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#+title: Genetics: Genomics
#+filetags: :genetics:lecture_notes:
#+STARTUP: latexpreview



* 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) (see[[id:e43a2223-ffee-4372-81c6-9520ca97450d][Genetics: 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.