Personal_Knowledge_Base/Biology_and_Chemistry/20241112162414-genetics_genomics.org

Genetics: Genomics

• Structural Genomics
• Restriction Fragment Length Polymorphisms (RFLPs)
• Variable Number Tandem Repeats (VNTRs)
• Contiguous Regions
• Sequencing the Human Genome
• Functional Genomics
• Comparitive Genomics

Structural Genomics

• Deals with the location of genes:

  • Genetic maps – Shows distance between genes in Morgans. Only good up to 50 Morgans, because beyond this, independent assortment can be assumed and thus no actual distance can be attributted.
  • Cytological maps – Uses flourescence to locate genes on a chromosome.
  • Physical map - Displays the actual bases.

Restriction Fragment Length Polymorphisms (RFLPs)

• Mutations that change the length of DNA fragments produced from REN digests. The mutation happens within the sequence that a particular REN recognizes.
• They are small nucleotide polymorphisms (SNPs).
• They segregate as codominant alleles.
• They are a useful tool in creating genetic maps.

Variable Number Tandem Repeats (VNTRs)

• Large areas of tandem repeats.
• The number of times it repeats is different in each person.
• Happen at different loci.
• They are not genes.
• They can produce a genetic fingerprint when all loci are analyzed.

Contiguous Regions

• Using different clones, they can be overlapped to form the gene to form a contiguous map.

  • Large DNA regions are fragmented so that they are easier to work with. BACs or YACs are often used.
  • Fragments are analyzed for overlapping regions, acheived by looking at restriction sites.
  • Once all overlapping positions are determined, they can be put together to create a complete map, giving the positions of genes on the chromosome.

Sequencing the Human Genome

• Collin's team mapped clone by clone.
• Venter used whole-genome sequence using computer software.
• 30-35K genes were found ot be in the genome.
• Exons are only 1.1% of the genome while introns are 24%.
• About 75% of the genome is intergenic space.

Functional Genomics

• Study of gene products: mRNA and proteins

• Microarray technologies examine expression of entire genomes (transcriptome) (seeGenetics: Techniques of Molecular Genetics)

  • A gene chip is used. gene-specific oligonucleotide probes are added to the chip.
  • RNA is extracted from experimental and control tissues.
  • RT-PCR is used to create cDNAs. The cDNAs are dyed with flourescence.
  • The binding of a cDNA to a probe in the microarray chip means that a the specific template RNA was present, which in turn means that particular gene was being expressed.
• Can answer questions such as: What is normal? What is abnormal? What has changed based on the conditions?

Comparitive Genomics

• The word homologous can refer to common ancestry or to analog proteins in prokaryotes vs. eukaryotes, or different species.

• Bioinformatics provides information from DNA sequences:

  1. Can provide protein data/identify similar proteins with known functions.
  2. Hints to crucial amino acids

  3. Can provide exon data. Sheds insights on those that show high conservation, which usually is found in exons.

     • conservation means that mamy different species have the same DNA sequence. This means that the sequence must be important and have a specific function.