Micro T2

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Major reasons: control microbial growth

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1.prevention/ treatment of infection (general)
2. prevention of infection
3. prevention of food spoilage

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sterilization

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complete destruction of all microbes on an object

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disinfection

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the reduciton or inhibition of microbial growht on a NON-LIVING object

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antisepsis

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the reduction or inhibition of microbial growth on LIVING tissue

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bacterial death curve

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bacteria die at a fixed exponential rate:
log plot: straight downward sloping line (like death phase)

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How to harm bacteria

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1. damage cell wall
2. change or distroy membrane permeability
3. damage protines and or nucleic acids: messes up enzyme or inhibit dna replication/protein synth
4. physical or chemical agents

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(4) of harm bacteria

Physical agents

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1. heat
2. moist heat
3.dry heat
4. cold
5. dessication
6. Filtration
7 osmotic pressure treatment
8. Radiation

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1. heat-

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i.quickly denatures protiens;
ii. damage membrane (more fluid)
iii. denatures DNA and RNA

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2. moist heat

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i. boiling
ii.autoclaving
iii. pasteurization

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boiling

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kills most bacteria in 10 min, endospores and viruses resistant.
30 min for water

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autoclaving

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moist heat under dry pressure. 121C 15psi 2atm
- sterilizing culture media and lab instruments.

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pasteurization

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short duration/ high temp treatment of food (72C for 15 sec)
- does not sterilize but kill bacterial

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dry heat

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kills by oxidizing effect, can denature proteins and dna
ie flaming loop used to transfer bacteria
methods
- incineration (combustion)
- dry ovens

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4) cold

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inhibits bacterial growth ; does not kill
- refrigeration and freezing are common uses of cold to inhibit bacterial growth

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5) dessication

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removal of water- often stops growth.
-does not kill
- endospores resistant
- lyophilization (freeze drying)- combo of dessication and freezing; preserve microbs n food

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6) filtration

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passage of a liquid or gas through a filter w/ pores small enough to retain miroorganism
- membrane can eliminate most bacteria
- cannot remove toxins

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7) osmotic pressure treatment

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use of salts . causes plasmolysis
- preserve food
salt n sugar ;"cure" meat n preserve fruits

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8) radiation

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kills bacteria
- ionizing radiation (gamma rays, x-rays)- can cause large scale mutations
- non-ionizing radiation (UV, microwaves) can cause abnormal base linkages in DNA (thymine dimers) n heat(microwaves)

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chemical agents

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1. disinfectants
2. heavy metals

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disinfectants

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1. halogens
2. alcohols
3. surfacants;
4. phenol and phenolic
5. aldehydes

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chemical agent- disinfectants
Halogens (1)

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- chlorine
clorine +h20= hypochlorous acid; stron oxidizing agent. disrupts enzymes
- compressesd clorine ; drinking water n pools (1ppm small)
-hypochlorite; swimming pools
- clorox: sodium hypochlorite
pros; ills bacterial cells endosproes, fungi, virues and algae
congs; not effective @ basic pH. unstable esp if light

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hypochlorite

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swimming pools

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sodium hypochlorite

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clorox: household disinfectnat

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chemical disinfect
halogens (2)

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-iodine ; denature enzymes
-in tincture; in alcohol;antiseptic
-ionodine tablets: disinfect drinking water

-F and Br dangerous

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chem disinfect
2. Alcohols

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- dissolve membrane lipids and denaturing proteins
- ethanol and isopropyl alcohol
- antiseptic of surfaces

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chemical

surface acting agents (surfactants)

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- detergents soaps
- chemical structure: long chain hydrocarbon w/ a charged "head"; ampipathic ( like phospholipids
detergents: disrupt cell membrane; cleansing agents and emulsiiers
- soap (an anionic detergent) not disinfectant ; acts emulsification ; removes germs

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chemicals
surface acting agents II:

quaternary ammonium salts (quats)

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- cationic detergents (ammonium ion bound to 4 other groups)
- disrupt plasma membrane
- n alkyl dimethyl benzyl ammonium

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chemicals:

Disinfectants

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- disrupt plasma membrane
- denature proteins
- lister to disinfect wounds
-toxic; just used as throat lozenges
-used in some lysol n household disinfectants-=qw

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chemicals: disinfectants

aldehydes

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- organic compounds w/ terminal CHO

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chem

formaldehyde

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inactivate proteins and nucleic acids
- very toxic, limited use

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formalin

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-liquid preservative, dissolving fomaldehyde gas in water

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glutaraldehyde

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- two terminal CHO groups
- less toxic and very effective
- ie sterilization of medical instruments

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heavy metals

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work by inactivating proteins by interacting with funcitonal groups
-Hg, silver, Cu Zn

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chemical food preservatives

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-1. weak organic acids:
- ie benzoic acid and sorbic acid: sodium salts
2. Nitrite salts: prevents germination of C. botulinum endospores in meat & preservative

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who is more susceptible to control of
- bacteria
- viruses

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- GRAM- POSITIVE generally more suceptible than gram-negative bacteria
- endospores are very resistant
- ENVELOPED viruses MORE SUSCEPTIBLE to chemicals than nonenveloped ones

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genetics

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study of genes

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genes

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-units of info made of DNA:
-carry info about particular traits
-basis of heredity :

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DNA structure

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polymer of nucleotides which come from : A-T G-C
- found as double -helix
-two antiparallel strands are joined by hydrogen bonds b/w the bases

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the central dogma of molecular biology

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DNA--> RNA--> Protein

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replication

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dna copies itself b4 cell division in a process called replicaiton

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transcription

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dna makes an mRNA copy of itself during this process

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translation

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mRNA directs the synthesis of a protein

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gene n proteins

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gene; holds the informaiton necessary to build a particular protein
protein: direct producers of phenotypic trait

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genetic recombination process of bacteria

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1. NO SEXUAL LIFE CYCLE
2 transformation
3. conjucation
4. transduction

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recombination

transformation

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- discovreed by griffith ; lead to the idea that dna is genetic material
- experiment: streptococcus pneumoniae bacteria and mice

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smooth strain of s. penumoniae

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- illness in mice (b/c capsule)
- inject live smooth: death
-inject dead smooth strain: live
- inject live rough ; live
- mix living rough and dead smooth: death

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griffith experimental reason

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soething form dead smooth cells was able ot transform the rough cells into smooth cells.
- transforming agent was DNA

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transformation

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the uptake of naked DNA by a cell
- lateral transformation of info

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recombination

conjugation

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transfer of genetic material from one bacteria (the donor) to another ( the recipient) by direct contact
- F factor ; plasmid
-

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how conjucation works

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the plasmid copies itself and directs the formaiton of a pilus, through which the copy (or a piece) moves to a recipient cell

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Recombination

conjugation: F factor

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- contain F factor referred to as F+; and can change cells w/o it to with it (F- -->F+)
HFR high frequency of recombination

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Recombination

Transduction

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the transfer of bacterial genes from one cell to another mediated by a bacteriophage

(viruses infect: replicates own DNA and degrades the bacterial DNA.

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Transduction: how

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bacterial genes become incorporated into the new infective phage particles.
- if this phage infects another bacterium, these new genes can be transferred to the new cell --> allows it to express a new trait.

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transduction: 2 types

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Generalized: any bacteriophage involved
- any gene may be transferred

specialized: only Temperate phage may be involved: (phages which integrate into the bacterial chromosome)
- only the adjacent to their integration sites may be transferred.

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Taxonomy

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the science of classificaiton of organisms

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purpose of taxonomy

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to show evolutionary relationships b/w groups
- to provide a means of identifying organisms

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Taxonomy

two methods of classificaiton

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*Phylogenetic- reflects ancestry (evolutionary relationships) (nucleic acid ; only non observable)
- phenetics: observable characteristics ; the goal is practical: ID and common language

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Taxonomy

5 kingdom system

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1. monera
2. protista
3. fungi
4. plantae
5. animalia

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5 kingdom system

Monera

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1. unicellular prokaryotes (bacteria)
2. based on cellular organization

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5 kingdom system
protista

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1. unicellular eukaryotes (protozoa, algae
2. based upon cellular organization

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5 kingdom system
fungi

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1. multicellular heterotrophs
2. external digestion (yeast, mold, mushrooms)
3. based on nutritional pattern

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5 kingdom system
plantae

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1. multicellular autotrophs (plants)
2. based upon nutritional pattern

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5 kingdom system

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1. multicellular heterotrophs
2. internal digestion(animals)
3. based upon nutritional pattern

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progenote

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hypothetical 1st living organism where 1st animal came

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The three Domains

define domain

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considered to be a new lvl apart from kingdom
- based on the fact that cells are really of 3 fundamental types
1. eukarya (eukaryotes)
2. bacteria (most bacteria)
3. archaea (archaebacteria) - no peptidoglycan in cell walls, extreme environments and strange biochemistry.
molecular studies, of DNA not very related to eubacteria

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domains (2) under kingdom monera

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domain bacteria
domain archaea

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what kingdoms are under domain eukarya

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1. kingdom prosista
2.kingdom plants (green algae closely related)
3. fungi
4. animalia

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linnaean taxonomic hierarchy

7 tiers (8 if inc domain)

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Domain, Kingdom, Phylum (division), Class, Order, Family, Genus, Species
- most inclusive to least inclusive
- genus and species italicized

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all
Human beings

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Domain-eukarya
kingdom-animalia
phylum-chordata
class- mammalia
order-primates
family- hominidae
genus-homo
species- sapiens

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dogs

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domain- eukarya
kingdom- animalia
phylum- chordata
class- mammalia
order- carnivora
family- canidae
genus- canis
species- familiaris

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bacteria (e.coli)

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domain - bacteria
kingdom- monera
phylum- gracilicutes
class- scotobacteria
order- enterobacteriales
family- enterobacteriacieae
genus- escherichia
species- coli

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tree of bacterial phylogeny

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order of earliest (to latest divergence)
1. green non sulfur bacteria
2. proteobacteria
--- gram-pos (bacteria and mycoplasms)
--- cyanobacteria
3. chlamydias
-- green sulfur bacteria
-- spirochetes

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How are bacteria classified

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- "Bergey's Manual of DETERMINATIVE bacteriology"
-1st 1923 last 1994
-observable characteristics or phenetics;

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characteristics to classify bacteria (8)

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1. Morphological characteristics (shape)
2. differential staining (gram stain)
3. nutritional pattern
4. relationship w/ Oxygen
5. biochemical charac (catalase +/-)
6. serological analysis-ability of specific antibodies ot react w/ specific microbe
7. phage typing - can bacteria be infected w/ same phage
8. protein and DNA Sequencing

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bacterial classification : new

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Bergey's Manual of SYSTEMATIC bacteriology"
-1980s: 2003 (2nd)
- phylogeny

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Define
species

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a group of potentially interbreeding organisms that can produce viable offspring
-- this def does not work for bacteria: NO SEX

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bacterial species

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a population of cells with similar characteistics ; (subjective)
- convention >3% differences; membership in diff species
- both sexual and non-sexual def are ways of getting at similarities

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viral classification:
viral species

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- not alive; not classified in KPCOFGS
- viral species- a populaiton of viruss that have similar characteristics
- some classify by--> who they can infect; not common usage

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Bacterial classification

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DOMAINS
- eubacteria
- archaea
KINGDOM
- Monera (in five- kingdom system)

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Bergey's Manual of DETERMINATIVE bacteriology
; characteristics to classify bacteria

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1. gram stain (cell wall type)
2. cellular morphology (rod, coccus, etc)
3. oxygen requirements (obligate anaerobe, etc)
4. Nutritional patterns (chemoautotrophs)

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systematic manual basis

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base entire scheme on phylogeny

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4 divisions ( phyla)

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1. Gracilicutes (gram-negative)
2. firmicutes (Gram-pos)
3. tenericutes (mycoplasmas; no cell wall!)
4. mendosicutes (archaebacteria; have strange cell walls w/ no peptideogycan

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DIvision I: Gracilicutes

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Gram negative bacteria
1. class : oxyphotobacteria
2. anoxyphotobacteria
3. scotobacteria

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class 1: oxyphotobacteria

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1. the cyanobacteria
2.aerobic photosynthesizers
3.primary producers in aquatic ecosystems
4. rep genus: oscillatoria

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class 2 anoxyphotobacteria

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1. DIvision (phylum): gracilicutes
2. grene and purple sulfur bacteria:
3. reduce sulfur compounds as electron donor
4 rep genus green: chlorobium
5. rep genus Purple: chromatium

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Green and purple non-sulfur bacteria

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1. Gracilicutes
2 class; anoxyphotobacteria
3. do NOT use reduced sulfur compounds as electron donor
4. rep genus Green: chloroflexus
5. Rep genus purple: rhodospirillum:

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scotobacteria

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- Division (phylum): gracilicutes
-class: scotobacteria
1. family: spriochaetacea
2. fam: spirillaceae
3. fam; vibrionaceae

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spirochaetacea

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1. division: gracilicutes
2. class; scotobacteria
3. family spirochaetaceae
4. sprial in shap, possess axial filament
5. rep Genera: Treponema: cuases syphilis
6. rep genera: Borrelia: causes lyme disease

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Spriillacea

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1. division: gracilicutes:
2. class: scotobacteria
3. microaerophilic, sprial shaped motile flagellum
4. rep genus; ehliobacter: causes stomach ulcers (helix)

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vibrionaceae:

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1. division: gracilicutees
2. class scotobacteria
3. facultative anerobic
4. curved, motile flagellum
6. rep genus Vibirio causes cholera

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Family enterobacteriaceae

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facultative anaerobic rods (colon)
1. escheria (coli)
2. salmonella
3. shigella
4. klebsiella
5. serratia
6. yersinia

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Vibirio

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family: vibrionaceae:
1. division: gracilicutees
2. class scotobacteria
3. facultative anerobic
4. curved, motile flagellum
6. rep genus Vibirio causes cholera

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escherichia (coli

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1. division (phylum) gracilicutes
2.family enterobacteriaceae (the enterics)
3. facultative anerobic rods
4. norm microbiota: food poisoning. used in research

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salmonella

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1. gracillicutes
2. class enterobacteria
3. facultative anerobic rods
4. causes food poisoning and typhoid fever

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shigella

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1. gracillicutes
2. class scotobacteria
3. family enterobacteriaceae
4. casues dysentery

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klebsiella

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1. Div: gracilicutes
2. class: scotobacteria
3. family enterobacteriaceae
4. morm microbiota
colon
5. cause bacterial pneumonia

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serratia

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1. Div: gracilicutes
2. class scotobacteria
3. family enterobacteriaceae
4. nosocomial infection (hosptital)

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yersinia

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1. div; gracilicutes
2. class: scotobacteria:
3. family: enterobacteria
4. plague (black death)

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chlamydias and rickettsias

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1. gracillicutes
2. scotobacteria
3. obligate parasiites
4. chlamydia- STD
5. Rickettsia: rocky Mountain spotted fever

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Chemoautotrophs

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1. gracillicutes
2. scotobacteria
3. oxides reduced sulfur, iron , and nitrogen compounds (muddy sediments)
4. thiobacillus.
5. ferroxidans

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Aerobic rods and cocci

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1. gracilicutes
2. scotobacteria
3. pseudomonas: ubiquitous lives in soil/H2O;
-- food spoilage; opportunistic infections
4. nisseria: gonorhea: diplococcus
5. bordetella: whooping cough
6. rhizobium; fixes atmospheric nitrogen 4 plants

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Division
Firmicutes

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Gram Pos Bacteria
class: firmibacteria: rods and cocci
1. Family Micrococcaceae
2. streptococcaceae
3. Family Bacillaceae
4. family mycobacteriaceae

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Micrococcaceae

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1. division: firmicutes;
2. gram post bact
3. class firmibacteria
4. cocci ; grapelike clusters
5. rep genus: staphylococcus:
- food poisoning
- wound infection
-boils
-toxic shock syndrom

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family streptococcaceae

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1. firmicutes
2. gram pos
3. class firmibactiera
4. cocci ; linear chains
5. rep gen: streptocuoccus:
- soar throat and scarlet fever

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bacillaceae

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1. Firmicutes
2. gram pos bact
3. class firmibacteria
4. endospore- forming rods: ***** the only endospore formers
5. rep genus: bacillus: causes anthrax
5. clostridium : botulism and tetanus

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mycobacteriaceae

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1. firmicutes
2. gram pos
3. class firmibacteria
4. family mycobacteriaceae
5. acid-fast, non-spore forming rods
6. mycobacterium (fungi) - Tuberculosis & leprosy

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Firmicutes

Class 2: thallobacteria

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the actinomycetes
1. filamentous (looks like fungal type growth) most live in soil
2. rep gen : streptomyces
-- produces many antibiotics inc streptomycin.

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DIvision III
Tenericutes

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Bacteria lacking a cell wall
1. class1: mollicutes (Mycoplasmas)
2. rep genus Mycoplasma
-- may cause bacterial pneumonia

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division IV
Mendosicutes

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THe archeabacteria
- have unusual cell wall: no peptidoglycan
1. extreme Halophiles
2. extreme Thermophiles
3. Thermoacidophiles
4. Methanogens

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Extreme halophiles

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1. div: mendoscutes
2.Class: archeabacteria
3. unusual cell walls no peptidoglican
4. salt lovers
5. rep gen. Halobacterium:
- photosynthesizes using bacteriophodopsin ;
- req. high salt concntrations

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extreme thermophiles

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1. div; Mendosicutes
2. class:Archeabacteria
3. heat lovers
4. rep gen; sulfolobus, thermoccus:
70C - 100C live in deep sea vents, volcanoes, hot springs

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thermoacidophiles:

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1.Mendosicutes:
2. class: archaebacteria
3. thermoplasma: pH2 , 60C

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methanogens

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1. mendosicutes
2. class; archaebactria
3. ch4 producers
4. rep gen: methanobacterium : turn organic waste, carbon dioxide and hydrogen gas into methane: (sewage treatment plants)

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Genus list for phylogenic trea

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proteobacteria:
-thiobacillus
- pseudomonas
-rhizobium
-bordatella
-neisseria,
-rickettsia
-salmonella
-shigella
-klebsiella
-serratia
-yersinia-
-Vibrio
-helobacter

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genus list for phylogenic tree

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gram pos/ mycoplasmas:
-staphylococcus,
-streptococcus
-bacillus
-clostridium
-mycoplasma
-mycobacterium
-streptomyces

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genus list for phylogenic tree

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- cyanobacteria: oscillatoria
-chlamydias: chlamydia
-green sulfur bacteria: chlorobium
- green non-sulfur bacteria: chloroflexus
- spirochetes: treponema, borrelia

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arecheabacteria genera

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-extreme halophiles; halobacterium
-methanogens; methanobacterium
-thermoacidophiles- thermoplasma
-extreme thermophiles: thermococcus
- extreem thermophiles (volcanic) sulfolobus