OMICS: Lect 15 Flashcards
Human Genome Sequence
- determine entire seq of human genome.
- identify and map genes in human genome.
- find single nt polymorphisms.
- shows how few genes we have
Annotation
-identifying the functions of open reading frame. Challenges: miss aspects of genome -very small ORF -small genes w/i larger genes -genes on opposing DNA strands -gene not translated into protein -other unknown RNA species
Why is it that chrom 13, 18 and 21 are only autosomes that can be found as trisomy and compatible w/ life?
- because size of chrom doesn’t always correlate w/ size by gene content. (Alt splicing ->resulting in many genes, RNA editing)
- these have the smallest gene content.
Duplications in the genome
- 50% of genome is repetitive sequence.
- STR (di, tri or tetra) and VNTR (slightly longer repeats); highly polymorphic regions.
- Transposons (LINES and SINES “Alu element) -> most repetitive DNA in genome.
- Pseudogenes: vestigial, duplicated and processed pseudogenes.
Pseudogenes
- Vestigial: now dormant. Ex: humans have the Vit C gene but it doesn’t function.
- Duplicated genes: not expressed. Ex: one of the globin genes in the B globin locus is not expressed.
- Processed pseudogenes: introns are removed from primary transcript by nl splicing, poly A tail added. Rev transcription and integration then yield a processed pseudogene which does not contain introns and has an A-rich tract at it’s 3’ end.
Transposons leads to a disease by?
- integrating into a critical spot in a genome, disrupt a gene and cause disease.
- as repetitive sequence may lead to misalignment during meiosis and gene disruption.
DNA fingerprinting
- may be used to settle paternity issues via PCR.
- use highly polymorphic single locus regions like STR or VNTR loci.
Multiplex PCR:
an example of STR/VNTR PCR genotyping.
Gene/chrom duplication or amplification occurs in a variety of ways:
- error in homologous recombination, retrotransposition event or duplication of an entire chrom.
- duplicated gene can evolve faster and the second copy of the gene is free from selective pressure.
- In a-thalessemia; due to repetitive struct of the a-cluster, deletions are the common disease causing mechanism for a-thal.
Red-green color blindness?
explained by unequal intragenic recombination btwn a pair of X-chrom during meiosis.
Chromosomal Microarray Analysis:
- can detect birth abnormalities.
- allows overview of the genome.
- > 1000s of probes immobilized on a solid support.
-CGH and SNP
CGH
- comparing one genome to another.
- gives copy number variation
- important in pediatrics and diagnosis of developmental abnormalities.
- can detect smaller del or insertions than G-banding.
- diagnostic tool
SNP chip
- single nucleotide polymorphisms
- may inform haplotype and pharmacogenomics.
- data collection tool
Haplotype
- combination of alleles at different chromosomal loci that are transmitted together.
- HapMap describes common patterns of human genetic variation.
Genome wide assoc. studies
- an attempt to uncover genetic determinants of multifactorial diseases (environmental and more than one genetic component)
- created by scanning 1000s of SNP
- search for genetic variations assoc w/ a particular disease.
- > finding genetic variations that contribute to common, complex disease such as autism, asthma, cancer, diabetes type I/II, heart disease and mental illnesses.
Transcriptome
- all mRNA in a particular cell under a particular condition.
- use of cDNA microarrays to determine the genes expressed
- allows comparison of expressed genes btwn nl and diseased states.
Proteomics
- number of genes does not equal number of proteins because genes can have:
1. multiple start sites
2. alternate splicing
3. RNA editing
4. most proteins are modified (phosphorylation, glycosylation)
At low pH,
At high pH,
At the isoelectric point
the protein has a +ve charge.
the protein has a -ve charge.
the protein has no net charge.
Mass Spectrometry
- finds out what the identity of the protein is.
- fragments the protein w/ an electrical charge and then the mass is calculated.
- allows identification of minute amounts of a molecule.
Epigenome
DNA methylation patterns on CpG repeats/islands are important in gene regulation.
-methylation of CpG islands are assoc. w/ reduced gene expression of nearby genes. (reduced expression of tumor suppressor genes)
Fragile X
- result of excessive methylation pattern.
- expansion of a CGG repeat (CG gets methylated)
- reduced expression of FMR1 gene; leads to mental impairment.
- trinucleotide repeat disorder
- combo of genome duplication and epigenetic control
