GDC

• Chromatin


  Double stranded helical structure of DNA

  
• Nucleosome


  DNA wrapped around histone proteins
• Chromatosome


  Nucleosome and H1 histone

  
• Chromosome


  Formed from 2 sister chromatids

  
• Nuclear genome


  3 x 10^9 base pairs and contains about 25,000 genes
• Coding DNA


  10% of nuclear genome
• Non-coding DNA


  90% of nuclear genome
• Pseudogene


  Once worked but no longer works. Not transcribed, but if it is, is not translated, but if it is, doesn't work
• Gene fragments


  Not quite a pseudogene. A bit of a gene that is copied or dropped. NUMT (nuclear mitochondrial inserts)

  
• Introns


  Aren't translated. Sometimes partly transcribed then edited out of mRNA
• Extragenic DNA

  75% of nuclear genome
• Unique or low copy number

  60% of extragenic DNA
• Moderate to highly repetitive

  40% of extragenic DNA
• Tandemly repeated or clustered repeats


  Particular sequence repeated in tandem
• Interspersed repeats


  Sequence found all over genome. Various types of elements (LINEs, SINEs, Alu)
• Mitochondrial genome


  16,500 base pairs (1/180,000th of nuclear genome size) and contains 37 genes which are crowded into DNA sequence about 270 x more densely than nuclear genes

  
• Typical gene


  Contains a 5' UTR (untranslated region) directly upstream of initiation codon and a 3' UTR immediately following translation termination codon, with introns and exons in between. Transcription occurs in a 5' to 3' direction. Promoter: upstream of start of transcription site. This is where RNA polymerase binds and begins transcription. Transcription factors: regulate interaction between RNA polymerase and promoter region

  
• Exons and introns


  • Number of exons and introns in a gene is highly variable, but correlates to overall size of gene. Exons are minority and introns are majority. HBB gene (haemoglobin β): 3 exons and 2 introns. DMD gene (Duchenne muscular dystrophy): 79 exons

  
• Gene size and exon content

  • Gene < 10 kb (tRNA, histone H4, α-interferon): contain 0 introns. Gene < 100 kb: % of exons ↓ as gene length ↑. Gene > 100 kb (factor VIII, CFTR, Dystrophin): exon content is < 1%. Majority is intron

  
• Genes within genes

  Small genes within introns of larger genes. NF1 (neurofibromatosis gene) is found within a large intron, and it contains 3 genes transcribed in opposite direction (OGMP, EVI2A and EVI2B)

  
• Gene densities

  • 6p21.3: on chromosome 6. In < 1 million bases, there are > 7 genes. Xp21.2: on X chromosome. Dystrophin gene stretches over 2.4 million bases

  
• Gene families


  • Members may exhibit high sequence homology (shared ancestry). Sometimes contain a highly conserved domain or a very short conserved motif. Superfamilies, clustered genes, and often associated with truncated and non-processed pseudogenes
• Tandemly repetitive DNA

  • Satellite DNA (100 kb to several Mb, 5 bp - 5 kb, located in heterochromatin particularly at centromeres)
  • Minisatellite DNA (0.1 - 20 kb, 6 - 64 bp, scattered but concentrated near telomeres)
  • Microsatellite DNA (< 100 bp, 1 - 5 bp, dispersed throughout genome)

  
• Tandemly repetitive DNA


  Number of repeats is highly variable. When passing onto offspring, there is a high chance (1 in 200) that number of repeats will ↑/↓ allowing for variability. High variability of repeated expression means that it is a useful genetic marker and can be used as basis for DNA fingerprinting

  
• Ultracentrifugation of satellite DNA

  DNA has a density of 1.8 g/ml. Filling DNA with a CsCl solution (like NaCl but very dense) and then centrifuging (100,000 rpm) causes DNA to float at 1.8

  
• Repetitive DNA sequences are often associated to pseudogenes as genes are duplicated and can either develop a different function or become a pseudogene (loss of function)

  
• Tandemly repetitive DNA


  • Satellite DNA (100 kb to several Mb, 5 bp - 5 kb, Heterochromatin particularly at centromeres)
  • Minisatellite DNA (0.1 - 20 kb, 6 - 64 bp, Scattered but concentrated near telomeres)
  • Microsatellite DNA (< 100 bp, 1 - 5 bp, Dispersed throughout genome)

  
• Repetitive DNA sequences


  • Number of repeats is highly variable, When passing onto offspring, there is a high chance (1 in 200) that number of repeats will ↑/↓ allowing for variability
  • High variability of repeated expression means that it is a useful genetic marker and can be used as basis for DNA fingerprinting

  
• Ultracentrifugation of satellite DNA

  1. DNA has a density of 1.8 g/ml, Filling DNA with a CsCl solution and then centrifuging (100,000 rpm) causes DNA to float at 1.8 g/ml layer, Dye is added to stain DNA, and banding is observed

  2. Satellite band: banding outside of main DNA band, These bands are highly repetitive DNA sequences of C and G repeats (< density than A and T)

  
• Dispersed repetitive DNA


  • SINE (Alu 0.3 kb, 1,000,000 copies, 7% of genome, MIR 0.13 kb, 400,000 copies, 1.7% of genome)
  • LINE (LINE-1 (Kpn) 6.1 kb (but most are truncated), 300,000 copies, 5% of genome)
  • Others (Various 0.4 kb, 800,000 copies, 10% of genome)

  
• Alu repeats


  • Can arrive at a new site by transposition of an active copy, Once inserted, it will gradually accumulate mutations until it is incapable of further transposition, Almost always appear within non-coding introns because they will interrupt gene if expressed in exon, which will cause a mutation and will be lost from population over time due to natural selection
• Heterochromatin: regions that are gene poor and highly variable
• Oxidative phosphorylation


  Produce ATP for cell
• Cells contain between 200 and 100,000 mitochondria, Erythrocytes contain no mitochondria
• Mitochondrial DNA (mtDNA)


  • Unlike nuclear DNA, mtDNA is naked (not associated with histones or other proteins) and is circular
  • Gene rich, containing little junk DNA: 13 protein-coding genes, 2rRNA genes, 22 tRNA genes (so many because genetic code of mtDNA is slightly different to that used in nuclear genes)
  • ↑ mutation rate than nuclear DNA, due to influence of free radicals and ROS
  • 1/180,000th size of nuclear genome

  
• Mitochondrial DNA code differences

  • UGA (Stop in nuclear genes, Tryptophan in mitochondrial genes)
  • AGA (Arginine in nuclear genes, Stop in mitochondrial genes)
  • AGG (Arginine in nuclear genes, Stop in mitochondrial genes)
  • AUA (Isoleucine in nuclear genes, Methionine in mitochondrial genes)

  
• Mitochondrial DNA inheritance


  • Found in males and females, Inherited from mothers, because sperm does not contribute its mitochondria to fertilised egg, Can be used to investigate female-specific migration history
• Mendel's 0th law: genes are particulate and come in different forms known as alleles
• Mendel's 1st law (segregation)

  Organisms have 2 copies of each gene but transmit only 1 to each offspring, Which one is transmitted is chosen at random, If you are heterozygous for 2 different alleles, these alleles will segregate from each other in your offspring
• Mendel's 2nd law (independence of assortment)


  Where alleles for > 1 gene are segregating, segregation at each gene occurs independently of others (exception is during linkage (if genes are very close together, then they are more likely to be inherited together))