the relaxed euchromatin state
  • "Reader" proteins read the modifications by interacting with the modified residues
  • Recruits "writer" enzymes (transferases) that add more permissive modifications to histone tails
  • In the repressive state, reader proteins bind to repressive histone tail modifications and recruit co-repressors and "eraser" enzymes (e.g. deacetylases, demethylases, dephosphorylases)
• Recent EM tomography and cryo-EM studies challenge the existence of the 30 nm fibres. However, it has been found that they are not always there and are actually rarely seen because they are a transient transition state between the beads on a string and higher order chromatin folding.
• Metaphase checkpoint


  Are chromosomes attached to bipolar spindles?
• G1/S checkpoint


  • Delays progression until conditions are favourable
  • Determines if cells go to S-phase or G0
• G0 (quiescence)


  Cells enter dormancy
• G2/M checkpoint


  Checks for DNA damage
• Sister chromatids


  • Newly replicated chromosomes
  • Attached at the centromere
• Centromere


  DNA region where sister chromatids remain joined after S-phase
• Microtubules


  Proteinaceous filaments involved in structure, transport and motility
• Kinetochore


  Proteinaceous region of centromere that binds spindle microtubules (tubulin)
• Centrosome


  Organelle that serves as MTOC (microtubule organising centre)
• Daughter cells inherit identical DNA content (2n = 46 chromosomes = 23 chromosome pairs)
• However, daughter cells can have different fates
• Meiosis


  Germline reductive division
• Mitotic recombination


  The physical exchange of DNA between non-sister chromatids in a chromosome pair during prophase I
• Chiasmata


  • Points of contact between homologous chromosomes (non-sister chromatids)
  • Sites of crossing over
• Mandelian inheritance


  • Haploid germ cells (egg and sperm) are products of meiosis
  • Haploid germ cells form a diploid organism by fertilisation
  • Mutations present in germ cells are inherited by progeny
  • Heterozygous parents each contribute an allele