L6&7 - Genomiccs & genome projects Flashcards
How is an organisms genomic sequence obtained?
- Obtain the organisms genomic DNA
- Break the DNA into small fragments
- Obtain the DNA sequence from all the fragments
- Search for overlaps of identity between the DNA sequences of the different fragments to ‘reconstruct’ the genome sequence
- Fill in any missing ‘gaps’ in the genome
The computer plays a major role in genome sequencing, reassembling the complete genomic sequence from the fragments
Why are model organisms important?
Small genome – value for money
Easy organisms to manipulate
Provide information on fundamental biological processes
Technology development
Why is it important to look at history of diease?
It is important to look into history because some infections that have occurred in the past may occur again so it can provide valuable insight
How many genes are in the human genome?
30,000 – 40,000
How many reading frames are there for each gene?
3 reading frames on each strand – 6 open reading frames
Takes every triplet from the start until it finds a stop codon – ATG to stop codon = a gene
What are some major issues in identifying genes within genomes?
Identification of RNA splice site
How big is a valid open reading frame?
Identification of RNA splice site
How is this an issue?
ATG may be separated – computer cannot detect this
Make the DNA into RNA and then splicing occurs – this removes the sequence inbetween (intron) the A & the TG
How big is a valid open reading frame?
Anything less than 50 could just be by chance
However, some genes are smaller than 50
What can computer analyses of protein sequence tell us?
Prediction of function – roles for model organsims
Prediction of protein localisation
Prediction of protein domains/modification
PREDICTION OF FUNCTION
Understanding the location of a protein can also give some idea of its function
Eg. if a protein is associated with a ribosome it is likely to be involved in translation
What does a Blast value give us?
Blast value = probability of homology being due to chance
The lower the number the higher the chance of being real homology
Other benefits of studies in model organsims
Functional Characterisation of Mutant Proteins
Understanding human genome variation
PREDICTION OF PROTEIN LOCALISATION
Analysing the protein using the PSORTII programme gives you predictions of where the protein is
– Have to figure out what’s real – only a guideline of where to look
– Have to test it in a lab
Can check using microscopy
– Using light microscopy, nuclear staining & fluorescent markers
PREDICTION OF PROTEIN DOMAINS/MODIFICATION
To understand function/regulation of the protein use a range of programmed to predict potential functional domains & protein modification sites
Use various programmed including BLAST to identify conserved domains
Search for potential serine/threonine/tyrosine phosphorylation sites for example using NetPhos programme
Uses of genome sequences within an organsim
Identification of regulatory sequences
Characterisation of protein families
