21 Genomes and their Evolution Flashcards
What is genomics?
The study whole sets of genes (genome) and their interactions,
What is bioinformatics?
The application of computational methods to the storage and analysis of biological data.
What is a map of all the genes in an organism called?
A cytogenetic map
What is a cytogenetic map?
A map of the locations of all the genes i.e. the entire genome
What are the basic approaches to sequencing a genome?
The ’Three-stage approach’ and the ‘Whole-genome shotgun approach’
What basic approach did the Human Genome project use to sequence the genome?
The ’Three-stage approach’
What is the ’Three stage’ approach to genome sequencing?
A linkage map is used to determine the location of genetic markers i.e. restriction sites (RFLPs) and other polymorphisms.
Then ‘physical mapping’ which involves the hysical mapping ordering of large over-lapping fragments cloned in YAC and BAC (bacterial artificial chromosome) vectors, followed by ordering of smaller fragments cloned in phage and plasmid vectors.
Finally ‘DNA sequencing’ which is the determination of nucleotide sequence of each small fragment and assembly of the partial sequences into the complete genome sequence
What is YAC?
Yeast Artificial Chromosome (basically just a BAC but from a eukaryotic yeast)
How does the ‘Whole-Genome Shotgun Approach’ sequence a genome?
It basically skips the linkage map and physical mapping stages.
Cut the DNA from many copies of an entire chromosome into overlapping fragments short enough for sequencing. Then clone the fragments in plasmid or phage vectors.
Sequence each fragment i.e. using the dideoxy method
Because the fragments are overlapping their order can be determined using analysis by a computer. Thus the entire genomes sequence can be determined.
What is DNA from a group of species called?
A metagenome
What is a metagenome?
DNA from a group of species that is collected from an environmental sample.
What is metagenomics?
The analysis of a metagenome (collection of DNA from a range of species from an environmental sample)
What is the analysis of a metagenome called?
Metagenomics
What is the point of metagenomics?
With analysis the genomes of the individual species can be isolated.
This means a sample can be taken where many different bacteria species are, such as in the soil, and each individual species can have its genome sequenced.
(this avoids the need to culture specific bacteria from a mixture)
What is ‘reverse genetics’?
A form where the actual genotype is determined (sequenced)
This contrasts with classical genetics where the genotype is inferred from from the phenotype
What is the determination function of a gene called?
Gene annotation
What is gene annotation?
The determination of all the protein coding genes and the functions they have i.e. regulated x, lead to breast cancer
How are protein coding genes determined?
By scanning the sequenced genome for known promotor and terminator regions.
Besides looking for promoter regions, how can the protein coding regions be determined?
By comparing it with known samples of mRNA sequenced from from cDNA libraries.
These known mRNA sequences are called ‘expressed sequence tags’
What are ‘expressed sequence tags’?
Known mRNA sequences that have been collected from cDNA sequences.
They are used in gene annotation for the determination of gene coding regions.
What are ‘ESTs’?
Expressed sequence tags (known mRNA sequences that are inferred from sequenced cDNA)
How can the function of a gene be determined?
- Compare it to genes of a known function.
- Sequence it and predict its shape and thus possible binding sites
- Block or disable the gene and see how this affects phenotype.
What are all the proteins encoded by a genome called?
The ‘proteome’
What is a ‘proteome’?
All the genes encoded by a genome
What is the analysis of a proteome called?
Proteomics
What is an analysis of all the proteins encoded by a genome called?
Proteomics
What is proteomics?
An analysis of all the proteins encoded by a gene
How long is a typical bacterial genome?
between 1 and 6 million base pairs (Mb)
What does ’Mb’ refer to?
Million base pairs
How long is a typical archae genome?
1-6 mb (same as bacteria)
How long is a typical eukaryotic genome?
Yeast have 12 Mb, Fruit Flies have 165Mb while humans have 3,000 Mb
How many genes does a typical human have?
22,000
How does number of genes per Mb vary between organisms?
It is generally much higher in bacteria and archaea than it is is eukaryotes. Complex eukaryotes i.e animals tend to have the fewest
How does the number of genes vary between organisms?
Bacteria tend to have 1,700 to 4,400 whereas humans have only 22,000
What explains why humans have so few genes and why we have not many genes per Mb?
- Large sections of non-transcriped “junk” DNA increases length and thus allows crossing over to occur
- Alternative RNA splicing leads to new proteins without more genes
- Variation in the way carbohydrates are added to proteins increases the number of forms
- The effects of miRNA
What are pseudogenes?
Former genes that have accumulated muta- tions over a long time and no longer produce functional proteins
What are former genes that due to an accumulation of mutations no longer produced functioning proteins called?
Pseudogenes
What is much of the non-coding region of DNA composed of?
repetitive DNA
What is ‘repetitive DNA’
Sequences that are present in multiple copies in the genome.
