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Flashcards in Genome Organisation Deck (13):

What is a genome?

Genome consists of all the DNA w/in the cell (i.e. the chromosomes)
-majority of bacteria have singular chromosomes
-also not always DNA - can be RNA (many viruses have RNA)
-smaller organisms will have smaller genomes
-ranges in size across kingdoms & phyla


Bacteria Genome

-Most have circular chromosome w/ single DNA molecule several million bp in length (some have multiple chromosomes & few w/ linear)
E. coli:
-double stranded ring
-Can have genes on both strands
-Most of space on single chromosome taken up by genes, are efficiently organised (referred to as a COMPACT GENOME)
-approx. 5000 kbp (is relatively small - is why E. coli is good to work with)


Define Gene

Gene = part of DNA that encodes a product that carries out a role in the cell
-definition of gene can be debatable as 1 gene can encode multiple products.
-start position determines the product - can get 3 diff. products from 1 sequence depending on starting nucleotide.

Products either structural (ribosomes, cell wall, RNA [RNA has regulatory function in cell]) or functional (enzymes)


How cell knows where a gene is

Open Reading Frame


Prokaryote Gene organisation

-Need signals at start and end of gene to tell where protein begins & ends
-Open Reading Frame: region that encodes the protein
-starts with an ATG (or AUG in RNA) start codon & ends w/ a stop codon (UGA, UAA, UAG)
-Codon: group of 3 bases/nucleotides that are read together
-Polygenic Operons: common in prokaryotes (e.g. lac operon) - where a group of genes are turned on or off together.
-If cell can't make on of genes, switches operon off (ensures resources aren't wasted)
-Genes co-transcribed, but translated separately (might need different amounts)
-Prokaryotes tend to have genes w/in genes


Eukaryotic Genomes

-Tend to be larger than prokaryote
-Multiple linear chromosomes (prok. tend to have circular)
-No relationship between size and complexity
-DNA comes from nuclear, mitochondrial and chloroplast (in plants)
-although DNA from the latter 2 is small, there can be many organelles w/in cell - so it adds up
-Most of DNA is non-coding & many genes interrupted by introns

Segmental duplications: Regions greater than 1000bp that are almost identical in sequence (esp. in multicellular organisms)
-make up approx. 4% in humans.


The Human Genome

-Intron definition

~3.2 x 10^9 bp
-28% transcribed to RNA - only 1.25% encodes proteins
-Human introns longer than other organisms
-45% genome = parasitic DNA (sines, retroviruses, transposons)
-Variable nucleotide repeats (used for fingerprinting) ~3%
-8% is duplicated segments
-Number of genes = 25000 to 70 000

*Is a lot of spare space and parasitic DNA in eukaryotes

INTRON: Non-encoding segment of DNA w/in a gene
-sometimes makes up larger amount than actual gene
-Can get alternate patterns of splicing which gives variant forms of the protein (i.e. 1 version where intron is retained, another version where it is removed)


Mobile Elements (2)

Mobile Element: A type of DNA that can move around w/in the genome.

1. DNA Transposons (found in all species - v. abund. in bacteria)
2. Retro Elements (Or retrotransposons) - those that transpose through a RNA intermediate (needs reverse transcriptase)


Transposons - Characteristics & Functions

-Characterised by inverted repeats (CTAG........GATC) on either side of transposable element [3-12bp long]
-NOT part of element & DON'T move with it
-Range in size from 1 - 100kbp
-Carry multiple antibiotic resistant genes
-Makes up approx. 43% of our genome
-Limited by methylating DNa in regions where transposons common (methylation usu. suppresses transcription)
-Major drivers of evolution of the genome (opossum seems to have evolved separately - genome consists of only 2% MGEs
-low amounts of MGEs generally = low amounts of evolution

In human Genome:
-lots more than just genes - are a lot of repeats (e.g. tandem repeats)


Tandem Repeats

-Short sequence motif that is repeated multiple times.
-Repeat 1 - 15 bases long
*Can be several thousands of repeats at a locus
-Are the mini satellites and microsatellites (are a v. sig. portion of the genome)
-Mainly occur at telomeres and centromeres
-no. @ locus is highly variable w/in a species (i.e. between individuals)
-unknown - are used for forensic DNA fingerprinting and parental idenfication
-Bacteria & viruses don't have them - different species have different amounts.


Retro Elements (retroviruses)

-Move via a RNA intermediate (called retro because go from DNA -> RNA -> DNA)
-reverse transcriptase responsible (all cells have this enzyme)
2 Consequences:
-Development of psuedogenes: mRNA transcript of gene spontaneously reverse transcribed back into chromosomal DNA (psuedo b/c doesn't have coding region/regulatory proteins)
-RNA in food (external source) can be integrated into genome (via cDNA)



-Structure at ends of chromosomes that protect the chromosome from damage - w/out them enzymes w/in cell will chew up DNA & degrade it [linear]
-bacteria's circular DNA solves this prob.
-Involved a complicated folding of DNA at ends
-Also provides means of replicating ends of chromosome
-Sequences synthesized by telomerase (enzyme)



-Small, usu. circular DNA molecules
-Are replicons found in cell in addition to the chromosome
-found in bacteria, plants, animals & fungi
-bacterial plasmids commonly associated w/ antibiotic resistance (can be huge prob.)
-can move from species to species & carry multiple resistances between species
-can be used to clone DNA
-density of genes constant: 1000 bp = 1 gene
-larger genome usu. means more genes (only works w/ prokaryotes)



Transposition: Movement of a transposable element from one location to another
Common features;
-Staggered breaks made in target DNA
-Transposable element is joined to ss ends of target DNA
-DNA is replicated at ss gaps

-transposase enzyme used to make staggered breaks in DNA & to integrate transposable element into new site

Transposition may be;
-Replicative: new copy of trans. element introduced at a new site while old copy remains at original site
-Non-replicative: Trans. element excises from old site and inserts at new site w/out an increase in the number of copies

*retrotransposons use relicative only