bacteria which normally reside in or on another organism

sum of all the species living in or on a healthly host

bacteria is setting up shop

not the same as infected because does not cause disease

keeps bad bacteria away

enzymatic reactions (break down fiber)

make certain vitamins humans can't make

dry and acidic so most microbes have a hard time living there

bacteria grow inside pores and sweat glands because moist and warm

direct contact pathogen

for some, normal flora on skin and repiratory tract; others dangerous pathogen

pyogenic-giving rise to pus

produce hemolysins and other toxins but not as flesh eating as Streptococcus pyogenes

causes: 1) imepitgo-localized

2) food poisoning-S. aureus produces enterotoxin; intoxication

halotolerant

3) toxic shock syndrome-bacteria go systemic

methocillin-resistant Staphylococcus aureus

makes propionl acid, a cause of acne

normal flora on skin

keeps bacteria numbers in check

has lysozyme-breaks peptidoglycan bonds

gets rid of food, dilutes nutrients for bacteria 

mucous membranes on check and gum

gums

more likely to have bacteria

bacteria secrete polysaccharides which make a matrix or biofilm over the enamel

causes dental carries

normal flora

tube through which you take in, digest, or absorb food and eliminate the wastes

bacteria numbers decrease as you move down

upper GI tracts less colonized because acidic

normal flora for some 

causes gastric ulcers

direct contact pathogen

enteric bacteria cause disease in intestine

bacteria have to withstand bile

normal for some in nasopharynx

can cause pneumonia in compromised host

phenotypes of pathogen that helps them cause disease

the more virulent an organism is, the less cells needed to cause disease

weakened bacteria

can become attenuated due to lack of selected pressure when used in lab

number of organisms needed to kill half of the host

high virulence, low LD50

low virulence, high LD50

attached with pili or capsule via specific interactions

recognized specific molecules on host cell

good attachment allows for invasion

can invade and be a localized disease

gram negative cells (LPS)

lipid A is the toxic protion

on bacteria outermembrane and not secreted by the call

causes edema and fever

pyrogenic

age

stress

nosocomial

smoking

alcohol use

 genetics

what we have to resist infection

nonspecific ways to resist

different for each individual

ability to recognize non-self

act on it whether or not your body has seen it before

have seen before

immune system has a memory of what it's seen before

phagocyte

white blood cell

phagocyte

white blood cell

PMN "polymorphonuclear neutrophile" type of neutrophile

non-self molecule

specific region of a molecule

specific responce to specific region

foreign molecule on which immune system responds

T Cells

cellular response/immunity

regonizes Ag in the context of MHC molecules

doesn't recognize "free" Ag in serum

specific fit between T Cell surface molecule (the T Cell Receptor) and Ag

humoral immunity

antibody recognizes Ag

from the B cell

secretes anitbodies

cell surface molecules which mark different cells

bases for tissue typing

on all cells except RBCs and sperm

looks different from person to person

recognized by Tc Cells

on immune cells

recognized by TH Cells

cytotoxic T Cells

recognize MHCI

poisons cells

kills phagocyte which ate bacterium

kills virus infected cells (virus puts Ag on surface of MHCI molecule)

does not attack cells with self Ag

produces cytotoxic enzymes

help the rest of the immune system

does not recognize a viral cell and then kill it but helps immune system cells

when MHCII is holding Ag, TH cells stimulate it to produce cytokine

huge class of molecules which stimulate other cells of the immune system 

bases for memory

stimulated by TH Cells

boost immune response

major Ig class at mucosal surfaces

mucosal immunity

a series of proteins that cause cells to lyse

Ab bind to Ag and calls in complements which breaks cell

neutralize toxins (physical bonding of Ab ties up activity of Ag)

opsomization

complement

make immune response

nature-exposed to pathogen

artificial-immunized with shot

airborne pathogen

not normal flora

causes: strep throat

scalet fever

post streptococcal infection

rheumatic fever

PSGN

necrotizing fascittis

Streptococcal toxic shock syndrom

virulence factors: hemolysins

erythrogenic toxin

impetigo

caused by Streptococcus pyogenes

beefy red throat

acute infection-first part of infection

localized

not normal flora

virulence factor of Streptococcus pyogenes

generates rash over the body

Scarlet Fever

more systemic

sequelae-sequels to strep disease

rheumatic fever

PSGN

necrotizing fasciitis

Streptococcal toxic shock syndrome

some of the bacteria have Ag to which you make a lot of Ab to

Ab attacks host heart tissue

flesh eating strep

death of tissues

work quickly

only certain stains

can have on skin or internal tissues

huge immune response that can kill you

organs shut down

blood goes to source of infection (which is ever) cause blood pressure to drop

enlarge all blood vessels at once

airborne pathogen

normal flora

cause of bacteria pneumonia

"pneumonococcal pneumonia"

Ag causes lung macrophages which dialate openings which brings fluid into the lungs

very sick, high mortality rate

airborne pathogen

causes diptheria-severe resipiratory disease

fatal in unvaccinated areas

Virulence Factor: diphtheria toxin: a cytotoxin blocks breathing by creating a pseudomembrane in back of throat

DTaP vaccine uses diphtheria toxoid

airborne pathogen

causes pertussis "whooping cough"

makes several toxins

DTaP vaccine

airborne pathogen

slow growing

causes leprosey

disfigures

organisms walled off in lesions-makes harder to treat

armadillo carries

can grow inside macrophages

airborne pathogen

cronic and lethal lung infection

highly contagious (more contagious when ruptured)

long term antibiotics

presense of tuverculus in lungs

constant cough

multiple drug-resistant strains

TB Skin test used to monitor exposure of mycobacterium-like organism

vaccine doesn't elicit a very good immune response and makes you test positive for life

airborne pathogen

causes bacterial meningitis-infection in brain and spinal fluid

extremely lethal

very cytotoxic

happens in epidemics

causes "meningococcal meningitis"

normal flora for some

in nasopharnx

airborne pathogen

causes upper respiratory infection

"Hib" vaccine to prevent ear infection

causes otitis media-middle ear infection

can also cause systemic disease

airborne pathogen

Mycoplasma pneumonia "walking pneumonia"

don't have a peptidoglycan wall

very small with a small genome so have to live inside another cell for nutrients and an osmotically balanced environment

Staph has:

1) halotolerance

2) catalase positive

3) coagulase

STD

causes gonorrhea

urethra discharge 

changes its antigens

leading cause of infertility and can lead to PID

infected mother could pass to child in child's eye and causes blindness

STD

causes syphilis

spirochetes-spiral, thin organisms

1* syphilis-localized infection; chancre

2* syphilis-rash

3* syphilis- rash goes away but syphilis goes on to affect central nervous system; blindness, demensia, death

congenital syphilis-baby borne with; spirochetes go through placenta and can cause miscarriage

STD

may cause vaginitus urethritis (less likely than gonorrhoeae)

can cause PID

leading cause of NGU-nongonococcal urethritis (asymptomatic chlamydia infection)

STD virus

can go latent (dormant)

type 1-cold sores

type 2-genital herpes

most common infectious disease

can use topical anti-viral medications

STD virus

infects TH Cells

compromises immune system

person dies from opertunisitc pathogen

changes Ag

STD virus

causes genital warts

some strains lead to cancer

Arthopod transmitted disease

causes typhus

spread by lyce

huge epidemics in highly populated areas or places with unsanitary conditions

Arthropod transmitted disease

causes Rocky Mountain Spotted Fever

spread by tick

rash, headache, pain

some people die, others clear out on their own

Arthropod transmitted disease

causes Lyme disease

emerging disease

transmitted by deer tick (more likely to get if live near deer)

sometimes get characteristic rash

chronic joint pain, chronic fatigue

Antropod transmitted disease

causes Black Plague

fleas from rat or prairie dog

one of the earliest documentations of guerilla warfare (Crimeon War)

settle in lymph nodes and make them swell (called bubose)

replicate inside phagocytes and releases tons of cytotoxins

causes Pneumonic Plague (inhale organisms, quick death)

soil borne pathogen

causes tetanus

can get from puncture womb

strict anaerobe

makes potent neurotoxin (infects nervous system)

exotoxin

causes: lock jaw (spastic paralysis) aka 'sardonic smile'

DTap vaccine

soil borne pathogen

causes anthrax

cutaneous anthrax

inhalation anthrax

localized skin infection caused by exposure of broken skin to spores

begins localized but can go systemic

"wool sorter's disease"

several cytotoxin

necrosis

goes systemic

lots of neucrotic damage

quick death

vaccine but not used in general public

soil borne pathogen

exotoxin: BT toxin

harmless to humans but kills insect larvae

crops engineered with gene for BT Toxin 

advantage: decreased use of pesticides

disadvantage: pest resistance, can't control pollination, allergeis

large group of bacteria which inhabit the instestine of humans and animals

if found in water, indicates fecal contamination

water borne pathogen

also spread by shellfish

vaccine but not very good

acts on intestine

causes cholera

mostly in eastern hemisphere

non invasive

attach to intestinal epithelial cells and releases enterotoxin which actives adenylate cyclase

increases cAMP

chloride ions leave cell

water leaves cell

watery diarrhea "rice water stool"

die if body doesn't flush out in time

water borne protist

causes Giardiasis

get from drinking downstream from a beaver

"backpacker's diarrhea"

trophozoite: swimming and feeding form

encyst: cyst form during harsh conditions

water borne protist

causes GI Disease

common in countries where human waste is used as a fertilizer

amebic dysentery-bloody diarrhea; invade and lyse tissues which leaves holes in intestinal epithelial cells which can let other organisms into your blood stream

once in blood stream can cause harm to organs which can lead to death

water borne protist

free living amoeba

causes meningocephalitis

extremely fast acting

headache and then die

more apparent in warm shallow waters

air borne pathogen

doesn't grow well on nutrient agar

manifests itself like pneumoniae

can cause death

water borne pathogen

not normal flora (some people can have but their normal flora keeps the organism in check)

causes Typhoid fever-affects GI system

severe GI disease

high fever

more systemic disease

causes food borne intoxication

GI 

more common 

outbreaks due to improper canning

anaerobes

food borne intoxication

anaerobe

causes botulism

botulism toxin

causes infant botulism (infant injects the spores from raw honey)

paralysis baby

wound botulism (injected with spores via puncture wound leads to flaccid paralysis)

neurotoxin

causes flaccid paralysis by blocking the release of acetyocoline at the nueromuscular junction

food borne infection

causes Salmonellosis

generic food poisoning

very common (lots of animals and humans harbor in intestine)

food borne infection

enterotoxigenic E. coli

traveller's diarrhea

raw fruits and vegetables

food borne infection

enteropathogenic E coli

causes diarrhea in small children

disease in some

food borne infection

enteroinvasive E. coli

going through intestinal wall into bloodstream

causes ulserative lesions in bowel which leave path for other organisms

food borne infection

enterohemorrhagic E. coli

can be fatal

make shiga-like toxin

causes bloody diahhrea

holes in tissue (cytotoxic)

kidney failure

food borne infection

causes serious blood disentary

less common than EHEC

shiga toxin-causes bloody disentary

food borne infection

pyscrotolerant-can still replicate in refridgerator on in cold food

can cause miscarriage

food borne infection

serious intestinal disease, diarrhea

normal flora in gut

oppertunistic pathogen

"C dif"

cause problems during flora imbalance and because of certain antibiotics

never quite get rid of

reduce number of microbes so less likely to spread

not sterile

time required to decimate (leave a tenth of) a microbial population

independent of population size

time required to kill all the organisms at a given temperature

population dependent

more contaminated, more time needed to kill all the organisms

minimal inhibitory concentration

lowest concentration of chemical needed to inhibit grown of bacteria

semi-quantitative

semi-quantitative

if bacteria doesn't grow up to disc, no inhibition

i know the rest

chemicals which kill microbial growth within a living organism

use against bacteria and fungi

naturally-occuring: made from mold and bacteria

synthetic: chemical changes to naturally-occuring antibiotics

cell wall :)

metabolic pathway :)

cell membrane :(

DNA synthesis :(

RNA synthesis :(

protein synthesis

antibiotics which work on cell wall

penicillin

cephalosporin

prevents transpeptidation

most bacteria have developed resistance against

B-lactam antibiotic

less suseptible to B-lactamase cleavage

wider spectrum

look like base pairs and get incorporated into DNA or RNA strands

next time DNA or RNA gets used, it is ineffective

used in anti-viral drugs

viruses transcribe faster so pick up analogs faster

-mycins

tetracycline

chromosomes or plasmid

1) decreased uptake of the drug

2)increase efflux of the drug

3) in activate drug (B-lactamase)

4)modify target

5) modify enzymes in pathway or change pathway

cell membrane

chromosomal DNA

ribosomes

cell membrane

true nucleus

chromosomal DNA

membrane-bound organells

ribosomes

cytoskeleton

characteristic of the bacteria cell

nucleus not defined by membrane

"nucleus like"

electrons as energy source focused with magnets

two types: transmition electron microscopy

scanning electron microscope

father of cell biology

developed microscope

first to look at microrganisms

plant cell walls

1600s

first to describe bacteria under a microscope

1600s

disproved notion of spontaneous generation

1800s

developed germ theory of disease (microbes when left to grow cause disease)

discovered relationships between microbes and disease

developed Koch's Postulates (criteria for microbes developing into a disease)

1)pathogen must be present in all cases of the disease and absent from healthy animals

2)suspected pathogen must be grown in pure culture

3)cells from a pure culture of the suspected pathogen must cause disease in a healthy animal

4)suspected pathogen must be reisolated and shown to be the same as the original

an organism that fails to meet Koch's postulates:

may still be a pathogen

not all organisms can grown in pure culture

not all people get sick when they have the bacteria

chemical energy

chemo-organotrophs (carbon, organic)

chem-lithotrophs (inorganic)

"light eating"

do not have chloroplasts because chloroplasts are membrane bound

sunlight

atmosphere

aquire C from CO2

organic compounds

aquire C from organic compound

breakdown reactions

chemoogranictrophs

make energy

enzyme pathways on which reactions occur in order to harness more net energy by harvesting energy at each point

energy requirements

Gibbs Free Energy-free energy held in a molecule; available energy in a molecule

more bonds = more available energy

input energy: endergonic

release energy: exergonic

proteins which speed up reactions

required by some enzymes

aka cofactors

has no catalytic metabolic activity by itself

small molecule with three components: ribose (5-C sugar)

N-rich base

one or more P ions

substrate-level phosphorylation

oxidative phosphorylation

catalyzed by a kinase

transfer P to high energy intermediate to ADP to make ATP

synthesis of ATP using ATPsynthase

enzyme using energy of proton gradient across the cytoplasmic membrane

anaerobic conditions

doesn't use exogenus electron acceptor

electron acceptors and donors will resupply themselves

internally-balanced redox-system

conversion of glucose to CO2 and H20

Phases:

1)Glycolysis

2)Phase II

3)Phases III

4)Phase IV

splittig of glucose in a series of steps

occuring in cytoplasm

02 is not required or used in this phase

overall, glucose is oxidized and NAD+ is reduced

2 ATP net are formed using substrate-level phosporilization

if oxygen is present:

2 pyruvate form 2 acetyleCoA and 2 CO2

2 NADH form 2NAD+

occurs in cytosol

pyruvate is oxidized, NAD+ is reduced to form NADH

2 Acetyle CoA

overall oxidation of molecules

per crank of CAC (per glucose)

NADH-3(6)

FADH2-1(2)

ATP-1(2)

CO2-2(4)

electron transport system coupled with oxidative phosphorylation

where most ATP is made

electron transport chain

NADH gives electron to ETC

(NAD+ oxidized and then reused)

some players in ETC are proton pumps

(creates proton gradient which in turn makes ATP)

O is last electron acceptor

ATPsynthase is a motor turned by protons flowing through it

motor takes ADP and adds P to make ATP using the energy from the protons turning the motor

Per NADH donor: 3ATP

Per FADH2 donor: 2 ATP

in mitochondria containing cell you end up with less ATP because PHASE II occurs in mitochondria

series of membrane bound molecules that alternately accept electrons and pass them down

REDOX chain

no ETC

Glucose becomes 2 pyruvate which becomes:

yeast

mixed acid

lactic acid

NAD+ is the limited agent

internal balance of NAD+

reduction of pyruvate

time it takes for one cell to split to two 

doubling time

N = Ninitial + 2^n

1) lag

2) exponential/log

3) stationary phase

4) death

elongation

taking in macromolecules

assimulating nutrients

adjusting to temperatuer

stopped growing

ruptured

DIED!!!!

physically count on microscope slide 

alive and dead

bacteria count based on cloudiness

counts alive and dead

pass light through sample to measure absorbance

more absorbance, more growth

O.D.

measures alive and dead

absorbance at particular wavelength 

use visible wavelength

doubles as growth doubles

how many bacteria are alive

serial dilutions and then plate

denature (disruption of protein's 3D structure) at high temperature

hyperthermophile-has proteins and bonds which are more resistant to unfolding

saturated vs unsaturated

tighter, harder to disrupt with fatty acid

saturated with H

can bend, easier to disrupt with heat

allows for some membrane fluidity at low temperature

phospholipid monolayer

one attachment

attached more strongly from head to tail

internal pH is neutral

sodium pumps bind with -OH so H+ can form 

Acidophiles-like low pH

bacteria have a certain internal concentration of salt

if placed in high salt environment, H2O leaves, cell shrivels to prevent this

halophiles synthesize more salt and retain it better

"aero"-oxygen

Aerobes:

obligate (O2 required)

facultative (O2 not required but grow better with it)

microaerophilic (required at levels below atmosphere)

Anaerobes:

aerotolerant (not required)

obligate (lethal)

shape of a bacteria

cocci (coccus)

bacilli (bacillus)

spirilli (spirillum)

thicker and more extensive

peptidoglycan layer

stains purple

more amino acids, more elaborate peptides, more glycan layers

cell wall: peptidoglycan

teichoic acid and lipoteichoic acid cause fever

thinner layer of peptidoglycan

have another membrane outside of peptidoglycan

stains pink

endotoxin

lipid A is the toxic portion

cell wall: peptidoglycan, periplasm (space between membranes), outer membrane

outer membrane:

phospholipid bilayer

proteins

looser structure, leakier

phospholipids not as closely tight

porins (big proteins which form channels in membrane)

LPS (lipopolysaccharide-extends out and very toxic to host)

endotoxin-fever

made up of two alternating sugars: N-acetylglucosamine "G"

N-acetylmuramic acid "M"

glycosidic bond-bond between two sugars

a few amino acids attacted by peptide bonds

form petido

an enzyme with antibacterial properties 

cleans glycans and disrupts bonds

1) deliver sugars into cell

2) repair glycosidic bonds

3)transpeptidation-step inhibited by penicillin

(penicillin only works when bacteria is releasing autolysins)

made of polysaccharids

sugar layer on outside of cell

attachment (to solid surface or each other)

helps pathogenic bacteria resist phagocytosis (cells with this feature cause disease)

insoluable droplets that are separate from the rest of the cell

not a separate compartment

protein "cages"-can fill with gas produced by the cell; increases buoyancy

photosynthetic organisms

especially photoautotroph

some but not all cells have

structures which are protective (protect from heat and dessication-drying out)

protective coating

vegetative cell creates in lag phase

germination returns to vegetative cell state

some have

protein extension used for motility

a stretch of DNA which encodes something

can be defined more narrowly or more broadly depending on what you are talking about

bacteria cells have one chromosome made of DNA

chromosomal DNA

in bacteria, divided into functional units called genes

all DNA codes for something

the building blocks of nucleotides are nucleic acids

nucleotide + nucleotides = nucleic acid

made up of sugar-P- chain attached to nucleotide

three covalent bonds between A and T

two covalent bond between G and C

messenger (mRNA) says which amino acid to bring in

transfer (tRNA) brings amino acids to ribosome

ribosonal (rRNA) makes up ribosomes

catalyzed by an enzyme RNApolymerase (holoenzyme)

two functional subunits:

sigma factor: protein which recognizes area on DNA where the start site is (promoter)

core enzyme

gene is defined by start and stop points

RNAP hops on to promoter and pulls in nucleiotides and hooks together

sequence promoter recognizes, most common promoter sequence

2 types in e coli:

rho-dependent

rho-independent

rho is a protein that binds to certain RNA sequences

destabilizes to complex

RNA comes off

recognizes RNA sequence that transcriped DNA from sequence

mRNA is unstable, MUST BE TRANSLATED NOW

2 areas of inverted repeats

structures of RNA base pair and form loop followed by stretch of U's

breaks off because U's aren't very strong

rRNA

tRNA

express genes only when needed

physical interestion where DNA binding protein recognizes DNA

know certain proteins are DNA-binding proteins

shut down gene expression by blocking RNApolymerase access

bound by binding protein-repressor protein

lac operon

arg operon

genes needed for utilization of lactose

use lactose (disaccaride of glucose and galactose) for energy source

lac promoter/lac operator/lacZ/lacY/lacA

repressor is bound unless lactose is present

lactose binding to operson makes repressor fall off

has genes that encode enzymes needed for synthesis of argenine (amino acid)

promoter/operator/argC/argB/argH

encourages more DNApolymerase binding rather than prevent

activator proteins-binds and encourages/increase DNApolymerase binding

nucleiode that gives you a feel for the energy feel in the cell

levels inversely proportional to ATP

ATP high, cAMP low

ATP high when glucose high

cAMP helps activator protein bind

cAMP-receptor-protein

activator protein for lac operon to CRP (only binds when high)

encodes repressor protein

not in operson because has it's own promoter

set operons that are coordinately regulated

can turn on multiple operons

use to cause disease

make pili to attach to cells and cytotoxin (regulon can turn both on at once)

bacteria sense how many of them are there

respond to population size

make small molecules and make more if others present until you make enough for gene expression

virus that infects bacteria

"phage"

a particle (not a cell) made of a nucleic acid gonome (DNA or RNA) plus protein coat (capside)

cannot replicated without living cell

like living things in that genetic info on nucleic acid can mutate and allow the virus to adapt to its environment

enveloped virus: has envelope

naked virus: does not have envelope

nucleic acid plus a capsid

means "the particle"

does or does not have a lidip envelope

viruses are specific to cells they can attach to and replicate them

virus which infects bacteria doesn't infect us

also specific to part of body in multicell

lysis "break"

lyse cells open

virus attaches to cell's protein, lipid or sugar

protein coat remains outside

virus wins because stronger than chromosomes in cells

keep replicating inside cell until it burst

"restrict" incoming DNA

use restiction endonucleases-cleave NA and double stranded DNA

cleave NA at very specific recognition sequences

cooresponding DNA (methalase-prevents cleavage of won RNA; modify chromosomal DNA to protect from restiction endonucleasis)

restition endonucleasis only works on double stranded DNA

"temperate" phage

not as virulent

phage is lysogenic

phage can do lysogeny

bacterium is lysogenized

doesn't always lyse the host

can integrate into host chromosome and becomes part of it; replicated and transcribed with it

cell's phenotype changes with addition of viral DNA

lysogenic can go lytic but not vis versa

lysogenic orgin

introduces integrated phage into cell

state of the genome of a temperate virus when it is replicating in synchrony with that of the host, typically integrated into the host genome

virus injects RNA into a cell

reverse transcriptase

virus has RNA and must reverse transcriptase to DNA and then integrate into cell

a change in DNA sequence

(wt)

normal sequence

choose organisms you want from the population

all will grow

can grow in absence of nutrient

wt (wild types) are prototrophs

to screen for nutritional auxotrophs

have replica

what you do if you can't select for something

all grow

screening process

doesn't have certain protein

mutants don't grow

a screening process

how you get change and how often

spontaneous and induced

a mistake in replication

happen at certain rate

DNAPolymerase (enzyme makes DNA)-makes mistakes

proofreads (corrects most mistakes)

net mistakes are spontaneous mutations

chemicals can change DNA (mutagen gives rise to mutants)

high-energy radiation

UV light

test using bacteria to assess mutantenicity of a bacteria

1)take an auxotroph such as 'his-' auxotroph

2) plate 'his-' auxotroph onto minimal medium without his

3) cells left mutated back to prototrophy

4) A-UV light before plating increase mutation rate back to phototrophy

B-disc soaked with chemical in middle if cells around it the chemical is mutagenic

the way bacterial cells transfer genetic information

3 mechanisms:

transformation

transduction

conjugation

Possible fates:

1)exogenous DNA can be digested through restriction digestion (results in no phenotypic change)

2) if exogenous DNA has it's own replicating system then phenotypic changes will occur

piece of DNA which will get replicated 

need "ori"-origin where DNA will be replicated by attracting DNApolymerase

extrachromosomal piece of DNA (very small) that get replicated

naturally occuring in many bacteria

if cell dies the plasmids can enter other cells

integrates into chromosome and replicated with big replicon

getting in and recombinging with chromosome is rare

base homology

prokaryotes and eukaryotes

switching out parts of DNA in places where there is homologous sequencing

nick-one of the strands of DNA gets broken 

genotype and phenotype changed

uptake of naked DNA (not enclosed in virus, ex:plasmid)

rare (degraded, replicate self, integrated into DNA)

when bacteria take up DNA, it can "transform" phenotype

stuff from dead bacteria cells can be mixed with live bacteria cells

those that uptake DNA are "competent" DNA

compentence can be increase to increase transferring

phage bring in DNA from one DNA to another

generalized: Lytic phage

specialized: lysogenic phage (integrate into bactorial chromosome)

"bacterial mating"

2 cells come together

donor and recipiant via pilus (structure donor cell makes)

pilus draws close together and the DNA from donor travels through pilus to recipiant

must have conjugative plasmid in order to be a donor

(has the genes for making the pilus and moving DNA)

most common "F" plasmid (recipiant F-, donor F+)

plasmid cut and transfered as replicates (so each cell has plasmid, = 2F+ cells)

want plasmid because contain an advantage most bacterial resistances on plasmids

manipulating DNA

cloning DNA

recombinant DNA

rBGH

insulin

rHBV

bacterial colony from binary fussion

lots of copies (enough so you can work with it)

bovine growth hormone

use gene for BGH and add in so cell produces a lot of BGH

a recominat

put human insulin gene and put on plasmid

e coli cell taken and now makes lots of insulin 

use manipulated e coli

enzymes which cleave DNA at very specific sequences

cut out DNA to put in plasmid

sites they recognize are usually palyndromes (read same one way as the other)

cut so ends are "sticky"

methalyse

vector-carrier

carries in DNA of interest

transform: plasmids

infect: phage (take out part of virus you don't want expressed; harder to manipulate; use when you have a big piece of DNA because phage and accomidate larger chunks of DNA)

most commonly used vector

naturally occuring if nonchromosomal, then nonessential (have some useful feature)

with recominant, took plasmids and made more useful

must have ori

polylinker (useful to have)-aka multiple cloning site

must have selectable marker (gene that does something so that you can select for cells that get the plasmids; because transformation extremely inefficient; only grow up ones that have plasmid)

penicillinase or B-lactamase

gene encdoes enzyes that cleave pencillin

another way to clone DNA of interest

polymerase chain reaction

amplyify DNA to a lot

heat stable DNA polymerase won't distable in heat

"Taq" polymerase

isolated from organism that can live in hot springs

Thermus aquaticus

for bacteria, reproduce asexually

within a species you have strains (each strain has different characteristics)

group of strains that show a high degree of similarities in several traits

traits use to define based on DNA

DNA-DNA hybridization

2 organisms/strains in same species must have a >97% identity in rRNA gene sequence (use rRNA because change gradually)

how well the DNA strands go togethers

must be >70%

take an organism's genomic DNA, shear into small pieces, heat to break H bonds, mix with untaged DNA strands (will base pair if same)

if second organism is too different, it won't rehybridize

see how much double stranded DNA verses how many single stranded DNA

use radiolables

picture of systematics (based on DNA sequence) that show evolutionary relationship

Domain

Phylum (proteobacteria is the largest)

Class 

Order

Family

Genus

Species