Genome Organisation Flashcards
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
Codon
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.
- DNA Transposons (found in all species - v. abund. in bacteria)
- 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)
Function:
-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)
Function:
-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)
Telomeres
- 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)
Plasmids
- 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
- bacterial plasmids commonly associated w/ antibiotic resistance (can be huge prob.)
- density of genes constant: 1000 bp = 1 gene
- larger genome usu. means more genes (only works w/ prokaryotes)
Transposition
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
