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Prokaryotic Organisms
Bacterial structure, observation techniques and exploitation
122
Biochemistry
Undergraduate 1
01/31/2013

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Cards

Term
What are the three reasons to why bacteria are important?
Definition
Abundace, distribution and activities.
Health and disease
Food and Biotechnology
Term
How many bacteria are on the planet?
Definition
10 to the power of 30
Term
What five organic atoms are bacteria usually involved in?
Definition
Carbon, nitrogen, oxygen, phosphorus and sulphur
Term
Which bacterium can live in the extreme condition of the antartic?
Definition
Psychrophiles
Term
What was used to construct the phylogenetic tree of life?
Definition
rDNA
Term
How do Archea differ from prokaryotes?
Definition
They have unique meatbolic processes and DNA regulation similar to Eukaryotes
Term
How are bacteria able to live in every possible environmental niche?
Definition
They have a diverse metabolic rate so can survive of a range of molecules
Term
What is the main artificial way our human body can build up a defense to bacteria?
Definition
Vaccinations
Term
Give an example of a recombinant protein produced through biotechnology?
Definition
Human Insulin
Term
Give an example of a biological drugs produced through biotechnology?
Definition
Humanised monoclonal antibodies
Term
Give an example of a natural product drugs produced through from biotechnology?
Definition
Antibiotics
Term
Give an example of a fine chemicals produced through biotechnology?
Definition
Vitamins
Term
Give an example of a industrial enzymes produced through biotechnology?
Definition
Proteases
Term
In what century were bacteria originally discovered?
Definition
17th Century
Term
What did Louis Pasteur do?
Definition
Created the pasteurisation method through his swan-necked vial
Term
What is Koch's germ theory of disease?
Definition
Pathogenic organisms cause disease
Term
When was the second 'Golden Age' of Microbiology?
Definition
20th Century
Term
What did Cyanobacteria do to make the earth inhabitable?
Definition
Produced oxygen
Term
Where is sophisticated life thought to have began?
Definition
At the stromatolites
Term
Outline the steps involved in the crystal violet gram stain?
Definition
1)Flood the smear with cyrstal violet for 1 minute
2)Add iodine solution for 1 minute
3)Decolourise smear with alcohol for 20 seconds
4)Counterstain with safranin for 1-2 minutes
Term
What colour do gram-positive bacteria go when treated with crystal violet?
Definition
Pink
Term
What colour do gram-negative bacteria go when treated with crystal violet?
Definition
Purple
Term
Why does the crystal violet gram stain work?
Definition
The gram-negative bacteria has an outer membrane which is less likely to hold onto pigment
Term
Outline the steps involved in preparing an electron microscope sample?
Definition
Cell fixed, cell dehydrated, cell embedded in glass, cell sectioned and then cell stained
Term
Waht three things did we learn about bacteria through electron microscopy?
Definition
Cells had a lack of compartmentalisation, cells had no nuclear envelope and cells had no obvious organelles/cytskeleton
Term
How is a sample prepared for Cryoelectron microscopy?
Definition
The samples are 'flash frozen' live.
Term
What is the advantage of using Cryoelectron microscopy?
Definition
You get a 3D reconstruction
Term
What are the two disadvantages of using Cryoelectron microscopy?
Definition
Poor contrast and 600nm depth limit
Term
Waht is flurescence microscopy?
Definition
Imagining through a high powered opticla lens
Term
What are the two types of flurescence micrscopy?
Definition
Immunofluorescence and GFP's
Term
What does GFP stand for?
Definition
Green Fluorescent Proteins
Term
How does Immunofluorescnce microscopy work?
Definition
A fluorescent antibody can bind to specific targets in the cells and then they can be detected
Term
What is the advantage of using Immunofluorescnce microscopy?
Definition
Detects wild type proteins
Term
What are the three disadvantages of using Immunofluorescnce microscopy?
Definition
Cells need to be fixed, there are some fixation artifacts and there is no time lapse imaging
Term
Where does the GFP come from?
Definition
The jellyfish Aequoria
Term
How does GFP microscopy work?
Definition
GFP binds to gene and then when that gene is transcribed the GFP will glow on the protein.
Term
What are the two advantages of using GFP micrscopy?
Definition
There are many colour variants for different proteins and can be done on living cells
Term
What is the disadvantage of using GFP micrscopy?
Definition
Fusion of proteins would cause fusion of colours which could be misleading
Term
What is FtsZ?
Definition
The divisionary protein in the centre of bcateria that is similar to eukaryotic microtubules
Term
What is MreB?
Definition
A protein in bacteria which i similar to eukaryotic actin
Term
How were MreB and FtsZ identified?
Definition
Using GFP microscopy
Term
Why is teh bacterial cell wall an ideal trget for antibiotics?
Definition
The wal is essential to growth, only present in bacteria and would cause cell lysis and instant death is damaged
Term
What molecule is present in gram-positive cell walls?
Definition
Anionic polymers
Term
What is the order of the cell wall/membranes in gram-positive bacteria?
Definition
An inne cell membrane surrounded by a thick outer petidoglycan cell wall.
Term
Which molecule makes up a bacterial cell wall?
Definition
Peptidoglycan
Term
What is the order of the cell wall/membranes in gram-negative bacteria?
Definition
Two cells membranes with a layer of peptiodoglycan cell wall between them
Term
What is the S-layer?
Definition
An additional outer layer present in some archea and bacteria
Term
What are endospores?
Definition
A condensed bacteria formede during starvation?
Term
What is the endospore cycle?
Definition
1)Cell divides internally into spore and cell
2)Spore forms a cortex
3)Spore is coated in Ca2+ ions
4)Cell disolved and spore released?
Term
When is the spore turned back into a bacterium?
Definition
When favourable condituions and reappeared
Term
How can we observe the spore cycle of bacteria?
Definition
Using GFP microscopy
Term
Which factor is present in the mother cell of a bacteria?
Definition
Factor E
Term
Which factor is present in the spore?
Definition
Factor F
Term
What colour does Factor E glow?
Definition
Red
Term
What colour does Factor F glow?
Definition
Green
Term
What are biofilms?
Definition
Large colonies/clumps of bacteria that have their own micro-ecosystem
Term
Give an example of a biofilm?
Definition
Plaque on teeth
Term
What is the capsule?
Definition
A polysaccharide layer attached to the cell wall that plays an important role in teh formation of biofilms
Term
What are pili and fimbrae?
Definition
Extensions of the bacteria that are involved in movement and conjugation
Term
What is the purpose of the flagella?
Definition
It can rotate at high speeds to provide a long tail that the bacteria can use to swim
Term
What are the six shapes of bacteria?
Definition
Coccus, Rod, Spirillum, Spirochete, Budding and Filamentous
Term
How long is the bacterial chromosome?
Definition
1mm
Term
What is a nuceloid?
Definition
A highly condensed chromosome
Term
How long is the average bacterial gene?
Definition
1,000 bp
Term
What is an operon?
Definition
A section of the bacterial chromosome that contains genes that all code for similar things
Term
What is a plasmid?
Definition
An additional piece of circular DNA that holds additional genes for the bacterium
Term
What are the majority of plasmid genes involved in?
Definition
Conjugation
Term
Where are antibiotic resistance genes contained in a bacteria?
Definition
On the plasmid
Term
What are the three other mobile genetic elements?
Definition
Bacteriophages, Transposons and Integrons
Term
What are integrons?
Definition
Sections of DNA that accumilate useful genes and then insert themselves into organisms
Term
What is the core genome?
Definition
The fundamental genes contained on the chromosome
Term
Waht is the pan genome?
Definition
The core gene and all the additional genes present on plasmids etc.
Term
What are pathogenicity islands?
Definition
Clusters of pathogenic genes in the core genome of a bacteria
Term
How are pathogenicity islands identified?
Definition
Through their high G/C content and with comparisons to similar non-pathogenic organisms
Term
How much does it cost to sequence the genome of a bacteria?
Definition
$100
Term
What are the three main methods we use to sequence a genomre?
Definition
Sanger, Balasubramanian and Klenerman and Oxford Nanopore
Term
How does Balasubramanian and Klenerman sequencing work?
Definition
1)DNA is fragmented and many copies of of the same fragment are added to microchips.
2)Coloured tags are added to teh microchip and one anneals
3)As it anneals the colour is emitted and is recorded by a computer
Term
What are the four steps involved in genome sequencing?
Definition
Preparation, Sequencing, Assembly, Analysis
Term
What happens during the preparation and sequencing stages of genome sequencing?
Definition
DNA is fragmented and then each contig is sequenced
Term
What is a contig?
Definition
An overlapping sequence of DNA
Term
What happens during the assembly stages of genome sequencing?
Definition
The contigs are lined up in a logical order
Term
What happens during the analysis stages of genome sequencing?
Definition
As not all the contigs can be sequenced correctly by a computer it must be analysed by human eye to piece together the final genome
Term
How is sequencing analysis usually done?
Definition
By comparinge the contigs of one organism with a sequenced genome of another
Term
What is the new revolutionary way that bacterial phenotypes are linked to the genotype?
Definition
Sequence the mutant and the parent of the mutant and look to see what mutation caused it by comparing the genome
Term
Why is the new revolutionary way of bacterial gene identification revolutionary?
Definition
There is no need for time consuming genetic mapping, populations can be tracked as teh evolve and adapt and it is applicable to all haploid organisms
Term
How is comparing genomes linked to phylogentics and evolution?
Definition
can see which mutations have caused a species divergence and produce a more accurate tree of life
Term
How is comparing genomes linked to health and disease?
Definition
By comparing the genome we can work out which genes are pathogenic and which are non-pathogenic so we can defeat antibiotic resistant bacteria like MRSA
Term
What are the three ways of measuring bacterial growth?
Definition
Viable cell count, turbidity and microscopic counting
Term
Each colony on an agar is supposed to represent what?
Definition
A single viable cell
Term
What are the three disadvantages of using the viable cell count method?
Definition
It only measures the viable cells, underestimates the number of cells in clusters and its very dull and slow
Term
What are the two advantages of using the turbidity method?
Definition
It's simple and can be done continously due to it being non destructive
Term
What are the two disadvantages of using the turbidity method?
Definition
It measures all cells (including thos dead) and it has a low sensitivity
Term
What is the advantages of using the microscopic count method?
Definition
Can acoomodate for clumping and chaining
Term
What is the disadvantage ofusing the microscopic count method?
Definition
You can't tell which are live and which are dead cells and its very laborious
Term
What is Flow cytomery?
Definition
Measure of particles in a microfluidic flow.
Term
What is FACS?
Definition
Combining flow cytometry with flurescent light to detect when the cells flow off to make the process automated
Term
What does FACS stand for?
Definition
Fluorescence Activated Cell Sorting
Term
Outline the bacterial cell cycle?
Definition
1. Duplications of organelles
2. Elongation
3. Septum cleavage
4. Segragation mid cell to form two daughter cells
Term
How long does it take for the entire genome of a bacterium to be replicated?
Definition
40 minutes
Term
What is the replication conundrum?
Definition
The bacterium can divide in 20 minutes but DNA requires 40 minutes to be replicated
Term
What is the solution to the replication conundrum?
Definition
They initiate DNA replication in the previous cycleusig a multifork approach with four OriC
Term
What does the Min system of bacterial cell division do?
Definition
Inhibits division at the poles
Term
What does the NO system of bacterial cell division do?
Definition
Inhibits division in the nucleoid
Term
How does the DNA segragate into teh two daughter cell?
Definition
As the cell elongates the NO regions break allowing a inhibitor free zone to form where segrgation can occur
Term
What does FtsZ tubulin do in a bacterium?
Definition
Forms the contractile ring that segragetes the cells and forms the poles
Term
How do other bacteria replicate differently?
Definition
No segregation forms long bracnhes and some bacteria grow inside other bacteria like bacteriophages or even form fruiting bodies to eat other bacteria
Term
Name four types of food produced from bacteria?
Definition
Yoghurt, cheese, sauerkraut and Natto
Term
What is the other way in which bacteria been used in the past besides food?
Definition
Waste water treatment
Term
What is biomining?
Definition
Unsing bacteria to extract important minerals
Term
How does biomining work?
Definition
Impure metal is disolved then precipitated and then bacteria can be used to gain the metal from the precipitate
Term
What two metals have bacteria been used for in biomining?
Definition
Gold and Copper
Term
What is bioremediation?
Definition
Using bacteria to clear up oil spills or solve the eutrophication problem from pesticides, fertlisers and xenobiotics
Term
What is biotechnology?
Definition
Harnessing microorganisms to make industrial products
Term
What three things are we currently using biotechnology for?
Definition
Medical reasons, chemical reasons and transgenic plants
Term
Why would we want to produce an antibiotic using fermentation rather than synthesis?
Definition
You can maximise the yeild, make it continous and minimise the costs
Term
What are semisynthetic antibiotics?
Definition
Traditional antibiotics that have been metabolised by a bacterium to give it extra properties
Term
What is the advantage of semisythnetic antibiotics?
Definition
The extra properties of teh durgs can be used to combat antibiotic resistance
Term
What is recombinant theraputics?
Definition
The introduction of foreign genes into an organism to produce an unatural response
Term
What are industrial enzymes?
Definition
Enzymes that have been isolated to be reused again and again
Term
WHy would we want bacteria to produce some aminoa acids?
Definition
The essential amino acids can then be sold as vitamins to those deficient in that amino acid
Term
What are bioplastics?
Definition
Biodegradable plastics that can be metabolised by bacteria
Term
What is T-DNA transfer?
Definition
The addition of bacterial plasmids into plants making them transgenic and immune to some plant infections
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