Bioinformatics: Week 1 Part 1 Flashcards
- Genomes – types and differences
- Nuclear genome – in cell nucleus of eukaryotic organisms: Size + ploidy = NB
- Mitochondrion genome: Organellar genome
- Chloroplast genome: Organellar genome
- Endosymbionts/parasites/endophytic bacteria genomes
- Genome sizes and examples thereof, evolutionary benefit of expanding genome
• Most genomes = diploid
• Polyploid e.g., bread wheat
✓ DD of bread wheat was added by humans. Thus, it’s hexaploidy (AABBDD)
✓ Evolutionary benefit to expanding genome:
leads to genome plasticity
that enhances adaption as new functions can be acquired via insertions,
acceptance of transposons and rearrangement of the genome
- Core aims of genome studies is to:
• Establish an integrated Web-based database + research interface
• Assemble physical + genetic maps of the genome
• Generate + order genomic and expressed gene sequences
• Identify + annotate the complete set of genes encoded within the
genome
• Characterize DNA diversity
• Compile atlases of gene expression
• Accumulate functional data, including biochemical + phenotypic
properties of genes
• Provide resources for comparison with other genomes
- Types of genome analyses/studies – also examples thereof
no 4 and no has the same answer
- Genome models and examples thereof and advantages
• Genomic model organisms: organisms that have a relatively small genome.
In many instances the smallest genome is sequenced of a representative
group of organisms e.g., Arabidopsis Italiana has been sequenced because it
has the smallest genome of all dicotyledon species.
Advantages:
It is easy, quick + cost effective to start with smallest genome and use it for reference in studies and expand from it
e.g., Xenopus laevis which is used to manipulate its amount of
egg cells
- Major features of the human genome
No . 6 table
7.1 Model organisms – types
Types of model organisms
Genetic model organisms
Genomic Model organisms
Experimental Model organisms
• Genetic model organisms: organisms from which genetic mapping
populations can be made of; organisms that can be used in population
genetics + can easily locate positioning/locations on chromosomes
✓ Best Genetic Model organism: Drosophila Melanogaster aka fruit fly
✓ Model for development + mapping populations
✓ If mapping can be done, genetic studies follows
✓ Also need mapping populations to find out the genetic composition of the
genome e.g., where are which genes located?
• Genomic model organisms: organisms that have a relatively small genome.
In many instances the smallest genome is sequenced of a representative
group of organisms e.g. Arabidopsis Italiana has been sequenced because it
has the smallest genome of all dicotyledon species. It is easy, quick + cost
effective to start with smallest genome and use it for reference in studies and
expand from it e.g. Xenopus laevis which is used to manipulate its amount of
egg cells
• Experimental model organisms: organisms that is used to manipulate or
insert DNA into embryos
7.2 Model organism 1 and 2 definitions
•Model organism1: non-human species that is extensively studied to understand biological phenomena, with the expectation that discoveries made in the organism
model will provide insight into the workings of other organisms.
•Model organism2: species that has been widely studied, usually because it is easy to maintain and breed in a laboratory setting and has particular experimental
advantages.
7.3 Model organisms - Examples
Rat, mouse, fruitfly, plant, sea urchin, nematode and frog
- Criteria for selection of model organisms – old test
- Genome size: small
- Generation time: lots of new generations in a short time period
- Accessibility: organisms are easily accessible
- Easy to manipulate and study
- Genetics: you must be able to make mapping populations
- Conservation of mechanisms
- Potential economic benefit
8.1 Genome size- evolutionary benefits
increasing the genome size, it increases
plasticity and enhances adaption
New function acquired with insertion of new genome.
• The larger the genome the more ability to acquire more function
8.2 Genome Plasticity
Genome plasticity: genome can allow for insertions, acceptive of transposons and rearrangement.
This enables adaption which increases the survivability of the
species in different environments
Genome plasticity allows changing and adaption for new function
9.1 Organellar genomes – features and applications Mitochondrion genome (7)
• Mitochondrion genome
✓ Double stranded
✓ Mostly circular, but there is linear mitochondrial DNA in some protozoa +fungi
✓ Super coiled
✓ CG content differs greatly with that of nuclear and mitochondrial DNA.
✓ No histones or similar proteins
✓ Multiple copies of genomes in mitochondria located in multiple mei nucleoid
regions.
✓ Gene content is similar in number + function among mitochondrial genomes in different species (but can differ greatly in size)
9.2 Organellar genomes – features and applications Chloroplast genome (7)
Chloroplast genome
✓ Double stranded
✓ Circular
✓ Super coiled
✓ CG content differs greatly with nuclear + mitochondrial DNA
✓ Chloroplast DNA = larger than nuclear + mitochondrial DNA
✓ They are between (80-800) kb but have a large non-coding regions.
✓ Copies of chloroplast DNA varies across species, but there is a universal generic code for chloroplast protein synthesis
9.3 Main difference between plant, animal + fungal DNA:
entire animal genome encodes for product
plant + fungal genomes have extra DNA that does not code for product
