micro exam 2

bacterial chromosomes

• DNA bent into lobes

  • makes some parts of the DNA more accessible than others

  • each lobe can be called a domain

DNA structure

• polymer of nucleotide monomers

• double stranded helix

  • pair bonding: w/ antiparallel strand, but can also loop & bond to itself

• supercoiled

  • packaging into small space

  • coiling & uncoiling

DNA replication in bacteria

• NO mitosis! - no lining up & separating

• make copy of chromosome & cell splits down the middle

• no introns to remove, no splicing, no RNA processing

  • more straightforward & faster

• euks have more flexibility & customizability (ex. if they want membrane bound proteins vs free, can splice to make that happen)

• NO histones

  • have DNA binding proteins that wind DNA similarly

• inverted repeat: same thing but backwards (complement)

  • stem loop structure

• melt DNA: makes 2 strands dissociate

  • temperature range is small - comes apart at once

  • temp depends on how many A-T vs C-G

supercoiling and domains

when looping, bacteria can make double stranded break (via DNA gyrase) & tie it so it is permanently supercoiled

genetic elements

• bacterial chromosome

  • usually circular

  • 0.6-10 mb

  • contains most or all genes

• plasmids

  • small, independently replicating of chromosome

  • carries non-essential genes (DON’T want to put critical genes on plasmids bc they sometimes get lost)

  • easy to move

  • come & go

  • HAVE to have place to start replication (ori)

• transposons

  • mobile genetic elements

• viruses

  • have protein coated extracellular form to travel between cells → different from plasmids!

  • obligate intracellular parasites

DNA replication

• requires:

  • template

  • primer (DNA pol 3 doesn’t know how to start replication w/o)

  • nucleotides

  • enzymes:

    • DNA pol:

      • DNA pol 1

      • DNA pol 3: does most of the replicating

    • helicase: unwinds helix

    • primase: lays down promers

    • ligase: seals nicks in DNA

    • single stranded binding protein: keeps strand from tangling

semi-conservative: parent strand is a part of the new daughter strand

theta structure: circular chromosome replicating

replication fork

origin of replication

replication proceeds 5’ → 3’

lagging & leading strand: bacterial complex does lagging & leading strands at the same time

once replication is done, still have to add finishing touches:

• DNA pol 3 doesnt have exonuclease activity: cant break down primers

• so DNA pol 1 comes in, removes RNA primer, & replaces it w/ DNA

• DNA ligase then ties last bond together

proofreading

• DNA pol 3 sometimes makes mistakes

• strand bulges & DNA pol feels that & fixes mistake:

  • has 3’ → 5” exonuclease activity, goes back, cuts wrong nucleotide, & adds right one

• proofreading polymerases are more accurate but slower

transcription

• DNA → RNA

• different types of RNA transcribed:

  • mRNA: messenger

  • rRNA: ribosomal

  • tRNA: transfer

• coding region: translated into polypeptide

• regulatory region: determines whether the gene will be expressed

• untranslated region (UTR): where formatting info is

• contains transcriptional start & stop points - only reads certain regions vs replication that reads everything

• bacterial polymerase is much different than euk

• transcribes RNA complement of DNA strand

• process of transcription:

  • requirements:

    • DNA template

    • RNA polymerase

      • core enzyme: α, α, β, β’

        • does the transcribing, but bad at recognition

      • holoenzyme: addition of σ factor

        • σ allows for promoter recognition

        • different σ allows RNA polymerase to recognize different genes (regulates genes)

    • nucleotide bases

  • initiation: RNA pol & σ bind to promoter

    • promoter: specific sequence of DNA, where transcription starts

      • consensus sequence: mostly the same sequence

        • the more similar the sequence is to ideal, the stronger the promoter & the more often that gene is expressed (regulation)

  • elongation: RNA pol opens DNA helix, adds, & joins new bases

  • termination: RNA pol comes across terminator & leaves DNA

    • stem loop: common terminators

units of trascription

• operon: multiple genes controlled by one promoter

  • often regulated by operator

  • used for speed, not precision (ex. precision of number of specific products: genes on operon often work together, but if one product dies, then can’t precisely bring up the # of that specific product)

    • ex. rRNA genes (16S, 23S, 5S) are transcribed together

• ORF: open reading frame

  • long run w/ no terminator

  • place where gene probably is

• euks add 5’ caps & poly A tails to protect product, but bacteria don’t bother - wastes too much time & energy

translation

• making proteins from mRNA

• requirements:

  • mRNA template

  • tRNA for each amino acid

  • amino acids

  • ribosomes

  • other proteins

    • elongation factors

    • releasing factors

    • chaperones

• anticodon on tRNA recognizes codon on mRNA

• cant go backwards & make RNA from proteins: there are many different codons that code for the same amino acid

• tRNA:

  • contains internal base pairing

  • some bac dont use all codons so they dont have to make as may tRNAs

• importance of reading frame: ribosome must start at proper base or else will translate gibberish (frameshift mutation)

ribosomes

• large complexes

• most RNA in cells is rRNA

• contains subunits:

  • large: 50S

  • small: 30S

• lots of antibiotics act on proteins in ribosomal subunits (bc theyre different than eukaryotic subunits)

• some bac dont start at AUG (Met), some start at a Lysine

• stop codons dont code for an amino acid

folding and processing

• proteins fold as they leave the ribosome, but some need additional work:

  • processing: add things (sugars, lipids, carbohydrates) & fold more to make finished products

  • once folded, cant be replicated once protein denatures (ex. bac have trouble w/ heat shock bc have no control over internal temp)

• chaperones: makes sure proteins dont un-fold/go somewhere theyre not supposed to & form plaques

  • can help proteins fold properly

  • use ATP

selenocysteine & pyrrolysine

• non-standard amino acids

• additions added to amino acids post translationally

protein secretion

• bac dont have vesicles, so how to proteins get across membrane?

• have specialized secretion systems

• using ATP to move proteins across the membrane

gene regulation

• cells need to adapt to their environment

• efficiency:

  • want to scavenge molecules over making it themselves

• regulate product at different levels

  • regulate enzyme

  • regulate gene (turn it off)

  • make transcript, but dont translate it

• some genes expressed constitutively

feedback inhibition

• protein, not DNA - affects enzymes, not genes

• end product shuts down process (homeostasis)

  • end product acts as regulatory molecule

• often allosteric - 2nd site on enzyme that regulates function

• inhibits at the beginning of the pathway - so cell doesn’t waste energy making products it’s not going to use

• shared pathways can cause issues - if there’s a lot of one amino acid being made, it can shut down the pathway for other amino acids & cause deficiencies

covalent modification

• covalent bonds are harder to make & break

• allows for dial efficiency of enzyme - dont want all or nothing, sometimes only want a bit

  • do when having too much/too little of a product are equally as bad

inteins

• protein

• sometimes make a protein that should’ve had an intron that should’ve been spliced out, but they read thru for efficiency & splice at the amino acid level

• free piece is often regulatory

regulation of translation

• message stability

  • mRNA degrades rapidly: after translated, don’t need it anymore, & if it’s around for longer than needed, may produce more product than intended

regulation of transcription

• regulated by DNA binding proteins: sequence specific

  • transcription factors

  • often dimers

  • binds DNA (often @ major groove) & sterically hinders anything from binding

  • several types:

    • zinc finger

    • helix-turn-helix

    • leucine zipper

  • since genome is so large, common to run across the same sequence (just by chance), so have inverted repeats spaced specifically apart to make sequence more rare

repression

• regulatory sequence usually next to promoter

• operator: often between promoter & genes

  • if protein (repressor) is bound to operator, then RNA polymerase is blocked

• ex. arginine synthesis

  • repressor needs co-repressor to bind

    • co-repressor is often what you’re making (feedback inhibition)

  • w/ things like arginine, default of operon is on bc w/o arginine, you die

induction

• presence of substrate stimulates transcription

• default is off

• by positive control:

  • ex. maltose operon

    • controls transcription of enzymes that digest maltose

    • dont want to have enzymes around when they arent needed

    • promoter is weak, needs activator protein which needs inducer (maltose!) to bind

• sometimes activator binding site & promoter are right next to each other, other times, they’re not - DNA has to fold to bind

• by de-repression:

  • lac operon: default is off

    • repressor protein default is to bind, then when inducer binds, repressor falls off & transcription proceeds

    • also has additional layer of regulation: glucose

    • lac operon is off even when lactose is present, but only when glucose is also present

      • preferentially use glucose, lactose less efficient energy source

      • presence of glucose inhibits cAMP formation

      • cAMP + CAP binding is required for RNA polymerase binding, so w/o cAMP, CAP cant bind & operon is off

global control (of transcription)

regulation responds to cell’s overall state rather than a single gene’s signal

• catabolite repression: use the best form of energy first (glucose)

• stringent response: amino acid starvation, tells the cell “you’re dying, start breaking things down for energy & don’t synthesize/replicate”

• heat shock:

  • layers of regulation, 1st: overarching regulation, 2nd: more specific

  • layers at RNA level to detect temp

    • only translate if temp is above threshold

2-component systems

bacteria sense environmental signal & change gene expression in response

1. sensor kinase

   • in cytoplasmic membrane

   • binds substrate outside of cell - detects environmental signal

   • adds phosphate when it senses something

2. response regulator

   • what is phosphorylated by sensor kinase

   • brings DNA & activates/represses transcription

phosphatase

bacteria do this bc they dont have a nucleus, so they can put these things right next to each other

porins

• the size of porins depend on osmolarity of environment

  • if in gut of bear: lots of nutrients, but lots of toxins ∴ need small porins

  • if in stream: not a lot of nutrients ∴ need large porins

  • need to adjust porin size based on environment

quorum sensing

• bacteria behave differently if it’s by itself or in a group

  • autocrine: secrete & respond to compound (if bac is by itself, there is nothing to respond to)

    • uses as a measure of cell density & adjusts behavior based on density

      • cells will hide more it it’s alone, but if in a group, can send out group toxins

chemotaxis

• movement towards/away from chemicals

• changing direction of flagella motor

• regulation of protein function, not gene transcription

• have collection of methyl accepting chemotaxis proteins, they get methylated to change phosphorylation cascade to suppress motor switching or stall it

• makes small adjustments in real time

viruses overview

• obligate intracellular parasites

• steals cellular machinery to make more viruses - lack their own metabolic pathways

  • stops cells from doing what they’re supposed to do

• protein encoded extracellular form to move from cell to cell

• most are very small

viral nucleic acids

• viruses have different ways to store their genes:

• some are DNA:

  • double stranded

  • single stranded:

    • pos: less to carry

    • neg: no backuo

• some are RNA:

  • double stranded & single stranded

  • pos: no transcription ∴ dont have to carry the genes for this task

  • neg: not stable, difficult to maintain

• some shuttle between DNA & RNA

  • retroviruses: RNA → DNA, rare, weird

    • have to bring their own polymerases bc host cells cant carry out this action

viral structure

• virion: extracellular form

• core: contains genetic material (nucleic acid - DNA or RNA), & sometimes a few proteins

• capsid: proteins that surround genome

• envelope: lipid bilayer surrounding capsid

  • made from stolen lipids: piece of cytoplasmic membrane from last host cell - only found in animal viruses (bc they font have cell wall ∴ virus can peacefully leave cell instead of blowing it up)

viral shape

• capsids self assemble

• helical: plant & bacteria viruses

  • length determined by genome size

  • ex. tobacco mosaic virus

• icosahedral: sphere made of planes

  • enveloped or naked

  • ex. HPV

• complex: combining forms

  • icosahedral head & helical tail

  • ex. bacteriophage

viral life cycle

1. attachment

   • critical, why viruses are species specific

   • very specific - virus binds specific receptor on specific host cell

     • can only do one thing, only knows how to run one type of machine

   • when they jump species, usually bad: covid, rabies

2. penetration

   • injecting genome/DNA/RNA into host cell

   • bacterial: only nucleic acid is injected

   • animal: whole virion is engulfed

3. uncoating

   • only in animal - capsid is removed

4. synthesis

   • making components to create new viruses

   • early proteins, nucleic acids, late proteins

5. assembly

   • putting together components to create new virus

6. release

   • usually lysis

plaque assay

• plate lawn of bacteria-phage mixture

• bacteria create lawn of growth except for plaques

  • plaque: place on lawn where bacteria dont grown bc virus causes bacterial cells to explode

viral replication

• how viruses replicate varies on type of viral nucleic acid

  • ex. DNA/RNA, double/single stranded, coding (+)/non-coding (-)

• sometimes can use host cell’s enzymes, sometimes have to bring their own

  • if virus has RNA genome, host cell doesnt have enzymes to replicate RNA

• double stranded intermediate still required for single stranded viruses

one step growth curve

plaque forming units appear suddenly - virus replicates silently inside cells until they lyse & release many viruses at once

viral overlapping genes

• viruses have small, efficiently designed genomes

  • genes/enzymes/proteins virus needs/uses first gets translated first, when stuff it uses later gets translated later

• some open reading frames (ORFs) overlap - risky but has pros

  • increases number of genes per kb of nucleic acid - allows virus to remain tiny

  • complicates transcription & replication

bacteriophage

• have to think ahead:

  • since virus builds itself inside host cell, & outside host cell it cant do anything on its own - it has to pack itself w/ everything it needs in order to infect new host cell once it’s on its own

    • ex. pack w/ ATP/energy to infect host cell

• concatemer: long, continuous DNA molecule that contains multiple copies of the same DNA sequence

  • host cell replicates viral genome via rolling circle replication

  • bacteriophage cuts up genome to package into separate viruses - just hoping that each one has intact genome

    • since they make billions of copies, it’s ok if a million don’t work

• infection of bacteriophage:

  • tail fibers bind to specific part of host cell (most likely LPS)

  • tail fibers retract when they hit the right surface (retract using prepackaged ATP)

    • retraction allows for teeth to meet cell

    • remade tension in tail hammers through bacterial peptidoglycan layer to allow for genome to be injected into the cell

viral receptors

• flagella, mating pilus, iron transport protein, ACE 2 (covid)

• uses a piece of the cell’s physiology

  • cells dont evolve receptors for viruses to use, viruses find something cell already has to use for infection

lambda

temperate bacteriophage: can alternate between lytic life cycle & lysogenic life cycle

• has double stranded DNA

lysogeny

• doesnt kill host (at least not right away)

• viral DNA integrates into host chromosome

  • lambda DNA cuts to create cos sites (sticky ends) that match the host cell’s DNA

  • ligates own DNA into host: prophage (when virus is integrated into chromosome)

  • every time cell replicates, it replicates virus too

• stays dormant in host cell until host starts to die/conditions dont look good

  • then turns lysogenic path into lytic path (removes itself from genome, replicates itself, packages, & blows up host)

animal viruses

• classified by type of nucleic acid & presence of envelope

• no relationship between shape/size & deadliness

• pathways of infection:

  • lytic: infect, replicate, & immediately lyse

  • persistent: cells survive & continue to produce virus, only making a few copies slowly

  • latent: delay between infection & symptoms - goes dormant until something happens & virus decides to replicate

  • transformation: changes cell to cancer cell

• animal cells dont have cell wall ∴ virus doesnt have to blow up cell to get out

(+) RNA viruses

• virus genome is essentially mRNA

  • high risk, but allows for small genome to move across cell membrane quickly w/o trouble

• lots of viruses are single stranded RNA

• (+) strand = coding

• (-) strand = non-coding, complement to (+)

• viral RNA looks like the cell’s own RNA, so when given to ribosome, it will translate it

• BUT virus has to bring its own polymerase to replicate RNA from RNA

• ex. poliovirus does this

  • only has 7 genes

• w/ virus only having (+) RNA strand, sometime in lifetime HAVE to make (-) strand to replicate more (+)

  • SO at some point, virus has to become double stranded RNA, which host cell doesnt have, so host knows immediately it is foreign & can eliminate

(-) RNA viruses

• genome is complement of mRNA

• ex. rhabdovirus - rabies

• ex. influenza

  • genome is broken up into fragments that can be traded out/easy for gene exchange (why we need flu shot every year)

  • 2 proteins on surface of influenza cell

    • hemagglutinin: clumps blood cells

    • neuraminidase: shaves membrane to leave

double stranded DNA viruses

• enveloped

• herpes virus

  • latent/dormant in neurons

• pox virus

  • small pox (30% mortality rate) - irradicated

  • large, complex viruses (~300 genes)

retroviruses

• enveloped

• (+) RNA → DNA

  • uses reverse transcriptase to use RNA template for DNA synthesis

  • then uses host polymerase to make double stranded DNA

  • then integrates into host genome (long latency period)

• very few RNA viruses are retroviruses

• ex. HIV

viruses in plant cells

since plants have plasmodesmata, some viruses dont bother to even leave cell, just moves between from cell to cell

prions

infectious protein

forces host proteins to misfold (misfolding leads to abnormal function)

DNA mutation

• change in nucleic acid sequence

• rare at any particular nucleotide, but we have a lot of them, so its bound to happen

• bacterial mutations are “easy” to detect bc haploid

• genes named: gldA, gldB…

• proteins named: GldA, GldB…

• mutants often named: Gld- or ∆gldA

types of mutations:

• substitutions: replacement of one base w/ another (ex. A for G)

  • can be silent: no change in phenotype

  • can be missense: change on amino acid

    • can cause faulty protein

• insertions & deletions: frameshifts

• revertants: mutations changed back to wild type, not intentional (but good)

• suppressors: compensatory mutations show up in another part of the pathway to help the cell work even with the mutation

mutation rates:

• viruses have more mutations than other microorganisms bc they focus on being small & fast, not accurate

• RNA genomes are way more prone to mutations - RNA repair mechanisms dont exist

mutagens

• anything that increases the rate of mutation

• ex. chemical, radiation

• called carcinogens in humans

• base analogs

  • looks similar to normal nucleotide, can be added into strand & cause the wrong nucleotide to be added

SOS system

• RecA: protein, primary sensor & activator of SOS response

• LexA: represses DNA repair mechanisms

  • when LexA comes in contact with RecA, it degrades, allowing for DNA repair mechanisms to start

• during double stranded breaks - have error prone repair pathway

  • error DNA is better than no DNA - last resort

ames test

• asks: does this compound interact w/ DNA that causes damage

• filter paper w/ compound you’re testing to see if it’s a mutagen

• using auxotroph

  • mutant that has defect in some metabolic pathway

  • requires specific nutrient to grow bc it doesnt make it

• plate auxotroph on plate w/o nutrient it needs

  • see some colonies: mutants (either revertant/suppressant)

  • only see colonies if mutation occurs

transposons

• mobile genetic elements

  • movement is mediated by insertion sequences (IS)

  • IS can move by themselves

  • genes can be sandwiched between insertion sequences

    • transposase

    • often antibiotic resistance genes

  • can have inverted repeats: if at the ends of a sequence, most likely the sequence that moves

  • transposons can:

    • move & take genes with

    • move & disrupt genes (& promoter issues)

    • duplicate genes

      • can be good: another copy of gene in case one breaks

        • can give evolution a set of genes to play with to evolve (can sometimes evolve up a new capability)

      • can be bad: get too many products

Tn4351

• transposon found in Bacteroides

• carries 2 antibiotic resistance genes that are found in 2 different phylum of bacteria (Bacteroides & E.coli)

• suggests that this transposon has been in both E.coli & Bacteroides & picked up these genes on its way

bacterial DNA transfer

• in theory: all bac are identical bc of binary fission

• but can transfer DNA horizontally: transfer DNA from one organism to another

  • vs vertically (transfer DNA from one generation to the next)

  • fairly common

  • spread of antibiotic resistance genes

  • multiple mechanisms

1. live cells can pick up genes from dead cells

   • ex. live S cells kill mice, heat killed S cells have no effect, live R cells have no effect - but combining live R cells & heat killed S cells kill mice

   • R cells have taken up genes from S cells to become deadly

2. bacteria can grab free floating DNA

   • ex. Trp- cells are unable to grow on plates lacking tryptophan, but adding Trp+ DNA into solution, Trp- cells are able to uptake the DNA & form recombinant colonies

recombination

• physical exchange of DNA

• DNA fragments (other than plasmids) must integrate into the chromosome to be maintained - if not, it is broken down to nucleotides for the cell to use

• mechanism: donor DNA & recipient DNA requires some sequence homology

  • after recipient DNA is nicked, can combine w/ chromosome: strand invasion

  • strands are then weaved together & nuclease has to come in & fix - but doesnt really know which strand is which, so it doesnt revert back to the original sequence

  • some of recipient DNA is now a part of chromosome

transformation

• when cells die, DNA gets broken up into ~50kb fragments

• free naked DNA is floating in solution

• competent cells can uptake these strands

  • can be dangerous (if strands are viruses), but good for uptaking nucleotides (expensive to make from scratch)

1. DNA binding proteins on outside of cell ONLY when cell wants to uptake DNA (competent cells)

2. nuclease degrades one strand as it’s entering the cell (making it single stranded

2.5. if there is homology, sometimes pair bond & piece of DNA is incorporated into chromosome: RARE (but also common bc so many bacteria)

3. breaks down strand to chew up for nucleotides to replicate own chromosome before replication

• recombination during this process is a mistake in the system (2.5)

• DNA transforms better when organisms are similar bc more chance of sequence homology for recombination

transduction

• DNA transfer from cell to cell through a virus (phage)

• bacteriophage cant tell which DNA is its own - only looks for DNA that is the right length

• during viral DNA packaging, the virus can mistakenly package the host DNA instead of its own genome

• the bacteriophage then infects a new cell w/ the host cell’s DNA

  • bc bacteriophage only targets specific cell type, so cells are similar ∴ high chance of homology & chance of recombination

• bacteriophage doesnt want this bc doesnt help w/ replication

specialized transduction

• when bacteriophage integrates its DNA into host chromosome, when it takes it out it can sometimes take up a few kb of the host chromosome & replicate it

  • then packages & injects bacteriophage DNA + part of host chromosome into new cell

  • bc phage only cuts certain amount of DNA, part of phage’s own genome is often left behind - usually makes phage defective

  • this part of bacterial chromosome is then transferred to another bacteria allowing for horizontal gene transfer

plasmids

• replicate independently of chromosome

• usually circular

• small (1-1,000kb)

• bacteria make their own plasmids

• have copy numbers of 1-100 (chromosome copy number is 1)

• incompatibility groups: “this town ain’t big enough for the both of us”

  • two plasmids are not able to inhabit same cell at the same time

• transfer from cell to cell by conjugation

  • conjugation: DNA transfer through cell to cell contact

    • involves pilus (donor cell produces sex pilus)

    • replicative transfer: both cells end up w/ copy of plasmid

    • can “mobilize” parts of the chromosome

• types of plasmids:

  • resistance: carry genes for antibiotic resistance

  • virulence plasmids: carries genes that makes the virus worse

    • turns harmless/less harmful viruses into worse strains

• HAS to have origin of replication - can use host enzymes to replicate, but need to have its own ori

• once a plasmid gets a resistance gene, it tends to collect many others

  • resistance = incentive for cell to keep plasmid around

• uses: can add any gene/DNA into plasmids & they will replicate inside bacteria

  • ex. human insulin

• plasmids are different from lysogenic viruses bc plasmid doesnt make protein encoded extracellular form: cant go outside the cell

F plasmid

• conjugative plasmid in E.coli

• can integrate into chromosome & recombine

• was used to help map E.coli genome:

  • plasmid was integrated into known spot, cells allowed to mate for specific, increasing times, then interrupted & read genome

• bacterial DNA is very plastic - can lose/gain pieces of chromosome really fast

restriction endonucleases

• cause double stranded breaks in DNA at specific sequences

• defense mechanism against viruses

• methylation of DNA protects own DNA

  • host cell methylated own DNA to prevent cutting at restriction enzyme sites

  • if cell encounters piece of DNA that isnt methylated, it knows it’s not its own, so it chops it up (ex. viral DNA)

• recognizes 4-8 base pairs

cloning

• gene of interest is isolated on a plasmid so we can use it

• vector: usually plasmid - thing you dont care about that carries the gene you do care about

  • plasmids are good bc:

    • replicate independently of chromosome

    • can insert into any cell we want

PCR

• technique used to produce large amounts of specific sequence

• primer reads template strand one way, while another primer reads the other way of opposite strands to amplify

gene knockouts

• specific genes targeted for disruption

• requires coned gene of interest in suicide vector: cant replicate on its own in host cell

• randomly break genes until you find something important that is necessary for function

  • insert antibiotic resistance gene in the middle of gene of interest: gene is broken, but cell is now antibiotic resistant

    • if you see colonies forming, shows that gene is not necessary

genome size

• looking at the total size of the genome vs the size of ORFs doing each task

  • ex. little genome vs big - only need one gene for polymerase, but different percentage of the genome

• as an organism gets bigger, it needs more of certain genes

  • ex. w/ more things (ex. clothes) comes more decisions to make

  • w/ a bunch of metabolic pathways, have to decide which to turn on

• most pathogens that are dedicated pathogens are usually very small: they lose interesting genes to become specialists

  • ex. criminals are criminals bc they cant do anything else

• core genomes:

  • different species can overlap in specific genes

  • how big does overlap have to be in order to be the same species?