Capitulo 5

• A person's whole set of chromosomes received from the parents makes up their genome
• Except for viruses, which may have ssDNA, dsDNA, ssRNA, or dsRNA genomes

  all genetic information in an organism takes the form of double-stranded DNA
• A single linear or circular molecule makes up the genome in many viruses and prokaryotes
• • In eukaryotes, the mitochondrial, and chloroplas genomes are small circular DNA molecules, , whereas the nuclear genome is made up of linear chromosomes
• What is the C-Value?

  The C-value, is the amount of DNA per haploid cell
• What is the C-Value Paradox?

  The amount of DNA in a haploid cell of an organism is not related to its evolutionary complexity, and this in known as the C-value paradox.
• there is no correlation between the presumed evolutionary complexity and the number of chromosomes.
• The DNA has the ability for denaturation and renaturation or re-annealing
• What is the Cot Curve used for?

  is used to estimate the complexity of the sequence of a genome
• In DNA denaturation and renaturation experiments, the following steps are required:

  • (a) Shear the DNA to a size of around 400 bp.

  • (b) Heat the DNA to 100 °C to denature it.

  • (c) Cool gradually while taking samples at periodic intervals.

  • (d) Calculate the percentage of DNA that is single-stranded at each time point.
• What is Cot½


  is the Cot value at which half of the DNA has reannealed
• The size or complexity of the genome and the quantity of repetitive DNA present in the genome both influence the form of a Cot curve for a specific species.
• • Physically, it will take longer for any one sequence to encounter its complementary sequence in the solution the higher the genome size
• It will take longer for any two complementary sequences to encounter each other and reanneal if the genome is more complex
• repeated DNA sequences anneal fast
• unique (non-repeated) sequences anneal slowly
• Why do Highly repetitive sequences Reanneal fast?

  1. Because there are many copies in the genome and (2) low sequence complexity
• Why do single copy DNA reanneal slowly?

  because the sequences are unique
• The degree of repetitiveness can be determined of each segment can be calculated using the Cot½ values and the proportion of the genome that comprises each segment.
• Non-repetitive DNA (unique DNA) makes up the majority of the structural genes (much of it is transcribed).
• Eukaryotic genome

  Can be classified by its abundance and by its function
• Unique sequence (single-copy, low-copy, non-repetitive DNA) Sequences present as one or a very few copies per genome. Contains most genes and includes introns, regulatory sequences and other DNA of unknown function
• Moderately repetitive DNA Sequences present 10-10,000 copies per genome. Generally dispersed repeats corresponding to highly conserved multigene families (functional genes and pseudogenes) and transposable elements. Occasionally clustered
• Highly repetitive DNA Sequences present 100,000-1,000,000 copies per genome. Generally found as tandem repeats although some superabundant (dispersed) transposable elements also fall into this class, e.g., Alu elements.
• Genic DNA Genes, i.e., DNA which is expressed. Genic DNA may be further classified as mDNA (protein encoding), rDNA, tDNA, snDNA, etc. representing the different classes of gene product.
• Regulatory DNA role is the regulation of gene expression the regulation of DNA function
• Intergenic DNA, spacer DNA Introns and the DNA which separate genes from each other
• Satellite DNA Highly repetitive DNA play a role in chromosome function.
• Selfish DNA role appears to be to mediate its own replication and survival within the genome
• Junk DNA DNA with no assigned function.
• Methods that can be used to quantify the amount of dsDNA created during renaturation.

  As O.D. decreases over time, it may be utilized to calculate how much double-stranded DNA was produced

  A hydroxyapatite column may be used to run a DNA sample which only allows ssDNA to pass through and keeps only dsDNA

  S1 nuclease treatment breaks down ssDNA, and quantity of dsDNA can be determined in the sample.

  renaturation will take a longer time for fragment of larger sizes
• DNA's ability to reassemble depends on the complexity of its sequence
• DNA-DNA denaturation, renaturation, and hybridization procedures can be used to examine the sequence complexity of eukaryotic DNA.
• dsDNA unwinds into ssDNA by heating
• • DNA renaturation is governed by second order kinetics and is dependent on a chance collision of the complementary strands
• A higher Cot½ indicates a slower reaction since Cot½ is the product of the concentration and time needed to proceed halfway through a reaction.
• Cot½ will reflect the entire length of all the various sequences (represented only once) in a genome, which will be smaller than the total length of DNA in a genome.
• genome's kinetic complexity.

  When there is repetition, Cot½ will reflect the entire length of all the various sequences (represented only once) in a genome, which will be smaller than the total length of DNA in a genome.
• • Unineme structure

  A chromosome is formed of a single continuous length of DNA double helix.

  • Prokaryotic and eukaryotic chromosomes both have linear gene organization
• Semiconservative DNA replication • Confirmed in Escherichia coli by Mesleson and Stahl (1958) and in Vicia faba by Taylor et al. (1957)