71 lines
3.2 KiB
Org Mode
71 lines
3.2 KiB
Org Mode
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:PROPERTIES:
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:ID: 3c1042b7-41e6-4830-a7b9-68a8d1d3b46f
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:END:
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#+title: Genetics: Genomics
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#+filetags: :genetics:lecture_notes:
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#+STARTUP: latexpreview
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* Structural Genomics
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- Deals with the *location* of genes:
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* 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.
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* Cytological maps -- Uses flourescence to locate genes on a chromosome.
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* Physical map - Displays the actual bases.
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* Restriction Fragment Length Polymorphisms (RFLPs)
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- Mutations that change the length of DNA fragments produced from REN digests. The mutation happens within the sequence that a particular REN recognizes.
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- They are small nucleotide polymorphisms (SNPs).
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- They segregate as codominant alleles.
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- They are a useful tool in creating genetic maps.
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* Variable Number Tandem Repeats (VNTRs)
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- Large areas of tandem repeats.
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- The number of times it repeats is different in each person.
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- Happen at different *loci*.
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- They are not genes.
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- They can produce a genetic fingerprint when all loci are analyzed.
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* Contiguous Regions
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- Using different clones, they can be overlapped to form the gene to form a contiguous map.
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* Large DNA regions are fragmented so that they are easier to work with. BACs or YACs are often used.
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* Fragments are analyzed for overlapping regions, acheived by looking at restriction sites.
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* Once all overlapping positions are determined, they can be put together to create a complete map, giving the positions of genes on the chromosome.
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* Sequencing the Human Genome
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- Collin's team mapped clone by clone.
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- Venter used whole-genome sequence using computer software.
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- 30-35K genes were found ot be in the genome.
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- Exons are only 1.1% of the genome while introns are 24%.
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- About 75% of the genome is intergenic space.
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* Functional Genomics
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- Study of gene products: mRNA and proteins
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- Microarray technologies examine expression of entire genomes (transcriptome) (see[[id:e43a2223-ffee-4372-81c6-9520ca97450d][Genetics: Techniques of Molecular Genetics]])
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* A gene chip is used. gene-specific oligonucleotide probes are added to the chip.
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* RNA is extracted from experimental and control tissues.
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* RT-PCR is used to create cDNAs. The cDNAs are dyed with flourescence.
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* 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.
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- Can answer questions such as: What is normal? What is abnormal? What has changed based on the conditions?
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* Comparitive Genomics
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- The word *homologous* can refer to common ancestry *or* to analog proteins in prokaryotes vs. eukaryotes, or different species.
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- Bioinformatics provides information from DNA sequences:
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1. Can provide protein data/identify similar proteins with known functions.
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2. Hints to crucial amino acids
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3. Can provide exon data. Sheds insights on those that show high *conservation*, which usually is found in exons.
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* conservation means that mamy different species have the same DNA sequence. This means that the sequence must be important and have a specific function.
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