Microbial Diversity Flashcards
Define a strain - how are bio- morpho- and sero- vars differentiated
Variant of the same species
Bio - biochemically
Morpho - morpholgically
Sero - different antigenic properties
3 main classification methods
Phenotypic
Genotypic
Phylogenetic
Phenetic classification is based on how organisms look or behave - what are the 3 sections of this
Morphologically - shape, size and structural features
Physiologically - what an organisms does
Ecologically - Life-cycle patterns
Give 3 limitations of phenetic classification
Behavioural groupings may be wrong due to convergent evolution
Unculturables cannot be studied phenotypically
Microbes can tranfer DNA leading to a change in phenotype
What does genotypic classification compare
Genetic similarity
How does nucleic acid base composition work
50% more energy is required to break the bonds between G-C in comparison to A-T so measuring energy input to denature DNA tells you the base composition
What piece of equipment is used to measure how much energy was required to melt the DNA
Spectrophotometer
Why does less than 10% difference not necessarily correlate to relatedness
Base proportions maybe similar but sequences may be different
Give 1 advantage and disadvantage of NABC
Unculturables can be studied
Must have enough pure DNA
Define hybridisation
Act of annealing 2 different single strand of DNA together
How does nucleic acid hybridisation work
If single strands of DNA from two different organisms are hybridised the proportion of binding shows how similar the 2 sequences are
Outline how the first organisms DNA is prepared
DNA is denatured and a single strand is affixed on to a filter or membrane
Outline how the second organisms DNA is prepared
DNA is sheared and labelled with a detectable molecule then denatured
How is the unhybridised DNA removed once the fragments and the strand have been mixed
Removal by washing of the filter
What is NAH effective at and give 1 disadvantage
Separating closely related organisms
Shows similarities but not what those similarities are
What is phylogenetic classification based on
Predicted evolutionary relationships
What mutations considered as in terms of time - what does more mutations infer
Molecular chronometers - more mutations suggest more time passed
Give 1 disadvantage of molecular chronometers
Rate of sequence change can vary overtime - assumes that amount of change increases linearly with time
Give 2 advantages of phylogenetic classification
- Can study unculturables
- Labs work only has to occur once - comparisons can be made once you have the genetic sequence
What rRNA is used is used for P and E
P - 16s rRNA
E - 18s rRNA
Give 2 reasons why rRNA are used in phylogenetic classification
- Universally distributed
- Moderately well conserved - too much and they wouldn’t change enough for differences to be observed - too little and changed would be too rapid and there would be no similarities
How are enough 16s rDNA genes accquired
Amplification using PCR
In the phylogenetic tree of life - what does more mutations mean
More distantly relatedness
Why does denaturing gel electrophoresis work on 16s rDNA whereas normal gel electrophoresis doesn’t
There is an addition of a gradient of denaturing chemicals - where the DNA denatures is controlled by the DNA sequence
Normal gel electrophoresis wont work as it functions on the size of molecules - all of the 16s rDNA molecules from PCR will be the same size
Why will denatured rDNA move slower in electrophoresis
The rDNA is less aerodynamic
Why is rRNA more advantageous than rDNA (2)
- rRNA can be examined without breaking open the sample
- PCR not required as there are many more ribosomes hence more rRNA
What is the name given to short sections of nucleotides that are unique to different taxonomic ranks
Oligonucleotide signature sequences
How are oligonucleotide sequences detected - FISH
A probe (small strand of complementary nucleic acid) is labelled with a fluorescent dye and hybridises with the sequence
Fluorescent in-situ hybridisation
