Bio 120 lecture 2 2011 2012

BIOLOGY 120 LECTURE 2

DIVERSITY OF MICROORGANISMS(Chapters 10-13 : Microbiology by Tortora 9th ed.)

Parungao-Balolong 2011Tuesday, June 21, 2011

Lecture Outline

•Classifications of Microorganisms

•Prokaryotes

•Eukaryotes

•Viruses, Viroids, Prions


Lecture Outline


•Prokaryotes

•Eukaryotes



Classification of Microorganisms

•Taxonomy (REVIEW)

•Science of classifying organisms

•Provides universal names for organisms

•Provides a reference for identifying organisms


THE 3 DOMAIN SYSTEM


THE 3 DOMAIN SYSTEM


Prokaryotic vs Eukaryotic Organelles


The ENDOSYMBIOTIC Theory


Scientific Names

Parungao-Balolong 2011

Scientific Binomial Source of Genus Name Source of Specific Epithet

Klebsiella pneumoniae Honors Edwin Klebs The disease

Pfiesteria piscicida Honors Lois Pfiester Disease in fish

Salmonella typhimurium Honors Daniel Salmon Stupor (typh-) in mice (muri-)

Streptococcus pyogenes Chains of cells (strepto-) Forms pus (pyo-)

Penicillium chrysogenum Tuftlike (penicill-) Produces a yellow (chryso-) pigment

Trypanosoma cruzi Corkscrew-like (trypano-, borer; soma-, body)

Honors Oswaldo Cruz

Tuesday, June 21, 2011

Taxonomic Hierarchy


DEFINING “SPECIES”•Eukaryotic species: A group of closely related

organisms that breed among themselves

•Prokaryotic species: A population of cells with similar characteristics

• Clone: Population of cells derived from a single cell

• Strain: Genetically different cells within a clone

• Viral species: Population of viruses with similar characteristics that occupies a particular ecological niche


DOMAIN EUKARYA•Animalia: Multicellular; no cell walls;

chemoheterotrophic

•Plantae: Multicellular; cellulose cell walls; usually photoautotrophic

•Fungi: Chemoheterotrophic; unicellular or multicellular; cell walls of chitin; develop from spores or hyphal fragments

•Protista: A catchall for eukaryotic organisms that do not fit other kingdoms


PROKARYOTES: DOMAIN BACTERIA & ARCHAEA


NAMING YOUR UNKNOWN MICROBE


Bergey’s Manual of Determinative Bacteriology

Provides identification schemes for identifying bacteria and archaea

Morphology, differential staining, biochemical tests

Bergey’s Manual of Systematic Bacteriology

Provides phylogenetic information on bacteria and archaea

Based on rRNA sequencing

Approved Lists of Bacterial Names

Lists species of known prokaryotes

Based on published articles


IDENTIFYING YOUR UNKNOWN MICROBE

•Morphological characteristics: Useful for identifying eukaryotes

•Differential staining: Gram staining, acid-fast staining

•Biochemical tests: Determines presence of bacterial enzymes


USEFUL TESTS


BIOCHEMICAL TESTS SEROLOGY (e.g. ELISA, AGGLUTINATION

TESTS, WB)


USEFUL TESTS


GENETIC TESTS(DNA base composition, PCR,

RNA sequencing, etc)

PHAGE TYPING


USEFUL TESTS


MICROARRAYS (Gene Expression Assays,

Metabolomics, etc)

FISH (uses DNA

probe, antibody, antigen, etc)


WHICH TESTS SHOULD YOU USE?


DICHOTOMOUS KEYS


VIDEO: DICHOTOMOUS

KEY


CLADOGRAMS


Lecture Outline


•Prokaryotes

•Eukaryotes



THE PROKARYOTES


PROTEOBACTERIA

•includes most of the Gram negative, chemoheterotrophic bacteria

•presumes to have risen from a common photosynthetic ancestor

•largest taxonomic group of bacteria

•5 classes: alphaproteobacteria, betaproteobacteria, gammaproteobacteria, deltaproteobacteria, epsilonproteobacteria


ALPHAPROTEOBACTERIA


IMPORTANT GENERA


Caulobacter (found in lakes) Hyphomicrobium (found in lakes)


IMPORTANT GENERA


Agrobacterium (tumor)

Rhizobium (nodules)


BETAPROTEOBACTERIA


IMPORTANT GENERA & Features


Sphaerotilus (forms sheaths)

Spirillum (forms sheaths)

Fimbriae and Capsules =

Pathogenicity


GAMMAPROTEOBACTERIA




Pseudomonas(opportunistic)

Legionella (cooling towers)

Vibrio (marine)




Proteus(swarming; peritrichous flagella)


DELTAPROTEOBACTERIA


Bdellovibrio(prey on other bacteria)

Myxococcus(aggregates)


EPSILONPROTEOBACTERIA


Helicobacter(stomach cancer)


NON-PROTEOBACTERIA; GRAM NEGATIVE BACTERIA


Fusobacteria

Chlorobium


FIRMICUTES




Clostridium Epulopiscium Lactobacillus/ Streptococcus

Staphylococcus


ACTINOBACTERIA




Actinomycetes (Actinomyces, Frankia, Nocardia, etc)


THE PROKARYOTES


THE PROKARYOTES


DOMAIN ARCHAEA

•Hyperthermophiles

•Pyrodictium

•Sulfolobus

•Methanogens

•Methanobacterium

•Extreme halophiles

•HalobacteriumParungao-Balolong 2011


SMALLEST AND BIGGEST BACTERIA

•Thiomargarita (750 µm)

•Nanobacteria (0.02 µm) in rocks


ISSUES: NON-CULTIVABLE PROKARYOTES

•Use of Culture-Independent methods (e.g. PCR)

•Pelagibacter ubique (Discovered by FISH technique)

•ExtremophilesParungao-Balolong 2011


Lecture Outline


•Prokaryotes

•Eukaryotes



WHO ARE THEY?


THE FUNGI


DIMORPHISM & REPRODUCTION IN FUNGI


VARIOUS FUNGAL SPORES•ASEXUAL

SPORES

•Sporangiosphore

•Conidiospore

•Arthrospore

•Blastoconidium

•Chlamydospore

•SEXUAL SPORES

•Zygospore

•Ascospore

•Basidiospore


VARIOUS FUNGAL SPORES


VARIOUS FUNGAL SPORES


LICHENS (FUNGI + ALGAE)


THE ALGAE


REPRESENTATIVE GROUPS


THE PROTOZOA


THE PROTOZOA


THE PROTOZOA


Plasmodium Cryptosporidium


THE PROTOZOA


Cellular Slime Molds


THE PROTOZOA

Parungao-Balolong 2011Plasmodial Slime Molds


THE HELMINTHS


THE HELMINTHS


TREMATODES


THE HELMINTHS


TREMATODES


THE HELMINTHS

Parungao-Balolong 2011CESTODESTuesday, June 21, 2011

THE HELMINTHS

Parungao-Balolong 2011NEMATODES (egg infects humans)Tuesday, June 21, 2011

THE HELMINTHS

Parungao-Balolong 2011NEMATODES (adult infects humans)Tuesday, June 21, 2011

VECTORS (Arthropods)


Lecture Outline


•Prokaryotes

•Eukaryotes



VIRUSES• Contain DNA or RNA

• Contain a protein coat

• Some are enclosed by an envelope

• Some viruses have spikes

• Most viruses infect only specific types of cells in one host

• Host range is determined by specific host attachment sites and cellular factors


VIRUSES : ARCHITECTURE


Helical Viruses

Polyhedral Viruses

Enveloped Viruses

Complex Viruses


HOW ARE THEY NAMED?

• Family names end in -viridae.

• Genus names end in -virus

• Viral species: A group of viruses sharing the same genetic information and ecological niche (host)

• Common names are used for species

• Subspecies are designated by a number


EXAMPLE Herpesviridae

Herpesvirus

Human herpes virus

EXAMPLE Retroviridae

Lentivirus

Human

immunodeficiency virus

HIV-1, HIV-2


GROWING VIRUSES


Plaques

Cell Culture

Embryonated Eggs


LIFE CYCLE


LIFE CYCLE


LIFE CYCLE


Lytic cycle: Phage causes lysis and death of host

cell. Lysogenic cycle: Prophage DNA incorporated in host


LIFE CYCLE


Lytic cycle: Phage causes lysis and death of host cell.

Lysogenic cycle: Prophage DNA incorporated in

host DNA.Tuesday, June 21, 2011

VIRUS MULTIPLICATION




VIRUS MULTIPLICATION (DNA Virus)


VIRUS MULTIPLICATION (+ strand RNA Virus)


Maturationand release

Entryand uncoating

Translation and synthesisof viral proteins

RNA replication by viral RNA-dependent RNA polymerase

Uncoating releasesviral RNA and proteins.

Nucleus

Attachment

Viralprotein

Capsidprotein

Cytoplasm

Host cell

– strand is transcribedfrom + viral genome.

+ strand

mRNA is transcribedfrom the – strand.

Capsid

RNA

Viralgenome(RNA)

ssRNA; +or sense strand;Picornaviridae

(a)


VIRUS MULTIPLICATION (- strand RNA Virus)



Entryand uncoating




Nucleus

Attachment

Viralprotein

Capsidprotein

Cytoplasm

Host cell

– strands areincorporatedinto capsid

The + strand (mRNA) must firstbe transcribed from the – viralgenome before proteins canbe synthesized.

Additional – strands aretranscribed from mRNA.

Capsid

RNA

Viralgenome(RNA)

ssRNA; – orantisense strand;Rhabdoviridae

(b)


VIRUS MULTIPLICATION (dsRNA Virus)



Entryand uncoating




Nucleus

Attachment

Viralprotein

RNA polymerase initiates production of– strands. The mRNA and – strands form thedsRNA that is incorporated as new viral genome.

Cytoplasm

Host cell

mRNA is produced inside thecapsid and released into thecytoplasm of the host.

Capsid

RNA

Viralgenome(RNA)

dsRNA; + or sensestrand with – or antisense strand; Reoviridae

Capsid proteins and RNA-dependent RNA polymerase

(c)



(Comparing Notes : RNA

Viruses)


VIRUS MULTIPLICATION (Retrovirus)


DNA vs RNA VIRUSES• DNA: Cellular enzyme

transcribes viral DNA in nucleus

• DNA, reverse transcriptase: Cellular enzyme transcribes viral DNA in nucleus; reverse transcriptase copies mRNA to make viral DNA

• RNA, + strand: Viral RNA is a template for synthesis of RNA polymerase.

• RNA – strand: Viral enzyme copies viral RNA to make mRNA in cytoplasm

• RNA, double-stranded: Viral enzyme copies – strand RNA to make mRNA in cytoplasm

• RNA, reverse transcriptase: Viral enzyme copes viral RNA to make DNA in cytoplasm.


VIRUSES & CANCER

• CANCER

• Activated oncogenes transform normal cells into cancerous cells.

• Transformed cells have increased growth, loss of contact inhibition, tumor specific transplant and T antigens.

• The genetic material of oncogenic viruses becomes integrated into the host cell's DNA.


VIRUSES & CANCER•Oncogenic DNA

viruses

•Adenoviridae

•Heresviridae

•Poxviridae

•Papovaviridae

•Hepadnaviridae

•Oncogenic RNA viruses

•Retroviridae

•Viral RNA is transcribed to DNA which can integrate into host DNA

•HTLV 1

•HTLV 2


LATENT vs PERSISTENT VIRAL

INFECTIONS

• Latent viral infections

• Virus remains in asymptomatic host cell for long periods

• Cold sores, shingles

• Persistent viral infections

• Disease processes occurs over a long period; generally is fatal

• Subacute sclerosing panencephalitis (measles virus)


PRIONS• Infectious proteins

• Inherited and transmissible by ingestion, transplant, and surgical instruments

• Spongiform encephalopathies: Sheep scrapie, Creutzfeldt-Jakob disease, Gerstmann-Sträussler-Scheinker syndrome, fatal familial insomnia, mad cow disease

• PrPC: Normal cellular prion protein, on cell surface

• PrPSc: Scrapie protein; accumulates in brain cells forming plaques


VIROIDS

•Infectious RNA; e.g., potato spindle tuber disease.


MAJOR PLANT VIRUSES


FAMILY OF VIRUSES


ssDNA dsDNA

Human ParvovirusHuman Respiratory

Infections Wart VirusesSmallpox; Cowpox

Herpes Simplex 1 and 2 Hepatitis B


FAMILY OF VIRUSES


ssRNA (-)

ssRNA (+)

Rhinovirus Hepatitis E

RubellaDengue

SARS

Rabies Ebola Mumps Hepatitis D

InfluenzaHantavirus Lassa Fever


FAMILY OF VIRUSES


ssRNA, 2 strands dsRNA

HIV Rotavirus


ISSUES: CROSSING BARRIERS


Documents

Bio 120 lecture 2 2011 2012