Lecture 1 Flashcards
what are the subjects covered in the test for november 1st
all the green block topics on the lecture 1 slides- the exam is worth 50%
what is taxonamy? what is it based upon?
it is a form of classification based on shared characteristics- related to shared behaviour, diet, genetics and appearance
what is phyologeny?
measures the evolutionary relationships between organisms- come into its own own over the last few decades via modern techniques of genetic analysis- genetic sequence analysis and the studies of the divergence of the species through time relates to the development of phylogeny
what are the steps of taxonomic classification for microbes?
- classification- ordering the organisms into groups based on shared properties
- nomenclature- naming the classified organisms
- identification- obtaining data on the properties of an unknown organism and determining which species it belngs to,, based on direct comparison to known groups
what are some traditional properties used in bactrial classification?
microscopy/morphology
response to oxygen
mode of energy synthesis/ source of carbon
biochemical, enzymatic tests
what is a molecular and genetic method to help classify bacteria
- Choose appropriate molecular markers for a gene family
- Amplify and sequence
- Create evolutionary model
- Phylogenetic tree analysis and construction
what is the Basis of phylogeny (the evolutionary relationship between organisms)
- All living things have genes which mutate
randomly (base changes) at low frequency - All progeny will carry the mutation (base changes)
- Organisms differing by a few DNA base changes have diverged more recently in evolutionary time than organisms that differ by more bases
what is a key property of many archaea?
they hare extremophiles
-methanogens
-hyperthermophiles
-psychrophiles
-acidophiles
-barophiles
what are the main gram positives (including mycoplasmas)?
- high G+C (% of nutrogenous bases in DNA or RNA that are guanine or cytosine) such as mycobacteria or Actinomycetes
- low G+C such as Bacillis
what are the most common gram negative bacterias
-Alpha
-Beta
-Gamma
-Delta
-Epsilon
How and why is taxonomy important?
- What phenotypic and chemotaxonomic methods could you use to help
with classification of a previously unrecorded microbe?
How and why is taxonomy important? - You may encounter genotypic and phenotypic systems for classifying
organisms. What are the relative benefits in using each of these? - Since Woese, Archaea are accepted as a separate domain of life in the
“Three Domain” model. Why may Woese have experienced resistance to his
proposal for reclassification in this way? Focus on differences and similarities
between archaea and bacteria.
What phenotypic and chemotaxonomic methods could you use to help with
classification of a previously unrecorded microbe?
Genotypic – classification on the basis
of genetic similarities- genotypic structures such as analysing their 16s rRNA comparing a molecular marker such as a gene family.
Phenotypic – physical; structural, or
metabolic features- i.e you could use morphology/microscopy to analyse and compare the shape of the bacteria, their reaction to oxygen, their ability to be motile; if they are spore forming, rod shaped, cocci, budding
- level of response to oxygen i.e anaerobes or aerobes
Chemotaxonomic – phenotypic
classification which measures degree
of similarity of biochemical
composition of organisms, e.g. Raman
spectroscopy
-RNA / DNA / GC
- what Fatty acids they have, using biochemical tests such a gram stain to determine their cell wall structure.
what are Aerobes
Thrive in the presence of O2
(e.g. Bacillus)
what are Microaerophiles
Require O2 but cannot tolerate 21%.
Campylobacter grows at ~5% O2
what are Anaerobes
Cannot tolerate O2
(e.g. Clostridia)
what are Facultative anaerobes
Prefer O2 but will grow without (e.g.
E. coli)
You may encounter genotypic
and phenotypic systems for
classifying organisms. What are
the relative benefits in using each
of these?
Using phenotypic systems that rely on traditional taxonmy the drawbacks may be that for example organisms that have divereged by a difference of millions of years ago from another species may appear to have been identically related i.e macaques and lemars share the same order of primates with humans but lemars diverged 63 million years ago whilst macaques diverged 25 million years ago so there are drawbacks with determining how long closely related species may be.
genotypic classification and analysis may help determine which species can survive in certain temperature environments and conditions, i.e analysis of their cell wall may help determine what antibiotic they would be resisitant too.
they are more about calculating the differences and providing specific information.
traditional taxonomy is more simple and easy to comprehend and detail
- Since Woese, Archaea are accepted as a separate
domain of life in the “Three Domain” model.
Why may Woese have experienced resistance to his proposal for reclassification in this way? Focus on differences and similarities between archaea and bacteria
Similarities:
* The two types generally share shape, size, and microscopic
appearance (rods, cocci, spirals, coiled etc.)
* Differentiation difficult with just a microscope (although
some are distinguished by their square-edged appearance)
* Like bacteria, Archaea multiply by binary fission and if motile
move primarily by means of flagella.
Differences:
* Despite morphological similarities some Archaea are
more angular / square shaped than bacteria
* Archaea do not have peptidoglycan –
- some have no cell wall
- may have protein S-layers
- may have polysaccharide walls
- may have pseudopeptidoglycan
* Archaea genes are more similar to eukaryotes than
bacteria
* Different 70S ribosome and more complex RNA
polymerase
read the tora microbiology textbook
