Microbial Genomes Flashcards
Central dogma of life
-all cells store their genetic information as DNA
-dna replication is the first step in cell division
-genetic info of DNA is copied to RNA in transcription
-open reading frames from mRNA are converted to proteins via translation
-non encoding RNAs such rRNAs are not converted to proteins
DNA structure
-polymer comprised of strings of nucleotide monomers
-nucleotides are comprised of 4nucleobasesattached to deoxyribose which carried a phosphate
-nucleosides lack a phosphate group
-nucleosides are connected via phosphodiestee bonds
-all linear DNA has a 5’end and a 3’ end
-two complementary DNA strands run anti parallel
DNA base pairs
-C and T are pyrimidines
-A and G are purines
-AT base pairs has a weaker interaction with 2 hydrogen bonds
-CH base paid has a stronger interaction with 3hydrogen binds
-base paring alllws identical copies to made and for information to be converted to RNA and protein
Differences between DNA and RNA
-RNA contains 2’ hydroxyl group on its ribose sugar that is absent in DNA
-THIS MAKES RNAless chemically stable since the 2’ OH can attack sugar phosphate backbone casing hydrolysis of the phosphodiester bond
-T replaced by U similar but lacks a methyl group
-RNA usually single stranded
Structure of prokaryotic chromosomes
-chromosome circula, not simple relaxed circle - extensive supercoilig
-many proteins involved in structring the chromosome
-required to make DNA compact enough to fit
nuceloid
- region of cell containing the nculeus
-not membrane bound but similar concept of nucelus
-prokaryotic
organization of prokaryotic genomes
-bacteria and archaea almost alway have one circular chromosome
-vibrio cholera has two circular chromosomes
-streptomyces have linear chromosomes
organization of eukaryotic genomes
-multiple linear chromosomes
-saccharomyces cerevisiae has 16 chromsomes that vary in size
-eukaryotes (including mcirobes) generally have larger and less compact genomes than prokaryotes (few genes per kb)
-eukaryotic microbes are smaller and more compact genomes than higher eukaryotes because they have fewer introns
genes and genomes
-85-90% protein coding genes
-genes can run in either direction and can overlap
-genes often organized into functionally related clusters
-genes of a related function can also be scattered around chromosome
genes
-segments of genetic material that encode a functional protein or RNA
core genomes
-genes present in all members
-usually conserved genes important for biology of that lineage
-present in all genomes
genome composityion
-in prokaryotic genomes as size increases so does number of genes
-some funtions like translation and DNA replication essentially constant in all genomes
-genes that encode specialized functions for adapting to different environemnts or operating in different lifestyles increase in larger genomes
genome sizes
-endosymbionts and parasites can have very small genomes and rely on host for many functions
-mycoplama has a very small genome (smallest genome capbable of independetn life?)
-free living bacteria have larger genomes (ie ecoli)
-some bacteria with complex life cycles have genomes as large as 15Mb
functionally related clusteres
-function of surrounded genes can offer insight into a genes function
pan genome
-all genes present in any member
- any gene in any and all genomes
core and pan genomes of salmonells
-many lineages of salmonells that have different ecologies and virulence proeperties
-they all share a lot of common genes important to. basic salmonella lifestyle (core)
-different lineages also encode many unique genes that give them their unqiue properties
genomic islands
-unique genes of a particular genome often dound in blocks of genes
-large blocks = genomic island
-small block = genomic island
synteny
-genomes of closely related lineages often exhbit significant synteny
-homologus genes arranged in same order in their genomes
-often represented horizontally acquired genes
-in many cases the genes have a related function that confers that lineage with umique properties
salmonella pathogenicity island
bacyeriphages
viruses that infect bacteria
-archaea are also infected by similar viruses
prophages
-some bacteriphages known as temeprate phage can integrate into bacterial genomes where they become part of the genome called prophage
-prophage content can vary from strain to strain
-prophage can carry cargo genes that have nothing to do with phage biology-can provide bacterial. host with usrful new genes
-many important bacterial toxins are encode by prophages
plasmids
-typically ciruclar DNA molecules and replicated in cytoplasm
-encode non essential accessory genes
-genes important under certain conditions such as AMR
-vary in size
-can vary in copy number
-contain genes to ensure their replication using host DNA replication machinery
