Genome Features and Transposition Flashcards
What makes up a genome?
- DNA or RNA
- Genes- encode biological information
- Genome replication/segregation – to allow genome to be inherited
What is c-value?
• Amount of DNA/number of kilo-bases per haploid cell
What types of organisms have the smallest genomes?
• Viruses
How does polarity of virus genomes affect transcription?
- +ve can be translated immediately by host machinery
- –ve requires synthesis of +ve RNA using viral encoded RdRp
What can make up the viral genome?
- Genes for genome replication (e.g. polymerase)
- Genes for coat proteins
- Genes that reflect different life history (lytic vs lysogenic)
What characterises prokaryotic genomes?
- Uni or multi-chromosome number (in nucleoid)
- Circular mostly, sometimes linear
- Small
- No histones
- High gene density
- Most non coding regions for gene regulation (e.g. promoters)
- Not much repetitive DNA
- Operon structure
- Genome size varies but gen density relatively constant
- Chromosome type and number varies
- Sometimes plasmids part of genome
What other type of genetic material can exist in prokaryotes? What does it encode?
- Plasmids
- Extra chromosomal
- Coexist with main chromosome
- Range of functions encoded
- Dispensable for host function (usually) – not essential to live
Are all plasmids dispensable?
• No, some are considered part of genome
How can the genome be arranged in prokaryotes?
• Loops anchored to protein core then supercoiled to release tension stress
What are non-coding regions associated with in prokaryotes?
• Gene regulation
How does gene density differ among bacteria?
• Relatively constant
What makes up the eukaryotic genome?
• Nuclear and organelle genomes
What are features of the chloroplast genome?
- All circular
- Ds supercoiled DNA
- Similar size and gene content to land plants
- Most genes for photosynthesis
- Chloroplast enzyme subunits encoded for by nucleus
- Operon-like clusters of photosynthetic and ribosomal genes
- Use standard genetic code
What are features of the mitochondria genome?
- Most genomes circular
- Ds supercoiled DNA
- Bigger variation in size but similar gene content to metazoans
- Human mtDNA has codes for oxidative phosphorylation
- Non-standard genetic code
- Yeast mtDNA less compact because of introns and inter-genic spaces
What are nucleoids?
- In organelles, house the genomes
- Variable number of chromosomes inside
- Variable number of nucleoids per organelle
What are features of the nuclear genome?
- Multi chromosome (one two or more copies)
- Linear DNA molecules
- Chromosome number varies but no link to complexity of organisms
- Genome size doesn’t link to complexity
Does genome size correlate with chromosome number in eukaryotes?
• No
How are euchromatin and heterochromatin different?
- Euchromatin (stain light, less condensed, easy access)
- Heterochromatin (stain dark, very condensed, hard access)
How are Facultative heterochromatin and Constitutive heterochromatin different?
- Facultative heterochromatin for different cells expressing different genetic material
- Constitutive heterochromatin for same genetic material in each cell
What is the C value paradox and what does it suggest about eukaryotes?
- Amount of DNA in haploid cell not precisely related to evolutionary complexity
- Similar organisms can differ greatly in genome size
- Suggests variable gene density in eukaryotes and other elements in genome
What are the types of inter-genic sequences?
• Unique and repeated
What are the types of repeated inter-genic sequences?
• Tandem repeats and interspersed
What constitutes the nuclear genome of a human?
- 46% repetitive DNA
- 35% Unique DNA
- 5% introns
- 1.5% Protein-coding DNA
How can genomes vary? How can this be measured?
- By base composition (melt curve analysis, density gradient centrifugation)
- By complexity (re-association kinetics)
- By gene composition (nucleic acid hybridisation)
What is Tm?
• Temperature at which half DNA is ss
What is the relationship between Tm and GC content?
- More GC content = larger Tm
- Stronger bonds so harder to melt
How can melt curves differ between species?
- GC composition differs between species
- Even if same GC composition, nucleotide distribution differs so still different curves