CHAPTER 5

- PARASITES
o Ecto vs endoparasites:
 Ectoparasites live ON the surface of other organisms, ex: ticks and lice
 Endoparasites live IN other organisms, ex: worms
o Obligate vs facultative:
 Obligate: need host for at least some part of life cycle
 Facultative: free living, don’t need a host but can use one
o Permanent/temporary/accidental
 Permanent- once they invade the host they remain on it
 Temporary- feed on host then leave, ex: mosquitoes
 Accidental- invade organism other than their host, ex: deer tick on human
o Hyperparasitism- parasites that have their own parasites
- Vectors: agents of transmission, can transmit disease, different types, ex: malaria needs
mosquito (vector) to move from host to host
o Biological vector- parasite goes through part of life cycle in the vector
o Mechanical- parasite does not go through any part of its life cycle in the vector
- Hosts:
 Definite host: holds the parasite while it reproduces sexually
 Can be an intermediate host, but if the sexual part of the cycle
occurs it is called definite
 Intermediate host: holds parasite during other part of developmental
cycle
 Reservoir host: infected organisms that make parasites available for
transmission to other hosts
 Definite and intermediate hosts can be reservoir hosts
o Host specificity=range of hosts in which a parasite can mature/how many it can
actually infect (ex: some are very specific and only infect humans)
- Ways parasites evade host defenses:
o 1. Encystment- formation of outer covering that protects from environmental
conditions, like an egg that protects the parasite, prevents immune system of
host from recognizing it as a threat
o 2. Changing surface antigens- parasite changes antigens faster than the host can
produce antibodies against it, immune system can’t destroy it
o 3. Invading host cells- immune system won’t attack self
- Eukaryotic cell reproduction
o Reproduction: all have linear chromosomes that divide during mitosis, “ends” of
linear chromosomes require a special means of replication that bacteria don’t
need (they have circular chromosomes)
 Mitosis=asexual reproduction, each daughter cell receives full set of
daughter chromosomes
 Steps: prophase, metaphase, anaphase, telophase
 Meiosis=sexual reproduction, most can also do this
  Sexual life cycles alternate between diploid (2n) and haploid (n)
 2 haploids (gametes) join=diploid cell
o Advantages of haploid and diploid for parasites??
 If its requires a human host, the haploid form requires less resources and
generates fewer varieties of coat proteins that could set off the host’s
immune system
 Diploid form generates combinations of genes that could be
advantageous if the environment changes or the parasite enters a new
host
- Types of MICROBIAL eukaryotes (other multicellular parasites that are NOT TRUE
microbes= helminths and arthropods)
o Fungi: grow in chains called hyphae, absorptive nutrition (digest many complex
plant polymers), most nonmotile
o Microsporidians: spore forming organisms, closely related to fungi
o Algae: protists that have chloroplasts/do photosynthesis, can be single celled or
filaments or sheets
 Ex: chlamydomonas
o Alveolates: protists with flagella or cilia, can be free-living or host dependent
parasites, mostly single cells, complex multilayered outer covering called the
cortex
o Amebas: single celled, highly variable shape, have pseudopods for motility
o Trypanosomes: protists with flagella, complex parasitic life cycles involving
developmental staged within hosts
o Helminths: multicellular worms (roundworms, tapeworms, and flukes)
o Arthropods: insects such as fleas and lice, also non-insects such as mites

- FUNGI AND MICROSPORIDIANS

o Can produce sexually or asexually
 Asexual-
 hyphae fragmentation
 spores- a) condiospore: uni or multicellular, not enclosed in a sack
o b) sporangiospore: within a sack, more organized
 Sexual- fusion of nuclei from 2 opposite mating strains of the same fungal
species to form a zygosporangium (2n)  sporangium will grow from a
stalk off it with haploid (n) spores inside  spores released
o Filamentous fungi: expand by mitosis until they run out of nutrients  undergo
meiosis to form gametes  gametes develop into spores for dispersal
 2 haploid cells fuse to form
the zygote (2n)  (The tips
of the 2n mycelium)
undergoes meiosis to form
haploid ascospores (spores)
within a pod (ascus) 
 mitosis occurs to form 8 spores  disperse until they germinate in a
region with fresh resources / eventually released into environment

 Ex: ascomycete fungi such as aspergillus

o All except yeasts are multicellular
o Chemoheterotrophs
o Multicellular form septate or non-septate hyphae
 Septate=cells separated by cell wall
o Unicellular form psuedohyphae
 Psuedohyphae=not true hyphae, result of asexual reproduction  yeasts
bud out and give rise to smaller cells
 Ex: candida albicans (yeast infection)

o Single-celled yeasts:
 Advantages: rapid growth and dispersal in aqueous environments
 Some are asexual and some alternate between 2n and n forms (both
forms are still a single cell)
 Haploid cells undergo several generations of mitosis and budding
(vegetative growth)
 With lack of nutrients… haploid cells can develop into gametes
and undergo meiosis
o Importance: use cellulases to decompose dead plant matter  nearly all plants
depend on symbiotic fungi (mycorrhizae) to help roots absorb water and
minerals from the soil
 Also- food source, produce antibiotics (metabolic wastes of fungi)
 To invade a host, they need 1) proximity to host 2) ability to penetrate
host 3) ability to digest and absorb nutrients from cells
 Healthy people don’t have many fungal infections because they
are easy to fight
 Only ~200 fungi are human pathogens
o Medically important fungi:
 Important in immunocompromised patients
 Fungi grow slower than bacteria and virusescan cause very bad
infections before you realize
 1. Zygomycota- mainly saprophytes, have coenocystic hyphae and
haploid nuclei, can do sexual or asexual reproduction (usually asexual via
sporangiospores)
 ex: black mold
 Mucor genus- can cause necrotizing infection
 2. Microsporidia-
unicellular fungi,
obligate intracellular
parasites, NO

mitrochondria/peroxisomes/centrioles  need to live inside host cell,

cause chronic diarrhea in humans, spores can pierce host cell membrane
like a needle to invade
 ex: Enterocystozoan bieneusi
 3. Ascomycota- some are edible (mushrooms), others cause food spoilage
or are human pathogens, can have septate hyphae and cup-shaped
fruiting bodies (ascocarps), produce condiospores (asexual reproduction)
 ex: aspergillus sp (allergy or infection), tricophyton, microsporum
(skin infections), penicillin, candida albicans (yeast infection)
 4. Basidiomycota- have basidia (club shaped structures that produce
basdiospores aka spores produced through budding) within fruiting
bodies (basidiocarps), decomposers, lot are human pathogens
o think mushroom head=basidia, whole shroom=basidiocarp
  ex: Cryptococcus neoformans – cause lung infection in
immunocompromised
o fungal infections: mycosis
 systemic mycosis=deep within body
 subcutaneous mycosis=beneath skin
 cutaneous mycosis=hair, skin, nails
 superficial mycosis=localized (ex: hair shaft)
 opportunistic mycosis=caused by normal microbiota or environmental
fungi that normally don’t cause disease but will if given opportunity (ex:
in immunocompromised)
o economic effects of fungi
 saccharomyces cerevisiae: bread, wine, HBV vaccine (can genetically
modify to be a vaccine bc they reproduce quickly)
 Trichoderma: cellulose
 Taxomyces: taxol
 Entomophaga: biocontrol
 Coniothyrium minitans: kills fungi
 Paecilomyces: kills termites, is a yeast, stops growing after termites die

PROTOZOA
- “first animal”
- all unicellular
- some are intestinal parasites  don’t need O2 for growth
- structure:
o all have a plasma membrane (“plasmalemma”)
o some have a pellicle: bands of protein outside the membrane that add rigidity
o some need specialized structures to take in food
 cytosome- to take in food by phagocytosis
 cytoproct- for exocytosis of waste
o some have distinct cytoplasms layers under the membrane called the ectoplasm
and endoplasm
o
- life cycle:
o vegetative form- trophozoite  protozoan in metabolically active growth stage,
actively destroying host, absorbing nutrients from host, can be inside of cell and
feeding etc, some protozoa only exist in this form while others produce cysts
o encystment- similar to an egg or a spore, protects cell during lack of O2 or
nutrient conditions, also happens a lot when changing hosts, cysts are passed in
waste
- reproduction:
 o asexual- binary fission, budding, or schizogony
 SCHIZOGONY= multiple fission, nucleus undergoes multiple divisions
before the cell divides
 Schizont=cell with many nuclei inside
 Merozoites= product of division


o sexual- conjugation (2 haploid cells fuse, micronucleus from each fuses)=
syngamy
- medically important protozoa:
o Metamonada: group of parasites with flagella, lots in aquatic streams, anaerobic
metabolism/no mitochondria, reproduce via binary fission
 Order Diplomonadida
 Example: Giardia Lambia -> STD
 Causes bad diarrhea
o Acquired by contact with cysts in water, food, or hands
o Diagnosed by cysts present in feces
 Trophozoite form also passed in stool but don’t
survive outside
 Found in aquatic streams, spread by animals, anaerobic, have
special type of mitochondria called ‘mitosomes’ (not used for ATP
synthesis like normal mitochondria, do something with iron to
produce proteins they need to survive)
 Each cyst has 4 nuclei
o Each nuclei have 4 associated flagella
 Order Parabasalia
 Example 2: Trichomonas vaginalis
 Has no cyst stage, only trophozoites
 Infection found in vagina or urethra (but can be found in men
too), can cause infertility, transmitted by sex, toilet seat, towels
 Passed directly from host to host only
 Symbiotic relationship with animals (ex: termites)
 No mitochondria
o Euglenozoa
 Group of parasites with flagella, common in aquatic streams, anaerobic
metabolism/no mitochondria
 2 groups - 1. Euglenoids 2. Hemoflagellated
 euglenoids don’t infect humans
 Trypanosoma examples- African sleeping sickness
  Leishmania examples- leishmaniasis
 Order Euglenoids
 Use flagella to move (at anterior end near the eye spot)
o Red eye spot= senses light, important because it is a
photoautotroph (needs light to produce ATP)
 Have a pellicle- semi rigid membrane
 Order Trypanosomatida
 Elongated cell with a single flagellum
 Have unqiue organelle called the ‘kinetoplast’ = special
mitochondria that provides energy for the flagellum
 Genus Trypanosoma : need to convert to several forms during life
cycle in order to infect a host
o 1. Slender form and an undulating membrane- proliferates
in the blood stream
o 2. Stumpy form- does not proliferate in mammals, only
insects
 Trypanosoma spp./Sleeping sickness
o life cycle:
 Fly takes a blood meal and injects T. brucei into
human bloodstream
 T. brucei multiplies by binary fission  can cross
BBB and enter spinal fluid, can infect glands and
lymph
 Fly takes a blood meal and ingests T. brucei
 T. brucei transforms into infectious stage in the fly
and multiplies sexually in salivary glands (M and F
gametes fuse)
 fly cycle takes about 3 weeks, humans are
main reservoir
 fly=definite host
 Leishmania spp.
 Sandfly/mosquito=definite host
 Creates a wound in human gut so it can’t absorb nutrients, body
becomes weaker overtime
 Many types, transmitted via mosquito, can only kill it during the
active stage
 Life cycle:
o Mos takes blood meal and injects promastigote stage into
humans
o Macrophages phagocytize the promastigotes
o Promastigotes turn into amastigotes within the
macrophages (can be diagnosed)
o Amastigotes multiply in cells of various human tissues
 o Mos takes blood meal and ingests infected macrophages
o Macrophages burst and amastigotes transform back into
promastigotes in midgut
o Cells divide in midgut and migrate to proboscis
o Amebozoa
 Voracious predators- consume other protists and bacteria, can be several
mm in size
 Infectious stage- trophozoites (with pseudopods)
 Several types, free living in soil or water, thin and flat shape, can cause
malnutrition and diarrhea
 1. Lobed amebas with large bulkly pseudopods that extend the
lobes of the cytoplasm through cytoplasmic streaming
 2. Filamentous amebas with thin needlelike psuedopods
 Example: E. histolytica
 Most invasive
o Doesn’t usually affect humans unless
immunocompromised
 Invades cells by secreting enzymes that damage the intestines
 Pass in feces as both trophozoites and cysts
 Can only diagnose by cysts
o All cysts look slightly different
 Acquired only by ingesting cysts from soil/water/feces
 Example 2: Acanthamoeba spp.
 Found in water (mostly), contact lenses, dental treatment units,
dialysis machines, ventilation/AC systems, vegetables
 Don’t reproduce often
o No flagellated cycle
o Do have trophozoites- replicate by mitosis- this form
infects
 Opportunistic? Infect us because they came across a host
o Enter through eyes, nose, or mouth or broken skin in
water
o Can cause encephalitis
 Example 3: Naegleria fowleri
 “brain eating ameba”
 has a flagellated form that actively swims- seen more in the
summer (only cysts in winter)- penetrates nose underwater 
meningoencephalitis  death in sleep
o trophozoites in CSF and brain tissue
o occasionally can find flagellated form in CSF as well
o Apicomplexa
 Major group of parasites (infect humans and other animals)
  Have an apical complex: specialized structure that facilities entry of the
parasite into a host cell, allows parasite to become intracellular (can
digest parts of the cell with enzymes)
 Has a complex life cycle- involves transmission between several hosts
 Non motile in mature form
 Elaborate cell cortex- alveoli, pores, microtubules
 Reductive evolution- lost flagella and cilia
 Genus Plasmodium
 Plasmodium falciparum (malaria): life cycle involves 2 hosts
(human and mosquito), definite host=mosquito
 Genus Babesia
 Babesia microti: causes babesosis…emerging human pathogen
spread by deer ticks (also blood transfusions or blood contact),
life cycle involves 2 hosts, definite host=tick

HELMINTHS (worms)
- Bilaterally symmetrical, have a head and a tail, 3 distinct tissue layers=triploblastic
o Tissue layers- ectoderm, mesoderm, endoderm
- Nematodes (roundworms): cylindrical, digestive tube with anus
o Hermaphrodites and male reproductive forms
o Adults- live most of life cycle in the digestive tract
o Larvae- cause their damage in other organs
o Enterobius vermicularis: enterobiasis or pinworm
 Most prevalent infection in US and Europe (25-50% of pop. possibly
infected)
 Causes malabsorption of nutrients, anorexia (related to host’s immune
response), secondary bacterial infection at site of scratching
 Definite host=humans
o Ancylostoma duodenale: hookworm
 Common in south US and tropical regions around world
 Larvae grow in soil and feed on other microbes until they contact host
skin (usually bare feet)
 Definite host=humans (or other mammals)
o Ascaris lumbricoids: ascariasis (neglected tropical disease)
 Largest nematode parasite to the human intestine (grow to F: 20-35cm
M: 15-30cm within human digestive tract)  can be lethal
 Grow indefinitely in digestive tract and can obstruct the intestines
 Transmitted by ingestion of eggs from soil
 Definite host=humans
- Trematodes (flukes): oval shaped flatworms, digestive tube with cecum (no outlet)
o Infect many kinds of animals, but most require a mollusk as their primary host
o All hermaphrodites
 o Have a mouth, pharynx, and digestive tube, but tube ends in one or more
pouches called caeca  must expel waste back out the mouth
o Usually has two suckers- one near mouth and one on ventral side of body
o Different species prefer different organs (liver vs lungs vs intestines)
o Definite host=humans
o Life cycle is complex and involves several hosts
o 2 types of fluke infections occur in humans:
 1. Tissue flukes- attach to bile ducts, lungs, or other tissues
 lung: Paragonimus westermani
 liver: Fasciola hepatica
 2. Blood flukes- found in blood in some stages of their life cycle
 genus Schistosoma- various species
- Cestodes (tapeworms): parasitic flatworms, absorb nutrients through their skin
o Head structure called the scolex with suckers that attach to intestinal
walls
o Hermaphroditic: Grows a long chain/ ‘tail’ of segments/proglottids
containing both male and female reproductive structures in each
segment
o Transmitted through larvae in uncooked meat
 Different species
 Taenia solium- pork
 Taenia saginata- beef
 Diphyllobothrium- fish

ARTHROPODS
- Make up the largest group of living organisms- as many as 80% of all animal species
belong to phylum Arthopoda
- Arthropods=invertebrate animals with an exoskeleton and jointed appendages, includes
insects and arachnids (spiders and mites)
- Many are free living; others are parasites with complex life cycles
- Ectoparasites= some attach to surface of a vertebrate host (Others burrow into the
flesh)
o Some suck blood and fall off, others inject eggs to develop inside host
- Can be acquired from environment or other infected hosts
- Can transmit disease  vectors
- Arachnid parasites: 8-legged mites and ticks
o mites cause…
 mange- in animals
 scabies- in animals or humans- caused by Sarcoptes scabiei
 mites attached to skin using suckers at burrow under using special
mouthparts and cutting surfaces on their front legs
 lay eggs as they borrow  hatch into larvae
  larvae come out of skin and attach to a hair follicle where they
feed and molt until they reach the adult stage
o ticks: resemble mites in their 8-legged form, but are larger and don’t burrow into
skin, ectoparasites
 suck blood for nutrients to produce eggs, then fall off to disperse their
progeny
 ex: Deer tick lxodes scapularis carries the spirochete of Lyme disease
(Borrelia burgdorferi)
- insect parasites:
o sucking lice- wingless ectoparasites that suck blood then produce eggs
 tend to be very specific to one host species
 different species also have a preference for different body sites
(ex: head lice, body lice, public lice)
 difficult to remove because their eggs attach firmly (need lice shampoo)
o bedbugs- Cimex lectularius
 detect host by exhaled CO2
 suck hosts blood and leave to lay eggs (not noticed by host)
 were nearly eradicated in US in mid-20th century by DDT and other
pesticides
 now they are resistant to those pesticides and need newer
chemicals with toxic side effects to kill them

CHAPTER 9
- Cell elongates when it grows, there isn’t more cells
- Efficient replicating- once they have the needed nutrients most will replicate very
quickly
o Limiting nutrients controls growth
o In our body iron controls bacterial growth- not readily available in the body,
bacteria have to remove the iron from the carrier
- Nutritional factors
o C is only needed
by autotrophs
o H- most need
o O- not all need
o N- essential for all
o P- most need
o S- all need
o K- all need
o Mg-
o Na- not all
o Ca- needed for cell
wall
o Fe- needed for respiration
 o Certain bacteria need specific nutrients
 Ex: legionella pneumophila needs cysteine to grow
 Ex: Streptococcus pyrogenus- needs alanine and glutamate to grow
- Culture media: solid vs semi solid vs liquid
o Solid- has agar, no nutrient source, isolated from algae, some bacteria can
degrade it
o Liquid- liquid broth with nutrients
o Semi-solid- less than 0.8% agar, jelly like
- Minimal vs complex medium
o Minimal- chemically defined, you know exactly what was added and
concentration
 Ex: M9 medium
o Complex- chemically non-defined
 Ex: luria bertani- don’t know exact amounts of bacto tryptone or bacto
yeast extract
- Culture medium: when you prepare nutrients for microbial growth
- Sterile medium - no microbes growing and no possibility of it happening
- Inoculum- introduce microorganisms into culture medium
- Some bacteria need very specific nutrients to grow (like nucleic acids, etc)
o Estimated about 60% can’t be cultured in lab bc conditions can’t be replicated
- Ways of obtaining carbon
o Heterotrophs- rely on other organisms to produce their C source
o Autotrophs- use Co2 discarded by heterotrophs to make complex things made of
C, H, and O
o Phototrophs- extract energy from light
o Chemotrophs- use energy from redox reactions, remove electrons from high
energy compounds to produce lower energy compounds
 Lithotrophy
 Organotrophy
- Obtaining nitrogen
o Essential for all organisms- used for proteins, nucleic acids, etc
o Makes up 79% of earths atomosphere- but this is unavailable to most organisms
o First N must be fixed in the cycle
 N2 removed from air (nitrogen fixers)ammonia (nitrifers)nitrate
(denritifiers)N2
- Most bacteria rely on binary fission: cell wants to grow to 2x size  Dna replication
occurs  cell will elongated to 2x size  septum of division starts forming  cell
separates
o Regulations to make sure daughter cells contain same genetic material
o Random mutations can occur but should be clones
- Asymmetrical binary fission- cell buds off to form new cell
o Low G+C gram positive organisms do this
- The epulopiscium life cycle- FtsZ (protein that produces the septum)  separates an
area of the cell from the main area (DNA has already been replicated) offspring is
engulfed in mother cell and grows  once its big enough the mother cell will die and
the offspring will emerge
o One of the longest bacterial cells- adapted by doing this (would be too hard to
do binary fission)
- Batch culture system- will find in test tube or Erlenmeyer flask
o Phase 1: lag phase- when you start a new culture you start with a very low
number of cells, move from high to low density, no increase in # of living cells
o Phase 2: log phase- exponential increase in number of cells (12416)
o Phase 3: stationary phase- when a nutrient is limited (usually iron), death rate
and growth rate are equal, may be prolonged for a long time
o Phase 4: death phase- lots of death, very limited nutrients, lots of toxic waste
byproducts, may be prolonged for a long time
- Continuous culture systems
o Continuous culture: in open systems where fresh medium is continually added to
a culture and an equal amount of culture is constantly siphoned off, bacterial
populations can be kept in exponential phase at a constant cell mass for long
periods of time
o Chemostat: continuous culture system in which the diluting medium contains a
growth-limiting amount of an essential nutrient
 Flow rate is same as max duplication time rate
 Inoculate a reactor, allow bacteria to grow for a while in that reactor,
need to reach a certain number, only start flow after that, allows cells to
adapt to new media, have flow going in and out at same rate, if a cell
divides the new cell will leave system  cell # is always constant
 Cells are always in exponential phase because there are always new
nutrients coming in

 If you inoculate and start flow with small # of cellslose all cells
o Biofilms: in nature microorganisms will grow mostly as biofilms, complex
dynamic communities of bacteria that “talk” to each other like we do in a
community, depend on the community, microbiome in our body is a biofilm
 Cells are protected from antibiotics- more resistant bc antibiotic may not
even reach them
 Surrounded by slime called exopolymeric substance- contains proteins,
DNA, carbs, lots of other things  can inactivate certain antibiotics or
bind to it
 Cycle of growth 1. Bacteria attaches to surface (decides to stay or go)
2. (if it stays) starts to grow to form a microcolony and 3. produces
polymeric substance  4. biofilm matures and forms colonies
(mushroom like structures)  5. eventually environment inside becomes
too toxic and biofilm will disperse
  When in biofilm the cells downregulate their flagella gene  NO
FLAGELLA
 When cells leave biofilm  upregulate flagella  FLAGELLA
 Flow rate for biofilm is MUCH HIGHER than duplication rate (chemostat is
equal)  want to increase flow so much that only cells attached to
surface will remain, nutrients are passing really fast, if bacteria doubles
every hour  want a flow that changes min 6 times in an hour=no
chance any bacteria will remain floating around
- Environmental limits on microbial growth

o Any limits beyond norm for humans to survive are considered “extreme”
o Extremophiles=organisms that can survive in extreme environments
o Every molecule in a cell will be affected by a change in environment and will
probably die unless it can adapt really quickly
o Physical requirements: pH, T, moisture, hydrostatic pressure, osmotic pressure,
radiation
o Chemical requirements: availability of C, N, S, P, trace elements, organic
compounds, oxygen
o Temperature:
 Bacteria CANNOT control their T- has same T as environment
 Psychrophiles- growth rate highest below 5-15°C (will grow in fridge),
some can infect humans but rare
 Mesophiles- optimum 35°C (infect our bodies)
 Thermophiles- 40-60°C, rarely infect humans
 Hyperthermophiles- 90°C optimum (can survive in boiling water), usually
archaea, do not infect humans
 Adapt to different T by changing lipid membrane permeability- depends
on fatty acid composition
 T decrease= fatty acids will decrease in size
(saturatedunsaturated)
 Lots of unsaturated fatty acids=membrane gelling=transport
process very slow and growth is limited
 At optimum T proteins are working at max
  Above optimum proteins denature
o Pressure
 Normal land 0.98atm
 Depth of ocean 365atm
 Mariana trench (lowest point in sea) 1085atm
 Barophiles: prefer high pressure/high weight
 Piezophiles: prefer high pressure, another name
 Cell membrane changes: Fatty acids shorten in length- adaptation to
survive high pressure, become more unsaturated
o Water availability/Na concentration/molarity
 How much solute is present- different [Na]
 Normal Na=moderate halophiles
 Ones that live in the ocean
 Extreme halophiles=high [Na]
 Nonhalophile=low [Na]
 Hypertonic solution- cell inside shrinks (cell wall protects whole cell)
 Hypersaline habitats- different shades of pink represent amount of water
 Dark pink=less water=more bacteria (salt loving ones)
o Microbial response to change in pH
 Acidophiles=low pH
 ATP synthase activity increases- more ATP produced in acidic
environment
 Neutralophiles=netural pH
 Compatible with life, normal body pH
 Alkaliphiles= high pH
 pH alters protein shape (and cell membrane) – alters protein activity too
o Oxygen

 Atmosphere contains 21% O2

 test tube environment: top of test tube has most contact with O2,
bottom has very low O2
 top- aerobic
 middle- microaerophilic
  bottom- anaerobic
 Bacteria that use O2 as terminal e- acceptor= aerobic organisms/aerobic
respiration (obligate aerobes)
 Most bacteria are anaerobic- O2 is toxic (obligate anaerobes)
 obligate anaerobes usually lack all 3 enzymes
 Facultative anaerobic organisms- have certain enzymes to detoxify O2
radicals and can undergo fermentation, prefer aerobic respiration, lack of
O2 will do fermentation, can do both at same time
 Aerotolerant anaerobes- strictly anaerobic, but are not harmed by
presence of O2, contain certain enzymes (superoxide dismutase and
catalase or peroxidase)  protect from ROS
 ROS= reactive oxygen species, they are byproduces of aerobic
respiration that must be detoxified
 Even organisms that don’t do aerobic respiration need way to
break down ROS that forms from O2 in atm.
 have SOD but not catalase
 Microaerophiles- grow at low O2 concentration (1-10%), need certain
amount of CO2 (~5%)
 Lot of organisms in our body (despite humans having aerobic
respiration)
 Decreased amount of SOD and/or catalase
 Problem with oxygen?? Can oxidize numerous chemicals in our cells 
can lead to cell injury or death
 Several (3) enzymes convert O2 byproducts (ROS) to something
less harmful
 These rxn’s use an e- donor (reduced compound) to oxidize
peroxides to water  limits damage caused by peroxidation of
lipids in cell membranes
o Catalase: converts hydrogen peroxide to water and oxygen
2H2O2 O2 + 2H2O
o Superoxidie dismutase: most organisms have it, breaks
down powerful superoxide anions generated by aerobic
metabolism
 2 O2- + 2H+  H2O2 + O2
o peroxidase: X—(2H+) + H202  2H2O + oxidized-X
- What happens if cell can’t adapt to environment? Goes dormant
o normal cell undergoes vegetative growth- 1 cell becomes 2
o stress triggers different cycle=sporulation (ONLY bacillus or clostridium species
can undergo this)
 stage 1: septum begins to form near one pole (asymmetrical), DNA
replicates and moves to that pole/extends into an axial filament (DNA is
very compacted)
  stage 2: the septum separates the forespore from the mother cell, DNA is
pumped through the septum until each compartment has a full
chromosome
 stage 3: mother cell engulfs the forespore, which surrounds it with a
second membrane
 stage 4: mother cell chromosome disintegrates
 stage 5: forespore develops a cortex layer made of peptidoglycan
between original forespore membrane and the second membrane from
the mother cell, coat proteins are deposited on the outer membrane
 called an exosporangium now
 stage 6: dipicolinic acid is synthesized and Ca is incorporated into the
spore core
 stage 7: mother cell releases spore once it is completely formed
 cell germinates and either goes back to vegetative growth or repeats
sporulation
 spore only gives 1 cell= method of survival=spore has chance to revert
back into active state
 not a method of replication cell is dormant

- Agar: usually needed to culture bacteria, complex polysaccharide (most prokaryotes

cannot use as a nutrient source, ones that can are not human pathogens)
o Used to use gelatin instead of agar
o Liquid at 100°C // solid at ~40°C
- Culture media types
o Selective (vs nonselective): encourages growth of certain organisms and
discourage others, will have a growth inhibiting additive (bile salts, crystal violet,
or an antibiotic)
 Crystal violet- resist gram positive
 Antibiotic- select for antibiotic resistant bacteria
 Examples of media:
 mannitol salt agar- both selective and differential, has high salt
concentration, selects against organisms that don’t grow in salt,
has mannitol on it
o mannitol- carbohydrate, allows differentiation between an
organism that uses mannitol, uses pH detector  if it uses
mannitol salt it turns yellow, if it doesn’t pH doesn’t
change so neither does color
 when organism uses a carb it undergoes
fermentation through glycolysis changes pH of
media  pH indicator turns media yellow
o can SELECT for salt loving organisms, and DIFFERENTIATE
for what they use (mannitol)
 o ex: used to select for staphylococcal species (will turn
yellow)
 MacConkey agar- both selective and differential, has bile salts,
crystal violet, and lactose
o Bile salts and crystal violet- select against gram positive
o Lactose- differentiate between organisms that use lactose
as a carb source (ecoli loves lactose), detect change in pH/
use of lactose by presence of pink color
 Ecoli will turn media very pink
 Blood agar: NOT selective (most will grow in it), differential for
certain reaction (ability to degrade RBCs)
o Clear areas=blood has been degraded, Beta-hemolysis
o Green colonies= blood has been partially degraded, alpha-
hemolysis
o No change= blood not degraded, gamma-hemolysis
o Differential media: use biochemical properties of organism that will grow in that
media to differentiate between species that both grow in the media
o Enrichment media: want to encourage growth of specific organism
 Fastidious; needs lot of nutrients, sometimes we can’t even tell what they
need, sometimes need other bacteria to be present to grow, take a long
time to grow
 Winogradsky column: developed in 19th century, mainly used to study
interactions between soil organisms, different colors will develop in the

column
 Oxygen vs sulfur cycle
o Top of column = aerobic zone
o Bottom of column= sulfate zone
 o As you go up column sulfur gradient changes- different
reactions happen that are dependent on each other

- Culturing bacteria
o Pure culture- one bacterium gives rise to one colony (all colonies look the same)
 Use agar, do a dilution of culture, streak plate=dilution of culture
 Streak plate purpose is to be able to capture an isolated colony from one
type of bacteria
 When trying to isolate one from a patient its challenging to figure
out which one bc there are so many types of bacteria need to
use differentiation etc.
o Once you have isolated colony you can grow it in liquid use inoculate for
several tests
- Enumeration of bacteria (2 ways)
o Spread plate: allows to enumerate how many viable bacteria there are in sample
 Pipette culture onto agar, spread evenly, incubate  should have
isolated colonies
o Pour plate: add agar ON TOP of culture, mix, then incubate  colonies grow on
top and within agar (only grow within IF they are fermentative), each colony
supposedly comes from ONE bacterium cell (how you estimate how many cells
you have)
- Dilution for counting: dilute cells enough that you have a countable amount of colonies
(between 30-300), can do 2 fold, 10 fold, etc.
o 1 in 2/ 2 fold- if you have 2mL (1 solute, 1 dilutant)
o usually do 1 in 10 (or 1 in 100): 1mL culture in 9 mL of dilute  if too many
colonies you can repeat for a total of 1 in 100  repeat again is 1 in 1000 etc.
until you have between 30-300 colonies
o usually plate 100 microliters or 0.1 mL- to count take number of colonies and
 CFU/mL= # of colonies/ (dilution x volume plated)
 1 in 10,000= 10^-4
 50/ (10^-4 x .1 mL) = 50/ 10^-5 = 50 x 10^5= 5x10^6 CFU/mL
- Counting by filtration: use filter with smaller pore than bacteria, collect bacteria in filter
then put in petri dish, allow to grow, and count
o Can also do a serial dilution and then filter
o Each colony comes from 1 bacteria- can count
- Total cell counts: account for dead and live cells together, don’t need to wait 24 hours
for colonies to grow, usually need a stain
o Important because can underestimate amount of bacteria
 o Fluorescence stain: Usually green for live, red for dead (exception- red cell but
still alive, just damaged/can’t replicate)
 Damaged cell is still producing toxins, just not reproducing—counting just
viable cells will not account for this
o Not all living bacteria are VIABLE- these can still cause harm too
o Some antibiotics do not kill bacteria, but limit their growth- important to note
because bacteria will start growing again after antibiotics stop
- Counting chambers: count bacteria in squares, for bacteria on line of square count 2
sides
- FACS sorting (fluorescence-activated cell sorter)- sorts based on fluorescence and size
o Culture goes down- Laser shines and light scatters from cell- can tell size and
type of fluorescence, bacteria are sorted two different sides of microscope based
on charge, can study cells on each side
 Scatter=size
 Larger cells= different types of bacteria or cells are actively
dividing
 Fluorescence= can detect for certain things based on fluorescent
component, can tell % of bacteria that have that trait (ex: ecoli)
- Turbidity estimation:
o Other ways above can be too long, too expensive, etc
o Turbidity of a culture= degree to which the liquid medium has become cloudy
because of microbial growth
 Can be measured in real time using a spectrophotometer
 Optical density=decrease in intensity of light due to scattering of light
o Turbidity estimation vs viable count- bacterial curve (lag phase, exponential
phase, etc) is shifted a bit
 Can’t use to estimate past stationary phase: underestimates death of
cells because light will reflect off living and dead cells the same
 Assessing if antimicrobial is effectively killing bacteria—can’t use turbidity
 Good for estimation of TOTAL cells, not VIABLE cells
- Preserving bacterial cultures:
o Deep freezing: -50°C to 95°C
o Lyophilization (freeze drying): frozen -54°C to -72°C and dehydrated in a vacuum

Chapter 4
- Thomas Brock- discovered certain bacteria can live in boiling water  what other
extreme environments can bacteria live in (bottom ocean, volcanos, high alt)
- Bacteria produce proteins used in research and medicine
- Shorenella- bottom of ocean, O2 is scare, grows long appendages so it can seek limited
O2 in environment, digest toxic wastes, generates electricity
- Prokaryotes can be found everywhere on planet
o Abundant on body
 o Prokaryotes/bacteria outnumber human cells 10:1 or 1:1  large % of cells in
body are prokaryotic not eukaryotic
- PCR finds up to 10k bacteria per gram of soil – most not even identified
- Prokaryotes essential to ecosystems
o part of soil formation and stabilization process – can metabolize plant
substances and release products  release back to soil to increase soils fertility
o abundant in air
o found everywhere on earth
o metabolically flexible- can turn on/off genes for pathways depending on
nutrients around them
o preform vital functions for life on earth- ex: plants and animals rely on
prokaryotes for nitrogen fixation (N ammonia)
o clean up environment- some can degrade toxins that pollute water and soil
o BAD: some are human pathogens, can contaminate food
 Less than 1% are human pathogens
- Normal microbiota=collection of bacteria, archaea, eukaryotic microbes that colonize
our bodies= GOOD GUYS (protect from pathogens)
o Permanent or transient
 Permanent- live symbiotically in host, protect by occupying niches
pathogens could, produce acids that interfere with bacteria, produce
bacteriocins (compounds that kill other bacteria)
 Transient- temporary (hours, days, or weeks)
o Some parts of body are MICROBE FREE  spinal fluid
 Blood used to be though to be microbe free but not true
- Types of symbiotic relationships (normally host and microbiota benefit)
o Microbial ecology=study of this
o Microbiota is usually commensalism- we benefit, other unaffected
Type Population A Population B
Mutualism Benefitted Benefitted
Amensalism Harmed Unaffected
Commensalism Benefitted Unaffected
Neutralism Unaffected Unaffected
Parasitism Benefitted Harmed

- Locations of commensal microorganisms:

o Skin- staph
o Oral cavity- streptococcus (more in areas less exposed to oxygen), candida,
Neisseria
o Upper respiratory tract- streptococcus (less), fusobacterium, candida, Neisseria
o Intestines- bacteriodes, ecoli, LOTS OTHERS
o Urogenital tract- Corynebacterium, ureaplasma
o Etc.
- Changes in microbiota overtime
 o 16S analysis- based on 16SrRNA
 baby doesn’t have commensal microbiota until birth
 breastfed vs formula vs solid food=different microbial composition
 breastfed has more proteobacteria, bacteroidetes, actinobacteria but less
firmicutes
 proteobacteria almost disappear with solid food but “others” increase
 healthy child microbial compositon doesn’t change much from solid food
 antibiotic treatment changes it during treatment
 malnutrition changes composition (large # of proteobacteria,
responsible for lots of infections)
 adult has more firmicutes and bacteroidetes decrease
 obestity changes (more proteobacteria)
 elderly
 65-80: pretty similar
 over 100: many more actinobacteria (kinda like reverting to being
a baby again)
o overall DNA composition- bacteria DNA present in human

Taxonomy
- prokaryotic
species
assigning is
hard because no
sexual

reproduction
o can’t classify based on interbreeding
o hard to classify based on appearance
- used to be based on shape, patterns, biochemical differences
- now nucleotide sequences are used
- Bergey’s manual- handbook of classification
- ARCHAEA- cell membrane has ether linkages with branches isoprene chains, no
peptidoglycan (pseudomurein instead), genomes are larger and more complex
o PHYLUM CRENARCHAEOTA- mainly hyperthermophiles, very diverse, all aquatic,
most abundant microorganism in oceans, some are able to grow at T up to 113°C
 GENUS SULFOLOBUS- prefer 70-80°C, some are acetophiles (prefer pH 2-
3), aerobic or anaerobic
  GENUS THERMOPROTEUS- strictly anaerobic, 85°C, have flagella, have
cell membrane with lipid MONOlayer, autotrophs, synthesize ATP by
reducing sulfur and use CO2 or CO as carbon source, leading example of
earliest life form on planet
o PHYLUM EURYARCHAEOTA
 CLASS METHANOBACTERIA, METHANOCOCCI, METHANOMICROBIA
 Called methanogens- All can produce CO2 in presence of O2,
produce methane, can reproduce at wide variety of temperatures,
thought to be the bacteria that live on mars
 CLASS HALOBACTERIA- need very high concentrations of NaCl in aquatic
environments, one is oldest organism on earth
- BACTERIA- cell membrane has ester linkages with fatty acids, peptidoglycan
o GRAM NEG OR GRAM POS
 GRAM NEG  PROTEOBACTERIA or NONPROTEOBACTERIA
 GRAM POS  LOW G+C OR HIGH G+C
o GRAM NEG PHYLUM PROTEOBACTERIA
 Alphaproteobacteria- oligotrophs (can live in low nutrient envrionments),
many are human pathogens
 Betaproteobacteria- eutrophs (need many nutrients), often grow
between aerobic and anaerobic areas (ex: human intestines), some are
human pathogens
 Pathogen examples:
o Burkholderia- aerobic, motile, single polar flagellum or tuft
flagella, known for contaminating drugs and hospital
equipment
o Bordetella- aerobic, non-motile, chemoheterotrophic, ex:
whopping cough
o Neisseria- ex: gonorrhea, inhabit mucus membranes,
diplococci, aerobic, non-motile
o Legionalleles- rod or coccoid shape, motile, aerobic, love
warm water, cause pneumonia, intracellular (can survive
and produce in amoebas and survive antibiotics)
o Vibrionales- includes vibrios, anaerobic, most common
organism that causes disease, ex: cholera
o Pasteurellales- causes sepsis in cattle, rarely affects
humans, non-motile
 Gammaproteobacteria- largest subgroup, great variety, most diverse
class of gram negative bacteria
 GENUS Beggiatoa- only one species, aquatic sediments, between
aerobic and anaerobic
 GENUS Franscisella- grow only on complex media, need blood and
tissue extract to grow, aerobic, facultative intracellular parasites,
causes type of pneumonia
  GENUS Pseudomonadales-
o Pseudomonas- metabolically diverse, polar flagella (single
or tufts), aerobic, opportunistic pathogens, common in
soil, ex: UTI, sepsis
o Moraxella- aerobic, coccobacillus, ex: pink eye
o Acinetobacter- occurs in pairs, aerobic, motile, respiratory
pathogens primarily
 ORDER Enterobacteriales- facultative anaerobic organisms, some
motile, called enteric (inhabit intestines), produce bacteriocins
o Examples (GENUSES)
 salmonella- almost all pathogenic
 Shigella- only found in humnas, pathogen
 Klebsiella- UTIs, or normal
 Serratia
 Proteus- swarming motility in gut (normal), can
cause UTIs
 Yersinia- not common in humans, but is the plague
 Escherichia- ecoli (several types), usually not
pathogenic, naturally in gut, high levels cause
disease
 EHEC (enterohemorragic)- bloody diarrhea
 ETEC (enterotoxigenic)- watery
 EPEC- (enteropathogenic)- bloody and
watery
 EIEC (enteroinvasive)- invades epithelial
cells, mucoid bloody and fever
 EAEC (enteroadherent)- adheres to
intestinal cells, causes damage, watery
 EAggEC (enteroaggregative)- clumps
intestinal cells, chronic mucoid watery
 Deltaproteobacteria- some are predators to other bacteria, some
important to sulfur cycle
 Epsilonbacteria- slender gram negative rods, smallest class, anaerobic
 Campylobacter- one polar flagellum, gastroenteritis, can cause
spontaneous abortion and food born disease
 Helicobacter- multiple flagella, peptic ulcers, stomach cancer
o GRAM NEG PHYLUM NONPROTEOBACTERIA- phototrophic bacteria (undergo
photosynthesis). Oxygenic (typical) vs anoxygenic (uses H2S instead of H2O)
photosynthesis
 Purple sulfur bacteria- oxidize hydrogen sulfide into elemental sulfur and
sulfuric acid, purple from pigments they produce (bacterial chlorophylls
and keratinoids), anaerobes, live in water
 Green sulfur bacteria- use sulfide for oxidation and produce large

amounts of green bacteriochlorophyll, part of greenhouse
gasesproduce methane
 Purple nonsulfur bacteria- similar to other purple, but use H rather than
H sulfide for oxidation, facultative anaerobes, usually pinker
 Green nonsulfur- similar to other green but use substrates other than
sulfur for oxidation
o GRAM POS LOW G+C  FIRMICUTES

 LOW GC= low amounts of guanosine and cytosine

 Mycoplasmatales
 Mycoplasma- very small, have undergone degenerative evolution
(lost genetic material they don’t need), highly pleomorphic, can
produce filaments and resemble fungi
 Clostridiales
 Clostridium- obligated anaerobes, rod shape, contain endospores
(usually distend the cells)
o Species: clostridium difficil (CDIFF)- cause disease after
taking antibiotics (they are resistant)
 Epulopiscium- among largest known bacteria (can see with naked
eye), symbiotic with sturgeon fish
o Hard to classify because it was so big, no membrane
enclosed nucleus, small flagella, but based on 16SRNA
 Bacillales
 Bacillus- facultative anaerobes, rod shape, contain endospores
o Bacillus anthax- causes anthrax
 Staphylococcus- facultative anaerobes, cocci shape, grow well in
areas of low moisture (like our skin), and high osmotic pressure
 o Toxic shock syndrome, food poisoning, infect surgical
wounds
 Listeria- facultative anaerobe, rod shape, infections have a fatality
rate of around 20%
o Food poisoning (dairy products)- difficult to track bc
incubation period is 3-70 days  can survive in phagocytic
cells
 Lactobacillales
 Streptococcus- facultative anaerobic, coccus shape, produce
enzymes that produce connective tissue, can destroy phagocytic
cells, some species are non-pathogenic and used to produce dairy
products
o B-hemolytic- produce emulsion on blood agar
o Non-B-hemolytic
 Enterococcus- facultative anaerobic, coccus shape, live in areas of
body high in nutrients but low in O2 (GI tracts, oral cavity), in
large numbers in human stool, very resistant to antimicrobials
(problem in hospitals)

 HIGH G+C = ACTINOBACTERIA

 Filaments are much smaller than fungi
 Mycobacterium- aerobic, occasionally have filaments, rod shape, distinct
cell wall (lot of mycolic acid)
 Slow growing- more likely to be pathogenic
 Fast growing
 Corynebacterium- aerobic, pleomorphic, skin commensal, coccus or
bacillus
  Propionibacterium- anaerobic or microaerophilic, rod shape, forms
propionic acid, known to produce holes in swiss cheese and acne
 Gardnerella- facultative anaerobic, highly pleomorphic, causes vaginitis,
gram variable
 Streptomyces- aerobic, filamentous, has reproductive asexual spores
(each can germinate into a new colony), in soil, can degrade nutrients in
soil and transport them into cell, produce musty odor geosmin (rain
smell), produce most antibiotics
 Actinomyces- facultative anaerobes, filamentous
 Nocardia- aerobic, filamentous that fragment into short rods

Chapter 11 &12
BACTERIAL GENOMES- Every organism has a unique DNA sequence
for that species in its genome- Flow of genetic information: Parent cell
DNAexpression, recombination, replication
o Expression- genetic info is used within a cell to produce the proteins
needed for the cell to function
Includes transcription and translationo Recombination- genetic info
can be transferred between cells of the same
generation, results in new combinations of geneso Replication- genetic
info can be transferred between generations of cells, result
is 2 daughter cells- A cell’s genotype always stays the same, but shows
different phenotypes based on environmental conditions
BACTERIAL DNA REPLICATION- DNA synthesis has 3
phasesinitiation, elongation, and termination
o Initiation- involved unwinding the helix, priming, and loading of the
DNA polymerase enzyme complex
o Elongation- sequential extension of DNA by adding DNA nucleotide
triphosphates (dNTPs= ATGC) with release of pyrophosphate, followed
by proofreading
o Termination- DNA helix is completely duplicated and replication
stops
^GUANASINE
BACTERIAL DNA REPLICATION

RNA TRANSCRIPTION BACTERIA

- Bacteria use 1 RNA polymerase to transcribe all their genes
(eukaryotes use 3)o RNA polymerase doesn’t need the 3’-OH
group (/primer) to add a nucleotide to the strand like DNA
polymerase does
- RNA polymerase has polypeptide subunits- some bacteria like
th
E.coli have a 6 subunit sigma that allows it to bind to a specific
promotor/for specific genes to be transcribed o Sigma binds to a
specific promotor region that’s similar across all bacterial cells
- RNA polymerase does the job of unwinding the DNA double
helix, and sealing it, as it moves
 - Template strand=antisense strand RNA produced is
complementary to this strand o RNA is identical to nontemplate
strand (besides with U instead of T)
- Promotor=where transcription is initiated o Like a start codon o
5’->3’ EUKARYOTES - basically the same as prokaryotes
except- genes that encode polypeptides have exons (coding) and
introns (non-coding) cut out introns before protein synthesis
(‘RNA splicing’)- Eukaryotes have to move the RNA outside the
nucleus for transcription, have factors that make mRNA survive
longer (5’ cap, poly-A tail, etc.)

TRANSLATION
- protein synthesis o 3 nucleotides=amino acid=building block of
proteino 20 common amino acidso amino acids are encoded by
more than one codon= redundancy= ’degeneracy’ o AUG- start
codono 3 stop codons/nonsense codons: UAA UAG UGA
eukaryotic translation immediately stops at a stop codon
 prokaryotic translation doesn’t because there might be another
start codon after?o a few unique amino acids have been found in
bacteria
- Translation requires: mRNA template, tRNAs, ribosomes, and
various enzymatic factors
- Ribosomes- rRNA and proteins
o Amount of each varies depending on the organismo Dissociate into
large and small subunits when they are not synthesizing proteins,
come back together at the initiation of translation o Small subunit binds
mRNA templateo Large subunit binds tRNAs
- tRNA- in cytoplasm, 60-90 types, ‘holds’ an amino acid and adds it to
the specific codon on the mRNA template
o every cell makes 61 different tRNAs- there is one for each possible
amino acid/codon
o can bond to itself to create a 3D structurepositions the amino acid
binding site/ “CCA amino acid binding end” at the 3’ end, and an
anticodon at the other/5’ end
o aminoacyl tRNA synthases link tRNA to its amino acid

- polyribosomes:o prokaryotes can have multiple RNA polymerases

transcribe a single bacterial
gene while multiple ribosomes translate the mRNA transcripts into
polypeptides fast protein production
transcription and translation can occur simultaneously because both
occur 5’-3’, both occur in cytoplasm, and the RNA transcript is not
processed once it is transcribed
o eukaryotes can’t do transcription and translation at the same time
polyribosomes can still form but only after RNA synthesis is
complete and
the RNA is moved out of the nucleus Mechanism of translation (very
similar in pro/eukaryotes)
Example: Ecoli 1. Initiation
- initiation complex forms: mRNA template, small 30S ribosome, 3
initiation factors (GTP, initiator tRNA with fMET)
o initiator tRNA interacts with corresponding AUG start codon and
bindso first tRNA binds to the P site instead of the A site so there is
room for the next
oneo there is a sequence of amino acids on the mRNA before the AUG
codon=
ribosome binding site/Shine-Dalgarno sequenceinteracts with rRNA of
the
ribosome and the 30S ribosome binds to it, followed by the 50S-
eukaryote initiation complex differs in a) initiator tRNA is a different
one b) doesn’t bind
to Shine-Dalgarno site, instead recognizes 5’ cap on mRNA and tracks
along the mRNA
(5’-3’) until it finds the AUG codon, where the 40S subunit will bind,
followed by the 60S 2. Elongation
- A site- binds incoming charged tRNA’s- P site- binds charged tRNA’s
that have polypeptides that have joined the growing chain,
but not yet detached from the tRNAo Peptide bonds form between A
site and P site amino acids- catalyzed by peptidyl
transferase- E site- releases tRNA’s to be recharged with free amino
acids- Proceeds with single-codon movements of the ribsome called a
‘translocation event’
o 1 translocation event- charged tRNAs enter A site, move to P site,
leave at E site o ‘steps’ are induced by conformational changes that
move the ribosome 3 base
pairs down in the 3’ direction 3. Termination
- occurs at a nonsense/stop codon- when a stop codon aligns with the A
site it is recognized by release factorsP site
amino acid detaches from its tRNAnew polypeptide is released -
ribosome subunits detach

o prokaryotic don’t disassemble right away because they synthesize so

quickly??

**something in notes about only 1 ribosome

DNA MUTATIONS AND REPAIR
- for a mutation to become inheritable: 1) base sequence must
change 2) cell must fair to repair the change
- what causes mutations: o spontaneous mutation rate=1 in 1
billion replicated base pairs exposure to a mutagen can increase
rate x1000
• mutagens are often also carcinogenso chemical mutagens: act like or
modify nucleotide bases
reactive O molecules (ex: H2O2)
superoxide radicals (.O2-)
intercalating agents- slide between DNA double helix bases
and distort the molecule so DNA replication creates a frameshift
mutation
• ex: acridine orange
certain biological processes (mutator strains) o physical agents:
x- rays: causes breaks in DNA backbone, can also modify bases (ex:
C becomes Upoint mutation)
• used to sterilize- powerful damage to DNA/proteins/cellsUV
radiation- causes pyrimidine dimers=ex: linked thymines (stalls DNA
replication), DNA polymerase may replicate the dimer incorrectly (point
or frameshift mutation possible)o Oxidation of nucleotides (makes a
mutagen):
A normally based pairs by H bonds with T or Ureactive O molecule
(like a radical) binds to A and alters itwill H bond with C instead
(wrong)one strand of daughter DNA is altered
• HNO2 is another example - classes of mutations:
o point mutation/base substitution: single nucleotide is changed
silent- same amino acid is still coded for, no effect on protein
missense- different amino acid is coded for (effects vary,
sometimes protein still functional)
nonsense- changes a sense codon to a stop codon (proteins shorter
than they should be, rarely functional)
o insertion/deletion: one or more nucleotides added or subtracted
frameshift- add/del in not a multiple of 3 (all amino acids after are
changed)o inversion: DNA fragment is flipped in orientation in relation
to DNA on the other
side REPAIR
- types of DNA repair:o base excision repair: recognizes a specific
damaged base and removes it
nuclease will cut the strand, helicase removes the damage, DNA
polymerase adds missing bases, ligase repairs cut area
o methyl mismatch repair: requires recognition of the methylation
pattern in DNA bases
o SOS (save our ship) repair: coordinated cellular response to damage
that can introduce mutations in order to save the cell
o DNA recombination: the process of ‘crossing over’ and exchange of
2 DNA helices
o Photoreactivation: photolyase binds to T dimer, in the presence of
light the dimer breaks apart and restores base pairing
REGULATION OF GENE EXPRESSION- Primary purpose in
prokaryotes: Producing excess proteins wastes ATP - Primary purpose in
eukaryotes: cell differentiation
o Malfunctionscancer and other diseases in humans - Levels of gene
regulation:
o Changing the DNA sequence: some microbes change the DNA
sequence to activate/disable a gene
Ex: Phase variation (variation of protein expression)
• Penicillin resistant bacteria: if you stop taking penicillin, the bacteria
don’t need the gene, can remove it

• When gene is active it is transcribed

o Control of transcription: can be regulated by protein repressors,

activators, and alternative sigma factors
Normal transcription goes left to right- flip it=deactivates
Only prokaryotic (eukaryotic have exons and enzones)
Sigma factors- recognize a promotor sequence for
transcription, having different sigma factors allows for recognition
of slightly different promotor sequences, environmental conditions
stimulate the cell to change the sigma factor to the one that will
produce the proteins it needs in those conditions
o Translational control: control of transcription initiation sequences that
recognize specific repressor proteins

o Posttranslational control: control of proteins that are already made

(activate, deactivate, or degrade a protein)
Mainly eukaryotes- Operons: bacteria/archaea have them, group of
genes close together that are controlled
by a single promotor, allows quick transcription of all of the genes at the
same time (usually needed for a specific process, ex: ecoli needs to
digest lactose, all genes that code for enzymes needed for this are on the
same operon)
o Some operons are constantly turned on because they code for genes
that are always needed (ex: for DNA replication, cell maintenance)
o Usually 2-3 geneso Operon parts= regulatory gene + control region
+ structural geneso Transcription factors are activated by external
stimulio Inducers- A) inducer- reverse effects of repressors by binding
to them and
changing the conformation to make it unable to bind to the operator
anymore,
proteins are produced B) corepressor- binds to repressors, no proteins
produced - Repressible vs Inducible operons
o Repressible- transcription is induced in absence of X, then repressed
in presence of X/when X is plentiful
Ex: trp operon in Ecolio Inducible- transcription is repressed in
absence of X (proteins not needed in
absence of X), then transcription is induced in presence of X Ex: lac
operon in Ecoli
Where activators/RNA polymerase

bindsPROTEINS ARE PRODUCED Codes for production of transcription

Code for production of proteins

factorsrepressor/activator/inducer

Repressor- binds to operator and blocks transcription of structural genes Activator- binds to
promoter to facilitate RNA polymerase binding and transcription of structural genes

Inducer- small factor that EITHER interacts with a repressor or activator

Where repressors bind/RNA polymerase is BLOCKEDPROTEINS NOT PRODUCED

- Some genes respond to changes inside the cell, others respond to

outside influences o 1. Sensing intracellular environment: different
regulatory proteins bind to
specific compounds to determine the concentration of the compound in
the cell ex: dtx (diphtheria toxin genekills host cells for iron)
HIGH Fe: dtxR repressor binds with Fe, which binds to the regulatory
regionno toxin producedLOW Fe: dtxR comes off the regulatory
regiontoxin is produced
o 2. Global Regulators: proteins that affects the expression of many
different genes
ex: cAMP receptor protein (CRP) of Ecoli and related species
Ecoli prefer glucose as an energy source, when glucose is
depleted growth slows (seen on the curve), and the enzymes
needed to digest lactose will be expressed (second, less steep
growth)
When glucose levels are low, cells produce less ATP, which is
recognized by an enzyme EIIA, that activates conversion of
remaining ATP to cAMP
Increasing cAMP binds to create the protein CRP, which binds
to the promotor site of the lac operon, which encourages RNA
polymerase to bind
The repressor must also be removed for transcription to occur,
which happens in the presence of lactose
Genes are transcribed that produce the enzymes needed for
lactose digestion
When glucose levels are high, there is no cAMP/CRP and the
operon is repressed, no lactose enzymes are produced
 SUMMARY: for the lac operon to be activatedneed 1)
low glucose (so cAMP is produced) 2) lactose (so the repressor
is removed)
• Lac operon will operate SOME if there is glucose AND lactose (no
cAMP, but repressor is removed)
o 3. Sensing the extracellular environment: commonly used by bacteria
to relay information from outside/environment to inside, relies on a
serious of two- component protein phosphorylation relay systems
Ex: sensor kinase PhoQ in Salmonella senses magnesium and pH
outside the cell
Useful in bacteria because they can sense the environment and
activate transcription quickly if needed

- the system is composed of a sensor kinase on the cell membrane and

proteins within
the cell
- 1. the sensor kinase detects conditions outside the cell- 2. Signal
triggers/prevents autophosphorylation of ATPADP and releases a
phosphate
- 3. The phosphate binds to a response regulator in the cytoplasm, which
activates the regulator
- 3b. the regulator binds to the operator and activates/represses
production of the genes
- 4. Phosphatase removes the P from the regulator and proteins are
produced/not produced again

GENETIC RECOMBINATION
- vertical gene transfer: occurs during reproduction between 2
generations of cells, how DNA is most often transferred, parent
celldaughter cells
- horizontal gene transfer/lateral gene transfer: prokaryotic cells,
how asexual reproduction can still have genetic recombination,
occurs between cells of the same generation/between any two cells
o (a) transformation- DNA is taken in from the environmento (b)
transduction- bacteriophage injects DNA into the cello (c)
conjugation- DNA transferred between cells through a cytoplasmic
bridge
- (a) transformation: importing free DNA from the environment into
bacterial cells o carried out by specific protein
complexes=transformasomeo natural transformation vs artificial
natural ex: Streptococcus, Bacillus, Haemophilis, Neisseriacan be
manipulated to be made artificially competent: E.coli, Salmonella • via
electroporation- brief electrical pulse ‘shoots’ DNA across the
membraneo process: (for gram positive??)
1. Competence factor (CF) is synthesized and exported from the cell
2. As cell numbers rise, external CF levels riseactivates a
sensor kinase
3. The sensor kinase transfers a signal/a phosphate to an
activatortranscription of transformasome genes
4. Transformasome binds extracellular DNA1 strand is
transported, 1 is degradedDNA incorporated into the
chromosome
- (b) transduction: gene transfer mediated by a bacteriophage vectoro
discovered in Salmonella by Joshua Lederberg in 1952o bacteriophages
have a core nucleic acid covered by a protein coato specialized
transduction- the viral gene becomes integrated into the host
chromosomecopies of phage DNA include the gene from the
hostviruses inject that host gene into new cells
can make the new host pathogenic o why transduction is significant:
transfer gene from one bacterial cell to another, alters genetic
characteristics of recipient cell
incorporation of phage DNA into a bacterial chromosome
demonstrates a close evolutionary relationship between the
prophage and the host bacterial cell
the fact that a prophage can remain for long periods of time in
a cell suggests a similar mechanism for the viral origin of cancer

the viruses bring along genes from their previous host (or
hosts), so if this type of virus infects us, the type of DNA
incorporated into us might belong to another animaltransgenic?
Way to study gene linkage via chromosome mapping
- (c) conjugation: requires contact between donor and recipient cell for
gene transfer
o transfers larger amounts of DNA than transformation or transduction
o discovered by Joshua Lederberg in 1946
1. pilus of F+ (donor) cell attaches to recipient cellpilis contracts,
pulling cells together2. one strand of F+ plasmid DNA transfers to F-
3. F- makes a complementary strand and becomes a F+ cellF+ cell also
makes a new strand to restore the plasmid

o HFR CELLS- F plasmid becomes incorporated into the chromosome

Hfr=high frequency recombination
Can therefore transfer genes from the chromosome to the next
cell— plasmid excision from the chromosome is not precise = F’
cell
Can map genes on bacterial chromosomes- sometimes the
bacterial cell will try to transfer the entire chromosome into F- cell,
but it takes too long so it will cut off at a point, genes closer to
origin area of chromosome will go first
- Why conjugation is significant:o Contributes to genetic variationo
Increase genetic diversity (compared to other mechanisms)- larger
amount of
DNA is transferredo May represent an evolutionary stage between
asexual processes and the actual
fusion of whole cells (gametes)o Plasmids are self-transmissible and
can sometimes be promiscuous (moment a
cell has one it can transfer it, not super regulated)
o Some gram + bacteria have self-mating plasmids that don’t form a F
pili- instead secrete peptide compounds which simulate nearby bacteria
that contain the plasmid they want to mate with them
Bacteria only
- plasmids: mostly circular, double stranded, extrachromosomal
DNA o self-replicate by same mechanism as any other DNAo lot
of them have a function that allows bacteria to surviveo require a
lot of energy from the cell, will kick the plasmid out if not needed
- Plasmid functions (know them):
o 1. F plasmids direct synthesis of protein towards the pili (important
for
transferring genetic info between cells)cells with an F+ plasmid have
the gene to form the pilus
o 2. *** Resistance (R) plasmids carry genes that provide resistance to
antimicrobials (chloramphenicol, arsenic, etc.)
also have genes to control conjugation and transfer of the plasmid
between cells of the same species and different species
1 R plasmid often has genes coding for resistance to multiple
antibiotics o 3. Virulence plasmids (neurotoxin) cause disease signs and
symptoms (ex: strep
throat bacteria is only dangerous if it has the plasmid)o 4. Tumor
inducing plasmids cause tumor formation in plants (often used to move
genetic info into plant cells)o 5. Genes for catabolic enzymes- not
essential for cell growtho 6. Bacteriocinogen plasmid- direct synthesis
of bacteriocins (kill bacteria)
Prokaryotes and Eukaryotes- Mobile genetic elements: transposons
o All life formso Different from plasmids in that they can’t replicate
outside a larger DNA
moleculeo Have a transposase gene (and inverted repeat sequences),
that codes for the
enzyme transposaseenzyme facilitates recombination between the
repeats transposon is cut from original location and ‘pasted’ into a new
location
Transposon in the new location may have disrupted the code for a
particular geneaffects protein production from that gene

o Example: bacterial transposons can relocate genes from

chromosomes to plasmids- can add multiple antibiotic resistant genes on
a single R plasmid
o Transposon library- compilation of transposons for many genes of
bacteria