BIOL1020 Module 6 - Genomics

4 Pages
102 Views
Unlock Document

Department
Biology
Course
BIOL1020
Professor
Dr Paul Ebert
Semester
Spring

Description
Genomics Genomics and sequencing Gene: a segment of DNA needed to contribute to a function by encoding a protein Genetics: study of the function of individual genes and their effects Genome: the entire DNA content and hereditary material possessed by an organism (may refer to nuclear, mitochondrial or chloroplast genome) Genomics: study of the functions and interactions of all genes in the genome 1977: first DNA genome sequenced (E coli bacteriophage) 2001: first human genome Sequencing before 2001 1. Cloning  Fragment genome into small pieces  Insert each piece into vector (plasmid)  Insert plasmid into bacteria and grow each as individual strain 2. Ordering: Determine position of each clone along chromosome using various techniques (i.e. electrophoresis) 3. Sequencing: determine nucleotide sequence of each fragment 4. Assembling: use computer to manage data Next generation sequencing (2009-2013) Use PCR instead (service sequences purified DNA) – costs about $3000  Massively parallel sequencing occurs in lab Assembling: computational and highly automated Soon the genome sequence of any organism will be known  Personalising treatment and drug administration? Clinical genome sequencing Genome sequencing will become a clinical test at birth Most drugs currently wasted due to incompatibility with patient genotypes  Causes financial waste and harm to patients Every human genome known -- ethical issues must be very well managed Bioinformatics How to find genes amongst nucleotides:  Start and stop codons  Translate from RNA sequence  Look at related species and proteins (available in public domain) Why are amino acid sequences similar? (characteristics preserved as important for protein function)  Regulatory sites on proteins  Amino acids essential for structure  Catalytic sites  Hydrophobic and hydrophilic domains Why aren’t nucleic acid sequences similar?  Non-translated regions  Redundancy of the genetic code  More than one nucleotide sequence that can encode same protein  Many matches by chance alone If sequences of two genes are similar:  Initial assumption is that functions are similar  Phenotypes of mutations will be similar  Knowledge of one organism can be applied to other similar ones ‘omics technologies Genomics: sequence similarity of genes/proteins Transcriptomics: abundance of every transcript – which genes are expressed? Proteomics: abundance of nearly every protein - what proteins are expressed? Metabolomics: abundance of all major metabolites – final output of gene expression Transcriptomics All transcripts are chemically quite similar but:  Not every cell type expresses same type of genes  Splice variants from same transcript  Developmental stages have different transcripts  Environmental stressors change transcripts Bacterial genomics Fewer than 1% of bacteria have been grown in the lab – great diversity Microbial fuel cells: fuel cells powered by bacteria that produce electrons as they eat What makes bacteria conducive to genomic study?  Haploid (only 1 copy of each gene)  Small genome size (4.6 million bp) – correlates to physical size  Easy to genetically manipulate  Short generation times  Asexual reproduction (genotype remains constant)  Can be frozen and stored indefinitely  Great diversity and biosynthetic capacity No clear link between genome size and reproduction rate Genome size correlates with lifestyle  Smaller bact
More Less

Related notes for BIOL1020

Log In


OR

Join OneClass

Access over 10 million pages of study
documents for 1.3 million courses.

Sign up

Join to view


OR

By registering, I agree to the Terms and Privacy Policies
Already have an account?
Just a few more details

So we can recommend you notes for your school.

Reset Password

Please enter below the email address you registered with and we will send you a link to reset your password.

Add your courses

Get notes from the top students in your class.


Submit