Gene expression in eukaryotes

• How is genome organised into eukaryotes?

  linear DNA organised into chromatin
• how is the genome organised in prokaryotes?

  circular DNA
• why are eukaryotic genomes generally so large?

  The number of genes

  The amount of non-coding DNA
• why is there more gene in eukaryotes?

  The have a greater complexity
• Why is there a large amount of non-coding DNA?

  In prokaryotes- most DNA codes for proteins

  In eukaryotes- Most DNA does not encode protein or RNA
• What does most of the non-codig sequences consist of?

  Gene regulatory sequence (e.g promoters)

  Introns (non-coding sequences within genes)

  Sequences of no known function (including repetitive DNA sequences - junk DNA)
• What is a promotor?


  The part of the gene that controls its transcription
• What is an exon?


  Transcribed sequence that is represented in the final mRNA
• what is an intron?

  Intervening sequence in the transcribed region that is not represented in the final mRNA
• what are the types of repetitive sequences?

  interspersed repetitive DNA

  Tandemly repetitive (satellites) DNA
• What is a interspersed repetitive DNA?

  Repeated units scattered throughout the genome

  single unit 100-10,000 bp

  copies not necessarily identical, but closely related

  Makes up 25-40% of most mammaliam genomes
• what is used for detection of interspersed repeats in human chromosomes?


  FISH: Fluorescent in situ hybridization, green fluorescence shows location of Alu repeat sequences around the human genome
• What are tandemly repetitive (satellite) DNA?

  Length of a single repetitive region

  Satellites DNA is located at telomeres and centromeres - suggesting a structural role

  Some genetic disorders are caused by abnormally long stretches of a repetitive sequence within a gene
• what are the types of satellites?

  • Regular satellites DNA: 100,000-10 million bp per site
  • Minisatellites DNA: 100-100,000 bp per site
  • Microsatellite DNA: 10-100 bp per site
• What is the structure of chromatin?

  Composed of proteins and DNA

  Chromatin is an intricate form of packaging for DNA (10,000 fold compaction)
• Why is chromatin packed in the way it is?

  to be accessible for transcription and replication
• what are the two types of chromatin?

  Heterochromatin

  euchromatin
• What is heterochromatin?

  Highly condense during interphase, not actively transcribed
• what is euchromatin?

  Less condense during interphase, able to be transcribed
• where does packing of chromatin begin?

  Nucleosome
• what is a histone?

  Proteins with positively charged amino acids that bind to the negatively charged DNA
• what attaches nucleosome?

  Histone H1
• Describe the nucleosome:

  • core of 8 histone molecules
  • histone H1 attached
  • 200bp of DNA wrapped arounf each histone octamer
• looped domains of the 30nm chromatin fibre, during interphase, most of the chromosome is in this form euchrromatin
• when is heterochromatin formed?

  This highly condensed chromatin also occurs during interphase in some region of the chromosome
• what is the diameter of euchromatin?

  30nm
• what is the diameter of heterochromatin?

  300nm
• what is the long-term control of gene expression called?

  Cellular differentiation
• What are the stages regulation of gene expression?

  1. DNA unpacking
  2. transcriptional control
  3. RNA processing control
  4. RNA transport and localization control
  5. mRNA degradation control
  6. translation control
  7. protein activity control
• What are the chemical modification of chromatin?

  DNA methylation

  Histone acetylyation
• what is DNA methylation?

  attachment of methyl groups

  Triggers formation of a compact chromatin structure

  Associated with inactive DNA

  Accounts for genomic imprinting in mammals
• what is histone acetylation?

  Attachment of acetyl groups to histones

  Acetylated histones grip DNA less tightly

  Acetylation/deacetylation is involved in switching genes on and off
• How changes in DNA methylation and histone acetylation affect chromatin structure:

  closed chromatin: DNA methylated, Histone not acetylated

  Open chromatin: DNA unmethylated, Histone acetylate
• what are the 3 types RNA polymerase:

  RNA polymerase I: ribosomal RNA

  RNA polymerase II: messenger RNA (mRNA)

  RNA polymerase III: small RNAs e.g tRNA
• when does transcription begin?

  RNA polymerase binds to a promoter
• what does a promoter determine?

  Where the transcription of the gene is initiated

  The rate of transcription
• What is TATA box?

  Provides the site of initial binding of the transcription initiation machinery.

  Located 10-35bp upstream of the transcription start site
• what must form before transcription?

  Preinitiation complex
• Describe the formation of preinitiation complex:

  1. Binding of TFIID: includes the TATA-binding protein (TBP) + TATA-associated proteins
  2. Sequential addition of other general transcription factors - first TFIIA and TFIIB
• How is the rate of transcription in eukaryote modulated?

  The interaction between the transcription initiation complex and the basal promoter is very ineffecient so would produce very low level of gene expression.

  The process is regulated by specific transcription factor. (activator or repressor)

  These bind to proximal control element and distal control elements (grouping of which are called enhancers)